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Revision Tasks Age Author
14357 Directory Listing
Modified 2 years, 2 months ago
Mon Nov 30 20:37:50 2020 UTC
marios
Log:
Merged TPs branch back to mainline
14335 Directory Listing
Modified 2 years, 3 months ago
Sun Oct 18 03:48:33 2020 UTC
gary
Log:
more helpful raditive lifetime report
14321 Directory Listing
Modified 2 years, 3 months ago
Wed Oct 14 01:00:07 2020 UTC
gary
Log:
improve documentation for Jin papers
14318 Directory Listing
Modified 2 years, 3 months ago
Tue Oct 6 22:35:21 2020 UTC
marios
Log:
docs/latex/common/bibliography2.bib
  - Updated NIST ASD reference.

14317 Directory Listing
Modified 2 years, 3 months ago
Tue Oct 6 03:12:23 2020 UTC
gary
Log:
helpful comments for debugging phfit.dat
14316 Directory Listing
Modified 2 years, 3 months ago
Mon Oct 5 20:53:05 2020 UTC
gary
Log:
further limit number of elements for load leveling.  There were five to ten percent changes in monitored values due to change in cooling.
14314 Directory Listing
Modified 2 years, 4 months ago
Sat Oct 3 17:41:47 2020 UTC
gary
Log:
update branching ratio for electron - H3+ dissociation after extensive
discussions with Gargi Shaw.  The BR in UMIST seems to be a guess and caused the chemistry to fail
in igm_primal on Ubuntu / OracleStudio.  This change had little effect on the test suite.  The
revised BR was changed to its older value.
14313 Directory Listing
Modified 2 years, 4 months ago
Sat Oct 3 17:36:55 2020 UTC
gary
Log:
varlues have drifted a bit, updated H3+ branching ratio in mole_co_base
14312 Directory Listing
Modified 2 years, 4 months ago
Sat Oct 3 00:43:07 2020 UTC
gary
Log:
15 percent speedup by turning off rate elements
14310 Directory Listing
Modified 2 years, 4 months ago
Thu Oct 1 19:17:31 2020 UTC
marios
Log:
tsuite/auto/fix_input_scripts_wl.pl
  - Ported changes to look for suggested wavelength, instead of assuming it is
    always 3 lines after the emitted warning.  First implemented on the Priyanka
    branch in late Aug 2020.

docs/LineLabels.txt
  - Updated to current wavelengths.

14304 Directory Listing
Modified 2 years, 4 months ago
Mon Sep 28 23:31:34 2020 UTC
gary
Log:
minor speedups for the three slowest sims in the test suite
14302 Directory Listing
Modified 2 years, 4 months ago
Sun Sep 20 00:32:30 2020 UTC
gary
Log:
test new ISM abundances mixture
14300 Directory Listing
Modified 2 years, 4 months ago
Sun Sep 20 00:20:02 2020 UTC
gary
Log:
add Hensley Draine 2020 ISM gas phase abundances as optional abn file
14298 Directory Listing
Modified 2 years, 4 months ago
Sat Sep 19 20:46:21 2020 UTC
gary
Log:
ADS link to published Morisset paper
14294 Directory Listing
Modified 2 years, 4 months ago
Thu Sep 17 02:41:16 2020 UTC
gary
Log:
grid options to subsection
14263 Directory Listing
Modified 2 years, 4 months ago
Sun Sep 6 23:57:45 2020 UTC
gary
Log:
further update to McCall CR-related rates from r14260
14262 Directory Listing
Modified 2 years, 4 months ago
Sun Sep 6 23:40:49 2020 UTC
gary
Log:
add MOINTOR SET ERROR 0.1 to chemistry-dependent sims to acknowledge inherent
stability of ISM chemistry.  Most monitors had the 0.1 error introduced through experience, but this
make error floor more uniform
14260 Directory Listing
Modified 2 years, 4 months ago
Sun Sep 6 13:54:52 2020 UTC
gary
Log:
remove two CR rates since moved to
mole_co_base.dat and updated to McCall 2004, GS 
14259 Directory Listing
Modified 2 years, 4 months ago
Sun Sep 6 13:42:42 2020 UTC
gary
Log:
update and improve comments related
to various chemistry data files we use.
14258 Directory Listing
Modified 2 years, 4 months ago
Sat Sep 5 21:07:41 2020 UTC
gary
Log:
rollback r14255-14256 until we understand differences in tsuite better
14256 Directory Listing
Modified 2 years, 4 months ago
Sat Sep 5 14:40:41 2020 UTC
gary
Log:
Gargi Shaw removed duplicate reads of reactions files
14255 Directory Listing
Modified 2 years, 4 months ago
Sat Sep 5 12:52:13 2020 UTC
gary
Log:
Gargi Shaw removed old duplicate reaction to silense comment
14236 Directory Listing
Modified 2 years, 5 months ago
Tue Aug 25 20:47:58 2020 UTC
rjrw
Log:
Improved fix for multiplet handling

14235 Directory Listing
Modified 2 years, 5 months ago
Tue Aug 25 20:14:38 2020 UTC
rjrw
Log:
Trap for reported undefined behaviour

14232 Directory Listing
Modified 2 years, 5 months ago
Mon Aug 24 15:16:26 2020 UTC
gary
Log:
limit number of levels for Na I to prevent problems with linear algebra
14230 Directory Listing
Modified 2 years, 5 months ago
Sat Aug 22 17:41:58 2020 UTC
rjrw
Log:
Add const annotation

14229 Directory Listing
Modified 2 years, 5 months ago
Sat Aug 22 16:52:03 2020 UTC
rjrw
Log:
Tweak atom_leveln eigen-analysis coding to update it and make
it simpler to enable if required for failure analysis

14207 Directory Listing
Modified 2 years, 5 months ago
Thu Aug 13 15:08:28 2020 UTC
gary
Log:
diagnostics for physical state of sim upon abort or reporting arrays
14199 Directory Listing
Modified 2 years, 5 months ago
Fri Aug 7 17:45:02 2020 UTC
marios
Log:
adf042stout.py
  - Revert changes in r14007.

14182 Directory Listing
Modified 2 years, 6 months ago
Tue Aug 4 02:20:09 2020 UTC
gary
Log:
update H3+ rates to Indriolo+2012
14181 Directory Listing
Modified 2 years, 6 months ago
Tue Aug 4 02:19:43 2020 UTC
gary
Log:
update H3+ rates to Indriolo+2012
14178 Directory Listing
Modified 2 years, 6 months ago
Mon Aug 3 20:19:20 2020 UTC
gary
Log:
discern big botch gt 9 sigma
14176 Directory Listing
Modified 2 years, 6 months ago
Mon Aug 3 00:39:47 2020 UTC
gary
Log:
recognize special case where essentially all Ca is atomic but high charge states are slightly negative.  Code converged away from problem state so solution was positive.
14165 Directory Listing
Modified 2 years, 6 months ago
Sun Jul 26 23:07:01 2020 UTC
gary
Log:
fix user suppled density label dat -> sden
14163 Directory Listing
Modified 2 years, 6 months ago
Sun Jul 26 19:20:16 2020 UTC
gary
Log:
tsutie/auto/agn_S_curve_grd - add SAVE SPECIES command with long label to test against buffer overrun

data/LineList_BLR.dat
data/LineList_BLR_Fe2.dat
data/LineList_HII.dat
data/LineList_NLR.dat
replacd C  3 977, which picked up a very weak recombintion line, with the correct Stout transition,
C  3      977.020A		# type: t, index=1, 5 Elow=0   Stout, 1s2.2s2 1S0 -- 1s2.2s.2p 1P1


14161 Directory Listing
Modified 2 years, 6 months ago
Sat Jul 25 23:42:12 2020 UTC
gary
Log:
double limit on NCHLAB as per Fran comment o thread Buffer Overflow with save species densities
14159 Directory Listing
Modified 2 years, 6 months ago
Sat Jul 25 20:04:20 2020 UTC
gary
Log:
add optical depth at 1 Ryd to overview
14157 Directory Listing
Modified 2 years, 6 months ago
Sat Jul 25 19:12:28 2020 UTC
gary
Log:
want total (blnd) intensity of line
14153 Directory Listing
Modified 2 years, 6 months ago
Sat Jul 25 17:19:12 2020 UTC
gary
Log:
improve formatting and comments
14150 Directory Listing
Modified 2 years, 6 months ago
Thu Jul 23 22:36:23 2020 UTC
gary
Log:
update CR H2 dissoc as per  2020RNAAS...4...78S
14148 Directory Listing
Modified 2 years, 6 months ago
Mon Jul 20 13:13:31 2020 UTC
gary
Log:
references for AGN_Jin*.sed
14104 Directory Listing
Modified 2 years, 7 months ago
Wed Jun 24 23:46:10 2020 UTC
gary
Log:
add aastex63.cls, the current version,
and copy needed sumbols to macros.tex
14059 Directory Listing
Modified 2 years, 8 months ago
Tue May 26 00:27:24 2020 UTC
gary
Log:
ref to Goldsmith and Langer 1978
14056 Directory Listing
Modified 2 years, 8 months ago
Sun May 24 13:00:35 2020 UTC
gary
Log:
add Dalgarno ref to CR secondaries
14007 Directory Listing
Modified 2 years, 8 months ago
Thu May 14 21:20:50 2020 UTC
marios
Log:
scripts/adf042stout.py
  - bugfix: Ignore all transitions and collisions with TP <= 1e-30.  Previously,
    collisions with conjugate transitions of TP <= 1e-30 were used on output,
    while the transitions were not.

13986 Directory Listing
Modified 2 years, 8 months ago
Fri May 8 03:58:19 2020 UTC
marios
Log:
data/ionization_potentials.dat
  - Updated ionization potentials to NIST values on May 01, 2020.

source/atmdat_readin.cpp
  - Updated magic number to current version: 20200501.

13967 Directory Listing
Modified 2 years, 9 months ago
Tue Apr 28 14:35:17 2020 UTC
gary
Log:
add Seaton 79 reference
13835 Directory Listing
Modified 2 years, 10 months ago
Tue Mar 31 21:15:12 2020 UTC
fguzman
Log:
PS-M non-degenerate case was depending on the species (nelem) instead of on the iso-sequence (ipISO). This is now corrected.
13700 Directory Listing
Modified 3 years ago
Thu Jan 30 20:10:07 2020 UTC
fguzman
Log:
correctly extrapolate to low temperature R-Matrix Anderson+00 cross sections for hydrogen
13648 Directory Listing
Modified 3 years ago
Sat Jan 25 03:19:19 2020 UTC
gary
Log:
typo fix
13647 Directory Listing
Modified 3 years ago
Sat Jan 25 03:06:19 2020 UTC
gary
Log:
the band lines only exist in main output when SAVE SPECIES is entered
13516 Directory Listing
Modified 3 years ago
Mon Jan 13 20:01:56 2020 UTC
fguzman
Log:
added crossreference to Vrinceanu2017
13514 Directory Listing
Modified 3 years ago
Mon Jan 13 16:49:50 2020 UTC
fguzman
Log:
Deprecated S62 for protons l-changing collisions in he-like. Now PS-M is the default for l<3. 

1) Cloudy calculates S62 results by scaling the energies to the protons mass, integrates to the maxwell rates (one single temperature) and and convert them to upsilons to store them.

2) The upsilons are later converted to rates again to be used in the CR matrix but the temperature used is the electron temperature, so the rates are underestimated.

3) The mass factor should go into more terms (energy) in the integration of the rates. From Giulio Del-Zanna 12/21/2019:

"I was able to reproduce the original Seaton's cross-sections
for the electrons but then got a bit lost for the protons as the mass goes in
different places. It is not so simple.  I am still having some problems with
my code at higher l. I also had a look at the Cloudy programs and I could not make
sense of the various conversions done at the end which you have mentioned.
The bit which calculates the cross section for the electrons is fine. "

4) PS-M already has the right solution for l<3 proton he-like collisions.

5) S62 gives the right solution for electron impact collsions.



13413 Directory Listing
Modified 3 years, 1 month ago
Mon Dec 30 00:16:32 2019 UTC
gary
Log:
change yahoo to groups.io
13410 Directory Listing
Modified 3 years, 1 month ago
Sun Dec 29 23:47:03 2019 UTC
gary
Log:
add third report to LineLables.in and improve
docs of each
13409 Directory Listing
Modified 3 years, 1 month ago
Sun Dec 29 23:46:08 2019 UTC
gary
Log:
update line label list
13312 Directory Listing
Modified 3 years, 2 months ago
Sun Nov 24 16:00:56 2019 UTC
gary
Log:
allow underflow of Aul for large n where
collisions dominate.  The radiative lifetime of the upper level
is substantially longer than the age of the Universe.
13231 Directory Listing
Modified 3 years, 3 months ago
Fri Oct 25 15:40:31 2019 UTC
fguzman
Log:
reintegrated branch IsoFujiandVR62 for Fujimoto and VR62 collisional theories
13199 Directory Listing
Modified 3 years, 3 months ago
Sat Oct 19 14:33:45 2019 UTC
gary
Log:
debug statement for maser
13182 Directory Listing
Modified 3 years, 3 months ago
Tue Oct 15 18:43:06 2019 UTC
marios
Log:
docs/latex/hazy1/conout.tex
  - Explain that level-resolved output of the 'save species' family of commands
    is reported in the same order as in the input database models (without the
    sorting done internally).

13168 Directory Listing
Modified 3 years, 3 months ago
Mon Oct 7 21:37:19 2019 UTC
fguzman
Log:
Fixing reference of Bautista Fe II data
13167 Directory Listing
Modified 3 years, 3 months ago
Mon Oct 7 20:19:20 2019 UTC
gary
Log:
Smyth+19 paper has appeared
13160 Directory Listing
Modified 3 years, 3 months ago
Sun Oct 6 23:23:40 2019 UTC
gary
Log:
add cross references and explicit restatement that grain options are present on abundances command, but think about NO GRAINS option to get full set of grains keywords.
13159 Directory Listing
Modified 3 years, 3 months ago
Sun Oct 6 23:13:05 2019 UTC
gary
Log:
add discussion
and figure showing effects of cosmic rays on low density gas
13158 Directory Listing
Modified 3 years, 4 months ago
Sat Oct 5 23:54:47 2019 UTC
marios
Log:
docs/latex/common/bibliography2.bib: Update NIST_ASD entry
13155 Directory Listing
Modified 3 years, 4 months ago
Fri Oct 4 22:39:32 2019 UTC
gary
Log:
Add another incident continuum point - these really should be exported to an external file.
13141 Directory Listing
Modified 3 years, 4 months ago
Thu Oct 3 20:53:56 2019 UTC
gary
Log:
put readme with script
13138 Directory Listing
Modified 3 years, 4 months ago
Thu Oct 3 20:09:11 2019 UTC
fguzman
Log:
patch to fix thermal command in iso-sequences
13110 Directory Listing
Modified 3 years, 4 months ago
Thu Sep 26 22:28:22 2019 UTC
gary
Log:
refs needed for c20 review paper
13107 Directory Listing
Modified 3 years, 4 months ago
Wed Sep 25 19:42:08 2019 UTC
gary
Log:
changed monitors from update 12.8 micron cs
We had used very old Hollenbach+ H0 collision rates.  The new values are
significantly smaller.  The electron CS are unchanged.  As a result
the line became a bit weaker in x-ray dominated gas where warm H0 excited
the line.
13106 Directory Listing
Modified 3 years, 4 months ago
Wed Sep 25 19:40:08 2019 UTC
gary
Log:
working files no longer needed
13105 Directory Listing
Modified 3 years, 4 months ago
Wed Sep 25 19:38:54 2019 UTC
gary
Log:
update e and H0 collision rates for Ne II 12.8 micron
# atomic hydrogen
# Wan, Y., Leiberman, P., Buenker, R., Loch, S. D., Schultz, D. R., & Stancil, P. C.  2019, \apj, 881, 3
# https://ui.adsabs.harvard.edu/abs/2019ApJ...881....3W

# electron collisions <=2000 K
# Wang, Q., Loch, S. D., Li, Y., Pindzola, M. S., Cumbee, R. S., Stancil, P. C., McLaughlin, B. M., & Ballance, C. P.  2017, \mnras, 469, 1225-1232
# https://ui.adsabs.harvard.edu/abs/2017MNRAS.469.1225W
# electron collisions >2000 K
# Electron CS: Griffin,D.C., Mitnik,D.M. & Badnell, N. R.,2001,JPhB,34,4401
13103 Directory Listing
Modified 3 years, 4 months ago
Wed Sep 25 15:21:01 2019 UTC
gary
Log:
add zone to print so we can work around
loss of information after the abort
13102 Directory Listing
Modified 3 years, 4 months ago
Tue Sep 24 22:25:02 2019 UTC
gary
Log:
the original data file for now
13101 Directory Listing
Modified 3 years, 4 months ago
Tue Sep 24 22:22:30 2019 UTC
gary
Log:
the predicted Ne II 12.8 is coming out about 2x different with new values.
this must be due to electron collisions since in ionized nebulae.  This needs further study
since electron CS did not change by much.  

This reverts to old data (as sim link) and adds old/new as separate files. 
13100 Directory Listing
Modified 3 years, 4 months ago
Tue Sep 24 20:31:50 2019 UTC
gary
Log:
atmdat_chianti.cpp - user friendly error message
ne_2.coll - update H0 and e collisions to  https://ui.adsabs.harvard.edu/abs/2019ApJ...881....3W
13089 Directory Listing
Modified 3 years, 4 months ago
Mon Sep 23 22:02:20 2019 UTC
gary
Log:
update recombination contribution to [O III] as per Christophe Morisset
recommendation.  Now about two times smaller at nebular temperature
13087 Directory Listing
Modified 3 years, 4 months ago
Mon Sep 23 16:52:29 2019 UTC
marios
Log:
atmdat_adfa.h
yield.h
  - Use LIMELM parameter instead of bare 30.

13082 Directory Listing
Modified 3 years, 4 months ago
Mon Sep 23 15:00:12 2019 UTC
marios
Log:
data/ionization_potentials.dat
  - Update to IPs derived from NIST with the script fetch-NIST-IP.py.
data/ionization_potentials.dat
source/atmdat_readin.cpp
  - Update magic number to day's date.

13073 Directory Listing
Modified 3 years, 4 months ago
Sat Sep 21 14:01:53 2019 UTC
gary
Log:
bugfix - trans class not defined when Fe turned off
13072 Directory Listing
Modified 3 years, 4 months ago
Sat Sep 21 00:45:22 2019 UTC
gary
Log:
grains*.in have stronger FeKa due to missing
two-electron Ka.  blr sim now asserts mean of gcc and llvm.  
These changes are result of r13071
13071 Directory Listing
Modified 3 years, 4 months ago
Sat Sep 21 00:42:52 2019 UTC
gary
Log:
bugfix for Fe Ka.  We did not include two electron Fe K.  The labels and wavelengths have been update to better represent physics of production and observed wavelength.  The new labels and wavelengths are:
175369	FeKa      1.78000A		# type: i, total intensity of Fe K-alpha line, grain, cold, hot, 1 and 2 electron
175370	FeK1      1.78177A		# type: i, H-like one-electron Ka
175371	FeK2      1.85000A		# type: i, He-like two-electron Ka
175372	FeKH      1.80000A		# type: i, fluorescent hot iron, Fe 18 - 23 times ionized
175373	FeKC      1.75000A		# type: i, fluorescent cold iron, less than or 17 times ionized
175374	FeKG      1.75000A		# type: i, grain production of cold iron
13012 Directory Listing
Modified 3 years, 4 months ago
Tue Sep 10 22:21:34 2019 UTC
gary
Log:
protect against turbulence of zero - we take its log
12985 Directory Listing
Modified 3 years, 4 months ago
Thu Sep 5 15:11:58 2019 UTC
gary
Log:
document source for two Fe II bands
12938 Directory Listing
Modified 3 years, 5 months ago
Tue Sep 3 12:21:56 2019 UTC
gary
Log:
add ADAS Fe IV.  This model has very approximate
energies for the lower terms but goes high enough to include
permitted transitions.  The existing Chianti model only has
forbidden transitions.
12936 Directory Listing
Modified 3 years, 5 months ago
Sat Aug 31 21:34:03 2019 UTC
gary
Log:
make it clear that DATABASE NAME MASTERLIST
replaces the default masterlist rather than supplement it
12934 Directory Listing
Modified 3 years, 5 months ago
Fri Aug 30 17:31:45 2019 UTC
gary
Log:
document default for set nFnu,
add TOTAL option to get all four components
12930 Directory Listing
Modified 3 years, 5 months ago
Thu Aug 29 21:45:41 2019 UTC
gary
Log:
update LineLabels - comments have changed
12928 Directory Listing
Modified 3 years, 5 months ago
Thu Aug 29 20:41:23 2019 UTC
gary
Log:
bugfix, test on size of tau needed to be in log branch
12924 Directory Listing
Modified 3 years, 5 months ago
Thu Aug 29 16:47:22 2019 UTC
gary
Log:
cross references for SPHERE command
12912 Directory Listing
Modified 3 years, 5 months ago
Fri Aug 23 13:23:48 2019 UTC
gary
Log:
reference to PAH review, add macro
for element H
12910 Directory Listing
Modified 3 years, 5 months ago
Thu Aug 22 19:31:18 2019 UTC
gary
Log:
add two Jin AGN SED papers cited in c19
12909 Directory Listing
Modified 3 years, 5 months ago
Thu Aug 22 19:03:50 2019 UTC
gary
Log:
extrapolate all SEDs to low-energy limit of code
use consistent units for SED points
add references to original papers
12908 Directory Listing
Modified 3 years, 5 months ago
Thu Aug 22 17:11:42 2019 UTC
gary
Log:
LineList_BLR_Fe2, Arnab Sakar add missing Fe II bands

FeII_bands.ini, improve comments in refer to Baldwin+04
12907 Directory Listing
Modified 3 years, 5 months ago
Tue Aug 20 01:09:58 2019 UTC
gary
Log:
The following sim was part of a large grid that explored high-density BLR emission properties and the only one that failed with an assert.  The error tolerance for Al I and Mg I was violated by ~50% on the first evaluation.  This patch allows progress to continue by not throwing the assert during search phase.  The problem only happened on the first evaluation and with this change goes to completion without incident.

=================

set save prefix "assert"
species "Fe+" dataset="Smyth19"
species "Fe+" levels=all
stop column density 23
stop temperature exceeds 1e7 K
print lines sort wavelength
print lines column
iterate
print last
hden 18
table SED "AGN_Jin12_Eddr_mid.sed"
phi(H) 21
normalize to "Inci" 1215 scale factor = 1215
12906 Directory Listing
Modified 3 years, 5 months ago
Sat Aug 17 22:44:29 2019 UTC
gary
Log:
the four SEDs discussed in Ferland+19 MNRAS submitted
reference will be added when available
12904 Directory Listing
Modified 3 years, 5 months ago
Sat Aug 17 11:43:48 2019 UTC
gary
Log:
ADS reference to published paper
12902 Directory Listing
Modified 3 years, 5 months ago
Thu Aug 15 15:07:03 2019 UTC
gary
Log:
two papers on IR CS
12901 Directory Listing
Modified 3 years, 5 months ago
Wed Aug 14 22:30:11 2019 UTC
gary
Log:
exercise save ionization means
12899 Directory Listing
Modified 3 years, 5 months ago
Wed Aug 14 17:36:47 2019 UTC
gary
Log:
line format explain
12893 Directory Listing
Modified 3 years, 5 months ago
Wed Aug 7 23:31:31 2019 UTC
fguzman
Log:
included option for Vriens in the Parser
12892 Directory Listing
Modified 3 years, 5 months ago
Wed Aug 7 21:33:33 2019 UTC
fguzman
Log:
updated Hazy 1 to the new n-changing collisions options
12891 Directory Listing
Modified 3 years, 5 months ago
Wed Aug 7 20:50:17 2019 UTC
fguzman
Log:
merged IsoLebedev branch into trunk
12870 Directory Listing
Modified 3 years, 6 months ago
Tue Jul 30 23:38:43 2019 UTC
gary
Log:
split He I 2 ^3P_J
12869 Directory Listing
Modified 3 years, 6 months ago
Tue Jul 30 23:38:28 2019 UTC
gary
Log:
split He I 2 ^3P_J
12866 Directory Listing
Modified 3 years, 6 months ago
Tue Jul 30 19:08:38 2019 UTC
gary
Log:
rm char some fine offensive
12864 Directory Listing
Modified 3 years, 6 months ago
Mon Jul 29 12:52:41 2019 UTC
peter
Log:
source/mole_h2.cpp:
  - Fix ticket #284: convergence failures due to underflow in Boltzmann factors.
tsuite/auto/h2_pdr_leiden_f1.in:
tsuite/slow/h2_pdr_leiden_f4.in:
tsuite/slow/h2_pdr_leiden_hack_f1.in:
tsuite/slow/h2_pdr_leiden_v1.in:
  - Fix botches resulting from code fix.

12862 Directory Listing
Modified 3 years, 6 months ago
Sat Jul 27 23:10:54 2019 UTC
gary
Log:
logic assumed that SDIV would not return negative
12860 Directory Listing
Modified 3 years, 6 months ago
Sat Jul 27 02:44:15 2019 UTC
gary
Log:
remove sentence saying HD is not computed
12858 Directory Listing
Modified 3 years, 6 months ago
Fri Jul 26 14:53:54 2019 UTC
peter
Log:
source/hydro_vs_rates.cpp:
  - Fix FP exceptions when running with -DFLT_IS_DBL.

12857 Directory Listing
Modified 3 years, 6 months ago
Thu Jul 25 20:37:03 2019 UTC
fguzman
Log:
fix typo in set save prefix in sims
12853 Directory Listing
Modified 3 years, 6 months ago
Wed Jul 24 21:41:51 2019 UTC
fguzman
Log:
fix bug on GetHelikeCollisionStrength(), Percival and Richard collisions are not resolved in l
12852 Directory Listing
Modified 3 years, 6 months ago
Wed Jul 24 20:41:58 2019 UTC
marios
Log:
source/TestSpecies.cpp
  - Add tests for elem_symbol_to_index(), isElementSym().
  - Check return value of parse_chemical().

12849 Directory Listing
Modified 3 years, 6 months ago
Wed Jul 24 13:05:58 2019 UTC
peter
Log:
source/grains.cpp:
source/grainvar.cpp:
source/grainvar.h:
  - Remove estimate of grain charge based on variation with Te during search phase.
    This code could lead to a failed assert and probably did not much good anyway.

12846 Directory Listing
Modified 3 years, 6 months ago
Tue Jul 23 20:45:15 2019 UTC
fguzman
Log:
average some monitors between platforms, after fixing heavy ions impact excitation for iso-sequences in rev. 12845
12845 Directory Listing
Modified 3 years, 6 months ago
Mon Jul 22 18:40:05 2019 UTC
fguzman
Log:
Heavy ions impact excitation is not treated any more for Percival and Richards 1978 ion-ion collisions. It was treated at the same level as the electrons
12844 Directory Listing
Modified 3 years, 6 months ago
Sat Jul 20 16:41:36 2019 UTC
gary
Log:
model of IGM in Perseus galaxy cluster
inspired by Hitomi observations of Fe complex
12843 Directory Listing
Modified 3 years, 6 months ago
Sat Jul 20 11:53:52 2019 UTC
gary
Log:
update line list with Fe III multiplet
12840 Directory Listing
Modified 3 years, 6 months ago
Fri Jul 19 18:25:55 2019 UTC
gary
Log:
as per email exchange with C Morisset,
Kiselius+14 calculation intended for E1 lines and where not
very good for forbidden lines.  These are important density
diagnostics and have been backdated to Irimia&Froese Fischer 2005
# 2005PhyS...71..172I.  
12838 Directory Listing
Modified 3 years, 6 months ago
Thu Jul 18 01:37:52 2019 UTC
gary
Log:
fix missed xref to deleted command, give correct
12837 Directory Listing
Modified 3 years, 6 months ago
Wed Jul 17 21:56:39 2019 UTC
fguzman
Log:
typo in the monitor temperature in the sim m17_p07.in
12834 Directory Listing
Modified 3 years, 6 months ago
Wed Jul 17 11:53:59 2019 UTC
marios
Log:
Merge cdTemp branch back into mainline
12828 Directory Listing
Modified 3 years, 6 months ago
Mon Jul 15 11:40:36 2019 UTC
gary
Log:
the updated dat file
12827 Directory Listing
Modified 3 years, 6 months ago
Sun Jul 14 20:17:57 2019 UTC
gary
Log:
increased number of levels for Fe III, drift over time, use mean of grid_extreme values
12826 Directory Listing
Modified 3 years, 6 months ago
Sun Jul 14 01:46:17 2019 UTC
gary
Log:
Abort when insane species is adjusted.  This is
a more sensible behavior since the user should be made aware of the problem.
The existing implementation did not raise a proper warning so the
insanity could go by unnoticed.
12821 Directory Listing
Modified 3 years, 6 months ago
Fri Jul 12 21:26:27 2019 UTC
gary
Log:
enough levels to caputer Fe III UV34
12820 Directory Listing
Modified 3 years, 6 months ago
Fri Jul 12 16:12:13 2019 UTC
gary
Log:
add Fe III UV 34 multiplet
12815 Directory Listing
Modified 3 years, 6 months ago
Thu Jul 11 16:23:10 2019 UTC
peter
Log:
source/grains_mie.cpp:
  - Add support for the Maxwell Garnett (1904) EMT.
docs/latex/common/bibliography2.bib
docs/latex/hazy1/vanhoof_grain_model.tex
  - Describe the new EMT.
data/fluffy.mix:
  - Update the EMT to a more sensible choice.
  - Fix comment.

12811 Directory Listing
Modified 3 years, 6 months ago
Wed Jul 10 17:35:36 2019 UTC
peter
Log:
data/stout/fe/fe_2/fe_2_Bautista18.coll:
data/stout/fe/fe_2/fe_2_Bautista18.nrg:
data/stout/fe/fe_2/fe_2_Bautista18.tp:
  - Fix level indices in Bautista data files.

12810 Directory Listing
Modified 3 years, 6 months ago
Wed Jul 10 17:05:17 2019 UTC
gary
Log:
Maryam add new Lodders SS abundances, 
use them in two test cases
12808 Directory Listing
Modified 3 years, 6 months ago
Tue Jul 9 18:13:45 2019 UTC
gary
Log:
add two bends needed for analysis of HST AGN observations
12807 Directory Listing
Modified 3 years, 7 months ago
Fri Jul 5 12:01:09 2019 UTC
peter
Log:
source/hydro_vs_rates.cpp:
  - Fix FP exception when running with -DFLT_IS_DBL.

12806 Directory Listing
Modified 3 years, 7 months ago
Tue Jul 2 22:05:41 2019 UTC
fguzman
Log:
adjusting monitors from auto due to reintegration of iso_collisions branch
12805 Directory Listing
Modified 3 years, 7 months ago
Tue Jul 2 18:27:56 2019 UTC
marios
Log:
source/atom_hyperfine.cpp
  - Revert to setting Lya occupation number to 0 if negative.  Add more
    detailed explanation to fixit().
tsuite/programs/hizlte/hizlte.txt
  - Update output of hizlte sim.

12803 Directory Listing
Modified 3 years, 7 months ago
Mon Jul 1 21:59:48 2019 UTC
fguzman
Log:
reintegrate iso_collisions branch into trunk
12800 Directory Listing
Modified 3 years, 7 months ago
Wed Jun 26 16:27:14 2019 UTC
peter
Log:
source/cpu.h:
  - Let NORETURN macro support the Oracle Studio compiler as well.

12796 Directory Listing
Modified 3 years, 7 months ago
Fri Jun 21 22:19:58 2019 UTC
fguzman
Log:
changed names of sims so they are not deleted by clean_tsuite.pl
12795 Directory Listing
Modified 3 years, 7 months ago
Wed Jun 19 11:15:55 2019 UTC
gary
Log:
the Tayal 2018 dataset
12794 Directory Listing
Modified 3 years, 7 months ago
Wed Jun 19 11:14:13 2019 UTC
gary
Log:
use three of the Fe II databases
12792 Directory Listing
Modified 3 years, 7 months ago
Tue Jun 18 22:15:01 2019 UTC
fguzman
Log:
changed monitors to ratio with case b Hummer and Storey predictions
12791 Directory Listing
Modified 3 years, 7 months ago
Tue Jun 18 21:24:48 2019 UTC
gary
Log:
update to correct Bautista data.  This cannot be parsed and returns error
stout/fe/fe_2/fe_2_Bautista18.nrg:2:1: PROBLEM ERROR: found trailing junk after token
  1.0   0.0     10.0

12789 Directory Listing
Modified 3 years, 7 months ago
Tue Jun 18 21:05:29 2019 UTC
fguzman
Log:
added case b simulations for 30000K: the highest temperature of Hummer & Storey
12788 Directory Listing
Modified 3 years, 7 months ago
Tue Jun 18 20:08:02 2019 UTC
gary
Log:
symlink default to Verner - we  will reconsider this
12787 Directory Listing
Modified 3 years, 7 months ago
Tue Jun 18 20:05:42 2019 UTC
gary
Log:
add Bautista and Smyth data sets
12783 Directory Listing
Modified 3 years, 7 months ago
Fri Jun 14 22:22:44 2019 UTC
peter
Log:
tsuite/auto/blr_f92.in:
tsuite/auto/blr_n13_p18.in:
tsuite/auto/blr_n13_p18_Z20.in:
tsuite/auto/blr_n14_p18.in:
tsuite/auto/blr_n14_p22.in:
tsuite/auto/blr_rnfb.in:
tsuite/auto/hii_coolstar.in:
tsuite/auto/pdr_leiden_v2.in:
tsuite/slow/feii_blr_n09_p18_Z20.in:
tsuite/slow/feii_blr_n11_p20_Z20.in:
tsuite/slow/feii_blr_n12_p19.in:
tsuite/slow/feii_blr_n12_p21_Z20.in:
tsuite/slow/feii_blr_n13_p18.in:
tsuite/slow/feii_blr_n13_p18_Z20.in:
  - Fix botches resulting from update to CODATA 2018.

12782 Directory Listing
Modified 3 years, 7 months ago
Fri Jun 14 19:28:42 2019 UTC
peter
Log:
data/*.opc:
  - Update grain opacity files as a result of r12781.

12781 Directory Listing
Modified 3 years, 7 months ago
Fri Jun 14 18:14:41 2019 UTC
peter
Log:
source/physconst_template.h:
  - Update physical constants to CODATA 2018.
  - Update astronomical constants to 2018 definition.
  - Add new constant MOL_MASS_CONST.
source/physconst.cpp:
  - Fix test for CONST_EXPR constants.

12780 Directory Listing
Modified 3 years, 7 months ago
Fri Jun 14 11:54:37 2019 UTC
marios
Log:
source/atom_hyperfine.cpp
  - Remove if-test against non-existent flag conv.lgLyaMaseCommentDone.

12779 Directory Listing
Modified 3 years, 7 months ago
Thu Jun 13 17:00:22 2019 UTC
marios
Log:
atom_hyperfine.cpp
  - Temporary fix: ASSERT non-negative photon occupation numbers in Lya _only_
    when not in search phase.
  - Remove comment that occupation numbers can be negative when the line mases -
    this is unphysical.
lines_service.cpp
  - Improve printf statement used with debugging.

12777 Directory Listing
Modified 3 years, 7 months ago
Wed Jun 12 13:51:35 2019 UTC
peter
Log:
source/parse_table.cpp:
  - Bug-fix: pad keyword with spaces so that unit is always correctly recognized.
source/parser.cpp:
  - Use real path to data file in error messages.
source/cpu.cpp:
source/cpu.h:
  - Export actual location of data file via open_data() if requested.
data/SED/pl1.sed:
  - Extend data range.
  - Exercise NUFNU and UNITS keywords.

12776 Directory Listing
Modified 3 years, 7 months ago
Wed Jun 12 00:17:04 2019 UTC
fguzman
Log:
He-like ions excitations rates use now Percival and Richards (1978) and only He atoms use Vriens and Smeets (1980)
12772 Directory Listing
Modified 3 years, 7 months ago
Tue Jun 11 17:11:16 2019 UTC
peter
Log:
source/Makefile:
  - Bug-fix: when creating dependencies, we should also use the -std=c++11 flag.

12770 Directory Listing
Modified 3 years, 7 months ago
Tue Jun 11 16:31:33 2019 UTC
marios
Log:
Reintegrated branch 21cm
12767 Directory Listing
Modified 3 years, 7 months ago
Fri Jun 7 21:16:57 2019 UTC
rjrw
Log:
Add max field width to quieten g++ 9.1.1 warning

12758 Directory Listing
Modified 3 years, 8 months ago
Tue Jun 4 13:04:38 2019 UTC
peter
Log:
source/Makefile:
  - Emit clear error message when whitespace is embedded in the installation path.

12757 Directory Listing
Modified 3 years, 8 months ago
Tue Jun 4 12:41:50 2019 UTC
gary
Log:
BPT paper
12755 Directory Listing
Modified 3 years, 8 months ago
Sat Jun 1 15:25:14 2019 UTC
gary
Log:
more helpful comment
12753 Directory Listing
Modified 3 years, 8 months ago
Fri May 24 18:21:30 2019 UTC
peter
Log:
source/parse_agn.cpp:
  - Fix bug reported by David Carr: optimizing the AGN command sets wrong initial
    temperature.

12751 Directory Listing
Modified 3 years, 8 months ago
Tue May 21 17:22:21 2019 UTC
peter
Log:
source/cdstd.h:
  - Fix compiler warnings or errors when compiling with openmpi and g++ 8 or later.

12750 Directory Listing
Modified 3 years, 8 months ago
Wed May 15 14:05:20 2019 UTC
peter
Log:
source/helike_einsta.cpp:
source/helike_einsta.h:
source/iso.cpp:
source/iso.h:
source/iso_create.cpp:
source/parse_atom_iso.cpp:
source/prt_lines_helium.cpp:
  - Remove code for He-like fine-structure mixing. This code was not working
    correctly and would also not have any impact for low-Z ions. The situation
    is different for high-Z ions like e.g. Fe XXV where the individual fine-
    structure components can be spectroscopically resolved, but that requires
    major changes in the code. See ticket #425 for details.

12749 Directory Listing
Modified 3 years, 8 months ago
Fri May 10 13:20:10 2019 UTC
gary
Log:
current LineLabels
12747 Directory Listing
Modified 3 years, 8 months ago
Wed May 8 15:54:26 2019 UTC
peter
Log:
docs/latex/hazy1/compos.tex:
docs/latex/hazy2/observed.tex:
  - Make some minor improvements to the discussion of the emergent spectrum.

12746 Directory Listing
Modified 3 years, 9 months ago
Fri May 3 15:19:23 2019 UTC
peter
Log:
source/cont_createpointers.cpp:
source/cont_gammas.cpp:
source/cont_setintensity.cpp:
source/init_sim_postparse.cpp:
source/ion_photo.cpp:
source/ion_recomb_Badnell.cpp:
source/iso_create.cpp:
source/mesh.cpp:
source/mole_reactions.cpp:
source/opacity.h:
source/opacity_addtotal.cpp:
source/opacity_createall.cpp:
source/parse_element.cpp:
source/prt_alltau.cpp:
source/prt_comment.cpp:
source/prt_header.cpp:
source/prt_lines_helium.cpp:
source/prt_lines_hydro.cpp:
source/rt_diffuse.cpp:
source/rt_ots.cpp:
source/rt_stark.cpp:
source/sanity_check.cpp:
  - Do not set up the helium model atoms when helium is not enabled. This was
    done to have access to the ionization potential of He^0 and He^+. This was
    needed in only a handful of places. These instances now use atmdat.EIonPot.
  - Protect access to the helium data with checks for dense.lgElmtOn[ipHELIUM]
    where needed.
source/save_do.cpp:
source/save_opacity.cpp:
  - Bug-fix: fix several save commands that would crash if save output was
    requested for an element that was not enabled. These will now give a useful
    error message.
source/cddrive.h:
  - Remove unused definitions.

12745 Directory Listing
Modified 3 years, 9 months ago
Tue Apr 30 14:56:52 2019 UTC
peter
Log:
source/abund.h:
source/abundances.cpp:
source/elementnames.cpp:
source/elementnames.h:
source/init_defaults_preparse.cpp:
source/input.cpp:
source/input.h:
source/parse_abundances.cpp:
source/parse_element.cpp:
source/parser.cpp:
source/parser.h:
  - Rewrite ABUNDANCES command such that the element symbol is mandatory to
    identify the element the abundance belongs to. This also implies that
    abundances can now be given in arbitrary order and the list of elements
    need not be complete.
  - Remove the ELEMENTS READ command. This is no longer needed as the info
    it gathers is now implicitly contained in the ABUNDANCES command.
  - Modify routine nelem_symbol_to_index() to be completely case-insensitive.
  - Create new methods t_input::peekarray() and Parser::peekNextCommand() to
    test what next command will be (needed to check for CONTINUE lines).
data/c84.ini:
data/fast.ini:
data/ism.ini:
docs/latex/hazy1/cmdintro.tex:
  - Remove ELEMENTS READ command.
docs/latex/hazy1/compos.tex:
  - Update documentation of the ABUNDANCES command.
  - Remove description of the ELEMENTS READ command.
  - Fix typo in the "Variable grain abundances" section.
tsuite/auto/*.in:
tsuite/slow/*.in:
  - Update syntax of ABUNDANCES commands (include '=').

12743 Directory Listing
Modified 3 years, 9 months ago
Sat Apr 20 12:36:44 2019 UTC
peter
Log:
tsuite/auto/hii_paris.in:
  - Fix failure due to Blnd 1860 not being found.

12742 Directory Listing
Modified 3 years, 9 months ago
Fri Apr 19 20:47:31 2019 UTC
gary
Log:
two bug fixes
12741 Directory Listing
Modified 3 years, 9 months ago
Fri Apr 19 18:36:04 2019 UTC
gary
Log:
add FUV Inci 1367A to get away from damped Lya
It is no longer possible to add the unattenuated incident continuum
with set nFnu add since extinction is included - we want true incident
to get EW
12740 Directory Listing
Modified 3 years, 9 months ago
Fri Apr 19 17:47:41 2019 UTC
peter
Log:
source/prt_lines.cpp:
docs/latex/hazy1/miscell.tex:
  - Support molecular species when using SET BLEND QUIET.
source/prt_lines_molecules.cpp:
data/blends.ini:
  - Move H2 blend to blends.ini.

12738 Directory Listing
Modified 3 years, 9 months ago
Fri Apr 19 15:17:14 2019 UTC
gary
Log:
correct errors in EW discussion
12736 Directory Listing
Modified 3 years, 9 months ago
Thu Apr 18 14:23:34 2019 UTC
peter
Log:
docs/latex/hazy1/conout.tex:
source/mole_h2_io.cpp:
  - Fix incorrect description of the SAVE H2 PDR command.

12732 Directory Listing
Modified 3 years, 9 months ago
Fri Apr 12 13:18:02 2019 UTC
peter
Log:
docs/latex/hazy1/miscell.tex:
  - Fix incorrect description of the NO MOLECULES command.

12731 Directory Listing
Modified 3 years, 9 months ago
Wed Apr 10 13:38:56 2019 UTC
peter
Log:
source/cddrive.cpp:
source/maincl.cpp:
  - Bug-fix: this is the third stab at reading the standard blends. The first
    implementation in r12725 didn't work in optimizer runs, and likely also not
    when running Cloudy as a subroutine. The second implementation in r12727
    fixed the first problem but not the second. This third implementation should
    work in all setups.

12730 Directory Listing
Modified 3 years, 9 months ago
Tue Apr 9 21:12:39 2019 UTC
marios
Log:
Typo
12727 Directory Listing
Modified 3 years, 9 months ago
Tue Apr 9 17:31:02 2019 UTC
peter
Log:
source/maincl.cpp:
source/parse_commands.cpp:
source/parse_init.cpp:
source/parser.h:
  - Bug-fix: the solution for reading the blend file adopted in r12725 doesn't
    work in optimizer runs. Fix that here.

12725 Directory Listing
Modified 3 years, 9 months ago
Tue Apr 9 15:03:20 2019 UTC
peter
Log:
source/parse_commands.cpp:
source/lines.cpp:
  - Read blends.ini by default.
source/cddrive.cpp:
source/parse_dont.cpp:
source/prt.h:
  - Create new command NO BLENDS to prevent reading blends.ini.
source/init_defaults_preparse.cpp:
source/parse_set.cpp:
source/prt.h:
source/prt_lines.cpp:
  - Rename prt.user_blend -> prt.blend
docs/latex/QuickStart/QuickStart.tex:
  - Add introductory section on blends.
docs/latex/hazy1/miscell.tex:
  - Document NO BLENDS command.
  - Update description of blends.ini.
docs/latex/hazy1/conout.tex:
docs/latex/hazy1/grid.tex:
  - Revert changes from r12703
tsuite/auto/*.in:
tsuite/slow/*.in:
tsuite/experimental/*.in:
tsuite/programs/vary_nete/vary_nete.cpp:
  - Remove INIT FILE "blends.ini" commands.
  - Add NO BLENDS command in various sims.

12723 Directory Listing
Modified 3 years, 9 months ago
Mon Apr 8 02:39:03 2019 UTC
gary
Log:
orion paper
12722 Directory Listing
Modified 3 years, 9 months ago
Mon Apr 8 02:22:31 2019 UTC
gary
Log:
updated LineLabels.txt at r12702
12720 Directory Listing
Modified 3 years, 10 months ago
Wed Apr 3 18:36:22 2019 UTC
peter
Log:
source/parse_save.cpp:
  - Always save to separate files when using the SAVE TRANSMITTED CONTINUUM
    command in a grid run. The code cannot read concatenated files back in.
source/parse_table.cpp:
  - Rewrite parser of the SAVE TRANSMITTED CONTINUUM using DataParser. This
    avoids problems when reading output generated in a grid run where the top
    comment line is missing for the second and following grid points.
source/save_do.cpp:
  - Ignore the UNITS keyword when writing SAVE TRANSMITTED CONTINUUM output.
    Support for that was not complete and the option is not really needed
    anyway.
docs/latex/hazy1/conout.tex:
  - Update documentation of the SAVE TRANSMITTED CONTINUUM command.

12719 Directory Listing
Modified 3 years, 10 months ago
Fri Mar 29 14:20:36 2019 UTC
gary
Log:
add paper
12713 Directory Listing
Modified 3 years, 10 months ago
Tue Mar 26 18:29:29 2019 UTC
peter
Log:
docs/latex/hazy1/cmdintro.tex:
  - Remove weird invisible character.

12712 Directory Listing
Modified 3 years, 10 months ago
Tue Mar 26 18:20:05 2019 UTC
gary
Log:
replace section 9.2.1 to xref to extended discussion
12711 Directory Listing
Modified 3 years, 10 months ago
Tue Mar 26 17:41:51 2019 UTC
gary
Log:
a work in progress
12710 Directory Listing
Modified 3 years, 10 months ago
Tue Mar 26 17:28:01 2019 UTC
peter
Log:
docs/latex/head_info.tex:
  - Remove non-UTF-8 characters in comments, thus avoiding the need for
    \UseRawInputEncoding.

12709 Directory Listing
Modified 3 years, 10 months ago
Tue Mar 26 15:26:26 2019 UTC
peter
Log:
source/lines.cpp:
source/prt_lines_helium.cpp:
  - Optimize setting up He-like blends by avoiding the use of findline().

12708 Directory Listing
Modified 3 years, 10 months ago
Tue Mar 26 00:11:29 2019 UTC
peter
Log:
tsuite/auto/rerun_parallel.pl:
tsuite/auto/run_parallel.pl:
tsuite/slow/rerun_parallel.pl:
tsuite/slow/run_parallel.pl:
  - These scripts did not call wl_checkall.pl.

12707 Directory Listing
Modified 3 years, 10 months ago
Mon Mar 25 23:51:56 2019 UTC
peter
Log:
tsuite/auto/func_LineList_BLR.in:
tsuite/auto/func_LineList_BLR_Fe2.in:
tsuite/auto/func_LineList_HII.in:
tsuite/auto/func_LineList_HeH.in:
tsuite/auto/func_LineList_He_like.in:
tsuite/auto/func_LineList_NLR.in:
tsuite/auto/func_LineList_PDR.in:
tsuite/auto/func_LineList_PDR_H2.in:
tsuite/auto/func_LineList_strong.in:
tsuite/auto/h2_pdr_leiden_f1.in:
  - Missed these scripts in r12703. They also need blends.ini as they read line
    list files.

12703 Directory Listing
Modified 3 years, 10 months ago
Mon Mar 25 19:36:51 2019 UTC
peter
Log:
source/prt_lines.cpp:
  - Remove hardwired blends and move them into init file blends.ini.
source/prt_final.cpp:
  - Do not look up "Blnd" 5007, but rather its components so that the code can
    run without including blends.ini.
source/lines.cpp:
  - Print suggestion to include blends.ini when a "Blnd" line is not found.
data/blends.ini:
  - New init file containing definitions for blends.
docs/latex/hazy1/conout.tex:
docs/latex/hazy1/grid.tex:
docs/latex/hazy1/miscell.tex:
  - Document the existence of the blends.ini file.
tsuite/auto/*.in:
tsuite/slow/*.in:
tsuite/experimental/dynamics_orion_recom.in:
tsuite/programs/vary_nete/vary_nete.cpp:
  - Include blends.ini were needed.

12702 Directory Listing
Modified 3 years, 10 months ago
Mon Mar 25 15:32:32 2019 UTC
gary
Log:
head_info.tex - silence newly installed grumpiness in LaTex 2018

compos.tex - improved emergent spectrum discussion in section 7.9.6

observed.tex -  improved emergent spectrum discussion in section 2.10

stopping.tex - add label for xref
12701 Directory Listing
Modified 3 years, 10 months ago
Sun Mar 24 17:07:24 2019 UTC
gary
Log:
usse consistent alias for Abel and Shaw Thesis papers
12700 Directory Listing
Modified 3 years, 10 months ago
Sat Mar 23 13:47:08 2019 UTC
gary
Log:
copyright year, to be parallel with code copyright
12699 Directory Listing
Modified 3 years, 10 months ago
Sat Mar 23 13:31:16 2019 UTC
gary
Log:
added refs to Orion
12687 Directory Listing
Modified 3 years, 10 months ago
Wed Mar 20 12:43:26 2019 UTC
gary
Log:
improve comments on NGC 5548 SED file
12680 Directory Listing
Modified 3 years, 10 months ago
Fri Mar 15 19:07:52 2019 UTC
peter
Log:
source/parse_table.cpp:
source/stars.cpp:
  - Rename the TABLE KS18 command to TABLE KS19. This is necessary because we
    added the grids in 2018 before the paper was accepted. But accepting the
    paper took a long time and was only done in 2019.
  - Also rename the data files ks18_qxx.ascii -> ks19_qxx.ascii.

12677 Directory Listing
Modified 3 years, 10 months ago
Fri Mar 15 16:12:52 2019 UTC
peter
Log:
source/save_do.cpp:
  - Fix incorrect return value.

12676 Directory Listing
Modified 3 years, 10 months ago
Fri Mar 15 14:58:26 2019 UTC
peter
Log:
source/parse_set.cpp
source/prt.h:
source/prt_lines.cpp:
  - Add keyword QUIET to the SET BLEND command that causes it to quietly ignore
    blends where a model atom has not been set up for any of the species in the
    blend. Currently does not work for molecular species.
source/species.cpp:
source/species.h:
  - Make first argument of parsespect() const char*.
source/iso_create.cpp:
  - Signal that iso sequence models have been set up using atmdat.chdBaseSources
    and atmdat.lgdBaseSourceExists.
source/atmdat.h:
  - Add comment.
docs/latex/hazy1/miscell.tex:
  - Document the new keyword.

12656 Directory Listing
Modified 3 years, 10 months ago
Tue Mar 12 18:21:18 2019 UTC
peter
Log:
docs/latex/common/bibliography2.bib:
docs/latex/hazy1/cont-shp.tex:
  - Update reference to Khaire & Srianand (2019).

12654 Directory Listing
Modified 3 years, 10 months ago
Fri Mar 8 02:23:52 2019 UTC
gary
Log:
further update to SED, using file sent by Mehdipour
12636 Directory Listing
Modified 3 years, 11 months ago
Wed Mar 6 14:47:04 2019 UTC
peter
Log:
source/cont_ipoint.cpp:
source/opacity_createall.cpp:
source/sanity_check.cpp:
  - Fix various tests in the code as discussed in ticket #421.
  - In ipLineEnergy(), allow line to occupy the same frequency cell as the
    ionization edge.

12633 Directory Listing
Modified 3 years, 11 months ago
Tue Mar 5 18:11:30 2019 UTC
peter
Log:
source/init_defaults_preparse.cpp:
source/parse_set.cpp:
source/prt.h:
source/prt_lines.cpp:
  - Add command SET BLEND allowing the user to create a custom blend.
source/parser.h:
source/prt_linesum.cpp:
source/save_line.cpp:
  - Refactor code for reading a list of lines into a separate routine.
source/maincl.cpp:
  - Avoid saving empty line when using -e command-line syntax.
tsuite/auto/hii_blister.in:
  - Exercise the SET BLEND command.
docs/latex/hazy1/miscell.tex:
  - Document the SET BLEND command.
docs/latex/variables.tex:
  - Add variable for maximum line label length.

12627 Directory Listing
Modified 3 years, 11 months ago
Mon Mar 4 18:46:28 2019 UTC
peter
Log:
source/atmdat_char_tran.cpp:
  - Move last of the Cobalt Blue translated common blocks into external data files.
data/ctiondata.dat:
data/ctrecombdata.dat:
  - New data files holding the charge transfer data.

12623 Directory Listing
Modified 3 years, 11 months ago
Sun Mar 3 17:50:57 2019 UTC
peter
Log:
source/lines.cpp:
source/lines.h:
  - Change addComponent() such that it enforces that blend components have type
    't' and are associated to a transition. In effect this forces them to be
    database lines.
source/prt.cpp:
  - Include transition type in SAVE LINE LABELS output.
source/prt_comment.cpp:
  - Remove test for non-collisional excitation of Blnd 4363 as this is now moot.
source/prt_final.cpp:
  - Replace Blnd 4363 -> O  3 4363.21.
source/prt_lines.cpp:
  - Fix blends as outlined in ticket #415.
data/LineList_BLR.dat:
data/LineList_BLR_Fe2.dat:
data/LineList_HII.dat:
data/LineList_NLR.dat:
data/LineList_strong.dat:
  - Remove Inwd 1035 as it is no longer predicted.
  - Replace Blnd 4363 -> O  3 4363.21 as the blend is no longer predicted.
tsuite/auto/*.in:
tsuite/slow/*.in:
  - Fix errors and botches resulting from the changes above.

12614 Directory Listing
Modified 3 years, 11 months ago
Tue Feb 26 21:43:47 2019 UTC
marios
Log:
Updated NIST reference
12612 Directory Listing
Modified 3 years, 11 months ago
Mon Feb 25 21:25:48 2019 UTC
marios
Log:
source/cool_save.cpp
  - In CoolSave(), make sure that negative cooling is not counted with
    double-checking the total cooling.

12610 Directory Listing
Modified 3 years, 11 months ago
Wed Feb 20 15:14:10 2019 UTC
peter
Log:
tsuite/auto/blr_level2.in:
tsuite/auto/rrc_o.in:
  - Fix wavelengths of RRC lines as a result of r12609.

12609 Directory Listing
Modified 3 years, 11 months ago
Wed Feb 20 14:00:58 2019 UTC
peter
Log:
source/cont_createpointers.cpp:
source/pressure_total.cpp:
source/save_opacity.cpp:
  - Remove the constant 0.9998787 used in conversions of the ionization thres-
    hold obtained with ph1() from eV to Ryd. The origin of this constant is not
    entirely clear and there is no obvious purpose for it. Using the constant
    is not done consistently as it is not used when supplying a photon energy to
    phfit() leading to the failures reported in ticket #407.

12605 Directory Listing
Modified 3 years, 11 months ago
Sun Feb 17 23:08:30 2019 UTC
marios
Log:
updated bibliography
12601 Directory Listing
Modified 3 years, 11 months ago
Fri Feb 15 18:18:21 2019 UTC
peter
Log:
source/init_defaults_preparse.cpp:
source/parse_commands.cpp:
source/parse_table.cpp:
source/rfield.h:
source/save_do.cpp:
  - Add support for SAVE TRANSMITTED CONTINUUM in luminosity mode.
source/save.h:
  - Modify magic number for SAVE TRANSMITTED CONTINUUM output, it is no longer
    compatible with previous versions.
source/parse_save.cpp:
  - Make keyword LAST default for SAVE TRANSMITTED CONTINUUM command. It would
    not work otherwise.
source/parse_commands.cpp:
  - Fix test for radius set.
source/cont_setintensity.cpp:
  - Move test for radius.lgPredLumin to parse_commands.cpp.
  - Remove duplicated tests for radius set.
source/parse_CMB.cpp:
source/parse_backgrd.cpp:
source/parse_blackbody.cpp:
source/parse_commands.cpp:
source/parse_f_nu.cpp:
source/parse_ionpar.cpp:
source/parse_table.cpp:
  - Remove many duplicated initializations of radius.Radius to default value.
source/radius.cpp:
  - Make default radius linear.
docs/latex/hazy1/conout.tex:
docs/latex/hazy1/cont-shp.tex:
  - Document the changes.
tsuite/auto/func_trans_lumi.dat:
tsuite/auto/func_trans_lumi.in:
tsuite/auto/func_trans_read_lumi_scale.in:
tsuite/auto/func_trans_save_lumi.in:
tsuite/auto/trans_lumi.dat:
  - New test suite cases to exercise the SAVE TRANSMITTED CONTINUUM command in
    luminosity mode.
tsuite/auto/pdr_minimal.in:
  - Modify comment.
tsuite/auto/checkall.pl:
tsuite/auto/clean_tsuite.pl:
tsuite/auto/list_broken.pl:
tsuite/auto/rerun_parallel.pl:
tsuite/auto/run_parallel.pl:
tsuite/auto/run_sequence.pl:
tsuite/auto/run_single.pl:
tsuite/auto/run_single_r.pl:
tsuite/experimental/run_sequence.pl:
tsuite/programs/run_programs.pl:
tsuite/rerun_parallel.pl:
tsuite/run_parallel.pl:
tsuite/run_service.pm:
tsuite/slow/rerun_parallel.pl:
tsuite/slow/run_parallel.pl:
tsuite/slow/run_sequence.pl:
  - Fix indentation.

12589 Directory Listing
Modified 3 years, 11 months ago
Wed Feb 13 16:49:19 2019 UTC
peter
Log:
This commit implements line disambiguation by optionally supplying either the
lower and upper level index, or the energy of the lower level. This is supported
by the following commands:

SAVE LINES EMISSIVITY
SAVE LINE LIST
PRINT LINE SUM
TABLE LINES
MONITOR LINE
OPTIMIZE LINES

The command SAVE LINE LABELS has been modified to include the necessary info
needed to do the line disambiguation. Also the following routines support line
disambiguation by accepting a parameter of type LineID:

LinSv::addComponent()
t_LineSave::findline()
cdLine()
cdEmis()
cdGetLineList()
prt_line_err()

Additionaly some line labels were modified to aid with disambiguation:

GrGC -> GrCC, GrCH
Inwd -> InwdBnd (for continuum bands)


source/atmdat.h:
source/atmdat_chianti.cpp:
source/atmdat_lamda.cpp:
source/prt.cpp:
source/prt_lines_hydro.cpp:
  - Update comment for SAVE LINE LABELS output.
source/cddrive.cpp:
source/cddrive.h:
source/cdgetlinelist.cpp:
source/prt.h:
  - Add interfaces that accept a LineID.
source/conv_itercheck.cpp:
  - Fix capitalization.
source/cool_dima.cpp:
  - Bug-fix: we should test that level 2 lines have upper level energy larger
    than the highest level in Stout/Chianti. This is still not safe as level 2
    lines have inaccurate OP energies.
source/init_defaults_preparse.cpp:
source/iter_startend.cpp:
source/lines.cpp:
source/lines.h:
source/monitor_results.cpp:
source/optimize.h:
source/optimize_func.cpp:
source/parse_optimize.cpp:
source/parse_save.cpp:
source/parse_table.cpp:
source/parser.cpp:
source/parser.h:
source/prt_linesum.cpp:
source/save.h:
source/save_do.cpp:
source/save_line.cpp:
  - Implement line disambiguation.
source/lines_service.cpp:
  - Fix typos.
source/prt_final.cpp:
  - Bug-fix: Change "He 1" 5875.64 -> "Blnd" 5875.66.
source/prt_lines_grains.cpp:
  - Change GrGC -> GrCC, GrCH.
source/prt_lines_helium.cpp:
  - Bug-fix: remove duplicate He 1 lines from the line stack.
source/prt_lines_molecules.cpp:
  - Remove trailing spaces in line labels.
source/species_pseudo_cont.cpp:
  - Change Inwd -> InwdBnd for continuum bands.
source/taulines.h:
  - Remove unused constant.
source/TestDataParser.cpp:
  - Update test of getLineID().
source/TestParser.cpp:
  - Add test of getLineID().
docs/latex/hazy1/conout.tex:
docs/latex/hazy1/define.tex:
docs/latex/hazy1/miscell.tex:
docs/latex/hazy1/optimize.tex:
  - Document the new syntax.
  - Document removal of the limits on the number of lines for the PRINT LINE SUM
    and SAVE LINES EMISSIVITY command.
  - Document the inward component of continuum bands.
docs/latex/hazy2/sub.tex:
  - Document the modified API for cdGetLineList().
  - Document the additional API for cdLine().
tsuite/auto/feii_t4n8_rt.in:
tsuite/auto/grains_hot.in:
tsuite/auto/grains_hot_wd01.in:
tsuite/auto/ism_opacity.in:
tsuite/auto/limit_caseb_h_den2_temp37.in:
tsuite/auto/limit_caseb_h_den2_temp4.in:
tsuite/auto/limit_caseb_h_den2_temp5.in:
tsuite/auto/limit_caseb_h_den2_temp5_coronal.in:
tsuite/auto/limit_caseb_he2_den8.in:
tsuite/auto/orion_hii_open.in:
tsuite/programs/mpi/mpi.cpp:
  - Disambiguate lines where needed.
  - Change GrGC -> GrCC.
  - Change Inwd -> InwdBnd for Fe 2 continuum bands.
data/LineList_BLR.dat:
data/LineList_BLR_Fe2.dat:
data/LineList_NLR.dat:
  - Disambiguate the Al 2 1670.79 line.
  - Change Inwd -> InwdBnd for Fe 2 continuum bands.

12585 Directory Listing
Modified 3 years, 11 months ago
Sun Feb 10 11:53:36 2019 UTC
peter
Log:
source/prt_lines.cpp:
  - Bug-fix: fix components for inward blend.

12584 Directory Listing
Modified 3 years, 11 months ago
Sat Feb 9 16:00:07 2019 UTC
peter
Log:
source/iso_level.cpp:
  - Bug-fix. See comment 8 in PR #358 for a detailed discussion.
tsuite/auto/pdr_minimal.in:
  - Add new test suite sim to guard against regression.

12576 Directory Listing
Modified 4 years ago
Mon Feb 4 16:10:52 2019 UTC
peter
Log:
source/rt_continuum.cpp:
  - Bug fix for #396: improve dilution factor.

12574 Directory Listing
Modified 4 years ago
Fri Feb 1 14:54:06 2019 UTC
peter
Log:
source/parse_metal.cpp:
  - Fix bug where METALS DEPLETE command would reset abund.ScaleMetals to 1. This
    made the effect of the METALS DEPLETE and the regular METALS command dependent
    on the sequence of the two commands.
docs/latex/hazy1/compos.tex:
  - Add clarification that the METALS DEPLETE and the regular METALS command can
    be combined to modify the depletion effect.

12572 Directory Listing
Modified 4 years ago
Mon Jan 28 12:49:06 2019 UTC
peter
Log:
docs/latex/hazy1/conout.tex:
  - Clarify SAVE XSPEC MTABLE command.

12570 Directory Listing
Modified 4 years ago
Mon Jan 28 12:08:02 2019 UTC
peter
Log:
source/input.cpp:
source/input.h:
source/monitor_results.cpp:
source/parse_grid.cpp:
  - The vector form of input_readvector() was far too restrictive concerning the
    format of the file it was reading. Replace routine with new version using
    the DataParser so that comments are allowed now.
  - Remove old-style array version of input_readvector().
docs/latex/hazy1/grid.tex:
docs/latex/hazy1/miscell.tex:
  - Document that arrays are allowed now.

12562 Directory Listing
Modified 4 years ago
Thu Jan 24 11:49:00 2019 UTC
peter
Log:
source/parse_table.cpp:
  - Rewrite TABLE SED parser using DataParser.
  - Add option FLAMBDA for TABLE SED files.
source/energy.cpp:
source/energy.h:
  - Add method StandardEnergyUnitNoAbort().
source/parser.cpp
source/parser.h:
  - Add methods getKeyword() and getKeywordOptional().
  - Update error/warning messages.
docs/latex/hazy1/cont-shp.tex:
  - Document changes.
  - Fix erroneous reference to non-existent file.

12560 Directory Listing
Modified 4 years ago
Wed Jan 23 14:53:54 2019 UTC
peter
Log:
source/parse_table.cpp:
  - Fix bug where TABLE SED files that have wavelengths in increasing order are
    rejected. This is not documented behavior.
docs/latex/hazy1/cont-shp.tex:
  - Explicitly state that both increasing and decreasing order of frequencies or
    wavelengths are allowed.
data/SED/Rubin.sed:
  - Reorder this file so that is has wavelengths in increasing order and
    exercises the new code.

12558 Directory Listing
Modified 4 years ago
Tue Jan 22 19:40:12 2019 UTC
peter
Log:
source/mole.h:
source/mole_species.cpp:
  - Speed up the code by partially reverting r12549. Using weak_ptr slowed down
    the code by 1%.
source/helike_einsta.cpp:
  - Speed up AngerJ() with two measures:
    - Use Bessel Jn for integer orders of the Anger J function.
    - Reduce number of qg32() calls by factor 4. The old method was overkill.

12554 Directory Listing
Modified 4 years ago
Mon Jan 21 07:53:48 2019 UTC
peter
Log:
tsuite/auto/func_grid_list.in:
  - This sim should have been sequential.

12552 Directory Listing
Modified 4 years ago
Sat Jan 19 15:09:57 2019 UTC
peter
Log:
source/parse_print.cpp:
  - Bug-fix: LINEAR keyword on PRINT LINES COLUMN command was not picked up.

12551 Directory Listing
Modified 4 years ago
Fri Jan 18 12:34:46 2019 UTC
peter
Log:
source/cddefines.h:
  - Start using nullptr.

12550 Directory Listing
Modified 4 years ago
Fri Jan 18 11:53:55 2019 UTC
peter
Log:
source/hydroeinsta.cpp:
source/iso_create.cpp:
  - Move initialization of same-n transation wavelengths to iso_create.cpp where
    they belong.
  - Remove fake transition energy for transitions outside Cloudy frequency range.

12549 Directory Listing
Modified 4 years ago
Fri Jan 18 10:55:37 2019 UTC
peter
Log:
source/conv_init_solution.cpp:
source/dense.cpp:
source/dynamics.cpp:
source/ion_trim.cpp:
source/mole.h:
source/mole_drive.cpp:
source/mole_eval_balance.cpp:
source/mole_priv.h:
source/mole_reactions.cpp:
source/mole_solve.cpp:
source/mole_species.cpp:
source/parse_species.cpp:
source/parser.h:
source/prt_zone.cpp:
source/radius_next.cpp:
source/save_line.cpp:
source/transition.h:
  - Replace count_ptr with shared_ptr.
  - Replace naked pointer in chem_nuclide with weak_ptr.
  - Add method el() to chem_nuclide to access weak pointer.
source/count_ptr.h:
  - Deleted.

12548 Directory Listing
Modified 4 years ago
Thu Jan 17 15:30:48 2019 UTC
peter
Log:
docs/latex/hazy1/cmdintro.tex:
  - Update discussion of the command line format.

12546 Directory Listing
Modified 4 years ago
Thu Jan 17 10:55:18 2019 UTC
peter
Log:
docs/latex/hazy1/ControllingModelAtoms.tex:
docs/latex/hazy1/cmdintro.tex:
docs/latex/hazy1/conout.tex:
source/TestDataParser.cpp:
source/TestThirdparty.cpp:
source/atmdat_chianti.cpp:
source/cddrive.cpp:
source/cdgetlinelist.cpp:
source/cpu.h:
source/helike_einsta.cpp:
source/iso.cpp:
source/parse_abundances.cpp:
source/parse_commands.cpp:
source/parse_interp.cpp:
source/parser.cpp:
source/parser.h:
source/prt_lines_helium.cpp:
source/thirdparty.cpp:
source/thirdparty.h:
tsuite/auto/agn_lex00_u0.in:
tsuite/auto/agn_lex00_u1.in:
tsuite/auto/agn_lex00_um1.in:
tsuite/auto/agn_warm_absorber_hiU.in:
tsuite/auto/blr_kk81.in:
tsuite/auto/blr_rnfa.in:
tsuite/auto/blr_rnfb.in:
tsuite/auto/coll_t5.in:
tsuite/auto/dynamics_wind.in:
tsuite/auto/func_abund_fluc.in:
tsuite/auto/func_stopline2.in:
tsuite/auto/hii_Um3.in:
tsuite/auto/hii_Um35.in:
tsuite/auto/hii_Um385.in:
tsuite/auto/limit_caseb_he_den2_temp4.in:
tsuite/auto/limit_caseb_he_den4_temp4.in:
tsuite/auto/limit_conserve.in:
tsuite/auto/limit_lte_he1_coll.in:
tsuite/auto/limit_lte_he1_nomole_iso_force.in:
tsuite/auto/limit_lte_he1_nomole_ste.in:
tsuite/auto/limit_lte_he1_nomole_ste_nocoll.in:
tsuite/auto/limit_lte_he1_nomole_ste_nocoll2.in:
tsuite/auto/limit_lte_he1_ste.in:
tsuite/crash/limit_lte_he1_nomole_ste_nocoll2.in:
tsuite/experimental/cosmo_recom.in:
tsuite/mpi/func_test_cycle2.in:
tsuite/mpi/run_parallel.pl:
  - This is the final merge from the (now poorly named) newcomment branch. This
    implements the first update of the input parser to make it check the scripts
    more strictly. From now on all characters in a command name that are typed
    will be checked. Abbreviating commands is still allowed, and the code now
    automatically determines the shortest unambiguous abbreviation (with a
    minimum of four. If a command is not recognized, but close to other commands,
    these will be suggested as alternatives.

12541 Directory Listing
Modified 4 years ago
Wed Jan 16 13:46:54 2019 UTC
peter
Log:
source/grid_xspec.cpp:
  - Bug-fix: fix erroneous allocation of grid.paramData.

12540 Directory Listing
Modified 4 years ago
Wed Jan 16 13:16:19 2019 UTC
peter
Log:
source/atmdat.h:
source/atmdat_chianti.cpp:
source/atmdat_lamda.cpp:
source/atmdat_readin.cpp:
source/atom_hyperfine.cpp:
source/cddefines.h:
source/cddrive.cpp:
source/cdinit.cpp:
source/cont_createmesh.cpp:
source/cont_createpointers.cpp:
source/cont_setintensity.cpp:
source/continuum.h:
source/geometry.h:
source/grains_qheat.cpp:
source/grid.h:
source/grid_xspec.cpp:
source/hcmap.cpp:
source/hcmap.h:
source/hyperfine.h:
source/init_coreload_postparse.cpp:
source/ion_solver.cpp:
source/iso.cpp:
source/iso.h:
source/iso_continuum_lower.cpp:
source/iso_cool.cpp:
source/iso_create.cpp:
source/iso_solve.cpp:
source/iterations.cpp:
source/lines.h:
source/lines_service.cpp:
source/mole.h:
source/mole_h2_create.cpp:
source/mole_reactions.cpp:
source/mole_species.cpp:
source/monitor_results.cpp:
source/opacity.h:
source/parse_atom_iso.cpp:
source/parse_crashdo.cpp:
source/parse_save.cpp:
source/parse_table.cpp:
source/prt_lines_continuum.cpp:
source/prt_linesum.cpp:
source/rfield.h:
source/rt_diffuse.cpp:
source/sanity_check.cpp:
source/save_average.cpp:
source/save_do.cpp:
source/save_fits.cpp:
source/secondaries.cpp:
source/secondaries.h:
source/service.cpp:
source/species.cpp:
source/species2.cpp:
source/taulines.h:
source/temp_change.cpp:
source/timesc.h:
source/zero.cpp:
  - Remove all remaining instances of MALLOC. Apart from specially aligned memory
    for SIMD instructions, we no longer use malloc(). The code is now leak-free!
  - The CRASH UNDEFINED STATIC command has been removed. Since static memory is
    always initialized, this command makes no sense.
  - The default CRASH UNDEFINED command has also been removed as we no longer
    allocate raw data on the heap.
  - The CRASH UNDEFINED STACK | AUTO command has been renamed to plain CRASH
    UNDEFINED as it is now the only variant left.
  - The CRASH BOUNDS HEAP command has been removed since we no longer allocate
    arrays this way.
  - The CRASH BOUNDS ARRAY command has been added to test the STL class "array".
tsuite/crash:
  - The crash test suite has been updated to reflect the changes above.
docs/latex/hazy1/miscell.tex:
  - Document the changes in the CRASH commands.

12539 Directory Listing
Modified 4 years ago
Wed Jan 16 07:46:12 2019 UTC
peter
Log:
source/cloudy.cpp:
source/init_defaults_preparse.cpp:
source/parse_commands.cpp:
source/parser.h:
  - Remove PLOT command. This method of plotting is obsolete.
source/parse_plot.cpp:
source/plot.cpp:
source/plot.h:
  - These files were deleted.
docs/latex/hazy1/conout.tex:
  - Remove documentation of PLOT command.
docs/latex/QuickStart/QuickStart.tex:
  - Fix typo.
tsuite/auto/agn_warm_absorber.in:
tsuite/auto/agn_warm_absorber_hiU.in:
tsuite/auto/blr_f92.in:
tsuite/auto/blr_fp89.in:
tsuite/auto/blr_kk81.in:
tsuite/auto/blr_nf84.in:
tsuite/auto/blr_nf84_45deg.in:
tsuite/auto/hii_coolstar.in:
tsuite/auto/hii_paris.in:
tsuite/auto/stars_rauch_3d.in:
tsuite/auto/stars_rauch_cowd.in:
tsuite/auto/stars_rauch_h+he.in:
tsuite/auto/stars_rauch_h-ca.in:
tsuite/auto/stars_rauch_h-ni.in:
tsuite/auto/stars_rauch_helium.in:
tsuite/auto/stars_rauch_hydr.in:
tsuite/auto/stars_rauch_pg1159.in:
tsuite/auto/stars_rauch_pg1159_ascii.in:
  - Remove PLOT command from these scripts.

12535 Directory Listing
Modified 4 years ago
Tue Jan 15 14:26:55 2019 UTC
peter
Log:
source/atmdat_readin.cpp:
source/atom_leveln.cpp:
source/atoms.h:
source/cddefines.h:
source/cont_createmesh.cpp:
source/dynamics.cpp:
source/dynamics.h:
source/h2.cpp:
source/h2_priv.h:
source/init_sim_postparse.cpp:
source/ion_recomb_Badnell.cpp:
source/iso_create.cpp:
source/iter_startend.cpp:
source/iterations.cpp:
source/iterations.h:
source/mole.cpp:
source/mole.h:
source/mole_h2.cpp:
source/parse_commands.cpp:
source/parse_print.cpp:
source/parse_radius.cpp:
source/parse_set.cpp:
source/parse_stop.cpp:
source/species2.cpp:
  - Remove more instances of MALLOC().

12534 Directory Listing
Modified 4 years ago
Tue Jan 15 10:00:49 2019 UTC
peter
Log:
source/cdinit.cpp:
source/h2_priv.h:
source/iso.h:
source/iso_create.cpp:
source/iso_radiative_recomb.cpp:
source/mole_h2_etc.cpp:
source/opacity.h:
source/opacity_createall.cpp:
source/temp_change.cpp:
  - Remove more instances of MALLOC().

12530 Directory Listing
Modified 4 years ago
Mon Jan 14 17:38:19 2019 UTC
peter
Log:
source/ionbal.cpp:
source/ionbal.h:
  - Remove more calls to MALLOC().

12529 Directory Listing
Modified 4 years ago
Mon Jan 14 12:54:47 2019 UTC
peter
Log:
source/parse_commands.cpp:
source/parser.h:
source/cloudy.cpp:
  - Remove the STATE command. This project has been abandoned.
docs/latex/hazy1/conout.tex:
  - Remove it from the documentation as well.
source/parse_state.cpp:
source/state.cpp:
source/state.h:
  - These files have been removed.
source/container_classes.cpp:
source/container_classes.h:
  - Remove support for saving state.
source/TestFlexArr.cpp:
source/TestMultiArr.cpp:
  - Remove tests of methods to save state.
source/atmdat.cpp:
source/atmdat.h:
source/atmdat_readin.cpp:
source/cdinit.cpp:
source/helike_recom.cpp:
source/struc.h:
source/taulines.cpp:
source/taulines.h:
  - Remove more instances of MALLOC().

12527 Directory Listing
Modified 4 years ago
Sun Jan 13 16:12:37 2019 UTC
peter
Log:
source/iso.cpp:
source/iso.h:
source/parse_atom_iso.cpp:
source/prt_lines_hydro.cpp:
  - Create new command DATABASE H-LIKE KEEP FINE STRUCTURE to retain the fine
    structure of H-like lines on the line stack.
docs/latex/hazy1/ControllingModelAtoms.tex
  - Document the new command.
tsuite/auto/limit_caseb_h_den2_temp37.in:
  - Exercise the new command and monitor some fine structure lines.

12526 Directory Listing
Modified 4 years ago
Sun Jan 13 11:53:47 2019 UTC
peter
Log:
Remove a lot of instances of MALLOC().

12523 Directory Listing
Modified 4 years ago
Fri Jan 11 11:41:04 2019 UTC
peter
Log:
source/monitor_results.cpp:
  - Fix alignment of headers.

12521 Directory Listing
Modified 4 years ago
Thu Jan 10 14:07:13 2019 UTC
peter
Log:
source/hydroeinsta.cpp:
source/sanity_check.cpp:
  - Make sure the code doesn't crash when activating same-n hydrogenic transitions,
    but do not activate them yet.

12520 Directory Listing
Modified 4 years ago
Thu Jan 10 10:50:59 2019 UTC
peter
Log:
source/helike_einsta.cpp:
source/helike_recom.cpp:
source/ion_recomb_Badnell.cpp:
source/iso_create.cpp:
source/iso_radiative_recomb.cpp:
source/iso_solve.cpp:
source/prt_alltau.cpp:
source/prt_comment.cpp:
source/prt_header.cpp:
source/prt_lines_hydro.cpp:
source/prt_zone.cpp:
source/rt_tau_init.cpp:
source/sanity_check.cpp:
  - Replace QuantumNumbers2Index[] with QN2Index().
  - Don't use data that are hardwired to a specific level sequence.
  - Fix incorrect test of quantum numbers in ion_recomb_Badnell.cpp.
source/iso.h:
source/iso.cpp:
source/helike_energy.cpp:
  - Modify QN2Index() such that it also matches unresolved levels with resolved
    parameters. This makes it more compatible with QuantumNumbers2Index[].
  - Refactor QN2Index() to take g as parameter, rather than j.
  - Make QN2ind() safer to use.
  - Refactor energy methods to take g as parameter, rather than j. Otherwise
    they cannot be used for H-like species.
  - Add new method hydro_energy().
source/prt_lines_helium.cpp:
tsuite/auto/pn_paris_fast.in:
  - Fix bug in generating wavelengths for He I Ca B lines.
  - Don't use data that are hardwired to a specific level sequence.
  - Replace QuantumNumbers2Index[] with QN2Index().
  - Refactor GetStandardHeLines() to use the DataParser.
  - Fix test suite sim to use the correct Ca B wavelength.
source/parse_commands.cpp:
  - The NO TIME command should suppress printing the PRNG seed.
docs/latex/hazy1/ControllingModelAtoms.tex:
  - Add caution when using small model atom with He-like species.
source/helike.h:
data/he1_case_b.dat:
  - Update magic number.
  - Update wavelengths.
  - Change level indices to quantum numbers.

12519 Directory Listing
Modified 4 years ago
Thu Jan 10 07:12:42 2019 UTC
peter
Log:
source/cddefines.h:
source/container_classes.h:
source/generic_state.h:
source/species_pseudo_cont.cpp:
source/thirdparty_quadpack.h:
  - Fix compiler warnings with g++ 9.

12514 Directory Listing
Modified 4 years ago
Wed Jan 9 12:43:15 2019 UTC
peter
Log:
source/rt_continuum_shield_fcn.cpp:
  - Remove two unused classes. These were causing compilation warnings with the
    Intel compiler.

12513 Directory Listing
Modified 4 years ago
Wed Jan 9 12:26:29 2019 UTC
peter
Log:
source/atmdat_adfa.cpp:
source/atmdat_adfa.h:
source/helike_cs.cpp:
source/helike_einsta.cpp:
  - Fix compilation errors with the Intel and Oracle compilers.
source/cdstd.h:
  - Add hack to work around bug in cpp versions prior to 6.1.0.
source/cddefines.h:
  - Add pure C++11 headers like <array> and <regex>. They can now be used safely.

12509 Directory Listing
Modified 4 years ago
Sat Jan 5 09:26:41 2019 UTC
peter
Log:
source/hydrocollid.cpp:
  - Remove dependency on QuantumNumbers2Index[] by using quantum numbers instead
    of level indices.
source/atmdat_adfa.cpp:
source/atmdat_adfa.h:
  - Refactor routines working with hydrogen collisional data to use quantum
    numbers instead of level indices.
data/h_coll_str.dat:
  - Change level indices to quantum numbers.

12508 Directory Listing
Modified 4 years ago
Sat Jan 5 06:56:11 2019 UTC
peter
Log:
source/helike_einsta.cpp:
source/helike_einsta.h:
source/iso_collide.cpp:
  - Refactor ForbiddenAuls() such that it no longer depends on QuantumNumbers2Index[].
  - Refactor he_1trans() to remove error1 and error2. These were never used. Also
    remove Enerwn and calculate this on the fly when needed. This makes it safe to
    call the routine for transitions that are not in the line stack.
  - Refactor helike_transprob_collapsed_to_collapsed() to remove Enerwn as parameter.
  - Refactor helike_transprob_collapsed_to_resolved() to remove Enerwn as parameter.
source/iso.cpp:
source/iso.h:
source/iso_error.cpp:
  - Create new method QN2Index(). This is a safe version of QuantumNumbers2Index[]
    that avoids out-of-bounds array access when a level is not present on the stack.
  - Modify iso_init_energies() to also read the hydrogenic level energies.
  - Add new method iso_put_error() that takes QNPair as argument, rather than level
    indices. This version will quietly return when at least one of the levels is not
    present on the stack.
data/hydro_energies.dat:
  - New data file with hydrogenic level energies. Only read, but not used yet.

12507 Directory Listing
Modified 4 years, 1 month ago
Thu Jan 3 11:19:44 2019 UTC
peter
Log:
source/helike_einsta.cpp;
  - Refactor he_1trans() such that it no longer needs ipLo, ipHi.
  - Remove getG() as the source of the bogus J values has been fixed.
  - Start converting ForbiddenAuls() to remove dependency on ipLo, ipHi.
source/helike.h:
source/helike_energy.cpp:
data/helike_energies.dat:
  - Move He-like level energies and ionization potentials into separate file
    (helike_energies.dat). The data are now stored in the iso_sp class.
  - Refactor helike_energy() such that it no longer needs ipLo, ipHi.
source/iso.cpp:
source/iso.h:
  - Add routine for reading helike_energies.dat called iso_init_energies().
  - Add methods for retrieving the energies for a given set of quantum numbers
    from iso_sp, called energy() and energy_ioniz().
source/iso_create.cpp:
  - Call iso_init_energies().
source/helike_cs.cpp:
  - Improve error checking.
source/parser.h:
source/TestDataParser.cpp:
  - Add new checkEOF() method.
source/physconst_template.h:
  - Add constants ELECTRON_MASS_U, PROTON_MASS_U, ALPHA_MASS_U, H_RYD_FACTOR,
    and HE_RYD_FACTOR.

12506 Directory Listing
Modified 4 years, 1 month ago
Wed Jan 2 07:22:59 2019 UTC
peter
Log:
source/helike_einsta.cpp:
source/helike_einsta.h:
  - Refactor TransProbs such that it uses quantum numbers rather than index.
  - Rewrite HelikeTransProbSetup() to use DataParser.
source/iso.h:
source/iso_create.cpp:
  - Remove iso_sp[][].IndexIfAllResolved[][][]. This is no longer needed.
source/helike.h:
data/he_transprob.dat:
  - Update file to include quantum numbers.

12505 Directory Listing
Modified 4 years, 1 month ago
Tue Jan 1 07:42:34 2019 UTC
peter
Log:
source/helike_cs.cpp:
  - Refactor HeCS array into map so that it no longer depends on QuantumNumbers2Index.
  - Rewrite parser for he1_cs.dat using DataParser.
source/helike_cs.h:
  - Do not export CSTemp and HeCS. This is not needed.
source/helike_einsta.cpp:
source/hydro_bauman.cpp:
source/iso.h:
  - Refactor Index into QNPair and QNPack structs.
  - Get rid of preprocessor macros.
source/iso_create.cpp:
  - Add routine getL() for converting e.g. 'P' -> 1.
source/parser.h:
  - Fix typo in comment.
source/thirdparty.h:
source/thirdparty_interpolate.cpp:
  - Refactor linint() so that it can work on realnum arrays as well.
source/helike.h:
  - Get rid of preprocessor macros.
  - Update magic number for he1_cs.dat.
data/he1_cs.dat:
  - Added J values in the file.

12495 Directory Listing
Modified 4 years, 1 month ago
Sat Dec 29 03:27:14 2018 UTC
peter
Log:
source/ran.cpp:
  - Fix compiler error with Mac Homebrew compiler.
source/species.cpp:
  - Fix warning with Homebrew g++ 8.

12493 Directory Listing
Modified 4 years, 1 month ago
Sat Dec 29 02:04:25 2018 UTC
peter
Log:
This is the third and final commit from the backtrace branch. Here the lgAbort
variable is replaced with throwing a cloudy_abort. This cleans up the code and
prevents it from producing lots of meaningless output when it soldiers on after
the abort. This behavior is no longer needed as we have a new method to create
stub output files for grid points that failed.

This commit also works around a mysterious bug where the headers of the gathered
output of a grid run would be missing. This was caused by the fact that a file
that was opened was positioned at the start, despite being opened in append mode.
This is worked around by explicitly positioning the file at the end. This should
not be needed, but it fixes he problem...

12491 Directory Listing
Modified 4 years, 1 month ago
Fri Dec 28 11:42:52 2018 UTC
peter
Log:
source/lines.cpp:
  - Second attempt to revert the 1% slowdown from r12481. See also r12490.

12490 Directory Listing
Modified 4 years, 1 month ago
Fri Dec 28 04:32:00 2018 UTC
peter
Log:
source/lines.cpp:
  - In r12481 the test suite slowed down by about 1%. The test case
    grid_h2coronal.in was badly affected. This is an attempt to fix this.

12488 Directory Listing
Modified 4 years, 1 month ago
Fri Dec 28 02:33:53 2018 UTC
peter
Log:
source/TestFlexArr.cpp:
  - Fix compiler warning from clang++.
source/capabilities.pl:
  - Improve detection of g++ compiler, as it may be called something like g++-7.
source/sys_llvm/Makefile.conf:
  - Remove -freciprocal-math flag as it may lead to miscompiled code.

12487 Directory Listing
Modified 4 years, 1 month ago
Thu Dec 27 05:21:57 2018 UTC
peter
Log:
source/ran.cpp:
source/ran.h:
source/thirdparty.cpp:
  - Bug-fix: fill_ran_pool() was hardwired to the global ran instantiation. This
    violates the intended design where it is OK to have multiple local
    instantiations. Remove this routine and pass a pointer to the routine for
    filling the pool to the ran_pool class instead.
  - Upgrade the xoroshiro128+ algorithm to v1.0. We had the 2016 version.
  - Clean up the classes and fix some errors in the comments.
source/TestRandom.cpp:
  - Add test to check that random number sequence is as expected. This validates
    that the PRNG algorithms in Cloudy are still identical to the ones posted by
    Blackman & Vigna.

12486 Directory Listing
Modified 4 years, 1 month ago
Tue Dec 25 21:17:54 2018 UTC
peter
Log:
source/TestRandom.cpp:
  - Restrict testing normal distribution to 4 sigma. Going out to 5 sigma makes
    the test too susceptible to shot noise.
  - Fix centering of the bins in TestRanNormal.
source/TestThirdparty.cpp:
  - Loosen tolerance a bit further as this test still fails on some platforms
    due to differences in roundoff error.

12485 Directory Listing
Modified 4 years, 1 month ago
Tue Dec 25 04:10:07 2018 UTC
peter
Log:
source/ran.cpp:
source/ran.h:
source/thirdparty.cpp:
source/thirdparty.h:
  - Add second PRNG algorithm named xoshiro256**. Blackman & Vigna now promote
    this as their all-purpose, rock-solid generator. So it would be strange if
    Cloudy did not support it. The previous algorithm xoroshiro128+ is retained
    as a second option.
source/ran.h:
source/mpi_utilities.cpp:
source/optimize_phymir.cpp:
  - Rename t_ran::reseed() -> t_ran::new_rank() as this method does not change
    the seed, so the old name was inappropriate.
  - Replace preprocessor functions with inline functions.
source/capabilities.pl:
  - Remove obsolete tests for g++ version as our minimum requirement is 4.8.1.
docs/latex/hazy1/cmdintro.tex:
  - Document the change in PRNG algorithm.

12484 Directory Listing
Modified 4 years, 1 month ago
Mon Dec 24 22:10:39 2018 UTC
peter
Log:
docs/latex/hazy1/cmdintro.tex:
  - Add description of our random number generator.

12483 Directory Listing
Modified 4 years, 1 month ago
Mon Dec 24 21:43:50 2018 UTC
peter
Log:
bibliography2.bib:
  - Add Marsaglia & Tsang (2000).

12481 Directory Listing
Modified 4 years, 1 month ago
Sat Dec 22 23:48:33 2018 UTC
peter
Log:
source/cddrive.cpp:
source/conv.cpp:
source/conv.h:
source/conv_base.cpp:
source/dense.cpp:
source/grains_mie.cpp:
source/grid_do.cpp:
source/ionbal.cpp:
source/lines.cpp:
source/lines.h:
source/monitor_results.cpp:
source/optimize.h:
source/optimize_phymir.cpp:
source/parse_commands.cpp:
source/parse_print.cpp:
source/parse_state.cpp:
source/prt.cpp:
source/prt_final.cpp:
source/save_fits.cpp:
source/service.cpp:
source/state.cpp:
source/state.h:
source/thirdparty.cpp:
source/version.cpp:
source/version.h:
  - Remove more instances of INPUT_LINE_LENGTH.

12480 Directory Listing
Modified 4 years, 1 month ago
Sat Dec 22 16:28:42 2018 UTC
peter
Log:
source/ran.cpp:
source/ran.h:
source/mc_escape.cpp:
source/TestRandom.cpp:
source/TestVectorize.cpp:
  - Fix compilation problems with -DFLT_IS_DBL in effect.
  - Rename ran.flt() -> ran.rnm() to make it clearer that it returns a realnum.
  - Reduce size of unit tests for random numbers to speed them up.

12479 Directory Listing
Modified 4 years, 1 month ago
Fri Dec 21 15:59:38 2018 UTC
peter
Log:
source/maincl.cpp:
source/cdinit.cpp:
source/ran.cpp:
source/ran.h:
  - Make using a random seed the default.
  - Add -s command line option to set fixed seed.
  - Remove all seed() methods.
  - Add print_seed() method.
source/parse_atom_h2.cpp:
source/parse_atom_iso.cpp:
source/parse_crashdo.cpp:
source/parse_set.cpp:
  - Remove option to set seed in various commands. Having user commands set the
    seed is difficult to control in grid an optimizer runs.
source/cddefines.h:
source/cpu.cpp:
source/cpu.h:
source/parse_commands.cpp:
source/service.cpp:
  - Print PRNG seed in main output, as well as ShowMe() and traceback output. It
    is useful to have a record of this for future reference.
source/mpi_utilities.cpp:
source/optimize_phymir.cpp:
  - Try to generate the same random number sequence for a given seed on a fork()
    vs. MPI run (assuming the number of ranks is identical).
source/mpi_utilities.cpp:
  - Use t_ran class to initialize random_shuffle().
source/capabilities.pl:
  - Improve optimization for MPI compilations.
docs/latex/hazy1/ControllingModelAtoms.tex:
docs/latex/hazy1/miscell.tex:
  - Document the changes.

12478 Directory Listing
Modified 4 years, 1 month ago
Wed Dec 19 00:15:15 2018 UTC
peter
Log:
source/prt.cpp:
  - Remove print statement. This was producing output during unit testing, which
    should be avoided. In this case the statement was not concidered to be
    sufficiently important to retain, so the simple fix is to remove it.

12477 Directory Listing
Modified 4 years, 1 month ago
Tue Dec 18 19:54:24 2018 UTC
peter
Log:
source/TestMultiArr.cpp:
  - Fix compiler warnings from clang++.
source/TestThirdparty.cpp:
  - Fix failed tests. These result from a different random number sequence
    generating different test cases.
source/ran.cpp:
source/ran.h:
  - Remove lgPrint option and export seed instead. This gives user more freedom
    when and where the seed will be printed.
  - Work around internal copiler bug in Oracle Studio compiler 12.6 when compiling
    convert_double(), etc. The new code is also guaranteed not to violate strict
    aliasing rules, so should be better anyway.

12476 Directory Listing
Modified 4 years, 1 month ago
Mon Dec 17 18:04:14 2018 UTC
peter
Log:
source/mpi_utilities.cpp:
source/optimize_phymir.cpp:
source/ran.cpp:
source/ran.h:
  - The random number class would seed MPI ranks correctly (i.e. making sure
    that each rank generates a different sequence). This was not the case for
    forked runs though, so fix that here.
  - Bug fix: aligned memory should be freed with posix_memalign_free().
  - Bug fix: make sure that the command parser only seeds the random generator
    once. Poor randomness could otherwise result in grid or optimizer runs.
  - Delete copy ctor and assignment operator for ran_pool and t_ran classes.
    These would not be safe.
  - Use /dev/urandom instead of local time (when available) to create random
    seed. This works better if multiple Cloudy jobs are started simultaneously
    in a script. They might otherwise get the same seed.
source/vectorize.h:
source/cpu.h::
  - Move definitions of posix_memalign() and posix_memalign_free() from
    vectorize.h to cpu.h since that seems a better place for them.
source/cloudyconfig_vs.h:
source/configure.sh:
  - Add test to determine if /dev/urandom is available to obtain a seed.

12475 Directory Listing
Modified 4 years, 1 month ago
Mon Dec 17 17:48:21 2018 UTC
peter
Log:
source/cddefines.h:
source/iso_error.cpp:
source/iso_radiative_recomb.cpp:
source/service.cpp:
  - The routine MyGaussRand() calculates a non-standard normal distribution that
    is truncated to 3 sigma (to avoid negative values). It is not appropriate to
    export such a non-standard routine, so make it internal to iso_error.cpp and
    rename it to TruncatedNormal() for clarity.

12474 Directory Listing
Modified 4 years, 1 month ago
Mon Dec 17 17:39:28 2018 UTC
peter
Log:
source/hydro_bauman.cpp:
  - Fix compiler warning about unused variable when compiling with -DNDEBUG.

12473 Directory Listing
Modified 4 years, 1 month ago
Mon Dec 17 17:37:25 2018 UTC
peter
Log:
source/cddefines.h:
source/mole_species.cpp:
  - In C++11 auto_ptr is deprecated. Since our auto_vec class is styled after
    auto_ptr, it will have the same deficiencies and should be removed.
source/TestAutoVec.cpp:
  - File deleted.

12470 Directory Listing
Modified 4 years, 1 month ago
Sat Dec 15 16:08:20 2018 UTC
peter
Log:
source/TestMain.cpp:
source/TestMesh.cpp:
source/TestRandom.cpp:
source/TestService.cpp:
source/TestThirdparty.cpp:
source/TestVectorize.cpp:
source/cddefines.h:
source/cdinit.cpp:
source/cdstd.h:
source/cpu.h:
source/ion_recomb_Badnell.cpp:
source/iso.h:
source/mc_escape.cpp:
source/mole_h2_create.cpp:
source/mole_h2_io.cpp:
source/parse_atom_h2.cpp:
source/parse_atom_iso.cpp:
source/parse_crashdo.cpp:
source/parse_set.cpp:
source/ran.cpp:
source/ran.h:
source/random_crash.cpp:
source/service.cpp:
source/thirdparty.cpp:
source/thirdparty.h:
  - This is a partial merge from the spindust branch to bring in the new random
    number generator class. The core of the class is in the files ran.h and
    ran.cpp. The existing routines based on the Mersenne twister algorithm have
    been removed and the code is moved over to the new class where possible. The
    code is based on the xoroshiro128+ algorithm which is both faster and better
    than Mersenne twister. The code is fully vectorized on supported platforms
    and is also aware of parallelization making sure that every rank generates a
    different random number sequence. RandGauss() has been replaced by a faster
    version based on the Ziggurat algorithm.
  - Add unit tests for the new random number infrastructure.
  - Add an improved implementation of the Dawson function.

12466 Directory Listing
Modified 4 years, 1 month ago
Fri Dec 14 18:11:26 2018 UTC
peter
Log:
source/abundances.cpp:
source/cont_setintensity.cpp:
source/grains.cpp:
source/grains.h:
source/grains_mie.cpp:
source/grains_qheat.cpp:
source/grainvar.cpp:
source/grainvar.h:
source/mole_h2_form.cpp:
source/mole_reactions.cpp:
source/mole_solve.cpp:
source/mole_species.cpp:
source/monitor_results.cpp:
source/prt_comment.cpp:
source/prt_final.cpp:
source/prt_lines_grains.cpp:
source/prt_zone.cpp:
source/radius_increment.cpp:
source/save_do.cpp:
  - Apply the rule of zero to all classes used in the grain code. Two classes
    had non-trivial destructors: GrainBin and GrainVar. This was because both
    had two arrays of pointers to data allocated with new. These have now been
    transformed into arrays of classes. Hence the destructors are no longer
    needed and can be deleted. This however leads to rather invasive changes
    in the code...
  - Use the DataParser in ReadAugerData().
  - Move class methods from grains.cpp to grainvar.cpp.
source/init_defaults_preparse.cpp:
source/zero.cpp:
  - Move the call to gv.clear() from zero() to InitDefaultsPreparse().
  - Remove the routine GrainZero().

12465 Directory Listing
Modified 4 years, 1 month ago
Fri Dec 14 13:57:06 2018 UTC
peter
Log:
source/hydro_bauman.cpp:
source/service.cpp:
source/service.h:
  - Speed optimization of H_Einstein_A(). The new version is almost a factor of
    five faster.

12462 Directory Listing
Modified 4 years, 1 month ago
Wed Dec 12 18:36:24 2018 UTC
peter
Log:
tsuite/auto/func_gaunt.in:
  - Delete this script as it uses DRIVE commands which no longer exist.
source/TestGaunt.cpp:
  - Move the functionality of the func_gaunt.in script into the unit tests. This
    is a better place for them anyway...
source/TestMain.cpp:
  - Disable backtrace since we are generating lots of errors on purpose.
source/cpu.cpp:
source/cpu.h:
  - New methods for disabling and (re-)enabling backtraces.

12461 Directory Listing
Modified 4 years, 1 month ago
Wed Dec 12 17:06:33 2018 UTC
peter
Log:
source/atmdat_gaunt.cpp:
source/atmdat_gaunt.h:
source/init_defaults_preparse.cpp:
source/parse_commands.cpp:
source/parse_drive.cpp:
source/parser.h:
source/prt_lines.cpp:
source/rt.h:
source/rt_continuum_shield_fcn.cpp:
source/trace.h:
  - Remove all DRIVE commands. They are obsolete and may no longer work.
docs/latex/hazy1/miscell.tex:
  - Remove the documentation.

12453 Directory Listing
Modified 4 years, 1 month ago
Sun Dec 9 23:24:21 2018 UTC
peter
Log:
This is the second merge from the backtrace branch. It implements "fixing"
missing or empty save files from a certain grid point (due to a crash of some
sort) by creating a stub version of the file from another successful grid
point. This is done by replacing all digits from the successful file with
zeroes.

Support for backtraces is improved on Macs. In the case of an FP exception or
segfault, the address of the location where the signal was generated is now
correctly substituted in the call stack. The Homebrew g++ compiler will now
produce a correct backtrace in debug mode (but still nothing in optimized
mode).

12442 Directory Listing
Modified 4 years, 2 months ago
Wed Dec 5 13:50:22 2018 UTC
peter
Log:
source/cddefines.h:
source/cpu.cpp:
source/cpu.h:
source/maincl.cpp:
source/parse_print.cpp:
source/parse_set.cpp:
source/service.cpp:
  - Remove the '-a' command line flag, the SET ASSERT ABORT command, and the
    OLD_ASSERT compiler flag. These all had the aim to modify the ASSERT macro
    such that it aborts rather than throw a C++ exception. This behavior was
    deprecated.
docs/latex/hazy1/miscell.tex:
tsuite/crash/ReadMe.txt:
  - Document the changes.
tsuite/crash/assert_abort.in:
  - Deleted.

12433 Directory Listing
Modified 4 years, 2 months ago
Tue Dec 4 16:46:12 2018 UTC
peter
Log:
source/cpu.cpp:
  - Fix warning from g++ 9 compiler.

12428 Directory Listing
Modified 4 years, 2 months ago
Thu Nov 29 12:08:38 2018 UTC
peter
Log:
source/sys_llvm/Makefile.conf:
  - Silence warning about unused command line arguments.

12427 Directory Listing
Modified 4 years, 2 months ago
Wed Nov 28 17:35:02 2018 UTC
peter
Log:
source/capabilities.pl:
  - Bug-fix: disabling position independent executables broke the configure.sh
    script for the Homebrew g++ compiler. This improves the test for support for
    the -no-pie and -fno-pie flags by the compiler.

12425 Directory Listing
Modified 4 years, 2 months ago
Wed Nov 28 15:17:46 2018 UTC
peter
Log:
tsuite/crash/*.in:
  - Make sure scripts are complete and up to date.
tsuite/crash/runall.pl:
  - Deleted.
tsuite/crash/run_parallel.pl:
tsuite/crash/run_sequence.pl:
tsuite/crash/checkall.pl:
  - Use standard scripts for running the test suite.
tsuite/crash/ReadMe.txt:
  - Update description of files.

12423 Directory Listing
Modified 4 years, 2 months ago
Tue Nov 27 22:50:21 2018 UTC
peter
Log:
source/Makefile:
source/capabilities.pl:
  - Improve code for disabling position independent executables. The -no-pie flag
    is only supported from g++ 6 onwards, so do not break older compilers.

12422 Directory Listing
Modified 4 years, 2 months ago
Tue Nov 27 22:15:40 2018 UTC
peter
Log:
source/Makefile:
  - Fix bashism in Bourne script. This would not run with /bin/dash (e.g.,
    under Ubuntu 18.04, /bin/sh is linked to /bin/dash).
source/configure.sh:
  - Disable creating position independent executables. This breaks addr2line.

12419 Directory Listing
Modified 4 years, 2 months ago
Tue Nov 27 17:30:02 2018 UTC
peter
Log:
source/Makefile:
source/sys_clang_analyzer/Makefile.conf:
source/sys_gcc_gcov/Makefile.conf:
source/sys_icc/Makefile.conf:
source/sys_icc/sys_icc_mac/Makefile.conf:
source/sys_llvm/Makefile.conf:
source/sys_oraclestudio/Makefile.conf:
  - Only use -fnon-call-exceptions flag when compiling cpu.cpp. Limited testing
    shows that this is enough to get the desired behavior. Hopefully this will
    revert the slowdown of the code with g++.
  - Add flag -fasynchronous-unwind-tables to compile options.
source/cddefines.h:
source/cpu.cpp:
  - Remove obsolete cases.
source/service.cpp:
  - Produce backtrace when TotalInsanity() is executed.

12417 Directory Listing
Modified 4 years, 2 months ago
Mon Nov 26 15:21:27 2018 UTC
peter
Log:
source/iter_end_chk.cpp:
  - Remove inappropriate call to TotalInsanity().

12416 Directory Listing
Modified 4 years, 2 months ago
Mon Nov 26 00:03:37 2018 UTC
peter
Log:
source/cpu.cpp:
  - Disable backtrace for Homebrew compiler on MacOS.
source/parse_crashdo.cpp:
  - Add missing keyword.

12415 Directory Listing
Modified 4 years, 2 months ago
Sun Nov 25 22:44:03 2018 UTC
peter
Log:
This is the first merge from the backtrace branch. This implements a proper
signal handler for various exceptions like floating point exceptions and
segmentation violations. These are then rethrown as a C++ exception so that grid
runs can recover from these. On supporting platforms a traceback at the point of
failure will also be generated.

This merge includes the following noteworthy changes:

- The commands CRASH SEGFAULT, CHASH ABORT, and CRASH GRID were added.
- A C++ exception cloudy_abort was added. This is currently not used (apart from
  the CRASH ABORT command) but should in time replace the lgAbort flag. Also the
  C++ exception bad_signal was added to handle OS exceptions like segfaults.
- The routine cdBacktrace() was added. This is intended for debugging and allows
  a non-invasive backtrace to be generated (meaning that execution will continue
  normally after cdBacktrace() exits). This is useful to figure out what code
  path was taken to get to the place where the cdBacktrace() call was inserted.
  Since it is non-invasive, cdBacktrace() can be called multiple times in a run.
- The main program has been modified to catch the new C++ exceptions. This will
  also affect all programs that call Cloudy as a subroutine.

12410 Directory Listing
Modified 4 years, 2 months ago
Wed Nov 21 14:02:57 2018 UTC
peter
Log:
source/cdinit.cpp:
source/cloudy.cpp:
source/cpu.cpp:
source/cpu.h:
source/grid.h:
source/init_defaults_preparse.cpp:
source/maincl.cpp:
source/mpi_utilities.h:
source/parse_optimize.cpp:
  - Merge p_lgMPISingleRankMode in t_cpu_i and lgParseOnly in t_grid into one
    state variable p_MPIMode in t_cpu_i.
  - Bug-fix: turn off trace output before we close the output file. This prevents
    spurious messages to stdout when running a grid with trace output on. 

12401 Directory Listing
Modified 4 years, 2 months ago
Mon Nov 19 00:40:51 2018 UTC
peter
Log:
source/cdinit.cpp:
  - Fix bug introduced by r12399.

12399 Directory Listing
Modified 4 years, 2 months ago
Sun Nov 18 22:55:29 2018 UTC
peter
Log:
Kearn Grisdale reported a bug in a grid run where some of the grid models
failed because a boundary of the TABLE STAR command was overrun. This resulted
in certain files being completely missing and also to incorrect values in
certain variables in the t_save class. This would then lead to hanging processes
in an MPI run. This commit fixes these problems.

source/cddrive.h:
source/cddrive.cpp:
  - Add new version of cdOutput() that takes a file pointer as argument.
  - Change type of filename from const char* -> const string& in cdOutput() as
    well as cdInput().
source/grid.h:
source/cloudy.cpp:
  - Add option to only parse the input and then exit.
source/cpu.cpp:
  - Bug-fix: only increment nFileDone if opening the file was successful.
source/parse_save.cpp:
source/init_defaults_preparse.cpp:
  - Bug-fix: only store file names of save files during the initial parsing.
    Later calls to cdMain() during a grid may not be successful, which would
    invalidate the list of filenames. This in turn can cause problems when
    the gathering of the output files is done after the grid has completed.
source/maincl.cpp:
  - Bug-fix: parse the original input script again if the last grid model of
    that rank failed. This assures that global structures like t_save hold
    correct information which is needed during the gathering of the output
    files. Write the output of this additional parsing run to a scratch file
    that is deleted when parsing is complete.
  - Bug-fix: a single "-" is accepted as command line argument (which would
    mean: read from standard input) but this is not treated correctly.
source/mpi_utilities.cpp:
  - Bug-fix: when grid models fail, certain output files may be absent. Make
    sure the code does not trip over that.
source/save.h:
source/parse_save.cpp:
source/save_do.cpp:
  - Bug-fix: make sure we can find the name of the SAVE GRID file, which allows
    us to open the file in SaveGrid() when this was not done during parsing
    (which can happen if there was an error in one of the lines parsed before
    the SAVE GRID command). This allows us to log the error under all circum-
    stances and make sure that the SAVE GRID output is complete.

12398 Directory Listing
Modified 4 years, 2 months ago
Thu Nov 15 03:31:19 2018 UTC
peter
Log:
source/hydro_tbl.cpp:
  - Fix use of undefined type uint.

12395 Directory Listing
Modified 4 years, 2 months ago
Thu Nov 8 21:27:30 2018 UTC
fguzman
Log:
There can't be critical l-mixing density without l-changing collisions, so we are not printing them when these collisions are shut down
12393 Directory Listing
Modified 4 years, 3 months ago
Fri Nov 2 15:29:34 2018 UTC
peter
Log:
source/parse_save.cpp:
  - Clarify header of the SAVE CONTINUUM BINS command.

12367 Directory Listing
Modified 4 years, 3 months ago
Thu Oct 11 13:30:43 2018 UTC
peter
Log:
source/hydro_bauman.cpp:
  - Remove debug statement.

12366 Directory Listing
Modified 4 years, 3 months ago
Mon Oct 8 15:18:43 2018 UTC
peter
Log:
source/iso.h:
source/hydro_bauman.cpp:
source/helike_einsta.cpp:
  - Also cache Auls calculated by H_Einstein_A_log10().

12365 Directory Listing
Modified 4 years, 3 months ago
Mon Oct 8 10:00:37 2018 UTC
peter
Log:
source/iso.h:
source/helike_einsta.cpp:
  - Removing the CachedAs array slowed down the test suite quite a bit. This
    indicates that calculating the He-like A values is more CPU intensive than
    was assumed. Here we introduce a new form of caching A values that does not
    get in the way of code development and hopefully recovers the CPU time lost
    in r12361.

12364 Directory Listing
Modified 4 years, 3 months ago
Sun Oct 7 14:38:02 2018 UTC
peter
Log:
source/hydro_tbl.cpp:
  - Fix compiler warning in ndebug runs.

12362 Directory Listing
Modified 4 years, 3 months ago
Sun Oct 7 13:40:00 2018 UTC
peter
Log:
source/iso_collide.cpp:
  - This test should not have been removed.

12361 Directory Listing
Modified 4 years, 3 months ago
Sun Oct 7 13:05:24 2018 UTC
peter
Log:
source/iso.h:
source/helike_einsta.cpp:
source/hydroeinsta.cpp:
source/iso_collide.cpp:
source/iso_create.cpp:
  - Delete the CachedAs array. Replacing the Bauman routines with tabulated data
    removed the strongest need for this array and has made it largely redundant.
    The implementation via CachedAs was fragile and got in the way of current
    development on the condensed branch. This change will lead to additional
    calls to he_1trans() and H_Einstein_A(). That most likely will not produce
    a significant increase in CPU time, but if it does a different solution for
    caching the data will have to be devised.

12360 Directory Listing
Modified 4 years, 3 months ago
Sat Oct 6 21:22:54 2018 UTC
peter
Log:
source/iso.h:
source/iso_create.cpp:
source/iso_solve.cpp:
  - Remove iso_collapsed_Aul_update() and iso_collapsed_lifetimes_update(). These
    routines perform no useful function as they only overwrite fields in the iso_sp
    data structure with identical values.

12358 Directory Listing
Modified 4 years, 4 months ago
Fri Oct 5 14:21:23 2018 UTC
peter
Log:
source/hydro_tbl.h:
source/hydro_tbl.cpp:
  - Revert r12357 and implement a better solution following the discussion on
    https://en.cppreference.com/w/cpp/language/static under "Constant static
    members". The constant p_stride can be odr-used as a parameter in a call
    to min(). Hence it needs a declaration at namespace scope, but without an
    initializer.

12357 Directory Listing
Modified 4 years, 4 months ago
Fri Oct 5 11:39:09 2018 UTC
peter
Log:
source/hydro_tbl.h:
source/hydro_tbl.cpp:
  - Work around compilation problem with g++ 7 in debug mode.

12354 Directory Listing
Modified 4 years, 4 months ago
Thu Oct 4 16:29:44 2018 UTC
peter
Log:
Until now we calculated photoionization cross sections and Einstein A values for
hydrogenic ions on the fly using the routines written by Robert Bauman. These
routines are very accurate and stable, but are also very slow (especially for
high values of the principal quantum number). In this commit we put these data
in external data files to circumvent the costly calculation, thus speeding up
the code significantly for large H- or He-like model atoms.

source/hydro_tbl.h:
source/hydro_tbl.cpp:
  - New class for holding tabulated data for hydrogenic ions.
source/hydro_bauman.h:
source/hydro_bauman.cpp:
  - Remove linear versions of routines for calculating photo cross sections
    or Einstein A values. These are no longer needed as these data have now
    been tabulated. Use these instead.
  - Remove routines for calculating the oscilator strengths of hydrogenic
    transitions. These were never used.
  - Vectorize the routine prodxx_log10().
source/hydroeinsta.cpp:
  - Add code for inserting Einstein A values for n,l -> n,l' transitions, but
    disable it for now as it trips SanityCheck(). Most likely the indices in
    QuantumNumbers2Index[] are no longer correct.
  - Remove hardwired Einstein A value for Lya lines.
source/parser.h:
  - Add methods for getting and setting the position in the data file.
source/prt_lines_hydro.cpp:
  - Merge collectSkipTrans() into lines_hydro(). This significantly speeds up
    the code for large hydrogenic models.
data/hydro_pcs.dat:
  - Photoionization cross sections for hydrogenic ions.
data/hydro_tpn.dat:
data/hydro_tpnl.dat:
data/hydro_tpnn.dat:
  - Transition probabilities for hydrogenic ions.

12335 Directory Listing
Modified 4 years, 4 months ago
Tue Sep 25 11:24:32 2018 UTC
peter
Log:
docs/latex/hazy1/grid.tex:
  - Improve documentation of the GRID LIST command
docs/latex/hazy1/miscell.tex:
  - Improve documentation of the MONITOR ... GRID command.

12332 Directory Listing
Modified 4 years, 4 months ago
Mon Sep 24 16:13:18 2018 UTC
marios
Log:
species.cpp
  - Code that converts the Stout / Chianti basename into a spectral label
    is now refactored into a function, db_basename_to_spectral().
    The new function converts, for instance, "c_2" to "C  2".
species.h
  - Expose the interface for db_basename_to_spectral().
  - Add Doxygen comments to spectral_to_chemical() and chemical_to_spectral().

12318 Directory Listing
Modified 4 years, 4 months ago
Fri Sep 21 16:44:54 2018 UTC
marios
Log:
source/atmdat_chianti.cpp
  - In atmdat_STOUT_readin(), initialize transition arrays only
    after all level energy processing has been completed.

12313 Directory Listing
Modified 4 years, 4 months ago
Wed Sep 19 14:57:44 2018 UTC
peter
Log:
source/cddefines.h:
source/cloudyconfig_vs.h:
source/configure.sh:
source/cpu.h:
source/parse_print.cpp:
source/thirdparty.cpp:
source/thirdparty.h:
  - Remove local definitions of __func__, erf(), and erfc(). These are now
    guaranteed by the C++11 standard.

12312 Directory Listing
Modified 4 years, 4 months ago
Wed Sep 19 13:54:11 2018 UTC
peter
Log:
source/cloudyconfig_vs.h:
source/configure.sh:
  - Detect presence of libc++ bug described in
    https://bugs.llvm.org/show_bug.cgi?id=17782
source/cddefines.h:
  - Add workaround for this bug.
source/cpu.cpp:
  - Force code to always work in the POSIX locale (a.k.a. C locale).

12308 Directory Listing
Modified 4 years, 4 months ago
Tue Sep 18 18:39:29 2018 UTC
peter
Log:
source/species_pseudo_cont.cpp:
  - Add virtual destructor to fix warnings from clang++ 6.0.1.

12305 Directory Listing
Modified 4 years, 4 months ago
Tue Sep 18 15:13:13 2018 UTC
fguzman
Log:
- Fixed Hazy description of top levels line printout

- Fixed bugs in save hydrogen [alpha] lines. Now "save hydrogen [alpha] lines" is printing integrated emissivities, that can be relative (default) or absolute.

- Highest level lines are decided in  iso_Max_Emitting_Level() in iso.cpp



12294 Directory Listing
Modified 4 years, 4 months ago
Tue Sep 11 08:40:15 2018 UTC
peter
Log:
data/stout/p/p_2/p_2.coll:
  - Update P II collision strengths to Tayal (2004).
tsuite/auto/blr_level2.in:
  - Update monitors.

12265 Directory Listing
Modified 4 years, 5 months ago
Thu Aug 30 11:03:46 2018 UTC
peter
Log:
data/stout/p/p_2/p_2.nrg:
data/stout/p/p_2/p_2.tp:
  - Update transition probability data by including Froese-Fischer data set. This
    fixes the problem of certain forbidden transitions being missing, such as the
    3P-1D lines in the near infrared.
tsuite/auto/blr_level2.in:
  - Fix botches resulting from change above.
  - Add monitor of one of the 3P-1D lines of P II.
tsuite/auto/hii_Um385.in:
  - Fix botch unrelated to the changes in P II.

12257 Directory Listing
Modified 4 years, 5 months ago
Fri Aug 17 08:34:06 2018 UTC
peter
Log:
docs/latex/hazy1/cmdintro.tex:
  - Further clarify the way the search path works.

12249 Directory Listing
Modified 4 years, 5 months ago
Mon Aug 13 11:23:39 2018 UTC
peter
Log:
source/prt_comment.cpp:
  - Fix erroneous zone numbers in certain comments.

12231 Directory Listing
Modified 4 years, 6 months ago
Fri Aug 3 21:58:14 2018 UTC
fguzman
Log:
the tag \rmxaa did not work, fixed with the full name of the journal
12184 Directory Listing
Modified 4 years, 6 months ago
Thu Jul 19 20:19:18 2018 UTC
gary
Log:
say what the comment char s
12183 Directory Listing
Modified 4 years, 6 months ago
Thu Jul 19 16:59:42 2018 UTC
fguzman
Log:
corrected hazy1, it is needed to specify iso-sequence in masers off command
12169 Directory Listing
Modified 4 years, 6 months ago
Fri Jul 13 17:02:51 2018 UTC
fguzman
Log:
Print departure coeffcient/critical densities/populations. Now if no iso-sequence is specified all possible iso-sequences are printed
12168 Directory Listing
Modified 4 years, 6 months ago
Thu Jul 12 18:39:07 2018 UTC
gary
Log:
explicitly state that level indices count from 1 not 0
12153 Directory Listing
Modified 4 years, 7 months ago
Thu Jul 5 22:19:42 2018 UTC
gary
Log:
papers from C17 local bibliography
12152 Directory Listing
Modified 4 years, 7 months ago
Thu Jul 5 21:19:04 2018 UTC
gary
Log:
ref to published version existed far below reference to aerXiv - now only one, but yet another alias
12151 Directory Listing
Modified 4 years, 7 months ago
Thu Jul 5 21:16:01 2018 UTC
gary
Log:
misplaced brace
12150 Directory Listing
Modified 4 years, 7 months ago
Thu Jul 5 21:12:55 2018 UTC
gary
Log:
update reference for C17, add c17 alias
12149 Directory Listing
Modified 4 years, 7 months ago
Thu Jul 5 21:07:32 2018 UTC
gary
Log:
improve comments
12148 Directory Listing
Modified 4 years, 7 months ago
Wed Jul 4 01:11:08 2018 UTC
fguzman
Log:
Reducied duplicated code in parse_print.cpp (Robin's solution)
12146 Directory Listing
Modified 4 years, 7 months ago
Tue Jul 3 14:36:22 2018 UTC
fguzman
Log:
Added command 'print critical density [h-like/helike] element'
which prints critical densities for l-mixing

Modified criterium for not enough resolved states warning. Now it is
based only on l-mixing collisions.


12145 Directory Listing
Modified 4 years, 7 months ago
Mon Jul 2 16:09:59 2018 UTC
peter
Log:
source/atmdat_chianti.cpp:
source/parse_species.cpp:
  - The SPECIES "Fe+6" LEVELS command was broken in r12144. Fix this.

12144 Directory Listing
Modified 4 years, 7 months ago
Mon Jul 2 15:22:55 2018 UTC
peter
Log:
source/atmdat_chianti.cpp:
source/parse_species.cpp:
source/species.h:
  - Add support for alternate datasets in the Stout database.
docs/latex/hazy1/ControllingModelAtoms.tex:
  - Describe the new SPECIES "Fe+6" DATASET="abc" command to enable an alternate
    dataset.
  - Fix additional typo.

12143 Directory Listing
Modified 4 years, 7 months ago
Fri Jun 29 11:58:36 2018 UTC
gary
Log:
effects of SPHERE command on line optical depths
12141 Directory Listing
Modified 4 years, 7 months ago
Sat Jun 23 13:16:17 2018 UTC
gary
Log:
correct citation year
12139 Directory Listing
Modified 4 years, 7 months ago
Thu Jun 21 21:08:20 2018 UTC
rjrw
Log:
Fix zoning botches which were found on wolkje but not cloud9

12138 Directory Listing
Modified 4 years, 7 months ago
Wed Jun 20 21:02:06 2018 UTC
rjrw
Log:
Re-enable assert, results now appear to be consistent between gcc & llvm mac.

#244 refers.

12137 Directory Listing
Modified 4 years, 7 months ago
Wed Jun 20 18:30:08 2018 UTC
rjrw
Log:
Update (zone count) monitors for bugfixes at front face r12134:12136

12136 Directory Listing
Modified 4 years, 7 months ago
Mon Jun 18 19:41:54 2018 UTC
rjrw
Log:
Convert explicit constant to named parameter

12135 Directory Listing
Modified 4 years, 7 months ago
Mon Jun 18 19:12:22 2018 UTC
rjrw
Log:
radius_next() needs to be called in zone 0 to set base values

12134 Directory Listing
Modified 4 years, 7 months ago
Sun Jun 17 19:28:28 2018 UTC
rjrw
Log:
Improve zone 0 thermal relaxation in iterations > 1

12131 Directory Listing
Modified 4 years, 7 months ago
Sat Jun 16 12:17:23 2018 UTC
rjrw
Log:
Remove monitor for blend with populations which underflow trimming limit

12130 Directory Listing
Modified 4 years, 7 months ago
Fri Jun 15 15:43:33 2018 UTC
marios
Log:
scripts/prep-bib.sh -- Add missing prompt
12129 Directory Listing
Modified 4 years, 7 months ago
Fri Jun 15 15:39:05 2018 UTC
marios
Log:
prep-bib.sh
  - On MacOS, set number of threads for compiling Cloudy to number
    of physical cores.
    (Hyperthreads on Mac sometimes cause the machine to freeze.)

12128 Directory Listing
Modified 4 years, 7 months ago
Fri Jun 15 15:06:38 2018 UTC
marios
Log:
prep-bib.sh
  - Inspect error files, output of 'db-ref-bib2json.pl', if present,
    before proceeding to generate PDFs.
  - Fix syntax error when reading from /dev/stdin
  - Generate the file ../tsuite/auto/func_lines.spclab, if not present.
    Resolve the number of threads (not including hyperthreads) on the machine
    and compile Cloudy, if needed.
    Then, move to tsuite/auto and run script 'func_lines.in' to generate
    the desired file.
  - Copy generated PDFs to docs/

12127 Directory Listing
Modified 4 years, 7 months ago
Fri Jun 15 12:41:15 2018 UTC
rjrw
Log:
Switch to modified ion trimming scheme as default

12125 Directory Listing
Modified 4 years, 7 months ago
Fri Jun 15 10:16:18 2018 UTC
rjrw
Log:
Command to enable revised trimming approach

12124 Directory Listing
Modified 4 years, 7 months ago
Fri Jun 15 09:45:36 2018 UTC
rjrw
Log:
Move NewTrim control variable to ionbal class

12123 Directory Listing
Modified 4 years, 7 months ago
Thu Jun 14 19:55:41 2018 UTC
marios
Log:
Make scripts/prep-bib.sh executable
12122 Directory Listing
Modified 4 years, 7 months ago
Thu Jun 14 19:34:30 2018 UTC
marios
Log:
scripts/db-ref-bib2json.pl -- Add comments about the error files that may be generated.
12121 Directory Listing
Modified 4 years, 7 months ago
Thu Jun 14 19:14:47 2018 UTC
marios
Log:
scripts/prep-bib.sh -- Add script to automate the generation of tables in TeX and PDF formats.
12120 Directory Listing
Modified 4 years, 7 months ago
Thu Jun 14 11:34:46 2018 UTC
peter
Log:
tsuite/programs/comp4/comp4.cpp:
  - Prevent warnings about grains being above the sublimation temperature.

12118 Directory Listing
Modified 4 years, 7 months ago
Wed Jun 13 20:46:33 2018 UTC
rjrw
Log:
Need to trim dynamics.Source for consistency

12117 Directory Listing
Modified 4 years, 7 months ago
Wed Jun 13 19:09:24 2018 UTC
rjrw
Log:
Mop up dynamics sources below IonLow for consistency

12116 Directory Listing
Modified 4 years, 7 months ago
Wed Jun 13 05:27:14 2018 UTC
rjrw
Log:
Tweak NewTrim code

12115 Directory Listing
Modified 4 years, 7 months ago
Wed Jun 13 05:15:06 2018 UTC
rjrw
Log:
Tweaks to revised trimming approach (not active by default)

12112 Directory Listing
Modified 4 years, 7 months ago
Wed Jun 6 12:27:10 2018 UTC
peter
Log:
source/parser.h:
source/parser.cpp:
  - Create new method getElement() for reading the full name of an element.
source/init_defaults_preparse.cpp:
source/parse_abundances.cpp:
source/parse_element.cpp:
source/parse_optimize.cpp:
  - Use this method in the OPTIMIZE COLUMN DENSITY, OPTIMIZE TEMPERATURE, and
    ELEMENT READ commands. This solves a bug reported by Francie Cashman.

12110 Directory Listing
Modified 4 years, 8 months ago
Thu May 31 12:54:04 2018 UTC
peter
Log:
source/parse_commands.cpp:
  - Fix optimization for the EDEN command.
docs/latex/hazy1/cont-shp.tex:
docs/latex/hazy1/miscell.tex:
docs/latex/hazy1/optimize.tex:
  - Fix documentation of the optimizer.

12108 Directory Listing
Modified 4 years, 8 months ago
Thu May 31 08:11:00 2018 UTC
peter
Log:
source/parse_map.cpp:
source/parse_save.cpp:
  - Check ordering of the lower and upper limit of the range of the MAP command.

12106 Directory Listing
Modified 4 years, 8 months ago
Wed May 23 09:46:41 2018 UTC
gary
Log:
add xref for SET TEMPERATURE
12105 Directory Listing
Modified 4 years, 8 months ago
Tue May 22 03:58:38 2018 UTC
peter
Log:
source/iso_create.cpp:
source/iter_startend.cpp:
source/mole.h:
source/optimize_phymir.cpp:
source/prt_final.cpp:
source/prt_lines_general.cpp:
source/prt_lines_helium.cpp:
source/prt_zone.cpp:
source/save_fits.cpp:
source/species.cpp:
source/version.cpp:
  - Fix compiler warnings by g++ 8.

12104 Directory Listing
Modified 4 years, 8 months ago
Mon May 14 15:19:30 2018 UTC
marios
Log:
Improve language on the 'limit' option of 'save line optical depths'.
12103 Directory Listing
Modified 4 years, 8 months ago
Mon May 14 15:13:42 2018 UTC
marios
Log:
Add column for specific optical depth to output of 'save line optical depths'.

source/parse_save.cpp
  - Introduce column name in output file header.
source/save_do.cpp
  - Print line specific optical depth.
docs/latex/hazy1/conout.tex
  - Document additional column.

12100 Directory Listing
Modified 4 years, 9 months ago
Fri May 4 15:16:13 2018 UTC
marios
Log:
Improve discussion of 'save line optical depth some' to discuss how the direction along which the optical depth is accumulated matters.
12099 Directory Listing
Modified 4 years, 9 months ago
Fri May 4 14:46:43 2018 UTC
peter
Log:
docs/latex/hazy2/lineatomparam.tex:
  - Improve discussion of absorption cross section and line-center optical depth.

12098 Directory Listing
Modified 4 years, 9 months ago
Tue May 1 19:25:49 2018 UTC
marios
Log:
docs/latex/hazy1/conout.tex: Clarify that damping constant calculation in 'save line optical depth' is over the last zone, whereas the optical depth is for the whole cloud
12095 Directory Listing
Modified 4 years, 9 months ago
Mon Apr 30 13:30:34 2018 UTC
peter
Log:
source/prt_comment.cpp:
  - Do not print warnings about grain sublimation when FUNCTION SUBLIMATION is
    in effect.

12094 Directory Listing
Modified 4 years, 9 months ago
Mon Apr 30 11:00:04 2018 UTC
peter
Log:
docs/latex/hazy2/lineatomparam.tex:
  - Update description of the Voigt profile and mean optical depths.

12092 Directory Listing
Modified 4 years, 9 months ago
Fri Apr 27 18:53:25 2018 UTC
marios
Log:
source/species.cpp: In trim_levels(): Do not report each level trimmed, just the final number of levels after trimming.  Remove temporary variable (aul).
12091 Directory Listing
Modified 4 years, 9 months ago
Tue Apr 24 13:20:27 2018 UTC
peter
Log:
data/ionization_potentials.dat:
  - New data file with accurate ionization potentials obtained from the Atomic
    line list and NIST.
source/atmdat.h:
source/atmdat_readin.cpp:
  - Add code to read the new data into atmdat.EIonPot[][].

12089 Directory Listing
Modified 4 years, 9 months ago
Mon Apr 23 14:25:45 2018 UTC
peter
Log:
source/grains.cpp:
  - Prevent failed assert when rfield.anu(ilo) is very close to the threshold, in
    which case yzero[ilo] may underflow to zero for carbonaceous materials. 

12087 Directory Listing
Modified 4 years, 9 months ago
Mon Apr 23 10:31:56 2018 UTC
peter
Log:
source/species.cpp:
  - Fix compiler warning by g++ 7.2.0 when compiling with -DNDEBUG: writing into
    array that may be too small to hold the output.

12086 Directory Listing
Modified 4 years, 9 months ago
Fri Apr 20 19:52:55 2018 UTC
marios
Log:
Minor typo in Hazy 1
12080 Directory Listing
Modified 4 years, 9 months ago
Wed Apr 18 11:57:15 2018 UTC
gary
Log:
add mix of lines to save line emissivity.  The 5199 
blend has zero emissivity, reported in ticket #415
12078 Directory Listing
Modified 4 years, 9 months ago
Wed Apr 18 01:21:46 2018 UTC
gary
Log:
add Hb to save emissivity file
12077 Directory Listing
Modified 4 years, 9 months ago
Tue Apr 17 19:44:50 2018 UTC
marios
Log:
Exercise command 'save lines, optical depths some' in tsuite
12075 Directory Listing
Modified 4 years, 9 months ago
Tue Apr 17 19:37:01 2018 UTC
marios
Log:
Report mean optical depths in the outupt of 'save lines optical depths' and 'save lines optical depths some'
12065 Directory Listing
Modified 4 years, 9 months ago
Mon Apr 16 11:27:33 2018 UTC
peter
Log:
docs/latex/hazy2/lines.tex:
docs/latex/hazy2/observed.tex:
  - Fix incorrect references to the PRINT CONTINUUM command.

12063 Directory Listing
Modified 4 years, 9 months ago
Mon Apr 16 11:12:26 2018 UTC
peter
Log:
docs/latex/hazy1/conout.tex:
docs/latex/hazy1/miscell.tex:
docs/latex/hazy1/optimize.tex:
docs/latex/hazy1/stopping.tex:
  - Fix incorrect references to the PRINT CONTINUUM command.

12061 Directory Listing
Modified 4 years, 9 months ago
Mon Apr 16 02:58:13 2018 UTC
gary
Log:
update citation for 2017 paper
12060 Directory Listing
Modified 4 years, 9 months ago
Mon Apr 16 02:53:51 2018 UTC
gary
Log:
update copyright year to 2019 in 
anticipation of C19 release.
12058 Directory Listing
Modified 4 years, 9 months ago
Mon Apr 16 01:47:01 2018 UTC
gary
Log:
bugfix for spherical intensity case.
Improve comment describing variable
12056 Directory Listing
Modified 4 years, 9 months ago
Mon Apr 9 13:02:58 2018 UTC
peter
Log:
source/cddefines.h:
  - Add support for realnum literals. Use as: 12_r, 12.4_r, or 12.4e-02_r.
source/TestDataParser.cpp:
source/TestThirdparty.cpp:
source/cont_createmesh.cpp:
source/mole_species.cpp:
source/parse_grid.cpp:
source/parse_set.cpp:
source/prt_final.cpp:
source/rt_diffuse.cpp:
source/save_do.cpp:
  - Convert realnum(0.) -> 0_r, etc.

12055 Directory Listing
Modified 4 years, 10 months ago
Fri Mar 30 12:42:21 2018 UTC
peter
Log:
tsuite/slow/pdr_xdr.in:
  - Fix botches in alldouble runs due to the fact that nzone has a bimodal
    distribution.

12054 Directory Listing
Modified 4 years, 10 months ago
Fri Mar 23 00:36:16 2018 UTC
marios
Log:
Minor typo in hazy 1.
12052 Directory Listing
Modified 4 years, 10 months ago
Mon Mar 19 16:16:25 2018 UTC
peter
Log:
source/vectorhash.h:
source/vectorhash.cpp:
  - New very fast vectorized algorithm to obtain checksums of a large  buffer.
source/md5datafile.cpp:
  - Renamed to:
source/vh128sum.cpp:
  - Main program to obtain checksum. This has been deliberately set up such that
    it does not depend on Cloudy. This avoids bloating the binary and spurious
    rebuilds.
source/Makefile:
source/cpu.cpp:
source/cpu.h:
source/prt_comment.cpp:
  - Use the new algorithm where appropriate. The checksums in the grain opacity
    files and the SAVE TRANSMITTED CONTINUUM output are still done using the old
    MD5 algorithm for backward compatibility. The new algorithm is used to check
    if data files have been modified and so reduces the overhead from this check.
source/vectorize_math.h:
  - Enhance vpack class.
source/TestVectorize.cpp:
  - Test the new algorithm.
scripts/generate_md5sums.sh:
  - Renamed to:
scripts/generate_checksums.sh:
  - Use new checksum algorithm.
  - Optimize script for speed.
  - Sort output alphabetically to get stable sequence.
data/checksums.dat:
  - New file with checksums.
data/md5datafiles.dat:
  - Deleted.

12050 Directory Listing
Modified 4 years, 10 months ago
Fri Mar 9 12:51:00 2018 UTC
gary
Log:
move details for running a model to an earlier subsection, so it appears in the TOC
12049 Directory Listing
Modified 4 years, 10 months ago
Thu Mar 8 19:48:12 2018 UTC
marios
Log:
Clarify units of the opacity() methods in the EmissionProxy classes
12048 Directory Listing
Modified 4 years, 10 months ago
Thu Mar 8 16:07:58 2018 UTC
marios
Log:
Replace hardcoded constant in the calculation of the absorption coefficient in abscf() with a constant variable, ABSOR_COEFF_CONST, defined in physconst_template.h
12047 Directory Listing
Modified 4 years, 10 months ago
Wed Mar 7 19:54:47 2018 UTC
marios
Log:
Use NIST energy for level 9 in Stout data for Mg10.  ADAS energy was used before.  The energy difference is about 0.02%.
12045 Directory Listing
Modified 4 years, 11 months ago
Tue Mar 6 21:48:14 2018 UTC
marios
Log:
Update He-like multiplet wavelengths, which were adjusted for refraction
12044 Directory Listing
Modified 4 years, 11 months ago
Tue Mar 6 20:17:25 2018 UTC
marios
Log:
lines_service.h
  - Remove SDIV() from wn2ang().
lines.cpp
  - Run wavelength through wn2ang() to account for refractive index.

12042 Directory Listing
Modified 4 years, 11 months ago
Tue Mar 6 18:20:24 2018 UTC
gary
Log:
make figure smaller on page
12041 Directory Listing
Modified 4 years, 11 months ago
Tue Mar 6 18:19:40 2018 UTC
gary
Log:
this figure did not display correctly due to large white space around figure itself.
12040 Directory Listing
Modified 4 years, 11 months ago
Mon Mar 5 17:55:57 2018 UTC
marios
Log:
Add another warning about running Cloudy below density of -6
12038 Directory Listing
Modified 4 years, 11 months ago
Fri Mar 2 15:27:29 2018 UTC
peter
Log:
source/stars.cpp:
  - Bug-fix: Starburst99 files were parsed wrong.

12032 Directory Listing
Modified 4 years, 11 months ago
Sun Feb 25 05:58:10 2018 UTC
peter
Log:
Fix svn file properties on many files.

12030 Directory Listing
Modified 4 years, 11 months ago
Fri Feb 23 18:59:20 2018 UTC
marios
Log:
Coding style changes suggested by Peter
12024 Directory Listing
Modified 4 years, 11 months ago
Wed Feb 21 22:44:16 2018 UTC
marios
Log:
source/species.h
source/species.cpp
  - Use string reference in input to chemical_to_spectral(),
    not the string itself.  Reduces smoke test execution time
    by ~2%.

12023 Directory Listing
Modified 4 years, 11 months ago
Wed Feb 21 04:00:07 2018 UTC
marios
Log:
Update He-like triplet labels and wavelengths, in the test suite, and the data/ line lists.
12022 Directory Listing
Modified 4 years, 11 months ago
Wed Feb 21 03:58:22 2018 UTC
marios
Log:
prt_lines_helium.cpp
  - Multiplets are now entered with the infrastructure for
    entering (hardcoded) blends to the line stack.
    This necessitates that all components be entered in
    the stack (this was the case in C13), or the blend
    methods will fail to identify the components.
  - Define new function, setup_multiplet(), to add components
    to a declared blend, and compute its average wavelength.
  - Remove function PutLineSum().
  - Eliminate insert_trans() function in favor of operating
    directly on a vector of transitions.
  - Remove function multiplet_sum(), because the addition of
    intensities is now done natively by LinSv methods.
lines.h
lines.cpp
  - Define t_LineSave::resetWavelength(() method to update wavelength
    after it has been entered into the vector.
  - Define LinSv::setBlendWavl() method to compute weighted average
    wavelength of blend.  The averaging is done on the wavenumber
    (energy) of each transition, and the reciprocal of that mean
    is taken as the blend wavelength.  In computing the average,
    each wavenumber is weighted by the produce gu*Aul, where gu
    is the degeneracy of the upper level, and Aul is the transition
    probability.

12021 Directory Listing
Modified 4 years, 11 months ago
Tue Feb 20 17:59:02 2018 UTC
marios
Log:
source/generic_state.cpp
  - In extractLevels(), switch to using atoi() from stod()
    for string conversions to integers.
    The use of stod() was opted for with designations such
    as '1e3' in mind, which, however, are not expected to be
    used much.
  - Check against zero value in the case where only one
    level is given (e.g., '[2]').  A zero value indicates
    atoi() failure, and is in any case an unacceptable choice.
source/TestGeneric.cpp
  - Update unit test.

12020 Directory Listing
Modified 4 years, 11 months ago
Tue Feb 20 14:55:51 2018 UTC
peter
Log:
source/md5datafile.cpp:
  - Fix failure to open files.

12019 Directory Listing
Modified 4 years, 11 months ago
Tue Feb 20 14:01:36 2018 UTC
peter
Log:
data/compile_tsuite_stars.in:
tsuite/README_STARS.txt:
  - Remove the last input script from the data directory and archive its contents
    in the test suite directory if we ever need to recreate the SED tables that
    are used in the test suite.

12018 Directory Listing
Modified 4 years, 11 months ago
Tue Feb 20 02:58:07 2018 UTC
marios
Log:
source/generic_state.h
source/generic_state.cpp
  - Convert functions getLevelsGeneric() and matchGeneric()
    to operate on C++-style strings.
  - Separate parsing of string that holds species and levels,
    e.g., "Cu+13[1:10]" into a function of its own, extractLevels().
  - New function operates exclusively on C++-style strings.
    Bug fix: Out-of-bounds C-style string copy is averted.
source/monitor_results.cpp
source/prt.cpp
source/prt_columns.cpp
source/save_do.cpp
source/save_species.cpp
source/species_pseudo_cont.cpp
  - Adjust calls to functions.
source/TestGeneric.cpp
  - Add unit tests for extractLevels().

12017 Directory Listing
Modified 4 years, 11 months ago
Mon Feb 19 14:23:40 2018 UTC
gary
Log:
small changes in bibtex entries
12016 Directory Listing
Modified 4 years, 11 months ago
Mon Feb 19 13:56:58 2018 UTC
gary
Log:
some new references
12014 Directory Listing
Modified 4 years, 11 months ago
Fri Feb 16 22:48:03 2018 UTC
marios
Log:
source/prt.cpp
  - Add checks in t_prt_matrix::prtRates() against the number of
    available levels, when printing the arrays that enter the solver.

12013 Directory Listing
Modified 4 years, 11 months ago
Fri Feb 16 22:46:30 2018 UTC
marios
Log:
Switch to C++ strings to overcome 10-char size limit in 'print arrays levels':
Species such as "Cu+13[1:10]" could not be read in correctly.

source/prt.h
  - Convert char arrays of t_prt_matrix to strings.
source/prt.cpp
  - Modify t_prt_matrix methods to operate on C++ strings.
  - Add check in t_prt_matrix::setSpecies() for balanced brackets, '[]'.
source/iso_create.cpp
source/mole_h2_etc.cpp
source/species.cpp
  - Use string methods for comparisons.
source/TestPrt.cpp
  - Add unit test for the t_prt structure.

12011 Directory Listing
Modified 4 years, 11 months ago
Wed Feb 14 17:28:08 2018 UTC
peter
Log:
docs/latex/common/bibliography2.bib:
docs/latex/hazy1/miscell.tex:
  - Document the addition of the Draine (2003) rfi files.

12009 Directory Listing
Modified 4 years, 11 months ago
Tue Feb 13 21:18:53 2018 UTC
marios
Log:
Delete Cloudy scripts from the data directory.  Keep functionality in shell script.

make_data.sh
  - Introduce new bash script.
    Converts one-line input decks into command-line runs via the -e option.
compile1grain.in
compile_helike.in
compile_hlike.in
compilegrains.in
compilestars.in
  - Remove Cloudy scripts (input decks).

12007 Directory Listing
Modified 4 years, 11 months ago
Tue Feb 13 18:09:52 2018 UTC
marios
Log:
data/LineList_He_like.dat
tsuite/auto/blr_kk81.in
tsuite/auto/hii_coolstar.in
tsuite/auto/hii_paris.in
tsuite/auto/igm_primal.in
  - Update two-photon continuum wavelengths.

12006 Directory Listing
Modified 4 years, 11 months ago
Tue Feb 13 17:03:54 2018 UTC
peter
Log:
source/grains_mie.cpp:
  - Bug-fix: prevent out_of_range exception.
data/gdraine03.rfi:
data/sdraine03.rfi:
  - Add refractive index data from Draine (2003).

12005 Directory Listing
Modified 4 years, 11 months ago
Tue Feb 13 11:39:30 2018 UTC
peter
Log:
Delete unwanted input scripts in the data directory

data/compile_gauntff.in:
data/opacity.in:
data/compileopac.in:
  - Obsolete. These commands are no longer supported.
data/compileatlas.in:
data/compilecostar.in:
data/compilerauch.in:
data/compilerauchold.in:
data/compilewerner.in:
  - Compiling single SED grids as shown in these scripts never worked.
data/compile_grains.in:
  - Redundant with data/compilegrains.in.
data/crash.in:
  - This script cannot work; it is also redundant with tsuite/scrash.
data/test.in:
  - This is a likely script name users may choose, so the presence of this file
    may well lead to confusion. Its presence is not needed as its functionality
    can easily be obtained with the "cloudy.exe -e test" syntax.

12004 Directory Listing
Modified 4 years, 11 months ago
Tue Feb 13 11:18:04 2018 UTC
peter
Log:
source/parse_compile.cpp:
source/parse_table.cpp:
source/stars.cpp:
source/stars.h:
  - Add new command TABLE KS18 to support the Khaire & Srianand (2018)
    extragalactic background calculations. This has a similar setup to the
    Haardt & Madau commands.
docs/latex/common/bibliography2.bib:
docs/latex/hazy1/cont-shp.tex:
  - Document the new command.
data/ks18_q14.ascii:
data/ks18_q15.ascii:
data/ks18_q16.ascii:
data/ks18_q17.ascii:
data/ks18_q18.ascii:
data/ks18_q19.ascii:
data/ks18_q20.ascii:
  - New files containing the KS18 data.

12000 Directory Listing
Modified 4 years, 11 months ago
Mon Feb 12 20:14:53 2018 UTC
marios
Log:
docs/LineLabels.txt -- Update to remove induced two-photon continuum entries
11999 Directory Listing
Modified 4 years, 11 months ago
Mon Feb 12 20:10:00 2018 UTC
marios
Log:
source/prt_lines_hydro.cpp
source/prt_lines_helium.cpp
  - Remove induced 2-photon continuum from line stack.
    Only the total is now reported for each of the H-like
    doublet, and the He-like singlet and triplet.
  - Set the wavelength to twice the Lyman wavelength.

11998 Directory Listing
Modified 4 years, 11 months ago
Fri Feb 9 22:14:41 2018 UTC
gary
Log:
missing option on command
11996 Directory Listing
Modified 4 years, 11 months ago
Thu Feb 8 13:30:09 2018 UTC
peter
Log:
Merge asciigrids branch onto the trunk. This branch reimplements the COMPILE
STARS command to do away with binary SED grid files and replace them with index
files pointing to the ascii files. Interpolation is now always done by reading
the ascii file directly and the (optional) index file helps speed up the process
by enabling the code to read only the SEDs it needs and simply skip the rest.
The compiled index files are still platform dependent (despite being simple
ascii files -- the position into a file stream is implementation defined) but
are now no longer dependent on the frequency mesh as rebinning is now done on
the fly during the interpolation process. Getting rid of the frequency mesh
dependence was the main driver for this development.

11992 Directory Listing
Modified 4 years, 11 months ago
Tue Feb 6 15:27:23 2018 UTC
marios
Log:
Update Stout references, and BibTeX file.

11991 Directory Listing
Modified 4 years, 11 months ago
Tue Feb 6 14:59:51 2018 UTC
marios
Log:
Refactor code to compute wavelength from energy, because it violates DRY.

source/lines_service.h
  - Define inline function, wn2ang(), to convert wavenumbers to
    wavelengths in Angstrom.  This encapsulates corrections for
    the refractive index of the atmosphere.
source/atmdat_chianti.cpp
source/atmdat_lamda.cpp
source/atmdat_lines_setup.cpp
source/atmdat_readin.cpp
source/iso_create.cpp
  - Replace repeated one-line code with function calls.

11989 Directory Listing
Modified 4 years, 11 months ago
Mon Feb 5 23:21:55 2018 UTC
marios
Log:
source/prt_lines_helium.cpp
  - Adjust comments to distinguish between the singlet and triplet
    two photon continuua of He-like ions.
docs/LineLabels.txt
  - Update labels.

11988 Directory Listing
Modified 4 years, 11 months ago
Mon Feb 5 23:17:51 2018 UTC
marios
Log:
docs/LineLabels.txt - updated to include new Al 3 transitions
11987 Directory Listing
Modified 4 years, 11 months ago
Mon Feb 5 22:16:54 2018 UTC
marios
Log:
Update Stout data for Al+2.  Collision strengths come from ADAS.
First 2 excited level energies come from NIST.

11986 Directory Listing
Modified 4 years, 11 months ago
Mon Feb 5 18:42:44 2018 UTC
marios
Log:
source/cont_createpointers.cpp
  - Set ipCont() and ipFine() to default values for transitions beyond
    the energy mesh bounds.

11984 Directory Listing
Modified 4 years, 11 months ago
Mon Feb 5 17:02:24 2018 UTC
marios
Log:
Generalize t_mesh method to check if energy is within the continuum mesh bounds.

source/mesh.h
  - Generalize method to operate on Energy class, instead of on a realnum variable.
    Method renamed to 'isEnergyBound()' from 'isWNbound()'.
source/atmdat_chianti.cpp
source/atmdat_lamda.cpp
source/cont_createpointers.cpp
  - Update method calls.
docs/LineLabels.txt
  - Update labels.

11981 Directory Listing
Modified 5 years ago
Fri Feb 2 19:09:59 2018 UTC
marios
Log:
source/iso_create.cpp
  - Report J=0 in configurations of triplets, which are reported
    as comments in the output of 'save lines labels'.
    With this change, '2^3P_0' does not miss the '_0'.
    J>0 values are reported, just as they were.
docs/LineLabels.txt
  - Update line comments.

11978 Directory Listing
Modified 5 years ago
Fri Feb 2 16:33:07 2018 UTC
marios
Log:
Only treat transitions with energies within the continuum energy mesh limits.

source/mesh.h
  - Define new method, isWNbound(), to check that a given wavenumber
    falls within the bounds of the continuum energy mesh.
source/atmdat_chianti.cpp
source/atmdat_lamda.cpp
  - Compute wavelength for transitions with energies within the mesh
    bounds.
source/cont_createpointers.cpp
  - Only setup pointers for baseline transitions with energies
    within the mesh bounds.

11972 Directory Listing
Modified 5 years ago
Wed Jan 31 22:53:31 2018 UTC
marios
Log:
Update output files of docs/SpeciesLabels.in, i.e., LineLabels.txt and SpeciesLabels.txt
11971 Directory Listing
Modified 5 years ago
Wed Jan 31 22:47:48 2018 UTC
marios
Log:
iso_create.cpp
  - Change comments in output of 'save lines labels' for H-like ions
    to report the principal quantum number, except for n=1 and n=2,
    for which we use spectroscopic notation.

11969 Directory Listing
Modified 5 years ago
Wed Jan 31 15:23:20 2018 UTC
peter
Log:
source/maincl.cpp:
source/service.cpp:
source/service.h:
  - Add support for the -e command line flag. This allows Cloudy commands to be
    entered directly on the command line, e.g.
      cloudy.exe -e test
    to execute the smoke test.
docs/latex/QuickStart/QuickStart.tex:
docs/latex/hazy1/cmdintro.tex:
  - Document this new feature.

11967 Directory Listing
Modified 5 years ago
Tue Jan 30 17:00:40 2018 UTC
peter
Log:
tsuite/auto/stars_rauch_pg1159_ascii.in:
  - New test case to detect regressions from the fix in r11966. This sim also
    implements a test for reading directly from an ascii file.

11966 Directory Listing
Modified 5 years ago
Mon Jan 29 14:43:12 2018 UTC
peter
Log:
source/stars.cpp:
  - Fix bug reported by Will Henney: SED is truncated in the wrong place if zero
    flux values are embedded in the middle of the SED. This can happen in PoWR
    grids, but the problem also already existed in certain Kurucz and Rauch grids.
  - Add code for correctly rebinning SEDs that have zero flux values.
  - Fix debug code for dumping the contents of a stellar atmosphere file.

11962 Directory Listing
Modified 5 years ago
Fri Jan 26 12:54:04 2018 UTC
gary
Log:
update email address
11960 Directory Listing
Modified 5 years ago
Wed Jan 24 21:58:06 2018 UTC
fguzman
Log:
fixed tsuite/programs/complink.sh to allow compiler options and pick up correct header files
11958 Directory Listing
Modified 5 years ago
Wed Jan 24 16:29:57 2018 UTC
peter
Log:
docs/latex/hazy1/conout.tex:
  - Document units of normalized Xspec spectrum.

11956 Directory Listing
Modified 5 years ago
Wed Jan 24 16:21:34 2018 UTC
peter
Log:
source/save_do.cpp:
  - Fix comment.
source/save_fits.cpp:
  - Normalize Xspec spectra to 1 photon/cm^2/s/keV if normalization is requested.

11955 Directory Listing
Modified 5 years ago
Mon Jan 22 21:06:51 2018 UTC
marios
Log:
Added human-readable BibTeX code for 2017 Revista paper
11954 Directory Listing
Modified 5 years ago
Mon Jan 22 15:23:14 2018 UTC
marios
Log:
fixed monitored value
11953 Directory Listing
Modified 5 years ago
Fri Jan 19 18:22:31 2018 UTC
marios
Log:
Update Stout data for "S 5".  Collision strengths come from ADAS.

data/LineList_BLR.dat
data/LineList_BLR_Fe2.dat
data/LineList_NLR.dat
source/prt_lines.cpp
  - Update "S 5" wavelengths.
data/chianti/masterlist/CloudyChianti.ini
data/stout/masterlist/Stout.ini
  - Update species lists to use Stout for "S 5" by default.
data/stout/s/s_5/s_5.coll
data/stout/s/s_5/s_5.nrg
data/stout/s/s_5/s_5.tp
  - Update atomic data to use ADAS.
    NIST energies are used for the first 19 excited levels.

11952 Directory Listing
Modified 5 years ago
Fri Jan 19 17:12:13 2018 UTC
gary
Log:
update monitored value
11951 Directory Listing
Modified 5 years ago
Fri Jan 19 17:03:48 2018 UTC
gary
Log:
adjust monitor for slow drift up
11949 Directory Listing
Modified 5 years ago
Thu Jan 18 18:52:50 2018 UTC
gary
Log:
update Badnell RR, DR to results of
https://www.aanda.org/component/article?access=doi&doi=10.1051/0004-6361/201731243
11948 Directory Listing
Modified 5 years ago
Thu Jan 18 18:51:35 2018 UTC
gary
Log:
update Badnell RR, DR data to results of
https://www.aanda.org/component/article?access=doi&doi=10.1051/0004-6361/201731243
11947 Directory Listing
Modified 5 years ago
Thu Jan 18 18:36:28 2018 UTC
marios
Log:
Update Stout data for Mg10.  Collision strengths come from ADAS.

data/LineList_BLR.dat
data/LineList_BLR_Fe2.dat
data/LineList_NLR.dat
source/prt_lines.cpp
  - Update Mg10 wavelengths.
data/chianti/masterlist/CloudyChianti.ini
data/stout/masterlist/Stout.ini
  - Update species lists to use Stout for Mg10 by default.
data/stout/mg/mg_10/mg_10.coll
data/stout/mg/mg_10/mg_10.nrg
data/stout/mg/mg_10/mg_10.tp
  - Update atomic data to use ADAS.
    NIST energies are used for the first 7 excited levels.

11945 Directory Listing
Modified 5 years ago
Thu Jan 18 12:20:15 2018 UTC
peter
Log:
source/save_fits.cpp:
  - Bug-fix: the wrong array was being saved into the FITS file.

11943 Directory Listing
Modified 5 years ago
Sat Jan 13 17:34:23 2018 UTC
gary
Log:
add missing strong UV lines
11942 Directory Listing
Modified 5 years ago
Sat Jan 13 15:12:24 2018 UTC
gary
Log:
add missing line
11941 Directory Listing
Modified 5 years ago
Sat Jan 13 14:24:54 2018 UTC
gary
Log:
add lines, model, to show effects of suppressed DR
11940 Directory Listing
Modified 5 years ago
Fri Jan 12 04:22:03 2018 UTC
fguzman
Log:
fix botch from clang in radegund on blr_n14_p22 sim
11937 Directory Listing
Modified 5 years ago
Thu Jan 11 21:47:04 2018 UTC
gary
Log:
Maryam extends NGC5548 SED to radio/x-ray
as used in AGN STORM campaign modeling, and provided by Jerry Kriss
11936 Directory Listing
Modified 5 years ago
Thu Jan 11 14:17:41 2018 UTC
gary
Log:
as per PvH suggestion, do not recommend
alias to cloudyconfig.h, rather include sys_gcc on the include path
11935 Directory Listing
Modified 5 years ago
Thu Jan 11 14:12:53 2018 UTC
gary
Log:
make continuum output more useful for testing optically thick brems absorption
11934 Directory Listing
Modified 5 years ago
Thu Jan 11 14:10:25 2018 UTC
gary
Log:
improve comment on DR suppression, put SET DIEL.. command in alphabet order in section of hazy
11933 Directory Listing
Modified 5 years ago
Wed Jan 10 17:29:50 2018 UTC
fguzman
Log:
Masers are allowed by default now.

A new command has been included to disable  masers using database pasers. It's in section 12.4.8 of Hazy.

The command "Save hydrogen lines [alpha]" has been fixed and is reporting optical depth even when these are negative

11932 Directory Listing
Modified 5 years, 1 month ago
Sun Dec 24 17:38:47 2017 UTC
gary
Log:
reminder that header file must exist in source when building in sys_xxx
11931 Directory Listing
Modified 5 years, 1 month ago
Sun Dec 24 17:35:02 2017 UTC
gary
Log:
do not print sing-time header when no-times in active, so the programs/comp4 file1.txt file2.txt will agree
11930 Directory Listing
Modified 5 years, 1 month ago
Fri Dec 22 12:53:05 2017 UTC
gary
Log:
make it clear that the 5548 SED is the green fit in the Figure in the quoted paper
11929 Directory Listing
Modified 5 years, 1 month ago
Thu Dec 21 21:49:40 2017 UTC
gary
Log:
clarify two save transmitted continuum reports
11928 Directory Listing
Modified 5 years, 1 month ago
Wed Dec 13 06:35:06 2017 UTC
peter
Log:
source/Makefile:
  - Clean up correctly on Mac Darwin systems.

11924 Directory Listing
Modified 5 years, 1 month ago
Mon Dec 11 12:08:46 2017 UTC
peter
Log:
source/cloudy.cpp:
  - Fix bug introduced by r11883: the number of warnings would be reset to zero
    after the last iteration, but before the code exits. Therefore the presence
    of warnings would not be correctly indicated by the return code.

11920 Directory Listing
Modified 5 years, 2 months ago
Tue Dec 5 09:37:46 2017 UTC
peter
Log:
tsuite/auto/coll_t5.in:
  - Fix botches resulting from r11919.

11919 Directory Listing
Modified 5 years, 2 months ago
Tue Dec 5 08:18:29 2017 UTC
peter
Log:
source/ion_recomb_Badnell.cpp:
  - Fix DR suppression factor for H-, He-, and Ne-like sequences.

11917 Directory Listing
Modified 5 years, 2 months ago
Mon Dec 4 02:13:44 2017 UTC
peter
Log:
source/save_fits.cpp:
  - Workaround for incomplete C++11 support in Oracle Studio 12.5.

11916 Directory Listing
Modified 5 years, 2 months ago
Mon Dec 4 02:04:56 2017 UTC
peter
Log:
source/cdinit.cpp:
  - Fix memory leak.

11914 Directory Listing
Modified 5 years, 2 months ago
Thu Nov 30 17:45:38 2017 UTC
peter
Log:
tsuite/programs/vary_nete/vary_nete.cpp:
  - Fix wavelengths.

11912 Directory Listing
Modified 5 years, 2 months ago
Wed Nov 29 16:50:57 2017 UTC
peter
Log:
source/cdinit.cpp:
  - Clear input deck when running Cloudy as a subroutine.
source/cpu.cpp:
  - Augment error message.
tsuite/programs/collcool/collcool.cpp:
tsuite/programs/collion/collion.cpp:
tsuite/programs/comp4/comp4.cpp:
tsuite/programs/hazy_coolingcurve/hazy_coolingcurve.cpp:
tsuite/programs/hazy_kmt/hazy_kmt.cpp:
tsuite/programs/hizlte/hizlte.cpp:
tsuite/programs/template.cpp:
tsuite/programs/vary_nete/vary_nete.cpp:
tsuite/programs/varyn/varyn.cpp:
  - Fix programs test suite.
tsuite/programs/run_programs.pl:
  - Prepare script for running in the nightly test runs.
tsuite/programs/HelloWorld.cpp:
  - Fix indentation.

11910 Directory Listing
Modified 5 years, 2 months ago
Mon Nov 27 16:20:36 2017 UTC
peter
Log:
tsuite/auto/h_t4_conemis.in:
tsuite/auto/h_t4_conemis_lon.in:
tsuite/auto/heatomt10.in:
tsuite/auto/heatomt10lon.in:
tsuite/auto/heiont10.in:
  - Remove instances of the SAVE SPECTRUM command. This no longer exists.

11909 Directory Listing
Modified 5 years, 2 months ago
Mon Nov 27 15:28:03 2017 UTC
peter
Log:
source/grid.h:
source/grid_xspec.cpp:
source/mpi_utilities.cpp:
source/save.h:
source/save_do.cpp:
source/save_fits.cpp:
  - Bug-fix: the SAVE XSPEC command was missing covgeo factors for the reflected
    components.
  - Bug-fix: there was an off-by-one bug in the frequency range of the SAVE XSPEC
    command.
  - Bug-fix: including multiple SAVE XSPEC commands could lead to a segfault.
  - Bug-fix: The RANGE keyword on the SAVE XSPEC command would have side effects
    on other instances of the SAVE XSPEC command. Multiple instances  are now
    completely independent.
  - Add option to normalize spectra at a given frequency using the new NORMALIZE
    keyword on the SAVE XSPEC command.
  - Refactor SAVE XSPEC and SAVE FITS commands so that they automatically pick
    up changes in the way continua are saved. They were out of sync with the
    SAVE CONTINUUM command.
source/parse_save.cpp:
source/quantumstate.h:
source/save_do.cpp:
source/species2.cpp:
  - Bug-fix: fix incorrect normalization of the reflected components in the
    SAVE CONTINUUM command.
  - Remove the SAVE NLTE7 [ CONTINUUM ] commands. They are no longer needed.
  - Remove the SAVE OUTWARD CONTINUUM command, this is redundant with the
    SAVE CONTINUUM command.
  - Remove the SAVE SPECTRUM command. This is not documented and no longer
    maintained.
source/cddrive.h:
source/cdspec.cpp:
  - The file cdspec.cpp has been removed. Delete deprecated routine cdSPEC() and
    move cdSPEC2() to save_do.cpp.
source/rfield.h:
  - Fix incorrect comments.
docs/latex/hazy1/conout.tex:
docs/latex/hazy1/grid.tex:
docs/latex/hazy2/sub.tex:
  - Update documentation: remove deleted commands/routines and add description
    of new options. Also add some clarifications.

11905 Directory Listing
Modified 5 years, 2 months ago
Fri Nov 24 13:31:48 2017 UTC
peter
Log:
source/parse_stop.cpp:
  - Bug-fix: make sure the column density is parsed correctly when the species
    label contains a number, as in STOP COLUMN DENSITY "N+2" 10.
tsuite/auto/func_stopcol.in
  - Test this feature in a new script.

11904 Directory Listing
Modified 5 years, 2 months ago
Tue Nov 21 17:40:36 2017 UTC
peter
Log:
scripts/NistExtractor/NistExtractor.py:
  - Update script for the latest version of the ASD web interface.

11901 Directory Listing
Modified 5 years, 2 months ago
Mon Nov 20 12:05:49 2017 UTC
peter
Log:
tsuite/auto/blr_hizqso.in:
tsuite/auto/nlr_lex00.in:
tsuite/auto/nlr_liner_grains.in:
tsuite/auto/orion_hii_open.in:
tsuite/auto/pdr_orion_veil.in:
tsuite/auto/pn_paris_fast.in:
tsuite/slow/feii_blr_n13_p22_Z20.in:
  - Fix (near) botches resulting from r11900.

11900 Directory Listing
Modified 5 years, 2 months ago
Mon Nov 20 10:41:55 2017 UTC
peter
Log:
source/ion_recomb_Badnell.cpp:
  - Fix bug introduced in r9952. Also rename ionchar -> c10 for clarity.

11899 Directory Listing
Modified 5 years, 2 months ago
Thu Nov 16 14:38:03 2017 UTC
gary
Log:
more helpful comment
11898 Directory Listing
Modified 5 years, 2 months ago
Wed Nov 15 14:22:50 2017 UTC
gary
Log:
NSF17 references
11897 Directory Listing
Modified 5 years, 2 months ago
Tue Nov 14 13:27:56 2017 UTC
gary
Log:
references
11896 Directory Listing
Modified 5 years, 2 months ago
Mon Nov 13 13:53:17 2017 UTC
gary
Log:
references for NSF17
11895 Directory Listing
Modified 5 years, 2 months ago
Sat Nov 11 05:26:04 2017 UTC
gary
Log:
references for NSF 2017 proposal
11892 Directory Listing
Modified 5 years, 2 months ago
Thu Nov 9 11:55:26 2017 UTC
peter
Log:
source/Makefile:
source/sys_llvm/Makefile.conf:
  - Revert Makefile changes from r11889 and implement better solution that works
    for clang++.

11890 Directory Listing
Modified 5 years, 2 months ago
Wed Nov 8 14:18:48 2017 UTC
peter
Log:
source/vectorize_log.cpp:
source/vectorize_math.h:
source/vectorize_sqrt_core.h:
  - Fix bugs in avx512 code.
  - Enable avx512 optimizations on complient hardware.

11889 Directory Listing
Modified 5 years, 2 months ago
Wed Nov 8 13:22:16 2017 UTC
peter
Log:
source/Makefile:
  - In r10308 vectorize.cpp was renamed to vectorize_reduce.cpp. This change was
    overlooked in the Makefile, pessimizing the code because reduction loops were
    not properly vectorized any longer.
source/sys_llvm/Makefile.conf:
  - Enable vectorization of reduction loops also for clang++.

11887 Directory Listing
Modified 5 years, 3 months ago
Thu Nov 2 18:13:57 2017 UTC
peter
Log:
source/parse_grid.cpp:
  - Prevent division by zero when lower and upper bound of grid range are equal.

11883 Directory Listing
Modified 5 years, 3 months ago
Tue Oct 31 17:31:43 2017 UTC
peter
Log:
source/atmdat.h:
source/species.cpp:
  - Use DataParser to parse masterlist files.
data/chianti/masterlist/ChiantiOriginal.ini:
data/chianti/masterlist/CloudyChianti.ini:
data/chianti/masterlist/CloudyChiantiAll.ini:
data/chianti/masterlist/CloudyChiantiFe.ini:
data/chianti/masterlist/CloudyChiantiNe.ini:
data/chianti/masterlist/CloudyChiantiSelect_P_Up.ini:
data/chianti/masterlist/CloudyChiantiSelect_Ti_Up.ini:
data/chianti/masterlist/masterlist.ions:
data/chianti/masterlist/masterlist.ions.v6:
  - Fix comment characters.
source/cddrive.cpp:
source/cloudy.cpp:
source/prt_comment.cpp:
source/service.cpp:
source/warnings.cpp:
source/warnings.h:
  - Modify t_warnings class to use C++ strings and vectors, thus removing any
    arbitrary limitations.
  - Modify t_warnings class to take in warnings. etc., at any stage during each
    iteration. The class gets reset at end of each iteration.

11881 Directory Listing
Modified 5 years, 3 months ago
Tue Oct 24 16:36:37 2017 UTC
peter
Log:
source/atmdat.h:
source/broke.h:
source/cosmology.h:
source/dense.h:
source/hcmap.h:
source/heavy.h:
source/hextra.h:
source/init_coreload.cpp:
source/ionbal.h:
source/iso.cpp:
source/iso.h:
source/optimize.h:
source/struc.h:
source/taulines.cpp:
  - Move more code from InitCoreload() to individual ctors.
source/atmdat_chianti.cpp:
source/atmdat_gaunt.cpp:
source/atmdat_lamda.cpp:
source/atmdat_readin.cpp:
source/cddrive.cpp:
source/cpu.cpp:
source/cpu.h:
source/grains_mie.cpp:
source/grid_do.cpp:
source/isotopes.cpp:
source/maincl.cpp:
source/mole_dissociate.cpp:
source/mole_h2_coll.cpp:
source/mole_h2_io.cpp:
source/mole_species.cpp:
source/mpi_utilities.cpp:
source/optimize.cpp:
source/parse_abundances.cpp:
source/parse_drive.cpp:
source/parse_init.cpp:
source/parse_optimize.cpp:
source/parse_save.cpp:
source/parse_table.cpp:
source/parser.cpp:
source/species.cpp:
source/species_pseudo_cont.cpp:
source/stars.cpp:
source/vary_input.cpp:
  - Move open_data() over to const string& arguments.

11879 Directory Listing
Modified 5 years, 3 months ago
Tue Oct 24 14:48:28 2017 UTC
peter
Log:
source/cddrive.cpp:
source/grid.h:
source/init_coreload.cpp:
source/maincl.cpp:
  - Never call grid_do() when already inside a grid. This can happen if there is
    a rogue keyword VARY remaining on some input line.

11877 Directory Listing
Modified 5 years, 3 months ago
Tue Oct 24 11:49:52 2017 UTC
peter
Log:
source/parse_set.cpp:
  - Bug fix: when using SET PREFIX command, check that quoted string is present.
source/parse_set.cpp:
source/conv_base.cpp:
source/init_defaults_preparse.cpp:
source/mpi_utilities.cpp:
source/radius_first.cpp:
source/save.h:
source/save_do.cpp:
  - Remove dependency on INPUT_LINE_LENGTH for save.chHashString.

11875 Directory Listing
Modified 5 years, 3 months ago
Tue Oct 24 10:24:02 2017 UTC
peter
Log:
source/input.cpp:
source/input.h:
source/parser.cpp:
  - Add helpful message if an old-style comment was found in the input script.

11874 Directory Listing
Modified 5 years, 3 months ago
Thu Oct 19 10:10:04 2017 UTC
peter
Log:
source/grains_mie.cpp:
  - Fix compiler warning about unused constant.

11872 Directory Listing
Modified 5 years, 3 months ago
Wed Oct 18 13:35:48 2017 UTC
peter
Log:
This is the third merge from the newcomment branch. These are the highlights
of this commit:

- Use new version of read_whole_line() everywhere and remove old version of
  read_whole_line(). This avoids dependencies on fixed-length C-style strings
  while parsing data files.
- Remove any dependencies on fixed-length C-style strings from the input parser.
- Add new class DataParser for parsing data files.
- Rewrite the parser for the Stout data files using DataParser. Testing the
  files is stricter now. This unearthed various errors and also corruption in
  the Stout data files.
- Update to new Stout database format with magic numbers 17 09 05.
- Fix the errors in the Stout data files found by the new parser. These appear
  to have little impact on the modeling as the errors tend to be in fairly
  high lying levels.
- Rewrite the parser for line list files using DataParser.

There are no user-visible changes other than that the arbitrary limit on the
input line length has been removed. Checking data files is stricter now when
they are parsed by DataParser (this includes line list files). Gradually more
data files will be moved over to using DataParser in the future.

11865 Directory Listing
Modified 5 years, 3 months ago
Sun Oct 8 12:36:42 2017 UTC
gary
Log:
reject index files
11864 Directory Listing
Modified 5 years, 3 months ago
Sat Oct 7 11:52:47 2017 UTC
gary
Log:
how to download entire LAMDA database
11853 Directory Listing
Modified 5 years, 4 months ago
Tue Sep 26 20:18:03 2017 UTC
gary
Log:
typo
11852 Directory Listing
Modified 5 years, 4 months ago
Mon Sep 25 19:08:08 2017 UTC
peter
Log:
source/iso_radiative_recomb.cpp:
source/optimize.h:
source/optimize_phymir.cpp:
  - Fix remaining compiler warnings with g++ 8.

11850 Directory Listing
Modified 5 years, 4 months ago
Fri Sep 22 10:54:57 2017 UTC
peter
Log:
source/iso_radiative_recomb.cpp:
source/maincl.cpp:
  - Fix two compiler warnings from the g++ 8 compiler.

11847 Directory Listing
Modified 5 years, 4 months ago
Thu Sep 14 01:34:42 2017 UTC
marios
Log:
data/stout/c/c_2/c_2.coll
 - Update comment to give detailed provenance of
   the effective collision strength data for the
   C II 157.7 micron line.

11846 Directory Listing
Modified 5 years, 4 months ago
Tue Sep 12 12:19:36 2017 UTC
peter
Log:
docs/latex/hazy1/cmdintro.tex:
  - Update Hazy 1 as a result of r11845.

11845 Directory Listing
Modified 5 years, 4 months ago
Tue Sep 12 12:08:55 2017 UTC
peter
Log:
source/cpu.cpp:
  - Make saving to a non-local file a fatal error. This avoids problems in grid
    runs.
source/radius_next.cpp:
  - Fix comment.

11843 Directory Listing
Modified 5 years, 4 months ago
Sun Sep 10 15:16:47 2017 UTC
peter
Log:
source/TestFlexArr.cpp:
source/TestInput.cpp:
source/TestMultiArr.cpp:
  - Fix unit tests.

11841 Directory Listing
Modified 5 years, 4 months ago
Sun Sep 10 15:02:08 2017 UTC
peter
Log:
Merging the searchpath branch to the trunk.

This finalizes the work on the search path for reading data files. The code now
consistently adheres to the following rules:

 - Output files are always written to the local directory. If a user tries to
   supply a path to a different location between double quotes, a warning will
   be issued and only the last part of the path will be used. As an example, if
   the user requests to write to "dir/name.txt", the output will actually go to
   "name.txt". This also applies to internal calls to open_data().
 - Input files are always searched along the search path. This is consistently
   done for all files, so that one single rule applies to all commands. This
   applies both to input files supplied by the user between double quotes and
   data files. The only exception is the main input script, which must reside
   in the local directory. This was already enforced before these changes and
   has been retained since supplying a path to the script would not work in grid
   runs.

The default search path is to look in the local directory first, and then in the
standard Cloudy data directory. If a data file is needed in a subdirectory, then
the code will look in that subdirectory and the root of the directory. As an
example, if the code wants to read Stout.ini, it will look in these locations:
  <local_dir>/stout/masterlist/Stout.ini
  <local_dir>/Stout.ini
  <cloudy_data_dir>/stout/masterlist/Stout.ini
  <cloudy_data_dir>/Stout.ini
The first file that is found in this list will be used. This makes it easier to
override masterlist files and other files in subdirectories. The user can alter
the search path by defining the environment variable CLOUDY_DATA_PATH at run
time. Using the file path.h or defining CLOUDY_DATA_PATH during compilation was
deprecated and these possibilities have been removed now.

Initialization of the search path has been altered to make it impossible to read
data files from a global constructor. This is too dangerous as we have very
little control over the code during that phase.

Tests for (unsigned) long long and 64-bit integers have been removed as these
are guaranteed by the C++11 standard.

Hazy now has two new sections giving a detailed explanation of the search path.

11838 Directory Listing
Modified 5 years, 4 months ago
Sun Sep 10 01:09:05 2017 UTC
fguzman
Log:
minor bug introduced in rev 11837
11837 Directory Listing
Modified 5 years, 4 months ago
Sat Sep 9 22:27:43 2017 UTC
fguzman
Log:
fix bug in high n collisional excitation rates for H-like iso-sequences, as in commit 11815 but for H-like
11834 Directory Listing
Modified 5 years, 4 months ago
Sat Sep 9 13:29:59 2017 UTC
peter
Log:
docs/latex/hazy1/miscell.tex:
  - Remove description of dead command.

11828 Directory Listing
Modified 5 years, 4 months ago
Wed Sep 6 12:04:25 2017 UTC
peter
Log:
source/cddrive.cpp:
  - Bug-fix: behavior of cdTemp() did not agree with documentation in Hazy 2.
    Fixed in such a way that the behavior introduced by the labels branch is
    now used consistently by cdColm(), cdIonFrac(), and cdTemp().
source/service.cpp:
  - Fix bug in trimTrailingWhiteSpace() where string was not erased if it was
    all whitespace.
docs/latex/hazy2/sub.tex:
  - Document the behavior introduced by the labels branch.

11826 Directory Listing
Modified 5 years, 4 months ago
Wed Sep 6 11:41:10 2017 UTC
peter
Log:
docs/latex/hazy1/miscell.tex:
  - In r11824 the DRIVE CASE B command should also have been removed from Hazy.

11824 Directory Listing
Modified 5 years, 4 months ago
Wed Sep 6 11:17:06 2017 UTC
peter
Log:
source/parse_drive.cpp:
  - Remove broken DRIVE CASE B command.

11823 Directory Listing
Modified 5 years, 5 months ago
Sun Sep 3 15:14:16 2017 UTC
gary
Log:
NistExtractor was not included, an oversight
11820 Directory Listing
Modified 5 years, 5 months ago
Sun Sep 3 02:03:01 2017 UTC
gary
Log:
formatting errors or curiosities
11819 Directory Listing
Modified 5 years, 5 months ago
Sat Sep 2 21:37:57 2017 UTC
gary
Log:
rm invalid A=inf, 0, and <1e-30 (we ignroe these by design)
11817 Directory Listing
Modified 5 years, 5 months ago
Sat Sep 2 21:31:24 2017 UTC
gary
Log:
more helpful comment
11815 Directory Listing
Modified 5 years, 5 months ago
Fri Sep 1 20:52:02 2017 UTC
fguzman
Log:
fix bug in high n collisional excitation rates for He-like iso-sequence
11810 Directory Listing
Modified 5 years, 5 months ago
Sun Aug 27 13:48:24 2017 UTC
peter
Log:
source/prt_comment.cpp:
  - Change caunin() -> bangin().

11809 Directory Listing
Modified 5 years, 5 months ago
Sun Aug 27 13:43:40 2017 UTC
peter
Log:
source/cpu.cpp:
source/prt_comment.cpp:
  - Demote caution about md5sum mismatch in data files to a note.
data/continuum_mesh.ini:
  - Update history.

11807 Directory Listing
Modified 5 years, 5 months ago
Sun Aug 27 12:53:53 2017 UTC
peter
Log:
source/cpu.cpp:
  - Remove unnecessary printout of md5sum values.

11806 Directory Listing
Modified 5 years, 5 months ago
Sun Aug 27 12:49:28 2017 UTC
peter
Log:
source/prt.h:
source/cddrive.cpp:
source/init_defaults_preparse.cpp:
  - Fix ticket #394: using prt.lgPrintTime before it is properly initialized.

11804 Directory Listing
Modified 5 years, 5 months ago
Sun Aug 27 10:34:21 2017 UTC
peter
Log:
source/grid.h:
source/grid_xspec.cpp:
source/maincl.cpp:
source/mpi_utilities.cpp:
source/optimize_phymir.cpp:
source/parse_save.cpp:
source/save_do.cpp:
source/save_fits.cpp:
source/service.h:
  - Fix ticket #399: SAVE XSPEC produces faulty FITS files when using fork-based
    parallelization.

11802 Directory Listing
Modified 5 years, 5 months ago
Sat Aug 26 13:15:36 2017 UTC
gary
Log:
add the Lodders 09 abundances.  We give her isotope ratios but overlooked the total abundances/
11797 Directory Listing
Modified 5 years, 5 months ago
Wed Aug 23 09:22:55 2017 UTC
peter
Log:
This is the second merge from the newcomment branch. These are the highlights
of this commit:

- Remove all comment characters other than '#' and '##'. This closes ticket #391.
- Remove the arbitrary limitation to NKRD input lines.
- Fix bug due to overly permissive parsing of line labels.
- Fix several bugs in FFmtRead().
- Continue moving the parser over to using C++-style strings. The end goal will
  be to remove the arbitrary limitation to INPUT_LINE_LENGTH characters on a
  line. This conversion is not complete yet. To facilitate this, a new version
  of the routine read_whole_line() was created that can read arbitrary length
  lines from a FILE* into a C++-style string.
- Remove input.chDelimiter as this is a duplication of what is in the cpu class.
  Use cpu.i().appendDirSeparator() now.

This results in the following user-visible changes:

- Comments in scripts starting with anything other than '#' or '##' will be
  rejected by the parser.
- The user can include more than NKRD lines in scripts.
- Parsing line labels is stricter. A quoted species label must start in the first
  column. Entering the wavelength is mandatory now. Nothing other than a comment
  is allowed after the wavelength.
- To make copy / paste easier, the SAVE LINE LABELS command now prints a hash
  symbol before the line label comment.
- Line list files can now use a field of stars as the EOF marker.

11790 Directory Listing
Modified 5 years, 5 months ago
Fri Aug 18 18:16:06 2017 UTC
gary
Log:
we do not report realloc in release version
11781 Directory Listing
Modified 5 years, 5 months ago
Tue Aug 15 05:34:12 2017 UTC
peter
Log:
source/cpu.cpp:
  - Bug-fix: abort on failure to open file when using AS_DEFAULT mode.

11778 Directory Listing
Modified 5 years, 5 months ago
Tue Aug 15 04:11:30 2017 UTC
peter
Log:
Merge minor bug fixes from newcomment branch.
11774 Directory Listing
Modified 5 years, 5 months ago
Mon Aug 14 13:07:24 2017 UTC
gary
Log:
Two changes after problems at most recent workshop:
species2.cpp:  allow negative populations during search phase.  These occur when
the simulation is unphysical and in the process of failing.
temp_change.cpp: suggest ways to debug failures due to temperature extremes exceeded.
11770 Directory Listing
Modified 5 years, 5 months ago
Mon Aug 14 09:56:32 2017 UTC
peter
Log:
tsuite/auto/blr_fp89.in:
tsuite/auto/blr_kk81.in:
tsuite/auto/blr_rnfa.in:
tsuite/auto/blr_rnfb.in:
tsuite/auto/coll_t4.in:
tsuite/auto/nlr_lex00.in:
tsuite/auto/nlr_paris.in:
tsuite/auto/pn_fluc.in:
tsuite/auto/pn_ots.in:
tsuite/auto/pn_paris.in:
tsuite/auto/pn_paris_cpre.in:
tsuite/auto/pn_paris_fast.in:
tsuite/slow/feii_blr_n12_p19_Z20.in:
  - Missed comment character updates in these files.

11769 Directory Listing
Modified 5 years, 5 months ago
Mon Aug 14 09:12:20 2017 UTC
peter
Log:
Merge newcomment branch to the trunk.

This implements fixes for the bugs listed in PR #391 (to be precise, only the
part that is intended to be merged to c17_branch).

These are the main changes:

- Remove "c " and "C " as a valid comment character.
- Make "#" the comment character for visible comments ("c " used to do that).
- Add "##" as a new comment character for hidden comments.

A script called ccc.pl was already added to assist the user in the modification
of their input scripts.

In the process several other bugs in the parser were fixed (mostly in the
treatment of init files). As a result of these fixes the limit of a single init
file has been removed (there no longer is a limit) and users can now use init
files inside other init files.

11766 Directory Listing
Modified 5 years, 5 months ago
Fri Aug 11 21:48:27 2017 UTC
gary
Log:
trivial changes page ref -> section ref
11764 Directory Listing
Modified 5 years, 5 months ago
Fri Aug 11 12:15:29 2017 UTC
peter
Log:
source/cool_save.cpp:
source/heat_save.cpp:
  - Remove arbitrary limit to the number of heating or cooling agents printed.

11756 Directory Listing
Modified 5 years, 6 months ago
Sat Aug 5 19:02:03 2017 UTC
peter
Log:
source/init_defaults_preparse.cpp:
source/mpi_utilities.cpp:
source/parse_save.cpp:
source/save.h:
  - Bug-fix: process_output() was parsing the input file to figure out the names
    of the save files. This was done incorrectly. Now the names are saved during
    regular parsing, avoiding the need for duplicate parsing.

11754 Directory Listing
Modified 5 years, 6 months ago
Sun Jul 30 12:00:45 2017 UTC
gary
Log:
update N IV data to 
Electron impact excitation of N$^3+$ using the B-spline R-matrix method: importance of the target structure description and the size of the close-coupling expansion 
Fernández-Menchero, L., Zatsarinny, O., & Bartschat, K.
2017, Journal of Physics B Atomic Molecular Physics, 50, 065203
 http://adsabs.harvard.edu/abs/2017JPhB...50f5203F 
11753 Directory Listing
Modified 5 years, 6 months ago
Sun Jul 30 12:00:22 2017 UTC
gary
Log:
update N IV data to 
Electron impact excitation of N$^3+$ using the B-spline R-matrix method: importance of the target structure description and the size of the close-coupling expansion 
Fernández-Menchero, L., Zatsarinny, O., & Bartschat, K.
2017, Journal of Physics B Atomic Molecular Physics, 50, 065203
 http://adsabs.harvard.edu/abs/2017JPhB...50f5203F 
11741 Directory Listing
Modified 5 years, 6 months ago
Fri Jul 21 18:39:17 2017 UTC
peter
Log:
scripts/ccc.pl:
  - New perl script to convert comment characters to the new syntax.

11737 Directory Listing
Modified 5 years, 6 months ago
Thu Jul 20 15:04:57 2017 UTC
peter
Log:
source/parse_compile.cpp:
source/stars.cpp:
  - Bug-fix: allow additional dots to be embedded in the names of grid files.

11735 Directory Listing
Modified 5 years, 6 months ago
Wed Jul 19 16:13:40 2017 UTC
peter
Log:
source/cpu.h:
source/maincl.cpp:
source/mole_species.cpp:
source/prt_comment.cpp:
source/save_fits.cpp:
  - Fix warnings from the g++ 7 compiler. There are two categories: fall-through
    in a switch statement (for which the new FALLTHROUGH macro is defined) and
    possible string overflow in sprintf() statements.

11733 Directory Listing
Modified 5 years, 6 months ago
Wed Jul 19 14:38:48 2017 UTC
peter
Log:
tsuite/auto/clean_tsuite.pl:
  - Also remove the file warnings.txt.
tsuite/clean_tsuite.pl:
  - Remove obsolete statement.

11731 Directory Listing
Modified 5 years, 6 months ago
Wed Jul 19 13:28:38 2017 UTC
peter
Log:
source/prt_lines.cpp:
  - Remove duplicate definitions of Blnd 1304 and Blnd 8446 introduced by r11730.

11730 Directory Listing
Modified 5 years, 6 months ago
Wed Jul 19 11:59:18 2017 UTC
peter
Log:
This commit fixes ticket #393.

data/stout/masterlist/Stout.ini:
data/stout/masterlist/StoutAll.ini:
source/atmdat_chianti.cpp:
  - Move setting the number of levels for O I to masterlist file.
  - Increase number of levels from 25 -> 29 so that we can capture the old 6lev
    model atom completely.
source/prt_lines.cpp
  - Add Blnd entries that are equivalent to the 6lev entries in c13 and older.

11724 Directory Listing
Modified 5 years, 7 months ago
Tue Jul 4 22:16:52 2017 UTC
gary
Log:
add list of species labels
11723 Directory Listing
Modified 5 years, 7 months ago
Sat Jul 1 18:08:42 2017 UTC
gary
Log:
average of gcc c9 / all double ubuntu
11721 Directory Listing
Modified 5 years, 7 months ago
Tue Jun 27 17:31:45 2017 UTC
gary
Log:
continuum_bands.ini:
Add Swift SX and HX bands.
Update magic number.

cont_createpointers.cpp:
improved diagnostic report of bad bands
update magic number
11720 Directory Listing
Modified 5 years, 7 months ago
Wed Jun 21 18:34:39 2017 UTC
fguzman
Log:
updated bibliography
11718 Directory Listing
Modified 5 years, 7 months ago
Fri Jun 9 18:44:54 2017 UTC
gary
Log:
add references for H, He recombination predictions
11714 Directory Listing
Modified 5 years, 8 months ago
Fri Jun 2 05:18:28 2017 UTC
peter
Log:
tsuite/auto/checkall.pl:
  - Script now also checks for WARNING messages in the output.

11712 Directory Listing
Modified 5 years, 8 months ago
Thu Jun 1 17:37:23 2017 UTC
gary
Log:
the offical ADS bibdesk appeared, 12 hr after the announcement
11708 Directory Listing
Modified 5 years, 8 months ago
Thu Jun 1 11:53:43 2017 UTC
gary
Log:
this updates the reference to the 2017 review to the arXiv version.
It has not propagated to the ADS yet so that reference is incomplete.
11705 Directory Listing
Modified 5 years, 8 months ago
Wed May 31 20:57:17 2017 UTC
gary
Log:
start on updating link to ADS version of Cloudy review
11702 Directory Listing
Modified 5 years, 8 months ago
Wed May 31 18:39:00 2017 UTC
gary
Log:
demote two warnings to cautions.
atmdat_chianti.cpp:  Chianti has no radiative decays from one very highly
excited level.  We are moving away from Chianti and the message will likely
go away if we ever update this species.

dynamics.cpp: two comments about adding other command line options.
11700 Directory Listing
Modified 5 years, 8 months ago
Wed May 31 18:29:20 2017 UTC
gary
Log:
tomorrow will be the first release of this gold version
11697 Directory Listing
Modified 5 years, 8 months ago
Mon May 29 18:26:19 2017 UTC
gary
Log:
explain non-radiative transitions in SAVE LINE LIST and
how to get atomic data report
11695 Directory Listing
Modified 5 years, 8 months ago
Mon May 29 16:39:28 2017 UTC
gary
Log:
 correct typos and give better explain of LONG option
11692 Directory Listing
Modified 5 years, 8 months ago
Sun May 28 23:25:43 2017 UTC
gary
Log:
adjust nzone to average of gcc on cloud9/wolkje
11689 Directory Listing
Modified 5 years, 8 months ago
Sun May 28 19:20:20 2017 UTC
gary
Log:
silence warning about degenerate zeroed out contributors to H iso sequence multiplets, in release versions.  
11688 Directory Listing
Modified 5 years, 8 months ago
Sun May 28 19:16:57 2017 UTC
gary
Log:
update line list for new Rydberg
11686 Directory Listing
Modified 5 years, 8 months ago
Sun May 28 15:16:58 2017 UTC
gary
Log:
fix two wavelengths - warnings were hidden with all the chemistry noise
11684 Directory Listing
Modified 5 years, 8 months ago
Sun May 28 14:50:21 2017 UTC
gary
Log:
fix two wavelengths - missed since warning was lost in flood of chemistry warnings
11682 Directory Listing
Modified 5 years, 8 months ago
Sun May 28 02:35:18 2017 UTC
gary
Log:
fix spelling
11681 Directory Listing
Modified 5 years, 8 months ago
Sun May 28 01:53:26 2017 UTC
gary
Log:
add line labels file - critical documentation
11679 Directory Listing
Modified 5 years, 8 months ago
Sat May 27 21:29:51 2017 UTC
gary
Log:
add comment giving rev number to make it easy to find files containing explicit lists of ISO sequence wavelengths
11678 Directory Listing
Modified 5 years, 8 months ago
Fri May 26 21:04:11 2017 UTC
gary
Log:
The updates the Rydberg constants used to derive level energies and line wavelenghts
for the H I iso-electronic sequence, see iso_create.cpp:160.  The worst case was
He II where optical lines could be off by half an Angstrom.  The Warning
about using new chemistry rates is demoted to a comment, making it possible to see
other warnings emitted by the code during the test suite.  This exposed a large
number of incorrect line wavelengths.

11676 Directory Listing
Modified 5 years, 8 months ago
Fri May 26 16:29:57 2017 UTC
peter
Log:
source/stars.cpp:
  - Add new routine lgValidMesh().
  - Use lgValidMesh() in lgValidBinFile() to validate the full frequency mesh.
  - In GetBins() make sure ener[] has the correct size before writing to it.
    Remove unnecessary check on size of grid->ident.

11674 Directory Listing
Modified 5 years, 8 months ago
Fri May 26 03:32:49 2017 UTC
peter
Log:
source/stars.cpp:
  - Bug-fix: in lgFileReadable() only count .ascii files in pc.nFound.

11673 Directory Listing
Modified 5 years, 8 months ago
Thu May 25 16:43:14 2017 UTC
peter
Log:
source/mesh.cpp:
  - Fix outdated comments.

11672 Directory Listing
Modified 5 years, 8 months ago
Thu May 25 15:21:33 2017 UTC
peter
Log:
source/cont_createpointers.cpp:
source/mesh.cpp:
  - Fix incorrect order of tests by moving the ASSERTs in ContCreatePointers()
    into ValidateEdges(). That way the edge energies are checked before the
    iso pointers.

11669 Directory Listing
Modified 5 years, 8 months ago
Mon May 22 16:55:24 2017 UTC
peter
Log:
source/stars.cpp:
  - Prevent confusing error message when scratch[i] underflowed to zero.

11667 Directory Listing
Modified 5 years, 8 months ago
Tue May 16 12:44:09 2017 UTC
gary
Log:
update website for Veusz
11663 Directory Listing
Modified 5 years, 8 months ago
Sun May 14 02:11:19 2017 UTC
gary
Log:
update wavelengths
11660 Directory Listing
Modified 5 years, 8 months ago
Sat May 13 15:12:29 2017 UTC
gary
Log:
update test suite documentation included in Hazy2
11654 Directory Listing
Modified 5 years, 8 months ago
Tue May 9 22:51:11 2017 UTC
peter
Log:
docs/latex/hazy2/coninter.tex:
  - Update description of the frequency mesh.
docs/latex/hazy2/limits.tex:
  - Fix typo.

11652 Directory Listing
Modified 5 years, 9 months ago
Fri May 5 22:40:30 2017 UTC
gary
Log:
remove paragraph that is no longer true
11650 Directory Listing
Modified 5 years, 9 months ago
Wed May 3 12:45:53 2017 UTC
gary
Log:
increase default ndimOpacityStack to silence comment
11643 Directory Listing
Modified 5 years, 9 months ago
Mon Apr 24 17:02:18 2017 UTC
gary
Log:
Stancil update Ne2, 3 CS to published version of Wang et al 17
11642 Directory Listing
Modified 5 years, 9 months ago
Mon Apr 24 17:01:42 2017 UTC
gary
Log:
Stancil update Ne2, 3 CS to published version of Wang et al 17
11641 Directory Listing
Modified 5 years, 9 months ago
Sun Apr 23 17:44:45 2017 UTC
gary
Log:
revert r11640 - Phillip files have broken format
11640 Directory Listing
Modified 5 years, 9 months ago
Sun Apr 23 17:29:34 2017 UTC
gary
Log:
These updated CS files were provided by Phillip Stancil and represent the final published version of the data.
11639 Directory Listing
Modified 5 years, 9 months ago
Tue Apr 11 13:54:24 2017 UTC
marios
Log:
source/rt_line_one.cpp
  - Add debugging statement for RT of spectral line.

11635 Directory Listing
Modified 5 years, 10 months ago
Sat Mar 25 17:11:34 2017 UTC
gary
Log:
more meaningful nickname
11634 Directory Listing
Modified 5 years, 10 months ago
Fri Mar 24 18:50:12 2017 UTC
marios
Log:
Bugfixes in connection to optical depths of individual lines.

source/rt_line_one_tau_reset.cpp
  - Bugfix: Reset optical depth of individual lines between successive
    iterations.
source/emission.h
source/emission.cpp
  - Introduce variable to hold the value of the Voigt function at line center.
source/rt_line_one.cpp
  - Store Voigt profile central value.
source/rt_line_one_tauinc.cpp
  - Bugfix: Use line center optical depth for individual lines.
    This rationalizes the comparison against the fine continuum
    optical depths, and eliminates a bug in the output of
    'print lines optical depth', which occasionally reported higher
    optical depth for a line than the total optical depth at the same
    wavelength.
source/pressure.cpp
source/radius_next.cpp
  - Use central line Voigt profile for opacities when computing radiation
    pressure, or the radial step due to line heating.

11632 Directory Listing
Modified 5 years, 10 months ago
Fri Mar 24 16:21:41 2017 UTC
gary
Log:
add fran
11629 Directory Listing
Modified 5 years, 10 months ago
Tue Mar 21 14:06:51 2017 UTC
gary
Log:
add labels to ISM figure
11628 Directory Listing
Modified 5 years, 10 months ago
Mon Mar 20 16:34:36 2017 UTC
gary
Log:
add better nickname
11627 Directory Listing
Modified 5 years, 10 months ago
Sun Mar 19 12:52:50 2017 UTC
gary
Log:
add h0 macro
11626 Directory Listing
Modified 5 years, 10 months ago
Sat Mar 18 20:56:29 2017 UTC
marios
Log:
Increase precision in 'save fine opacity' output
11624 Directory Listing
Modified 5 years, 10 months ago
Fri Mar 17 20:54:06 2017 UTC
marios
Log:
source/prt_met.cpp
  - Add column headers to the output of 'print lines optical depth'.

11623 Directory Listing
Modified 5 years, 10 months ago
Sun Mar 12 14:01:26 2017 UTC
gary
Log:
warning about Tayal  S data (which we do not now use)
11622 Directory Listing
Modified 5 years, 10 months ago
Wed Mar 8 03:18:24 2017 UTC
gary
Log:
proper cite for first chianti paper
11621 Directory Listing
Modified 5 years, 11 months ago
Fri Mar 3 17:40:52 2017 UTC
fguzman
Log:
fixed item Black1987 in bibliography2.bib
11620 Directory Listing
Modified 5 years, 11 months ago
Fri Mar 3 17:24:51 2017 UTC
gary
Log:
update ads bibtex for Black1987
11618 Directory Listing
Modified 5 years, 11 months ago
Thu Mar 2 19:15:21 2017 UTC
gary
Log:
only print OpacityCreate1Element resize in developer
11616 Directory Listing
Modified 5 years, 11 months ago
Mon Feb 27 21:20:44 2017 UTC
marios
Log:
tsuite/auto/agn_warm_absorber_hiU.in - remove 'print line faint 10' command
11614 Directory Listing
Modified 5 years, 11 months ago
Mon Feb 27 21:12:13 2017 UTC
marios
Log:
source/init_coreload.cpp
  - Model H-like ion of highest-Z element with 5 collapsed levels.
tsuite/auto/agn_warm_absorber_hiU.in
  - New model to track Fe and Zn H- and He-like ions.

11610 Directory Listing
Modified 5 years, 11 months ago
Sun Feb 26 02:17:24 2017 UTC
gary
Log:
add many X-ray XUV lines
11608 Directory Listing
Modified 5 years, 11 months ago
Sun Feb 26 01:23:40 2017 UTC
gary
Log:
changes due to increased number of collapsed levels
11606 Directory Listing
Modified 5 years, 11 months ago
Sat Feb 25 23:38:17 2017 UTC
gary
Log:
min of 2 collapsed levels for H and He sequences
increase collapsed levels for abundant elements to 5 for He like, previous commit had done this for H like
11604 Directory Listing
Modified 5 years, 11 months ago
Wed Feb 22 21:50:45 2017 UTC
marios
Log:
By default use 5 resolved and 5 collapsed levels for H-like C, N, O, Ne, Si, Mg, S, Fe
11603 Directory Listing
Modified 5 years, 11 months ago
Mon Feb 20 15:49:32 2017 UTC
gary
Log:
Do not report lines from top 4 collapsed levels in H-like iso-sequence.  These lines can be in error by a factor of two due to proximity to top of model.
11602 Directory Listing
Modified 5 years, 11 months ago
Sat Feb 18 14:31:00 2017 UTC
gary
Log:
values must be on single line in the file
11600 Directory Listing
Modified 5 years, 11 months ago
Sat Feb 18 13:57:38 2017 UTC
gary
Log:
fix error in Brackett line n\'-n and improve wl
11599 Directory Listing
Modified 5 years, 11 months ago
Fri Feb 17 11:58:13 2017 UTC
peter
Log:
tsuite/auto/blr_f92.in:
tsuite/auto/blr_n14_p22.in:
tsuite/auto/pdr_th85ism.in:
tsuite/slow/pdr_xdr.in:
  - Readjust performance monitors that have been botching since r11582 on certain
    platforms. These monitors have a large spread, and in some cases have a
    bimodal distribution. In two cases the error margin was also increased.

11595 Directory Listing
Modified 5 years, 11 months ago
Tue Feb 14 20:23:47 2017 UTC
gary
Log:
Christophe Morisset\'s H II region sims
along BPT diagram
11593 Directory Listing
Modified 5 years, 11 months ago
Tue Feb 14 15:06:45 2017 UTC
peter
Log:
source/grains.cpp:
  - Relax ASSERTs in PE_init() following the report by Miguel Pereira Santaella.
  - Remove redundant casts to realnum in UpdatePot1(). 

11592 Directory Listing
Modified 5 years, 11 months ago
Mon Feb 13 18:46:22 2017 UTC
marios
Log:
fix minor errors in a few of the tsuite/auto/limit*.in sims
11590 Directory Listing
Modified 5 years, 11 months ago
Sat Feb 11 17:13:55 2017 UTC
gary
Log:
surprising collection of mistakes in this one sim
11588 Directory Listing
Modified 5 years, 11 months ago
Sat Feb 11 16:48:33 2017 UTC
gary
Log:
example did not include required keyword ZONE,
improve comment in cpp
Typo pointed out by Miguel Pereira Santaella
11587 Directory Listing
Modified 5 years, 11 months ago
Sat Feb 11 15:34:07 2017 UTC
gary
Log:
correct year on Fran's second paper
11586 Directory Listing
Modified 5 years, 11 months ago
Fri Feb 10 13:54:45 2017 UTC
gary
Log:
bring multiple alias for same paper together - if both used in same paper a mess results
11584 Directory Listing
Modified 5 years, 11 months ago
Fri Feb 10 12:39:41 2017 UTC
peter
Log:
source/cpu.cpp:
  - Don't print messages about md5sum mismatches when the NO TIME command is in
    effect. It would break repeatability tests.

11582 Directory Listing
Modified 5 years, 11 months ago
Fri Feb 10 11:05:08 2017 UTC
peter
Log:
data/stout/masterlist/Stout.ini:
  - Set default size of the N I model atom to 50 levels. This recovers the pumping
    discussed in Ferland+ (2012) ApJ 757, 79.
tsuite/auto/*.in:
tsuite/slow/*.in:
  - Fix test suite botches resulting from this change.

11581 Directory Listing
Modified 5 years, 11 months ago
Thu Feb 9 20:24:05 2017 UTC
gary
Log:
kappa paper
11580 Directory Listing
Modified 5 years, 11 months ago
Thu Feb 9 16:56:39 2017 UTC
gary
Log:
add publisher
11579 Directory Listing
Modified 5 years, 11 months ago
Thu Feb 9 13:36:58 2017 UTC
gary
Log:
move alias together
11578 Directory Listing
Modified 5 years, 11 months ago
Thu Feb 9 12:35:36 2017 UTC
gary
Log:
fix year for Fran's two photon paper
11577 Directory Listing
Modified 5 years, 11 months ago
Mon Feb 6 13:35:02 2017 UTC
gary
Log:
add comment that optional minimum number of levels
can appear after species label in Stout masterlist file
11575 Directory Listing
Modified 5 years, 11 months ago
Sun Feb 5 20:00:38 2017 UTC
gary
Log:
two small problems noted by Christophe
[O II] blend wavelength changed to 3729 to be consistent with C13
Add N II 2141 blend, which was present in C13
11574 Directory Listing
Modified 5 years, 11 months ago
Sun Feb 5 03:21:29 2017 UTC
gary
Log:
improve comments to collisional topoff
11572 Directory Listing
Modified 6 years ago
Fri Feb 3 12:58:03 2017 UTC
peter
Log:
source/mesh.h:
  - Do not read data files in global constructors. If the operation fails, the
    resulting exception cannot possibly be caught, leading to a hard crash of the
    program.
  - Avoid using physical constants in global constructors.

11571 Directory Listing
Modified 6 years ago
Thu Feb 2 20:56:50 2017 UTC
gary
Log:
alias adjustments
11570 Directory Listing
Modified 6 years ago
Thu Feb 2 18:27:13 2017 UTC
gary
Log:
two photon paper alias
11569 Directory Listing
Modified 6 years ago
Thu Feb 2 18:24:04 2017 UTC
gary
Log:
two photon paper alias
11566 Directory Listing
Modified 6 years ago
Tue Jan 31 07:33:52 2017 UTC
peter
Log:
source/prt_lines.cpp:
  - Add missing Ne 4720 blend.

11565 Directory Listing
Modified 6 years ago
Mon Jan 30 15:51:19 2017 UTC
gary
Log:
add Frans two photon paper
11564 Directory Listing
Modified 6 years ago
Sun Jan 29 22:28:42 2017 UTC
gary
Log:
reerences from localbib file in another paper
11561 Directory Listing
Modified 6 years ago
Wed Jan 25 06:14:39 2017 UTC
peter
Log:
source/cpu.h:
  - Add checks for a version of the compiler that fully supports C++11.
source/hydro_bauman.cpp:
source/rt_diffuse.cpp:
  - Remove obsolete pragmas.

11553 Directory Listing
Modified 6 years ago
Mon Jan 23 23:04:51 2017 UTC
rjrw
Log:
Remove code which is dead after last commit

11552 Directory Listing
Modified 6 years ago
Mon Jan 23 22:45:37 2017 UTC
rjrw
Log:
Remove unnecessary N*N search through line numbers in data read

11550 Directory Listing
Modified 6 years ago
Sun Jan 22 12:09:38 2017 UTC
peter
Log:
tsuite/auto/run_sequence.pl:
tsuite/slow/run_sequence.pl:
  - Optimize run sequence.

11547 Directory Listing
Modified 6 years ago
Sun Jan 22 11:47:12 2017 UTC
peter
Log:
source/Makefile:
source/capabilities.pl:
  - Make sure we pick up the correct runtime libraries when using g++ under FreeBSD.

11544 Directory Listing
Modified 6 years ago
Sun Jan 22 10:55:26 2017 UTC
peter
Log:
tsuite/run_service.pm:
  - Fix determination of number of cpus on modern BSD systems.

11541 Directory Listing
Modified 6 years ago
Sat Jan 21 16:50:46 2017 UTC
peter
Log:
tsuite/auto/split.pl:
tsuite/auto/test_grid.pl:
  - Repace the csplit command with our own split.pl script. The former doesn't
    work as intended under FreeBSD. This also reduces our dependence on external
    commands.

11537 Directory Listing
Modified 6 years ago
Sat Jan 21 11:12:08 2017 UTC
peter
Log:
source/capabilities.pl:
  - Precompiling headers doesn't work with gcc under FreeBSD 11.0-RELEASE. Here
    we disable this feature on all BSD variants to be on the safe side.

11531 Directory Listing
Modified 6 years ago
Wed Jan 18 08:01:24 2017 UTC
peter
Log:
source/cpu.cpp:
  - Enable FP traps when using the Oracle Developer Studio 12.5 compiler. This
    compiler no longer enables FP traps by default.

11523 Directory Listing
Modified 6 years ago
Tue Jan 17 19:48:43 2017 UTC
gary
Log:
change ionization oscillation warning to caution, caution to note, as per discussion on google group
11521 Directory Listing
Modified 6 years ago
Tue Jan 17 07:18:53 2017 UTC
peter
Log:
source/cddefines.h:
source/cpu.h:
source/container_classes.h:
source/atmdat_chianti.cpp:
source/parse_crashdo.cpp:
  - Remove pragmas to disable warning 4127 with MSVS, they are no longer needed.
  - Replace macro STATIC_ASSERT() with standard C++11 static_assert() calls.

11516 Directory Listing
Modified 6 years ago
Thu Jan 12 22:03:36 2017 UTC
gary
Log:
use correct year in nickname for Fran's 2017 paper
11515 Directory Listing
Modified 6 years ago
Thu Jan 12 15:31:41 2017 UTC
gary
Log:
define the nicknames used in the Stout database,
this resolves missed references in c17, c18 ms
11513 Directory Listing
Modified 6 years ago
Thu Jan 12 12:27:15 2017 UTC
gary
Log:
needed to vary eden for 2-level approximation plot
11510 Directory Listing
Modified 6 years ago
Wed Jan 11 09:52:56 2017 UTC
peter
Log:
source/cpu.h:
source/cpu.cpp:
  - Modify check_data() so that it can operate on a file for which the path is
    already known.
  - Test the MD5 checksum for all data files being read by open_data()
source/species.cpp:
  - Remove handcoded MD5 checksum tests. These are done in open_data() now.
source/thirdparty.h:
source/thirdparty.cpp:
  - Add routine MD5datastream() that calculates the MD5 checksum of an already
    open data stream.
source/version.cpp:
  - Bug-fix: avoid race condition between constructing t_version and the C++
    string Url.

11509 Directory Listing
Modified 6 years ago
Mon Jan 9 11:17:38 2017 UTC
peter
Log:
source/cddefines.h:
source/service.cpp:
source/TestVectorize.cpp:
  - Remove MyMalloc_avx() and MALLOC_AVX() as these are not safe on Windows.
    The allocated memory needs a special routine to be freed in Visual Studio.
source/vectorize.h:
  - Use special routine to free memory allocated with posix_memalign() on Windows.
source/opacity.h:
source/rfield.h:
source/cont_createmesh.cpp:
source/cool_eval.cpp:
source/rt_continuum.cpp:
source/temp_change.cpp:
  - Convert arrays that used to be allocated with MALLOC_AVX() into vector_avx.

11508 Directory Listing
Modified 6 years ago
Mon Jan 9 09:53:34 2017 UTC
peter
Log:
source/vectorize.h
  - Do not use preprocessor macros to define inline functions.
source/service.cpp
  - Add missing header dependency.

11506 Directory Listing
Modified 6 years ago
Sun Jan 8 13:00:51 2017 UTC
peter
Log:
source/cpu.h:
source/cpu.cpp:
source/prt_comment.cpp:
  - Downgrade md5sum mismatch to a caution.
  - Generate caunin() call when md5sum mismatches were found.
source/version.cpp
  - Fix file name in print statements and comment.

11504 Directory Listing
Modified 6 years ago
Sat Jan 7 16:33:21 2017 UTC
peter
Log:
source/version.cpp:
source/mole_reactions.cpp:
  - Set lgReleaseBranch to true for beta releases.

11503 Directory Listing
Modified 6 years ago
Sat Jan 7 10:44:49 2017 UTC
peter
Log:
source/save_fits.cpp:
  - Fix compiler warning from LLVM/clang++ 3.6.2.

11502 Directory Listing
Modified 6 years ago
Fri Jan 6 15:20:49 2017 UTC
gary
Log:
report number of Lya scatterins in 21 cm save file
11501 Directory Listing
Modified 6 years ago
Fri Jan 6 07:20:55 2017 UTC
peter
Log:
source/cloudyconfig_vs.h:
source/grains_mie.cpp:
  - Better solution for r11490.

11499 Directory Listing
Modified 6 years ago
Fri Jan 6 04:18:07 2017 UTC
peter
Log:
library/UnitTest++/src/tests/TestTestMacros.cpp:
  - Fix compiler warning about code that will no longer work in C++11.

11498 Directory Listing
Modified 6 years ago
Fri Jan 6 03:57:07 2017 UTC
peter
Log:
source/Makefile:
source/sys_clang_analyzer/Makefile.conf:
source/sys_gccBounds/Makefile.conf:
source/sys_icc/Makefile.conf:
source/sys_llvm/Makefile.conf:
source/sys_oraclestudio/Makefile.conf:
  - Switch language standard from C++98 to C++11. 
source/vectorize.h:
source/atmdat_gaunt.h:
source/atmdat_gaunt.cpp:
source/quantumstate.h:
source/TestVectorize.cpp:
  - Use vector_avx<> as our first C++11 feature.
source/sys_gcc_native:
  - Deleted. No longer needed as native compilations are the default now.
source/sys_solstudio:
  - This version of the compiler does not support C++11, use sys_oraclestudio instead.
source/sys_IBMxSeries:
source/sys_pSeries:
source/sys_open64:
source/sys_pgcc:
source/sys_pgccBounds:
  - Delete unsupported platforms and compilers.

11497 Directory Listing
Modified 6 years ago
Thu Jan 5 23:48:04 2017 UTC
gary
Log:
added papers
11496 Directory Listing
Modified 6 years ago
Thu Jan 5 22:27:31 2017 UTC
gary
Log:
add Eric paper
11495 Directory Listing
Modified 6 years ago
Thu Jan 5 21:21:22 2017 UTC
marios
Log:
dynamics.cpp
  - In DynaStartZone(), reverse order in another while-loop for finding correct
    upstream bin.

11494 Directory Listing
Modified 6 years ago
Thu Jan 5 19:21:09 2017 UTC
marios
Log:
dynamics.cpp
  - In DynaStartZone(), test in while-loop to find correct upstream bin now
    checks for valid index before attempting to fetch relevant values.
    This exploits short-circuit logic, and prevents out-of-bounds memory access.
  - Bugfix: In DynaNewStep(), while-loop to find correct upstream bin pointed to
    one bin past the correct one.

11492 Directory Listing
Modified 6 years, 1 month ago
Thu Jan 5 05:14:22 2017 UTC
peter
Log:
source/cddrive.cpp:
  - Fix preprocessor macro for MSVS.
  - Fix typos.

11490 Directory Listing
Modified 6 years, 1 month ago
Tue Jan 3 19:37:27 2017 UTC
gary
Log:
GNU math extensions not available in VS
11489 Directory Listing
Modified 6 years, 1 month ago
Tue Jan 3 17:45:36 2017 UTC
marios
Log:
BiblioToTeX.pm
  - Add option 'all' to clean-up script to remove the example TeX file,
    as well as the two scripts (for running and cleaning up).
    Instructions are printed on screen and in the script itself.

11485 Directory Listing
Modified 6 years, 1 month ago
Tue Jan 3 00:17:46 2017 UTC
marios
Log:
db-species-tex.pl
  - Include those molecules in the output table, for which we do not
    have a model for their structure (energy levels, and transition rates).
  - Do not include those labels from the output of 'save species labels'
    that indicate cosmic rays, photons, electrons, and grains.

11484 Directory Listing
Modified 6 years, 1 month ago
Mon Jan 2 19:06:29 2017 UTC
marios
Log:
BiblioToTeX.pm
  - Refactor run script into own function.
  - Create cleanup script to erase byproducts of running LaTeX on the example
    TeX file, as well as the scripts (mktable*.sh and cleanup*.sh) themselves.
    Only the PDF files are preserved.

11483 Directory Listing
Modified 6 years, 1 month ago
Mon Jan 2 18:50:32 2017 UTC
marios
Log:
db-species-tex.pl
  - Include molecules at the end of main LaTeX table.
  - Format molecule labels with superscripts (for isotopes and charge)
    and subscripts, as per chemical notation.

11480 Directory Listing
Modified 6 years, 1 month ago
Mon Jan 2 00:53:37 2017 UTC
marios
Log:
Add another pdflatex run to the 'mktable-species-db-list.sh' script
11478 Directory Listing
Modified 6 years, 1 month ago
Sun Jan 1 23:24:19 2017 UTC
gary
Log:
silence warning of use of possibly uninit var in VS15
11477 Directory Listing
Modified 6 years, 1 month ago
Sun Jan 1 22:36:35 2017 UTC
gary
Log:
alias for mem alloc func on windows
http://stackoverflow.com/questions/33696092/whats-the-correct-replacement-for-posix-memalign-in-windows
11475 Directory Listing
Modified 6 years, 1 month ago
Sun Jan 1 02:19:17 2017 UTC
gary
Log:
bring trunk and c17_branch versions into sync
11472 Directory Listing
Modified 6 years, 1 month ago
Sat Dec 31 17:57:44 2016 UTC
marios
Log:
energy.cpp: Improve confusing error message
11471 Directory Listing
Modified 6 years, 1 month ago
Sat Dec 31 17:21:10 2016 UTC
gary
Log:
drift up, mean of four compilers
11470 Directory Listing
Modified 6 years, 1 month ago
Sat Dec 31 17:16:56 2016 UTC
gary
Log:
update from compiling database
11469 Directory Listing
Modified 6 years, 1 month ago
Sat Dec 31 13:04:11 2016 UTC
gary
Log:
needed to comile to PDF
11468 Directory Listing
Modified 6 years, 1 month ago
Sat Dec 31 01:22:09 2016 UTC
gary
Log:
missing Lykins2015
11466 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 30 19:48:57 2016 UTC
marios
Log:
scripts/BiblioToTeX.pm: force test TeX into one column output
11465 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 30 19:35:55 2016 UTC
marios
Log:
scripts/BiblioToTeX.pm
  - New functions to write as a comment in the given file,
    the command-line invocation used that generated the file.
scripts/db-ref-json2tex.pl
  - Increase width for columns that hold the data citations from 4cm to 5cm.
  - Use \nodata command in deluxeTable mode, instead of leaving the column
    blank.
  - Write command-line invocation in output TeX table.
scripts/db-species-tex.pl
  - Allow more than one digit before dot in value to '-bc'.
  - Use two vertical columns to separate groups of columns, when more than
    one are used, without separating columns (-bc=0cm) in regular mode
    (not deluxeTable).
  - Use \nodata command in deluxeTable mode, instead of leaving the column
    blank.
  - Bugfix: Write data for the specified number of columns, even when we've
    run out of data (affects appearance at end of table, in regular mode --
    not deluxeTable).
  - Write command-line invocation in output TeX table.

11464 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 30 18:07:27 2016 UTC
gary
Log:
update H-H2 coll to Lique 2015
11463 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 30 02:37:42 2016 UTC
marios
Log:
scripts/BiblioToTeX.pm
  - Convert HTML code for '&' to ASCII.
  - Rename test TeX file from 'test-xxx.tex' to 'xxx-list.tex'.
    Also rename script for producing PDF file of prepared table.
scripts/db-ref-bib2json.pl
  - Do not report empty .coll files to empty_files.txt. 
scripts/db-ref-json2tex.pl
  - Explain in the table description the meaning of the double dagger symbol
    that appears next to some of the species names.
docs/latex/common/bibliography2.bib
  - Resolve conflicts between cross-reference human-readable codes.
data/stout/c/c_3/c_3.coll
data/stout/c/c_3/c_3.tp
data/stout/f/f_6/f_6.coll
data/stout/f/f_6/f_6.tp
data/stout/fe/fe_9/fe_9.coll
data/stout/fe/fe_9/fe_9.tp
data/stout/o/o_5/o_5.coll
data/stout/o/o_5/o_5.tp
  - Remove redundant line of field of stars, the last occurence of which is
    used as the delimeter between the data and the refs by the ref-gathering
    script, db-ref-bib2json.pl. 
    The field of stars appearing after the references prevented the latter from
    being resolved.

11462 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 30 02:12:36 2016 UTC
gary
Log:
use Lique 2015 for H - H2 coll
11461 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 30 02:11:45 2016 UTC
gary
Log:
use Lique 2015 for H - H2 coll
11460 Directory Listing
Modified 6 years, 1 month ago
Thu Dec 29 22:43:24 2016 UTC
gary
Log:
correct overenthusiastic removal of redundant data - h2 vs hd
11459 Directory Listing
Modified 6 years, 1 month ago
Thu Dec 29 21:35:16 2016 UTC
gary
Log:
remove unused / redundant code
11458 Directory Listing
Modified 6 years, 1 month ago
Thu Dec 29 21:21:16 2016 UTC
gary
Log:
Fe III cooling significantly larger due to Badnell Balance collision data
11457 Directory Listing
Modified 6 years, 1 month ago
Thu Dec 29 21:07:45 2016 UTC
gary
Log:
Lique 2015 H H2 data now default
11456 Directory Listing
Modified 6 years, 1 month ago
Thu Dec 29 20:26:58 2016 UTC
gary
Log:
update Fe III to Badnell & Balance 2014ApJ...785...99B
11455 Directory Listing
Modified 6 years, 1 month ago
Thu Dec 29 20:23:41 2016 UTC
gary
Log:
add Badnell Ballance Fe III reference
11454 Directory Listing
Modified 6 years, 1 month ago
Thu Dec 29 18:16:05 2016 UTC
marios
Log:
tsuite/auto/limit_casea_h_den_temp.in
tsuite/auto/limit_caseb_hhe_den_temp.in
  - Increase number of resolved and collapsed levels for H, in order to improve
    agreement for a few line monitors that were close to botching.

11453 Directory Listing
Modified 6 years, 1 month ago
Thu Dec 29 15:21:21 2016 UTC
gary
Log:
add reference for H2 X energies
11452 Directory Listing
Modified 6 years, 1 month ago
Thu Dec 29 15:13:16 2016 UTC
marios
Log:
Update H2 ground electronic state energies to the calculations of Komasa et al. (2011).

data/h2/energy_X.dat
  - Update H2 energies to Komasa+2011.
    File update courtesy of Kyle Kaplan.
data/LineList_PDR_H2.dat
  - Update H2 wavelengths.
source/prt_lines_molecules.cpp
  - Update hardwired H2 wavelengths.
source/save_do.cpp
  - Update hardwired H2 wavelengths.
  - Drop duplicate wavelength (3.48542 after the update, 3.48530 before).
tsuite/slow/h2_th85orion.in
  - Update monitor line H2 wavelengths.

11450 Directory Listing
Modified 6 years, 1 month ago
Wed Dec 28 22:57:41 2016 UTC
peter
Log:
source/TestThirdparty.cpp:
  - Slightly relax error bounds for unit tests of Bessel functions.

11449 Directory Listing
Modified 6 years, 1 month ago
Wed Dec 28 21:02:24 2016 UTC
gary
Log:
more helpful error message
11447 Directory Listing
Modified 6 years, 1 month ago
Wed Dec 28 20:47:44 2016 UTC
gary
Log:
use stop species column density in tsuite, change to no experimental in hazy
11441 Directory Listing
Modified 6 years, 1 month ago
Tue Dec 27 16:12:32 2016 UTC
marios
Log:
dynamics.cpp
  - Bugfix: Scale iso-seq level populations by scalingZoneDensity(), instead
    of the hydrogen density.  This has been broken since the reintegration of
    newmole, and has caused advection sims to not be able to converge to a
    solution.

11440 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 23 06:02:37 2016 UTC
marios
Log:
uninclude-headers.pl
  - Add option '-d' (dry run) to produce the summary file, but change no source
    files.  This is useful to run before updating the source.
  - Notify user of output file name.

11439 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 23 05:38:28 2016 UTC
marios
Log:
TestMesh.cpp
  - Remove redundant header.
headers.pm
  - Bugfix: Load-balancer did not cover all array indices.
  - Bugfix: Escape header file names to properly handle exceptional cases,
    such as UnitTest++.h.
uninclude-headers.pl
  - Adjust extra compiler flags to point to UnitTest++/src. 
  - Remove object files from previous run.
  - Bugfix: Escape header file names to properly handle exceptional cases,
    such as UnitTest++.h.
  - Exit if 'cloudyconfig.h' does not exist, as this leads the code to run
    ad infinitum.

11438 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 23 02:14:03 2016 UTC
marios
Log:
uninclude-headers.pl
  - Remove temporary files from a previous run, if present, before starting.
headers.pm
  - Simplify load-balancing, making an exception for the case that we have no
    files to process than threads, instead of specifically for just 1 thread.

11437 Directory Listing
Modified 6 years, 1 month ago
Thu Dec 22 20:16:26 2016 UTC
marios
Log:
Script show-src-hdr-tree.pl not included in previous commit
11436 Directory Listing
Modified 6 years, 1 month ago
Thu Dec 22 20:14:32 2016 UTC
marios
Log:
show-src-hdr-tree.pl
  - Add script that shows the header dependencies of a source file in
    a Christmas Tree layout.

headers.pm
  - Adapt to accommodate Tree layout for source files.

atmdat_dielrec_fe.cpp
cont_createmesh.cpp
save_line.cpp
  - Remove redundant headers.

11430 Directory Listing
Modified 6 years, 1 month ago
Wed Dec 21 22:51:16 2016 UTC
gary
Log:
do not report the duplicate reactions in beta release
11427 Directory Listing
Modified 6 years, 1 month ago
Wed Dec 21 20:41:52 2016 UTC
gary
Log:
update checksum
11424 Directory Listing
Modified 6 years, 1 month ago
Wed Dec 21 12:34:41 2016 UTC
gary
Log:
rm empty file
11423 Directory Listing
Modified 6 years, 1 month ago
Tue Dec 20 20:04:25 2016 UTC
marios
Log:
Increase the number of resolved levels for H and He, and / or relax
line error for limit_case[ab] sims.

11422 Directory Listing
Modified 6 years, 1 month ago
Tue Dec 20 19:26:56 2016 UTC
gary
Log:
two monitors drift, mean of cloud9 & wolkje
11421 Directory Listing
Modified 6 years, 1 month ago
Tue Dec 20 16:05:52 2016 UTC
marios
Log:
Add comment to global.cpp explaining the purpose of the file.
11419 Directory Listing
Modified 6 years, 1 month ago
Tue Dec 20 15:38:40 2016 UTC
marios
Log:
Add missing header to collision.cpp
11418 Directory Listing
Modified 6 years, 1 month ago
Tue Dec 20 12:45:33 2016 UTC
peter
Log:
source/ion_recomb_Badnell.cpp:
  - Add secondary autoionization to the code for DR suppression. Code provided
    by Dragan Nikolic.
source/parse_test.cpp:
  - Fix botches in the smoke test.
tsuite/auto/*.in:
tsuite/slow/*.in:
  - Fix botches.

11417 Directory Listing
Modified 6 years, 1 month ago
Tue Dec 20 11:59:15 2016 UTC
peter
Log:
source/parse_commands.cpp:
  - Give error message when the keyword LINEAR is omitted on the LUMINOSITY command.

11416 Directory Listing
Modified 6 years, 1 month ago
Tue Dec 20 00:43:30 2016 UTC
marios
Log:
Add missing header files with function declarations (obtained with the gcc
option -Wmissing-declarations).
The following functions have been declared STATIC:
  - in conv_init_solution.cpp, FindTempChangeFactor()
  - in helike_einsta.cpp, scqdri()
  - in iso_radiative_recomb.cpp, iso_radrecomb_from_cross_section()
  - in mole_h2_create.cpp, compareEnergies(), also disabled (#if 0).
  - in prt_final.cpp, PrintCenterLine() 
  - in rt_continuum_shield_fcn.cpp, RT_continuum_shield_fcn_point() 
  - in thirdparty_quadpack.cpp, xerror_() 

11415 Directory Listing
Modified 6 years, 1 month ago
Mon Dec 19 22:51:12 2016 UTC
marios
Log:
source/uninclude-headers.pl
  - Do not test header files exposing the interface of corresponding source
    files.  E.g., species.h should appear in species.cpp regardless of
    whether it'd pass the compilation test of the script.
  - Bugfix: glob did not produce list of source files.
source/headers.pm
  - Update to include compilation flag that requires function declarations
    (does not apply to inline functions).
source/cont_createmesh.cpp
source/cool_eval.cpp
source/global.cpp
source/h2.cpp
source/parse_species.cpp
source/rt_diffuse.cpp
source/species.cpp
source/taulines.cpp
  - Restore includes of header files that contain function declarations.
source/gammas.h
  - Forward declaration of struct t_phoHeat.

11414 Directory Listing
Modified 6 years, 1 month ago
Mon Dec 19 15:26:34 2016 UTC
marios
Log:
Use intrinsic Case B line predictions in monitors.
11413 Directory Listing
Modified 6 years, 1 month ago
Sat Dec 17 16:17:31 2016 UTC
marios
Log:
Bugfix: In 'monitor case b', set the linetype to 1 ('emergent') for calls to cdLine().
Previously, it was set to the default value of -1, which triggered a number of
warnings in the test suite.

11412 Directory Listing
Modified 6 years, 1 month ago
Sat Dec 17 15:55:04 2016 UTC
marios
Log:
source/uninclude-headers.pl
  - Allow list of source files to be specified on the command-line, instead of
    checking all the source files at every run of the script.

11411 Directory Listing
Modified 6 years, 1 month ago
Sat Dec 17 15:27:22 2016 UTC
marios
Log:
Update source/uninclude_headers.pl and remove unneeded / duplicate headers from source files.

11410 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 16 22:53:50 2016 UTC
gary
Log:
one more -- broke string search
11409 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 16 22:51:23 2016 UTC
gary
Log:
more copyright years
11408 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 16 22:30:56 2016 UTC
gary
Log:
missed in source unpdate due to wrong year
11407 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 16 22:24:23 2016 UTC
gary
Log:
two more updates
11406 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 16 22:13:49 2016 UTC
gary
Log:
step one in updating copyright year
11405 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 16 19:40:19 2016 UTC
fguzman
Log:
increase error on pdr_co_fully simulation t pass gcc 6.2.0: documented on the sim
11404 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 16 19:33:40 2016 UTC
fguzman
Log:
increase error on pdr_co_fully simulation
11403 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 16 19:31:00 2016 UTC
gary
Log:
hack to fix thrown assert in igm_primal on
some compilers.  This is the second time this sim and element
has required upward revision.  The alternative, according to the comments,
would be to sort variables so that matrix elements are added from
smallest to largest. 
11402 Directory Listing
Modified 6 years, 1 month ago
Fri Dec 16 02:20:52 2016 UTC
fguzman
Log:
test suite fixes for bug fix on P&R h-like rate coefficients on rev 11401
11401 Directory Listing
Modified 6 years, 1 month ago
Thu Dec 15 23:11:47 2016 UTC
fguzman
Log:
fixed bug in PR78 n-changing effective coefficients. Multipoles were counted as dipoles
11400 Directory Listing
Modified 6 years, 1 month ago
Thu Dec 15 21:30:12 2016 UTC
marios
Log:
Allow advection runs to proceed beyond the initial relaxation runs.

11399 Directory Listing
Modified 6 years, 1 month ago
Tue Dec 13 23:32:30 2016 UTC
gary
Log:
This makes it possible to change the shape of the Lya source function at line center.  The default continues to be the Planck function at the 2p/1s excitation temperature.  The new SET LYA 21CM command makes it possible to use the gas KINETIC temperature or S_nu = CONSTANT.  There is no change in the default functionality of the code.
11397 Directory Listing
Modified 6 years, 1 month ago
Mon Dec 12 19:11:04 2016 UTC
marios
Log:
source/rt_line_driving.cpp: update print statement, and disable it with if(0), instead of commenting out
11396 Directory Listing
Modified 6 years, 1 month ago
Sat Dec 10 22:14:00 2016 UTC
marios
Log:
tsuite/experimental/dynamics_orion_recom.in: Update line labels
11395 Directory Listing
Modified 6 years, 1 month ago
Sat Dec 10 21:43:20 2016 UTC
marios
Log:
auto/time_cool*.in: Fix save file prefixes
11389 Directory Listing
Modified 6 years, 1 month ago
Wed Dec 7 01:24:33 2016 UTC
marios
Log:
source/monitor_results.cpp
  - Compute the error for the "monitor departure coefficient" commands
    for a species or an iso-sequence element as the deviation of the
    monitored quantity from the computed mean.  Previously, the largest
    departure in the species model was reported as the error.
  - For the departure coefficient of H-, use the given value for the
    error calculation, instead of the hardcoded 1 used.
docs/latex/hazy1/miscell.tex
  - Document new behavior, and eliminate the discussion on the specific
    meaning on the error depending on the exact sub-command.
  - List the species ("C+4") syntax as a new sub-command.

11380 Directory Listing
Modified 6 years, 2 months ago
Sun Nov 27 23:16:34 2016 UTC
peter
Log:
source/TestQuadpack.cpp:
  - Fix unit test failures on openSUSE Leap.

11379 Directory Listing
Modified 6 years, 2 months ago
Wed Nov 23 19:38:57 2016 UTC
marios
Log:
typo in hazy
11378 Directory Listing
Modified 6 years, 2 months ago
Tue Nov 22 21:14:33 2016 UTC
marios
Log:
Bug fix: report 'monitor line case b' wavelengths with all significant digits.
11377 Directory Listing
Modified 6 years, 2 months ago
Mon Nov 21 18:41:35 2016 UTC
marios
Log:
data/pdr_leiden_hack.ini -- update command
11376 Directory Listing
Modified 6 years, 2 months ago
Mon Nov 21 18:07:32 2016 UTC
fguzman
Log:
fix bug introduced on rev 11372 for thermal command
11375 Directory Listing
Modified 6 years, 2 months ago
Mon Nov 21 13:30:31 2016 UTC
marios
Log:
Document command 'set density tolerance'
11374 Directory Listing
Modified 6 years, 2 months ago
Fri Nov 18 22:15:53 2016 UTC
marios
Log:
Introduce new command "monitor line Case B" to monitor the ratio of lines
against the Hummer & Storey predictions.

11373 Directory Listing
Modified 6 years, 2 months ago
Fri Nov 18 21:49:42 2016 UTC
gary
Log:
several serious errors did not start with PROBLEM
so were not automatically detected
11372 Directory Listing
Modified 6 years, 2 months ago
Fri Nov 18 21:20:41 2016 UTC
fguzman
Log:
modified thermal parsing and removed maxwell integration from non-thermal defaults
11371 Directory Listing
Modified 6 years, 2 months ago
Fri Nov 18 13:59:50 2016 UTC
peter
Log:
source/hydrocollid.cpp:
  - Optimize CS_PercivalRichards78() for speed. No change in functionality.

11370 Directory Listing
Modified 6 years, 2 months ago
Thu Nov 17 03:09:05 2016 UTC
fguzman
Log:
fix botches on the dat files of the grid sims due to the reintegration of RydDep branch
11369 Directory Listing
Modified 6 years, 2 months ago
Wed Nov 16 11:12:17 2016 UTC
peter
Log:
source/ion_recomb_Badnell.cpp:
  - Prevent debug.txt from picking up output of PRINT RECOMBINATION command.

11368 Directory Listing
Modified 6 years, 2 months ago
Mon Nov 14 22:43:41 2016 UTC
fguzman
Log:
updated tsuite after RydDep reintegration
11367 Directory Listing
Modified 6 years, 2 months ago
Mon Nov 14 22:39:57 2016 UTC
fguzman
Log:
reintegrated RydDep into trunk
11363 Directory Listing
Modified 6 years, 2 months ago
Sun Nov 13 11:17:55 2016 UTC
peter
Log:
source/thirdparty.h:
source/thirdparty.cpp:
  - Replace Cephes versions of the Bessel K and I functions with Boost versions.
    These are faster and possibly also more accurate than the Cephes versions.
  - Add new routines bessel_k0_k1(), bessel_i0_i1(), and their scaled versions.
    These are faster than calling bessel_k0() and bessel_k1() by eliminating
    redundant calls to math library functions.
  - Add new helper routines ratevl_x_y() for efficiently evaluating rational
    function approximations.
source/helike_cs.cpp:
  - Use the new bessel_k0_k1() routine to speed up my_Integrand_S62::operator().
source/TestThirdparty.cpp:
  - Make existing tests more accurate and also add new tests.
source/vectorize.h:
  - Fix compiler error when compiling with a C++11 complient compiler.

11360 Directory Listing
Modified 6 years, 2 months ago
Thu Nov 10 14:48:00 2016 UTC
peter
Log:
source/cddefines.h:
source/container_classes.h:
source/parse_crashdo.cpp:
  - Fix warnings from the Oracle Studio 12.5 compiler.

11359 Directory Listing
Modified 6 years, 2 months ago
Thu Nov 10 12:20:15 2016 UTC
gary
Log:
clarify the xi definition
11356 Directory Listing
Modified 6 years, 3 months ago
Sat Nov 5 01:50:31 2016 UTC
gary
Log:
extend limits of default Crab SED to be like C13,
document that 5548 SED is exactly as published, no extrapolation done.
11355 Directory Listing
Modified 6 years, 3 months ago
Fri Nov 4 14:32:09 2016 UTC
peter
Log:
source/sys_oraclestudio/Makefile.conf:
  - Prevent miscompiling CS_l_mixing_PS64_expI() for -xarch=avx2_i.

11353 Directory Listing
Modified 6 years, 3 months ago
Fri Nov 4 11:52:50 2016 UTC
peter
Log:
source/Makefile:
  - Omit u flag on the ar command to avoid warning messages from modern versions
    of ar which work in deterministic mode by default. See e.g. Comment 1 in
    https://bugzilla.redhat.com/show_bug.cgi?id=1155273

11347 Directory Listing
Modified 6 years, 3 months ago
Mon Oct 31 14:50:01 2016 UTC
gary
Log:
more useful debug print statement
11341 Directory Listing
Modified 6 years, 3 months ago
Tue Oct 25 19:21:50 2016 UTC
marios
Log:
Hazy1 - Add missing verb.
11340 Directory Listing
Modified 6 years, 3 months ago
Tue Oct 25 19:18:08 2016 UTC
marios
Log:
docs/latex/CompileAll.pl
  - Fix cross-references between Hazy 1 & Hazy 2

11339 Directory Listing
Modified 6 years, 3 months ago
Tue Oct 25 18:49:25 2016 UTC
gary
Log:
clarify how the resolving power changes the line intensities in the save continuum output
11338 Directory Listing
Modified 6 years, 3 months ago
Tue Oct 25 18:36:19 2016 UTC
marios
Log:
Remove extraneous references to Kingdon, Ferland, & Feibelman (1995)
11337 Directory Listing
Modified 6 years, 3 months ago
Tue Oct 25 17:45:34 2016 UTC
marios
Log:
docs/latex/common/aas_macros_v61.sty
  - Add journal macros from AASTeX v6.1.
docs/latex/head_info.tex
  - Switch to using the new AAS macros.
docs/latex/common/bibliography2.bib
  - Add missing reference to Akras et al. (2015).
docs/latex/hazy1/miscell.tex
  - Use C13 citation macro.

11336 Directory Listing
Modified 6 years, 3 months ago
Mon Oct 24 23:11:53 2016 UTC
fguzman
Log:
updated citation of He paper
11335 Directory Listing
Modified 6 years, 3 months ago
Mon Oct 24 21:57:45 2016 UTC
gary
Log:
Remove assert that total atom and ion density is positive.  Similar assert remains for total density being positive, after molecules are added.  

Following sim threw the assert I removed:
hden 0
set eden 0
set dr 0
stop zone 1
init "honly.ini"
coronal equilibrium log 1

At head of trunk 100% of H is molecular so the removed assert tripped.  In C13 there was a trace atomic H, probably due to our previous practice of not allowing rates to go to zero.  100% molecular is the right answer for this sim, which has no source of ionization, and is the answer we get.
11334 Directory Listing
Modified 6 years, 3 months ago
Mon Oct 24 14:33:03 2016 UTC
fguzman
Log:
fixed ambiguity of sqrt(integer) in helik_cs.cpp
11333 Directory Listing
Modified 6 years, 3 months ago
Mon Oct 24 06:04:20 2016 UTC
peter
Log:
source/helike_cs.cpp:
  - Fix warning from the LLVM compiler.

11332 Directory Listing
Modified 6 years, 3 months ago
Sun Oct 23 23:48:07 2016 UTC
gary
Log:
references in two photon paper
11331 Directory Listing
Modified 6 years, 3 months ago
Fri Oct 21 20:38:11 2016 UTC
fguzman
Log:
modified tsuite simulations according to the new l-changing rates
11329 Directory Listing
Modified 6 years, 3 months ago
Fri Oct 21 17:01:15 2016 UTC
fguzman
Log:
reintegration of Hlike_HS87 branch into trunk
11320 Directory Listing
Modified 6 years, 3 months ago
Fri Oct 14 18:53:24 2016 UTC
gary
Log:
add one ref
11311 Directory Listing
Modified 6 years, 4 months ago
Thu Sep 22 05:15:23 2016 UTC
peter
Log:
source/mole_eval_balance.cpp:
  - Only produce verbose output when TRACE MOLECULES is in effect.

11309 Directory Listing
Modified 6 years, 4 months ago
Thu Sep 22 04:49:40 2016 UTC
peter
Log:
docs/latex/hazy1/conout.tex:
  - Add missing documentation of the EVERY keyword.

11308 Directory Listing
Modified 6 years, 4 months ago
Wed Sep 21 21:22:27 2016 UTC
gary
Log:
give an example
11302 Directory Listing
Modified 6 years, 4 months ago
Sat Sep 10 13:51:53 2016 UTC
gary
Log:
explicit use of SED files often had incorrect case - this works on Mac and Windows, so was not detected, but will not work in Linux
11301 Directory Listing
Modified 6 years, 4 months ago
Fri Sep 9 22:10:35 2016 UTC
gary
Log:
remove lines which produced ambiguous finds
when going to n=200
11300 Directory Listing
Modified 6 years, 4 months ago
Wed Sep 7 20:15:18 2016 UTC
gary
Log:
remove extra He 1 lines
11299 Directory Listing
Modified 6 years, 4 months ago
Wed Sep 7 18:51:03 2016 UTC
gary
Log:
add HS C 6
11298 Directory Listing
Modified 6 years, 4 months ago
Wed Sep 7 18:31:02 2016 UTC
gary
Log:
tsuite auto add more complete HS line ratios,
for H1, He2 and O8.
Used evaluated number of levels in HS data rather than explicit comment,
improve comments 
11297 Directory Listing
Modified 6 years, 4 months ago
Wed Sep 7 18:24:16 2016 UTC
marios
Log:
scripts/HS-ratio-make.pl
  - Convert file from DOS to UNIX format.
  - Prompt user for input file name.
  - Prompt user for line label (was fixed to "O  8").
  - Label matching is now case-insensitive.

11294 Directory Listing
Modified 6 years, 4 months ago
Wed Sep 7 12:10:15 2016 UTC
gary
Log:
dat files to compare with HS Case B rates,
and Marios script to create them.  Not used yet.
11292 Directory Listing
Modified 6 years, 5 months ago
Mon Sep 5 11:19:06 2016 UTC
peter
Log:
source/prt_comment.cpp:
  - Bug-fix: protect against division by zero as TauTot() can be zero in the first iteration.
source/rt_tau_init.cpp:
  - Replace explicit constants 1e-20 with opac.taumin.

11291 Directory Listing
Modified 6 years, 5 months ago
Sun Sep 4 23:19:44 2016 UTC
gary
Log:
botches due to update in low-T CS for
Ne 2 and Ne 3 from http://arxiv.org/abs/1607.03158
11289 Directory Listing
Modified 6 years, 5 months ago
Sun Sep 4 14:59:50 2016 UTC
gary
Log:
svn merge  -r11270:11271 ^/branches/CSupdate
update low-T CS for IR lines of Ne 2 and Ne 3.
This cherry picks the Ne update on this branch.  The N 4
update will not be done.  Nigel is redoing that calculation
since the N IV] CS is 2x smaller than previous calculations
11285 Directory Listing
Modified 6 years, 5 months ago
Thu Sep 1 18:43:33 2016 UTC
gary
Log:
update O  5 wavelength
11283 Directory Listing
Modified 6 years, 5 months ago
Thu Sep 1 16:47:07 2016 UTC
fguzman
Log:
reintegrated RydDep after bugfixes
11279 Directory Listing
Modified 6 years, 5 months ago
Wed Aug 31 09:22:49 2016 UTC
peter
Log:
docs/latex/hazy1/ControllingModelAtoms.tex:
  - Fix examples where the ATOM command was still used.
  - Fix typo.
docs/latex/hazy1/conout.tex:
  - Change H_2 atom -> H_2 model.

11267 Directory Listing
Modified 6 years, 5 months ago
Sat Aug 20 16:16:32 2016 UTC
marios
Log:
Do not require 'Reference' label to mark the start of references in Stout data files.  Use last field of stars instead.
11266 Directory Listing
Modified 6 years, 5 months ago
Sat Aug 20 15:50:07 2016 UTC
marios
Log:
Fix bug in grep call in db-ref-bib2json.pl
11265 Directory Listing
Modified 6 years, 5 months ago
Sat Aug 20 15:15:43 2016 UTC
marios
Log:
Report Stout data files with missing data and / or references to an output file
11264 Directory Listing
Modified 6 years, 5 months ago
Sat Aug 20 14:27:01 2016 UTC
marios
Log:
Update references in bibtex and json for new Stout species
11263 Directory Listing
Modified 6 years, 5 months ago
Sat Aug 20 14:19:20 2016 UTC
marios
Log:
Guard against no references in the Stout data file.
11262 Directory Listing
Modified 6 years, 5 months ago
Sat Aug 20 12:50:59 2016 UTC
gary
Log:
wrong file name
11261 Directory Listing
Modified 6 years, 5 months ago
Sat Aug 20 12:33:02 2016 UTC
gary
Log:
state dependencies, and where to find out about them
11248 Directory Listing
Modified 6 years, 5 months ago
Wed Aug 17 20:12:34 2016 UTC
gary
Log:
reintegrate CSupdate branch,
update O V  and F VI to #http://adsabs.harvard.edu/abs/2014A%26A...566A.104F
update wavelength for O V lines that changed slightly in NIST
abort when blend fails
11245 Directory Listing
Modified 6 years, 5 months ago
Wed Aug 17 09:06:26 2016 UTC
peter
Log:
tsuite/auto/fix_input_scripts.pl:
  - Make wavelength matching more versatile.

11225 Directory Listing
Modified 6 years, 6 months ago
Tue Aug 2 17:37:06 2016 UTC
rjrw
Log:
Minor tidying of iso_collapsed_lifetimes_update()

11223 Directory Listing
Modified 6 years, 6 months ago
Mon Aug 1 08:16:09 2016 UTC
peter
Log:
source/Makefile:
  - Further improve the Makefile by removing the dependency on a directory. This
    could still lead to spurious recompilations.

11219 Directory Listing
Modified 6 years, 6 months ago
Sun Jul 31 17:40:45 2016 UTC
peter
Log:
This commit fixes various problems in the Makefile pertaining to running the
unit tests. Also fix several omissions in the svn:ignore property in sys_xxx.

source/Makefile:
  - Create new target testclean for cleaning up only the files pertaining to
    the unit tests.
  - Fix missing dependency on cloudyconfig.h for compiling the unit tests.
  - Reorganize compiling the unit test library. This is now done entirely
    inside the sys_xxx directory to avoid interference with other sys_xxx
    directories.
  - Create dependency files for Test*.o.
  - Avoid unnecessary recompilations when creating runtests.exe.

11216 Directory Listing
Modified 6 years, 6 months ago
Sat Jul 30 14:23:30 2016 UTC
marios
Log:
In 'monitor departure', first excited level is 2 (not 1).
11211 Directory Listing
Modified 6 years, 6 months ago
Fri Jul 29 22:36:34 2016 UTC
gary
Log:
second try - file had picked up a windows eof and did not commit in first try
11209 Directory Listing
Modified 6 years, 6 months ago
Fri Jul 29 21:57:07 2016 UTC
gary
Log:
Hazy2 cover figure, with permission of first autho
11208 Directory Listing
Modified 6 years, 6 months ago
Fri Jul 29 19:59:52 2016 UTC
rjrw
Log:
Set chConfig() values for ExtraLyman and Satellite states to
something vaguely relevant, in case anyone ever reads them...

11207 Directory Listing
Modified 6 years, 6 months ago
Fri Jul 29 18:59:41 2016 UTC
gary
Log:
Matt updates to better retain energy level state information
11206 Directory Listing
Modified 6 years, 6 months ago
Fri Jul 29 15:37:16 2016 UTC
marios
Log:
Account for EXCITED keyword in 'monitor departure coeff SPECIES'. Removed fixit.
11205 Directory Listing
Modified 6 years, 6 months ago
Fri Jul 29 15:26:51 2016 UTC
marios
Log:
bugfix: Get all the levels for a species given to 'monitor departure coeff' without the '[]' notation.
11204 Directory Listing
Modified 6 years, 6 months ago
Fri Jul 29 11:52:08 2016 UTC
peter
Log:
This commit fixes various problems that prevented the unit tests from being run
with compilers other than g++ or outside the source directory.

library/UnitTest++/Makefile:
  - Always use g++ to generate dependencies. It may not work for other compilers.
source/Makefile:
  - Add the -DSYS_CONFIG flag when compiling unit tests.
  - Add -I${SRCDIR} when compiling unit tests so that the header files are found.
  - Do not use optimization when compiling the unit test library.
source/sys_icc/Makefile.conf:
  - Add NO_TRAP_FLAGS.
source/sys_llvm/Makefile.conf:
  - Reduce level of optimization to avoid reordering of expressions. This breaks
    the vectorized math routines.
source/sys_solstudio/Makefile.conf:
  - Reduce level of optimization to avoid changes in FP rounding. This breaks
    pow10() and pow10f().
source/TestMain.cpp:
  - Disable FPE traps. They may lead to spurious crashes in the unit tests.
source/TestMultiArr.cpp:
  - Avoid warnings about unused expressions.
source/TestThirdparty.cpp:
  - Avoid ambiguous overloads.
source/sys_oraclestudio/*
  - Add support for the new Oracle Developer Studio 12.5 compiler.

11203 Directory Listing
Modified 6 years, 6 months ago
Thu Jul 28 19:09:20 2016 UTC
gary
Log:
template file did not include SAVE MONITOR
11202 Directory Listing
Modified 6 years, 6 months ago
Thu Jul 28 19:04:56 2016 UTC
gary
Log:
Case B sims for H, testing intensities and departure coefficients, and a coronal case at 1e5 K
the monitored departure coefficients are wrong - they should be <=1
makes no sense that the coronal case is so different from the photo case at 1e5 K
11201 Directory Listing
Modified 6 years, 6 months ago
Thu Jul 28 15:58:03 2016 UTC
gary
Log:
adjust monitor to means of 6 platforms
11200 Directory Listing
Modified 6 years, 6 months ago
Thu Jul 28 15:03:55 2016 UTC
marios
Log:
Allow the "monitor departure coefficients" command to accept a level or level
range as part of the input species, using the syntax of "save species".

11198 Directory Listing
Modified 6 years, 6 months ago
Thu Jul 28 12:58:03 2016 UTC
gary
Log:
adjust monitor so 32 bit all double does not botch
11195 Directory Listing
Modified 6 years, 6 months ago
Thu Jul 28 03:19:28 2016 UTC
gary
Log:
Peter's \ae
11194 Directory Listing
Modified 6 years, 6 months ago
Thu Jul 28 03:12:36 2016 UTC
gary
Log:
the image
11191 Directory Listing
Modified 6 years, 6 months ago
Wed Jul 27 22:51:13 2016 UTC
gary
Log:
new cover image, Wikipedia public domain
11189 Directory Listing
Modified 6 years, 6 months ago
Tue Jul 26 19:44:56 2016 UTC
gary
Log:
remove redundant definition of Hb in line stack
11188 Directory Listing
Modified 6 years, 6 months ago
Tue Jul 26 19:21:56 2016 UTC
gary
Log:
remove unneeded variable continua from cooling coronal sim
11185 Directory Listing
Modified 6 years, 6 months ago
Mon Jul 25 22:49:57 2016 UTC
gary
Log:
typo
11184 Directory Listing
Modified 6 years, 6 months ago
Mon Jul 25 22:32:44 2016 UTC
gary
Log:
remove redundant first entry of H 1 Lya into line stack.
correct inadvertent change TOTL to He 1 rather than H  1

11183 Directory Listing
Modified 6 years, 6 months ago
Mon Jul 25 22:17:28 2016 UTC
gary
Log:
missed one default Hb
11182 Directory Listing
Modified 6 years, 6 months ago
Mon Jul 25 22:04:45 2016 UTC
gary
Log:
revert r11178 for helium, He-like lines triplet to ground all have same wavelength
11181 Directory Listing
Modified 6 years, 6 months ago
Mon Jul 25 16:42:04 2016 UTC
peter
Log:
source/TestThirdparty.cpp:
  - Bug-fix: slightly relax test to allow it to pass on AVX2 platform with g++ 4.8.5.

11178 Directory Listing
Modified 6 years, 6 months ago
Mon Jul 25 12:43:06 2016 UTC
gary
Log:
converting TOTL to H  1 and He 1
11177 Directory Listing
Modified 6 years, 6 months ago
Sun Jul 24 20:56:17 2016 UTC
gary
Log:
update C III to 2014A&A...566A.104F
11176 Directory Listing
Modified 6 years, 6 months ago
Sun Jul 24 18:36:48 2016 UTC
gary
Log:
update C III to 2014A&A...566A.104F, CS significantly smaller
11175 Directory Listing
Modified 6 years, 6 months ago
Sun Jul 24 18:34:39 2016 UTC
gary
Log:
update C III to 2014A&A...566A.104F, CS significantly smaller
11174 Directory Listing
Modified 6 years, 6 months ago
Sun Jul 24 18:34:01 2016 UTC
gary
Log:
update C III to 2014A&A...566A.104F, CS significantly smaller
11173 Directory Listing
Modified 6 years, 6 months ago
Sat Jul 23 19:42:17 2016 UTC
gary
Log:
Matt's small change to retain all level energy digits in ADF04 files
11172 Directory Listing
Modified 6 years, 6 months ago
Fri Jul 22 12:28:57 2016 UTC
peter
Log:
source/vectorize_math.h:
  - Bug-fix: avoid calling vecfun_partial() or vecfun2_partial() when there is
    no work left to do. This leads to unnecessary computations, and can even
    lead to spurious crashes when x[] and y[] are the same array.

11167 Directory Listing
Modified 6 years, 6 months ago
Thu Jul 7 14:09:26 2016 UTC
gary
Log:
start on fixing WL in hazy - this was not done during move to external databases
11166 Directory Listing
Modified 6 years, 6 months ago
Thu Jul 7 13:33:13 2016 UTC
peter
Log:
tsuite/auto/run_sequence.pl:
tsuite/slow/run_sequence.pl:
  - Create the option to skip test suite sims by putting their names in a file skip.dat.
    The presence of this file is obviously optional.

11165 Directory Listing
Modified 6 years, 6 months ago
Thu Jul 7 11:22:04 2016 UTC
gary
Log:
TOTL -> Blnd for true blends
TOTL -> H  1 for old style Lya and Hb
11160 Directory Listing
Modified 6 years, 7 months ago
Mon Jul 4 19:47:49 2016 UTC
gary
Log:
update Fe 9, Ni 11, to Stout with Badnell data.
Limit Aul to keep gf within range of float. 
11159 Directory Listing
Modified 6 years, 7 months ago
Sun Jul 3 18:16:43 2016 UTC
gary
Log:
needed for latex to compile
11156 Directory Listing
Modified 6 years, 7 months ago
Fri Jul 1 20:39:59 2016 UTC
marios
Log:
tsuite/slow/time_cool_cp* now let cool to 10,000 K; monitors updated
11141 Directory Listing
Modified 6 years, 7 months ago
Tue Jun 28 02:33:49 2016 UTC
marios
Log:
Revert commits r11140 r11136 r11135 r11133.
Development continued on branch.

11140 Directory Listing
Modified 6 years, 7 months ago
Mon Jun 27 20:25:20 2016 UTC
marios
Log:
source/pressure_total.cpp
  - Restore 3/2 factor in enthalpy calculation.
    Parameter used with cooling timescale calculation, now consistent
    with r11135.
source/dynamics.cpp
  - Reduce recombination timestep to 3% of shortest thermal timescale
    (was 4%).

11138 Directory Listing
Modified 6 years, 7 months ago
Mon Jun 20 08:54:59 2016 UTC
gary
Log:
use the same command as Hazy1 sec 9.9
11137 Directory Listing
Modified 6 years, 7 months ago
Mon Jun 20 06:33:03 2016 UTC
peter
Log:
source/stars.cpp:
  - Add support for interpolating CoStar models straight from the ASCII file. Not
    used at the moment.
  - Remove duplicated code in RebinFind().
  - Fix minor inconsistency in output.

11136 Directory Listing
Modified 6 years, 7 months ago
Sun Jun 19 00:19:32 2016 UTC
marios
Log:
More detailed debugging print statement in t_timesc::calc_therm_timesc_minmax()
11135 Directory Listing
Modified 6 years, 7 months ago
Thu Jun 16 22:31:48 2016 UTC
marios
Log:
Use isochoric specific heat when computing the min, max thermal timescales over all zones
11134 Directory Listing
Modified 6 years, 7 months ago
Thu Jun 16 10:00:01 2016 UTC
peter
Log:
source/parse_compile.cpp
  - Get rid of call to ContCreateMesh(). The frequency mesh has been set up already.
  - Add informative message.
source/stars.cpp
  - Refactoring to remove duplicated code for writing ascii files.
  - Create intermediate ascii file for the CoStar grids. Define new ascii file syntax
    to support the CoStar grids. The old ascii file syntax is still supported.
docs/latex/hazy1/vanhoof_atmosphere_grids.tex:
  - Document the new ascii file syntax for CoStar grids.

11133 Directory Listing
Modified 6 years, 7 months ago
Wed Jun 15 14:55:27 2016 UTC
marios
Log:
Improved thermal timescale calculations.  Introduced specificHeat parameter.

source/timesc.h
source/timesc.cpp
  - Defined new variable and method for calculating the thermal time scale
    in the current zone.
  - Renamed the old calc_therm_timesc() to calc_therm_timesc_minmax().
  - Moved the calculation of the Compton timescale from IterStart() to
    a new method, calc_compton_timesc().
source/pressure.h
source/pressure.cpp
  - Defined new parameter for gas specific heat and set default value to 3/2. 
source/parse_constant.cpp
  - Set the specific heat variable to 5/2 with 'constant gas pressure'.
source/age_check.cpp
  - Replaced loop for calculation of time_therm timescales with method call.
  - Moved Compton timescale calculation from IterStart().
source/dynamics.cpp
  - Used cooling timescale in this zone when setting initial timestep,
    instead of calling calc_therm_timesc_minmax() with a zone 1 argument.
  - Used specific heat parameter instead of 5/2 in the calculation of dCooldT().
source/pressure_total.cpp
  - Replaced 3/2 with specific heat parameter in enthalpy calculation in the
    time static case.
source/zone_startend.cpp
  - Forced calculation of thermal timescale for this zone.
source/save_do.cpp
  - Replaced cooling timescale calculation with precomputed cooling in
    current zone.  Previous calculation also compared the thermal energy
    to the total heating.
source/conv_init_solution.cpp
  - Corrected first zone cooling in struc.coolstr for dynamical effects.
source/iter_startend.cpp
  - Removed Compton and longest thermal timescale calculations.
source/radius_increment.cpp
  - Removed longest thermal timescale calculation from radius_increment().
source/parse_save.cpp
  - Typo.

11132 Directory Listing
Modified 6 years, 7 months ago
Wed Jun 15 07:55:16 2016 UTC
peter
Log:
source/stars.cpp:
  - Bug fix: make sure the correct error message is printed in GridInterpolate() when
    the requested file is missing.

11131 Directory Listing
Modified 6 years, 7 months ago
Wed Jun 15 06:30:51 2016 UTC
rjrw
Log:
Check for bad format of Hummer-Storey file (should quieten
warnings on some g++ versions)

11130 Directory Listing
Modified 6 years, 7 months ago
Wed Jun 15 02:19:43 2016 UTC
gary
Log:
replace html file, which contained much
of the information on the wiki, with a more helpful txt file
giving an overview with links to the wiki.
11129 Directory Listing
Modified 6 years, 7 months ago
Tue Jun 14 10:02:52 2016 UTC
peter
Log:
source/cddefines.h:
source/service.cpp:
source/heat_save.cpp:
source/hydro_bauman.cpp:
  - Remove the last remaining instances of CALLOC() from the code.

11127 Directory Listing
Modified 6 years, 7 months ago
Mon Jun 13 11:28:41 2016 UTC
peter
Log:
source/prt_header.cpp:
  - Bug-fix: make sure the luminosity is not printed in the intensity case, as
    stated in Hazy 2. Problem reported by Vital Fernandez.

11126 Directory Listing
Modified 6 years, 7 months ago
Mon Jun 13 10:04:02 2016 UTC
peter
Log:
This commit adds support for the TABLE HM12 command.

source/stars.h:
source/stars.cpp:
  Major refactoring of the code.
  - Restucture code so that InitGrid() and InterpolateRectGrid() can work directly
    on an ascii file.
  - Create new option to do liner interpolation instead of logarithmic.
  - Modify TABLE STAR LIST command so that it can work directly on an ascii file.
  - Modify TABLE STAR "file.ascii" command so that it can work directly on an ascii
    file.
  - Fix problems in the code for preserving discontinuous edges. Review Edges arrays
    and correct problems where necessary.
  - Add new routine HaardtMadauInterpolate() for interpolating Haardt & Madau (2005,
    2012) models using the stellar grid infrastructure.
  - Remove progress bar when compiling. With the speed of modern computers this is
    no longer needed.
  - Make FreeGrid() a destructor of the stellar_grid class.
  - Remove all remaining uses of MALLOC/CALLOC.
  - Remove all remaining goto's.
  - Reduce use of preprocessor.
source/parse_table.cpp:
  - Remove read_hm05().
  - Rewrite TABLE HM05 code to use HaardtMadauInterpolate().
  - Add TABLE HM12 command, also using HaardtMadauInterpolate().
source/cddrive.cpp:
source/cont_createmesh.cpp:
  - Make sure that the frequency mesh is fully set up in cdDrive().
source/parse_compile.cpp:
  - Remove statement encouraging users to throw away ascii files.
source/cont_ffun.cpp:
  - Update comment.
data/hm05_galaxy.ascii
data/hm05_quasar.ascii
data/hm12_galaxy.ascii
  - Data files for the TABLE HM05 and HM12 commands. Frequency edges have been
    re-tweaked in the HM05 files.
data/haardt_madau_galaxy.dat:
data/haardt_madau_quasar.dat:
  - The original data files used by the TABLE HM05 command. Deleted.
tsuite/auto/stars*.in:
  - Add SAVE CONTINUUM command where needed.
  - Fixed some typos.
tsuite/auto/igm_lalpha_hm12.in:
tsuite/auto/igm_lalpha_noisosub_hm12.in:
  - New sims for exercising the Haardt & Madau (2012) grid.
docs/latex/hazy1/cont-def.tex:
docs/latex/hazy1/cont-shp.tex:
docs/latex/hazy1/miscell.tex:
docs/latex/hazy1/vanhoof_atmosphere_grids.tex:
docs/latex/common/bibliography2.bib:
  - Update documentation to reflect the changes above.

11125 Directory Listing
Modified 6 years, 7 months ago
Mon Jun 13 05:03:33 2016 UTC
peter
Log:
source/prt_comment.cpp:
  - Improve wording of confusing comment.

11120 Directory Listing
Modified 6 years, 8 months ago
Thu Jun 2 22:26:02 2016 UTC
marios
Log:
Adapt scripts/db-ref-bib2json.pl to support references given in the new format.

Typically, each file contains one field of stars, i.e., a line that holds only
stars, to signify the end of data, and beginning of the references.  Under the
new format, an additional field of stars may be used to separate the references
from general user comments.  This is meant to simplify parsing the references.

An additional complication exists in some files, which contain more than one
fields of stars before the references.  This means that if the field of stars
that begins the user comments section is absent, the script may report actual
Stout data as references.  The way around this limitation is to require the
keyword 'Reference' as a section header in such cases. 

11119 Directory Listing
Modified 6 years, 8 months ago
Thu Jun 2 20:56:48 2016 UTC
marios
Log:
Stout bibliography updates.

data/stout/ni/ni_15/ni_15.tp
  - Fix broken link
data/stout/refs.json
docs/latex/common/bibliography2.bib
  - Update bibliography and refs.
scripts/db-ref-bib2json.pl
  - Drop blank 'name' fields from refs.json.
  - Fix bug when ADS link in line is prepended by 'text:'.
    The two ':' threw the parser off.

11118 Directory Listing
Modified 6 years, 8 months ago
Thu Jun 2 15:37:09 2016 UTC
marios
Log:
Improvements to dataset bibliography processing scripts.

scripts/BiblioToTeX.pm
  - Sanitize bibcodes to convert URL-encoded strings to plain ASCII.
    This prevents A&A entries to be entered multiple times to bibliography2.bib.
    Before this update, that happened because the '&' in the 'A&A' part of the
    bibcode was encoded on the URL as '%26', and the search done for that string
    would find no such matches in the ASCII file.
scripts/db-ref-bib2json.pl
  - In Stout, allow the header line "Reference:" to contain reference
    (e.g., an ADS link).

11116 Directory Listing
Modified 6 years, 8 months ago
Wed Jun 1 22:58:33 2016 UTC
gary
Log:
revert 11115 - tests show issues with tiny gf that underflow
while being considered as a valid line, causing thrown assert
11115 Directory Listing
Modified 6 years, 8 months ago
Wed Jun 1 18:32:54 2016 UTC
gary
Log:
Matt update Ni XI to 	
Del Zanna, G.; Storey, P. J.; Badnell, N. R.
http://adsabs.harvard.edu/abs/2014A%26A...566A.123D
11112 Directory Listing
Modified 6 years, 8 months ago
Mon May 30 18:08:06 2016 UTC
marios
Log:
Report specific optical depth in the output of PRINT LINE OPTICAL DEPTH.

source/emission.h
source/emission.cpp
  - Define class variables and methods for optical depth due to emitting
    species alone.
  - Clarify difference to TauIn() in method comments.
source/prt_met.cpp
  - Add extra column for specific optical depth.
source/rt_line_one_tauinc.cpp
  - Calculate specific optical depth.
docs/latex/hazy1/conout.tex
  - Update documentation of PRINT LINE OPTICAL DEPTH.

11111 Directory Listing
Modified 6 years, 8 months ago
Sat May 28 18:11:58 2016 UTC
marios
Log:
Fix the width of the species portion of a transition label to NCHLAB-1 characters.
Drop optional argument to TransitionProxy::chLabel() method.

11110 Directory Listing
Modified 6 years, 8 months ago
Fri May 27 22:07:02 2016 UTC
rjrw
Log:
Add year to Hummer reference

11109 Directory Listing
Modified 6 years, 8 months ago
Fri May 27 17:06:28 2016 UTC
marios
Log:
Do not report species of zero column density with PRINT LINE OPTICAL DEPTH.

source/prt.h
  - Remove prme(); now a STATIC function.
source/prt_met.cpp
  - Check against non-positive column densities.
  - Move code of H2_Prt_line_tau() as body of diatomics loop.
  - prme() now STATIC to file.
  - Remove 2 spaces in front of emission line label.
  - Align output into columns.
  - Add the same amount of space between columns as in the main
    line intensity output.
source/transition.h
source/transition.cpp
  - Allow optional parameter to TransitionProxy::chLabel().
    A non-zero value resizes the species label, padding with
    empty spaces if needed.
source/h2_priv.h
source/mole_h2_io.cpp
  - Remove optical depth reporting method H2_Prt_line_tau().

11106 Directory Listing
Modified 6 years, 8 months ago
Thu May 26 19:21:49 2016 UTC
marios
Log:
Fix bug in PRINT RECOMBINATION.  Suppress the He-like DR rates (\todo).

source/ion_recomb_Badnell.cpp
  - Adjust ion range when reporting suppression factors, to avert crashes.
  - Extend the calculation of DR suppression factors to the He iso-seq.
  - Store DR density suppression factors.
  - Explain 'mean' and 'mean+' data sources.
  - Set all element numbers of PRINT RECOMBINATION to physics scale (i.e., H is 1).
source/ionbal.h
source/ionbal.cpp
  - Allocate space for DR density suppression factors.
source/iso_radiative_recomb.cpp
  - Apply density suppression to He iso-sequence.  Remove 2 \todo's.
  - Improve error message when disparities arise between He-like DR rates
    computed by Cloudy and rates computed by Badnell.
docs/latex/hazy1/conout.tex
  - Update documentation, emphasizing the meaning of 'mean' DR rates.
tsuite/auto/func_test.in
  - Exercise PRINT RECOMBINATION.
tsuite/auto/coll_coronal.in
tsuite/auto/coll_t5.in
tsuite/auto/func_hotgas_coolstar.in
  - Update monitors due to He-like DR density corrections.

11105 Directory Listing
Modified 6 years, 8 months ago
Thu May 26 05:35:55 2016 UTC
peter
Log:
source/container_classes.h:
  - Fix outdated comment.

11104 Directory Listing
Modified 6 years, 8 months ago
Wed May 25 09:19:31 2016 UTC
peter
Log:
source/stars.cpp:
  - Fix typo in URL.

11102 Directory Listing
Modified 6 years, 8 months ago
Tue May 24 19:53:23 2016 UTC
gary
Log:
Matt adds Ni 15 from Del Zanna+ 14 
11101 Directory Listing
Modified 6 years, 8 months ago
Tue May 24 07:09:53 2016 UTC
peter
Log:
source/cddrive.cpp:
  - Bug-fix: prevent spurious crashes due to overflow when running with -DFLT_IS_DBL.

11099 Directory Listing
Modified 6 years, 8 months ago
Fri May 20 17:02:25 2016 UTC
gary
Log:
update Co III to Storey calculation
http://adsabs.harvard.edu/abs/2016MNRAS.459.2558S
11097 Directory Listing
Modified 6 years, 8 months ago
Tue May 17 21:36:04 2016 UTC
marios
Log:
Set minimum optical depth (opac.tlamin, opac.taumin) to 0.

When incrementing the optical depth of a line, make sure the relevant element
is ON.  This suppresses bogus optical depths of lines from species that are
turned off, but one of their lines overlaps with an emission line from a species
that is actually turned on.

11096 Directory Listing
Modified 6 years, 8 months ago
Tue May 17 13:05:52 2016 UTC
gary
Log:
adjust to midpoint of all wolkje runs.
Monitoring number of zones to such high precision is not standard
in the test suite.  Losen to 2% which is still much higher than
our default precision of 5%.  Data follows:
nzone  platform
802trunk_alldouble_32bit
805trunk_bounds
810trunk_icc_32bit
811trunk_ndebug
811trunk_solstudio
811trunk_solstudio_32bit
814trunk_llvm_32bit
815trunk_gcc
816trunk_gcc_32bit
818trunk_icc
821trunk_llvm
822trunk_llvm_bounds

11092 Directory Listing
Modified 6 years, 8 months ago
Fri May 13 22:17:18 2016 UTC
fguzman
Log:
fixed bug in Debye cutoff and PS64 for h-like was calculating multipoles. Brackett alpha line in h_outpp.in and h_outsp.in goes back to old values
11086 Directory Listing
Modified 6 years, 8 months ago
Wed May 11 20:17:59 2016 UTC
gary
Log:
adjust nzone, which was drifting up and was near botched
after removing Case B
11079 Directory Listing
Modified 6 years, 9 months ago
Fri May 6 14:14:29 2016 UTC
rjrw
Log:
Extract common factor from AngerJ integrand

11078 Directory Listing
Modified 6 years, 9 months ago
Fri May 6 12:49:33 2016 UTC
rjrw
Log:
Pass reference-to-const for performance following usual C++ guidelines

11071 Directory Listing
Modified 6 years, 9 months ago
Sun May 1 17:42:18 2016 UTC
marios
Log:
New command "PRINT UTA REFERENCES" reports the citations for the UTA data
used in a simulation.

11070 Directory Listing
Modified 6 years, 9 months ago
Wed Apr 27 19:35:27 2016 UTC
gary
Log:
Update documentation to recommend using
Database H-like Lyman pumping off
rather than Case B when doing homework-problem PDR sims.

Also update the copy of the test sutie included in Hazy2.
11069 Directory Listing
Modified 6 years, 9 months ago
Wed Apr 27 16:48:15 2016 UTC
gary
Log:
update comments to reflect replacing case B with 
Database H-like Lyman pumping off
11068 Directory Listing
Modified 6 years, 9 months ago
Wed Apr 27 16:20:44 2016 UTC
gary
Log:
bugfix - command only worked with list
11067 Directory Listing
Modified 6 years, 9 months ago
Wed Apr 27 16:19:33 2016 UTC
gary
Log:
conout.tex - clarify meaning of species internal structure

optdepth.tex - clarify what case B command does.
11066 Directory Listing
Modified 6 years, 9 months ago
Tue Apr 26 20:36:52 2016 UTC
gary
Log:
This replaces the "Case B" command in
PDR sims with a command that explicitly disables Lyman line
pumping in H I.  The satisfies the purpose of the Case B command
but the intention should be clearer.  
11065 Directory Listing
Modified 6 years, 9 months ago
Thu Apr 21 14:05:38 2016 UTC
marios
Log:
Reinstate "SET UTA KISIELIUS ON".

11064 Directory Listing
Modified 6 years, 9 months ago
Wed Apr 20 22:13:26 2016 UTC
marios
Log:
Define "SET UTA OFF" command; delete the Behar UTA data, and
the "SET UTA GU06 OFF" command.

source/parse_set.cpp
  - Define "SET UTA OFF" command to not load _any_ UTA lines.
    Use of the command renders the simulation unphysical.
  - Delete "SET UTA GU OFF" command.
source/atmdat.h
source/atmdat.cpp
source/ionbal.h
source/ionbal.cpp
  - Move UTA flags to atmdat struct from ionbal class.
source/atmdat_readin.cpp
  - Remove Behar02 data.
source/conv_base.cpp
  - Remove test against boolean ionbal.lgInnerShellLine_on.
    This is now achieved by the size of the UTA vector.
source/parse_dont.cpp
  - Disable "no UTA ionization" command.
    Instruct to use "set UTA off" and exit.
docs/latex/common/bibliography2.bib
docs/latex/hazy1/miscell.tex
  - Update documentation of 'set UTA' commands.
  - Remove 'no UTA ionization' command.
  - Remove 'set UTA Gu06 off' command.
data/UTA/UTA_Behar.dat
  - Deleted.

11062 Directory Listing
Modified 6 years, 9 months ago
Sat Apr 16 07:24:37 2016 UTC
peter
Log:
source/atmdat_readin.cpp:
  - remove unused variable.

11061 Directory Listing
Modified 6 years, 9 months ago
Sat Apr 16 07:21:09 2016 UTC
peter
Log:
source/iso_level.cpp:
  - Fix compilation error with Solaris Studio compiler due to using a C++11 feature.

11060 Directory Listing
Modified 6 years, 9 months ago
Fri Apr 15 23:25:31 2016 UTC
marios
Log:
Refactor source/atmdat_readin.cpp to move separate functionality into separate
functions.  Factored magic number checks into separate functions.

11059 Directory Listing
Modified 6 years, 9 months ago
Thu Apr 14 17:14:46 2016 UTC
marios
Log:
Remove the last vestiges of the WNW Fe 2 lines.

These are the only lines included in the level1.dat file,
which is now removed.  The supporting TauLines vector, and
related infrastructure have been removed from the source.
Hazy 1 & 2 have been updated.

11058 Directory Listing
Modified 6 years, 9 months ago
Wed Apr 13 20:48:24 2016 UTC
marios
Log:
Convert the input to "print arrays levels" to include "[:]",
if no brackets are given.  Reword documentation.

11057 Directory Listing
Modified 6 years, 9 months ago
Tue Apr 12 20:55:29 2016 UTC
marios
Log:
Define new command 'print arrays levels', designed to report the matrix that
enters the solution for the level populations.  The command 'print arrays'
has been redefined as 'print arrays ionization'.

source/parse_print.cpp
source/generic_state.h
source/generic_state.cpp
  - Split matchGeneric() into two functions, one that determines the levels,
    and one that compiles a vector of genericState species.
source/prt.h
source/prt.cpp
  - Define new class to handle the UI (both input and output) for
    'print arrays levels'.
docs/latex/hazy1/conout.tex
  - Document new command.
  - Update documentation of 'print arrays', to include 'ionization' keyword.
tsuite/auto/func_fulltrace.in
  - Update 'print arrays' command to include 'ionization' keyword,
    and exercise new 'print arrays levels' command.

11055 Directory Listing
Modified 6 years, 9 months ago
Thu Apr 7 09:39:47 2016 UTC
peter
Log:
source/prt_lines_general.cpp:
  - Fix compiler warnings in 32-bit g++ compilations.

11052 Directory Listing
Modified 6 years, 10 months ago
Wed Apr 6 04:49:33 2016 UTC
peter
Log:
source/mole.h:
  - Fix compilation error with the latest version of the libstdc++ headers.

11050 Directory Listing
Modified 6 years, 10 months ago
Mon Apr 4 17:45:38 2016 UTC
marios
Log:
Drop iso-seq hardwired cooling and heating line stack entries (Hlin & Clin).
Update tsuite sim label.

11049 Directory Listing
Modified 6 years, 10 months ago
Mon Apr 4 16:14:07 2016 UTC
marios
Log:
Reset iso-seq cooling lines on the stack to 'c', and heating to 'h' (from 'i'); fix line comments.
11048 Directory Listing
Modified 6 years, 10 months ago
Sun Apr 3 23:20:53 2016 UTC
marios
Log:
Enter the iso-sequence species heating and cooling onto the line stack.

11047 Directory Listing
Modified 6 years, 10 months ago
Sun Apr 3 21:29:03 2016 UTC
gary
Log:
generate hint at what might have gone wrong - the user may have intended the ALL keyword so the list is not on their mind
11042 Directory Listing
Modified 6 years, 10 months ago
Sat Apr 2 01:00:25 2016 UTC
marios
Log:
Eliminate ambiguous description of the last column in the output of 'save species lines'.
11041 Directory Listing
Modified 6 years, 10 months ago
Sat Apr 2 00:48:31 2016 UTC
marios
Log:
Update Hazy 1 description of 'save species lines'.  Document meaning of gbar values of -1.
11040 Directory Listing
Modified 6 years, 10 months ago
Fri Apr 1 20:41:10 2016 UTC
marios
Log:
Force 'save species lines' to be treated as part of the 'save species' family of
commands.  Extend functionality to also include iso-sequences.
source/save_do.cpp
source/save_species.cpp
  - Move the 'save species lines' algorithm from SaveDo() to SaveSpecies().
source/iso_create.cpp
  - Copy the iso-seq numLevels_local and numLevels_max parameters to
    their species counterparts.
source/parse_save.cpp
  - Force the 'save species lines' command to be treated by the 'save species'
    algorithm.

11039 Directory Listing
Modified 6 years, 10 months ago
Fri Apr 1 18:06:06 2016 UTC
marios
Log:
Fix format for g's in 'save species lines'
11038 Directory Listing
Modified 6 years, 10 months ago
Fri Apr 1 18:04:12 2016 UTC
marios
Log:
Get rid of most of local variables in 'save species lines'
11037 Directory Listing
Modified 6 years, 10 months ago
Fri Apr 1 17:59:15 2016 UTC
marios
Log:
Set is_gbar() for all made-up CS.
11036 Directory Listing
Modified 6 years, 10 months ago
Fri Apr 1 17:38:30 2016 UTC
marios
Log:
Change the column order in the output of 'save species lines'
11035 Directory Listing
Modified 6 years, 10 months ago
Thu Mar 31 22:24:28 2016 UTC
marios
Log:
Replace ASSERT() with an if-statement in dground(), conv_base.cpp,
to suppress out-of-bounds compiler warnings.

11034 Directory Listing
Modified 6 years, 10 months ago
Thu Mar 31 20:42:57 2016 UTC
marios
Log:
Isolate into a function the header of 'save species lines' that prints
the species levels.  Report the species & spectral labels, as well as
the database of origin for the species.

11033 Directory Listing
Modified 6 years, 10 months ago
Thu Mar 31 19:52:32 2016 UTC
marios
Log:
prt_lines_helium.cpp
  - Improve transition comments -- those were
    the last ones with non-descript comments.
conv_base.cpp
  - Remove stray print statement.

11032 Directory Listing
Modified 6 years, 10 months ago
Thu Mar 31 18:48:36 2016 UTC
marios
Log:
source/conv_base.cpp
  - Fix off-by-one error in maximum ion stage in dground().
source/prt_lines_helium.cpp
  - Report transition in comment of He-like line.

11031 Directory Listing
Modified 6 years, 10 months ago
Thu Mar 31 16:18:21 2016 UTC
marios
Log:
Improve the ASSERT of a valid ion in dground(), conv_base.cpp
11030 Directory Listing
Modified 6 years, 10 months ago
Tue Mar 29 20:30:42 2016 UTC
marios
Log:
scripts/ -- comment improvements
11029 Directory Listing
Modified 6 years, 10 months ago
Tue Mar 29 19:26:05 2016 UTC
marios
Log:
scripts/db-ref-bib2json.pl -- Account for the presence of the number of levels
at end of each line in masterlist files.

11028 Directory Listing
Modified 6 years, 10 months ago
Tue Mar 29 15:28:55 2016 UTC
marios
Log:
Added section in Hazy 1 pointing to the database bibliography scripts.
11027 Directory Listing
Modified 6 years, 10 months ago
Tue Mar 29 07:13:30 2016 UTC
marios
Log:
rename sim feii_t4.in to feii_t4n8_rt.in
11026 Directory Listing
Modified 6 years, 10 months ago
Tue Mar 29 07:10:46 2016 UTC
marios
Log:
reintegrate stout6 branch -- move FeII to Stout database
11024 Directory Listing
Modified 6 years, 10 months ago
Tue Mar 29 07:04:38 2016 UTC
marios
Log:
scripts/db-ref-bib2json.pl
  - Compare obtained references against stored refs data for each file.  Prevent
    erasing data in non-interactive mode.
  - Process only ADS links.  Previously, lines containing 'NIST' also processed.
  - Define new global for interactive processing, instead of nonInteractive, to
    eschew confusion.
data/stout/refs.json
  - New order of species in terms of increasing Z, ion stage.
docs/latex/common/bibliography2.bib
  - Add reference to Laha+2016.

11023 Directory Listing
Modified 6 years, 10 months ago
Mon Mar 28 23:40:52 2016 UTC
marios
Log:
update bibliography-related scripts
11002 Directory Listing
Modified 6 years, 10 months ago
Mon Mar 21 14:19:51 2016 UTC
peter
Log:
Fix botches resulting from r11001.

11001 Directory Listing
Modified 6 years, 10 months ago
Mon Mar 21 12:43:32 2016 UTC
peter
Log:
data/chem_species.dat:
  - Add missing species HTiS+.
data/mole_co_base.dat:
  - Remove charge transfer reaction already present in ChargTranEval().
data/mole_ti.dat:
  - Fix typo in reaction: TiNH+ should be HNTi+.
  - Remove charge transfer reaction already present in ChargTranEval().
source/atmdat_char_tran.cpp:
  - Fix typo in comment.
source/mole.h:
source/mole_reactions.cpp:
source/mole_species.cpp:
  - Create counter for the number of reactions a species is involved in.
source/molcol.cpp:
source/save_do.cpp:
  - Use this counter to suppress output of species for which no reactions exist.
    This is done in the main output and the SAVE MOLECULES command, but not the
    SAVE SPECIES command since that would have the side effect of removing all
    atomic species that are not involved in reactions (e.g. all higher ionization
    stages of atomic species).

10990 Directory Listing
Modified 6 years, 10 months ago
Sun Mar 13 20:05:49 2016 UTC
marios
Log:
Improve error message in 'no lines' commands.
10987 Directory Listing
Modified 6 years, 10 months ago
Wed Mar 9 21:31:55 2016 UTC
marios
Log:
Hazy typo.
10975 Directory Listing
Modified 6 years, 11 months ago
Thu Feb 25 19:00:27 2016 UTC
marios
Log:
In time integrations, do not print the cumulative (intrinsic, emergent) line
list in the main output when the 'SET CUMULATIVE OFF' command is issued.

10954 Directory Listing
Modified 6 years, 11 months ago
Sun Feb 21 11:23:23 2016 UTC
rjrw
Log:
Remove stray character in comment

10944 Directory Listing
Modified 6 years, 11 months ago
Thu Feb 18 10:31:00 2016 UTC
peter
Log:
source/atom_leveln.cpp:
  - Demote PROBLEM message to a CAUTION to prevent a flood of messages in minor.txt
    in test suite runs. There were hunderds of them and they prevented us from
    seeing any other messages in that file.

10940 Directory Listing
Modified 6 years, 11 months ago
Tue Feb 16 12:16:24 2016 UTC
peter
Log:
tsuite/auto/igm_z3.in:
tsuite/auto/igm_z3_thick.in:
  - These two sims were overlooked in r10937.

10939 Directory Listing
Modified 6 years, 11 months ago
Tue Feb 16 12:12:43 2016 UTC
peter
Log:
source/conv_init_solution.cpp:
tsuite/auto/func_test_cycle.in:
tsuite/auto/func_test_grid.in:
  - Disable printing DEBUG statements in the test suite.

10938 Directory Listing
Modified 6 years, 11 months ago
Tue Feb 16 12:02:44 2016 UTC
peter
Log:
source/rt_continuum.cpp:
  - Change call to TestCode() into a call to fixit().

10937 Directory Listing
Modified 6 years, 11 months ago
Tue Feb 16 11:20:40 2016 UTC
peter
Log:
tsuite/auto/dynamics_orion_flow.in
tsuite/auto/dynamics_veryfast.in
tsuite/auto/dynamics_veryfast_rec.in
tsuite/auto/hii_blister.in
tsuite/auto/hii_paris.in
tsuite/auto/nova_dqher.in
tsuite/auto/orion_hii_pdr_fast.in
tsuite/auto/pn_paris.in
tsuite/auto/pn_paris_cpre.in
tsuite/auto/pn_paris_fast.in
  - Disable printing the emergent spectrum since the normalizing line is not
    defined on the emergent line stack.
tsuite/auto/time_cool_cd_noaccu.in:
  - Switch normalization line to O  8" 18.9732A and adjust faint limit.

10932 Directory Listing
Modified 6 years, 11 months ago
Fri Feb 12 12:00:17 2016 UTC
rjrw
Log:
Fix error inadvertently introduced at r10375

10931 Directory Listing
Modified 6 years, 11 months ago
Thu Feb 11 19:54:05 2016 UTC
gary
Log:
add ADS ref to Laha+ paper
10924 Directory Listing
Modified 6 years, 11 months ago
Mon Feb 8 09:33:48 2016 UTC
peter
Log:
tsuite/auto/func_t3_linesintroff.in:
  - Fix wrong save prefix.

10923 Directory Listing
Modified 6 years, 11 months ago
Mon Feb 8 09:04:56 2016 UTC
peter
Log:
tsuite/auto/agn_blr_albedo.in
tsuite/auto/limit_lte_he1_nomole_ste_nocoll2.in
tsuite/slow/dynamics_HII_PDR.in
tsuite/slow/grid_extreme.in
  - Disable printing the emergent spectrum to avoid error messages about a
    non-existing normalization line in the emergent spectrum.
tsuite/auto/func_test_cycle.in:
  - Switch normalization line to "H  1" 4861.36A. Do not disable printing the
    emergent spectrum as it is important to include as much output as possible
    for the repetition test.
tsuite/auto/func_t3_linesintroff.in:
  - New sim to exercise the PRINT LINES INTRINSIC OFF command.

10922 Directory Listing
Modified 6 years, 11 months ago
Sat Feb 6 18:51:38 2016 UTC
rjrw
Log:
Transfer C 3H 1909 to re-enable Blnd 1909 emergent diagnostics

10921 Directory Listing
Modified 7 years ago
Thu Feb 4 14:17:17 2016 UTC
peter
Log:
tsuite/auto/h_otsopen.in
tsuite/auto/h_otspp.in
tsuite/auto/h_otssp.in
tsuite/auto/h_outopen.in
tsuite/auto/h_outpp.in
tsuite/auto/h_outsp.in
tsuite/auto/h_t4_conemis_thick.in
tsuite/auto/hhe_otspp.in
tsuite/auto/hhe_otssp.in
tsuite/auto/hhe_outpp.in
tsuite/auto/hhe_outppff.in
tsuite/auto/hhe_outsp.in
tsuite/auto/hlike_c.in
tsuite/auto/hlike_o.in
tsuite/auto/limit_casea_h_den13.in
tsuite/auto/limit_caseb_h_lot.in
tsuite/auto/limit_caseb_h_n8.in
tsuite/auto/limit_caseb_he2_den8.in
tsuite/auto/limit_casec_h_den2.in
tsuite/auto/limit_casec_h_den5.in
  - Replace normalization lines that are not defined in the emergent spectrum with
    equivalent lines from the hydrogenic iso-electronic sequence (mostly Hbeta).
  - Adjust monitors where necessary.

10920 Directory Listing
Modified 7 years ago
Wed Feb 3 23:00:31 2016 UTC
peter
Log:
source/cont_gammas.cpp:
  - Bug-fix: prevent spurious crashes in the 32-bit all-double run caused by r10809.
    The new ASSERT should catch any serious errors in the upstream code while we
    revert to the situation before r10809 otherwise.

10916 Directory Listing
Modified 7 years ago
Mon Feb 1 22:39:00 2016 UTC
marios
Log:
Added sim to exercise 'print lines off' command.
10915 Directory Listing
Modified 7 years ago
Mon Feb 1 20:25:06 2016 UTC
rjrw
Log:
Convert a #define to a static const variable

10914 Directory Listing
Modified 7 years ago
Mon Feb 1 20:19:32 2016 UTC
rjrw
Log:
Allow leading spaces in LAMDA comments in file format tests, to
cope with some variant files in the wild; provide somewhat more
helpful output when corrupted data files are found.

10913 Directory Listing
Modified 7 years ago
Mon Feb 1 19:53:40 2016 UTC
marios
Log:
tsuite/ -- Expedite sims that exercise the 'set cumulative [flux| off]' commands.
10912 Directory Listing
Modified 7 years ago
Mon Feb 1 05:51:17 2016 UTC
marios
Log:
db-ref-toTeX.pl -- Report 'baseline' when no collisional data. Guard against undef cross-refs.
10911 Directory Listing
Modified 7 years ago
Mon Feb 1 04:35:30 2016 UTC
marios
Log:
New bibliography entries.
10910 Directory Listing
Modified 7 years ago
Mon Feb 1 04:28:03 2016 UTC
marios
Log:
Minor changes in Stout references.  Added JSON file holds summary of data.
10909 Directory Listing
Modified 7 years ago
Mon Feb 1 04:25:51 2016 UTC
marios
Log:
scripts/ -- Some minor improvements.

db-ref-gather.pl
 -  Implemented -f flag to force ADS queries when the bibcode is present in the
    Cloudy bibliography.  (Mainly for testing.)
 -  Improved author list resolution to process author names not separated by
    commas, and either led or followed by given name initials.
 -  When preprocessing refs, match either name or bibcode; only name done
    previously.

10908 Directory Listing
Modified 7 years ago
Thu Jan 28 19:38:02 2016 UTC
gary
Log:
minor update
10907 Directory Listing
Modified 7 years ago
Thu Jan 28 19:18:18 2016 UTC
marios
Log:
scripts/ -- Improvements in Perl scripts that handle references and TeX tables.
db-ref-gather.pl
 -  Include Perl module installation instructions.
 -  Include script usage examples.
db-ref-toTeX.pl
 -  Include script usage examples.
 -  Use new function to make existence of JSON file mandatory.
db-species-tex-table.pl
 -  Include script usage examples.
BiblioToTeX.pm
 -  Separate requirement that JSON file exists to a new function.
 -  Include bibliography in the example minimal TeX, only when asked.

10906 Directory Listing
Modified 7 years ago
Wed Jan 27 19:16:32 2016 UTC
gary
Log:
description of various scripts
10905 Directory Listing
Modified 7 years ago
Wed Jan 27 18:53:30 2016 UTC
marios
Log:
scripts/ -- Add scripts to gather references from the atomic data bases,
and generate TeX table reports.

10904 Directory Listing
Modified 7 years ago
Wed Jan 27 12:36:09 2016 UTC
gary
Log:
copyright year
10903 Directory Listing
Modified 7 years ago
Tue Jan 26 23:40:16 2016 UTC
gary
Log:
additional details in response to query from a user
10899 Directory Listing
Modified 7 years ago
Tue Jan 26 23:01:35 2016 UTC
gary
Log:
inproved discussion of coarse and fine continua, in response to query on user group
10895 Directory Listing
Modified 7 years ago
Mon Jan 18 14:22:30 2016 UTC
peter
Log:
docs/latex/hazy2/observed.tex:
  - Improve description of how to calculate equivalent widths with Cloudy.

10894 Directory Listing
Modified 7 years, 1 month ago
Thu Dec 24 06:16:56 2015 UTC
peter
Log:
source/mole_reactions.cpp:
  - Fix warning by g++ 6.0.0 about misleading indentation.
  - Fix calls to exit() rather than cdEXIT().

10893 Directory Listing
Modified 7 years, 1 month ago
Tue Dec 15 19:13:32 2015 UTC
marios
Log:
Added sims in tsuite/auto to exercise the 'set cumulative' options 'flux' and 'off'.
10891 Directory Listing
Modified 7 years, 1 month ago
Thu Dec 10 18:22:39 2015 UTC
marios
Log:
Add comment to the if-statement in set_xIntensity() that triggers a warning in the output when the isotropic correction is high.
10890 Directory Listing
Modified 7 years, 1 month ago
Thu Dec 10 18:12:11 2015 UTC
marios
Log:
Revert the time sims to printing out the line blocks.
10889 Directory Listing
Modified 7 years, 1 month ago
Thu Dec 10 00:15:05 2015 UTC
fguzman
Log:
corrected Anderson ref in bibliography2
10888 Directory Listing
Modified 7 years, 1 month ago
Wed Dec 9 04:51:01 2015 UTC
marios
Log:
Exercise command 'print lines off' in test suite.
10887 Directory Listing
Modified 7 years, 1 month ago
Wed Dec 9 04:33:56 2015 UTC
marios
Log:
Typo in command 'print line off'.
10886 Directory Listing
Modified 7 years, 1 month ago
Wed Dec 9 04:27:01 2015 UTC
marios
Log:
Enable commands to turn off printing of the intrinsic and emergent line blocks.

source/prt.h
source/init_defaults_preparse.cpp
  - Define and initialize boolean logical variables for the commands.
source/parse_print.cpp
  - Define commands as options to 'print lines off'.
source/prt_final.cpp
  - Disable both instantaneous and time-cumulative spectra.
docs/latex/hazy1/conout.tex
  - Document new commands.

10885 Directory Listing
Modified 7 years, 1 month ago
Tue Dec 8 23:40:02 2015 UTC
marios
Log:
Add note to the main output when isotropic subtraction is significant.

source/parse_dont.cpp
docs/latex/hazy1/miscell.tex
  - Added keyword 'isotropic' to 'no lines continuum subtraction'.
  - Update Hazy 1: 'save lines emissitivity' not affected by isotropic
    background correction.
source/lines.h
source/iter_startend.cpp
  - Define boolean variable to report if any lines significantly affected
    by isotropic continuum subtraction.
source/lines_service.cpp
  - Boolean flag raised when for any line the correction exceeds 50% of
    the emissivity.
source/prt_comment.cpp
  - Add note to the main output that when isotropic correction
    significant.
tsuite/auto/igm_lalpha.in
  - Exercise 'no lines isotropic continua subtraction'.
tsuite/auto/igm_lalpha_noisosub.in
  - Sister sim to igm_lalpha.in that does not involve line intensity
    corrections.

10884 Directory Listing
Modified 7 years, 1 month ago
Tue Dec 8 23:03:47 2015 UTC
marios
Log:
Add (disabled) print statements in set_xIntensity() and RT_line_pumping()
10882 Directory Listing
Modified 7 years, 1 month ago
Tue Dec 8 16:26:14 2015 UTC
fguzman
Log:
small corrections on NLTE7 defined case
10881 Directory Listing
Modified 7 years, 2 months ago
Sun Dec 6 13:16:29 2015 UTC
gary
Log:
document why we cannot use current Ti 2 model
NIST has almost no transitions between lowest dozen levels.  They should
produce strong IR forbidden lines.
10880 Directory Listing
Modified 7 years, 2 months ago
Fri Dec 4 01:39:30 2015 UTC
marios
Log:
In the main line output, report normalization line (label & wl) in the error message when intensity small or zero.
10879 Directory Listing
Modified 7 years, 2 months ago
Thu Dec 3 17:26:45 2015 UTC
peter
Log:
source/cddefines.h:
  - Improve fp_equal(). When the arguments are subnormal numbers, a larger
    value for epsilon should be used.

10878 Directory Listing
Modified 7 years, 2 months ago
Thu Dec 3 13:56:35 2015 UTC
marios
Log:
source/dynamics.cpp -- Disable DEBUG output by default.
10877 Directory Listing
Modified 7 years, 2 months ago
Thu Dec 3 11:55:53 2015 UTC
peter
Log:
source/atmdat_chianti.cpp:
  - Bug-fix: the code will now use the N levels with the lowest energy, rather
    than the first N levels in the data file. This affected both stout and
    chianti.
  - Bug-fix: the code will swap ipLo and ipHi if necessary. This only affected
    stout files.
  - Bug-fix: the test for ipLo or ipHi >= nMolLevs was in the wrong place (i.e.
    before getSortedLevel() was called). This only affected stout files.

10876 Directory Listing
Modified 7 years, 2 months ago
Wed Dec 2 14:19:14 2015 UTC
marios
Log:
Separate total and net emissivities in lincom().

docs/latex/hazy1/conout.tex
  - Remove explanation for bkg-corrected emissivity.
source/lines_service.cpp
  - Separate the total emissivity from the net (bkg-corrected) emissivity in the
    lincom() parameter list.
  - Calls to lincom() use the same value for the total and net emissivities,
    except for the call from lindst() that is invoked with a transition object.
  - Rename xInten to xEmiss to improve clarity.
source/transition.cpp
  - Use uncorrected intensity with the Inwd component in PutLine().

10875 Directory Listing
Modified 7 years, 2 months ago
Wed Dec 2 03:32:29 2015 UTC
marios
Log:
hazy1 - Explain that by default emissivities are corrected for isotropic continua.
10874 Directory Listing
Modified 7 years, 2 months ago
Tue Dec 1 22:29:43 2015 UTC
rjrw
Log:
Code for memory high-water-mark diagnostic

10873 Directory Listing
Modified 7 years, 2 months ago
Sun Nov 29 16:02:29 2015 UTC
marios
Log:
Transfer r9471 and r9472 to the trunk.

r9471: Separate the two roles of xIntensity(): emitted vs observed

Previously, the xIntensity property of the emission class was used to hold the
amount of energy emitted in a line, and well as the observed line intensity
after correction for isotropic continua.
The meaning of the xIntensity() method depended on the context, which could lead
to bugs down the road.
Here, xObsIntensity() is introduced to hold the intensity corrected for isotropic
background radiation fields, which is eventually reported to the user.
xIntensity() now holds the total emitted energy.
This eliminates the need to keep track of whether the correction has been
applied when we update the line intensity on the stack.
Correction-specific functions have been dropped.

r9472: Remove phots() storage and method from emission class
Function phots() introduced to emulate old method's functionality.

source/emission.cpp
source/emission.h
  - Define storage and method for xObsIntensity, the observed intensity
    in a line, corrected for isotropic continua.
source/lines_service.h
source/lines_service.cpp
  - Calculate gross and net (after continuum subtraction) photons
    with a single function, set_xIntensity().
  - Drop correction functions corr_xIntensity(), and set_corr_xIntensity().
  - lindst(Transition, ...) now works with xObsIntensity().
source/prt_lines_helium.cpp
source/prt_lines_hydro.cpp
  - Multiplet summation goes over xObsIntensity().
  - Use of PutLinePreCorr() dropped in favor of PutLine().
  - Refactor randomization code into a function.
source/transition.h
source/transition.cpp
  - PutLine() now works with xObsIntensity().
  - Drop PutLinePreCorr() functions.
  - phots() function defined to return number of emitted photons,
    uncorrected for isotropic background continua.

10870 Directory Listing
Modified 7 years, 2 months ago
Fri Nov 27 05:43:12 2015 UTC
peter
Log:
source/lines.h:
  - Fix compiler warnings when using -DNDEBUG.

10869 Directory Listing
Modified 7 years, 2 months ago
Thu Nov 26 00:34:14 2015 UTC
fguzman
Log:
adapted NLTE7 definitions to NLTE9 and new set up of cloudy
10868 Directory Listing
Modified 7 years, 2 months ago
Wed Nov 25 04:39:04 2015 UTC
peter
Log:
source/optimize.h:
source/grid_do.cpp:
source/init_defaults_preparse.cpp:
source/parse_optimize.cpp:
  - Abort optimization run if an OPTIMIZE INCREMENT command was found that does
    not follow a command that is being varied.

10862 Directory Listing
Modified 7 years, 2 months ago
Tue Nov 24 18:07:51 2015 UTC
gary
Log:
svn merge --reintegrate ^/branches/15atmdat
10858 Directory Listing
Modified 7 years, 2 months ago
Tue Nov 24 10:50:11 2015 UTC
gary
Log:
all SAVE FEII options are now used
10856 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 23 21:22:57 2015 UTC
marios
Log:
Add reference to Kaastra & Mewe inner shell lines
10855 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 23 21:18:00 2015 UTC
marios
Log:
Declare bands defined in data/continuum_bands.ini as transferred lines.
10854 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 23 21:13:08 2015 UTC
marios
Log:
Declare blend-member recombination lines, and the FeII bands as 't' lines.
The lines are entered onto the stack with lindst(), but not added to the
outward beam.

source/prt_lines.cpp
  - Enter recombination lines of blends onto the stack as transferred lines
    with lindst() -- the lines are not added to the outward beam.
source/prt_lines_general.cpp
  - Redeclare species cooling 'lines' with a line info of 'c' (for cooling).
source/prt_lines_lv1_k_zn.cpp
  - Enter the FeII bands onto the line stack as transferred 'lines'
    with lindst() -- the lines are not added to the outward beam.

10853 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 23 19:43:45 2015 UTC
gary
Log:
remove leading space so that we can copy/paste sets of lines when PRINT LINE COLUMN used
10852 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 23 19:00:22 2015 UTC
gary
Log:
give reference for UTA paper
10849 Directory Listing
Modified 7 years, 2 months ago
Sun Nov 22 14:10:12 2015 UTC
gary
Log:
add UTA / satellite lines to emission line stack
10848 Directory Listing
Modified 7 years, 2 months ago
Sat Nov 21 15:12:12 2015 UTC
gary
Log:
clean up save ionizing/interactive continuum
10847 Directory Listing
Modified 7 years, 2 months ago
Sat Nov 21 14:34:35 2015 UTC
gary
Log:
update readme for ADF04 data files.

Table SED - remove nuFnu keyword - this is a property of the
data files and is within the file. 
10845 Directory Listing
Modified 7 years, 2 months ago
Thu Nov 19 21:45:20 2015 UTC
marios
Log:
source/cont_createpointers.cpp -- Improve error message for non-positive gf()
10843 Directory Listing
Modified 7 years, 2 months ago
Thu Nov 19 13:53:44 2015 UTC
marios
Log:
Fix typo.
10841 Directory Listing
Modified 7 years, 2 months ago
Wed Nov 18 20:18:43 2015 UTC
rjrw
Log:
Fix minor typo

10837 Directory Listing
Modified 7 years, 2 months ago
Tue Nov 17 15:11:42 2015 UTC
gary
Log:
add a few very low ionization lines
10836 Directory Listing
Modified 7 years, 2 months ago
Tue Nov 17 14:41:10 2015 UTC
gary
Log:
make documentation for emergent emission more general and correct
10835 Directory Listing
Modified 7 years, 2 months ago
Tue Nov 17 13:57:33 2015 UTC
marios
Log:
Add overlooked isotropic continua correction for FeII 1787A.
10834 Directory Listing
Modified 7 years, 2 months ago
Tue Nov 17 03:54:42 2015 UTC
marios
Log:
Improve upon r10820 to pass 32-bit/all-double runs.

source/lines.h
  - Rewrite if clauses for ASSERTs in checkEmergent().
source/lines_service.cpp
  - Zero out lines with very low photon emission rates in set_xIntensity().

10833 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 16 22:14:42 2015 UTC
marios
Log:
FeII 1787A now entered on line stack with linadd() instead of PutLine().
10832 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 16 20:43:18 2015 UTC
gary
Log:
svn merge --reintegrate  ^/branches/15atmdat
10831 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 16 20:09:47 2015 UTC
rjrw
Log:
Convert MALLOCed arrays into vectors

10827 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 16 12:38:33 2015 UTC
gary
Log:
remove database stout maximum from coll_t series
due to time and memory use.  Fix comment for monitor in coll_t7.in

Full databases are exercised in grid_h2coonal, embellish comments there
10826 Directory Listing
Modified 7 years, 2 months ago
Sun Nov 15 16:52:38 2015 UTC
rjrw
Log:
Fix authors in reference

10825 Directory Listing
Modified 7 years, 2 months ago
Sun Nov 15 14:30:09 2015 UTC
rjrw
Log:
Attribute threshold cell to high energy heating if above
secondary ionization threshold

10824 Directory Listing
Modified 7 years, 2 months ago
Sat Nov 14 22:20:07 2015 UTC
gary
Log:
change in cooling due to including all levels
10823 Directory Listing
Modified 7 years, 2 months ago
Sat Nov 14 22:16:01 2015 UTC
gary
Log:
atmdat_chianti.cpp - silence warning the some levels have the same energy - this work well.
> coll_t?.in - use full stout database - we do need to test that as we develop it.  The sims run much more slowly as a result.
> continuum_bands.ini - include the [o III] line as a test 
10822 Directory Listing
Modified 7 years, 2 months ago
Sat Nov 14 21:09:54 2015 UTC
marios
Log:
Update Matt's script to deal with negative and absent Bethe limits
10821 Directory Listing
Modified 7 years, 2 months ago
Sat Nov 14 20:19:48 2015 UTC
gary
Log:
Matt Lykins scripts to convert Fortran-only ADF04 format into language neutral Stout format
10820 Directory Listing
Modified 7 years, 2 months ago
Fri Nov 13 21:45:55 2015 UTC
marios
Log:
Transfer only legitimate emission lines.

source/lines.cpp
  - Declared new type of line -- 't', for transferred.
source/lines.h
  - Define LineType() method to obtain the line type (eg, transferred).
  - Force zero intensity and emissivity for blends that contain
    non-transferred components.
  - Set the emergent intensity and emissivity to the intrinsic values at the
    optically thin limit only for transferred lines.
  - Define checkEmergent() method to assert that for transferred lines the
    emergent intensity is not greater than the intrinsic, and that for all
    others the emergent intensity is zero.
source/transition.cpp
  - PutLine now inserts line on the stack as a transferred line.
source/lines_service.cpp
  - Compute the emergent intensity only for tranferred lines.
source/prt_lines_continuum.cpp
  - Suppress emergent line intensities of the incident radiation at the H-beta
    and Lya wavelengths.
source/prt_lines_general.cpp
  - Convert H beta and Lya line types to transferred.
source/prt_lines_lv1_k_zn.cpp
  - Do not transfer hardwired FeII lines.  Insert them on the line stack with
    linadd() instead of PutLine().
source/cool_iron.cpp
  - Correct for isotropic continua, now that the hardwired FeII lines are not
    entered into the stack with PutLine().
source/prt_final.cpp
  - Call the checkEmergent() method when the emergent or cumulative emergent
    line intensities are reported.
tsuite/auto/orion_hii_open.in
  - Remove non-transferrable blends.

10819 Directory Listing
Modified 7 years, 2 months ago
Fri Nov 13 19:22:07 2015 UTC
gary
Log:
monitor cooling
10818 Directory Listing
Modified 7 years, 2 months ago
Fri Nov 13 19:16:35 2015 UTC
marios
Log:
Match output monitor strings to input strings; 'cool' and 'heat' changed to 'ctot' and 'htot', resp.
10817 Directory Listing
Modified 7 years, 2 months ago
Fri Nov 13 12:22:45 2015 UTC
gary
Log:
add reference for continuum lowering we use
10816 Directory Listing
Modified 7 years, 2 months ago
Thu Nov 12 14:02:21 2015 UTC
marios
Log:
Command renamed 'save lines, zone cumulative' to highlight spatial integration.

10812 Directory Listing
Modified 7 years, 2 months ago
Tue Nov 10 16:19:30 2015 UTC
marios
Log:
tsuite/auto/orion_hii_open.in -- Add emergent line monitors.
10811 Directory Listing
Modified 7 years, 2 months ago
Tue Nov 10 07:34:53 2015 UTC
rjrw
Log:
Move loops to native C style indexing

10810 Directory Listing
Modified 7 years, 2 months ago
Tue Nov 10 00:04:14 2015 UTC
gary
Log:
fix order of energy index if not specified properly - this mimics behavior of chianti parser
10809 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 9 18:58:31 2015 UTC
rjrw
Log:
Convert MAX2() to ASSERT() test in cont_gammas.  Improved coding now works
without floor, but keep ASSERT() for safety.

10808 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 9 18:32:13 2015 UTC
marios
Log:
source/monitor_results.cpp -- List line type as last column in monitors output.
10807 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 9 18:08:56 2015 UTC
marios
Log:
Add 'save monitors' to free cooling time integration sims.
10806 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 9 17:06:24 2015 UTC
rjrw
Log:
Slight reorganization of GammaBn()

10805 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 9 16:25:47 2015 UTC
rjrw
Log:
Introduce temp variable to make code look more uniform

10804 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 9 14:33:09 2015 UTC
rjrw
Log:
"save line optical depth some", and break apart some of the
save line infrastructure coding

10803 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 9 12:21:22 2015 UTC
rjrw
Log:
Improve accuracy of ExtraLymanLine optical depths,
if they switch attribution across layer

10802 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 9 11:19:43 2015 UTC
rjrw
Log:
Add ExtraLymanLines to line stack (for print out, and
access by monitors and save line commands)

10801 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 9 09:16:26 2015 UTC
rjrw
Log:
Move some static variables internal to routine into
class, so multiple save lines commands will operate
as expected

10800 Directory Listing
Modified 7 years, 2 months ago
Mon Nov 9 08:42:44 2015 UTC
rjrw
Log:
Optimize loop in diatomics::gs_rate()

10799 Directory Listing
Modified 7 years, 2 months ago
Sun Nov 8 23:23:57 2015 UTC
rjrw
Log:
Update format of line labels for "save line" commands

10798 Directory Listing
Modified 7 years, 2 months ago
Sun Nov 8 23:01:31 2015 UTC
rjrw
Log:
Allow more than one "save line" command in the input

10797 Directory Listing
Modified 7 years, 2 months ago
Sun Nov 8 20:42:42 2015 UTC
rjrw
Log:
Move remaining uses of isCat into line initialization

10796 Directory Listing
Modified 7 years, 2 months ago
Sun Nov 8 19:37:02 2015 UTC
rjrw
Log:
Convert more use of isCat() to enumerations

10795 Directory Listing
Modified 7 years, 2 months ago
Sun Nov 8 18:16:56 2015 UTC
rjrw
Log:
Start to convert use of isCat() to enumeration

10794 Directory Listing
Modified 7 years, 3 months ago
Thu Nov 5 16:20:37 2015 UTC
marios
Log:
hazy1 -- Improve description of monitored line types.

10793 Directory Listing
Modified 7 years, 3 months ago
Wed Nov 4 22:27:57 2015 UTC
marios
Log:
hazy1 -- Improve description of options to 'monitor line' command.

10792 Directory Listing
Modified 7 years, 3 months ago
Wed Nov 4 19:52:07 2015 UTC
gary
Log:
discussion of options on monitor line command
10791 Directory Listing
Modified 7 years, 3 months ago
Tue Nov 3 20:54:54 2015 UTC
gary
Log:
fix references and broken label definitions
10790 Directory Listing
Modified 7 years, 3 months ago
Tue Nov 3 20:16:28 2015 UTC
gary
Log:
upgrade O III cs to Storey+14
10787 Directory Listing
Modified 7 years, 3 months ago
Tue Nov 3 19:29:22 2015 UTC
gary
Log:
correct name of Fe II bands file
10786 Directory Listing
Modified 7 years, 3 months ago
Tue Nov 3 19:28:33 2015 UTC
gary
Log:
off by one bug
10785 Directory Listing
Modified 7 years, 3 months ago
Tue Nov 3 18:54:29 2015 UTC
marios
Log:
docs/latex -- Non-existent 'set line vacuum' commands replaced with 'print line vacuum'.

10782 Directory Listing
Modified 7 years, 3 months ago
Mon Nov 2 03:53:59 2015 UTC
rjrw
Log:
Improve inward emission estimate at first iteration

Assume inward and outward optical depths are equal, if no
better estimate is available.  Obviously this isn't correct
locally, but it will tend to make the average over the layer
correct.  In general, this biases the inward and outward
line predictions in the first iteration towards the (probably
more numerous) low optical depth transitions.  Note that the
first iteration predictions are already subject to warnings
as to their accuracy.

10781 Directory Listing
Modified 7 years, 3 months ago
Fri Oct 30 13:00:44 2015 UTC
gary
Log:
Ryan's explain of dlaw wind
10780 Directory Listing
Modified 7 years, 3 months ago
Thu Oct 29 20:49:11 2015 UTC
marios
Log:
Add comment description of data/SED/update_Trapezium.pl
10779 Directory Listing
Modified 7 years, 3 months ago
Thu Oct 29 20:27:34 2015 UTC
marios
Log:
Hazy -- Add basic description of 'table trapezium' command.
10778 Directory Listing
Modified 7 years, 3 months ago
Thu Oct 29 20:18:06 2015 UTC
marios
Log:
New command: 'table Trapezium'.
source/parse_table.cpp
 -  Add new command.
data/SED/update_Trapezium.pl
 -  Automate generation of Trapezium SED ('Trapezium.sed') from transmitted
    continuum file in Trapezium/.
data/SED/Trapezium.sed
 -  Add new SED file.
data/SED/ReadMe.txt
 -  Add description of Trapezium.sed, and instructions for updating it.

10777 Directory Listing
Modified 7 years, 3 months ago
Thu Oct 29 14:40:10 2015 UTC
marios
Log:
Hazy - Replace TODOs in Hazy 1 with references to Hazy 2 sections.
10776 Directory Listing
Modified 7 years, 3 months ago
Thu Oct 29 12:55:30 2015 UTC
gary
Log:
better integrate discussion of isotropic continua.
There are two outstanding TODOs in this commit - references to the
continuum bands discussion in Hazy2
10775 Directory Listing
Modified 7 years, 3 months ago
Thu Oct 29 11:55:35 2015 UTC
peter
Log:
tsuite/auto/run_sequence.pl:
  - Fix typo.

10774 Directory Listing
Modified 7 years, 3 months ago
Thu Oct 29 11:12:10 2015 UTC
gary
Log:
minor changes in line formatting for nicer viewing in terminal
10773 Directory Listing
Modified 7 years, 3 months ago
Thu Oct 29 11:02:48 2015 UTC
peter
Log:
tsuite/auto/run_sequence.pl:
tsuite/slow/run_sequence.pl:
  - Update run sequence for the test suite.

10769 Directory Listing
Modified 7 years, 3 months ago
Tue Oct 27 21:17:49 2015 UTC
gary
Log:
make save chianti more useful
10768 Directory Listing
Modified 7 years, 3 months ago
Tue Oct 27 19:42:47 2015 UTC
marios
Log:
docs/latex/hazy1/dynamics-time.tex
docs/latex/hazy1/hazy1.tex
 -  Enhance Cover image description with a reference to Hazy 1 section.
 -  Center Cover image.
docs/latex/cleanAll.pl
 -  New facility to remove intermediatex files (e.g., *.aux).
docs/readme.txt
 -  Add brief description of cleanAll.pl

10767 Directory Listing
Modified 7 years, 3 months ago
Tue Oct 27 18:31:49 2015 UTC
gary
Log:
options when working with latex
10766 Directory Listing
Modified 7 years, 3 months ago
Tue Oct 27 18:22:39 2015 UTC
gary
Log:
change stop to Av - had been temperature so model did not converge.
10765 Directory Listing
Modified 7 years, 3 months ago
Mon Oct 26 19:19:26 2015 UTC
marios
Log:
Update hazy1 cover figure.
10761 Directory Listing
Modified 7 years, 3 months ago
Fri Oct 23 13:25:34 2015 UTC
rjrw
Log:
Document AddressSanitizer workaround required for some systems

10760 Directory Listing
Modified 7 years, 3 months ago
Thu Oct 22 19:15:04 2015 UTC
marios
Log:
docs/latex/CompileAll.pl
 -  Kill program when either of the pdflatex or bibtex commands fails.
 -  Automate number of recompilations, but enforce an upper limit to guard
    against infinite loops.

10759 Directory Listing
Modified 7 years, 3 months ago
Wed Oct 21 23:18:56 2015 UTC
marios
Log:
Add missing publisher to bibtex entry (Allen1973).
10758 Directory Listing
Modified 7 years, 3 months ago
Wed Oct 21 22:49:40 2015 UTC
rjrw
Log:
Set up links between Hazy documents

10757 Directory Listing
Modified 7 years, 3 months ago
Wed Oct 21 21:48:15 2015 UTC
rjrw
Log:
Fix mis-formatted bibliography item

10756 Directory Listing
Modified 7 years, 3 months ago
Wed Oct 21 21:39:15 2015 UTC
rjrw
Log:
Remove lines already input common include file ../head_info.tex

10755 Directory Listing
Modified 7 years, 3 months ago
Wed Oct 21 20:52:45 2015 UTC
marios
Log:
Fix subscripting error of iLineType in lgMonitorCheck()
10754 Directory Listing
Modified 7 years, 3 months ago
Tue Oct 20 15:17:41 2015 UTC
marios
Log:
Update description of 'save average hydrogen' to not promise full exercise of cdTemp(), eg, the 21cm option.
10753 Directory Listing
Modified 7 years, 3 months ago
Tue Oct 20 15:12:52 2015 UTC
marios
Log:
Fix typos.
10752 Directory Listing
Modified 7 years, 3 months ago
Tue Oct 20 14:22:08 2015 UTC
marios
Log:
Replace free-free emission and absorption hard-wired numbers with constants.
FREE_FREE_EMIS and FREE_FREE_ABS are defined at global scope.

10751 Directory Listing
Modified 7 years, 3 months ago
Tue Oct 20 05:04:13 2015 UTC
marios
Log:
Moved time_cool_cp* sims to slow.
10750 Directory Listing
Modified 7 years, 3 months ago
Sun Oct 18 19:56:14 2015 UTC
marios
Log:
Merge dyna2 back into mainline.
10738 Directory Listing
Modified 7 years, 3 months ago
Fri Oct 16 07:07:52 2015 UTC
rjrw
Log:
Actually, don't do that -- the version with C in the first column
will break things

10737 Directory Listing
Modified 7 years, 3 months ago
Fri Oct 16 07:06:50 2015 UTC
rjrw
Log:
Make handling of comments in linelist input consistent with
elsewhere

10736 Directory Listing
Modified 7 years, 3 months ago
Fri Oct 16 06:50:46 2015 UTC
rjrw
Log:
Catch first problem for #347 input, and fail in a less
drastic fashion for bad expressions (i.e. return like in other
cases with a missing number/expression)

10735 Directory Listing
Modified 7 years, 3 months ago
Fri Oct 16 06:15:06 2015 UTC
rjrw
Log:
End run if no number is provided on line, or expression syntax is garbled

10734 Directory Listing
Modified 7 years, 3 months ago
Fri Oct 16 01:27:13 2015 UTC
gary
Log:
update missed Ne III wavelengths - energies were updated
10732 Directory Listing
Modified 7 years, 3 months ago
Thu Oct 15 19:02:50 2015 UTC
gary
Log:
add LAMDA molecular lines to our PDR linelists
10731 Directory Listing
Modified 7 years, 3 months ago
Thu Oct 15 17:46:00 2015 UTC
gary
Log:
reference
10730 Directory Listing
Modified 7 years, 3 months ago
Thu Oct 15 17:07:50 2015 UTC
gary
Log:
svn merge --reintegrate ^/branches/15atmdat
The McLaughlin collision strengths test to be about 3/4 as
large as the old Chianti values.  The following compares old
Stout with new McLaughlin data

15.5509m  CS
Chianti: 0.7501
Stout: 0.5899

36.0036m CS
Chianti: 0.2345
Stout: 0.1839

3868.75A CS
Chianti: 0.7022
Stout: 0.5740

10727 Directory Listing
Modified 7 years, 3 months ago
Thu Oct 15 13:22:58 2015 UTC
gary
Log:
small changes and TODOs
10726 Directory Listing
Modified 7 years, 3 months ago
Thu Oct 15 09:27:05 2015 UTC
peter
Log:
source/ion_recomb_Badnell.cpp:
  - Fix compiler warning when compiling with -DNDEBUG.

10725 Directory Listing
Modified 7 years, 3 months ago
Wed Oct 14 22:37:13 2015 UTC
marios
Log:
docs/latex/CompileAll.pl
 -  Allow individual directories in command line.
    Now, if only 'hazy1' needs to be recompiled, one may tell the script so.
    No arguments in the command line invokes the default behavior: the
    documentation in all subdirectories is compiled.

10723 Directory Listing
Modified 7 years, 3 months ago
Wed Oct 14 22:09:44 2015 UTC
marios
Log:
Add functions to identify transitions by wavelength and by quantum numbers.

10720 Directory Listing
Modified 7 years, 3 months ago
Wed Oct 14 17:46:03 2015 UTC
gary
Log:
increase accuracy of reported wavelength
10718 Directory Listing
Modified 7 years, 3 months ago
Wed Oct 14 17:06:31 2015 UTC
gary
Log:
update smoke test after chnage in coll suppression DR
10717 Directory Listing
Modified 7 years, 3 months ago
Wed Oct 14 12:51:18 2015 UTC
gary
Log:
update DR suppression r10716
10716 Directory Listing
Modified 7 years, 3 months ago
Wed Oct 14 04:52:08 2015 UTC
peter
Log:
source/ion_recomb_Badnell.cpp:
  - Update the DR suppression treatment to the "detailed" treatment supplied by
    Dragan Nikolic. This version will be described in the upcoming Nikolic+ paper.

10715 Directory Listing
Modified 7 years, 3 months ago
Wed Oct 14 03:33:53 2015 UTC
peter
Log:
source/species.h:
  - Remove overlooked instance of set_NaN() in ctor of species.

10714 Directory Listing
Modified 7 years, 3 months ago
Tue Oct 13 21:05:47 2015 UTC
marios
Log:
Parametrize maximum number of significant figures in I/O wavelength strings.

10713 Directory Listing
Modified 7 years, 3 months ago
Tue Oct 13 13:39:57 2015 UTC
marios
Log:
Default constructor for the species class defined.

source/species.cpp
 -  Function SpeciesJunk() removed.

10711 Directory Listing
Modified 7 years, 3 months ago
Mon Oct 12 14:29:58 2015 UTC
marios
Log:
Peter's fix to the possible memory leak reported by valgrind.
dBaseSpecies has been converted a vector of species.
dtor of species class has been defined.

10710 Directory Listing
Modified 7 years, 3 months ago
Fri Oct 9 21:19:00 2015 UTC
marios
Log:
Add functionality to not report isotropic continua in spectra and band fluxes.

Two commands have been added: "no isotropic continua report", and the option
"no isotropic" to the "save continuum" family of commands.  The first affects
both the output of the "save" commands, as well as the band fluxes reported in
the lines' array in the main output.  The option does not affect all of the
"save commands".  By default, all sources of radiation are included.

10708 Directory Listing
Modified 7 years, 3 months ago
Thu Oct 8 22:33:44 2015 UTC
gary
Log:
correct tabs for save output
10707 Directory Listing
Modified 7 years, 3 months ago
Wed Oct 7 22:06:52 2015 UTC
gary
Log:
species.cpp - more helpful error message

mostly remove variables left over from move to stout database
10701 Directory Listing
Modified 7 years, 4 months ago
Tue Oct 6 20:41:19 2015 UTC
marios
Log:
Convert 'STATIC' keyword to 'static' for vector in iso_create.cpp
10700 Directory Listing
Modified 7 years, 4 months ago
Tue Oct 6 20:35:39 2015 UTC
marios
Log:
Take advantage of the conversion of species member variable database to string.
10699 Directory Listing
Modified 7 years, 4 months ago
Tue Oct 6 20:26:43 2015 UTC
rjrw
Log:
Convert database member variable in species into string

10695 Directory Listing
Modified 7 years, 4 months ago
Tue Oct 6 13:00:04 2015 UTC
marios
Log:
Do not allocate new memory for each isoseq species entry to mole.species to gain
access to the isoseq string ("H-like", "He-like").  Instead, store this info once
per isoseq, and point each species to the appropriate memory.  The previous
implementation of separate calls to MALLOC/new per species leaked memory.

10694 Directory Listing
Modified 7 years, 4 months ago
Mon Oct 5 21:37:34 2015 UTC
gary
Log:
exercise save option
10693 Directory Listing
Modified 7 years, 4 months ago
Mon Oct 5 19:56:16 2015 UTC
marios
Log:
Move H2 collions commands from 'set atomic data' to 'database H2'.

10690 Directory Listing
Modified 7 years, 4 months ago
Fri Oct 2 19:49:46 2015 UTC
marios
Log:
Report the underlying database for each species in the 'save species labels' output.

docs/latex/hazy1/conout.tex
 -  Update 'save species labels' command description.
source/generic_state.h
source/generic_state.cpp
 -  Add database() method to genericState class.
source/iso_create.cpp
 -  Allocate memory to store the species iso-sequence as a string.
source/save_species.cpp
 -  Add database string to the output of 'save species labels'.
 -  Bugfix: Check against the current species list size for reporting an error,
    when a list of species (terminated by 'end of species') is requested.
    Previously, the check was done against the list read-thus-far, so the
    error message was emitted only when the first species was not identified.

10689 Directory Listing
Modified 7 years, 4 months ago
Fri Oct 2 18:59:21 2015 UTC
gary
Log:
use metals command rather than list of all metals
10688 Directory Listing
Modified 7 years, 4 months ago
Fri Oct 2 18:28:02 2015 UTC
marios
Log:
Add wl_checkall.pl to rerun_parallel.pl
10687 Directory Listing
Modified 7 years, 4 months ago
Fri Oct 2 18:26:03 2015 UTC
marios
Log:
tsuite -- renamed checkall_wl.pl to wl_checkall.pl
10685 Directory Listing
Modified 7 years, 4 months ago
Fri Oct 2 17:52:57 2015 UTC
marios
Log:
complink-template.sh
 -  Added script to guide compilation of template.cpp.

readme_template.txt
 -  Added compilation instructions, highlighting the role of SYS_CONFIG.

collcool/collcool.txt
collion/collion*.txt
collion/collion.txt
hazy_coolingcurve/hazy_coolingcurve.txt
hazy_kmt/hazy_kmt.txt
hizlte/hizlte.txt
vary_nete/vary_nete.txt
varyn/varyn.txt
 -  Updated programs' output.

10684 Directory Listing
Modified 7 years, 4 months ago
Fri Oct 2 17:49:36 2015 UTC
gary
Log:
silence comment when lgTalk false.  The other comments in this file are followed by aborts so the comments must be made in all cases.  This one is an exception - it is just a comment.
10683 Directory Listing
Modified 7 years, 4 months ago
Fri Oct 2 17:34:29 2015 UTC
marios
Log:
checkall_wl.pl:
 -  Bugfix: Error message check was accidentally skipping, instead of processing,
    line. Function now more in line with counterpart in fix_input_scripts_wl.pl.
 -  Minor optimization: pass ref to array

10680 Directory Listing
Modified 7 years, 4 months ago
Fri Oct 2 16:55:19 2015 UTC
marios
Log:
Update checkall_wl.pl to the new wavelength mismatch error message.
10679 Directory Listing
Modified 7 years, 4 months ago
Fri Oct 2 16:17:15 2015 UTC
marios
Log:
Remove all double-quoted filenames from input line.  Doing only the first caused the parser to trip up against filenames that contained Cloudy keywords (e.g., VARY).
10678 Directory Listing
Modified 7 years, 4 months ago
Fri Oct 2 02:22:59 2015 UTC
marios
Log:
Improved description of 'no lines continuum subtraction'.  Added missing references.
10677 Directory Listing
Modified 7 years, 4 months ago
Thu Oct 1 22:54:50 2015 UTC
marios
Log:
Renamed tests_remove_asserts.pl to tests_remove_monitors.pl
10676 Directory Listing
Modified 7 years, 4 months ago
Thu Oct 1 22:53:56 2015 UTC
marios
Log:
Update tests_remove_asserts.pl to remove monitor commands.
10675 Directory Listing
Modified 7 years, 4 months ago
Thu Oct 1 22:44:25 2015 UTC
marios
Log:
Fix typo in fix_input_scripts_wl.pl
10674 Directory Listing
Modified 7 years, 4 months ago
Thu Oct 1 22:43:42 2015 UTC
marios
Log:
Reverted r10673 -- included draft update of tsuite/programs/readme_template.txt
10673 Directory Listing
Modified 7 years, 4 months ago
Thu Oct 1 21:15:44 2015 UTC
marios
Log:
Fix typo in fix_input_scripts_wl.pl.
10672 Directory Listing
Modified 7 years, 4 months ago
Thu Oct 1 21:08:48 2015 UTC
marios
Log:
Updated fix_input_scripts_wl.pl to new line mismatch report message.
10668 Directory Listing
Modified 7 years, 4 months ago
Thu Sep 24 10:09:52 2015 UTC
peter
Log:
source/sanity_check.cpp:
  - Fix g++ 4.9.2 warning when compiling with -DNDEBUG.

10667 Directory Listing
Modified 7 years, 4 months ago
Thu Sep 24 09:22:21 2015 UTC
peter
Log:
source/collision.h:
source/conv_itercheck.cpp:
source/helike_einsta.cpp:
  - Fix g++ compiler warnings when compiling with -DNDEBUG.

10665 Directory Listing
Modified 7 years, 4 months ago
Wed Sep 23 10:44:27 2015 UTC
peter
Log:
source/grains.cpp:
  - Bug-fix: fix problems introduced by r10414. Comparing between realnum and double
    variables can lead to spurious failures, so avoid comparing mixed types.

10664 Directory Listing
Modified 7 years, 4 months ago
Mon Sep 21 22:17:24 2015 UTC
marios
Log:
Set comment of He-like two photon transitions to refer to singlet transitions.
10663 Directory Listing
Modified 7 years, 4 months ago
Mon Sep 21 21:57:00 2015 UTC
marios
Log:
Optimize comment string generation for isoseq line stack entries.

source/iso.h
source/prt_lines_hydro.cpp
  - Moved function iso_comment_tran_levels() from header file and made it
    work with GenerateTransitionConfiguration().
  - Comment strings are now created only when the lines are entered to the
    line stack. 
  - Removed fixit() calling for use of the comment generated by
    GenerateTransitionConfiguration().
source/prt_lines_helium.cpp
  - Comment strings are now created only when the lines are entered to the
    line stack. 
source/transition.cpp
source/transition.h
  - Converted GenerateTransitionConfiguration() to return a string, and
    removed the second (ref to string) argument.

10661 Directory Listing
Modified 7 years, 4 months ago
Sun Sep 20 22:11:34 2015 UTC
marios
Log:
Add missing header file to prt_lines_hydro.cpp
10660 Directory Listing
Modified 7 years, 4 months ago
Sun Sep 20 22:07:23 2015 UTC
marios
Log:
Create more informative comments to H-like and He-like line stack entries.
Each comment is composed of the isosequence, followed by the indices of the
lower and upper levels of the transition (ground level index is 1), and,
finally, by the configurations of the upper and lower levels, respectively.

10659 Directory Listing
Modified 7 years, 4 months ago
Sun Sep 20 21:59:24 2015 UTC
marios
Log:
Do not enter those H-like fine structure (FS) transitions onto the line stack
that have been reset to a zero intensity.  FS transitions between two shells
are coadded and reported as one line, while the component FS lines are reset
to a zero intensity.  Without this patch, a number of lines with identical
wavelengths and zero intensities may appear in the spectrum in the main output.

10655 Directory Listing
Modified 7 years, 4 months ago
Sat Sep 19 11:26:07 2015 UTC
gary
Log:
cross reference two different sets of
commands that adjust H2 collisions
10654 Directory Listing
Modified 7 years, 4 months ago
Thu Sep 17 19:53:57 2015 UTC
marios
Log:
Change variable names for in-file transition energy levels, and use consistently across database read-in functions.
10647 Directory Listing
Modified 7 years, 4 months ago
Tue Sep 15 21:07:45 2015 UTC
marios
Log:
docs/quickstart -- List data reporting commands in the quickstart guide.
10646 Directory Listing
Modified 7 years, 4 months ago
Tue Sep 15 20:44:39 2015 UTC
marios
Log:
hazy1 -- Advertise the new 'save lines labels' output in the 'Species' chapter.
10645 Directory Listing
Modified 7 years, 4 months ago
Tue Sep 15 20:38:32 2015 UTC
marios
Log:
hazy1 -- Move misplaced description of emission line comments under the 'save lines labels' command.
10644 Directory Listing
Modified 7 years, 4 months ago
Tue Sep 15 17:54:50 2015 UTC
marios
Log:
Document the new information contained in the comments of the 'save line labels'
output for DB lines.

10643 Directory Listing
Modified 7 years, 4 months ago
Tue Sep 15 17:30:32 2015 UTC
marios
Log:
Modify the comment string for database transitions to include the energy levels.
The order of the levels is the same as it appears in the original data file.

10642 Directory Listing
Modified 7 years, 4 months ago
Tue Sep 15 17:12:44 2015 UTC
gary
Log:
xiang wang update date to Storey+15 in press
10640 Directory Listing
Modified 7 years, 4 months ago
Mon Sep 14 17:32:02 2015 UTC
gary
Log:
svn merge --reintegrate  ^/branches/H2Lique
add Lique (2015) H2 collision data, but do not use by default
10637 Directory Listing
Modified 7 years, 4 months ago
Mon Sep 14 11:50:46 2015 UTC
peter
Log:
source/stars.cpp:
  - Relax another test of the frequency mesh in compiled atmosphere files. The old
    test tripped in runs with -DFLT_IS_DBL in use.

10636 Directory Listing
Modified 7 years, 4 months ago
Mon Sep 14 10:21:54 2015 UTC
peter
Log:
source/grains_mie.cpp:
source/parse_table.cpp:
source/stars.cpp:
  - Relax tests on the lower and upper bound of the mesh. They are defined in MHz
    and MeV, respectively, so are somewhat sensitive to updates of the fundamental
    constants.

10635 Directory Listing
Modified 7 years, 4 months ago
Mon Sep 14 09:38:28 2015 UTC
peter
Log:
source/physconst.cpp:
source/physconst_template.h:
  - Update fundamental constants to CODATA 2014 values.
source/mesh.cpp:
  - Slightly relax test on the ionization edges. This is needed since the CODATA
    update changed the value of EV1RYD by a relative amount 3.6e-8, marginally
    tripping the old test on the He^+ ionization potentials derived from ADfA
    (which are stored in eV). The new test should still be safe. However, it
    would be better to store H-like ionization potentials in Ryd rather than eV
    since they are known to greater accuracy than the accuracy of the eV unit.

10634 Directory Listing
Modified 7 years, 4 months ago
Fri Sep 11 18:16:26 2015 UTC
gary
Log:
spaces to isolate the warning in the printout
10627 Directory Listing
Modified 7 years, 5 months ago
Sun Aug 30 14:31:56 2015 UTC
gary
Log:
BUGFIX underflow when EXTRA=-DFLT_IS_DBL
10626 Directory Listing
Modified 7 years, 5 months ago
Sun Aug 30 14:21:50 2015 UTC
gary
Log:
update Si II electron collision data to Laha+ 2015
10625 Directory Listing
Modified 7 years, 5 months ago
Sat Aug 29 15:00:52 2015 UTC
gary
Log:
clean up species command
10624 Directory Listing
Modified 7 years, 5 months ago
Tue Aug 25 22:55:53 2015 UTC
rjrw
Log:
Fix for routine to convert spectroscopic to chemical
notation

10623 Directory Listing
Modified 7 years, 5 months ago
Tue Aug 25 21:39:46 2015 UTC
rjrw
Log:
Re-enable LOG option for TABLE ISM (was disabled inadvertently)

10619 Directory Listing
Modified 7 years, 5 months ago
Mon Aug 24 20:09:15 2015 UTC
fguzman
Log:
bug in the calling of function CS_l_mixing_VOS12(...), arguments gLo and nelem+1.-ipHE_LIKE. are swapped.
10615 Directory Listing
Modified 7 years, 5 months ago
Sat Aug 22 22:42:55 2015 UTC
gary
Log:
a bit on species level defaults, and CMB not part of table ISM
10614 Directory Listing
Modified 7 years, 5 months ago
Sat Aug 22 15:17:42 2015 UTC
rjrw
Log:
Print diagnostic for mis-spelt species names

10610 Directory Listing
Modified 7 years, 5 months ago
Wed Aug 19 17:37:52 2015 UTC
rjrw
Log:
Quieten unused variable warnings under g++ 5.1.1

10601 Directory Listing
Modified 7 years, 5 months ago
Sun Aug 16 15:43:37 2015 UTC
gary
Log:
Hazy1 - specify units in SAVE LINES ARRAY output
QSG - add section discussing what triggers the calculation stopping
on the lowest temperature, and how that interacts with other
stopping criteria.
10600 Directory Listing
Modified 7 years, 5 months ago
Sun Aug 16 15:41:55 2015 UTC
gary
Log:
add SAVE LINES, ARRAY to an open and closed
geometry - this command was not used in the test suite
10590 Directory Listing
Modified 7 years, 5 months ago
Wed Aug 12 22:32:34 2015 UTC
gary
Log:
small changes in plot
10589 Directory Listing
Modified 7 years, 5 months ago
Wed Aug 12 19:46:36 2015 UTC
gary
Log:
explain provenance of SEDs
10588 Directory Listing
Modified 7 years, 5 months ago
Wed Aug 12 19:42:03 2015 UTC
gary
Log:
two sets of stellar atmospheres
10587 Directory Listing
Modified 7 years, 5 months ago
Wed Aug 12 19:32:15 2015 UTC
gary
Log:
renaming files
10586 Directory Listing
Modified 7 years, 5 months ago
Wed Aug 12 19:29:44 2015 UTC
gary
Log:
rename to WMbasic
10585 Directory Listing
Modified 7 years, 5 months ago
Wed Aug 12 19:28:43 2015 UTC
gary
Log:
two types of O star stellar atmospheres
10583 Directory Listing
Modified 7 years, 5 months ago
Tue Aug 11 18:53:49 2015 UTC
marios
Log:
tsuite/programs/collion -- update headers to indicate ion stage
10571 Directory Listing
Modified 7 years, 6 months ago
Tue Aug 4 17:51:46 2015 UTC
gary
Log:
continuum_bands described in two locations,
both now say that not transmission function is used
10569 Directory Listing
Modified 7 years, 6 months ago
Mon Aug 3 16:58:59 2015 UTC
gary
Log:
svn merge --reintegrate ^/branches/LAMDA
update LAMDA to mid 2015 version.  We had been using 2010
10561 Directory Listing
Modified 7 years, 6 months ago
Sun Aug 2 01:56:53 2015 UTC
gary
Log:
 Changes in the TABLE SED command
By default we will now use only the tabulated data and set the SED to zero outside this.
The EXTRAPOLATE option is a keyword within the SED file which says to do a Rayleigh Jeans extrapolation.

The default units for the intensity are F_nu.  The nuFnu option can be entered within the
SED to signify those uses.

Two new AGN SEDs are introduced, for Mrk 509 and NGC 5548.

Add photon occupation number as last column in SAVE INCIDENT CONTINUUM.

SAVE CONTINUUM output will give luminosity in the luminosity case.  The old behavior,
the luminosity divided by the inner area of the cloud, is used if the
SET SAVE LUMINOSITY OLD command is given.

TABLE SED uses linear units, never logs.

Also add ReadMe.txt to tsuite pointing to wiki.

This message should have been part of r10560
Stackoverflow recommends this as the easiest way to add to a 
commit message.
10560 Directory Listing
Modified 7 years, 6 months ago
Sun Aug 2 01:46:34 2015 UTC
gary
Log:
svn merge --reintegrate  ^/branches/lumin3
10550 Directory Listing
Modified 7 years, 6 months ago
Wed Jul 29 19:21:52 2015 UTC
gary
Log:
confirm that global variable not changed during loop
10545 Directory Listing
Modified 7 years, 6 months ago
Tue Jul 28 22:05:07 2015 UTC
gary
Log:
move asserts on loop limits before start of loop - Robin reported this routine was significant time sink
10541 Directory Listing
Modified 7 years, 6 months ago
Tue Jul 28 21:10:13 2015 UTC
gary
Log:
note about checking on limit to number of iterations, and checking whether low-T limit set outer edge
10540 Directory Listing
Modified 7 years, 6 months ago
Tue Jul 28 02:12:04 2015 UTC
gary
Log:
Robin suggestion for compiling in Lex
10539 Directory Listing
Modified 7 years, 6 months ago
Mon Jul 27 21:09:42 2015 UTC
rjrw
Log:
Assert to quieten a clang-analyzer warning

10536 Directory Listing
Modified 7 years, 6 months ago
Mon Jul 27 14:23:57 2015 UTC
gary
Log:
update BLR spectrum as per comment by poster on yahoo group
10530 Directory Listing
Modified 7 years, 6 months ago
Sun Jul 26 19:26:42 2015 UTC
gary
Log:
Implement test whether ITERATE TO CONVERGENCE converged.  We did not issue
a warning when sim was not converged so it was not possible to check large grids 
for convergence problems.

If the sim has not converged when it stops, there is logic to check whether
the sim stopped due to too-low a temperature.   If so it advises use of different
stop condition.  Today, this is the most common reason for convergence problems.
When the sim stops due to low temperature the column density and line
optical depths change from iteration to iteration.

10529 Directory Listing
Modified 7 years, 6 months ago
Sun Jul 26 15:10:24 2015 UTC
rjrw
Log:
Add comment on origin to license.txt

10527 Directory Listing
Modified 7 years, 6 months ago
Fri Jul 24 19:03:03 2015 UTC
gary
Log:
no longer used - handled by external databases
10526 Directory Listing
Modified 7 years, 6 months ago
Fri Jul 24 18:02:25 2015 UTC
gary
Log:
more on the definition of xi
10524 Directory Listing
Modified 7 years, 6 months ago
Thu Jul 23 23:02:02 2015 UTC
gary
Log:
adjust energy bounds for Xi parameter -
was using full ionizing radiation field but should be 1 - 1000 R
problem reported by ldar Khabibullin on yahoo group
10523 Directory Listing
Modified 7 years, 6 months ago
Thu Jul 23 23:00:20 2015 UTC
gary
Log:
cite papers that give explicit bounds
to Xi Tarter ionization parameter
10522 Directory Listing
Modified 7 years, 6 months ago
Thu Jul 23 22:59:33 2015 UTC
gary
Log:
monitor incident SED as set with Xi command 
we need to include this in at least one test case
10508 Directory Listing
Modified 7 years, 6 months ago
Sat Jul 18 13:02:19 2015 UTC
gary
Log:
stress importance of cosmic rays in neutral or molecular regions
10507 Directory Listing
Modified 7 years, 6 months ago
Sat Jul 18 12:46:48 2015 UTC
gary
Log:
update discussion of SED shape
10506 Directory Listing
Modified 7 years, 6 months ago
Sat Jul 18 12:28:24 2015 UTC
gary
Log:
use save rather than punch
10505 Directory Listing
Modified 7 years, 6 months ago
Sat Jul 18 12:17:08 2015 UTC
gary
Log:
rename punch to save
10504 Directory Listing
Modified 7 years, 6 months ago
Fri Jul 17 22:06:30 2015 UTC
gary
Log:
more helpful comment when option not found
10499 Directory Listing
Modified 7 years, 6 months ago
Thu Jul 16 17:57:34 2015 UTC
rjrw
Log:
Add another test case

10498 Directory Listing
Modified 7 years, 6 months ago
Wed Jul 15 15:22:39 2015 UTC
gary
Log:
add paragraph stressing that INTERPOLATE does J_nu and not nu J_nu.  This is a frequent source of error as per the queries on the user forum
10497 Directory Listing
Modified 7 years, 6 months ago
Wed Jul 15 15:02:32 2015 UTC
gary
Log:
update year -> 2016
10496 Directory Listing
Modified 7 years, 6 months ago
Tue Jul 14 19:01:23 2015 UTC
gary
Log:
diagnose error condition before fpe
Why does cddefines.h:1391 exist?  It is there to throw and fpe
why not print a domain error and stop, 
Would save a step in the dubugging.
10493 Directory Listing
Modified 7 years, 6 months ago
Mon Jul 13 18:41:12 2015 UTC
rjrw
Log:
Avoid SEGV #335 and produce diagnostic print

10491 Directory Listing
Modified 7 years, 6 months ago
Sat Jul 11 12:10:06 2015 UTC
gary
Log:
explain format of Nigel's OP date
10486 Directory Listing
Modified 7 years, 6 months ago
Wed Jul 8 19:38:09 2015 UTC
gary
Log:
this sim has started to throw a monitor but
did not have the SAVE MONITORS report to check on cloudtests
10485 Directory Listing
Modified 7 years, 6 months ago
Tue Jul 7 21:17:12 2015 UTC
rjrw
Log:
Fix upper limit to Vrinceanu QM summation

10482 Directory Listing
Modified 7 years, 7 months ago
Sun Jul 5 17:51:58 2015 UTC
gary
Log:
TODOs for number of observational items that should be enumerated
10481 Directory Listing
Modified 7 years, 7 months ago
Wed Jul 1 14:30:27 2015 UTC
peter
Log:
source/cont_ffun.cpp:
  - Set intensity to zero outside of a laser delta function.
source/grains.cpp:
  - Fix cancellation error in y2s() when grain charge is extremely high.
tsuite/auto/pdr_co_fully.in:
  - Fix botch in performance monitor.

10479 Directory Listing
Modified 7 years, 7 months ago
Fri Jun 26 19:50:23 2015 UTC
gary
Log:
fix for ticket #328 discussed in google
group post STOP COLUMN DENSITY [ATOMIC; NEUTRAL] command 
10477 Directory Listing
Modified 7 years, 7 months ago
Tue Jun 23 19:07:33 2015 UTC
rjrw
Log:
Add inline tag to file-local function

10476 Directory Listing
Modified 7 years, 7 months ago
Tue Jun 23 18:48:10 2015 UTC
rjrw
Log:
Compile-time switch to use Vrinceanu's QM form of the l-mixing CS

10475 Directory Listing
Modified 7 years, 7 months ago
Tue Jun 23 16:47:07 2015 UTC
rjrw
Log:
Source to reproduce another V et al figure

10474 Directory Listing
Modified 7 years, 7 months ago
Mon Jun 22 20:30:02 2015 UTC
peter
Log:
source/thirdparty.h:
source/thirdparty.cpp:
  - Replace the routine for evaluating Wigner six-j symbols with new version that
    accepts half-integer values. The angular momenta are passed as 2*j to allow
    half-integer values.
source/TestThirdparty.cpp:
  - Add further unit tests for SixJ().
source/helike_cs.cpp:
  - Fix bug where half-integer values were incorrectly passed to SixJ().

10470 Directory Listing
Modified 7 years, 7 months ago
Thu Jun 18 14:42:49 2015 UTC
peter
Log:
source/mole_h2_io.cpp:
  - Fix compiler warning when using -DNDEBUG.

10468 Directory Listing
Modified 7 years, 7 months ago
Tue Jun 16 19:55:38 2015 UTC
rjrw
Log:
Code to try to generate Fig 1 in VOS12, for comparison

10467 Directory Listing
Modified 7 years, 7 months ago
Mon Jun 15 22:15:45 2015 UTC
rjrw
Log:
Straightforward implementation of the QM probability expressions
in VOS12

10466 Directory Listing
Modified 7 years, 7 months ago
Mon Jun 15 21:19:22 2015 UTC
gary
Log:
Fran noticed reference to old perl script - name updated to current version.
10465 Directory Listing
Modified 7 years, 7 months ago
Mon Jun 15 20:57:23 2015 UTC
rjrw
Log:
Simple implementation of ultraspherical aka Gegenbauer polynomial
evaluation

10464 Directory Listing
Modified 7 years, 7 months ago
Sun Jun 14 23:33:39 2015 UTC
marios
Log:
coronal/ms-nei -- update common bib
10463 Directory Listing
Modified 7 years, 7 months ago
Sat Jun 13 22:08:39 2015 UTC
marios
Log:
source -- Improve 'save map' command output, and Cool_GA08() debug output.
source/hcmap.cpp
  - Modify output of 'save map' command: comment out non-plottable lines,
    and use tabs to delimit columns.
source/cool_eval.cpp
  - Add H2 line cooling column to GA08 debug output.

10462 Directory Listing
Modified 7 years, 7 months ago
Fri Jun 12 21:55:25 2015 UTC
peter
Log:
source/integrate.h:
source/helike_cs.cpp:
  - Create vectorized version of the 32-point Gaussian integrator.
  - Use this integrator for the Seaton (1962) collision strengths.
source/iso_level.cpp:
  - Make local scratch arrays static to save on memory allocations.
source/mole_reactions.cpp:
  - Optimize transcendental function calls in hmrate().

10461 Directory Listing
Modified 7 years, 7 months ago
Wed Jun 10 23:35:36 2015 UTC
gary
Log:
comments to cite process and paper
10460 Directory Listing
Modified 7 years, 7 months ago
Wed Jun 10 23:34:06 2015 UTC
gary
Log:
oops - undo previous commit
10459 Directory Listing
Modified 7 years, 7 months ago
Wed Jun 10 23:27:38 2015 UTC
gary
Log:
added comment -- reference to paper and theory
10458 Directory Listing
Modified 7 years, 7 months ago
Wed Jun 10 18:24:59 2015 UTC
marios
Log:
source/mole_eval_balance.cpp -- include Robin's response to adjusting the
molecular conservation tolerance as a comment.

10457 Directory Listing
Modified 7 years, 7 months ago
Mon Jun 8 04:34:27 2015 UTC
marios
Log:
tsuite -- update h2small close monitors
10456 Directory Listing
Modified 7 years, 7 months ago
Mon Jun 8 03:23:52 2015 UTC
marios
Log:
Minor bugfix in 'save H2 cooling per molecule'.

source/mole_h2_io.cpp
  - Bugfix, save file label set to 4 char long. 
data/h2/lte_cooling.dat
  - Minor update to LTE cooling data.

10455 Directory Listing
Modified 7 years, 8 months ago
Sat Jun 6 13:57:54 2015 UTC
marios
Log:
source/mole_eval_balance.cpp -- loosen tolerance to let igm_primal pass under llvm
10454 Directory Listing
Modified 7 years, 8 months ago
Fri Jun 5 02:08:30 2015 UTC
marios
Log:
source/mole_eval_balance.cpp -- tighten chemistry balance tolerance, from 2e-9 to 1e-9
10453 Directory Listing
Modified 7 years, 8 months ago
Thu Jun 4 22:05:38 2015 UTC
marios
Log:
source/cool_eval.cpp -- missed converting a STATIC variable to static
10452 Directory Listing
Modified 7 years, 8 months ago
Thu Jun 4 21:58:54 2015 UTC
marios
Log:
trunk -- reintegrated branches/h2small
10441 Directory Listing
Modified 7 years, 8 months ago
Wed Jun 3 19:10:33 2015 UTC
gary
Log:
see r327
The PDR sims in the test suite include the DOUBLE command for the reasons described in the Quick Start Guide, Section 8.3.3 on heads up for PDRs. There are two reasons why. First, the models stop at Av = 10, the convention for PDR models. Real PDRs do not stop but extend into an unmodeled background molecular cloud. That unmodeled material is approximated when the DOUBLE command is included.

If DOUBLE is not included then a PDR will be very optically thick at the shielded face, with most coolants affected by line transfer. As the outer edge is reached the lines will become optically thin, on the very surface of the shielded face. For a line like Lya the total optical depth might be 1e8 and the line photons become freely escaping when optical depths within a few are reached at the shielded face. Conditions will change greatly at the outer skin due to this. We don't now have logic to detect this condition and adjust the zoning to resolve this thin skin at the shielded face, because this does not occur when a PDR is set up with the DOUBLE command. Physically, it does not happen in nature, for a PDR, because of the unmodeled molecular cloud.

The PDR sim pdr_coolbb was added to exercise the code in an extreme radiative case. I forgot to include the DOUBLE command. As a result ITERATE TO CONVERGENCE failed and the answer depends on circumstances with lots of botches coming and going. This was due to an oversight on my part and I have now added the DOUBLE command and ITERATE TO CONVERGENCE.

This ticket is because it would be good if we could converge such models. It will take some development of the zoning logic for this circumstance. To exercise the problem comment out the DOUBLE command in the pdr_coolbb sim

10440 Directory Listing
Modified 7 years, 8 months ago
Tue Jun 2 06:57:11 2015 UTC
rjrw
Log:
Avoid preprocessor testing in mole_eval_balance.cpp

10439 Directory Listing
Modified 7 years, 8 months ago
Tue Jun 2 06:27:02 2015 UTC
rjrw
Log:
Reduce allocations in lgNucleiConserved

10436 Directory Listing
Modified 7 years, 8 months ago
Sun May 31 09:17:44 2015 UTC
peter
Log:
source/mole_reactions.cpp:
  - Fix expression for H2 formation rate to prevent underflow to zero in FLT_IS_DBL runs.
source/stars.cpp:
  - Make expression more robust against the g++ compiler bug.
tsuite/slow/h2_orion_hii_pdr.in:
  - Fix near botch.

10422 Directory Listing
Modified 7 years, 8 months ago
Thu May 28 18:34:19 2015 UTC
rjrw
Log:
Minor optimization and clarifying comment

10419 Directory Listing
Modified 7 years, 8 months ago
Thu May 28 14:06:59 2015 UTC
peter
Log:
source/mole_h2_form.cpp:
  - Bug-fix: prevent spurious failed assert when running with FLT_IS_DBL.

10418 Directory Listing
Modified 7 years, 8 months ago
Thu May 28 06:02:10 2015 UTC
rjrw
Log:
Eliminate some more superfluous log() calls

10417 Directory Listing
Modified 7 years, 8 months ago
Thu May 28 05:51:00 2015 UTC
rjrw
Log:
Avoid unnecessary calls to log()

10416 Directory Listing
Modified 7 years, 8 months ago
Wed May 27 21:44:05 2015 UTC
rjrw
Log:
Fixes to PS64 implementation: should be scaled by gLo,
exact formula for l -> l+1 coupling (as confirmed by
NRB email)

10415 Directory Listing
Modified 7 years, 8 months ago
Wed May 27 12:21:53 2015 UTC
peter
Log:
source/atom_hyperfine.cpp:
  - Fix overzealous assert to prevent spurious crashes in FLT_IS_DBL runs.

10414 Directory Listing
Modified 7 years, 8 months ago
Tue May 26 15:18:55 2015 UTC
peter
Log:
source/grains.cpp:
  - Further optimize UpdatePot1() and subsidiary routines for speed.

10413 Directory Listing
Modified 7 years, 8 months ago
Mon May 25 16:24:26 2015 UTC
peter
Log:
source/grains.cpp:
  - Vectorize calls to asinh() and sqrt() in y2s().
source/vectorize.h:
  - Increase static size of avx_pool from 6 to 30.
source/TestVectorize.cpp:
  - Add unit test for MALLOC_AVX().

10412 Directory Listing
Modified 7 years, 8 months ago
Fri May 22 21:05:22 2015 UTC
gary
Log:
Hazy - add reference to Porter+12 in ADS format, add erratum for this paper, quote this for Case B monitor

He I case B, add commented out monitor for case B at high precision.  These do not pass since we have migrated away from our published Case B predictions in some cases.

h_hs87 - add collapsesd levels at the top of the model atom
10411 Directory Listing
Modified 7 years, 8 months ago
Fri May 22 18:55:40 2015 UTC
rjrw
Log:
Include target charge factor in VOS12, for consistency with PS64

This appears to cancel in the implementation of VF01, though

10410 Directory Listing
Modified 7 years, 8 months ago
Wed May 20 14:01:31 2015 UTC
gary
Log:
exercise SAVE AGE command, save ages for coronal grid
10409 Directory Listing
Modified 7 years, 8 months ago
Wed May 20 07:56:38 2015 UTC
rjrw
Log:
Reorder some variable sets closer to the memory pattern

Avoid an unnecessary count_ptr<> creation in an inner loop

10408 Directory Listing
Modified 7 years, 8 months ago
Tue May 19 22:26:37 2015 UTC
gary
Log:
clarify a confusion during the workshop
10407 Directory Listing
Modified 7 years, 8 months ago
Tue May 19 22:08:00 2015 UTC
gary
Log:
fix typos noticed by participant in Warsaw Cloudy workshop
10406 Directory Listing
Modified 7 years, 8 months ago
Tue May 19 17:54:48 2015 UTC
rjrw
Log:
Add ctor/dtor to CollSplinesArray

10405 Directory Listing
Modified 7 years, 8 months ago
Tue May 19 16:47:53 2015 UTC
peter
Log:
source/parse_tlaw.cpp:
  - ParseTLaw() should not set the temperature. This can lead to bogus error
    messages from the TLAW TABLE command. Setting the temperature will be
    handled correctly by ConvTempEdenIoniz().

10404 Directory Listing
Modified 7 years, 8 months ago
Tue May 19 16:14:32 2015 UTC
peter
Log:
source/vectorize.h:
source/vectorize_exp.cpp:
source/vectorize_exp_core.h:
source/vectorize_hyper.cpp:
source/vectorize_hyper.h:
source/vectorize_log.cpp:
source/vectorize_math.h:
source/vectorize_sqrt.cpp:
source/TestVectorize.cpp:
  - Throw domain_error() for invalid arguments to vectorized math functions.
    This allows a more informative error message to be printed and is easier to
    recover from in grid runs.
source/cddefines.h:
source/cpu.cpp:
source/maincl.cpp:
tsuite/programs/template.cpp:
tsuite/programs/collcool/collcool.cpp:
tsuite/programs/collion/collion.cpp:
tsuite/programs/comp4/comp4.cpp:
tsuite/programs/hazy_coolingcurve/hazy_coolingcurve.cpp:
tsuite/programs/hazy_kmt/hazy_kmt.cpp:
tsuite/programs/hizlte/hizlte.cpp:
tsuite/programs/mpi/mpi.cpp:
tsuite/programs/vary_nete/vary_nete.cpp:
tsuite/programs/varyn/varyn.cpp:
  - Handle domain_error() exceptions correctly.
source/configure.sh:
  - Remove test for asinh() since the presence of this routine is guaranteed by
    the X/Open 6 and POSIX 2001 standards.
source/thirdparty.h:
  - Remove asinh() replacement.
source/parse_crashdo.cpp:
  - Add CRASH DOMAIN command for testing the catching of a domain_error() exception.
docs/latex/hazy1/miscell.tex:
  - Document the new CRASH DOMAIN command.

10403 Directory Listing
Modified 7 years, 8 months ago
Tue May 19 12:38:23 2015 UTC
gary
Log:
update reference for Zn II atomic data
fix typo in plot descriptions
10402 Directory Listing
Modified 7 years, 8 months ago
Tue May 19 06:24:07 2015 UTC
rjrw
Log:
Handle case where asinh() is not available using the cloudyconfig.h
infrastructure

10401 Directory Listing
Modified 7 years, 8 months ago
Tue May 19 06:14:31 2015 UTC
rjrw
Log:
Provide fallback fast_asinh routines for non-AVX platforms

10400 Directory Listing
Modified 7 years, 8 months ago
Mon May 18 21:42:23 2015 UTC
rjrw
Log:
Convert a deeply-nested pointer array to a multi_arr<>

10399 Directory Listing
Modified 7 years, 8 months ago
Mon May 18 20:38:34 2015 UTC
rjrw
Log:
Cache collider densities in type-safe object outside loops

10398 Directory Listing
Modified 7 years, 8 months ago
Mon May 18 08:51:52 2015 UTC
peter
Log:
source/vectorize_exp_core.h:
source/vectorize_log_core.h:
source/vectorize_sqrt_core.h:
source/vectorize_math.h:
  - Move common constants into vectorize_math.h.
source/vectorize.h:
source/vectorize_hyper.h:
source/vectorize_hyper_core.h:
source/vectorize_hyper.cpp:
source/vectorize_log.cpp:
  - Add vectorized routines vasinh() and vfast_asinh().
  - Update comments.
source/TestVectorize.cpp:
  - Add unit tests for vasinh() and vfast_asinh().

10397 Directory Listing
Modified 7 years, 8 months ago
Sun May 17 12:55:23 2015 UTC
gary
Log:
improve explain of dusty open
10396 Directory Listing
Modified 7 years, 8 months ago
Sun May 17 12:36:24 2015 UTC
peter
Log:
source/ion_recomb_Badnell.cpp:
  - Fix compiler warnings from LLVM compiler.

10395 Directory Listing
Modified 7 years, 8 months ago
Sun May 17 06:22:33 2015 UTC
peter
Log:
source/vectorize.h:
source/vectorize_sqrt.h:
source/vectorize_sqrt_core.h:
source/vectorize_sqrt.cpp:
  - Add new vectorized versions of the sqrt() and hypot() functions. These are
    not used yet.
source/vectorize_log.cpp:
source/vectorize_log_core.h:
  - Fix compilation errors when compiling for avx512f hardware.
source/vectorize_math.h:
  - Add support for vectorized functions with two arguments (like hypot(x,y)).
  - Create macros VECL_CONST and VECLL_CONST consistent with the equivalent
    32-bit macros VECI_CONST and VECII_CONST.
source/TestVectorize.cpp:
  - Add units tests for the new vsqrt() and vhypot() functions.

10394 Directory Listing
Modified 7 years, 8 months ago
Thu May 14 07:32:19 2015 UTC
peter
Log:
source/cpu.cpp:
  - Make flushing denormalized numbers to zero the default. This speeds up the
    code by around 2.5%.

10393 Directory Listing
Modified 7 years, 8 months ago
Thu May 14 06:55:32 2015 UTC
peter
Log:
source/ion_recomb_Badnell.cpp:
  - Implement the final version of the CollisSuppres() routine sent by Dragan Nikolic.
source/parse_test.cpp:
  - Fix botches in the smoke test.
tsuite/auto/*.in:
tsuite/slow/*.in:
  - Fix remaining botches.

10392 Directory Listing
Modified 7 years, 8 months ago
Thu May 14 06:34:10 2015 UTC
rjrw
Log:
Fix wavelength of He line to ve consistent with Ca B comparison

10391 Directory Listing
Modified 7 years, 8 months ago
Wed May 13 22:01:52 2015 UTC
rjrw
Log:
Document last commit

10390 Directory Listing
Modified 7 years, 8 months ago
Wed May 13 21:55:24 2015 UTC
rjrw
Log:
Make VOS12 l-mixing available as an option

10389 Directory Listing
Modified 7 years, 8 months ago
Wed May 13 21:36:04 2015 UTC
rjrw
Log:
Fix name of argument to VOS12, and load (inactive) code
to fix splitting of upward & downward cross sections for PS64

10388 Directory Listing
Modified 7 years, 8 months ago
Wed May 13 20:53:30 2015 UTC
rjrw
Log:
Reduced velocity should depend on reduced mass -- validated
by comparison with VOS2012 results via extended diagnostic
also in this commit.

10387 Directory Listing
Modified 7 years, 8 months ago
Wed May 13 06:22:38 2015 UTC
rjrw
Log:
Minor work on cross-validation of collisional cross sections

10386 Directory Listing
Modified 7 years, 8 months ago
Tue May 12 07:19:46 2015 UTC
gary
Log:
add column option to save line list file
10385 Directory Listing
Modified 7 years, 8 months ago
Tue May 12 06:54:28 2015 UTC
gary
Log:
add column option to line list ratio save
10384 Directory Listing
Modified 7 years, 8 months ago
Tue May 12 06:45:40 2015 UTC
rjrw
Log:
Enable reduced mass scaling of collision strengths, gets VF01 and PS64
to agree at expected level for non-electron colliders

10383 Directory Listing
Modified 7 years, 8 months ago
Tue May 12 06:07:44 2015 UTC
rjrw
Log:
Change of variables to improve speed & accuracy of (disabled) Romberg integration

10382 Directory Listing
Modified 7 years, 8 months ago
Tue May 12 05:05:27 2015 UTC
rjrw
Log:
Fix lower bound in (inactive) Romberg thermal integration

10381 Directory Listing
Modified 7 years, 8 months ago
Tue May 12 02:20:29 2015 UTC
peter
Log:
source/grains_qheat.cpp:
  - The changes in r10369 slowed down PDR models on 32-bit platforms without AVX
    support (but not on 64-bit platforms without AVX support). This change should
    gain back the lost speed. 

10380 Directory Listing
Modified 7 years, 8 months ago
Mon May 11 22:42:30 2015 UTC
rjrw
Log:
Start to implement VOS 2012 approximate rate for l-changing collisions

10379 Directory Listing
Modified 7 years, 8 months ago
Mon May 11 09:46:30 2015 UTC
peter
Log:
source/vectorize_exp.cpp:
source/vectorize_exp_core.h:
source/vectorize_log.cpp:
source/vectorize_log.h:
source/vectorize_log_core.h:
  - Add new vectorized vlog1p() routines.
  - Speed up the vlog() and vlog10() routines by reorganizing the test for domain
    errors.
  - Speed up the vexp10() and vlog10() routines by replacing divisions by constants
    with multiplications with the inverse constant
source/TestVectorize.cpp:
  - Update tests of the vlog() and vlog10() routines.
  - Add new tests for the vlog1p() routines.

10378 Directory Listing
Modified 7 years, 8 months ago
Mon May 11 03:59:52 2015 UTC
peter
Log:
source/cpu.cpp:
  - Prevent cautions about multiple instances of a data file when the paths are identical.

10377 Directory Listing
Modified 7 years, 8 months ago
Sun May 10 20:45:13 2015 UTC
peter
Log:
source/cpu.cpp:
  - Add code for removing duplicate entries in the search path. We cannot use this
    code now as it would break the code. It should be activated once the search
    path changes have been finalized.
  - Downgrade warning about multiple files with the same name along to search path
    to a caution. The code could be picking up the correct file, so a warning is
    not the correct message level.

10376 Directory Listing
Modified 7 years, 8 months ago
Sat May 9 01:19:46 2015 UTC
peter
Log:
source/cddefines.h:
source/vectorize_exp_core.h:
source/vectorize_exp.cpp:
source/TestVectorize.cpp:
  - Improve accuracy of exp10() and vexp10().
  - Correctly detect invalid arguments for all variants of the exponential
    functions. If the result would overflow to +Inf, an assert will trip. If the
    argument is NaN, then NaN is returned (causing an FPE in a trapping
    environment).
  - Update the unit tests according to the new behavior and tighten the tests
    for the (v)exp10() routines.
source/vectorize_math.h
  - Fix typo.

10375 Directory Listing
Modified 7 years, 8 months ago
Thu May 7 23:04:28 2015 UTC
rjrw
Log:
Remove static expressions from VF thermal integrand

10374 Directory Listing
Modified 7 years, 9 months ago
Thu May 7 06:45:48 2015 UTC
rjrw
Log:
Create iso-level lines in a more cache-friendly order

10373 Directory Listing
Modified 7 years, 9 months ago
Thu May 7 06:27:46 2015 UTC
rjrw
Log:
Improve order of some more matrix fills

10372 Directory Listing
Modified 7 years, 9 months ago
Wed May 6 06:07:51 2015 UTC
rjrw
Log:
Simplify expression for VF12 alphamax

10371 Directory Listing
Modified 7 years, 9 months ago
Tue May 5 15:18:26 2015 UTC
gary
Log:
two paragraphs were repeated
10370 Directory Listing
Modified 7 years, 9 months ago
Tue May 5 15:13:13 2015 UTC
gary
Log:
misspelled Jaques' name, although the reference is correct
10369 Directory Listing
Modified 7 years, 9 months ago
Mon May 4 19:42:56 2015 UTC
peter
Log:
source/vectorize_exp.h:
source/vectorize_exp.cpp:
source/vectorize_math.h:
source/TestVectorize.cpp:
  - Add vectorized versions of expm1().
source/cool_eval.cpp:
source/grains_qheat.cpp:
source/iso_cool.cpp:
source/rt_diffuse.cpp:
source/temp_change.cpp:
  - Use the the vectorized versions of expm1().
source/thirdparty.h:
source/configure.sh:
source/cloudyconfig_vs.h:
source/TestThirdparty.cpp:
  - Remove the replacements for expm1() and cbrt(). These are guaranteed by the
    POSIX.1-2001 and X/Open 6 standards, which we require.

10368 Directory Listing
Modified 7 years, 9 months ago
Sun May 3 11:33:09 2015 UTC
rjrw
Log:
Simple bisection for VF integral lower limit with Romberg; extract routines
to allow cross-validation of integrators

10367 Directory Listing
Modified 7 years, 9 months ago
Sat May 2 08:25:42 2015 UTC
rjrw
Log:
Fix solstudio warnings

10366 Directory Listing
Modified 7 years, 9 months ago
Fri May 1 07:09:45 2015 UTC
rjrw
Log:
Not-yet-enabled branches switching to Romberg integration of VF01 function

10365 Directory Listing
Modified 7 years, 9 months ago
Thu Apr 30 23:20:51 2015 UTC
rjrw
Log:
source/helike_cs.cpp:
	More minor clarifying reorganizations

10364 Directory Listing
Modified 7 years, 9 months ago
Thu Apr 30 23:01:54 2015 UTC
rjrw
Log:
Inline a function to simplify code

10363 Directory Listing
Modified 7 years, 9 months ago
Thu Apr 30 22:54:16 2015 UTC
rjrw
Log:
Factor some stuff out of VF01 integral, towards improving treatment
of integration range

10362 Directory Listing
Modified 7 years, 9 months ago
Thu Apr 30 21:59:27 2015 UTC
rjrw
Log:
Optimizations of VF01 integrand

10361 Directory Listing
Modified 7 years, 9 months ago
Wed Apr 29 06:49:01 2015 UTC
rjrw
Log:
Minor optimization of VF01 integral

10360 Directory Listing
Modified 7 years, 9 months ago
Tue Apr 28 22:51:04 2015 UTC
rjrw
Log:
Optimize fine profile addition

10359 Directory Listing
Modified 7 years, 9 months ago
Tue Apr 28 15:47:13 2015 UTC
peter
Log:
source/ion_recomb_Badnell.cpp:
  - In CollisSuppres() update functional form for Te dependence of A_N following
    the suggestion by Dragan Nikolic.
tsuite/auto/blr_n13_p22_Z20.in:
tsuite/auto/blr_rnfb.in:
tsuite/auto/coll_coronal.in:
tsuite/auto/coll_heat_only.in:
tsuite/auto/coll_t5.in:
tsuite/auto/coll_t6.in:
tsuite/auto/pdr_coolbb.in:
  - Update monitors as a result of the change above.

10358 Directory Listing
Modified 7 years, 9 months ago
Tue Apr 28 14:14:23 2015 UTC
peter
Log:
source/configure.sh:
source/cpu.h:
source/cpu.cpp:
  - Fix compiler warning on 32-bit systems by introducing INT64_LIT() and UINT64_LIT().

10357 Directory Listing
Modified 7 years, 9 months ago
Mon Apr 27 22:03:27 2015 UTC
rjrw
Log:
Minor optimizations

10356 Directory Listing
Modified 7 years, 9 months ago
Mon Apr 27 21:31:29 2015 UTC
peter
Log:
source/cpu.h:
source/parse_print.cpp:
  - Add support for int64 and uint64 on 32-bit systems.
source/vectorize_math.h:
  - Disable AVX support on systems that don't support uint64.

10355 Directory Listing
Modified 7 years, 9 months ago
Mon Apr 27 20:49:40 2015 UTC
peter
Log:
source/vectorize_exp.cpp:
source/vectorize_log.cpp:
  - Optimize AVX coding of v1logd() and v1logf(). This version is ~10% faster.
  - Optimize AVX512 coding of v1expd() and v1logd().

10354 Directory Listing
Modified 7 years, 9 months ago
Sun Apr 26 17:44:26 2015 UTC
peter
Log:
source/vectorize_math.h:
source/vectorize_exp.h:
source/vectorize_exp.cpp:
source/vectorize_log.h:
source/vectorize_log.cpp:
  - Add vectorized math functions that take scalar arguments. There are versions
    that take 4 and 8 arguments, and also 16 for single precision arguments.
  - Optimize vecfun() by avoiding the use of scalfun1() for non-aligned parts
    of the array. Copy arguments and use vecfun1() instead.
  - Fix minor bug in v1logf().
source/TestVectorize.cpp:
  - Test the new vectorized math functions.
source/cddefines.h:
  - Add routine exp10f().
source/atom_feii.cpp:
source/cool_eval.cpp:
source/grains.cpp:
source/grains_qheat.cpp:
  - Start using vectorized log() functions.
source/iso_create.cpp:
source/prt_lines_helium.cpp:
  - Hoist loop-invariants out of loop.
source/species2.cpp:
  - Use physconst constant instead of exp(1.0).

10353 Directory Listing
Modified 7 years, 9 months ago
Sun Apr 26 12:32:55 2015 UTC
rjrw
Log:
Less disruptive optimization of highen()

10352 Directory Listing
Modified 7 years, 9 months ago
Sun Apr 26 11:51:49 2015 UTC
rjrw
Log:
Revert r10351 -- has negative consequences when run through whole
suite, e.g. on convergence of blr_n13_p18_Z20

10351 Directory Listing
Modified 7 years, 9 months ago
Sun Apr 26 10:44:38 2015 UTC
rjrw
Log:
Vectorize highen()

10350 Directory Listing
Modified 7 years, 9 months ago
Sun Apr 26 09:59:42 2015 UTC
rjrw
Log:
Optimize memory access in funjac()

10349 Directory Listing
Modified 7 years, 9 months ago
Sun Apr 26 09:03:47 2015 UTC
rjrw
Log:
Use local reference for clarity in reduction loop

10348 Directory Listing
Modified 7 years, 9 months ago
Sat Apr 25 17:38:22 2015 UTC
rjrw
Log:
Cache-optimize line stack wavelengths

10347 Directory Listing
Modified 7 years, 9 months ago
Sat Apr 25 15:16:35 2015 UTC
rjrw
Log:
Convert sPradDat to a multi_arr<>

10346 Directory Listing
Modified 7 years, 9 months ago
Sat Apr 25 14:01:33 2015 UTC
gary
Log:
Adopt comment 14 in refee report for Stout data paper
10345 Directory Listing
Modified 7 years, 9 months ago
Thu Apr 23 15:34:48 2015 UTC
peter
Log:
source/vectorize_log.cpp:
  - Fix bugs in AVX2 code.

10344 Directory Listing
Modified 7 years, 9 months ago
Wed Apr 22 22:47:47 2015 UTC
rjrw
Log:
Optimize xMatrix fill

10343 Directory Listing
Modified 7 years, 9 months ago
Wed Apr 22 22:06:15 2015 UTC
rjrw
Log:
Further cache optimization

10342 Directory Listing
Modified 7 years, 9 months ago
Wed Apr 22 21:43:21 2015 UTC
peter
Log:
source/vectorize_math.h:
source/vectorize_log.h:
source/vectorize_log.cpp:
  - Add new vectorized routines for calculating log() and log10() (both single
    and double precision versions). These are not used anywhere yet.
source/cddefines.h:
source/container_classes.h:
source/vectorize.h:
  - Add bounds checking to the avx_ptr class.
source/TestVectorize.cpp:
  - Add unit tests for avx_pool, avx_ptr, allocator_avx<>, and the new vectorized
    log() math routines. 
source/Makefile:
source/sys_valgrind/Makefile.conf:
  - The _mm256_cmp_pd() commands in the vectorized log() routines trigger a bug
    in valgrind. To circumvent this problem, checks for arguments <= 0 are not
    done in valgrind runs. This is achieved by defining the VALGRIND macro. Also
    see this bug report: https://bugs.kde.org/show_bug.cgi?id=346476
source/parse_crashdo.cpp:
  - Exercise bounds checking for the avx_ptr class in the CRASH BOUNDS command.
docs/latex/hazy1/miscell.tex:
  - Update the documentation of the CRASH BOUNDS command.

10341 Directory Listing
Modified 7 years, 9 months ago
Wed Apr 22 21:26:16 2015 UTC
rjrw
Log:
Another small cache optimization

10340 Directory Listing
Modified 7 years, 9 months ago
Wed Apr 22 21:14:11 2015 UTC
rjrw
Log:
Optimize FeIISumBand by moving wavelength test into loop

10339 Directory Listing
Modified 7 years, 9 months ago
Wed Apr 22 20:47:59 2015 UTC
rjrw
Log:
Transpose FeII_Cont and FeII_Band arrays

10338 Directory Listing
Modified 7 years, 9 months ago
Wed Apr 22 07:29:38 2015 UTC
rjrw
Log:
Improve memory layout of FeII arrays

10337 Directory Listing
Modified 7 years, 9 months ago
Tue Apr 21 23:03:36 2015 UTC
rjrw
Log:
Another FeII cache optimization

10336 Directory Listing
Modified 7 years, 9 months ago
Tue Apr 21 22:52:57 2015 UTC
rjrw
Log:
Cache optimization of FeII model

10335 Directory Listing
Modified 7 years, 9 months ago
Sun Apr 19 20:34:47 2015 UTC
peter
Log:
source/capabilities.pl:
  - Disable AVX optimizations completely on Mac Darwin when using the homebrew
    g++ compiler. The assembler doesn't support AVX instructions.

10334 Directory Listing
Modified 7 years, 9 months ago
Sun Apr 19 12:35:06 2015 UTC
peter
Log:
source/cddefines.h:
source/cloudyconfig_vs.h:
source/configure.sh:
  - Prevent problems on platforms with broken support for AVX intrinsics (such as
    Mac homebrew g++).
source/rt_line_one.cpp:
  - Fix comment.

10333 Directory Listing
Modified 7 years, 9 months ago
Sun Apr 19 01:05:19 2015 UTC
peter
Log:
source/thirdparty.cpp:
  - Start vectorizing FastVoigtH() by splitting up the loops for the core and the
    damping wings.
source/rt_line_one.cpp:
  - Avoid initializing nCells_damp to needlessly large values.
source/cont_ipoint.cpp:
source/parse_drive.cpp:
  - Fix inconsequential typos.

10332 Directory Listing
Modified 7 years, 9 months ago
Sat Apr 18 12:58:21 2015 UTC
peter
Log:
source/grains_qheat.cpp:
  - Bug-fix: prevent reading uninitialized memory in expval. This can result in
    spurious FP exceptions.

10331 Directory Listing
Modified 7 years, 9 months ago
Fri Apr 17 16:10:55 2015 UTC
peter
Log:
source/atmdat_gaunt.cpp:
source/atmdat_gaunt.h:
source/atom_leveln.cpp:
source/cddefines.h:
source/cont_createmesh.cpp:
source/cool_eval.cpp:
source/grains.cpp:
source/grains_qheat.cpp:
source/iso_collide.cpp:
source/iso_cool.cpp:
source/iso_create.cpp:
source/iso_level.cpp:
source/quantumstate.h:
source/rt_continuum.cpp:
source/species2.cpp:
source/thirdparty.cpp:
  - Vectorize more calls to exp().
  - Optimize existing vexp() calls by using aligned memory, mostly from avx_pool.
source/container_classes.h:
  - Revert changes to flex_arr, using avx_ptr is now the preferred solution.
source/vectorize.h:
source/vectorize.cpp:
  - Create avx_pool for holding a pool of scratch arrays to be used vexp() et al.
  - Create avx_ptr for obtaining a scratch array from avx_pool.
  - Create allocator_avx for obtaining AVX aligned memory in a vector.

10330 Directory Listing
Modified 7 years, 9 months ago
Thu Apr 16 20:24:29 2015 UTC
rjrw
Log:
...and struc.gas_phase[][]

10329 Directory Listing
Modified 7 years, 9 months ago
Thu Apr 16 20:13:34 2015 UTC
rjrw
Log:
Cache fix struc.molecules

10328 Directory Listing
Modified 7 years, 9 months ago
Thu Apr 16 20:08:17 2015 UTC
rjrw
Log:
Cache-optimize struc.StatesElem

10327 Directory Listing
Modified 7 years, 9 months ago
Thu Apr 16 19:36:36 2015 UTC
rjrw
Log:
Make struc.xIonDense array more cache-friendly

10326 Directory Listing
Modified 7 years, 9 months ago
Wed Apr 15 17:04:53 2015 UTC
rjrw
Log:
Avoid division in inner loop test

10325 Directory Listing
Modified 7 years, 9 months ago
Tue Apr 14 19:28:21 2015 UTC
peter
Log:
source/temp_change.cpp:
source/rfield.h:
source/atmdat_gaunt.h:
source/atmdat_gaunt.cpp:
source/cool_eval.cpp:
source/atom_leveln.cpp:
source/iso_level.cpp:
source/species2.cpp:
source/thirdparty.h:
source/thirdparty.cpp:
  - This is the first installment of vectorizing exp() calls. The following tasks
    are vectorized:
    * Calculating the Boltzmann factors in temp_change().
    * Calculating the free-free Gaunt factors.
    * Calculating the ee brems spectrum.
    * Solving level pops in atom_leveln(), iso_level(), and dBase_solve().
    * Calculating the core of the Voigt profile.
source/cpu.h:
source/cddefines.h:
source/service.cpp:
source/stars.cpp:
source/opacity_createall.cpp:
source/cont_createmesh.cpp:
  - Remove obsolete macro REALLOC.
  - Add new macro MALLOC_AVX for returning memory correctly aligned for AVX access.    
source/container_classes.h:
  - Force flex_arr memory to be aligned on an AVX boundary. This is temporary code
    until a better method is in place to align a vector and valarray.

10322 Directory Listing
Modified 7 years, 9 months ago
Sun Apr 12 09:24:52 2015 UTC
peter
Log:
source/cont_setintensity.cpp:
  - Fix minor complaint in grid_extreme with the LLVM compiler by removing obsolete
    casts to realnum. These caused the H^0 density to underflow to zero.

10321 Directory Listing
Modified 7 years, 9 months ago
Sat Apr 11 21:58:18 2015 UTC
peter
Log:
source/helike_cs.cpp:
source/helike_einsta.cpp:
source/helike_energy.cpp:
source/helike_recom.cpp:
source/hydroreccool.cpp:
  - Make more data arrays "static const".

10320 Directory Listing
Modified 7 years, 9 months ago
Sat Apr 11 18:53:44 2015 UTC
peter
Log:
source/helike_recom.cpp:
  - Make data arrays "static const".

10319 Directory Listing
Modified 7 years, 9 months ago
Sat Apr 11 17:31:57 2015 UTC
peter
Log:
source/service.cpp:
  - Fix botched asserts in llvm runs. These were caused by the fact that exp10()
    is not accurate enough to be used in FFmtRead(). So we replace the call to
    exp10() with a lookup table. This should also be faster.
source/TestService.cpp:
  - Add unit test to assure that FFmtRead() meets our accuracy requirements.

10318 Directory Listing
Modified 7 years, 9 months ago
Sat Apr 11 15:32:04 2015 UTC
peter
Log:
source/service.cpp:
  - Add support for q == 1 in powpq().
source/TestVectorize.cpp:
source/TestService.cpp:
source/TestThirdparty.cpp:
  - Add unit tests for the vectorized reduction loops as well as various math functions.

10317 Directory Listing
Modified 7 years, 9 months ago
Sat Apr 11 13:40:04 2015 UTC
peter
Log:
source/species2.cpp:
  - Bug-fix: fix typo in species name.

10316 Directory Listing
Modified 7 years, 9 months ago
Sat Apr 11 09:41:49 2015 UTC
peter
Log:
source/vectorize_exp.cpp:
  - Fix compilation problem with the Solaris Studio compiler.

10315 Directory Listing
Modified 7 years, 9 months ago
Sat Apr 11 09:07:17 2015 UTC
peter
Log:
tsuite/auto/coll_coronal.in:
tsuite/auto/coll_t5.in:
tsuite/auto/coll_t6.in:
tsuite/auto/pdr_coolbb.in:
  - Fix botches due to r10314. This is a modification of the collisional DR
    suppression routine.

10314 Directory Listing
Modified 7 years, 9 months ago
Sat Apr 11 09:01:21 2015 UTC
peter
Log:
source/ion_recomb_Badnell.cpp:
  - Bug-fix: replace discontinuity in A_N by a gradual change as a function of Te.
    The functional form is arbitrarily chosen.

10313 Directory Listing
Modified 7 years, 9 months ago
Sat Apr 11 08:56:25 2015 UTC
peter
Log:
source/cddrive.cpp:
source/cont_ffun.cpp:
source/parse_commands.cpp:
source/parse_cosmic_rays.cpp:
source/parse_drive.cpp:
source/parse_stop.cpp:
source/prt_comment.cpp:
  - Clean up typecasts in and around exp10() calls.

10312 Directory Listing
Modified 7 years, 9 months ago
Fri Apr 10 17:50:26 2015 UTC
peter
Log:
source/cddefines.h:
source/thirdparty.h:
source/*.cpp:
  - Make single precision version of exp10() overloaded with the double precision
    version. This results in the expected behavior when using FLT_IS_DBL.
  - Replace many instances of pow(x,y) with more efficient alternatives.
  - Introduce new routine powpq(x) for calculating x to a rational power p/q.
  - Introduce cephes routines for calculating the incomplete gamma function.

10311 Directory Listing
Modified 7 years, 9 months ago
Wed Apr 8 12:10:40 2015 UTC
peter
Log:
data/cdms+jpl/convert_calpgm.cpp:
  - Prevent compiler warning with g++ 5.0.0.

10310 Directory Listing
Modified 7 years, 9 months ago
Wed Apr 8 11:39:09 2015 UTC
peter
Log:
source/TestVectorize.cpp:
  - Add unit tests for vectorized math routines.
source/vectorize_math.h:
  - Bug-fix: cap upper loop limit.
source/Makefile:
  - Remove cloudyconfig.h during regular clean.

10309 Directory Listing
Modified 7 years, 9 months ago
Tue Apr 7 13:40:00 2015 UTC
peter
Log:
source/*.cpp:
  - Replace all instances of pow(10,x) with exp10(x) (or exp10f(x) where appropriate).

10308 Directory Listing
Modified 7 years, 9 months ago
Tue Apr 7 12:52:00 2015 UTC
peter
Log:
source/capabilities.pl:
  - Disable AVX when using g++ versions prior to 4.6.0. These compilers appear
    to be producing sub-optimal code.
source/cddefines.h:
  - Include header immintrin.h when needed for AVX intrinsics.
  - Add new routines exp10() and exp10f() to replace pow(10.,x).
source/cpu.h:
  - Add new macro ALIGNED needed for the AVX intrinsics.
source/vectorize.h:
source/vectorize.cpp:
source/vectorize_exp.cpp:
source/vectorize_exp.h:
source/vectorize_math.h:
source/vectorize_reduce.cpp:
source/vectorize_reduce.h:
  - Reorganize existing code.
  - Add new vectorized routines for evaluating exp(), exp10(), expf() and exp10f().
    They are not used anywhere yet...

10307 Directory Listing
Modified 7 years, 10 months ago
Thu Apr 2 02:07:27 2015 UTC
peter
Log:
source/grains_qheat.cpp:
  - Bug-fix: avoid accessing uninitialized array elements when rfield.nPositive
    was increased after the last call to GrainDrive().
  - Bug-fix: protect call to rfield.ipointC() against out-of-bounds access.
source/prt_final.cpp:
  - Bug-fix: protect log10() function call against g++ compiler bug.
source/grains.cpp:
  - Add ASSERT.

10306 Directory Listing
Modified 7 years, 10 months ago
Wed Apr 1 01:06:08 2015 UTC
peter
Log:
source/grainvar.h:
source/grains.cpp:
  - Improve the initial estimate of the grain charge. This will speed up the search phase,
    but will have no impact deeper into the model. So mainly single-zone models will
    benefit from this change.
  - Remove obsolete variable gv.bin[nd]->dstpotsav and replace with gv.bin[nd]->ZloSave.
  - Bug-fix: make sure gv.bin[nd]->rate_h2_form_grains_ELRD is initialized in ctor. This
    prevents spurious FP exceptions.
source/grains_qheat.cpp:
  - Bug-fix: prevent FP exceptions when probability distribution is pathologically steep
    and qtemp[i] == qtemp[i+1].
source/mole_reactions.cpp:
  - Bug-fix: prevent spurious FP overflow when grain temperature is very low.
source/prt_final.cpp:
  - Bug-fix: prevent spurious FP exception due to inadequate protection against underflow
    to zero.
source/vectorize.h:
source/vectorize.cpp:
  - Add more reduction primitives.
docs/latex/hazy1/miscell.tex:
  - Fix outdated info regarding the SET NCHRG command.

10305 Directory Listing
Modified 7 years, 10 months ago
Tue Mar 31 07:19:42 2015 UTC
peter
Log:
source/vectorize.h:
source/vectorize.cpp:
  - Fix compilation errors when FLT_IS_DBL is in effect.

10304 Directory Listing
Modified 7 years, 10 months ago
Wed Mar 25 23:42:58 2015 UTC
peter
Log:
source/vectorize.h:
source/vectorize.cpp:
  - New code module with vectorization primitives, currently only routines for
    carrying out reduction loops.
source/Makefile:
  - Make sure that vectorize.cpp is compiled with more aggressive optimization
    options so that the reduction loops are vectorized.
  - Add option -march=native to g++ compilations for g++ versions 4.2.0 and later.
    This enables AVX instructions on supporting platforms.
source/cont_gammas.cpp:
source/grains.cpp:
  - Use the new vectorization primitives to speed up reduction loops.
source/container_classes.h:
  - Add new method ptr0() to the flex_arr class. This returns a pointer to the
    hypothetical element arr[0]. This pointer should be used when passing it to
    a routine that expects a pointer to an array like linint() or reduce_ab().
source/TestFlexArr.cpp:
  - Add unit test for the new prt0() method.
source/thirdparty_lapack.cpp:
  - Optimize some loops so that they vectorize by hoisting a common factor out
    of the loop.
  - Replace a hand-unrolled loop with a generic loop so that compiler can choose
    its own optimal unrolling factor.
source/grains.h:
source/grainvar.h:
source/grains.cpp:
source/grains_qheat.cpp:
  - Try speeding up some loops by hoisting common factors out of the loop.
  - Lots of general cleanup like removing unused code and combining declarations
    with the first use of a variable. No change in functionality.
  - Remove the obsolete routine HighestIonStage().
source/grains_mie.cpp:
  - Add check of the frequency mesh in an opacity file.
  - Initialize new array dstab1_x_anu[].
source/parse_table.cpp:
  - Exit if frequency mesh in the file doesn't match the one used by Cloudy.
source/capabilities.pl:
  - Bug-fix: fix test for g++ compiler.
  - Add test for support for the -march=native flag.
source/sys_llvm/Makefile.conf:
source/sys_mpi_llvm/Makefile.conf:
  - Replace flag -fno-math-errno with -ffast-math. This is possible now since
    we no longer trap FPEs with this compiler. So we may as well benefit from
    the additional optimizations...
  - Add flag -march=native so that we can use AVX instructions. This flag is
    supported at least since clang++ 2.8.
  - Make sure sys_mpi_llvm inherits the settings from sys_llvm.

10303 Directory Listing
Modified 7 years, 10 months ago
Thu Mar 19 18:33:51 2015 UTC
peter
Log:
source/grains_qheat.cpp:
  - Improve speed of the quantum heating code.

10302 Directory Listing
Modified 7 years, 10 months ago
Wed Mar 18 15:02:48 2015 UTC
peter
Log:
source/grains.cpp:
source/grains_qheat.cpp:
  - Optimize grain code by running loops up to rfield.nPositive.
  - Remove desperate attempt to converge probability distribution when initial
    step size is very small.
  - Optimize quantum heating code by moving code for determining p_max outside
    of TryDoubleStep().
  - Bug-fix: in TryDoubleStep() fix definitions of ulo and uhi and fix initial
    value for ipHi. This should assure continuous behavior of the interpolation
    of Phi[] both inside and outside the bounds of Phi[].
  - Improve accuracy of series expansion in log_integral().
  - Remove dead code.
source/rfield.cpp:
  - Modify routine setTrimming() so that it never inspects rfield.SummedCon[i]
    for i = rfield.nflux, guarantee that rfield.nPositive <= rfield.nflux.
source/stars.cpp:
  - Bug-fix: make sure that when an incoming SED has zero flux for a certain
    frequency, the interpolated SED also has zero flux for that frequency.
  - Update comment about compiler bug in g++.

10301 Directory Listing
Modified 7 years, 10 months ago
Mon Mar 16 22:33:42 2015 UTC
peter
Log:
tsuite/auto/grid_coronal_grains.in:
tsuite/auto/grid_coronal_grains.dat:
  - Fix typo.

10292 Directory Listing
Modified 7 years, 10 months ago
Fri Mar 13 17:27:11 2015 UTC
peter
Log:
source/iso_cool.cpp:
source/rt_diffuse.cpp:
  - Optimize iso_rad_rec_cooling_discrete() and RT_iso_integrate_RRC() further
    by hoisting loop invariants out of the loop and do a partial loop unroll.

10291 Directory Listing
Modified 7 years, 10 months ago
Fri Mar 13 13:24:22 2015 UTC
peter
Log:
source/iso_cool.cpp:
source/rt_diffuse.cpp:
  - Speed up code in iso_rad_rec_cooling_discrete() and RT_iso_integrate_RRC()
    by truncating the integral when the contributions from a single cell become
    too small. Tests show that using a relative cutoff of 1e-20 is a good
    compromise between speed and stability. Using 1e-15 would be slightly slower,
    most likely because convergence is already hampered (e.g., itrz goes up in
    blr_fp89). Using 1e-10 causes convergence failures and even an abort of one
    of the sims due to excess convergence failures.

10289 Directory Listing
Modified 7 years, 10 months ago
Thu Mar 12 10:13:30 2015 UTC
peter
Log:
source/mesh.h:
source/mesh.cpp:
  - Bug-fix: put call to p_SetupEdges() in the wrong place.
source/parse_table.cpp:
  - Fix compiler warning.

10288 Directory Listing
Modified 7 years, 10 months ago
Thu Mar 12 06:03:31 2015 UTC
gary
Log:
Document the optional keyword changing between f_nu and nu f_nu.
We want to move in the direction of the SED command being locally
defined in this directory, rather than Hazy, just as we do for
the stellar atmospheres.

10286 Directory Listing
Modified 7 years, 10 months ago
Wed Mar 11 17:21:07 2015 UTC
peter
Log:
source/mesh.h:
source/mesh.cpp:
source/sanity_check.cpp:
source/opacity.h:
source/cont_createpointers.cpp:
  - Add new routine ValidateEdges() that checks that the edges merged into the
    frequency mesh are consistent with the ionization edges used by Cloudy.

10285 Directory Listing
Modified 7 years, 10 months ago
Wed Mar 11 00:10:31 2015 UTC
peter
Log:
source/mesh.h:
  - Bug-fix: tweak the p_edges array to prevent problems when running with -DFLT_IS_DBL.
    The hydrogenic level energies are based on single precision ionization energies
    provided by t_ADfA::ph1(), so the edge energies hardwired into t_mesh should be
    lower by more than a relative factor FLT_EPSILON rather than DBL_EPSILON as was
    used in the old code.
  - Adjust O III 1D edge energy to the one used in the code. Add OIII 1S edge.
source/stars.cpp:
  - Add detailed check of the frequency mesh stored in the binary SED files.
  - Add work-around for compiler bug in g++ 4.8.2 on RHEL/CentOS 7.0.
source/prt_final.cpp:
  - Fix typo.
data/*.opc:
  - Recompile the grain opacity files on the new frequency mesh.
tsuite/auto/blr_f92.in:
tsuite/auto/pdr_coolbb.in:
tsuite/auto/pn_paris.in:
  - Fix a few (near) botches.

10284 Directory Listing
Modified 7 years, 10 months ago
Mon Mar 9 23:34:49 2015 UTC
rjrw
Log:
Move first level of indexing of rfield.conEmitLocal[][] out of loops

10283 Directory Listing
Modified 7 years, 10 months ago
Mon Mar 9 18:53:18 2015 UTC
peter
Log:
source/rfield.h:
source/cont_createmesh.cpp:
source/cont_ffun.cpp:
source/cont_setintensity.cpp:
source/init_defaults_preparse.cpp:
source/parse_interp.cpp:
source/parse_table.cpp:
source/stars.cpp:
  - Remove the last instances of NCELL. This creates more freedom to modify the
    frequency mesh resolution.
  - Modify the code for reading interpolated SEDs such that arbitrary size tables
    can be provided by the user (most notably with the INTERPOLATE command).
  - Simplify the code in ffun1().
docs/latex/hazy1/cont-shp.tex:
  - Document the change.
tsuite/auto/limit_lte_he1_nomole_ste_nocoll2.in:
  - Enable monitoring the H-like departure coefficients.
tsuite/auto/run_sequence.pl:
  - Tune the run sequence.

10282 Directory Listing
Modified 7 years, 10 months ago
Mon Mar 9 16:20:29 2015 UTC
peter
Log:
source/opacity_createall.cpp:
  - Protect statements about resizing the opacity stack prt.lgPrintTime so that
    they don't cause spurious failures in the repeatability tests.

10281 Directory Listing
Modified 7 years, 11 months ago
Sat Mar 7 19:12:01 2015 UTC
peter
Log:
Merge the newmesh branch to the trunk.

The newmesh branch creates a new class for the frequency mesh. This cleans up the
frequency mesh code and makes sure that all frequency mesh related parameters are
internally consistent. In the new class the edges of the cells are set up first and
anu() is defined as the midpoint between the edges. The code for fiddling the
frequencies using weighting with the incident radiation field has been deleted.

10269 Directory Listing
Modified 7 years, 11 months ago
Thu Mar 5 01:44:31 2015 UTC
peter
Log:
docs/latex/common/bibliography2.bib:
docs/latex/hazy1/miscell.tex:
  - Update some references.

10240 Directory Listing
Modified 7 years, 11 months ago
Sat Feb 21 18:48:12 2015 UTC
gary
Log:
add comment on postion of OTS fields
change print of insanity to call to TotalInsanity
10236 Directory Listing
Modified 7 years, 11 months ago
Sat Feb 21 10:16:58 2015 UTC
gary
Log:
sequential keyword needed on grid - produced
out of memory abort on radegund
10233 Directory Listing
Modified 7 years, 11 months ago
Thu Feb 19 14:17:18 2015 UTC
gary
Log:
minor updates to plot, readme for programs
10232 Directory Listing
Modified 7 years, 11 months ago
Thu Feb 19 14:13:25 2015 UTC
gary
Log:
compare same cooling function with default
setup, and large models.  This gives a sense of the error
introduced by the default assumptions.
10231 Directory Listing
Modified 7 years, 11 months ago
Thu Feb 19 14:08:16 2015 UTC
gary
Log:
add two grids that match existing coronal
tests, except that the large H2 model is turned on.  This will
document the differences between the full treatment and the
universal cooling formula adopted by default.
10228 Directory Listing
Modified 7 years, 11 months ago
Wed Feb 18 21:17:49 2015 UTC
marios
Log:
Replace code that generates species labels with calls to makeChemical().

10227 Directory Listing
Modified 7 years, 11 months ago
Wed Feb 18 17:51:04 2015 UTC
marios
Log:
Another replacement of code that generates line labels with chIonLbl().
10225 Directory Listing
Modified 7 years, 11 months ago
Wed Feb 18 17:22:52 2015 UTC
marios
Log:
Correct DEBUG_ENTRY for TransitionProxy::chLabel()
10224 Directory Listing
Modified 7 years, 11 months ago
Wed Feb 18 17:18:44 2015 UTC
marios
Log:
Remove obsolete comments from chIonLbl().
10223 Directory Listing
Modified 7 years, 11 months ago
Wed Feb 18 16:06:12 2015 UTC
marios
Log:
Replace line label construction with calls to chIonLbl().

10219 Directory Listing
Modified 7 years, 11 months ago
Tue Feb 17 22:53:17 2015 UTC
rjrw
Log:
Simplify inline coding for fixits

10209 Directory Listing
Modified 7 years, 11 months ago
Mon Feb 16 12:51:23 2015 UTC
gary
Log:
more precise statement
10187 Directory Listing
Modified 7 years, 11 months ago
Tue Feb 10 10:14:35 2015 UTC
peter
Log:
tsuite/programs/collcool/collcool.cpp:
tsuite/programs/collion/collion.cpp:
tsuite/programs/hazy_coolingcurve/hazy_coolingcurve.cpp:
tsuite/programs/hazy_kmt/hazy_kmt.cpp:
tsuite/programs/hizlte/hizlte.cpp:
tsuite/programs/mpi/mpi.cpp:
tsuite/programs/vary_nete/vary_nete.cpp:
tsuite/programs/varyn/varyn.cpp:
  - Remove obsolete test for NULL pointer.

10184 Directory Listing
Modified 7 years, 11 months ago
Mon Feb 9 18:17:56 2015 UTC
peter
Log:
source/Makefile:
  - Add phony targets echo-cxx and echo-cxxflags.
tsuite/programs/run_programs.pl:
  - Fix script by polling make for the correct compiler and flags.

10183 Directory Listing
Modified 7 years, 11 months ago
Mon Feb 9 17:42:28 2015 UTC
peter
Log:
source/optimize_func.cpp:
  - Fix alignment in output header.
tsuite/mpi/optimize_phymir.in:
  - Fix line IDs and wavelengths.
  - Update line strengths to the current Cloudy prediction.

10180 Directory Listing
Modified 7 years, 11 months ago
Mon Feb 9 11:56:32 2015 UTC
peter
Log:
tsuite/programs/collcool/collcool.cpp
tsuite/programs/collion/collion.cpp
tsuite/programs/hazy_coolingcurve/hazy_coolingcurve.cpp
tsuite/programs/hazy_kmt/hazy_kmt.cpp
tsuite/programs/hizlte/hizlte.cpp
tsuite/programs/mpi/mpi.cpp
tsuite/programs/vary_nete/vary_nete.cpp
tsuite/programs/varyn/varyn.cpp
  - Fix compilation errors due to the use of fopen().
tsuite/programs/template.cpp
  - Add example of how to open an output file correctly.

10179 Directory Listing
Modified 7 years, 11 months ago
Mon Feb 9 09:40:10 2015 UTC
gary
Log:
mv content htm to txt
10178 Directory Listing
Modified 7 years, 11 months ago
Mon Feb 9 09:32:17 2015 UTC
gary
Log:
move readme_template content to plain text file
10177 Directory Listing
Modified 7 years, 11 months ago
Mon Feb 9 09:29:22 2015 UTC
gary
Log:
more useful name for readme
10176 Directory Listing
Modified 7 years, 11 months ago
Mon Feb 9 09:28:07 2015 UTC
gary
Log:
update copyright year
10171 Directory Listing
Modified 7 years, 11 months ago
Sat Feb 7 04:37:46 2015 UTC
marios
Log:
drop accidentally added flag (-Wpedantic) from Makefile
10170 Directory Listing
Modified 7 years, 11 months ago
Sat Feb 7 03:19:18 2015 UTC
marios
Log:
save_linedata.cpp -- moved header into separate function
10169 Directory Listing
Modified 7 years, 11 months ago
Fri Feb 6 11:41:06 2015 UTC
gary
Log:
add debug print
10168 Directory Listing
Modified 8 years ago
Thu Feb 5 14:10:17 2015 UTC
gary
Log:
update copyright year.  

There must be a better way of doing this - a macro, or flag
within svn? 
10135 Directory Listing
Modified 8 years ago
Fri Jan 30 07:52:05 2015 UTC
rjrw
Log:
One more old-style species command

10134 Directory Listing
Modified 8 years ago
Thu Jan 29 23:04:21 2015 UTC
rjrw
Log:
species "nnnn" levels=all

10133 Directory Listing
Modified 8 years ago
Thu Jan 29 22:57:17 2015 UTC
rjrw
Log:
Add include guard and consistency-include for cool_eval.h

10130 Directory Listing
Modified 8 years ago
Thu Jan 29 22:21:00 2015 UTC
rjrw
Log:
Create new file to group the species command parser and the
routines which interpret its options

10129 Directory Listing
Modified 8 years ago
Thu Jan 29 22:01:04 2015 UTC
rjrw
Log:
Process species command options in order, to ensure consistent
behaviour in case of overlap

10128 Directory Listing
Modified 8 years ago
Thu Jan 29 20:46:11 2015 UTC
rjrw
Log:
Document "species 'name' lte" and the syntax-directed parsing

10127 Directory Listing
Modified 8 years ago
Thu Jan 29 20:40:25 2015 UTC
rjrw
Log:
Syntax-directed parsing of "species 'xxxx'" options

10124 Directory Listing
Modified 8 years ago
Thu Jan 29 07:39:56 2015 UTC
rjrw
Log:
species "xxx" LTE command

10123 Directory Listing
Modified 8 years ago
Thu Jan 29 07:15:50 2015 UTC
rjrw
Log:
Move command option type into parser infrastructure

10122 Directory Listing
Modified 8 years ago
Thu Jan 29 06:48:02 2015 UTC
rjrw
Log:
Fix a couple of issues which caused crashes when 'species "xxx" levels' was
implemented

10121 Directory Listing
Modified 8 years ago
Wed Jan 28 23:02:35 2015 UTC
rjrw
Log:
Document initial cases of SPECIES command

10120 Directory Listing
Modified 8 years ago
Wed Jan 28 22:45:43 2015 UTC
rjrw
Log:
Implement SPECIES "xxx" LEVELS nnn

10119 Directory Listing
Modified 8 years ago
Wed Jan 28 22:25:49 2015 UTC
rjrw
Log:
More steps towards SPECIES "xxx" LEVELS

10116 Directory Listing
Modified 8 years ago
Wed Jan 28 08:06:46 2015 UTC
rjrw
Log:
Implement "species XXX off" to disable individual molecules in chemistry

10115 Directory Listing
Modified 8 years ago
Tue Jan 27 21:06:18 2015 UTC
rjrw
Log:
Start to set up hooks for "species 'xxx' levels nnn" command

Awkward to implement, as the slots the data needs to be put in aren't
yet defined when the parser is active.

10113 Directory Listing
Modified 8 years ago
Fri Jan 23 21:25:20 2015 UTC
rjrw
Log:
Allow ParseSpecies to intercept string arguments

10111 Directory Listing
Modified 8 years ago
Thu Jan 22 20:01:23 2015 UTC
marios
Log:
Clarify latex table entry for Allen abundances
10110 Directory Listing
Modified 8 years ago
Thu Jan 22 19:42:39 2015 UTC
marios
Log:
Implement and document command 'abundances allen'.
10108 Directory Listing
Modified 8 years ago
Thu Jan 22 17:23:01 2015 UTC
marios
Log:
Added abundance table of Allen 1973, 'Astrophysical Quantities'
10106 Directory Listing
Modified 8 years ago
Mon Jan 19 01:07:31 2015 UTC
gary
Log:
confirm that we handle case with no incident SED
10105 Directory Listing
Modified 8 years ago
Sun Jan 18 17:49:47 2015 UTC
rjrw
Log:
Add "table read scale" as a command specifying shape and intensity

10104 Directory Listing
Modified 8 years ago
Sun Jan 18 10:31:34 2015 UTC
rjrw
Log:
Document "table read scale"

10103 Directory Listing
Modified 8 years ago
Sun Jan 18 10:11:18 2015 UTC
rjrw
Log:
Correct and test "table read scale" option.

Needed to generalize the handling of func_trans_read slightly, to
handle case with a second dependency

10102 Directory Listing
Modified 8 years ago
Sat Jan 17 20:56:24 2015 UTC
rjrw
Log:
Start towards implementing "table read scale x", #301 refers

-- needs to be tested and documented, so currently disabled
-- remove duplicated setting of radius.Radius in a couple of places

10101 Directory Listing
Modified 8 years ago
Sat Jan 17 18:36:19 2015 UTC
rjrw
Log:
Add comment about late validation of table read mesh; merge setting
of default values for tFluxLog & tslop

10100 Directory Listing
Modified 8 years ago
Sat Jan 17 18:12:16 2015 UTC
rjrw
Log:
rfield.tslop[] isn't actually used by "table read", as of r2631

remove misleading comment saying that it is, and set the whole array
to NaN to ensure this is the case.

10097 Directory Listing
Modified 8 years ago
Fri Jan 16 08:15:35 2015 UTC
rjrw
Log:
Start to tease apart "database" and "species" commands;
prevent string filename arguments from confusing other
database options (unlikely failure mode, but was previously
possible)

10096 Directory Listing
Modified 8 years ago
Fri Jan 16 07:34:17 2015 UTC
rjrw
Log:
species -> database in slow

10095 Directory Listing
Modified 8 years ago
Fri Jan 16 07:00:55 2015 UTC
rjrw
Log:
species -> database in auto suite

10094 Directory Listing
Modified 8 years ago
Thu Jan 15 23:56:03 2015 UTC
rjrw
Log:
species -> database in documentation

10093 Directory Listing
Modified 8 years ago
Thu Jan 15 23:40:56 2015 UTC
rjrw
Log:
Provide "database" as a synonym for "species", as step towards
generating a more uniform means of changing individual species
properties

10090 Directory Listing
Modified 8 years ago
Thu Jan 15 07:58:36 2015 UTC
rjrw
Log:
Specify Jeans mass scaling in terms of fundamental constants
not quoted number

10089 Directory Listing
Modified 8 years ago
Wed Jan 14 21:53:46 2015 UTC
rjrw
Log:
Enable fix to FeII damping

10088 Directory Listing
Modified 8 years ago
Tue Jan 13 22:21:25 2015 UTC
rjrw
Log:
Not-yet-enabled code to fix FeII line damping

10087 Directory Listing
Modified 8 years ago
Mon Jan 12 21:38:58 2015 UTC
rjrw
Log:
Absolute error test for zero quantity

10085 Directory Listing
Modified 8 years ago
Sun Jan 11 20:47:48 2015 UTC
rjrw
Log:
*all meta-species; move genericState into its own module

10084 Directory Listing
Modified 8 years ago
Sun Jan 11 19:06:14 2015 UTC
rjrw
Log:
Fix a couple of places the topmost level 1 line was being missed

10083 Directory Listing
Modified 8 years ago
Sun Jan 11 17:46:04 2015 UTC
rjrw
Log:
Small clarification of level 2 data input logic

10082 Directory Listing
Modified 8 years ago
Sun Jan 11 17:39:40 2015 UTC
rjrw
Log:
nUTA -> UTALines.size()

10081 Directory Listing
Modified 8 years ago
Sun Jan 11 17:28:47 2015 UTC
rjrw
Log:
nHFLines -> HFLines.size()

10080 Directory Listing
Modified 8 years ago
Sun Jan 11 16:12:40 2015 UTC
rjrw
Log:
Allow temperature to be used as a column in "save species"

10079 Directory Listing
Modified 8 years ago
Sun Jan 11 15:48:36 2015 UTC
rjrw
Log:
Special case syntax to allow other quantities to be saved

10078 Directory Listing
Modified 8 years ago
Sun Jan 11 15:07:26 2015 UTC
rjrw
Log:
Complete state labels for diatoms

10077 Directory Listing
Modified 8 years ago
Sun Jan 11 13:15:35 2015 UTC
rjrw
Log:
More details about save species, and clear unbalanced bracket error

10076 Directory Listing
Modified 8 years ago
Sun Jan 11 12:02:26 2015 UTC
rjrw
Log:
Add hook back from element/ion representation to corresponding
molecules

10075 Directory Listing
Modified 8 years ago
Sun Jan 11 11:29:26 2015 UTC
rjrw
Log:
Allow comments within save species list

10074 Directory Listing
Modified 8 years ago
Sun Jan 11 11:24:40 2015 UTC
gary
Log:
clarify and cross reference some options on species command
10073 Directory Listing
Modified 8 years ago
Sun Jan 11 11:05:53 2015 UTC
rjrw
Log:
Normalize indentation in save_average.cpp

10072 Directory Listing
Modified 8 years ago
Sun Jan 11 10:59:05 2015 UTC
rjrw
Log:
Remove "save column density" in favour of "save species column"

10071 Directory Listing
Modified 8 years ago
Sun Jan 11 10:46:00 2015 UTC
rjrw
Log:
Make requiring a list the default for save species

10070 Directory Listing
Modified 8 years ago
Sun Jan 11 10:02:08 2015 UTC
rjrw
Log:
And move SaveColumns to file-static routine in save_do.cpp

10069 Directory Listing
Modified 8 years ago
Sun Jan 11 09:51:45 2015 UTC
rjrw
Log:
Break apart PrtColumns routine

10068 Directory Listing
Modified 8 years ago
Sat Jan 10 23:54:20 2015 UTC
rjrw
Log:
Fix tabbing and don't lose the early items of the save species list...

10067 Directory Listing
Modified 8 years ago
Sat Jan 10 23:27:10 2015 UTC
rjrw
Log:
save species populations -> save species densities, as this seems
to make more sense as things now are; some documentation updates

10066 Directory Listing
Modified 8 years ago
Sat Jan 10 19:49:25 2015 UTC
rjrw
Log:
Consistent handling of the save species levels command

10065 Directory Listing
Modified 8 years ago
Sat Jan 10 19:38:24 2015 UTC
rjrw
Log:
Fix typo

10064 Directory Listing
Modified 8 years ago
Sat Jan 10 19:18:21 2015 UTC
rjrw
Log:
Move to slice-indexing of species

10063 Directory Listing
Modified 8 years ago
Sat Jan 10 16:40:53 2015 UTC
rjrw
Log:
Re-order save species output to one row per zone

10062 Directory Listing
Modified 8 years ago
Sat Jan 10 16:23:48 2015 UTC
rjrw
Log:
Refactor SaveSpeciesOne to use single loop to do all output cases

10061 Directory Listing
Modified 8 years ago
Sat Jan 10 12:16:04 2015 UTC
gary
Log:
one edit too many - return density to original value
10060 Directory Listing
Modified 8 years ago
Sat Jan 10 11:20:35 2015 UTC
rjrw
Log:
Fix labels for molecular transitions

10057 Directory Listing
Modified 8 years ago
Fri Jan 9 15:55:39 2015 UTC
gary
Log:
report cooling, rename H2 column density output
10055 Directory Listing
Modified 8 years ago
Fri Jan 9 10:25:59 2015 UTC
gary
Log:
give examples of saving state specific quantities
10053 Directory Listing
Modified 8 years ago
Wed Jan 7 08:04:28 2015 UTC
rjrw
Log:
Add comment on level indexed access in save species

10051 Directory Listing
Modified 8 years ago
Tue Jan 6 23:46:41 2015 UTC
rjrw
Log:
Revert 10050 -- the pimpl structure of the TransitionList means this
actually has no effect.

10050 Directory Listing
Modified 8 years ago
Tue Jan 6 23:27:21 2015 UTC
rjrw
Log:
AllTransitions only needs to be a collection of pointers, not a
deep copy

10049 Directory Listing
Modified 8 years ago
Tue Jan 6 22:48:07 2015 UTC
rjrw
Log:
Fix labels in save_species output, by making dBaseStates label into
chemical species, not spectroscopic one

10046 Directory Listing
Modified 8 years ago
Tue Jan 6 13:05:38 2015 UTC
gary
Log:
description of LAMDA versioning
10044 Directory Listing
Modified 8 years, 1 month ago
Sun Jan 4 22:34:44 2015 UTC
rjrw
Log:
Remove quantumState chLabel field now generated on-the-fly

10043 Directory Listing
Modified 8 years, 1 month ago
Sun Jan 4 20:06:20 2015 UTC
rjrw
Log:
Add level index to qState label.  Some still come out in
spectroscopic notation.

10042 Directory Listing
Modified 8 years, 1 month ago
Sun Jan 4 19:13:11 2015 UTC
rjrw
Log:
Use higher-level label where appropriate

10040 Directory Listing
Modified 8 years, 1 month ago
Sun Jan 4 14:43:53 2015 UTC
peter
Log:
source/quantumstate.cpp:
  - Fix compiler warning about mismatched type in print statement.

10038 Directory Listing
Modified 8 years, 1 month ago
Sun Jan 4 13:44:34 2015 UTC
gary
Log:
major reorganization of paper to improve logical order
move table to appendix
10036 Directory Listing
Modified 8 years, 1 month ago
Sun Jan 4 12:35:30 2015 UTC
rjrw
Log:
Add reference data for monotonic interpolation

10035 Directory Listing
Modified 8 years, 1 month ago
Sat Jan 3 20:24:21 2015 UTC
rjrw
Log:
Need to protect against underflow

10034 Directory Listing
Modified 8 years, 1 month ago
Sat Jan 3 20:13:13 2015 UTC
rjrw
Log:
Move to explicit setter for level label setters

10033 Directory Listing
Modified 8 years, 1 month ago
Sat Jan 3 18:52:13 2015 UTC
rjrw
Log:
Add label field to qList

10032 Directory Listing
Modified 8 years, 1 month ago
Sat Jan 3 17:31:37 2015 UTC
rjrw
Log:
Use quotes to protect level indices

10031 Directory Listing
Modified 8 years, 1 month ago
Sat Jan 3 17:03:27 2015 UTC
rjrw
Log:
Exercise "save species populations list"

10030 Directory Listing
Modified 8 years, 1 month ago
Sat Jan 3 16:56:26 2015 UTC
rjrw
Log:
Deal with one more place where a quantumState would confuse
save_species

10027 Directory Listing
Modified 8 years, 1 month ago
Sat Jan 3 16:12:58 2015 UTC
rjrw
Log:
Search and generate species properties via findGeneric, should
now allow access to level data

10026 Directory Listing
Modified 8 years, 1 month ago
Sat Jan 3 15:52:29 2015 UTC
rjrw
Log:
Do more of save_species via genericState interface

10025 Directory Listing
Modified 8 years, 1 month ago
Sat Jan 3 15:35:38 2015 UTC
rjrw
Log:
Start to get save species information via genericState
interface

10024 Directory Listing
Modified 8 years, 1 month ago
Sat Jan 3 15:22:25 2015 UTC
rjrw
Log:
Use genericState to tunnel molecule pointer in save_species.cpp

10022 Directory Listing
Modified 8 years, 1 month ago
Sat Jan 3 14:21:27 2015 UTC
rjrw
Log:
Provide hook from zone-based to global molecule data

10021 Directory Listing
Modified 8 years, 1 month ago
Sat Jan 3 13:33:26 2015 UTC
rjrw
Log:
Fix botched Hbeta monitor

10020 Directory Listing
Modified 8 years, 1 month ago
Sat Jan 3 11:39:33 2015 UTC
rjrw
Log:
And fix the fix for square brackets (had permed match and
replacement...)

10019 Directory Listing
Modified 8 years, 1 month ago
Sat Jan 3 11:37:16 2015 UTC
rjrw
Log:
Allow '[' and ']' level accessors in monitors

10018 Directory Listing
Modified 8 years, 1 month ago
Sat Jan 3 11:15:36 2015 UTC
gary
Log:
some fixes
10017 Directory Listing
Modified 8 years, 1 month ago
Sat Jan 3 10:12:33 2015 UTC
rjrw
Log:
Reinstate missing '*'

10016 Directory Listing
Modified 8 years, 1 month ago
Sat Jan 3 10:03:39 2015 UTC
rjrw
Log:
Roll back over-eager error checking

10015 Directory Listing
Modified 8 years, 1 month ago
Fri Jan 2 20:04:32 2015 UTC
rjrw
Log:
Add (but not enable) some more width-based blend definitions

10014 Directory Listing
Modified 8 years, 1 month ago
Fri Jan 2 18:47:05 2015 UTC
rjrw
Log:
Remove save string vector which can be shared with other
variants

10013 Directory Listing
Modified 8 years, 1 month ago
Fri Jan 2 18:23:10 2015 UTC
rjrw
Log:
Generate "save element" output from header strings

10012 Directory Listing
Modified 8 years, 1 month ago
Fri Jan 2 18:03:13 2015 UTC
rjrw
Log:
Extract generalized state query function into global scope

10011 Directory Listing
Modified 8 years, 1 month ago
Fri Jan 2 17:32:06 2015 UTC
rjrw
Log:
Extract 'clean' variant of cdColm functionality

10010 Directory Listing
Modified 8 years, 1 month ago
Fri Jan 2 16:57:36 2015 UTC
rjrw
Log:
Remove hand-coded pump diagnostic which duplicates value 
generated automatically by iso-sequence

10009 Directory Listing
Modified 8 years, 1 month ago
Fri Jan 2 16:48:34 2015 UTC
rjrw
Log:
Start to move "save element" towards using "save species" infrastructure

10008 Directory Listing
Modified 8 years, 1 month ago
Fri Jan 2 15:57:18 2015 UTC
rjrw
Log:
Improve cdColm error reportage

10007 Directory Listing
Modified 8 years, 1 month ago
Fri Jan 2 15:46:29 2015 UTC
rjrw
Log:
Handle other invalid level index case (too small)

10006 Directory Listing
Modified 8 years, 1 month ago
Fri Jan 2 11:26:44 2015 UTC
rjrw
Log:
Catch some more edge cases in spectrum normalization

10005 Directory Listing
Modified 8 years, 1 month ago
Fri Jan 2 11:15:03 2015 UTC
rjrw
Log:
Also normalize quoted spectra

10004 Directory Listing
Modified 8 years, 1 month ago
Fri Jan 2 11:13:36 2015 UTC
rjrw
Log:
Revert changes which came along inadvertently in r10002

10003 Directory Listing
Modified 8 years, 1 month ago
Fri Jan 2 11:09:10 2015 UTC
rjrw
Log:
Normalize common input error, with warning

10002 Directory Listing
Modified 8 years, 1 month ago
Fri Jan 2 10:39:32 2015 UTC
rjrw
Log:
Convert to more flexible [] form for level indexing of
species column densities

9996 Directory Listing
Modified 8 years, 1 month ago
Wed Dec 31 16:57:26 2014 UTC
gary
Log:
improve description of species

rename SAVE DATA SOURCES to SAVE DATA SOURCES

the test case that uses it
9995 Directory Listing
Modified 8 years, 1 month ago
Wed Dec 31 16:56:59 2014 UTC
gary
Log:
improve description of species

rename SAVE DATA SOURCES to SAVE DATA SOURCES
9994 Directory Listing
Modified 8 years, 1 month ago
Wed Dec 31 16:56:40 2014 UTC
gary
Log:
improve description of species

rename SAVE DATA SOURCES to SAVE DATA SOURCES
9993 Directory Listing
Modified 8 years, 1 month ago
Wed Dec 31 16:42:02 2014 UTC
gary
Log:
improve description of species

rename SAVE DATA SOURCES to SAVE DATA SOURCES
9989 Directory Listing
Modified 8 years, 1 month ago
Tue Dec 30 17:14:19 2014 UTC
rjrw
Log:
svn merge --reintegrate ^/branches/labels

9987 Directory Listing
Modified 8 years, 1 month ago
Tue Dec 30 08:57:34 2014 UTC
gary
Log:
one missed atom -> species
9986 Directory Listing
Modified 8 years, 1 month ago
Sun Dec 28 18:31:34 2014 UTC
gary
Log:
further adjustment, going to lower temperature,
including StoutAll.ini
The problem is that NIST are missing forbidden transtions for low
levels of these poorly studied species.  
9985 Directory Listing
Modified 8 years, 1 month ago
Sun Dec 28 17:28:27 2014 UTC
gary
Log:
tests over a wide range of ionization parameter
and gas kinetic temperature show that these four Stout baseline models
cause ill conditioned matrix and negative level populations.  This
is due to lack of TP data in NIST, which causes very small CS from
our g-bar approximation.  At low temperatures the level above the
new limit has no connection to low levels, hence the numerical problems.
9984 Directory Listing
Modified 8 years, 1 month ago
Tue Dec 23 19:38:17 2014 UTC
peter
Log:
source/prt_lines_hydro.cpp:
  - Bug-fix: prevent FPE with Solaris Studio 12.4 in the test case limit_compton_hi_t.in.

9979 Directory Listing
Modified 8 years, 1 month ago
Sun Dec 21 21:03:13 2014 UTC
rjrw
Log:
Make column width printout covariant with NCHLAB

9978 Directory Listing
Modified 8 years, 1 month ago
Sun Dec 21 15:41:03 2014 UTC
rjrw
Log:
Rationalize excited state access so far as is possible within
4 character limit

9977 Directory Listing
Modified 8 years, 1 month ago
Sun Dec 21 10:40:36 2014 UTC
rjrw
Log:
Catch failure mode when He is disabled (shows up in chianti_fe_cool)

9976 Directory Listing
Modified 8 years, 1 month ago
Sat Dec 20 19:13:26 2014 UTC
rjrw
Log:
Remove an unnecessary value, in favour of standard property

9975 Directory Listing
Modified 8 years, 1 month ago
Sat Dec 20 15:04:10 2014 UTC
rjrw
Log:
Print something in the fine structure columns of
"save element carbon" and "save element oxygen"

9974 Directory Listing
Modified 8 years, 1 month ago
Sat Dec 20 12:52:53 2014 UTC
rjrw
Log:
Patch over excited state column density printout with something
which looks plausible by comparison with old results.

This needs to be checked, and is intrinsically fragile.

9973 Directory Listing
Modified 8 years, 1 month ago
Sat Dec 20 07:48:39 2014 UTC
gary
Log:
Remove species with energy levels but no transition probabilities.  These were added as part of the baseline data NIST harvest.  Baseline data are based soley on NIST, have no collision strengths, but do have energies and TPs.  It is not possible to predict spectra for these species with the current data set.
9971 Directory Listing
Modified 8 years, 1 month ago
Fri Dec 19 19:44:06 2014 UTC
rjrw
Log:
Emergent line intensities were also shot (#309, #310)

9970 Directory Listing
Modified 8 years, 1 month ago
Fri Dec 19 16:33:33 2014 UTC
gary
Log:
Cites to three very recent papers on solar abundances for Z >= Ne.  

Final solar will be updated when this series of papers is complete (C, N, O and the light elements are not yet ready).
9969 Directory Listing
Modified 8 years, 1 month ago
Fri Dec 19 15:37:15 2014 UTC
rjrw
Log:
Enable revised line search mode -- passes test suite, see
how it works in practice...

9968 Directory Listing
Modified 8 years, 1 month ago
Fri Dec 19 10:33:24 2014 UTC
rjrw
Log:
Set up infrastructure for hopefully less fragile means of
defining static blends

9967 Directory Listing
Modified 8 years, 1 month ago
Fri Dec 19 09:42:44 2014 UTC
rjrw
Log:
Improvements to diagnostics and matching tests of
revised line search

9965 Directory Listing
Modified 8 years, 1 month ago
Thu Dec 18 17:10:01 2014 UTC
gary
Log:
the 7.1.4 update of Chianti
9964 Directory Listing
Modified 8 years, 1 month ago
Thu Dec 18 00:00:52 2014 UTC
rjrw
Log:
Handle case of no lines in narrow wavelength band better, with
comments to explain

9963 Directory Listing
Modified 8 years, 1 month ago
Wed Dec 17 23:38:04 2014 UTC
rjrw
Log:
Improvements to adapted line search algorithm

9960 Directory Listing
Modified 8 years, 1 month ago
Tue Dec 16 09:57:38 2014 UTC
gary
Log:
Warn that convergence problems are likely
if calculation stops due to lowest temperture
9959 Directory Listing
Modified 8 years, 1 month ago
Tue Dec 16 09:24:37 2014 UTC
gary
Log:
two suggestions in response to confused user
9958 Directory Listing
Modified 8 years, 1 month ago
Tue Dec 16 07:36:49 2014 UTC
gary
Log:
Make test for continuum renormalization factors double.
The factor itself was changed to double some time ago, but the test is on the
range of a float.  

User reported a trip on the test for a Starburst 99 SED in which the final
radiation field was reasonable, but the original SED was very intense,
while the scale factor was correspondingly small.  
9957 Directory Listing
Modified 8 years, 1 month ago
Mon Dec 15 19:25:16 2014 UTC
marios
Log:
ticket #281 -- move sanity check on radius from ParseCoronal to ParseCommands
9952 Directory Listing
Modified 8 years, 1 month ago
Sun Dec 14 18:10:08 2014 UTC
gary
Log:
svn merge --reintegrate  ^/branches/s3dr
9948 Directory Listing
Modified 8 years, 1 month ago
Fri Dec 12 17:09:12 2014 UTC
peter
Log:
source/*.cpp:
  - Fix many DEBUG_ENTRY() statements so that they have a uniform syntax. Most
    importantly remove spaces in front of the routine name.

9947 Directory Listing
Modified 8 years, 1 month ago
Fri Dec 12 16:37:08 2014 UTC
peter
Log:
source/cpu.cpp:
  - Generate warning when multiple files with the same name are found along the
    search path. Apart from this there is no change in functionality.

9946 Directory Listing
Modified 8 years, 1 month ago
Fri Dec 12 12:30:36 2014 UTC
gary
Log:
this assert had been part of the code for some time, but there is no
reason for it.  In principle the continuum can maser, and if levels
are are populated according to statistical weight the opacity will be zero.


The assert is likely a hold over from times where opacity expressions were poorly behaved.
9945 Directory Listing
Modified 8 years, 1 month ago
Thu Dec 11 20:33:01 2014 UTC
rjrw
Log:
No need to bother the heap with constant-size local vectors

9944 Directory Listing
Modified 8 years, 1 month ago
Thu Dec 11 18:27:38 2014 UTC
gary
Log:
update primordial He/H to Planck concordance
9943 Directory Listing
Modified 8 years, 1 month ago
Tue Dec 9 18:41:44 2014 UTC
rjrw
Log:
Remove needless variable increment

9942 Directory Listing
Modified 8 years, 1 month ago
Tue Dec 9 14:40:59 2014 UTC
peter
Log:
data/ac1-amcarb.rfi:
data/be1-amcarb.rfi:
  - Fix erroneous beta=2 extension of the laboratory refractive index data
    towards long wavelengths by removing that part of the file. For AC1
    amorphous carbon simply removing the extension was sufficient to get a
    plausible beta=1 slope. For BE1 amorphous carbon more points had to be
    removed because the longest wavelength laboratory data already showed a
    gradual change from beta=1 to higher values. A better fix would be to use
    data from Zubko et al. (1996) MNRAS 282, 1321, but these are currently not
    ready for use in Cloudy.

9941 Directory Listing
Modified 8 years, 1 month ago
Tue Dec 9 12:22:49 2014 UTC
peter
Log:
source/stars.cpp:
  - Allow comments to precede the data in a .ascii file.
  - Remove overzealous check of the first parameter on the TABLE STAR command.
source/parse_table.cpp:
  - Remove option to interpret the first parameter of the TABLE STAR command as
    a log if it is <= 10. This hampers using the TABLE STAR command for grids as
    a function of redshift, as e.g. in Haardt & Madau (2012).
  - Match all 5 characters of LINES in the TABLE LINES command to avoid confusion
    with the LINEAR keyword.
docs/latex/hazy1/cont-shp.tex:
docs/latex/hazy1/miscell.tex:
docs/latex/hazy1/vanhoof_atmosphere_grids.tex:
  - Document these changes.