/[cloudy]/tags/release/c07.02.02/source
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Sticky Revision:

Revision Tasks Age Author
2149 Directory Listing
Modified 14 years ago
Thu Jul 3 12:49:34 2008 UTC
peter
Log:
Create 3rd release tag - fixed runall.pl so that it runs the full auto test suite.

1974 Directory Listing
Modified 14 years, 2 months ago
Mon Apr 28 13:34:44 2008 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
comment out hydro cs check that fails at very high resolution continuum mesh
1964 Directory Listing
Modified 14 years, 2 months ago
Wed Apr 23 20:15:30 2008 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
update version number to C07.02.02, the last bug fix roll up
1890 Directory Listing
Modified 14 years, 3 months ago
Wed Mar 26 16:42:25 2008 UTC
peter
Original Path: branches/c07.02_branch/source
Log:
source/punch_do.cpp:
  Bug-fix for PR61 - division by zero in the PUNCH HYDROGEN IONIZATION command.

1880 Directory Listing
Modified 14 years, 3 months ago
Sat Mar 22 19:52:24 2008 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
BUGFIX charge transfer rate entered as reverse process - merge from R1879
1877 Directory Listing
Modified 14 years, 3 months ago
Sat Mar 22 19:02:17 2008 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
BUGFIX merge RP bug fix R1856 bug in interpolate command during grid runs
1753 Directory Listing
Modified 14 years, 5 months ago
Wed Jan 23 07:51:32 2008 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge r1752 bugfix roundoff with very small cells
1750 Directory Listing
Modified 14 years, 5 months ago
Sun Jan 20 14:09:51 2008 UTC
peter
Original Path: branches/c07.02_branch/source
Log:
source/parse_table.cpp:
source/cdgetlinelist.cpp:
source/parse.h:
source/zero.cpp:
source/cont_createmesh.cpp:
source/parse_punch.cpp:
source/rfield.h:
source/optimize_phymir.cpp:
source/ion_recomb_Badnell.cpp:
source/cont_ffun.cpp:
source/cloudy.cpp:
source/cdinit.cpp:
source/cddrive.cpp:
source/atom_feii.cpp:
source/hydrobranch.cpp:
source/maincl.cpp:
  - Bug-fix: fix PR45 - large grid fails on max no. of open file descriptors exceeded.
    This is largely a port of r1623, r1711, r1726, and r1728. There are still remaining
    issues with "special" punch commands; these require a more comprehensive bugfix.
tsuite/auto/blr_rnfb.in:
tsuite/auto/blr_kk81.in:
tsuite/auto/blr_rnfa.in:
  - Fix near-botches, largely a result of r1471.

1738 Directory Listing
Modified 14 years, 5 months ago
Fri Jan 11 15:25:10 2008 UTC
peter
Original Path: branches/c07.02_branch/source
Log:
source/punch_fits.cpp:
  Bug-fix: fix memory leak in he1n4t4.in.

1647 Directory Listing
Modified 14 years, 6 months ago
Sun Dec 9 12:37:43 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge bugfix r1646
1628 Directory Listing
Modified 14 years, 7 months ago
Fri Dec 7 15:30:31 2007 UTC
peter
Original Path: branches/c07.02_branch/source
Log:
source/parse_grain.cpp:
  Bug-fix - fix broken test if chOption was defined.
  Problem reported by Enrique PĂ©rez Montero.

1471 Directory Listing
Modified 14 years, 8 months ago
Fri Oct 26 14:06:09 2007 UTC
rporter
Original Path: branches/c07.02_branch/source
Log:
branches/c07.02_branch/source/iso_create.cpp - bug in stark broadening, "jj = jj" -> "jj = j"

branches/c07.02_branch/tsuite/auto - change asserts in three blr models as a result of above fix.
1467 Directory Listing
Modified 14 years, 8 months ago
Thu Oct 25 13:59:27 2007 UTC
peter
Original Path: branches/c07.02_branch/source
Log:
Merge various bug-fixes from the mainline:

r1439: fix convergence problems in stars_optimize[1-3].in

r1447: fix crash with g++ 4.2.x compilers.

r1454: fix compilation warnings on big-endian systems.

r1458: fix crashes with Sun Studio 12 compiler on IA32 due to unsafe FP comparison.

r1465: fix crashes with Sun Studio 11 compiler on Ultrasparc.

1438 Directory Listing
Modified 14 years, 8 months ago
Mon Oct 15 07:42:14 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
BUGFIX ion stage off by one in parse_set.cpp for set atomic data o 2 as command rev 1437
1362 Directory Listing
Modified 14 years, 10 months ago
Tue Sep 4 12:00:22 2007 UTC
rporter
Original Path: branches/c07.02_branch/source
Log:
bring trunk change r1356 into this branch as well (use linear instead of logarithmic interpolation in FITS files exported to XSPEC).
1345 Directory Listing
Modified 14 years, 10 months ago
Thu Aug 23 14:09:32 2007 UTC
peter
Original Path: branches/c07.02_branch/source
Log:
source/mole_h2.cpp:
  Port bug-fix r1344 from mainline. When searching for largest relative change during convergence, the wrong value was stored.

1289 Directory Listing
Modified 14 years, 11 months ago
Mon Jul 23 19:11:04 2007 UTC
rporter
Original Path: branches/c07.02_branch/source
Log:
branches/c07.02_branch/source/parse_punch.cpp 
branches/c07.02_branch/source/punch_average.cpp
  - fix memory links reported by Peter.  I fixed these in r1100 on the trunk, but neglected to copy them to this branch.  This does not fix the 4th leak Peter recently reported in he1n4t4.in. 


1286 Directory Listing
Modified 14 years, 11 months ago
Sun Jul 22 03:59:59 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge r1285, fix punch opacity bug
1268 Directory Listing
Modified 15 years ago
Fri Jul 6 21:53:18 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge RP r1263 on parse_optimize.cpp only

this fixes problem with grid upper limit being subject to roundoff error
1266 Directory Listing
Modified 15 years ago
Fri Jul 6 19:11:20 2007 UTC
peter
Original Path: branches/c07.02_branch/source
Log:
source/Makefile:
docs/quick_start_07_02.pdf:
data/rate05_feb17.csv:
  Fix file properties.

1253 Directory Listing
Modified 15 years ago
Tue Jul 3 19:55:01 2007 UTC
peter
Original Path: branches/c07.02_branch/source
Log:
source/opacity_addtotal.cpp:
source/cont_gaunt.cpp:
source/prt_final.cpp:
source/hydrolevelpop.cpp:
source/hydro_bauman.cpp:
source/helike_level.cpp:
source/mole_h_step.cpp:
source/rt_diffuse.cpp:
  These modifications make it possible to compile the release branch correctly with
  icc 9.0, 9.1, or 10.0 using the "-O3 -mp" flags on IA32, AMD64, and IA64. The only
  exception is the combination icc 10.0 on IA64 which has not been tested yet. 

1245 Directory Listing
Modified 15 years ago
Sat Jun 30 21:56:40 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge of r1244 - remove access data base of to do list
1234 Directory Listing
Modified 15 years ago
Wed Jun 27 18:57:10 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge r1224 bugfix ip fine pointers off by one
1226 Directory Listing
Modified 15 years ago
Tue Jun 26 21:32:06 2007 UTC
rporter
Original Path: branches/c07.02_branch/source
Log:
branches/c07.02_branch/source - bring in r1220 changes to transmission coefficients.
1212 Directory Listing
Modified 15 years ago
Sun Jun 24 23:46:24 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge r1211 - sanity check on continuum shape more tolerant of floating point imprecision
1201 Directory Listing
Modified 15 years ago
Tue Jun 19 01:10:00 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge r1200 bugfix
1198 Directory Listing
Modified 15 years ago
Sun Jun 17 01:38:18 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
bugfix merge of 1197 - did not print incident continuum correctly in both emergent and intrinsic continuum
1177 Directory Listing
Modified 15 years, 1 month ago
Fri Jun 8 16:11:56 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge of r1176 - do not include X collisional excitation de-excitation heating / cooling during search phase
1174 Directory Listing
Modified 15 years, 1 month ago
Wed Jun 6 18:51:48 2007 UTC
rporter
Original Path: branches/c07.02_branch/source
Log:
trunk/source/prt_columns.cpp - bug in PrtColumns, implicit assumption (that an insignificant column could not be found at a stage between two stages with significant columns) was invalid.  Print all columns and give -30 for instead of zero for small ones. 
1153 Directory Listing
Modified 15 years, 1 month ago
Thu May 24 16:50:42 2007 UTC
rporter
Original Path: branches/c07.02_branch/source
Log:
branches/c07.02_branch/source/ion_recomb_Badnell.cpp - break out of two while loops in index goes below zero.  Array bounds were exceeded.  No botches after fix. 
1146 Directory Listing
Modified 15 years, 1 month ago
Tue May 22 01:31:30 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge r1145 bugfix, high ion stage extended beyond top of ionization ladder, off by one counting error
1140 Directory Listing
Modified 15 years, 1 month ago
Mon May 21 16:10:22 2007 UTC
rporter
Original Path: branches/c07.02_branch/source
Log:
c07.02_branch/source/punch_fits.cpp - generic fits output (for single model) was broken, now fixed.  Also replace tabs in comments with spaces, so that fits output strictly adheres to standard.
1133 Directory Listing
Modified 15 years, 1 month ago
Thu May 17 21:19:29 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge R1132 
prt_comment.cpp - say that excited state column densities are not predicted when level 2 lines are turned off

prt_columns.cpp - no not print excited state column densities when level 2 lines are turned off

1131 Directory Listing
Modified 15 years, 1 month ago
Thu May 17 15:08:35 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge r1124 iter_startend.cpp set opac.E2TauAbsOut
1130 Directory Listing
Modified 15 years, 1 month ago
Thu May 17 14:37:08 2007 UTC
peter
Original Path: branches/c07.02_branch/source
Log:
source/prt_lines_continuum.cpp:
  Merge r1127 bugfix from mainline.

1126 Directory Listing
Modified 15 years, 1 month ago
Wed May 16 15:29:14 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
cdinit.cpp - set beta version flag to false so will not print beta header

parse_commands.cpp - merge Ryan Porter add of web site into header, rev 1104 and 1107

lines_service.cpp
lines_service.h
prt_lines_continuum.cpp, merge r1125 bugfix energy conservation in continuum bands

1098 Directory Listing
Modified 15 years, 2 months ago
Fri May 4 20:23:56 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge r1097 fix mole_h2.cpp format, extra parse_table.cpp %s
1093 Directory Listing
Modified 15 years, 2 months ago
Fri May 4 00:03:21 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge from r1092, add transmission coefficient to punch continuum
1088 Directory Listing
Modified 15 years, 2 months ago
Thu May 3 16:39:22 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge back of several merges of mainline into 07.02 branch.
rev 1087 - set initial value to beta version in cdinit.cpp - now set to 0 as it should be in rev, but reset to 1 on this merge, which will become rc1 of 07.02

rev 1086, revise readme_docs.htm

rev 1082, 1084, rename docs

rev 1081, ionbal.h, parse_set.cpp, and zero.cpp, implement set atomic data sulpher DR command, and revised treatment of DR guesses in ion_recomb_Badnell.cpp

ion_recomb_Badnell.cpp had several conflicts where were resolved by hand

*.in merge back rev 1081 changes due to S DR

1080 Directory Listing
Modified 15 years, 2 months ago
Tue May 1 16:59:13 2007 UTC
rporter
Original Path: branches/c07.02_branch/source
Log:
c07.02_branch/source/cdspec.cpp: added line transmission coefficient as multiplicative factor;
c07.02_branch/source/punch_do.cpp: added line transmission coefficient as multiplicative 
1077 Directory Listing
Modified 15 years, 2 months ago
Mon Apr 30 02:24:41 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge rev 1076, fix typo in stop H2 too large
1064 Directory Listing
Modified 15 years, 2 months ago
Fri Apr 20 17:13:30 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge of r1063, reorganized parse table so cannot be confused by string within double quotes
1060 Directory Listing
Modified 15 years, 2 months ago
Wed Apr 18 20:48:18 2007 UTC
rporter
Original Path: branches/c07.02_branch/source
Log:
source/helike_cs.cpp: he-like proton collisions bugfix, and a few other minor changes;
tsuite/auto/*.in: changes related to the proton collision change.
1057 Directory Listing
Modified 15 years, 2 months ago
Sat Apr 14 23:34:41 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge of r1055, fix too-short array dimension
1032 Directory Listing
Modified 15 years, 3 months ago
Fri Apr 6 12:56:10 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge r1031, wrong collider and OP transitions in g-bar guess of H2-He collision rates
1021 Directory Listing
Modified 15 years, 3 months ago
Fri Mar 30 02:28:26 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
BUGFIX - merge r1017 fixing thrown assert on some platforms
1012 Directory Listing
Modified 15 years, 3 months ago
Mon Mar 26 14:43:18 2007 UTC
peter
Original Path: branches/c07.02_branch/source
Log:
Merging r1011 from mainline
1006 Directory Listing
Modified 15 years, 3 months ago
Fri Mar 23 22:23:02 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
source - revisions from r1005
replace line_labels.txt with shorter file that does not include parts of transferred lines 
987 Directory Listing
Modified 15 years, 3 months ago
Wed Mar 14 18:05:26 2007 UTC
rporter
Original Path: branches/c07.02_branch/source
Log:
branches/c07.02_branch/source/lines_service.cpp: changes in HLineTransOpacSet to fix cache errors
trunk/source/lines_service.cpp: changes in HLineTransOpacSet to fix cache errors
branches/c07.02_branch/tsuite/auto/*: small changes in asserts as result of changes in HLineTransOpacSet
trunk/tsuite/auto/*: small changes in asserts as result of changes in HLineTransOpacSet
953 Directory Listing
Modified 15 years, 4 months ago
Tue Mar 6 20:46:08 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge of r952 - make diagnostic more helpful when first data file cannot be found
940 Directory Listing
Modified 15 years, 4 months ago
Sun Mar 4 19:31:57 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
make path.cpp simpler, and have unix as the default path
937 Directory Listing
Modified 15 years, 4 months ago
Sun Mar 4 15:50:58 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge of changes in path committed in r936
933 Directory Listing
Modified 15 years, 4 months ago
Sat Mar 3 21:36:17 2007 UTC
peter
Original Path: branches/c07.02_branch/source
Log:
Merged r932 from trunk.
928 Directory Listing
Modified 15 years, 4 months ago
Thu Mar 1 23:35:05 2007 UTC
peter
Original Path: branches/c07.02_branch/source
Log:
Merge r927 from mainline
920 Directory Listing
Modified 15 years, 4 months ago
Wed Feb 28 20:55:16 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
date.h - explain that day is now the subversion number, 00 for initial release

rest are merge of r919 on mainline
918 Directory Listing
Modified 15 years, 4 months ago
Wed Feb 28 02:08:09 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge r917
905 Directory Listing
Modified 15 years, 4 months ago
Mon Feb 26 12:18:37 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge r903 bugfix
900 Directory Listing
Modified 15 years, 4 months ago
Sun Feb 25 22:15:05 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge bugfix in r896
892 Directory Listing
Modified 15 years, 4 months ago
Sat Feb 24 20:35:03 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge r889
886 Directory Listing
Modified 15 years, 4 months ago
Sat Feb 24 11:32:57 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge of r885
878 Directory Listing
Modified 15 years, 4 months ago
Tue Feb 20 02:55:23 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
cdinit.cpp - lgRelease now true, this is a release version, so fixits will no longer print caution
path.cpp - now points to data within branch not trunk
runall.pl - uses release of branch
877 Directory Listing
Modified 15 years, 4 months ago
Mon Feb 19 23:41:40 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
path.cpp - merge r864 & 875 update comments
874 Directory Listing
Modified 15 years, 4 months ago
Mon Feb 19 20:15:26 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge of r872 (test on lgRelease for fixits) and r873 (rm Powell's method)
868 Directory Listing
Modified 15 years, 4 months ago
Mon Feb 19 12:18:15 2007 UTC
peter
Original Path: branches/c07.02_branch/source
Log:
Merged r867 bug fix from trunk.

866 Directory Listing
Modified 15 years, 4 months ago
Mon Feb 19 12:06:10 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
change date of 07.02.00 signifying initial release
863 Directory Listing
Modified 15 years, 4 months ago
Sun Feb 18 23:41:39 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge r859 (rjrw bugfix to H chemistry) and r862 (change wording of print citation command).
850 Directory Listing
Modified 15 years, 4 months ago
Sat Feb 17 17:37:06 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
merge of r849
845 Directory Listing
Modified 15 years, 4 months ago
Wed Feb 14 17:13:16 2007 UTC
gary
Original Path: branches/c07.02_branch/source
Log:
create new branch for C07.02 release
844 Directory Listing
Modified 15 years, 4 months ago
Wed Feb 14 17:06:48 2007 UTC
rporter
Original Path: trunk/source
Log:
Add a ''print citation'' command.
843 Directory Listing
Modified 15 years, 4 months ago
Tue Feb 13 20:40:54 2007 UTC
gary
Original Path: trunk/source
Log:
parse_puncch.cpp - BUGFIX logical flags for init clobber / no clobber of files was inverted

move PunchFilesInit from cdinit to cddrive

grains.cpp - upper limit on loop had MAX which consumed time - move to variable set before loop

grid_do.cpp - minor rm commented code

maincl.cpp - change filename to follow code naming convention

parse_crashdo.cpp - minor fix in comments




841 Directory Listing
Modified 15 years, 4 months ago
Fri Feb 9 18:49:59 2007 UTC
rjrw
Original Path: trunk/source
Log:
Some systems may need to call ranlib on the library, others may not have it.

837 Directory Listing
Modified 15 years, 4 months ago
Fri Feb 9 02:21:08 2007 UTC
gary
Original Path: trunk/source
Log:
remove optimize_amoeba.cpp and tsuite auto due to Robin & Peter license concerns
836 Directory Listing
Modified 15 years, 4 months ago
Fri Feb 9 00:18:37 2007 UTC
rporter
Original Path: trunk/source
Log:
trunk/source/iso_continuum_lower.cpp: bug in continuum lowering, all bases should FINALLY be covered on this.
835 Directory Listing
Modified 15 years, 4 months ago
Thu Feb 8 23:29:07 2007 UTC
gary
Original Path: trunk/source
Log:
cddefines.h - add visual studio pragma to disable warning on use of str functions

ion_recomb_Badnell.cpp - cosmetic changes

*.in revise asserted quantities after bugfix in r828

tsuite/programs adjusted perl script run_programs.pl to work with cpp source and g++ - also now executes the program.  
834 Directory Listing
Modified 15 years, 4 months ago
Thu Feb 8 21:44:34 2007 UTC
rjrw
Original Path: trunk/source
Log:
Fix programs/collion.cpp problem -- by making the PR14 kludge worse
:-(

Changed Makefile to generate a library of everything other than
maincl.cpp -- this makes it easier to build things in the programs
hierarchy.


833 Directory Listing
Modified 15 years, 5 months ago
Wed Feb 7 12:05:20 2007 UTC
gary
Original Path: trunk/source
Log:
atom_pop5.cpp - correct comments, no change in function
cool_carb.cpp - correct comments, no change in function
cool_nitr.cpp - add pumping of N0 by all level 2 lines, used as upper limit to pumped [NI] 5200 in prt_lines_lv1_li_ne.cpp
mole_h_step.cpp - correct comments, no change in function
nitro.h - add pump rate variable for NI pumping
prt_lines_lv1_li_ne.cpp - add pump rate as upper limit to amount of [NI] 5200 that can be produced
auto/pdr_co_fully_noneq.in - update results to change introduced by bugfix in r828
slow/h2_orion_hii_pdr.in - update results to change introduced by bugfix in r828
828 Directory Listing
Modified 15 years, 5 months ago
Tue Feb 6 07:58:55 2007 UTC
rjrw
Original Path: trunk/source
Log:
Correct bugs in mole_h_step.cpp (found due to checking consistency
with improved branches/newmole treatment).

825 Directory Listing
Modified 15 years, 5 months ago
Mon Feb 5 22:09:49 2007 UTC
gary
Original Path: trunk/source
Log:
cddrive.cpp - detect grid command in cdRead
parse_punch.cpp - default clobber/no clobber is clobber everything except grid, when default becomes no clobber.  cleaner logic for detecting clobber / no clobber on punch command

824 Directory Listing
Modified 15 years, 5 months ago
Sun Feb 4 22:59:31 2007 UTC
gary
Original Path: trunk/source
Log:
cdinit.cpp - rm unused header, fix typos
cont_createpointers.cpp - typos, rm unused code
mole_co_etc.cpp - rm unused headers
mole_co_solve.cpp - rm unused headers
parse_punch.cpp - rm unused header, typos, fix format error in fprintf, in punch linelist command rm second file name early so that it does not trigger keyword,
service.cpp - typo

parse_punch.cpp invert logic for clobber file, now do not clobber by default, clobber is used to turn on clobbering files

h2_orion_hii_pdr.in and h2_pdr_leiden_v4.in - update close asserted values
822 Directory Listing
Modified 15 years, 5 months ago
Sun Feb 4 18:14:11 2007 UTC
gary
Original Path: trunk/source
Log:
cddefines.h - disable more PCLint checks at start, and enable all at the bottom of the file
conv_base.cpp - add float format that was missing in print statement
parse_commands.cpp - correct format with error reported by g++
parse_punch.cpp - add tabs to punch physical conditions output
punch_do.cpp - add tabs to punch physical conditions output

sanity.txt, project.lnt - update source_hot for running pclint
820 Directory Listing
Modified 15 years, 5 months ago
Sun Feb 4 11:32:40 2007 UTC
peter
Original Path: trunk/source
Log:
source/punch_do.cpp:
source/parse_punch.cpp:
  - Add filling factor to output of PUNCH PHYSICAL CONDITIONS.

816 Directory Listing
Modified 15 years, 5 months ago
Thu Feb 1 23:16:19 2007 UTC
peter
Original Path: trunk/source
Log:
source/cddefines.h:
  Add fp_equal() to test equality of FP numbers.

815 Directory Listing
Modified 15 years, 5 months ago
Thu Feb 1 16:47:59 2007 UTC
gary
Original Path: trunk/source
Log:
atmdat_readin.cpp - move blocks defining heating per line absorption for UTAs out of atmdat_readin over to cont_createpointers.cpp.  Simpler code (only appears in a single loop) and able to use valence shell energies, which were not yet defined in atmdat_readin

cont_createpointers.cpp - define heating per line absorption for UTAs here rather than in atmdat_readin

conv_base.cpp - minor changes in comments and a debug print statement

parse_commands.cpp - atom rotor will now say to use atom co instead, although it will still parse the command for now.

service.cpp - PROBLEM and DISASTER strings are now printed when ShowMe is called and exiting with "something bad has happened" - this will now be picked up by our scripts.  MyAssert now also prints PROBLEM in addition to DISASTER

813 Directory Listing
Modified 15 years, 5 months ago
Thu Feb 1 15:45:36 2007 UTC
peter
Original Path: trunk/source
Log:
source/cont_ffun.cpp:
  Bug-fix for PR20: overzealous assert blows due to roundoff error.

812 Directory Listing
Modified 15 years, 5 months ago
Thu Feb 1 11:49:20 2007 UTC
peter
Original Path: trunk/source
Log:
source/interpolate.cpp:
  since this is mostly third-party code, renamed to ->
source/thirdparty_interpolate.cpp:
  - Change new[], delete[] -> malloc, free.
source/interpolate.h:
  merged into ->
source/thirdparty.h:
  - Added hunt_bisect_reverse().
source/ion_solver.cpp:
source/grains_qheat.cpp:
source/prt_lines_helium.cpp:
source/opacity_createall.cpp:
source/grains.cpp:
source/dynamics.cpp:
source/atmdat_2photon.cpp:
source/helike_recom.cpp:
  - Fix include statements.

811 Directory Listing
Modified 15 years, 5 months ago
Wed Jan 31 22:16:21 2007 UTC
rporter
Original Path: trunk/source
Log:
source/radius_first.cpp: determine "punch dr" printout based on logical flags rather than floating point equality.
809 Directory Listing
Modified 15 years, 5 months ago
Tue Jan 30 21:30:49 2007 UTC
peter
Original Path: trunk/source
Log:
source/interpolate.h:
source/interpolate.cpp:
source/prt_lines_helium.cpp:
source/dynamics.cpp:
source/helike_recom.cpp:
  - Remove third party interpolation software with unclear copyright.
source/conv_base.cpp:
  - Fix compiler warning.

805 Directory Listing
Modified 15 years, 5 months ago
Fri Jan 26 06:27:24 2007 UTC
gary
Original Path: trunk/source
Log:
these are a series of updates related to the Gu et al. 2006 UTA transition data
MAJOR CHANGE - bug fix in gu et al data set, do not use Kisielius data by default

UTA_Gu06.dat - this file was sent to me by Ming on the day that their paper was posted on astro-ph.  I had emailed asking for it.  Tests with Netzer showed that the data file was quite different from the version actually published in the ApJ.  The data file was updated to the published version but with integers for the roman numerals and an updated magic number

tests showed that the Kisielius UTA data set were very irregular and agreed poorly with Gu et al. data, which has smooth variation with charge.  Do not use Kisielius data by default any more - use Gu et al. 2006

source files changes are related to using this data file and including UTA line heating

the heat element of the UTALinies structure now contains the heating per UTA pump.  this is different from the usual meaning of heat in other instances of the EmLines structure.  heat is now set one time at setup and in several places protected against being set to zero (which is needed for usual EmLines data).  

atmdat_lines_setup.cpp - do not init heat to zero

atmdat_readin.cpp - update magic number for Gu data file, set heat as incident photon energy minus shell energy, set energyErg for UTALines (had not been set to anything before), define heat as heat per pump - Gu data set does not have upper and lower statistical weights defined, so use absorption oscillator strength to get Bul, define heat for all UTALines, not just new Gu data set,

ionbal.h - rename lgInnerShellRomas to lgInnerShell_Kisielius since paper is Kisielius et al., add **UTA_heat_rate to save heating per element and ion

conv_base.cpp - define UTA_heat_rate for all elements and ions

heat_punch.cpp - identify UTA heating as string when important

iso_create.cpp - do not zero UTALines heat since contains heat per pump
rt_tau_init.cpp - do not zero UTALines heat since contains heat per pump
rt_tau_reset.cpp - do not zero UTALines heat since contains heat per pump

zero.cpp - set up UTA heating array ionbal.UTA_heat_rate, do not use Kisielius data by default
heat_sum.cpp - define UTA heating as local var photo_heat_UTA, clean up comments

parse_dont.cpp - no uta command no longer has "romas" keyword - command is not only "no uta" with no options

parse_set - "set UTA" now has more options.  "set UTA Gu06" has keywords ON and OFF - default is ON.  "set UTA Kisielius" is new and has keywords ON and OFF and default is OFF - this is a change - had been used by default


*.in - these changed as result of changes in UTA treatment


804 Directory Listing
Modified 15 years, 5 months ago
Fri Jan 26 05:57:22 2007 UTC
gary
Original Path: trunk/source
Log:
cont_setintensity.cpp add dense.EdenExtra to very first guess of electron density
conv_init_solution.cpp assert H0 density gt zero since cannot be zero
dynamics.cpp update comments, replace 1 with true in bool
dynamics.h rm unused lgHeLIKE, improve comments
helike_level.cpp - update comments
hydrogenic.cpp - update comments
ion_collis.cpp - update comments
ion_photo.cpp - update comments
ion_recomb.cpp - update comments
mole_co_solve.cpp - update comments
parse_dont.cpp - update comments
parse_punch.cpp - add do nothing statemnet to empty clause

pressure_total.cpp, clean up comments, BUGFUX add H- to loop over particles, do not assert number of H species (this was left over from time when each species was explicitly written out, rather than a loop)
service.cpp - clean up comments in e2, ee1 functions, replace sexp(x) with exp(-x)

803 Directory Listing
Modified 15 years, 5 months ago
Thu Jan 25 01:55:03 2007 UTC
rporter
Original Path: trunk/source
Log:
bug in cosmic rays background, not properly parsed when varied in optimizer/grid runs.  Bug found by Gargi.
802 Directory Listing
Modified 15 years, 5 months ago
Wed Jan 24 01:13:43 2007 UTC
rporter
Original Path: trunk/source
Log:
source/parse_punch.cpp: malformed comment in last commit, suite passed fine, VS didn't catch this, cluster did.
801 Directory Listing
Modified 15 years, 5 months ago
Tue Jan 23 23:19:20 2007 UTC
rporter
Original Path: trunk/source
Log:
source/atom_seq_boron.cpp: added DEBUG_EXIT and DEBUG_ENTRY
source/cddrive.cpp: remove tabs in cdLine, changed to space
source/conv_init_solution.cpp:  let neutral hydrogen equal density equal zero instead of assert positive.
source/dynamics.cpp: moved header punch in DynaPunchTimeDep to parse_punch.cpp
source/helike_cs.cpp: replaced Bohr_rad with macro in physconst.h
source/helike_einsta.cpp: changed BohrRadiusCM to BOHR_RADIUS_CM
source/helike_recom.cpp: changed a debug loop
source/hydro_bauman.cpp: fixed typos and Bohr macro change
source/hydro_vs_rates.cpp: use global BOHR_RADIUS_CM
source/mole_h_step.cpp: fixed three typos
source/parse_print.cpp: BohrRadiusCM to BOHR_RADIUS_CM
source/parse_punch.cpp:  added "lg" in front of logical variable QHPunchFile_noclobber, made changes to allow for multiple output files in grid calculation.
source/parse_set.cpp: fixed incorrect "DIEL RECO" error message
source/physconst.h: changed to BohrRadiusCM to all-caps BOHR_RADIUS_CM
source/punch.h: changes associated with parse_punch.cpp changes
source/punch_average.cpp: changes associated with parse_punch.cpp changes
source/punch_do.cpp: changes associated with parse_punch.cpp changes
source/punch_line.cpp: changes associated with parse_punch.cpp changes
tsuite/auto/func_grid.in: added "punch total opacity" to test parse_punch.cpp changes with grid and separate output files.

793 Directory Listing
Modified 15 years, 5 months ago
Mon Jan 22 12:16:29 2007 UTC
gary
Original Path: trunk/source
Log:
cddefines.h, iter_startend.cpp, parse_drive.cpp, radius_increment.cpp, rt_tau_reset.cpp, sanity_check.cpp, service.cpp - remove unused second parameter from e2 function

slow/*.in - update asserted values after e2 function bug fix in r786
792 Directory Listing
Modified 15 years, 5 months ago
Mon Jan 22 07:20:39 2007 UTC
gary
Original Path: trunk/source
Log:
*.in - these changed as result of e2 bugfix r786

conv_base.cpp - only reevaluate UTA pump rates when lgRedoStatic is true, this will save some time

hydrobranch.cpp - init nd2 var to impossible value to prevent possibly use of uninit var warning

service.cpp - add change comment and date for PvH fix of e2 function.  This was a serious bug that had been in the code for some time, did change results, and worthy of a comment



791 Directory Listing
Modified 15 years, 5 months ago
Sun Jan 21 22:04:37 2007 UTC
peter
Original Path: trunk/source
Log:
source/cddefines.h:
source/service.cpp:
  - Add new version of FFmtRead(). Not yet activated.
source/rt_line_all.cpp:
source/mole_h2_io.cpp:
source/mole_h2.cpp:
source/lines_service.cpp:
source/cddrive.cpp:
source/stars.cpp:
source/mole_co_etc.cpp:
  - Fix various DEBUG_ENTRY / DEBUG_EXIT statements.

790 Directory Listing
Modified 15 years, 5 months ago
Sun Jan 21 14:00:21 2007 UTC
peter
Original Path: trunk/source
Log:
source/prt_lines_helium.cpp:
source/helike_recom.cpp:
  - Fix botched assert in stars_optimize1.in. This test case is very sensitive
    to the way interpolation is done in the routine TempInterp(). Hence use a
    different scheme that gives results closer to the old interp() routine from
    Bevington.

788 Directory Listing
Modified 15 years, 5 months ago
Wed Jan 17 12:27:31 2007 UTC
peter
Original Path: trunk/source
Log:
source/optimize_subplx.cpp:
source/service.cpp:
source/cddefines.h:
source/conv_pres_temp_eden_ioniz.cpp:
source/parse_commands.cpp:
source/radius_first.cpp:
source/thirdparty.h:
source/radius_next.cpp:
source/prt_lines_helium.cpp:
source/plot.cpp:
source/helike_recom.cpp:
  - Remove more Cobalt Blue and Bevington software and replace it with
    our own routines where needed. The replaced/removed routines are
    sign, vfmin, vfmax, istrstr (Cobalt Blue), interp (Bevington),
    and qip (unused).
source/thirdparty_bevington.cpp:
  - Deleted.

787 Directory Listing
Modified 15 years, 5 months ago
Wed Jan 17 00:14:51 2007 UTC
gary
Original Path: trunk/source
Log:
pdr_leiden_hack.ini - SET H2 SOLOMON command is now SET H2 SMALL MODEL

atmdat_readin.cpp - simplify evaluation of UTA ionization yield

ionbal.h rename ionbal.xInnerShellIonize to ionbal.UTA_ionize_rate to better reflect the physics of the process

hmi.h - separate out different representations of small model H2
cool_eval.cpp - clean up evaluation of distinct methods of the small model H2
iter_startend.cpp - only int H2 vars that are used

dense.h - fix typos

hydrobranch.cpp - init nd2 at line 52 to stop comment of possibly unit var

change all ASSERT( a == a) tests for NaN to ASSERT( !isnan(a) )

mole_h2.cpp fix typos, do not save old heat rate in case where large H2 is not evaluated

mole_h2_etc.cpp - fix typos

mole_h_drive.cpp add Burton et al. 1990 approximation to dissociation rates

mole_h_step.cpp - break apart Elwert and burton et al. approximation to dissociation rates

parse)set.cpp - change SET H2 SOLOMON to SET H2 SMALL MODEL, add "BHT90" option to use Burton et al. paper

orion_hii_pdr.in - changed values due to bug fix
786 Directory Listing
Modified 15 years, 5 months ago
Tue Jan 16 16:31:41 2007 UTC
peter
Original Path: trunk/source
Log:
source/service.cpp
  - Bug-fix. Fix problem in e2() with negative return values for very large tau.
source/thirdparty_bevington.cpp
source/conv_eden_ioniz.cpp
source/thirdparty.cpp
source/thirdparty.h
  - Replace Bevington linfit routine with open source version.
  - Bug-fix. Replace call to y0() -> bessel_y0(), y1() -> bessel_y1() in bessel_yn().

785 Directory Listing
Modified 15 years, 5 months ago
Tue Jan 16 06:03:11 2007 UTC
peter
Original Path: trunk/source
Log:
source/thirdparty_bevington.cpp:
source/thirdparty.cpp:
source/helike_cs.cpp:
  - Delete and replace software with incompatible or unclear licenses.
    Replacement routines are taken from the Cephes library.
  - remove gammafun and replace with standard mathlib function tgamma.
source/hydro_bauman.cpp:
  - Move factorial and log10_factorial into thirdparty.cpp to make
    them globally available.
source/service.cpp:
  - Replace e2 with better version using recursion relation. The old
    version had dreadful accuracy.
source/sanity_check.cpp:
  - Make check on e2 stricter now that it is better.
source/atom_pop5.cpp:
source/ion_solver.cpp:
source/conv_eden_ioniz.cpp:
source/cont_gaunt.cpp:
source/thirdparty_lapack.cpp:
source/hydrolevelpop.cpp:
source/atom_seq_beryllium.cpp:
source/helike_level.cpp:
source/prt_lines_helium.cpp:
source/atom_leveln.cpp:
source/mole_h_step.cpp:
source/atom_oi.cpp:
source/atom_feii.cpp:
source/mole_co_solve.cpp:
source/helike_recom.cpp:
  - Update includes.
  - Call replaced routines from thirdparty.cpp.
source/bevington.h:
source/lapack.h:
  - Deleted and merged into thirdparty.h.
source/thirdparty.h:
  - Included the above, added prototypes for new routines from Cephes.

784 Directory Listing
Modified 15 years, 5 months ago
Mon Jan 15 23:06:07 2007 UTC
rjrw
Original Path: trunk/source
Log:
...and final declaration of it.

783 Directory Listing
Modified 15 years, 5 months ago
Mon Jan 15 23:04:34 2007 UTC
rjrw
Original Path: trunk/source
Log:
Remove unused tridiag function which was close to Press et al source

779 Directory Listing
Modified 15 years, 5 months ago
Sat Jan 13 09:38:33 2007 UTC
peter
Original Path: trunk/source
Log:
source/cpu.h:
  - Add support for Portland Group compiler.
  - Improve detection of Linux platform.
source/cpu.cpp:
  - Fix compile problem on IA64 with Intel compiler.
source/hydro_bauman.h:
source/hydro_bauman.cpp:
  - General cleanup. Fix indentation. Add DEBUG_ENTRY and DEBUG_EXIT statements.    
  - Remove unused variables.
  - Replace braindead implementation of log10_factorial() with version that caches.
source/assert_results.cpp:
source/rt_diffuse.cpp:
  - Fix DEBUG_EXIT statements.
source/optimize_phymir.cpp:
source/parse_dont.cpp:
source/thirdparty.cpp:
  - Remove various unused variables.
source/cool_iron.cpp:
  - Remove unused routine Fe2Lev16(). This deletes the last of the fortran block
    data initializers!!
source/prt_lines_lv1_k_zn.cpp:
source/atomfeii.h:
source/atom_feii.cpp:
  - Update comments in view of the above.
source/mole_co_etc.cpp:
  - Remove unreachable statement.

774 Directory Listing
Modified 15 years, 5 months ago
Fri Jan 12 07:56:48 2007 UTC
peter
Original Path: trunk/source
Log:
source/hydro_bauman.cpp:
  Bug-fix for PR17. It appears that pgCC miscompiled the routine power in hydro_bauman.cpp.
  This routine is redundant and is therefore replaced with powi everywhere.

772 Directory Listing
Modified 15 years, 5 months ago
Thu Jan 11 08:20:11 2007 UTC
rjrw
Original Path: trunk/source
Log:
Calling CO_zero makes more sense here than CO_Init (CO_zero was split
from CO_Init in a previous version, so presumably just missed this case).


771 Directory Listing
Modified 15 years, 5 months ago
Wed Jan 10 06:30:30 2007 UTC
peter
Original Path: trunk/source
Log:
source/optimize_subplx.cpp:
source/opacity_createall.cpp:
source/hydro_vs_rates.cpp:
source/hydrobranch.cpp:
source/hydrocollid.cpp:
source/hydrogenic.h:
data/hydrobranch.dat:
  - Removing more block data initialization code. All the ones in active code have now
    been romoved! Moved hydrogenic branching ratios into new separate data file.
source/atmdat_adfa.cpp:
  - Minor improvements.
source/mole_co_reactions.cpp:
source/mole_co_etc.cpp:
  - Bug-fix for PR14. The CO network was leaking memory in optimizer runs. This is a
    temporary fix to stop the leaks.
source/parse_set.cpp:
source/mole_h_step.cpp:
  - Bug-fix: Branch for using constant H2 grain formation rate could not be reached.
    Bug discovered by Robin Williams and fixed by Nick Abel.

769 Directory Listing
Modified 15 years, 5 months ago
Tue Jan 9 21:54:09 2007 UTC
rjrw
Original Path: trunk/source
Log:
Add DEBUG_ENTRY() and DEBUG_EXIT() to CO network routines.

768 Directory Listing
Modified 15 years, 5 months ago
Tue Jan 9 19:40:22 2007 UTC
rjrw
Original Path: trunk/source
Log:
Add malloc protection where missing (mole_co_reactions.cpp); use
overall Cloudy scheme rather than local implementation (hash.cpp).


767 Directory Listing
Modified 15 years, 5 months ago
Tue Jan 9 15:48:48 2007 UTC
gary
Original Path: trunk/source
Log:
crash.in - add script with tests of crash command

cddrive.cpp - give more information if cdColm cannot find species

parse_crashdo.cpp - clean up commments, and output, remove unused header

parse_optimize.cpp - minor style and comment changes

punch_average.cpp - clean up, better diagnostics if something goes wrong

pn_paris.in - include punch average command
766 Directory Listing
Modified 15 years, 5 months ago
Mon Jan 8 16:04:03 2007 UTC
gary
Original Path: trunk/source
Log:
grains_qheat.cpp - change var power to ppower to get around error in pgCC - name collision?

with this change the code does compile with pgcc BUT USES INFINITE TIME.  The smoke test never ends.  We must have a loop that does not terminate.  

THIS IS A SHOW STOPPER.  pgcc is the only way we can test array bounds limits being exceeded.  it is critical that the code be able to compile and execute with this compiler.  
763 Directory Listing
Modified 15 years, 6 months ago
Sun Jan 7 19:44:45 2007 UTC
peter
Original Path: trunk/source
Log:
More general cleanup of the code; no change in functionality.

- A few more of the old fortran block data initializations have been
  transformed.
- A couple of cases where we still explicitly tested for failed MALLOC have
  been mopped up.
- A few last remaining cases where we used "type_t" have been fixed.

762 Directory Listing
Modified 15 years, 6 months ago
Sun Jan 7 14:26:08 2007 UTC
gary
Original Path: trunk/source
Log:
assert_results.cpp - add missing DEBUG_ENTRY, EXIT
cpu.h, add pragma to disable warning on if constant expression
helike_einsta.cpp - minor formatting
zero.cpp - add cast to double to float

*.in - changes caused by update H3+ rate to McCall et al. nature paper
761 Directory Listing
Modified 15 years, 6 months ago
Sat Jan 6 15:58:25 2007 UTC
peter
Original Path: trunk/source
Log:
General cleanup of the code.

- Move more platform/hardware specific stuff into cpu.h and cpu.cpp.
- cpu.h is now included in cddefines.h to make it available everywhere.
- Make a start in removing preprocessor macro function from cddefines.h.
- Convert more preprocessor defines into const int, etc.
- Fix compile problem of cpu.cpp on Windows boxes.

760 Directory Listing
Modified 15 years, 6 months ago
Sat Jan 6 00:59:56 2007 UTC
gary
Original Path: trunk/source
Log:
scripts - better load leveling

conv_fail.cpp - flush buffer before exit so that all print comes out

mole_h_step.cpp - turn on McCall H3+ DR rates, this changes many test suite results which will be updated after tests are complete - this had been debugged but not turned on in jan 06

prt_comment.cpp - do not print comment about maser lines in iso seq when levels are affected by topoff

prt_lines.cpp - fix typos

prt_lines_continuum.cpp - formatting

rt_diffuse.cpp - zero out arrays before abort return, prevents NaN from propagating into code during abort

service.cpp - add casts two places

agn_S_curve_grid.in - add output option

optimize_phymir.in - remove sequential so it runs in parallel
759 Directory Listing
Modified 15 years, 6 months ago
Fri Jan 5 17:39:17 2007 UTC
peter
Original Path: trunk/source
Log:
This commit touches nearly every file in the source directory. The main aim
was to clean up the code. These are the highlights.

- The constants in physconst.h have been updated to Codata 2002; also some new
  constants have been added.
- The code now detects the number of CPUs and the hostname on Windows boxes as
  well as Unix systems. The hostname has been moved into the cpu class.
- A constructor for t_dense has been created. The initialization in cdDefines
  has been moved into this constructor.
- A start has been made to convert preprocessor constants into const int,
  const double, etc. Similarly for constants that were defined as global vars.
- In a move to reduce the number of preprocessor statements in the code, new
  preprocessor macros DEBUG_ENTRY and DEBUG_EXIT have been defined. These
  replace the old #ifdef DEBUG_FUN -- futs( xxx ) -- #endif constructs. A new
  class t_debugprt has been created for this.

757 Directory Listing
Modified 15 years, 6 months ago
Thu Jan 4 20:28:17 2007 UTC
rjrw
Original Path: trunk/source
Log:
Move some more system dependencies into cpu.h.

756 Directory Listing
Modified 15 years, 6 months ago
Thu Jan 4 17:00:12 2007 UTC
peter
Original Path: trunk/source
Log:
source/yield.h:
source/atmdat_readin.cpp:
source/ion_photo.cpp:
source/punch_do.cpp:
source/ion_solver.cpp:
source/punch_opacity.cpp:
source/cddefines.cpp:
source/prt_lines.cpp:
source/cont_createpointers.cpp:
source/parse_dont.cpp:
source/cont_gammas.cpp:
  - The global struct yield clashed with system routine under Solaris -> turn
    it into a Singleton.
source/cpu.h:
source/cpu.cpp:
source/service.cpp:
source/zero.cpp:
source/cool_iron.cpp:
source/optimize_phymir.cpp:
source/grid_do.cpp:
source/optimize.h:
source/cdinit.cpp:
source/parse_optimize.cpp:
  - The isnan routine is not defined under Windows -> create MyIsnan and
    MyIsnanf to test for NaN and create preprocessor symbol isnan to access
    these routines.
  - Rename routines for setting NaN to set_nan and set_nanf; make them part
    of the t_cpu class so that they can be inlined.    
  - Move initialization of SNaN_Value into constructor of t_cpu; ditto for
    the initialization of the FP environment and the detection of the number
    of available CPUs. This solves bug where the number of CPUs was detected
    incorrectly.
source/parse_crashdo.cpp:
  - Create new crash test for the isnan functions.
source/cddefines.h:
  - Define types int64 and uint64 on LP64 platforms.
  - Create overloaded versions of pow2 and pow3.
source/cont_gaunt.cpp:
  - Work around problems with braindead imlementations of the complex class.
source/Makefile:
  - Force -O0 when compiling parse_crashdo.cpp.

754 Directory Listing
Modified 15 years, 6 months ago
Mon Jan 1 23:32:07 2007 UTC
gary
Original Path: trunk/source
Log:
readme_makefile.htm - add readme file for makefile in source directory
753 Directory Listing
Modified 15 years, 6 months ago
Mon Jan 1 16:02:18 2007 UTC
gary
Original Path: trunk/source
Log:
punch_average - create the punch average command to generate output for grid results

assert_results - add grid option to assert temperature to assert temperature for each grid point, fix typos

cont_ffun.cpp - do not accept input energies of zero in table read - this prevents crash on div by zero

grid_do.cpp - tidy up source, typos 

parse_optimize.cpp - typos

parse_print.cpp - print size of bool

parse_punch.cpp - infrastructure needed for punch average command, change key matching "ages" to " age" to not trigger on "average"

punch.h - infrastructure needed for punch average command

punch_do.cpp - infrastructure needed for punch average command

change series of agn_S_uxx sims into on grid sim, and assert temperatures using assert temperature grid - this one sim fully replaces all individual models with same testing

ism.in - change to ism abundances rather than orion - no reason for orion to be used

ism_hot_brems.in - add comments that abundances starburst multiplies existing abundances by scale factor

runsome_purify.dat - correct name of one sime

751 Directory Listing
Modified 15 years, 6 months ago
Thu Dec 28 06:22:02 2006 UTC
gary
Original Path: trunk/source
Log:
punch_do.cpp - BUGFIX - hide option did not work on punResuts command so all input lines were written, rename pop to popul and make local to if clause to avoid name collision, remove several occurancces of asserting bool==true (assert bool is enough!), 

parse_commands.cpp - fix typo in comment

rfield.h - fix comments, especially distinction between coarse and fine continua

struc.h - small typo

comp4 - update readme and output - add dust to first sim so that space is allocated.

750 Directory Listing
Modified 15 years, 6 months ago
Tue Dec 26 20:12:04 2006 UTC
gary
Original Path: trunk/source
Log:
cddrive.cpp - fix print formation when line not found

ion_nitro.cpp - small change in logic setting up trace flag in call to

ion_solver.cpp - - minor changes in print, add co chem ct recom and ionization to debug print - no change in routine's results

iter_startend.cpp - save and reset chemistry charge transfer that affect ionizatino of elements in ion_solver, for catalytic reactions

mole_co_drive.cpp - minor change in comments

mole_co_etc.cpp - detect if number of co species has increased after initial malloc, and stop.  this happens in tsuite/programs comp4 as reported in ticket 8

bugfix mole_h_step.cpp - change bug entered in R743 caused access violation - now do assert if ratei is correct value 

prt_comment.cpp - tidy print state - near lines 1424, but this print should not happen for levels within topoff - also cast bool to int for use in arith

reset chemical rates in iter_startend.cpp fixes ticket 7 in trac repsotiry, also causes changes in orion_hii_pdr.in - orion_hii_pdr_pp.in - and pdr_th85ism_cgto.in 

pn_paris.in - small drift in asserted values

748 Directory Listing
Modified 15 years, 6 months ago
Sun Dec 24 18:37:58 2006 UTC
gary
Original Path: trunk/source
Log:
helike_cs.cpp - comment out open mp call

parse_print.cpp - print size of char

func_test.in - print path

744 Directory Listing
Modified 15 years, 6 months ago
Fri Dec 22 23:39:05 2006 UTC
rporter
Original Path: trunk/source
Log:
The call to CO_zero at line 85 of optimize_func.cpp breaks the code.  It causes a zero malloc every time the optimizer or grid is run.  At any rate, the routine was already being called inside cloudy() at line 133.
743 Directory Listing
Modified 15 years, 6 months ago
Fri Dec 22 20:05:51 2006 UTC
rporter
Original Path: trunk/source
Log:
Fix in iso_continuum_lower when lowering changes during calculation.
Easier to read cdLine printout when it cannot find line.
Checks for NaN in various places in molecular network.
hydrolevel.cpp, prt_lines_hydro.cpp, and prt_lines_helium.cpp: numLevels_local should have been numLevels_max.
Two new asserts in hydrorecom.cpp.
New bool iso.lgLevelsEverLowered, needed because sometimes lowering happens and then is undone by end of calc.
parse_commands.cpp: don't complain about large deduced thickness if specified thickness is small.
prt_comment.cpp: remove dead code, make comment if continuum was ever lowered.
zero.cpp: initialize new boot iso.lgLevelsEverLowered.
limit_lte_h_t50_coll.in: hydro 1 and 2 ionizations change because of continuum lowering fix.
742 Directory Listing
Modified 15 years, 6 months ago
Fri Dec 22 15:45:55 2006 UTC
rjrw
Original Path: trunk/source
Log:
Avoid multiple allocations of molecular solver space when optimizing.

740 Directory Listing
Modified 15 years, 6 months ago
Wed Dec 20 01:08:45 2006 UTC
gary
Original Path: trunk/source
Log:
there changes were introduced by Ryan Porter

*.h are change of structure names from xxx_t to t_xxxx as per PvH comment
*.cpp are mostly "if (" to "if("


733 Directory Listing
Modified 15 years, 6 months ago
Mon Dec 18 21:56:25 2006 UTC
gary
Original Path: trunk/source
Log:
atmdat_2photon.cpp - introduced error in previous rev - logical flag was correct in r730, is correct now

two sims changed asserted continuum in ir as result of spline rather than linear interpolation, fix in r730
732 Directory Listing
Modified 15 years, 6 months ago
Mon Dec 18 21:09:51 2006 UTC
gary
Original Path: trunk/source
Log:
change int used for logical vars to bool
make all vars with names lgXXX vars boolian, all boolian vars have names lgXXX

remove macros for TRUE and FALSE
all TRUE -> true, all FALSE -> false

nearly all files changed as result of these changes, so also updated copyright year to 2007

730 Directory Listing
Modified 15 years, 6 months ago
Mon Dec 18 18:19:53 2006 UTC
rjrw
Original Path: trunk/source
Log:
Correct initial value of lgFirstCall in atmdat_2photon.cpp


729 Directory Listing
Modified 15 years, 6 months ago
Sun Dec 17 19:13:45 2006 UTC
gary
Original Path: trunk/source
Log:
small changes in formatting, no significant changes
728 Directory Listing
Modified 15 years, 6 months ago
Sat Dec 16 19:39:14 2006 UTC
peter
Original Path: trunk/source
Log:
No code change; only lots of cosmetic changes to correct the layout after the
removal of BadMalloc().

724 Directory Listing
Modified 15 years, 6 months ago
Fri Dec 15 17:23:25 2006 UTC
peter
Original Path: trunk/source
Log:
source/cddefines.h:
source/cdinit.cpp:
  - Add support for PathScale EKOPath compiler.
  - Start updating compiler detection for C++ compilers.

715 Directory Listing
Modified 15 years, 6 months ago
Wed Dec 13 17:15:20 2006 UTC
gary
Original Path: trunk/source
Log:
Set new date.

714 Directory Listing
Modified 15 years, 6 months ago
Wed Dec 13 17:07:27 2006 UTC
gary
Original Path: trunk/source
Log:
parse_compile.cpp - two commands, compile stars and compile grains, failed
with mallocing array of length zero in atmdat_readin because the chemistry
network had not been established when atmdat_readin was called. Fix is to not
call atmdat_reading or ContCreatePointers when parsing these two commands
since only continuum needs to be set up.

atmdat_readin.cpp now checks that chemistry network has been established
before this routine is called. This would only fail if there were a major
logical error in the order of calling setup routines.

711 Directory Listing
Modified 15 years, 6 months ago
Wed Dec 13 00:11:31 2006 UTC
rjrw
Original Path: trunk/source
Log:
Eliminated BadMalloc now MALLOC dies rather than returning on failure.

710 Directory Listing
Modified 15 years, 6 months ago
Tue Dec 12 22:15:46 2006 UTC
rjrw
Original Path: trunk/source
Log:
Merged in small changes from newmole r704:708

709 Directory Listing
Modified 15 years, 6 months ago
Tue Dec 12 22:07:14 2006 UTC
rjrw
Original Path: trunk/source
Log:
Make sure malloc and calloc are caught when NDEBUG is set -- memory
can run out for external reasons.


707 Directory Listing
Modified 15 years, 6 months ago
Tue Dec 12 02:40:31 2006 UTC
peter
Original Path: trunk/source
Log:
source/cddefines.h:
  Corrected comment.

706 Directory Listing
Modified 15 years, 6 months ago
Tue Dec 12 02:18:11 2006 UTC
peter
Original Path: trunk/source
Log:
source/cddefines.h:
  - Modify condition for using standard malloc and calloc.
  - Add definition for Singleton template.
source/parse_set.cpp:
  - Remove SET PATH command, print error message instead.
  - Use modified t_ADfA struct.
source/cdinit.cpp:
  - Pick up path from environment variable CLOUDY_DATA_PATH.
  - Remove call to phfit().
source/Makefile:
  - Use environment variable CLOUDY_DATA_PATH.
source/atmdat.h:
source/atmdat_adfa.cpp:
  - Modify t_ADfA class to use Singleton.
  - Merge global struct PhFitOn into t_ADfA.
source/punch_do.cpp:
source/grains_mie.cpp:
source/punch_opacity.cpp:
source/zero.cpp:
source/cont_setintensity.cpp:
source/ion_recomb_Badnell.cpp:
source/prt_lines.cpp:
source/cont_gammas.cpp:
source/pressure_total.cpp:
source/helike_cs.cpp:
source/opacity_createall.cpp:
source/hydrorecom.cpp:
source/iso_create.cpp:
source/cont_createpointers.cpp:
source/hydrocollid.cpp:
source/ion_collis.cpp:
source/helike_recom.cpp:
source/punch_linedata.cpp:
  - Use modified t_ADfA struct.

704 Directory Listing
Modified 15 years, 7 months ago
Fri Dec 8 23:22:02 2006 UTC
peter
Original Path: trunk/source
Log:
Merging newmole branch to the mainline.
695 Directory Listing
Modified 15 years, 7 months ago
Thu Dec 7 23:24:30 2006 UTC
peter
Original Path: trunk/source
Log:
source/cdinit.cpp:
  Remove duplicate prototype definitions.

691 Directory Listing
Modified 15 years, 7 months ago
Thu Dec 7 20:55:39 2006 UTC
gary
Original Path: trunk/source
Log:
these are various small changes that have occurred, also Ryan Porter's changes to get code to run as C++ on SDX

atom_feii.cpp __HP_aCC macro name change

cddrive.cpp rearrange logic for __HP_aCC for clock

cdinit.cpp for HP_aCC define fegettrapenable and fesettrapenable, use it to trap floating point

cpu.h rename cpu)t to t_cpu

iso_cool.cpp - rename __HP_aCC

lines.h, lines_service.cpp - fix typoes

mole_h_step.cpp - rename __HP_aCC

parse_ratio.cpp - rename __HP_aCC

parse_table.cpp - rename __HP_aCC

parse_punch.cpp, punch_dp.cpp - give both emergent and intrinsic line intensities for punch lines array 

parse_set.cpp - bugfix, do not allow punch line width larger than c


685 Directory Listing
Modified 15 years, 7 months ago
Wed Dec 6 00:14:43 2006 UTC
gary
Original Path: trunk/source
Log:
dayslow_master.pl - use icl rather than gcc for slow test suite
ion_solver.cpp - undo bug introduced in rev 622.  now looks at matrix elements to see if singular
rt_stark.cpp - resolved ambiguous overload
blr_n09_p18_Z20.in - add punch convergence error command
limit_hi_ion.in - renamed func_hi_ion.in to this since it tests code in high ionization limit 
682 Directory Listing
Modified 15 years, 7 months ago
Tue Dec 5 19:33:25 2006 UTC
peter
Original Path: trunk/source
Log:
source/atmdat_adfa.cpp:
  Promote ADfA.CF to double precision.

681 Directory Listing
Modified 15 years, 7 months ago
Tue Dec 5 17:17:30 2006 UTC
peter
Original Path: trunk/source
Log:
The main purpose of this commit is to split off the atomic data from Dima
Verner's Atomic Data for Astrophysics (ADfA) routines into separate data files
in the data directory. These used to be block data statements in the fortran
code and had been inlined as data initialization loops in the C code by the
fortran to C conversion program.

source/atmdat_h_photocs_fit.cpp:
source/atmdat_phfit.cpp:
source/atmdat_H_phot_cs.cpp:
source/atmdat_coll_ion.cpp:
source/atmdat_rad_rec.cpp:
source/atmdat_rec_lines.cpp:
source/atmdat_h_rad_rec.cpp:
  Deleted.
source/atmdat.h
source/atmdat_adfa.cpp
  New data structure and routines to store the ADfA data. All the routines
  accessing the data that used to be in the deleted files above have been
  moved here.
source/punch_do.cpp
source/punch_opacity.cpp
source/opacity_addtotal.cpp
source/helike.cpp
source/cont_gammas.cpp
source/pressure_total.cpp
source/opacity_createall.cpp
source/iso_create.cpp
source/cont_createpointers.cpp
  Multiple minor changes to deal with the new data layout.
data/phfit.dat
data/hpfit.dat
data/h_phot_cs.dat
data/rad_rec.dat
data/coll_ion.dat
data/h_rad_rec.dat
data/rec_lines.dat
  New files containing the data from the old block data statements.

source/grains_mie.cpp
  Add references to the origin of some of the routines.

676 Directory Listing
Modified 15 years, 7 months ago
Mon Dec 4 03:28:31 2006 UTC
gary
Original Path: trunk/source
Log:
helike_level.cpp - bugfix - trace threw fpe in limit_eden.in in print statement.  fix some comments.

limit_eden.in - add comments that this strongly affected by charge transfer.
674 Directory Listing
Modified 15 years, 7 months ago
Sun Dec 3 05:13:53 2006 UTC
peter
Original Path: trunk/source
Log:
source/cont_gaunt.cpp:
  Remove three more places where z.real() was used as l-value.

673 Directory Listing
Modified 15 years, 7 months ago
Sun Dec 3 03:35:34 2006 UTC
peter
Original Path: trunk/source
Log:
source/grains_mie.cpp:
source/cont_gaunt.cpp:
source/thirdparty.cpp:
  Avoid using z.real() and z.imag() as l-values, this may not be supported everywhere.

672 Directory Listing
Modified 15 years, 7 months ago
Sun Dec 3 01:47:28 2006 UTC
peter
Original Path: trunk/source
Log:
source/cddefines.h:
source/grains_mie.cpp:
source/cont_gaunt.cpp:
source/sanity_check.cpp:
source/helike_cs.cpp:
source/helike_recom.cpp:
source/thirdparty.h:
source/thirdparty.cpp:
  - Removed our crufty complex implementation in favor of the default C++ complex type.
  - Moved expnf(), gammafun(), and subsidiaries to thirdparty.cpp
source/math_complex.h:
source/math_complex.cpp:
  - Deleted.

670 Directory Listing
Modified 15 years, 7 months ago
Sat Dec 2 03:31:12 2006 UTC
gary
Original Path: trunk/source
Log:
parse_commands.cpp - updated line intensities asserted in smoke test - change due to Badnell DRD
all *.in - changes due to Badnell DR
668 Directory Listing
Modified 15 years, 7 months ago
Fri Dec 1 17:04:54 2006 UTC
peter
Original Path: trunk/source
Log:
tsuite/auto/stars_optimize1.in:
tsuite/auto/stars_optimize2.in:
tsuite/auto/stars_optimize3.in:
  Fix test suite failures due to new Badnell DR rates.
source/punch_colden.cpp:
  Fix compiler warning.

663 Directory Listing
Modified 15 years, 7 months ago
Thu Nov 30 22:48:32 2006 UTC
gary
Original Path: trunk/source
Log:
merge of r662 from newmole, ambiguous overload
656 Directory Listing
Modified 15 years, 7 months ago
Thu Nov 30 16:56:53 2006 UTC
gary
Original Path: trunk/source
Log:
head_punch.cpp - BUGFIX - fractional heating was evaluated as a double and cast to a float, then asserted to be positive.  Assert was thrown when underflow to zero was detected.  Now only do this if value is greater than SMALLFLOAT

parse_punch.cpp, punch.h, punch_colden.cpp, punch_do.cpp, punch some column densiteis now writes header info into string for one-time printout in grid calculations

*.in - continuing update of test suite after enabling Badnell DR

654 Directory Listing
Modified 15 years, 7 months ago
Thu Nov 30 03:33:19 2006 UTC
gary
Original Path: trunk/source
Log:
dynamics.cpp - comment within comment fixed

*.in - further updates of changes in test suite due to Badnell Dr

652 Directory Listing
Modified 15 years, 7 months ago
Thu Nov 30 00:23:16 2006 UTC
gary
Original Path: trunk/source
Log:
the big change below is enabling the Badnell DR rates.  a good fraction of the test suite results changed as a result.  the next merge will update part of the auto test suite, but not half.  with this rev by itself the test suite will certainly not pass cleanly, but there should be no fpes.

zero.cpp - turn on Badnell DR by default

mole_co_etc.c - CRITICAL BUG FIX - make sure this goes into Robin's newmole
delay including ice formation on grains until both molecule and ion solvers have had at least one pass.  Early evaluation before other solver had worked caused catastropic ice formation.

ion_solver.cpp - CRITICAL BUG FIX - make sure this goes into Robin's newmole
delay including source terms from chemistry solver until both ion and chem solvers have been called twice - prevents very large & bogus source terms from molecular network from upsetting the approach to a solution

punch_do.cpp 
punch out radius command introduced
minor rewrite of if logic to avoid block nesting limits in vs2005

parse_punch.cpp 
punch outer radius option

punch_colden.cpp
do not check on element and ion, so now possible to get molecular column densities

prt_comment.cpp
BUGFIX - fpe occured for VERY high ionization conditions where H0 abundance underflowed - protect against division

heat_sum.cpp 
BUGFIX - fpe occurred for VERY high ionization conditions when AtomicCollidDensity underflowed to zero - protect against division

dynamics.cpp
turn off CO network when advection is active - a conservation error developes which it cannot converge away from

conv_base.cpp
move IonChlor to before CO_drive call so that all elements within co mole network are evaluated before CO called
646 Directory Listing
Modified 15 years, 7 months ago
Wed Nov 29 03:19:18 2006 UTC
gary
Original Path: trunk/source
Log:
cddrive.cpp give units of column density for comment for cdColm

cddrive.h - same

punch_colden.cpp - finish punch some column densities

645 Directory Listing
Modified 15 years, 7 months ago
Wed Nov 29 01:59:43 2006 UTC
gary
Original Path: trunk/source
Log:
forgot to add punch_colden.cpp to handle some option on punch column density
644 Directory Listing
Modified 15 years, 7 months ago
Wed Nov 29 01:53:18 2006 UTC
gary
Original Path: trunk/source
Log:
add terminal option to punch wind command

add some option to punch column densities command

add emission lines to to pdr sims so that to check effects of badnell dr

638 Directory Listing
Modified 15 years, 7 months ago
Mon Nov 27 12:28:37 2006 UTC
gary
Original Path: trunk/source
Log:
atmdat_readin.cpp - add comment with data saying that changed from default behar to gu UTA data

*.in - these changes are in ionization of Fe due to differences between new Gu and older Behar data

636 Directory Listing
Modified 15 years, 7 months ago
Sun Nov 26 21:47:51 2006 UTC
gary
Original Path: trunk/source
Log:
updated Fe UTA to Gu et al. 2006

ionbal.h add global variable lgInnerShell_Gu06 to setlect between Gu or Behar UTA data

zero.cpp - use Gu 06 UTA data by default

parse_set.cpp - set UTA command introduced

atmdat_readin.cpp - option to use either gu or behar uta data, now gu uta by default, both replaced by Romas data where available

renamed UTA data files to UTA_author.dat for consistency

634 Directory Listing
Modified 15 years, 7 months ago
Sun Nov 26 01:48:06 2006 UTC
gary
Original Path: trunk/source
Log:
cddefines.h - add directives for PCLint

rm compiling.txt - info is old and web site if far better

remainder are comments or changed print statements
633 Directory Listing
Modified 15 years, 7 months ago
Sat Nov 25 15:10:05 2006 UTC
gary
Original Path: trunk/source
Log:
move evaluation of badnell dielectronic and radiative recombination from conv_base into ion_recom_Badnell

conv_base.cpp, abort when stop ntotalioniz reached

parse_stop.cpp - add stop nTotalIonize command

rest are corrections to comments

631 Directory Listing
Modified 15 years, 7 months ago
Fri Nov 24 23:21:44 2006 UTC
gary
Original Path: trunk/source
Log:
orion_hii_pdr.in - very weak co lines differ by about 20% between vs2005 and icl - assert mean of the two and increase error a bit
630 Directory Listing
Modified 15 years, 7 months ago
Fri Nov 24 20:02:58 2006 UTC
gary
Original Path: trunk/source
Log:
punch_do.cpp - corrections to comments
629 Directory Listing
Modified 15 years, 7 months ago
Fri Nov 24 14:09:11 2006 UTC
gary
Original Path: trunk/source
Log:
zero.cpp - turn on Badnell radiative recombination by default

zerologic.cpp - bugfix flag for printing continuum indices was on by default, should have been off

sims changes as result of using Badnell RR rather than older values
most changes were due to changes in the Mg+ and Al++ rec - no dramatic changes resuled, but some larger changes were
coll_t5 mg 2
igm_lalpha - mg 1,2 balance
pn_paris - mg 2 2798 a lot
stars tests - al 3 fraction changed a bit, al 2 and 4 also

628 Directory Listing
Modified 15 years, 7 months ago
Fri Nov 24 03:20:12 2006 UTC
gary
Original Path: trunk/source
Log:
several files have small changes in comments

cont_ipoint.cpp, parse_print.cpp, prt.h - implement print continuum indices command

parse_set.cpp - badnell option on set recom commands now has off option, to turn off once it is turned on


627 Directory Listing
Modified 15 years, 7 months ago
Thu Nov 23 22:04:32 2006 UTC
peter
Original Path: trunk/source
Log:
source/grains_mie.cpp:
source/cddefines.h:
source/thirdparty_lapack.cpp:
source/cdinit.cpp:
source/utilitymacros.h:
  Remove conditional compilation for C++, this is the standard now.

624 Directory Listing
Modified 15 years, 7 months ago
Thu Nov 23 14:44:29 2006 UTC
gary
Original Path: trunk/source
Log:
ion_solver.cpp - bring back RJRW code for other methods of solving system of ionization balance equaitons
622 Directory Listing
Modified 15 years, 7 months ago
Wed Nov 22 15:46:13 2006 UTC
gary
Original Path: trunk/source
Log:
update comments in several files

prt.h, zerologic.cpp, parse_print.cpp, add option "only element" to the print array command

ion_solver.cpp - detect very small H molecular abundances and use homogeneous case in this limit

616 Directory Listing
Modified 15 years, 7 months ago
Tue Nov 21 21:42:53 2006 UTC
rjrw
Original Path: trunk/source
Log:
Factored logic out of a loop in GrainTemperature for a small but 
measureable speedup.

613 Directory Listing
Modified 15 years, 7 months ago
Mon Nov 20 23:09:35 2006 UTC
gary
Original Path: trunk/source
Log:
nightly_copy_files_original.pl, nightly_copy_source.pl - change *.c to *.cpp in copying source to ftp dir and creating backups

elementnames.h - comments - this contains a constructor written by PvH, the first C++ code in cloudy.
611 Directory Listing
Modified 15 years, 7 months ago
Sun Nov 19 23:12:19 2006 UTC
peter
Original Path: trunk/source
Log:
source/punch_fits.cpp:
source/h2.h:
source/state.h:
source/punch_line.cpp:
source/dynamics.h:
source/thirdparty_lapack.cpp:
source/mole_h2.cpp:
source/punch.h:
source/dynamics.cpp:
source/state.cpp:
  Fix various warnings issued by g++ 4.2.0.

610 Directory Listing
Modified 15 years, 7 months ago
Sun Nov 19 19:20:36 2006 UTC
peter
Original Path: trunk/source
Log:
source/cddefines.cpp:
source/mole_co_etc.cpp:
source/elementnames.h:
source/zerologic.cpp:
  Fix various warnings issued by g++ 4.1.1.

604 Directory Listing
Modified 15 years, 7 months ago
Sun Nov 19 17:12:08 2006 UTC
peter
Original Path: trunk/source
Log:
Move the code to C++ - global rename *.c -> *.cpp
602 Directory Listing
Modified 15 years, 7 months ago
Sat Nov 18 18:31:37 2006 UTC
gary
Original Path: trunk/source
Log:
parse_commands.c - change asserted value of [OIII] 5007 for the smoke test.  result had drifted away from asserted value over past year.
601 Directory Listing
Modified 15 years, 7 months ago
Sat Nov 18 16:03:19 2006 UTC
peter
Original Path: trunk/source
Log:
source/stars.c:
  Rename val -> pval to prevent hiding variable in outer scope.
source/grains.c:
  Delete inactive code that is now being developed on separate branches.

600 Directory Listing
Modified 15 years, 7 months ago
Sat Nov 18 14:58:53 2006 UTC
gary
Original Path: trunk/source
Log:
a series of trivial changes correcting minor comments by the intel compiler.  no change in functionality of the code.
597 Directory Listing
Modified 15 years, 7 months ago
Tue Nov 14 22:21:19 2006 UTC
gary
Original Path: trunk/source
Log:
two changed file to compile as C++

cddefines.c - do not have second definition of same var - set string value in cddefines function instead

stars.c - ambiguous overloaded pow - added casts to double

input.txt - improve documentation

596 Directory Listing
Modified 15 years, 7 months ago
Sun Nov 12 16:40:07 2006 UTC
gary
Original Path: trunk/source
Log:
tfidle add alnte to phycon struc, the ln of the temperature
phycon.h - same

cool_oxyg.c - NA update [OIV] collision strength to Tayal 2006 - value is smaller so gas is warmer

atom_seq_boron - only changes in comments

atmdat_char_tran.c - use alnte rather than reevaluating

*.in - changes caused by decreased cooling in th [OIV] line

595 Directory Listing
Modified 15 years, 7 months ago
Sat Nov 11 14:22:52 2006 UTC
gary
Original Path: trunk/source
Log:
changes in comments and source code layout only
593 Directory Listing
Modified 15 years, 7 months ago
Sat Nov 11 13:33:27 2006 UTC
gary
Original Path: trunk/source
Log:
BUGFIX - index for current continuum was incremented before that continuum was fully defined.  fpe resulted.
586 Directory Listing
Modified 15 years, 8 months ago
Mon Nov 6 11:16:30 2006 UTC
peter
Original Path: trunk/source
Log:
source/optimize.h:
  Bug-fix: prevent possible buffer overrun in chOptimFileName.

584 Directory Listing
Modified 15 years, 8 months ago
Sat Nov 4 23:35:17 2006 UTC
peter
Original Path: trunk/source
Log:
source/optimize.h:
source/cddefines.c:
  - Expose length of chOptimFileName[] buffer to libmudflap.
source/reason.h:
source/iter_end_chk.c:
source/zerologic.c:
source/prt_comment.c:
  - Bug found by libmudflap: fix overflow of reason.chReason buffer.
source/cont_setintensity.c:
  - Bug found by libmudflap: fix out-of-bounds access of rfield.fine_anu[].

579 Directory Listing
Modified 15 years, 8 months ago
Sat Oct 28 22:22:59 2006 UTC
gary
Original Path: trunk/source
Log:
mole_h_step.c - TE correct energy conservation problem with his fit to the dissociation and heating rates for the small H2 in a very spherical geometry.  In this case the G0 at the illuminated face must be corrected for the spherical dilution of radiation.  also the direct heating.

problem manifested itself as non-conservation of energy in hydrogen-only spherical nebulae.

this rev will be added to the c06.02 branch

578 Directory Listing
Modified 15 years, 8 months ago
Sat Oct 28 22:15:21 2006 UTC
gary
Original Path: trunk/source
Log:
 conv_ioniz.c - comments

conv_pres_temp_eden_ioniz.c - comments

conv_temp_eden_ioniz.c - comments

mole_h_step.c - comments

parse_compile.c - comments 

parse_table.c - comments


577 Directory Listing
Modified 15 years, 8 months ago
Sat Oct 28 16:52:28 2006 UTC
peter
Original Path: trunk/source
Log:
source/parse_table.c:
source/stars.c:
source/stars.h:
  - Add support for the following new commands:
      TABLE STAR <grid> LIST
      TABLE STAR AVAIL
  - Replace grid_parms -> stellar_grid.

576 Directory Listing
Modified 15 years, 8 months ago
Wed Oct 25 17:50:17 2006 UTC
peter
Original Path: trunk/source
Log:
source/parse_table.c:
  Bug-fix: insert BSTAR/OSTAR keyword in optimizer command for TABLE STAR TLUSTY.

574 Directory Listing
Modified 15 years, 8 months ago
Tue Oct 24 19:49:53 2006 UTC
gary
Original Path: trunk/source
Log:
readme.txt - describe log files created by nightly rungs

atmdat_2photon.c - replace 29 in array size with LIMELM-1

cool_iron.c - rm unused var k

cpu.c - trivial formatting changes

grains_qheat.in and heatomt10lon.in - small changes in IR continuum, near 10 microns, for no apparent reason!!  only 5% change, will not track down

571 Directory Listing
Modified 15 years, 8 months ago
Fri Oct 20 16:24:32 2006 UTC
peter
Original Path: trunk/source
Log:
source/parse_table.c:
source/stars.c:
source/stars.h:
  - Add support for new Tlusty BSTAR2006 grid; added keyword to TABLE STAR TLUSTY
    command to choose between OSTAR2002 and BSTAR2006 grids.
  - COMPILE STARS "userfile.ascii" now always calls ValidateGrid().
  - Some minor improvements.
tsuite/auto/stars_ostar2002.in:
tsuite/auto/stars_ostar2002_all.in:
tsuite/auto/stars_ostar2002_3d.in:
  - Updated command syntax for TABLE STAR TLUSTY command.
tsuite/auto/stars_bstar2006_3d.in
tsuite/auto/stars_bstar2006_all.in
tsuite/auto/stars_bstar2006.in
  - New test cases for the BSTAR2006 grid.

570 Directory Listing
Modified 15 years, 8 months ago
Thu Oct 19 16:19:29 2006 UTC
peter
Original Path: trunk/source
Log:
source/cpu.c:
source/cpu.h:
source/cool_iron.c:
source/parse_crashdo.c:
source/zero.c:
  Remove SET_FLT_SNAN and SET_DBL_SNAN macros altogether and replace with the new
  and safer set_flt_snan, set_fltarr_snan, set_dbl_snan, set_dblarr_snan routines.

569 Directory Listing
Modified 15 years, 8 months ago
Wed Oct 18 21:29:20 2006 UTC
rjrw
Original Path: trunk/source
Log:
Add cache for (constant) interpolating coeffs in atmdat_2photon.c 
to shave some cycles.

565 Directory Listing
Modified 15 years, 8 months ago
Sat Oct 14 13:46:29 2006 UTC
gary
Original Path: trunk/source
Log:
cool_iron.c - minor changes to comments, set all of fe10 cs arrays to nan

mole_h2_io.c - small changes in comments

mole_h_step.c - small changes in comments

prt_lines_continuum.c - small changes in comments

stars.c - small changes in comments


562 Directory Listing
Modified 15 years, 8 months ago
Tue Oct 10 19:46:29 2006 UTC
rjrw
Original Path: trunk/source
Log:
Fix underflow problem with pgcc which showed up on pdr_co_fully_noneq.

561 Directory Listing
Modified 15 years, 8 months ago
Tue Oct 10 08:42:16 2006 UTC
gary
Original Path: trunk/source
Log:
put float cast in zero.c to prevent comment on demotion from double to float
560 Directory Listing
Modified 15 years, 8 months ago
Tue Oct 10 06:42:57 2006 UTC
rjrw
Original Path: trunk/source
Log:
More array size fixes.

559 Directory Listing
Modified 15 years, 8 months ago
Mon Oct 9 23:09:45 2006 UTC
rjrw
Original Path: trunk/source
Log:
More fixes for the new molecular network size on the reduced mass fill.

558 Directory Listing
Modified 15 years, 8 months ago
Mon Oct 9 19:49:23 2006 UTC
rjrw
Original Path: trunk/source
Log:
Fixed bug in use of reduced mass factors for turbulent corrections, 
and improved string handling in species code.

557 Directory Listing
Modified 15 years, 8 months ago
Mon Oct 9 13:42:03 2006 UTC
peter
Original Path: trunk/source
Log:
source/cpu.h:
source/cpu.c:
  SET_FLT_SNAN(X) and SET_DBL_SNAN(X) are now implemented as routines.
  This should guard against aliasing problems.

555 Directory Listing
Modified 15 years, 9 months ago
Sat Oct 7 20:12:23 2006 UTC
gary
Original Path: trunk/source
Log:
sets of trivial changes after running pclint on entire project.lnt
rm unused header files from several source

correct indentation errors

554 Directory Listing
Modified 15 years, 9 months ago
Fri Oct 6 21:25:56 2006 UTC
gary
Original Path: trunk/source
Log:
cddrive.c - elapsed time came out roughly 50% too long on visual studio or intel compiler 
553 Directory Listing
Modified 15 years, 9 months ago
Fri Oct 6 16:20:02 2006 UTC
peter
Original Path: trunk/source
Log:
source/stars.c:
  Bug-fix: fixed buffer overrun in GridInterpolate().

552 Directory Listing
Modified 15 years, 9 months ago
Fri Oct 6 10:05:35 2006 UTC
peter
Original Path: trunk/source
Log:
source/stars.c:
  Bug-fix: CompileAtmosphereCoStar made explicit assumptions about the size
  of the Edges array. Also fixed typographical error.

551 Directory Listing
Modified 15 years, 9 months ago
Fri Oct 6 02:04:38 2006 UTC
gary
Original Path: trunk/source
Log:
a wide range of trivial changes in response to compiling with /W4 on intel icl compiler, the windows version of icc.  many were static routines that had not been declared static.
550 Directory Listing
Modified 15 years, 9 months ago
Thu Oct 5 22:27:36 2006 UTC
rjrw
Original Path: trunk/source
Log:
Attempt to avoid triggering Intel compiler warnings by making routines 
file static or declaring in an include file.

549 Directory Listing
Modified 15 years, 9 months ago
Thu Oct 5 18:23:54 2006 UTC
rjrw
Original Path: trunk/source
Log:
Re-order loop for speed.

548 Directory Listing
Modified 15 years, 9 months ago
Thu Oct 5 01:54:33 2006 UTC
gary
Original Path: trunk/source
Log:
parse_print.c - gcc reported two errors - one macro in MS VS2005 float.h was not defined in cygwin, removed it, warning that ints were printed with long int format, fixed
due to first error did not compile with gcc

h2_orion_hii_pdr.in - change in OI intensity due to change in collision strength introduced two revs ago
547 Directory Listing
Modified 15 years, 9 months ago
Wed Oct 4 22:17:34 2006 UTC
gary
Original Path: trunk/source
Log:
cool_oxyg.c - update [OI] optical line collision strengths to Barklem,P.S.,2006,A&A (astroph 0609684) - collision strength for 6300,6363 double can be as much as 3x larger

parse_print.c - add some constants from float.h

*.in - update asserted line strengths - mainly effects of larger [OI] collision strength

546 Directory Listing
Modified 15 years, 9 months ago
Wed Oct 4 22:16:10 2006 UTC
rjrw
Original Path: trunk/source
Log:
Restructure element addressing data into nascent element object within mole.h

545 Directory Listing
Modified 15 years, 9 months ago
Wed Oct 4 19:25:04 2006 UTC
rjrw
Original Path: trunk/source
Log:
Add back declarations of rate functions which remain.

544 Directory Listing
Modified 15 years, 9 months ago
Wed Oct 4 17:47:25 2006 UTC
rjrw
Original Path: trunk/source
Log:
Removed old CO molecule implementation which is no longer used.

tags/newmole-0.1 contains reference version with both implementations 
available, depending on setting of NEWMOLE preprocessor macro, for 
intercomparison.

538 Directory Listing
Modified 15 years, 9 months ago
Tue Oct 3 15:20:08 2006 UTC
peter
Original Path: trunk/source
Log:
Merging newgrids branch.

This branch had several goals:

1. restructure the code for handling stellar atmosphere grids.

  The main reason for restructuring the code was that there was a lot of code
  duplication, leading to lots of trivial errors. The restructuring has split
  off all duplicated code into separate routines. There were also minor
  differences in the way each grid was set up, making them incompatible. These
  differences have been removed. Now the new structure is in place, adding new
  grids will be very easy. The code has been rewritten to handle grids with
  more than 2 dimensions. This enables interpolation in metallicity and
  possibly other parameters (e.g. Mdot).

2. updating the format of the ascii and binary atmosphere files.

  Since the changes above did break all existing binary atmosphere files,
  this was a good moment to update the format of both the ascii and binary
  files. The most important changes were that the ascii files got version
  numbers, and that the binary files for 32-bit and 64-bit versions of the
  code are now compatible.

3. add support for new grids, and update existing ones.

  - the Kurucz Atlas models have been updated to the most recent version,
    and support has been added for non-solar metallicities as well as the
    ODFNEW models.
  - The old Kurucz (1979) and Mihalas grids are no longer hardwired into
    the code, but are now split off and treated like any other grid.
  - Starburst99 output files are now transformed into the same format as
    the atmosphere grids. The TABLE STARBURST command has been retired.
  - the Rauch H-Ca grid has been updated to the final version.
  - 3-dim versions of the Rauch H-Ca and H-Ni grids have been added to
    enable interpolation in log(Z).
  - support has been added for the Rauch pure hydrogen, pure helium, H+He,
    and PG1159 grids.
  - support has been added for the Tlusty OSTAR2002 grid (all metallicities).
    The TABLE TLUSTY command has been retired.
  - support has been added for the WMBASIC grid of O-star models.

source/stars_atlas.c:
source/stars_costar.c:
source/stars_kurucz79.c:
source/stars_mihals.c:
source/stars_rauch02.c:
source/stars_rauch_old.c:
source/stars_rebinatmosphere.c:
source/stars_werner.c:
  Deleted and merged into
source/stars.c

source/stars.h:
source/cont_ffun.c:
source/parse_table.c:
source/parse_compile.c:
  Modified to support new grid structure.

tsuite/auto/stars_costar.in:
  Renamed to
tsuite/auto/stars_costar1.in

tsuite/auto/stars_kurucz.in:
  Renamed to
tsuite/auto/stars_kurucz79.in

tsuite/auto/stars_rauch.in:
  Renamed to
tsuite/auto/stars_rauch_h-ni.in

tsuite/auto/stars_rauchold.in:
  Renamed to
tsuite/auto/stars_rauch_h-ca.in

tsuite/auto/stars_mihalas.in:
tsuite/auto/stars_starburst99.in:
  Minor text changes.

tsuite/auto/stars_starburst99.dat:
  Deleted.

tsuite/auto/stars_wmbasic.in:
tsuite/auto/stars_atlas_3d.in:
tsuite/auto/stars_ostar2002.in:
tsuite/auto/stars_costar4.in:
tsuite/auto/stars_optimize1.in:
tsuite/auto/stars_rauch_3d.in:
tsuite/auto/stars_rauch_hydr.in:
tsuite/auto/stars_rauch_h+he.in:
tsuite/auto/stars_ostar2002_all.in:
tsuite/auto/stars_optimize2.in:
tsuite/auto/stars_rauch_helium.in:
tsuite/auto/stars_ostar2002_3d.in:
tsuite/auto/stars_atlas_all.in:
tsuite/auto/stars_rauch_pg1159.in:
tsuite/auto/stars_optimize3.in:
tsuite/auto/stars_atlas_odfnew_all.in:
tsuite/auto/stars_costar2.in:
tsuite/auto/stars_costar3.in:
  New test suite cases to test new grids.

source/mole_co_reactions.c
source/mole_co_step.c
  Fixed svn:eol-style property.

534 Directory Listing
Modified 15 years, 9 months ago
Sun Oct 1 12:28:50 2006 UTC
gary
Original Path: trunk/source
Log:
BUGFIX - under Cygwin & windows gcc io lib could put a carriage return at the end of a line.  as a result some null lines could begin with a cr.  we now interpret a cr as equivalent to a nl

h2_pdr_leiden_v2.in - change asserted molecular column densities from rjrw co network update in r532
533 Directory Listing
Modified 15 years, 9 months ago
Sat Sep 30 13:03:50 2006 UTC
gary
Original Path: trunk/source
Log:
changes in asserted values in test suite from rjrw merge of co chem network

532 Directory Listing
Modified 15 years, 9 months ago
Fri Sep 29 07:35:10 2006 UTC
rjrw
Original Path: trunk/source
Log:
Merged newmole changes r466:531 into trunk.

529 Directory Listing
Modified 15 years, 9 months ago
Thu Sep 28 16:57:49 2006 UTC
gary
Original Path: trunk/source
Log:
merging with newmole - various very small changes
528 Directory Listing
Modified 15 years, 9 months ago
Thu Sep 28 16:41:29 2006 UTC
gary
Original Path: trunk/source
Log:
small changes in merge with newmole
519 Directory Listing
Modified 15 years, 9 months ago
Sat Sep 23 17:08:11 2006 UTC
gary
Original Path: trunk/source
Log:
mole_co_solve.c - turn advection for co back on

others are comments

these are further steps in the merge
515 Directory Listing
Modified 15 years, 9 months ago
Fri Sep 22 10:36:26 2006 UTC
gary
Original Path: trunk/source
Log:
merging with nemole branch
513 Directory Listing
Modified 15 years, 9 months ago
Thu Sep 21 22:14:52 2006 UTC
gary
Original Path: trunk/source
Log:
further work on merge of Robin Williams' newmole branch with mainline.  

cdPrtWL added back to cddrive.c - needed for loc scripts, had been removed in previous rev

512 Directory Listing
Modified 15 years, 9 months ago
Thu Sep 21 11:11:09 2006 UTC
gary
Original Path: trunk/source
Log:
these changes are part of them merge of Robin Williams CO network branch back into the mainline 
511 Directory Listing
Modified 15 years, 9 months ago
Wed Sep 20 23:14:50 2006 UTC
gary
Original Path: trunk/source
Log:
atmdat_char_tran.c - comments, add commented out lines to change Fe and Mg ct

comments, moved vars in anticipation of major merge with Robin's source
509 Directory Listing
Modified 15 years, 9 months ago
Wed Sep 20 10:41:12 2006 UTC
gary
Original Path: trunk/source
Log:
changes in header files from Robin Williams development of newmole branch
501 Directory Listing
Modified 15 years, 9 months ago
Mon Sep 18 13:44:16 2006 UTC
gary
Original Path: trunk/source
Log:
input.c - bugfix - on gcc / cygwin the last char in a line is a cr not a nl - so "C" comment with no space was not detected.  now check on cr

parse_set.c - set hcorr did not set i before call to free format scanner - memory violation

add molecular trace convergence print

rest are changes in comments

500 Directory Listing
Modified 15 years, 9 months ago
Sat Sep 16 11:55:33 2006 UTC
gary
Original Path: trunk/source
Log:
update comments

ion_recomb.c - punch recomb coef now does old and new dr explicitly

add print option to test command to print all commands it issues


499 Directory Listing
Modified 15 years, 9 months ago
Tue Sep 12 10:39:18 2006 UTC
gary
Original Path: trunk/source
Log:
mole_co_drive.c - near line 475, add test on the H+/H ratio, and do not do the co network if H+/H>0.5.  this was added by NA to delay evaluation of the co network until conditions become appropriate.  It had little effect on the test suite results but should speed up the code.

orion_hii_pdr.in - - 0.1 dex changes in intensities of very optically thick CO lines as result of delaying evaluation of CO network until later.  this is down in the noise.  changed values and increased uncertainty in asserted co lines to 0.15 dex, the uncertainty in the column densities.
498 Directory Listing
Modified 15 years, 9 months ago
Sun Sep 10 15:21:52 2006 UTC
gary
Original Path: trunk/source
Log:
small changes in comments in several files

define co.lgCO_Init_called - set FALSE when cdinit called, set TRUE when CO_Init is called.  asserted to be true in co drive to make sure the init did occur


497 Directory Listing
Modified 15 years, 9 months ago
Sat Sep 9 18:28:13 2006 UTC
gary
Original Path: trunk/source
Log:
hydrogenic.h remove two flags that detected Lya masing for hydrogen alone - hydrogenic.h

prt_comment.c replaced with loop near line 1414 of prt_comment.c that detects masers for entire iso seq

*.in - remove confusing dust word from punch grains commands
496 Directory Listing
Modified 15 years, 10 months ago
Fri Sep 8 13:13:05 2006 UTC
gary
Original Path: trunk/source
Log:
grid routines altered by Ryan Porter so that punch does not output header for each grid point and third parameter on grid command is increment, as in a for loop, rather than the number of points

parse_punch changed to write header into string in all instances, then decide at end of routine whether to write the string, to implement not putting headers on each grid point

punch grid command introduced

punch options in func_grid.in changed to 

Ryan porter change more instances of iso.numLevels_max to iso.numLevels_local for continuum lowering


495 Directory Listing
Modified 15 years, 10 months ago
Thu Sep 7 01:49:21 2006 UTC
gary
Original Path: trunk/source
Log:
cddefines.h - improve comments

geometry.h variable AngleIllum was actually the direcional cosign.  split into two variables, AngleIllumRadian - angle away from normal in radians, and DirectionalCosin, the directional cosign

ParseDriveCmnd renamed to ParseDrive

parse_commands cnange call to ParseDriveCmnd to new name, rework illuminate command to keep two vars separate, add vary option to illuminate so that we can run grid with it

add drive E1 command

LineList_HeH.dat - add comments tha tfile needs lines that are not predicted by default

pdr_leiden_f1.in - add punch co chemistry


494 Directory Listing
Modified 15 years, 10 months ago
Tue Sep 5 14:50:13 2006 UTC
gary
Original Path: trunk/source
Log:
lgInputComment - comment line parser written - arg is string returns true if constant.  

combined input_init and input_readxx into input.c, add above command parser to this file

maincl.c - allow _, [, and ] char in comments

mole_co_solve.c line 83 - comment out advection for CO

parse_radius.c - create warning if outer radius set and radius being optimized since interpretation of second number changes when first becomes larger or smaller than second

pressure_total.c line 712, after conversation with Robin Williams, clean up branch on test for time variable with constant density vs variable density


492 Directory Listing
Modified 15 years, 10 months ago
Sat Sep 2 20:56:40 2006 UTC
gary
Original Path: trunk/source
Log:
comments updated in many files 

hydro and he-like iso sequences, Ryan Porter expand continuum lowering to include H-like sequences, many places iso.numLevels_max, the largest number of possible levels, (used to malloc space) replaced with iso.numLevels_local, the local number of levels if continuum has been lowered.

hydrogenic.c - now call iso_continuum_lower to lower H-like continua

logical variable iso.lgFullSize renamed to iso.lgLevelsLowered - this says if continuum has been lowered for numLevels_max

parse_hden - check order of magnitude of hydrogen density before doing 10^x (making linear rather than log) to prevent crash on errors like "hden 130" (which I did).  Code will make note of bad hden and stop

punch commands reorganised by Ryan Porter to work with grids.  No longer complain that punch cannot be used with optimize or grid commands. 

move calls to
	CO_Init();
	hmole_init();
	H2_Init();
from cdInit to zero - fixed bug where molecules did not converge in grids




489 Directory Listing
Modified 15 years, 10 months ago
Fri Aug 25 15:40:56 2006 UTC
gary
Original Path: trunk/source
Log:
these are a series of changes related to the grid command, and increasing the number of comments in the he-like code.  All changes to the source were made by Ryan Porter.

the grid command now requires three args, the lower and upper bounds, and the number of points.

in the orion_hii_pdr_xx models two changes - total pressure with magnetic field, and stop column density 22.  first is more realistic, second is because most molecular clouds have similar column densities, about long N 22.  these two had gone to column densities of 25.
487 Directory Listing
Modified 15 years, 10 months ago
Sun Aug 20 12:54:01 2006 UTC
gary
Original Path: trunk/source
Log:
lines_service - add routine ConvRate2CS to convert line deexcitation rate into collision strength

cool_oxyg update to Krems et al. H0 collision rate for [OI] emission

he1n2t4.in - wavelength of 10830 slightly different - this uses more sig fig for lines
486 Directory Listing
Modified 15 years, 10 months ago
Sat Aug 19 14:55:50 2006 UTC
gary
Original Path: trunk/source
Log:
cddrive.c, .h, lines_service, rm cdPrtWl for lines, this just called prt_wl, so now all routines call prt_wl

prt_lines_helium.c - mean wavelength of three lines of 2 ^3S - 2 ^3P multiplet is used, with label TOTL, rather than first line in the multiplet

change in multiplet wavelength required that several line list files also change


484 Directory Listing
Modified 15 years, 10 months ago
Fri Aug 18 18:03:13 2006 UTC
gary
Original Path: trunk/source
Log:
helike.h - update magic number for he-seq trans prob data file

helike_einsta - use Johnson As for up to & including Ar, higher Z use Lin et al
Johnson did not include higher than Ar so was extrapolation

helike_level - do not set PopLTE to zero for levels within lowered continuum

iso_cool - loop for coll ion cool - 3bod heat went to numLevels_max, should have been local to treat only levels that are active for this continuum -lowered model of atom

iso_ionize_recombine - similar change

prt_lines_helium - changes in prediction of satellite line intensities
2^3P - 2^3S multiplet wavelength now mean of three lines


483 Directory Listing
Modified 15 years, 10 months ago
Fri Aug 18 11:03:56 2006 UTC
gary
Original Path: trunk/source
Log:
small changes in comments and print statements

cool_oxyg.c - HN improve fit to OIII cs, better temp dependence

ion_recomb_Badnell.c - update Fe DR and RR to his astro post of aug 2006, does Fe8+ through Fe14+

change in fit to OIII cs and much larger fe dr changed several simulations

482 Directory Listing
Modified 15 years, 10 months ago
Thu Aug 17 11:54:52 2006 UTC
gary
Original Path: trunk/source
Log:
these mods allow compilation as a C++ code.  the struc names were embellished with an ending _t - this embellishments had been removed to make doxygen output more used, but broke class definiations in c++.  this change allows both doxygen and C++ to be happy

atmdat_readin.c  parse_atomhlike.c  parse_radius.c - overloaded pow function needed cast to float in first arg for C++ to compile
481 Directory Listing
Modified 15 years, 10 months ago
Wed Aug 16 11:52:57 2006 UTC
gary
Original Path: trunk/source
Log:
rfield.ConEmitLocal now 2d array - [depth][energy]

update bands_continuum.dat and magic number

cont_setintensity.c - print comment if ioniz par is far too high

geometry.nend_max is max number of iterations to do, used to define size of vector rfield.ConEmitLocal

ion_recom_Bandell.c - add more lower charge states for Fe from recent badnell paper

prt_lines_continuum.c work on na bands

pressure_total - 5/2 vs 3/2 around line 710 to do with PdV work in vary press model

radius_next.c comment out max dr from grain emission optical depth

rt_diffuse.c - rfield.ConEmitLocal[depth][energy] - new depth var for move to exact rt


480 Directory Listing
Modified 15 years, 10 months ago
Sun Aug 13 03:56:21 2006 UTC
gary
Original Path: trunk/source
Log:
radius_next.c add logic to dr zoning to not let ir continuum become thick to grain emission,

orion_hii_pdr.in - small changes in results, more zones needed
479 Directory Listing
Modified 15 years, 10 months ago
Sat Aug 12 17:09:41 2006 UTC
gary
Original Path: trunk/source
Log:
load leveling in night run scripts/nightly_run_tsuite.pl
update slow sims to catch up with past few weeks of changes
478 Directory Listing
Modified 15 years, 10 months ago
Sat Aug 12 08:23:45 2006 UTC
gary
Original Path: trunk/source
Log:
ion_recomb_Badnell.c - add Badnell dr for Fe+13

large number of test cases changed as result of bowen change, paris meeting turn on all badnell rr & dr, add three lex meeting x-ray models

477 Directory Listing
Modified 15 years, 10 months ago
Sat Aug 12 08:20:55 2006 UTC
gary
Original Path: trunk/source
Log:
NA modified some bands in bands_continuum.dat

cont_createpointers.c fixed bug in how wl was scanned off the data lines in this file - now require label to extend over first 4 then start number in col 6 - number had been scanned off starting in col 4 so could pick up end of label

the LineList_PDR.dat and LineList_PDR_H2.dat labels & wl changed

476 Directory Listing
Modified 15 years, 10 months ago
Sat Aug 12 08:17:31 2006 UTC
gary
Original Path: trunk/source
Log:
rt_ots.c - modify bowen yield following "meudon06" meeting with Daniel Pequignot & Hagai Netzer

this produced slightly brighter Hbeta in PN, other changes in blr

475 Directory Listing
Modified 15 years, 10 months ago
Fri Aug 11 23:20:23 2006 UTC
peter
Original Path: trunk/source
Log:
source/cdinit.c:
  Added support for Apple MacOSX. The OS is now properly detected,
  and FP exceptions are generated on Intel based systems.

474 Directory Listing
Modified 15 years, 10 months ago
Fri Aug 11 19:37:24 2006 UTC
gary
Original Path: trunk/source
Log:
update coll str for fe12 line to storey et al. 2005

atom_feii.c - add comments

atmdat_readin.c - chng magic numbers for level2.dat, fix comments and references

cool_dima.c add reference to mewe paper for g-bar coll stren

hot-issues udpate

more_h2_io.c also print product Aul hnu a_ul

prt_lines_hydro.c - comments update



471 Directory Listing
Modified 15 years, 10 months ago
Fri Aug 11 16:23:45 2006 UTC
peter
Original Path: trunk/source
Log:
source/stars_rebinatmosphere.c:
  Bug-fix - rebinning stellar atmosphere models could crash on certain platforms
  (e.g. Macbook pro) because y/x would be evaluated as y*(1/x). This crashes if
  x is a denormalized number. Problem reported by Dick Henry.

468 Directory Listing
Modified 15 years, 11 months ago
Mon Aug 7 09:38:43 2006 UTC
gary
Original Path: trunk/source
Log:
bands_continuum.dat - details of some continuum bands changed as per NA email of Jul 25.

cont_createpointers.c - magic number changed
467 Directory Listing
Modified 15 years, 11 months ago
Sun Aug 6 07:03:42 2006 UTC
gary
Original Path: trunk/source
Log:
bugfix - Robin Williams correct few matrix elements that were incorrect in CO network, in co_step 1 and 2.  also rename many chem variables to be more consistent.
465 Directory Listing
Modified 15 years, 11 months ago
Wed Aug 2 09:59:39 2006 UTC
gary
Original Path: trunk/source
Log:
atomic data upgrade - change O+2 and N+2 charge transfer recombintion with H0 to Barragan et al. ApJ, 636, 544 - these are substantially smaller than previous results, agreeing better with very old Butler & Dalgarno numbers

*.in changed as a result

rt_ots.c - commented out print statement 

464 Directory Listing
Modified 15 years, 11 months ago
Tue Aug 1 18:43:21 2006 UTC
gary
Original Path: trunk/source
Log:
cont_setintensity.c - generate warning that continuum is far too faint except when lgTSetOn is true, which holds for for constant temper, rather than ConstTemp==0 - second also happens when force temp is used.

mole_h_drive.c mole_h_step.c - trivial changes in formatting of source 

parse_commands.c - change comments

parse_constant.c - change comments

prt_comment.c - add DISASTER to error that occurs when luminosity is not conserved

463 Directory Listing
Modified 15 years, 11 months ago
Tue Aug 1 18:25:11 2006 UTC
gary
Original Path: trunk/source
Log:
bugfix - Robin Williams noted that two sets of matrix elements were incorrect in the CO network.  Nick Abel implemented the corrections.
461 Directory Listing
Modified 15 years, 11 months ago
Tue Aug 1 09:49:37 2006 UTC
gary
Original Path: trunk/source
Log:
cddefines.h - redefine macros for electrons, protons, and he+

cloudy.h, iterations.h - move defn of iter_end_check from cloudy to iterations 

cont_setintensity.c - print warning if incident continuum is surprisingly faint, also do not include radio continuum in this test since cmb itself could be significant

conv_init_solution.c - when ices are important do not let temperature change by much - large T changes with ices throws the solvers badly off

cool_iron.c, grains.c, ion_solver.c, iter_end_check.c, parse_commands.c - minor changes in comments or print statements

zero.c - init radiius.drNext to 1

func_trans_punch.in - last became missing on punch transmitted continuum - no idea how this happened

this runs test suite cleanly
455 Directory Listing
Modified 15 years, 11 months ago
Sat Jul 29 07:32:30 2006 UTC
gary
Original Path: trunk/source
Log:
move comment generated if C/O > 1 and going into cold gas.  was in parse_commands.c but moved to abundances.c
452 Directory Listing
Modified 15 years, 11 months ago
Wed Jul 26 12:48:32 2006 UTC
gary
Original Path: trunk/source
Log:
atmdat_char_tran.c - update mg0 & si0 charge trans ion with H+ to umist 05

atom_pop3 - assert physical quantities are >= 0

cool_oxygen - update [oii] and [oiii] collision strengths

grains.c - attempt at getting bakes hack to work with grain physics is turned off - this is critical for debugging hydro models.  heating now vastly too large and commented out

prt_final update [oiii] cs to be parallel with cool_oxygen


*.in - many changes in results due to CT and cs changes

bands_continuum.dat - NA add total lumin
451 Directory Listing
Modified 15 years, 11 months ago
Wed Jul 26 10:20:22 2006 UTC
gary
Original Path: trunk/source
Log:
cont_ffun.c - add comment to failure of table read command, suggesting that user forgot to put last on punch trans continuum command
450 Directory Listing
Modified 15 years, 11 months ago
Mon Jul 24 11:25:03 2006 UTC
gary
Original Path: trunk/source
Log:
Humeshkar Nemala update collision strengths

tidy up radius_increment.c

results of change in H-like coll strength and Mg0 Si0 charge trasnfer into slow test suite

pn_ots.in - change in ne cs detected
449 Directory Listing
Modified 15 years, 11 months ago
Mon Jul 24 00:33:24 2006 UTC
gary
Original Path: trunk/source
Log:
update to do list
447 Directory Listing
Modified 15 years, 11 months ago
Mon Jul 24 00:26:04 2006 UTC
gary
Original Path: trunk/source
Log:
atmdat_char_tran.c - do not let CT rates for Mg0 and Si0 with H+ fall below UMIST 05 rates
446 Directory Listing
Modified 15 years, 11 months ago
Mon Jul 24 00:21:10 2006 UTC
gary
Original Path: trunk/source
Log:
Ryan Porter update to hydrogenic collision strengths,
routine Hion_colldeexc_cs had been done by Ferguson as part of his PhD thesis
replace with routine CS_VS80 by Ryan Porter - cs are many dex smaller for hydrogenic levels

add option to do thermal average over collision strengths (set collision strneght thermal average on) by
default not done, considerably faster

radius_increment - threw asserts due to much smaller H-like collision strengths in above change - do not assert that various solvers agree when ionization fraction is tiny


444 Directory Listing
Modified 15 years, 11 months ago
Sat Jul 22 20:13:46 2006 UTC
gary
Original Path: trunk/source
Log:
Two additions by Nick Abel

print chemistry rates had CO option, added OH option

set chemistry non-equilibrium 
proton elimination - favor -> H over H+
neutrals - non-equil does not affect neutrals

set jura rate now has default of 3e-17 

443 Directory Listing
Modified 15 years, 11 months ago
Sat Jul 22 19:52:07 2006 UTC
gary
Original Path: trunk/source
Log:
bugfix cddrive.c - routine cdLine - if not lines exist at all, used to fail by accessing invalid array element, now declares insanity.  This can't happen but did when calling the routine with a NaN wavelength

minor changes in comments in other routines


441 Directory Listing
Modified 15 years, 11 months ago
Fri Jul 21 21:22:35 2006 UTC
gary
Original Path: trunk/source
Log:
BUGFIX - prt_final.c - The mean H0 gas temperature that is weighted by the 21 cm opacity should be weighted over radius but was weighted with respect to volume.  This is given with the label T(<nH/Tspin> in the final printout.  
440 Directory Listing
Modified 15 years, 11 months ago
Sun Jul 16 21:26:24 2006 UTC
gary
Original Path: trunk/source
Log:
conv_base.c - better print statements for set recom dr/rr badnell  print command
helike_o.in - minor change in output options
readme_docs.htm - update to reflect current contents of doc folder - van Hoof grains now here
438 Directory Listing
Modified 15 years, 11 months ago
Sun Jul 16 03:03:32 2006 UTC
peter
Original Path: trunk/source
Log:
source/parse_interp.c:
source/parse_table.c:
source/zero.c:
source/cont_setintensity.c:
  Fix memory leak when optimizing a model which uses a stellar atmosphere grid.

435 Directory Listing
Modified 15 years, 11 months ago
Thu Jul 13 11:57:10 2006 UTC
gary
Original Path: trunk/source
Log:
the DR rates in conv_base.c have been updated over the past few weeks to preprints and pre-publication values computed by Badnell & Gu.  these are not used by default and so have had no effect on the test suite.  however they are used in establishing a mean dr for ions that have no rates.  with this change the new dr rates are allowed to enter in the mean DR used for guesses.  

the test suite sims that changed tested ions that used these fake DR rates, so these changes represent real uncertainties.  
434 Directory Listing
Modified 15 years, 11 months ago
Wed Jul 12 15:33:19 2006 UTC
peter
Original Path: trunk/source
Log:
data/vanhoof_grain_model.tex:
data/vanhoof_grain_model.ps:
  Deleted.
data/vanhoof_grain_model.pdf:
docs/vanhoof_grain_model.pdf:
  Moved to more appropriate location.
source/grains_mie.c:
  Bug-fix - guard against roundoff error in mie_find_slope().

433 Directory Listing
Modified 15 years, 11 months ago
Wed Jul 12 14:19:15 2006 UTC
gary
Original Path: trunk/source
Log:
bugfix radius_increment.c - assert near 522 thrown for H-only gas with radiation at an angle.  missing factor of geometry.AngleIllum

bugfix - conv_base.c - factor of 1e-10 missing from c coefficients in Gu DR 

parse_commands.c - small change in comments



432 Directory Listing
Modified 15 years, 11 months ago
Tue Jul 11 14:55:49 2006 UTC
gary
Original Path: trunk/source
Log:
*.c, *.h - change format of to-do statements to be in doxygen format - old format was TODO[tab]priority[tab]statement

doxygen uses string \todo to enter into its to do list - priority is still in the strong but not recognized by doxygen
431 Directory Listing
Modified 15 years, 11 months ago
Tue Jul 11 14:52:15 2006 UTC
gary
Original Path: trunk/source
Log:
atmdat_char_tran.c correct N-H rates

prt_lines_lv1_li_ne - update recombination contribution for [NI] to Pequignot et al 1991, 
bugfix - charge transfer production of 5200 was missing factor of n(N+)

add recombination contributions to total 5200 and individual components, assuming proportional to 2D statistical weight

*.in - changes due to revised N-H charge transfer



418 Directory Listing
Modified 16 years ago
Sun Jul 9 14:35:09 2006 UTC
gary
Original Path: trunk/source
Log:
tabden renamed to dense_tabden

fabden renamed to dense_fabden

headers for each moved into dense.h

417 Directory Listing
Modified 16 years ago
Sat Jul 8 15:54:06 2006 UTC
gary
Original Path: trunk/source
Log:
update H - N charge transfer, also Mg IV collision strength

atmdat.h - add HCharExcRecTo_N0_2D, rate coef for H0 +N+ -> N0* charge transfer into excited state producing NI 5200

atmdat_char_tran.c - add Yun fits to Stancil H0+ - N0+ charge transfer

cool_nitr.c - minor change in comments 

prt_lines_lv1_li_ne.c - add H - N charge transfer excitation of NI 5200, in total NI line intensity, include CT and chem production - according to stat weight - not important in test suite

cool_magn - update mg iv 4.487 micron line collision strength

*.in - update predictions in test suite for sims that changed as result of updated H-N charge transfer rate

416 Directory Listing
Modified 16 years ago
Fri Jul 7 15:47:01 2006 UTC
gary
Original Path: trunk/source
Log:
gaunt.h defn of thermal gaunt factor calc moved to continuum.h, gaunt.h removed from project

public routine renamed from CalcThermAveGaunt to cont_gaunt_calc

415 Directory Listing
Modified 16 years ago
Fri Jul 7 13:04:16 2006 UTC
gary
Original Path: trunk/source
Log:

414 Directory Listing
Modified 16 years ago
Fri Jul 7 12:55:48 2006 UTC
gary
Original Path: trunk/source
Log:
*.h - minor change in formatting to make doxygen perform better - tags for strucs had been struct t_name { } name - changed to struct name { } name so class and name agree, making doxygen output more useful
413 Directory Listing
Modified 16 years ago
Thu Jul 6 20:40:42 2006 UTC
gary
Original Path: trunk/source
Log:
cool_neon.c - update collision strengths for NeII - NeV

mole_h_stop.c - comment change 

parse_crashdo.c - print statement had invalid argument - fixed

atmdat_char_tran.c - add commented out block of code for Terry Yun

*.in - updated asserted values that changed as result of change in neon collision strengths

412 Directory Listing
Modified 16 years ago
Tue Jul 4 02:32:32 2006 UTC
gary
Original Path: trunk/source
Log:
dynamics.c - do not turn off co molecules when time dependent recom is done

mole_h_step
do not include co cross terms when dynamics is being done
do not include co protons in proton sum

hydrogenic - comments changed

iter_startend - reset both H_sum_in_CO_save and hevmol_save[NUM_HEAVY_MOLEC]

dynamics_orion_flow.in - turn on co network and cosmic rays


411 Directory Listing
Modified 16 years ago
Tue Jul 4 02:31:41 2006 UTC
gary
Original Path: trunk/source
Log:
atmdat - fix typo in name in previous revision
410 Directory Listing
Modified 16 years ago
Mon Jul 3 22:53:40 2006 UTC
gary
Original Path: trunk/source
Log:
small changes in names of strucs in headers for doxygen xref to be more useful
408 Directory Listing
Modified 16 years ago
Mon Jul 3 02:02:03 2006 UTC
gary
Original Path: trunk/source
Log:
doxygen header comments updated
406 Directory Listing
Modified 16 years ago
Sun Jul 2 13:05:00 2006 UTC
gary
Original Path: trunk/source
Log:
add H_sum_in_CO to dense, this is sum of all protons in H-bearing molecules

phycon - add more exponentials on temperature, evaluate in tfidle

dynamics.c - add more physical quantities to punch time dependent

mole_h_step.c - had used locally defined variable nprot[mol] which was initialized to hmi.nProton[mol] - rm nprot and use hmi.nProt

mole_co_solve.c - add dynamics source and sink terms - has no effect now since co mole auto turned off when dynamics used




404 Directory Listing
Modified 16 years ago
Thu Jun 29 12:27:21 2006 UTC
peter
Original Path: trunk/source
Log:
source/parse_dont.c:
  Removed initialization of input.lgSetNoBuffering.

403 Directory Listing
Modified 16 years ago
Wed Jun 28 21:18:27 2006 UTC
gary
Original Path: trunk/source
Log:
small changes to r402

parse_dont.c - move FILE declaration to before first executable

parse_punch.c  use four char keywords for ease of search

402 Directory Listing
Modified 16 years ago
Wed Jun 28 17:36:15 2006 UTC
peter
Original Path: trunk/source
Log:
source/parse_radius.c:
  Bugfix - RADIUS command used setbuf() after I/O was done, replaced with fflush().
source/parse_commands.c:
  Bugfix - removed call to setbuf(), it should never have been there.
source/parse_dont.c:
source/cddrive.c:
  Bugfix - NO BUFFERING command used setbuf() after I/O was done, redirect ioQQQ to stderr instead.
source/parse_punch.c:
  Bugfix - issue setbuf() command only immediately after punch file is opened.
           PUNCH CONVERGENCE ERROR command would close file handle twice.
           various punch commands failed to reset lgNoClobber[punch.npunch].
source/cdinit.c:
  Bugfix - I/O on ioQQQ was attempted before it was initialized.

401 Directory Listing
Modified 16 years ago
Wed Jun 28 02:02:28 2006 UTC
gary
Original Path: trunk/source
Log:
add print statrement to dynamics.c to give total power radiated
399 Directory Listing
Modified 16 years ago
Tue Jun 27 21:01:22 2006 UTC
gary
Original Path: trunk/source
Log:
zero.c - bugfix - memory leave of several malloc'd vars

level1.dat - fix typo in description of gf - it and A are log if negative, linear if positive,
comment was incorrect

atom_feii.c bugfix - zero col arrays when number of levels trimmed down

396 Directory Listing
Modified 16 years ago
Tue Jun 27 12:57:26 2006 UTC
gary
Original Path: trunk/source
Log:
Mitchell Martin add Fe+13 - Fe+12 DR rates, at this time do not add to mean for
	dr since this changes mean significantly.  will update when Gu & Badnell
	numbers are also in

timesc.AgeCOMoleDest is now a vector for all CO species, keeps destruction timescale for all

bugfix - punch_do - every option was added to punch continuum - did not work at all,
	punch continuum punch first zone only.  fixed.

PAF complete update headers for doxygen

runbotched.pl and runcrashed.pl - rm nice from system run


390 Directory Listing
Modified 16 years ago
Mon Jun 26 15:50:51 2006 UTC
peter
Original Path: trunk/source
Log:
source/stars_kurucz79.c:
source/stars_rauch02.c:
source/stars_atlas.c:
source/stars_werner.c:
source/stars_costar.c:
source/stars_mihals.c:
source/stars_rauch_old.c:
  Fixed memory leak due to double allocation of arrays.

387 Directory Listing
Modified 16 years ago
Sun Jun 25 13:55:48 2006 UTC
gary
Original Path: trunk/source
Log:
bugfix - fix memory leak discovered by PvH - do not use conv.nTotalIoniz==0 to indicated initial call since this occurs during first call of each iteration.  on second and later iterations space was malloced again without freeing initial space - memory leak resulted - now use static flag within routine to indicate need to malloc space
386 Directory Listing
Modified 16 years ago
Sun Jun 25 13:26:13 2006 UTC
gary
Original Path: trunk/source
Log:
a series of small changes in names and doxygen comments

no change in working code

384 Directory Listing
Modified 16 years ago
Sun Jun 25 13:09:51 2006 UTC
gary
Original Path: trunk/source
Log:
bugfix - atom_feii.c - when FeII emission model atom was trimmed down, the optical depths were only evaluated through the active levels.  This meant that the UV transitions had their optical depth underestimated when the upper level population was no longer solved.  with this fix the upper level populations are set to zero and optical depths between lower levels with real populations and all upper levels possible is still evaluated.

bug manifested itself in orion veil sim - very cold gas so top of Fe+ was trimmed down, but UV lines are present in HST data.  
383 Directory Listing
Modified 16 years ago
Sat Jun 24 14:12:29 2006 UTC
gary
Original Path: trunk/source
Log:
add punch large feii to lines.in so line data is produced

remaining *.in add punch feii column density
381 Directory Listing
Modified 16 years ago
Sat Jun 24 01:03:45 2006 UTC
gary
Original Path: trunk/source
Log:
bugfix - atom_feii.c - punch lines data did not produce output for many resonance lines to high states with FeII due to mis set loop counter
380 Directory Listing
Modified 16 years ago
Fri Jun 23 11:52:21 2006 UTC
gary
Original Path: trunk/source
Log:
all doxygen related

included a readme_doxygen.txt in the doxygen directory.  explains how to run doxygen to create output,
what options are now in use, and the output

header files - work continues on adding doxygen markup
379 Directory Listing
Modified 16 years ago
Thu Jun 22 12:48:55 2006 UTC
gary
Original Path: trunk/source
Log:
these are a series of changes to allow constant pressure time dependent cooling of a single cell of gas

conv_init_solution.c - remove all updates of PresRamInit and PresTotlInit, these are now only set in presuree_total
conv_init_solution now calls ConvPresTempEdenIoniz rather than ConvTempEdenIoniz on second and later iterations.  this converges pressure too rathern than just temp

dynamics.c  - punch time output now includes total H density since this changes in constant pressure models

zero.c - set PresTotlInit and PresRamInit to NAN for safety
new var dense.lgDenseInitConstant introduced to give option to keep initial pressure constant from iteration to iteration

parse_constant - constant pressure now has keyword RESET to allow hden to be reset to keep initial pressure the same from iteration to iteration

iter_startend.c - no not set PresTotlInit - this is only done in pressure_+change

pressure_change - do not set PresTotlInit or PresRamInit 
for WIND and lgStatic case, allow constant pressure
NB - THIS IS NOT RIGHT YET - CONST PRESS AND TIME COMMAND INTERFERE

pressure_total - set PresTotlInit and PresRamInit if first zone


378 Directory Listing
Modified 16 years ago
Thu Jun 22 12:33:33 2006 UTC
gary
Original Path: trunk/source
Log:
header files updated with doxygen markup.

Doxyfile - updated to use source_hot and gernerate graphic cross references
377 Directory Listing
Modified 16 years ago
Sat Jun 17 15:51:34 2006 UTC
gary
Original Path: trunk/source
Log:
thermal.h - increase length of NCOLNT_LAB_LEN so that cooling labels can be longer and more informative

iso_cool.c - all iso-electronic coolants now have labels that start with IS to indicate that it is an iso-coolant

conv_fail.c - make diagnostic prints more informative

rt_ots.c - slight change in Lya OTS print diagnostics

376 Directory Listing
Modified 16 years ago
Thu Jun 15 02:16:39 2006 UTC
gary
Original Path: trunk/source
Log:
punch_do.c - revise comments around punch continuum command
375 Directory Listing
Modified 16 years ago
Thu Jun 15 00:19:46 2006 UTC
gary
Original Path: trunk/source
Log:
grain - change InitGrains to GrainsInit - noun verb is style
373 Directory Listing
Modified 16 years ago
Tue Jun 13 14:55:18 2006 UTC
gary
Original Path: trunk/source
Log:
remove casts to float in expressions that go to doubles
372 Directory Listing
Modified 16 years ago
Tue Jun 13 04:50:24 2006 UTC
gary
Original Path: trunk/source
Log:
mole.h - change reduced mass to double from float
zero.c - same

parse_crashdo.c - require keyword on crash bounds command

371 Directory Listing
Modified 16 years ago
Mon Jun 12 00:11:24 2006 UTC
gary
Original Path: trunk/source
Log:
update todo list in cool_sulf.c
370 Directory Listing
Modified 16 years ago
Sun Jun 11 23:53:32 2006 UTC
gary
Original Path: trunk/source
Log:
add var dense.density_low_limit - this is the lowest ion density (cm-3) we will allow on this
processor - used to trim ion limits

zero.c - int var dense.density_low_limit to 1000 times small float

dense.h - add dense.density_low_limit as double

rt_tau_inc.c - use dense.density_low_limit to determine whether to evaluate optical depth increments - if density of parent ion is less than this then do not evaluate

ion_trim - use dense.density_low_limit to adjust trim limits 

369 Directory Listing
Modified 16 years ago
Sat Jun 10 04:15:28 2006 UTC
gary
Original Path: trunk/source
Log:
conv_init_solution.c - on iterations after first, set initial temps, other physical variables, to previous iteration's converged temp in first zone, had always used init guess of first soln

dynamics.c - set const temp to 0 to turn off coronal equili command after relax, in time dependent models

mole_h2_etc.c - fix bug in h2 coll interpolation command found by Mitchell Martin

runall.pl - rm nice command for run all
368 Directory Listing
Modified 16 years ago
Sat Jun 10 03:49:40 2006 UTC
gary
Original Path: trunk/source
Log:
bugfix - when number of iterations is increased beyond limit set with iniital malloc was done, a realloc is done.  code did not set new memory to continued copies of values set in the existing memory, hence when more than default number of iterations were done unset memory was encounted.

this is an improvement but still not correct - the values in the three arrays controlled with the realloc will depend on the order of evaluation of the commands.  correct soln would be to preparse the input stream and check whether any set iterations occur, and derive the correct array size before any vars are set
365 Directory Listing
Modified 16 years, 1 month ago
Wed Jun 7 11:58:21 2006 UTC
gary
Original Path: trunk/source
Log:
bugfix - helike_recom.c - assert when temp went to exactly 1e10 since highest tabulated temp was also exactly 1e10.  

heat_sum - bugfix - needed total of neutral H and H in molecules to multiply cosmic ray density to obtain heating rate.  usually this was important only in neutral or molecular gas so code used different between total H density and H+ density.  but post of 06 jun 06 had cr dominated ionized gas, and wild fluctuations in temperature were produced by roundoff error in this difference - two numbers were nearly identical.  changed to two branches, old way when difference is large, and explicitly sum over H2 and H0 when mostly ionized.
NB - this should not be done this way - will contact Leiden participants to check what we decided
364 Directory Listing
Modified 16 years, 1 month ago
Wed Jun 7 11:41:54 2006 UTC
gary
Original Path: trunk/source
Log:
bugfix cool_eval, the thermal.chClntLab label length was increased from 4 to 10 in r255 but routine fndstr used internal chars that were only 5 long.  trace cooling then overwrote memory and threw an exception.  now macro NCOLNT_LAB_LEN is used for length (as it should have been)

mole_h2_etc.c - small change in comments and statement with no change in functionality

prt_comment.c - move of fortran style E formats (%10.2e) into more flexible %.2e

rt.h - doxygen markup fix

362 Directory Listing
Modified 16 years, 1 month ago
Tue Jun 6 22:40:12 2006 UTC
gary
Original Path: trunk/source
Log:
mole_co_priv.h and nitro.h - eol style had not been set since default properties had not been set on cumulus workstation.  corrected.

*.h - add doxygen markup - this consisted of changing struc member comments from /* comment */ to /** comment */

358 Directory Listing
Modified 16 years, 1 month ago
Tue Jun 6 18:18:29 2006 UTC
gary
Original Path: trunk/source
Log:
development work on time dependent recombination - this is being done in response to Orly Gnat & Amiel Sternberg's paper on time-dependent recombination - the heuristics now in the code did not work in this limit.  this is only the start of heuristic development for this recombination problem.

add time init to coronal equilibrium command to allow collisions to be only source initially, the turned off after nrelax time steps
357 Directory Listing
Modified 16 years, 1 month ago
Tue Jun 6 18:13:53 2006 UTC
gary
Original Path: trunk/source
Log:
cddrive.c & h - add routine cdEDEN_last - returns electron density in last computed zone
356 Directory Listing
Modified 16 years, 1 month ago
Tue Jun 6 18:10:00 2006 UTC
gary
Original Path: trunk/source
Log:
information in first columns of punch heating and punch cooling output were not the same, and also not as described in hazy.  updated punch routines so that each gives same information and in agreement with hazy.
354 Directory Listing
Modified 16 years, 1 month ago
Tue Jun 6 17:35:44 2006 UTC
peter
Original Path: trunk/source
Log:
source/cool_eval.c:
source/grains.c:
  Bug-fix: effect of SET GRAIN HEAT command depended on order of input statements.
  Bug-fix: PE heating was printed incorrectly in output when SET GRAIN HEAT in effect.
source/parse_set.c:
  SET GRAIN HEAT: set phycon.lgPhysOK to FALSE since energy conservation is violated.
source/grains_qheat.c:
source/grainvar.h:
  Cosmetic changes only.

353 Directory Listing
Modified 16 years, 1 month ago
Sat Jun 3 13:59:45 2006 UTC
gary
Original Path: trunk/source
Log:
parse_cosmic_ray - add cosmic rays equipartiton option to cosmic ray command

hextra.h 
define CR_EDEN_GAL_BACK_EV_CMM3 as Webber background cr energy density
cr_energydensity added
lg_CR_B_equipartition set true if equipartition

highen.c - if lg_CR_B_equipartition set true then derive cr energy density and ionization rate from B field

physconst.h small changes in some comments.

pressure_total - add todo to add cr pressure near line 204

zerologic - set some B equipartition variables to zero

orion_hii_pdr_pp.in - add punch temperature to get te & deriv

351 Directory Listing
Modified 16 years, 1 month ago
Fri Jun 2 17:03:21 2006 UTC
gary
Original Path: trunk/source
Log:
grains_qheat.c = add term to assert to allow set grains heat scale factor to no conserve energy
350 Directory Listing
Modified 16 years, 1 month ago
Fri Jun 2 16:35:54 2006 UTC
gary
Original Path: trunk/source
Log:
implement "set grain heating" command - command has a scale factor, parsed in parse_set.c
scale factor multiplies the grain heating rate in cool_eval.c
this is to allow tests similar to those in Allers et al. (2005; ApJ, 630, 368) in which they say that grain heating must be multiplied by a factor of three.  
NB - this is totally ad hoc and does not conserve energy!
349 Directory Listing
Modified 16 years, 1 month ago
Fri Jun 2 16:32:29 2006 UTC
gary
Original Path: trunk/source
Log:
assert_results - add three molecules to those whose column densities can be assertetd
cddrive.c - add three molecules to cdColm 
three added are CN, CH, and CH+

mole_co_etc.c - gather together rates that depend only on temp or rad field, and do not reevaluate them unless quantities have changed - several duplicate rates would found and removed, and two cases where rate multiply defined with second being incorrect were found.  this caused some changes in molecular column densities - not large

prt_lines_lv1_k_zn - make list of Fe 3 lines that come from model atom added by Blagrave


perl scripts - remove nice -n 5 since this pushed scripted runs to too low a priority

*.in - small effects of bug fixes in mole_co_etc.c

pdr_co_fully_noneq.in - add this with non-equil chem turned on
pdr_co_fully.in - add turbulence to this so that pdr_co_fully_noneq.in is totally parallel
348 Directory Listing
Modified 16 years, 1 month ago
Thu Jun 1 12:10:36 2006 UTC
gary
Original Path: trunk/source
Log:
parse_punch.c, punch.h, punch_do.c -
implement punch linelist command

service.c - small change in format of comments

runall.pl - clean up
347 Directory Listing
Modified 16 years, 1 month ago
Wed May 31 23:37:36 2006 UTC
gary
Original Path: trunk/source
Log:
punch chemistry command added

346 Directory Listing
Modified 16 years, 1 month ago
Wed May 31 16:04:39 2006 UTC
gary
Original Path: trunk/source
Log:
cosmic ray command now requires background keyword to work in terms of the galactic background

345 Directory Listing
Modified 16 years, 1 month ago
Wed May 31 16:01:41 2006 UTC
gary
Original Path: trunk/source
Log:
major refactoring of co chem files:
co chemistry refactored by Nick Abel to use global rate coefficients which are evaluated only in one place, and used elsewhere.  this uncovered bugs where the same rate was not used in different routines. 

orion_hii_pdr, orion_hii_pdr_pp, pdr_co_fully, and pdr_leiden_?3.in changed as a result of bug fix of inconsistent rates

moved nitrogen cooling variables out of coolheavy into nitro.h

hmole_reactions now called from CO_update_chem_rates in mole_co_etc.c

structure mole_co_priv created to hold rate coefficients in global name space

add files mole_co_priv.h and nitro.h

NI 5200 recombination from Pequitnot et al.  1991 (must fix reference) prt lines lv1 li ne line 302

342 Directory Listing
Modified 16 years, 1 month ago
Thu May 25 15:25:01 2006 UTC
gary
Original Path: trunk/source
Log:
bugfix - ion_trim.c could throw assert for very low density clouds when the abundance of atomic Li became so small that it underflowed to zero.  logic had raised lowest ion stage in this case and could end up with only one ion stage, Li+.  fix is to not raise lower stage even when its abundance has gone to zero due to underlow.
341 Directory Listing
Modified 16 years, 1 month ago
Thu May 25 15:22:37 2006 UTC
gary
Original Path: trunk/source
Log:
rm optimal.in from repo since this is generated by optim*.in scripts during nightly testing

weekly_backup.pl - change target drive to cumulus raid

svnbackup.pl - target changed to cumulus raid
340 Directory Listing
Modified 16 years, 1 month ago
Thu May 25 00:21:53 2006 UTC
gary
Original Path: trunk/source
Log:
added void to prototypes of void routines - pg compiler caught absence

func_grid.in - make 2D add comments

334 Directory Listing
Modified 16 years, 1 month ago
Sun May 21 13:21:23 2006 UTC
gary
Original Path: trunk/source
Log:
nightly_run_tsuite.pl - change nice to -n 2 from -n 5 to give more priority on lightning.

prt.c - small change in format for one print

TS ran clean
333 Directory Listing
Modified 16 years, 1 month ago
Sat May 20 21:52:32 2006 UTC
gary
Original Path: trunk/source
Log:
punch line optical depth command added

number off changes introduced by Ryan Porter:
assert_results.c - RP add options to suggest asserted line wavelength if no line found

cddrive, parse_commands, accept grid command as form of optimize grid

set line precision command now does 6 digits

328 Directory Listing
Modified 16 years, 1 month ago
Fri May 19 18:25:56 2006 UTC
gary
Original Path: trunk/source
Log:
bugfix - punch feii lines only did number of levels that were considered at end of calculation.  if gas at shielded face is cool then few FeII lines are output.  change so that number of levels malloced is done instead.
326 Directory Listing
Modified 16 years, 1 month ago
Fri May 19 00:53:23 2006 UTC
gary
Original Path: trunk/source
Log:
cont_ffun.c - bugfix - line 172, fix error where lookup we limited to nupper -
very fine continua such as stellar atmospheres can have VERY large values,
up to NCELL.  effect of bug was to truncate interpolated continuum after
nupper cells.

parse_interp.c - bugfix - line 260 - make sure interpolated continuum arrays are
zero between last entered values and NCELL

323 Directory Listing
Modified 16 years, 1 month ago
Tue May 16 13:23:44 2006 UTC
gary
Original Path: trunk/source
Log:
add lines to LineList* so that optical and HII region lines are also extracted

lines_service.c - correct citation to AQ

parse_optimize.c - optimize xspec also accepts optimize grid 

func_ion_increase.in - correct misnamed type of test in comment

321 Directory Listing
Modified 16 years, 1 month ago
Sat May 13 19:36:03 2006 UTC
gary
Original Path: trunk/source
Log:
parse_dont - improve error comment
parse_element - same
320 Directory Listing
Modified 16 years, 2 months ago
Tue May 9 17:59:23 2006 UTC
gary
Original Path: trunk/source
Log:
bugfix - abund_starburst.c format error in vary command

316 Directory Listing
Modified 16 years, 2 months ago
Tue May 9 14:07:35 2006 UTC
gary
Original Path: trunk/source
Log:
cool_nitr.c - small format change in a comment

LineList_PDR.dat, LineList_PDR_H2.dat, add optical H+ region lines

315 Directory Listing
Modified 16 years, 2 months ago
Mon May 8 09:25:22 2006 UTC
gary
Original Path: trunk/source
Log:
RT update lines_service.c so that h-like As for levels n > 15, scale with As for lower levels.  effects are important for fit to case b as per ferguson & ferland 97 - fixed discontinuity at higher levels, n >15, where As were not adjusted for density

*.in, small changes in asserted higher n lines at ~5% level
313 Directory Listing
Modified 16 years, 2 months ago
Fri May 5 19:36:23 2006 UTC
gary
Original Path: trunk/source
Log:
perl scripts, rename current to trunk

pressure.h, struc.h - change name PresRadCurr to pres_radiation_lines_curr to make clear that this is line radiation pressure not continuum

punch pressure, column title Prad changed to Prad(line) to make clear line not continuum

parse_atomhlike.c atom h-like pyman pump scale factor will be log if negative

add pressure to dynamics*.in


312 Directory Listing
Modified 16 years, 2 months ago
Fri Apr 28 01:53:20 2006 UTC
gary
Original Path: trunk/source
Log:
NB this version passes on vs and gcc, but h2_pdr_leiden_f1 throws fpe with pgcc - leaving for Madison so will update

rename struc.Hmole to He_mole
and COmole to be CO_mole

dynamics.c now saves info for co advevction

nElemCO[LIMELM][NUM_COMOLE_CALC] now replaces 
	int nHydr[NUM_COMOLE_CALC];
	int nCarb[NUM_COMOLE_CALC];
	int nOxyg[NUM_COMOLE_CALC];
	int nSili[NUM_COMOLE_CALC];
	int nNitr[NUM_COMOLE_CALC];
	int nSulp[NUM_COMOLE_CALC];
	int nChlo[NUM_COMOLE_CALC];

310 Directory Listing
Modified 16 years, 2 months ago
Mon Apr 24 21:27:12 2006 UTC
gary
Original Path: trunk/source
Log:
*.ini, change "print on" to "print on " - gcc on two new machines did not match on keyword - for some reason trailing space not added on with gcc

orion_hii_open.in - at print line optical depths to see HeI optical depths in orion

prt_alltau.c - changes in print helium optical depths - give lowest give continuum edges also give several explicit lines rather than cryptic code
305 Directory Listing
Modified 16 years, 2 months ago
Sat Apr 22 21:51:27 2006 UTC
gary
Original Path: trunk/source
Log:
merge Ryan porter's changes to both helike and grids code.  many were in response to lint.  

change DR for helike species to Badnell DR rates.  the set recom command does not change this.  This update changed results for species with H-like, He-like abundances, so a handful of *.in changed
304 Directory Listing
Modified 16 years, 2 months ago
Fri Apr 21 20:53:38 2006 UTC
gary
Original Path: trunk/source
Log:
with these changes the turbulence equipartition command works diferently in detail, in a clearer way, but should get the same result.

magnetic.c - magnetic energy density is no longer doubled, it is the real energy density.  The turbulent velocity now includes the heiles & troland F which is read in on the turbulence command 

parse_commands - turbulent pressure is only turned off with no turbulen command, equipartition leaves turb pressure in, so this term comes from real turbulent pressure not doubled mag pressure 

pressure total - cleaned up tests on which pressure to include, just mult by lg var don't test it


303 Directory Listing
Modified 16 years, 2 months ago
Thu Apr 20 14:48:23 2006 UTC
gary
Original Path: trunk/source
Log:
atom_feii, parse_punch, punch_do - implement range and relative options on punch feii populations command

feii_hirad.in, feii_blr_n09_p18.in - add punch feii populations range

301 Directory Listing
Modified 16 years, 2 months ago
Wed Apr 19 12:28:33 2006 UTC
gary
Original Path: trunk/source
Log:
conv_fail.c - give more useful message if code fails because we went into molecular gas without cosmic rays

ion_trim.c - identify case where hden has become very very small and floating abundances have underflowed below zero.  abort in this case.  previously had detected insanity with an assert.  now says to consider turning off the element or not running such low densities.

parse_crashdo.c - small change to comments

punch_line.c add tabs between numbers of punch line cumulative

feii*.in add punch feii level populations

h2*.in slow run - changes introduced by Nick Abel adding N2H+

300 Directory Listing
Modified 16 years, 2 months ago
Wed Apr 19 11:12:59 2006 UTC
gary
Original Path: trunk/source
Log:
small changes in punch pressure output format
299 Directory Listing
Modified 16 years, 2 months ago
Wed Apr 19 09:25:51 2006 UTC
peter
Original Path: trunk/source
Log:
source/cdinit.c:
  Fixed compilation problem when using Portland Group compiler.

297 Directory Listing
Modified 16 years, 2 months ago
Sat Apr 15 12:34:35 2006 UTC
gary
Original Path: trunk/source
Log:
NA break mole_co_step into two pieces, _1 and _2, to speed up compilation
remove mole_co_step

NA add N2H+ to chemistry

iter_startend better doc of problem with stop line command

some test cases had changes in SiO and H3+ as a result - botch but not big botch

292 Directory Listing
Modified 16 years, 2 months ago
Tue Apr 11 14:58:46 2006 UTC
gary
Original Path: trunk/source
Log:
parse_punch - punch feii lines now gives wavelength

atom_feii - several
read table of energies into new var Fe2Energies - in wavenumbers
energies are read in from file fe2energies.dat
routine FeIISumBand bug fix error in conversion wl to erg, use all wl instead
	error caused shift if spectrum.  also spectrum was always vacuum, is
	now air for wl > 2000A

large number of expanded tests on malloc changed to call to BadMalloc

feii_pump.in - results changed because of shift in spectrum

290 Directory Listing
Modified 16 years, 2 months ago
Mon Apr 10 18:11:00 2006 UTC
gary
Original Path: trunk/source
Log:
bands_continuum.dat - warn that continuum near pah features depends on continuum band width due to finite number of cells

copy_source.pl - active source is now source_hot which will update to ftp - only merged with source after passing tests the next day

prt_lines_lv1_k_zn.c - adjust comment
289 Directory Listing
Modified 16 years, 2 months ago
Mon Apr 10 13:38:48 2006 UTC
gary
Original Path: trunk/source
Log:
scripts changed to use gcc for day runs on lightning

remove unused header files from several source files

rt_line_all.c, rt_line_one.c - reevaluate line rt if ionization trim occurred

func_ion_increase.in - do not assert frac abun of highest fe stage since only forms in five zones, depends on zoning

288 Directory Listing
Modified 16 years, 3 months ago
Sat Apr 8 14:56:51 2006 UTC
gary
Original Path: trunk/source
Log:
major change for performance - rt_line_all.c - do not reevaluated some line details except when doing shielding or escape prob

rt_line_one.c - do not reevaluate all details of line when population is zero 

kshllenr.h - removed and vars moved to continuum.h
negdrg.h - removed and vars moved to grains.c
several source files that referred to these headers/and/or/strucs changed

punch_do.c - add hash to punch continuum every command
287 Directory Listing
Modified 16 years, 3 months ago
Fri Apr 7 01:34:53 2006 UTC
gary
Original Path: trunk/source
Log:
*.in - put element on before abundnance & ionization set

add two arrays to punch.h to implement every option on punch continuum command
286 Directory Listing
Modified 16 years, 3 months ago
Thu Apr 6 12:02:55 2006 UTC
gary
Original Path: trunk/source
Log:
parse_set.c - bugfit, did not recognize set hazy "xx" where xx is return or time

punch_do.c - minor change in output from punch hemis agn

rt_diffuse.c - "no free free" now also turns off continuous emission

rt_line_one.c - comments change
285 Directory Listing
Modified 16 years, 3 months ago
Wed Apr 5 02:01:52 2006 UTC
gary
Original Path: trunk/source
Log:
add helpful print statement when cannot open file that should be on the path - explain how to set the path
284 Directory Listing
Modified 16 years, 3 months ago
Wed Apr 5 00:52:41 2006 UTC
gary
Original Path: trunk/source
Log:
radius_next add logic to look at previous iteration on time dep recom to get dr

nlr_paris.in - bug in NI changed predicted ni int
283 Directory Listing
Modified 16 years, 3 months ago
Tue Apr 4 01:25:50 2006 UTC
gary
Original Path: trunk/source
Log:
bugfix - cool_nitr.c - array bounds incorrect

magnetic.c vary option on magnetic field command

parse_punch.c - every option for continuum

dynamics.c - read time factor on time command

atmdat_readin.c - malloc space for new struc vars

iter_startend.c - reset vars for depth & drad in struc

bugfix - mean.c could find negative B pressure for ordered field, crash on sqrt neg number

parse_set.c - minor change in comments

radius_next.c - start changes in recombination dr logic


282 Directory Listing
Modified 16 years, 3 months ago
Mon Apr 3 16:53:31 2006 UTC
gary
Original Path: trunk/source
Log:
revise optimized models with new [OII] As - reran at n=5 and used that spectrum as the one we are after.

pn_paris.in - [OII] revised

these are all trickle down effects of change in [OII] As
281 Directory Listing
Modified 16 years, 3 months ago
Sun Apr 2 21:47:30 2006 UTC
gary
Original Path: trunk/source
Log:
very minor change in format of a comment
280 Directory Listing
Modified 16 years, 3 months ago
Sat Apr 1 02:24:59 2006 UTC
gary
Original Path: trunk/source
Log:
pressure_total.c - include turbulent pressure in total pressure equation of state
parse_commands.c - no pressure option on turbulence command, optional factor F from Heiles & Troland

dynamics - move time elapsed into dynamics.h global namespace

prt_final.c - minor change in comment

279 Directory Listing
Modified 16 years, 3 months ago
Sat Apr 1 02:19:13 2006 UTC
gary
Original Path: trunk/source
Log:
cool_iron.c - add reference to Blagrave paper for model of fe3
cool_oxyg.c - set atomic data can select which [OII] As to use
parse_punch.c, punch_do,  time option on set hash
278 Directory Listing
Modified 16 years, 3 months ago
Sat Apr 1 02:16:40 2006 UTC
gary
Original Path: trunk/source
Log:
keep upper and lower column density of 21 cm level, punch it
276 Directory Listing
Modified 16 years, 3 months ago
Tue Mar 28 03:01:16 2006 UTC
gary
Original Path: trunk/source
Log:
cool_nitr.c - add reference for Tayal collision strengths
parse_commands.c - paren around logical test as per gcc 4.1 warnings
parse_print.c - print line optical depth faint triggered print faint - add further test on keys
stars_costar.c & state.c - correct fprint format as per gcc 4.1 warnings
275 Directory Listing
Modified 16 years, 3 months ago
Tue Mar 28 02:56:57 2006 UTC
gary
Original Path: trunk/source
Log:
update Badnell DR rates - badnell_dr.dat - new file from his web site, ion_recomb_Badnell.c - change to use only m=1 state, use new magic number (date he posted file)
272 Directory Listing
Modified 16 years, 3 months ago
Mon Mar 27 19:04:34 2006 UTC
gary
Original Path: trunk/source
Log:
bug fix - iter_startend.c - at two places StopCalc.chStopLabel, a line label that had been turned into CAPS was compared with LineSv[i].chALab which is in an undefined cap state.  fix is to convert LineSv[i].chALab to caps before comparing.  result of this - stop line command would miss correct line.

reported & fixed by Kevin Blagrave
270 Directory Listing
Modified 16 years, 3 months ago
Mon Mar 27 03:53:46 2006 UTC
gary
Original Path: trunk/source
Log:
include turb press with flag to turn off in punch output
265 Directory Listing
Modified 16 years, 3 months ago
Sat Mar 25 14:10:25 2006 UTC
gary
Original Path: trunk/source
Log:
bugfix - correct interaction between turbulent equipartition and set pressure 
264 Directory Listing
Modified 16 years, 3 months ago
Sat Mar 25 01:56:16 2006 UTC
gary
Original Path: trunk/source
Log:
turbulence now add rho v^2 term to total pressure except when turbulence equipartition is on
262 Directory Listing
Modified 16 years, 3 months ago
Fri Mar 24 18:11:59 2006 UTC
gary
Original Path: trunk/source
Log:
bug fix - for complex multi level atoms, the critical density given by the punch lines data command gave simply the ratio of the transition probability to the collision rate for that particular line.  With this fix zero will be printed for these cases to prevent confusion.  the to do list now includes doing a proper critical density for these species.
261 Directory Listing
Modified 16 years, 3 months ago
Fri Mar 24 11:52:21 2006 UTC
gary
Original Path: trunk/source
Log:
update to do list
259 Directory Listing
Modified 16 years, 3 months ago
Thu Mar 23 12:19:12 2006 UTC
gary
Original Path: trunk/source
Log:
a series of changes to implement time-dependent photoionization.  cont_createmesh.c, crease two additional continuum arrays to hold constant and varying continua, cont_ffun.c, cont_setintensity.c - separate continuum into these two parts.

dynamics.c - use the two separate continua and do not save old continuum

parse commands, look for TIME keyword on various continua intensity commands

prt_comment.c - generate caution if dynamics and U > 0.1 and warning if U > 1

257 Directory Listing
Modified 16 years, 3 months ago
Tue Mar 21 21:45:08 2006 UTC
gary
Original Path: trunk/source
Log:
punch file - punch time does not put iteration separator since don't want this for those punch that make one line per iteration

adjust zoning when keyword "recombination" appears on one of the time step commands.
256 Directory Listing
Modified 16 years, 3 months ago
Mon Mar 20 23:41:08 2006 UTC
gary
Original Path: trunk/source
Log:
two changes,
prt_lines_lv1_li_ne.c - Terry Yun add IR [N I] lines

dynamics.c and radius_next.c - add logic to not use continuum for radius next when in recombination front

255 Directory Listing
Modified 16 years, 3 months ago
Mon Mar 20 17:04:39 2006 UTC
gary
Original Path: trunk/source
Log:
change labels for iso cooling to make more sense.  char strings had to have longer length, created defn in thermal.h to save new length of string.
248 Directory Listing
Modified 16 years, 3 months ago
Sun Mar 19 05:04:34 2006 UTC
gary
Original Path: trunk/source
Log:
series of changes so that the size of vectors used to save information over iterations is no longer hardwired at 200 - now malloced initially and will realloc if more iterations are needed.  this was needed for the time command, in which an iteration is a time step.
247 Directory Listing
Modified 16 years, 3 months ago
Sat Mar 18 16:27:38 2006 UTC
gary
Original Path: trunk/source
Log:
bug fix time command
246 Directory Listing
Modified 16 years, 3 months ago
Sat Mar 18 01:08:25 2006 UTC
gary
Original Path: trunk/source
Log:
large number of changes that implement the time command - the code now does time dependent calculations!
245 Directory Listing
Modified 16 years, 3 months ago
Tue Mar 14 00:17:40 2006 UTC
gary
Original Path: trunk/source
Log:
bands_continuum.dat - add pah features and update magic number

cont_createpointers.c - update magic number for bands_continuum.dat, add trace continuum output for points in bands_continuum.dat

cool_nitr.c, coolheavy.h, prt_lines_lv1_li_ne.c - update N I to 5-level atom with better atomic data - Terry Yun

prt_lines_continuum.c - include bands in emergent continuum

nlr_paris.in, nova_dqher.in - changes due to updated N I atom


244 Directory Listing
Modified 16 years, 3 months ago
Mon Mar 13 18:21:52 2006 UTC
gary
Original Path: trunk/source
Log:
all bug fixes

fabden did not return a value, now returns negative density to indicate insanity 

iter_startend.c - comment within a comment fixed

lines_service.c - added assert to catch negative ipCont before access bad array element, add PROBLEM to a print statement indicating error

mole_h2_io.c - remove reference to Q(0) H2 line - that does not exist since Q must have non-zero J, led to array bounds error

prt_comment.c - volumn integration incorrectly accessed emergent "vol" which did not exist - this sanity check must work with intrinsic spectrum

state.c - printed size_of type with li format
243 Directory Listing
Modified 16 years, 3 months ago
Sun Mar 12 15:06:15 2006 UTC
gary
Original Path: trunk/source
Log:
hazy3_06_02.pdf - change opening index so pages are collapsed

parse_atomhlike.c - do not allow fewer than 5 levels so that Hb can be referenced

parse_drivecmnd.c - delete drive helium command which no longer worked

prt_comment.c - small change in format of prints

limit_veryveryfast.in - cleaned up atom levels commands, do not request 4 levels - imposed limit is now 5 to include Hbeta
242 Directory Listing
Modified 16 years, 3 months ago
Sun Mar 12 04:20:37 2006 UTC
gary
Original Path: trunk/source
Log:
various small changes propagating emergent continuum, change in atom h-like levels small, 
241 Directory Listing
Modified 16 years, 3 months ago
Sun Mar 12 01:52:09 2006 UTC
gary
Original Path: trunk/source
Log:
all changes are in computing the emergent continuum

old dst lin array removed and main sumlin made vector with two elements, first intrinsic spectrum second emergent.

print line emergent tells cdLine to get emergent rather than intrinsic


239 Directory Listing
Modified 16 years, 3 months ago
Sat Mar 11 16:52:12 2006 UTC
peter
Original Path: trunk/source
Log:
source/cddefines.h:
source/punch_fits.c:
  Add support for Mac Darwin systems. Fixed clash in htonl definition.

236 Directory Listing
Modified 16 years, 4 months ago
Thu Mar 9 12:07:22 2006 UTC
gary
Original Path: trunk/source
Log:
this has two different changes.

EMERGENT INTENSITY
lines_service.c - the emergent lines intensities are now computed for a closed geometry and include outward escape of radiation.  previously they had only been done for an open geometry, and only calculated the emission from the illuminated face of the cloud.

parse_print.c added option "print line emergent" will print emergent intensities in closed geometry.

EmLine demote several variables from double to float to limit size of structure and resulting core size.

test suite passed with one minor "problem"
235 Directory Listing
Modified 16 years, 4 months ago
Tue Mar 7 00:54:31 2006 UTC
gary
Original Path: trunk/source
Log:
put in option to have trailing letter on version number and date, so that versions like 06.02a are possible, this changed cdinit.c, grid_do.c, parse_commands.c, parse_init.c

update extra lyman line optical depths at end of iteration, rt_tau_reset.c

improve state put/get parse_state.c state.c state.h zero.c
228 Directory Listing
Modified 16 years, 4 months ago
Sun Mar 5 22:24:53 2006 UTC
peter
Original Path: trunk/source
Log:
source/cloudy.c:
source/abundances.c:
  Bug-fix. The grain number density printed in the header was wrong. Problem
  reported by R. Surendiranath.
source/grains.c:
source/grainvar.h:
  Modified meaning of gv.bin[nd]->dstfactor; for clarity of meaning
  gv.GrainMetal is no longer factored in.
source/mole_co_gas_grain.c:
  Bug-fix. Fixed errors in projected grain surface area and average speed of
  molecules. Also multiple minor improvements.

223 Directory Listing
Modified 16 years, 4 months ago
Sun Mar 5 13:49:40 2006 UTC
gary
Original Path: trunk/source
Log:
previously had added C+, Si+, and S+ ct with Mg0 and Fe0, and bug fix since these were not evaluated when CO chem was not done.  ct is now in and C+ and Si+ abundances are now much smaller.
222 Directory Listing
Modified 16 years, 4 months ago
Sun Mar 5 01:56:17 2006 UTC
gary
Original Path: trunk/source
Log:
clean up state save / retrieve - code now passes gcc & valgrind on cloud9
220 Directory Listing
Modified 16 years, 4 months ago
Sat Mar 4 18:46:34 2006 UTC
gary
Original Path: trunk/source
Log:
a series of changes to rework how the state variables are saved and read in the binary file.  nothing changed other than the state command.
219 Directory Listing
Modified 16 years, 4 months ago
Sat Mar 4 13:51:37 2006 UTC
gary
Original Path: trunk/source
Log:
These are a series of changes introduced by Nick Abel to improve chemistry network.

NA add charge transfer of Mg0 and Fe0 with C+, Si+, S+, these changes are in ion_iron.c and ion_magne.c and in several of the mole_co routines

Boltzmann factor was not present on several reactions that affected H-bearing molecules, their reference had been intended for warmer environments.  

mole_co_drive.c boost flag saying whether co has been calculated into global name space, part of mole.h, also evaluate ct rates when co not done

add missing flags to gas-grain freeze out reactions to remove loss terms when grain freeze cut is turned off

some ractions moved to other routines to rationalize the network

test suite runs cleanly with changes.

due to changess in charge transfer and boltzmann factor freeze out is now less severe when ice forms, when no ice in some low density models the CO column can be 0,5 - 1 dex larger.  affects mostly low-density PDRs.



218 Directory Listing
Modified 16 years, 4 months ago
Sat Mar 4 04:31:31 2006 UTC
gary
Original Path: trunk/source
Log:
bugfix iso_create.c - malloc at line 349 was EmLine ** and should have been ***

state.c - improve comments
217 Directory Listing
Modified 16 years, 4 months ago
Fri Mar 3 21:53:48 2006 UTC
gary
Original Path: trunk/source
Log:
save state option -
cloudy.c - move save state to below call to rt_tau_reset so that reset optical depths are saved

cont_createmesh.c - save size of three continuous optical depth arrays

state.c - save optical depth vars

prt_final.c - small bug fix - do not try to recover HeI and HeII line intensities when He is not turned on
216 Directory Listing
Modified 16 years, 4 months ago
Thu Mar 2 21:11:42 2006 UTC
gary
Original Path: trunk/source
Log:
change comments printed when sim extends into molecular gas but no cosmic rays present.  both parse_commands.c where initial warning is given, and service.c where abort print occurs.
214 Directory Listing
Modified 16 years, 4 months ago
Thu Mar 2 01:14:52 2006 UTC
gary
Original Path: trunk/source
Log:
comment out print statement in state.c
213 Directory Listing
Modified 16 years, 4 months ago
Thu Mar 2 00:15:32 2006 UTC
gary
Original Path: trunk/source
Log:
add state command to parse_commands.c

state.c & .h, support of new state command, allows code's current state to be saved for possible restart in later stage

at current rev all line structures have their state saved as external file.  this required saving the size of each set of structures, hence many state.h and state size vars added
211 Directory Listing
Modified 16 years, 4 months ago
Wed Mar 1 18:01:30 2006 UTC
gary
Original Path: trunk/source
Log:
bug fix - else was missing on test at line 142 - as result "atom h2 collisional dissociation off" turned off all collisions
210 Directory Listing
Modified 16 years, 4 months ago
Tue Feb 28 18:47:48 2006 UTC
gary
Original Path: trunk/source
Log:
ion_solver.c - do not print it negative number is closer to zero than -1e-9 - had been -1e-10 and high temp sim caused problemsm

parse_constant.c - use stored value of highest temp alllowed

service.c - change comments
206 Directory Listing
Modified 16 years, 4 months ago
Sat Feb 25 07:33:44 2006 UTC
gary
Original Path: trunk/source
Log:
all minor changes in comments or spellings - no source code changes
205 Directory Listing
Modified 16 years, 4 months ago
Tue Feb 21 20:53:47 2006 UTC
gary
Original Path: trunk/source
Log:
date update

203 Directory Listing
Modified 16 years, 4 months ago
Tue Feb 21 12:56:37 2006 UTC
gary
Original Path: trunk/source
Log:
LineList_PDR.dat and LineList_PDR_H2.dat add broad band continuum points contained in bands_continuum.dat to pick up dust emission in pdr models

bands_continuum.dat - add comment that wavelengths MUST be in microns

cont_createpointers.c - bug fix, wavelength used for ID of band was interpreted in ang rather than microns, id was wrong but numbers were correct

pressure_change.c - bug fix, for fabden checked pressure itself rather than change in pressure for generating warning.

202 Directory Listing
Modified 16 years, 4 months ago
Mon Feb 20 05:35:27 2006 UTC
gary
Original Path: trunk/source
Log:
prt_comment.c - T=1e10K now makes caution not warning that electrons are relativistic.  ee free-free is treated correctly in this limit so perhaps even caution is too strong.

service.c - remove stray comment

blr*.in adjust comments

doc_tsuite.htm - rerun to include new tests that were added
200 Directory Listing
Modified 16 years, 4 months ago
Tue Feb 14 20:57:18 2006 UTC
gary
Original Path: trunk/source
Log:
add comments to atom_pop5.c and sample call to cool_nitr.c

add two sims to test suite, func_t10.in and func_t30.in, that exercise the code at 3K and at 1e10K, the low and high temperature extreme where the code is designed to function.  They exposed several bugs which were fixed in rev 197 and 198, and merged onto c06_02_branch at 199
198 Directory Listing
Modified 16 years, 4 months ago
Tue Feb 14 20:31:46 2006 UTC
gary
Original Path: trunk/source
Log:
all following are bug fixes

atom_feii.c - line 1210 - reevaluate FeII collision strengths if number of levels has changed - fix crash at 3K when number of levels increased and NaN cs used, 

ion_recomb.c - line 218 indent branch checking on negative temp power

parse_constant.c - line 67 - do not allow temperatures greater than 1e10 K.  improve error statements when constant temperature is outside allowed Te range of code

tfidle.c - line 539 - add small increment to highest temp in look-up table - fix thrown assert when temperature of 1e10 K is set
197 Directory Listing
Modified 16 years, 4 months ago
Tue Feb 14 17:28:41 2006 UTC
gary
Original Path: trunk/source
Log:
bug fix - add test on tefac at line 217 of ion_recomb.c - at very low temperatures Nussbaumer & Storey fits to some DR rates go to +inf due to negative ff[ion].
196 Directory Listing
Modified 16 years, 4 months ago
Tue Feb 14 16:20:02 2006 UTC
gary
Original Path: trunk/source
Log:
add print constants to func_test so that contents of physconst.h are available.

change comment in prt_lines_molecules.c to say where H2_LinesAdd is located.
195 Directory Listing
Modified 16 years, 4 months ago
Mon Feb 13 14:09:35 2006 UTC
gary
Original Path: trunk/source
Log:
punch grains command output altered.  Now tab delimited fields.  Added sum of two column as last column.
188 Directory Listing
Modified 16 years, 4 months ago
Thu Feb 9 14:17:03 2006 UTC
gary
Original Path: trunk/source
Log:
stars_rauch02.c - but fix - number of stars in table had been copied from old file and not updated.

others are small changes in comments or addition of debug print features - no change in functionality.
187 Directory Listing
Modified 16 years, 4 months ago
Wed Feb 8 15:21:40 2006 UTC
gary
Original Path: trunk/source
Log:
badnell_dr.dat & badnell_rr.dat - remove special magic number, use his comment as version control
ion_recomb_Badnell.c - obtain magic number from comment rather than special line, should not be possible to use his recom data file straight from his web site

ion_carbo.c - comments on nussbaumer & storey dr
ion_recomb.c - use gentle exp(-1000K/Te) temp cuttoff for guesses of DR rates

lines_service.c - add debug print option

parse_punch.c - chng header output for punch ion con to make clear that continuum array index is on C not F scale

rt_diffuse.c - comments

sims - the changed boltzmann factor in the DR guess changes the ionization of 1-4 charged species that have no real DR rates, by  5 - 10%.

185 Directory Listing
Modified 16 years, 4 months ago
Wed Feb 8 13:57:48 2006 UTC
peter
Original Path: trunk/source
Log:
source/grains.c:
  Bug-fix. For small PAHs at the most negative charge it can happen that GrainChargeTemp()
  doesn't converge due to the fact that thermionic emissions become an important cooling
  source for the grain. The grain temperature will oscillate between two values and never
  converge. This is solved by bracketing the solution and using a bisection search for the
  correct grain temperature.

184 Directory Listing
Modified 16 years, 5 months ago
Tue Feb 7 02:31:59 2006 UTC
gary
Original Path: trunk/source
Log:
atmdat_dielrec_fe.c - add comments and reference

cdinit.c - say that compiled date is date cdinit.c was compiled

ion_recomb.c - reorganize logic to be simpler & clearer in kludge and low T dr

parse_set.c - no longer a steve option (was undocumented) but brought noise option out as a diel rec option

182 Directory Listing
Modified 16 years, 5 months ago
Sun Feb 5 15:58:50 2006 UTC
gary
Original Path: trunk/source
Log:
Terry Yun update ion_DR_Badnell.c to use date in badnell_dr.dat and badnell_rr.dat as magic numbers.

update dr file to 20060127, some fits changed, in impact on results

cont_setintensity.c - better explanation of error when intensity of continuum is specified outside range of table
181 Directory Listing
Modified 16 years, 5 months ago
Sat Feb 4 13:06:13 2006 UTC
gary
Original Path: trunk/source
Log:
LineList_PDR.dat and LineList_PDR_H2.dat - add HI and vs lines seen by Spitzer

cont_setintensity.c - bug where ffun would be evaluated outside range of frequency cell, lead to insanity later.  added min and max to keep mean energy within cell

major change is definition of mean Badnell DR recombination rates.  These are now used in place of the Kraemer kuldge for DR of higher charge ions.  highly ionized species are more ionized as a result.  this give a better representation of the temperature and charge dependence of the DR.  many sims changed as a result, in many cases mitigating the changes introduced when the Kraemer DR guesses were introduced.
179 Directory Listing
Modified 16 years, 5 months ago
Wed Feb 1 12:11:41 2006 UTC
gary
Original Path: trunk/source
Log:
add file iso_continuum_lower.c
commentes added to conv_base.c
178 Directory Listing
Modified 16 years, 5 months ago
Tue Jan 31 22:50:06 2006 UTC
gary
Original Path: trunk/source
Log:
return to lexington after two weeks in Pune.  Most ports were blocked so it was not possible to update repo for entire time.

major activity:
Ryan Porter updated iso levels to include continuum lowering for hydrogen like series.  not actually turned on but it could be.

xi command, parse of ionization parameter in parse_ionpar.c started in col 5 so often would miss start of number

printed H2 column density at end of standard output was total column density in protons not H2 molecules.  changed to total number of molecules.  only one print statement was affected.

170 Directory Listing
Modified 16 years, 5 months ago
Fri Jan 20 13:31:42 2006 UTC
gary
Original Path: trunk/source
Log:
Terry Yun update Badnell rr both source and data.

small change in comments on cool_sili.c

add radnell rr routine to ionbal.h

init vars in zero.c
164 Directory Listing
Modified 16 years, 5 months ago
Thu Jan 12 20:00:37 2006 UTC
gary
Original Path: trunk/source
Log:
add thermal destruction of ices for kinetic temperatures greater than 100K

changed CO ice on grains in h2_cr_grains.in and h2_solomon.in

update comments in bands_continuum.dat
163 Directory Listing
Modified 16 years, 5 months ago
Wed Jan 11 17:40:46 2006 UTC
gary
Original Path: trunk/source
Log:
changes in te powers in tfidle.c - no operational change, just in method of evaluation - no impact on results should be possible.
162 Directory Listing
Modified 16 years, 6 months ago
Sat Jan 7 16:41:15 2006 UTC
gary
Original Path: trunk/source
Log:
bands_continuum.dat - NA added several more bands with defn fro ipac web site

cddrive.c - cdColm - add H2vJ option for obtaining level-specific column densities for large H2 atom.  makes it possible to optimize H2 column densities.

cont_createpointers.c - update magic number for bands_continuum.dat
159 Directory Listing
Modified 16 years, 6 months ago
Fri Jan 6 12:40:17 2006 UTC
peter
Original Path: trunk/source
Log:
source/cdinit.c:
  Fix compiler and OS detection on SGI MIPS systems.
  Definition of signaling NaN is reversed on MIPS -> modify SNaN constants.
source/service.c:
  Definition of signaling NaN is reversed on MIPS -> modify MyMalloc().

156 Directory Listing
Modified 16 years, 6 months ago
Fri Jan 6 00:33:14 2006 UTC
gary
Original Path: trunk/source
Log:
NA add assert C2 and C3 column densities to assert_results.c
cddrive.c - cdColmn can now obtain C2 and C3 column densities
ion_DR_Badnell.c - minor change in format of comments
152 Directory Listing
Modified 16 years, 6 months ago
Wed Jan 4 15:54:02 2006 UTC
gary
Original Path: trunk/source
Log:
atmdat_char_tran.c - adjust format of atomic data refence - comment only
doc_* generated artifacts

prt_lines.c - add assert at end of routine to confirm that number of lines did not change from initial calls (ipass==0) where labels and wavelengths are set up, and later calls (ipass>0) where line intensities are added to stack.
151 Directory Listing
Modified 16 years, 6 months ago
Tue Jan 3 19:28:18 2006 UTC
gary
Original Path: trunk/source
Log:
Large block of reactions that involve C3 had been left out of previous merge with Nick's source.  These have now been added to mole_co_step.c
147 Directory Listing
Modified 16 years, 6 months ago
Tue Jan 3 17:08:12 2006 UTC
gary
Original Path: trunk/source
Log:
update comments in release_prepare.txt
146 Directory Listing
Modified 16 years, 6 months ago
Tue Jan 3 15:57:08 2006 UTC
gary
Original Path: trunk/source
Log:
replaced deleted date.h in scripts - this is needed for script to run
144 Directory Listing
Modified 16 years, 6 months ago
Mon Jan 2 23:16:04 2006 UTC
gary
Original Path: trunk/source
Log:
iso_cool.c - gcc fast complained about ambiguous {} - due to lack of asserts - added {}

parse_crashdo.c - change li to i in print as per gcc comment

prt_final.c - gcc found comment within comment

release_prepare.txt - update instructions
143 Directory Listing
Modified 16 years, 6 months ago
Mon Jan 2 22:33:59 2006 UTC
gary
Original Path: trunk/source
Log:
bands_continuum.dat - change comment to make clear that # is comment

dayslow_master.pl - change log file name so also starts dayslow.

scripts/readme.txt - explain bounds and log file name in dayslow_master.pl

parse_crashdo.c - output vars after crash should have occurred to keep lint happy
140 Directory Listing
Modified 16 years, 6 months ago
Mon Jan 2 08:29:23 2006 UTC
peter
Original Path: trunk/source
Log:
source/optimize_do.c:
source/optimize_phymir.c:
  Bug-fix: wr_continue() wrote uninitialized array members to continue file.

139 Directory Listing
Modified 16 years, 6 months ago
Mon Jan 2 06:33:17 2006 UTC
peter
Original Path: trunk/source
Log:
source/parse_crashdo.c:
  - Fixed CRASH UNDEF command so that it crashes both on little-endian and
    big-endian systems.
  - CRASH UNDEF now differentiates between static, automatic and heap variables
    by using the STATIC and STACK/AUTO keywords (HEAP is the default option).
  - CRASH BOUND also differentiates between static, automatic and heap variables
    using the same keywords as above. The user can supply the offset to be used:
    CRASH BOUND -2 means that array[-2] will be accessed 
    CRASH BOUND 2 means that array[ARR_SIZE+2] will be accessed 
  - Disabled icc warning about uninitialized var being used.
  - Many small changes.

138 Directory Listing
Modified 16 years, 6 months ago
Sun Jan 1 14:20:32 2006 UTC
gary
Original Path: trunk/source
Log:
update copyright year in all files
136 Directory Listing
Modified 16 years, 6 months ago
Sat Dec 31 14:14:29 2005 UTC
gary
Original Path: trunk/source
Log:
two versions of numLevels existed, with different interpretations.  this was a source of bugs. two changges:  global rename of iso.numLevels into iso.numLevels_max since this is initial value used to malloc arrays.  Second,helike.numLevels renamed to iso.numLevels_local since this is the value within the cloud, could be smaller if continuum lowering is important.
135 Directory Listing
Modified 16 years, 6 months ago
Fri Dec 30 14:54:37 2005 UTC
gary
Original Path: trunk/source
Log:
introduced bug in prt_lines_lv1_li_ne.c yesterday - would cause div by zero in sims with no H-ionizing radiation.  introduce test at line 694

minor change in print statement in cddrive.c 
134 Directory Listing
Modified 16 years, 6 months ago
Fri Dec 30 03:52:43 2005 UTC
peter
Original Path: trunk/source
Log:
source/cdinit.c:
  Fixed broken compiler detection for icc, as well as gcc on SGI MIPS.
  Added FPE trap support for HP compiler on sdx.
tsuite/auto/run_parallel.pl:
  Improved cleanup (leave all files from repository) and sequence of sims
  (make sure the long running ones are upfront).

133 Directory Listing
Modified 16 years, 6 months ago
Thu Dec 29 22:42:40 2005 UTC
gary
Original Path: trunk/source
Log:
change doc_atomic_data.pl so that it write ancillary files that all start with doc
132 Directory Listing
Modified 16 years, 6 months ago
Thu Dec 29 21:37:48 2005 UTC
gary
Original Path: trunk/source
Log:
rename extract_atomic_data.pl to doc_atomic_data.pl

add te40 to phycon struc

upgrade fit to recombination contribution to [OII] lines to Liu et al.
131 Directory Listing
Modified 16 years, 6 months ago
Thu Dec 29 20:19:48 2005 UTC
gary
Original Path: trunk/source
Log:
scripts - cosmetic changes

mean.c fix typo at line 166

programs - change calls to cdGet that reference routines with changed names
130 Directory Listing
Modified 16 years, 6 months ago
Thu Dec 29 19:37:34 2005 UTC
gary
Original Path: trunk/source
Log:
bug in parse_optimize.c - used chCard instead of cdCap - only VOLUME and not volume was accepted as option on optimize temperature.

many cdXXX routines in cddrive.c had a redundant "Get" in their names.  These (for example cdGetCooling_last) had get removed.

minor tweeks in define mean B and over space in mean.c
129 Directory Listing
Modified 16 years, 6 months ago
Thu Dec 29 13:51:38 2005 UTC
gary
Original Path: trunk/source
Log:
add cdB21cm routine to return mean magnetic field weighted by n(H0)/Tkin.  included this is printout at end of sim, in  prt_final.c
128 Directory Listing
Modified 16 years, 6 months ago
Thu Dec 29 03:24:13 2005 UTC
gary
Original Path: trunk/source
Log:
added option to cdLine to return simple mean temperature wrt vol or rad to mean.c
127 Directory Listing
Modified 16 years, 6 months ago
Wed Dec 28 23:17:23 2005 UTC
gary
Original Path: trunk/source
Log:
fixed bug in iso_cool.c where sum over he-like levels extended into states in the continuum in very dense models.  added limit_lte_he1_ste.in test case to test suite to detect such errors in future - this test confirms that He-dominated plasma goes to STE
124 Directory Listing
Modified 16 years, 6 months ago
Wed Dec 28 02:15:50 2005 UTC
gary
Original Path: trunk/source
Log:
update badnell_rr.dat to nigel's current version
edits in hot_issues.txt and to_do.mdb
collion now use Badnell DR data
122 Directory Listing
Modified 16 years, 6 months ago
Mon Dec 26 14:25:33 2005 UTC
gary
Original Path: trunk/source
Log:
variable name contained in a comment in these two sources was incorrect - changed to correct name.  code not changed, only comment.
121 Directory Listing
Modified 16 years, 6 months ago
Sun Dec 25 23:10:40 2005 UTC
gary
Original Path: trunk/source
Log:
minor changes in formatting, fabden now aborts rather than pressing on, as appropriate for release code.
119 Directory Listing
Modified 16 years, 6 months ago
Sun Dec 25 18:19:02 2005 UTC
gary
Original Path: trunk/source
Log:
cleaning up programs
118 Directory Listing
Modified 16 years, 6 months ago
Sun Dec 25 17:59:30 2005 UTC
gary
Original Path: trunk/source
Log:
added comp4.htm to repo
117 Directory Listing
Modified 16 years, 6 months ago
Sun Dec 25 04:12:40 2005 UTC
peter
Original Path: trunk/source
Log:
source/cddefines.h:
source/cdinit.c:
  Added support for Intel compiler on IA64 SGI systems.

116 Directory Listing
Modified 16 years, 6 months ago
Sun Dec 25 00:23:14 2005 UTC
peter
Original Path: trunk/source
Log:
source/cdinit.c:
  cdInit() - moved call to SetFPEnv(); it should be before the first FP operation.
tsuite/programs/vary_nete/vary_nete.htm
tsuite/programs/vary_nete/vary_nete.txt
tsuite/programs/hilohi/hilohi.htm
  Fixed svn:eol-style property.

113 Directory Listing
Modified 16 years, 6 months ago
Sat Dec 24 22:54:17 2005 UTC
peter
Original Path: trunk/source
Log:
source/cdinit.c:
  SetFPEnv() - added support for IA64 Linux systems.
source/parse_crashdo.c:
  Added test of SET_xxx_SNAN macros.

111 Directory Listing
Modified 16 years, 6 months ago
Sat Dec 24 15:00:39 2005 UTC
gary
Original Path: trunk/source
Log:
mostly work on programs to redo documentation and confirm that they all run

review of to_do data base with some small format changes in source
110 Directory Listing
Modified 16 years, 6 months ago
Sat Dec 24 03:58:39 2005 UTC
gary
Original Path: trunk/source
Log:
changes to program docs to make better describe their purpose. 
109 Directory Listing
Modified 16 years, 6 months ago
Fri Dec 23 22:13:00 2005 UTC
gary
Original Path: trunk/source
Log:
grain_ion_charge_transfer - grain ionization recombination of atoms and ions, deleted - it set two variables that were not used by the code.  The ionization / recombination is totally done with the gv structure.  Cleaned up ion_solver.c - this still contained old code by tri-diagonal solver.  

cleaned up files in source - formatting, references, TODO list.  no change in functionality.  Ran all perl scripts in source and adjusted their output files.  
107 Directory Listing
Modified 16 years, 6 months ago
Thu Dec 22 17:12:16 2005 UTC
gary
Original Path: trunk/source
Log:
VS reported error when compiling as C++ code - call to pow at line 758 had ambiguous overload in mole_h_drive.c - added cast to double.  Code now compiles as C++ with no errors or warnings with highest level of warnings set.
105 Directory Listing
Modified 16 years, 6 months ago
Thu Dec 22 16:17:59 2005 UTC
gary
Original Path: trunk/source
Log:
two independent changes here:

the uta directory below data should not have been included in the repository.  they were working files that were provided by Kisielius & Keenan.  Deleted.

Merged in Ryan Porters changes to the He-like iso sequence.  these made a finer grid on the tabulated recombination coefficients, used a higher order interpolation method for extracting these recombination coefficients, and adjusted the test suite to trace the changed asserts.  

set line precision command added by RP - increases number of digits in printed wavelength.

cdH2_Line was added to extract a particular H2 line from its quantum indices.

dielectronic recombination command changed to set direlectronic recombination

RP made changes to optimization code used to create xspec interface.

believe that test suite will run cleanly.
104 Directory Listing
Modified 16 years, 6 months ago
Wed Dec 21 17:07:21 2005 UTC
gary
Original Path: trunk/source
Log:
incorporate Badnell DR rates, although not on by default.
atmdat_readin.c - has call to ion_DR_Badnell.c init routin
ion_recomb.c incorporates DR code
several changes across header files and others to support this
agn_warm_absorber.in - update assert from previous change in Fe cs
101 Directory Listing
Modified 16 years, 6 months ago
Tue Dec 20 17:34:43 2005 UTC
peter
Original Path: trunk/source
Log:
source/cpu.h:
  Added pclint directives, modified comment.

96 Directory Listing
Modified 16 years, 6 months ago
Mon Dec 19 22:51:17 2005 UTC
gary
Original Path: trunk/source
Log:
these are a series of changes relating to multi-level models of Fe emission.  new multi-level models of FeIII, FeXI, and Fe XIII were introduced.  other changes were to infrastructure in support of these new models.  Some atomic data were updated, and other FeXI lines removed, from level1.dat.

correction to utilitymacros.h fixed warning issued by g++ when *.c renamed to *.cpp

agn_warm_absorber.in and blr_n09_p22_Z20.in had asserted results that changed as result of improved Fe emission.  Updated to current predictions.

h2_orion_hii_pdr.in - failures in CO chemistry were due to going so deep into the molecular cloud that grain temps fell to such small values that catalysis of H2 no longer occurred.  Cosmic rays still destroyed H2 so H had a transition from H2 to H0.  changed to stop at AV of 1000
95 Directory Listing
Modified 16 years, 6 months ago
Mon Dec 19 17:06:03 2005 UTC
peter
Original Path: trunk/source
Log:
source/parse_abundances.c:
  Bug-fix: gp.lgGreyGrain was not initialized (3 times).
source/parse_grain.c:
  Bug-fix: keyword REEVALUATE should have been NO REEVALUATE on grain vary command.

94 Directory Listing
Modified 16 years, 6 months ago
Sun Dec 18 20:31:20 2005 UTC
gary
Original Path: trunk/source
Log:
these are a series of changes that further increase the carbon chemistry and were introduced by Nick Abel.  The major thrust was to introduce molecules and reactions that will directly affect the C2 abundance. 

The asserted values in the *.in files were updated to reflect the answers obtained with this updated chemistry.

set attribute on readme_hazy_coolingcurve.htm - to eol native
92 Directory Listing
Modified 16 years, 6 months ago
Sat Dec 17 23:32:24 2005 UTC
gary
Original Path: trunk/source
Log:
The 14-level model of FeIII emission is now enabled and double checked.  
91 Directory Listing
Modified 16 years, 6 months ago
Sat Dec 17 19:05:58 2005 UTC
peter
Original Path: trunk/source
Log:
source/cpu.h:
tsuite/programs/run_programs.dat:
  Fixed svn:eol-style.

87 Directory Listing
Modified 16 years, 6 months ago
Sat Dec 17 15:47:09 2005 UTC
gary
Original Path: trunk/source
Log:
cool_iron.c - added kevin Blagrave model of FeIII atom.  
prt_lines_lv1_k_zn.c - This adds many FeIII lines.  several revs before FeII cooling was changed to Fe2c in output.  this rev change Fe III and Fe IV cooling to Fe3c and Fe4c by analogy.

blr_hizqso.in - added FeIII cooling changed intensities of two lines.
86 Directory Listing
Modified 16 years, 6 months ago
Sat Dec 17 15:14:04 2005 UTC
gary
Original Path: trunk/source
Log:
yesterday's change to ion_solver allows code to press on into regions where ices are well formed.  this causes some negative populations, code had aborted before yesterday's changes.  it now sets non-converged flag and presses on.  Also the limit to the fraction of O in ices was removed since we can now handle icy cases.  

As a result the three sims h2_cr_grains.in h2_solomon.in and h2_t500.in now make it to the requested number of zones.  They had been stopping due to ice formation.  Added assert on how many zones were computed and adjusted asserts to get current values.  There were mainly the values in place before ice stop criteria was in place.

minor change in comments in zero.c
85 Directory Listing
Modified 16 years, 6 months ago
Fri Dec 16 22:53:48 2005 UTC
gary
Original Path: trunk/source
Log:
ion_solver.c - when ices form deep in cloud the molecule solver can take many iterations to settle down.  During early stages the molecular network can be out of synch with the ion solver and the atomic density, the difference between the gas phase and molecule density, could be negative.  ion_solver.c was aborting when this happens, but tests show that the network and ionization ladder do eventually settle onto a good solution. chng is to now print a PROBLEM statement when this occurs, and set a non-convergence flag, but soldier on.

zero.c - the limit to the ice fraction is no longer needed due to above - change is to set ice fraction for stopping to >1 so will not occur.

prt_lines_lv1_li_ne.c - bug in [NII] 5755 recombination contribution reported and fixed by Kevin Blagrave.

several small formatting changes in comments
84 Directory Listing
Modified 16 years, 6 months ago
Fri Dec 16 16:17:25 2005 UTC
peter
Original Path: trunk/source
Log:
The changes in r79 didn't work with MS VS and icc: in general simply assigning
a signaling NaN to a floating point number can already raise an FPE. Here we
rewrite the code so that FP assignment is never used. The preprocessor symbols
FLT_SNAN and DBL_SNAN are replaced by preprocessor macros SET_FLT_SNAN( f ) and
SET_DBL_SNAN( d ).

source/cddefines.h:
  Remove definition of FLT_SNAN and DBL_SNAN.
source/cpu.h:
  Change definition of Float_SNaN_Value, Double_SNaN_Value.
  Add SET_FLT_SNAN( x ), SET_DBL_SNAN( x ).
  Replace BIG_ENDIAN -> CPU_IS_BIG_ENDIAN; LITTLE_ENDIAN -> CPU_IS_LITTLE_ENDIAN.
source/cdinit.c:
  Change initialization of Float_SNaN_Value, Double_SNaN_Value.
source/service.c:
  Use CPU_IS_BIG_ENDIAN, CPU_IS_LITTLE_ENDIAN.
source/cool_iron.c:
  Use SET_DBL_SNAN( x ).

83 Directory Listing
Modified 16 years, 6 months ago
Thu Dec 15 20:43:13 2005 UTC
gary
Original Path: trunk/source
Log:
these four files were correct on the branch but were not updated on the trunk when the merge was done.  for this merge I obtained a copy of the branch and trunk source and did a manual merge from the branch to the trunk.  This is the commit from that merge.
82 Directory Listing
Modified 16 years, 6 months ago
Thu Dec 15 20:06:34 2005 UTC
gary
Original Path: trunk/source
Log:
these are a series of changes related to a major bug discovered by Kevin Blagrave.  in cool_iron.c routine Fe7Lev8 had the excitation energies in wavenumbers but assumed they were in Kelvin.  The fix is to add another parameter to atom_levelN to allow either energy scale to be used.  Surprisingly none of the test suite sims changed as a result.  Files that contain calls to atom_levelN were changed for the extra parameter.
79 Directory Listing
Modified 16 years, 6 months ago
Thu Dec 15 16:11:57 2005 UTC
peter
Original Path: trunk/source
Log:
source/cddefines.h:
  Add new perprocessor symbols FLT_SNAN, DBL_SNAN, remove NaN.
source/cpu.h:
  Add cpu.Float_SNaN_Value, cpu.Double_SNaN_Value.
  Fixed bug caused by existing symbols BIG_ENDIAN, LITTLE_ENDIAN.
source/cdinit.c:
  Initialize cpu.Float_SNaN_Value, cpu.Double_SNaN_Value.
source/helike_create.c:
  Replaced NaN with DBL_MAX.
source/cool_iron.c:
  Replaced NaN with DBL_SNAN.
source/service.c:
  Fixed comment.

74 Directory Listing
Modified 16 years, 6 months ago
Thu Dec 15 00:52:04 2005 UTC
peter
Original Path: trunk/source
Log:
Merging uninitialized-vars branch.

source/cpu.h:
  Added. Holds CPU specific data.
source/cddefines.c:
  Allocate data in source/cpu.h.
source/cdinit.c:
  Initialize data in source/cpu.h. This will be used to determine if CPU is
  big-endian or little-endian.
source/service.c:
  Updated code in MyMalloc(). In debug mode, malloc'ed arrays will be
  initialized to signaling NaN where possible, increasing the chance to detect
  uninitialized variable bugs. Introduced NOINIT preprocessor symbol to
  disable this code for runs with e.g. valgrind.

69 Directory Listing
Modified 16 years, 6 months ago
Sun Dec 11 22:53:09 2005 UTC
gary
Original Path: trunk/source
Log:
update source with today's date so that branch repo will start cleanly.
68 Directory Listing
Modified 16 years, 6 months ago
Sun Dec 11 12:41:21 2005 UTC
gary
Original Path: trunk/source
Log:
copy_tsuite.pl now does both auto and slow dirs off tsuite 
it still needs to do the same programs

the h2_pdr_leiden sims had not been updated since NA increased the chem network to include molecules.  one sime, h2_orion_hii_pdr crashes - the only major problem with the test suite.  with these changes the auto will go cleanly as will the modified slow scripts.
63 Directory Listing
Modified 16 years, 7 months ago
Fri Dec 9 01:45:17 2005 UTC
gary
Original Path: trunk/source
Log:
two pdr models had issues where H2O condensed onto grains - due to dr too large when molecule density increased by great deal from zone to zone.  mods to radius_next.c
62 Directory Listing
Modified 16 years, 7 months ago
Thu Dec 8 23:06:06 2005 UTC
gary
Original Path: trunk/source
Log:
in zero.c made Torsten Elwert's approximation to the Solomon rates the default.  pdr_leiden_hack.ini - added command to make BD96 used for the hacked models.  many pdr models changed as a result, documented and changed the asserted values.
60 Directory Listing
Modified 16 years, 7 months ago
Thu Dec 8 00:04:14 2005 UTC
gary
Original Path: trunk/source
Log:
radius_next.c - add logic to follow changes in ices when they become more abundant that 1e-5 of main element.  ices form exponentially when grain temperature falls near the sublimation point.

This exposed a bug in the FeII optical depth routines.  atom_feii.c used the number of levels in the atom to reset optical depths, but this has been decreased in the orion_hii_pdr_cc sim since it went so deep in the molecular cloud.  The full range of levels is now reset.

several variable names were changed to follow the style of the code.

59 Directory Listing
Modified 16 years, 7 months ago
Wed Dec 7 03:50:42 2005 UTC
gary
Original Path: trunk/source
Log:
add license.txt and readme.txt to root of trunk

add print statement to trace output in pressure_total.c
57 Directory Listing
Modified 16 years, 7 months ago
Tue Dec 6 19:29:49 2005 UTC
gary
Original Path: trunk/source
Log:
end development of FeII branch.  The 16 level model of the lowest terms of Fe+ has been deleted and the large FeII model is always used.  
42 Directory Listing
Modified 16 years, 7 months ago
Mon Nov 28 03:52:34 2005 UTC
gary
Original Path: trunk/source
Log:
very small change in formatting
41 Directory Listing
Modified 16 years, 7 months ago
Mon Nov 28 01:58:34 2005 UTC
gary
Original Path: trunk/source
Log:
repaired bug introduced at line 1538 of mole_h_step.c to save time - did not reevaluate photo rate during early stages after bound compton was evaluated.   caused crash in limit_recoil_ion
40 Directory Listing
Modified 16 years, 7 months ago
Sun Nov 27 17:14:10 2005 UTC
gary
Original Path: trunk/source
Log:
end a series of changes dealing with H2 photo heating

heat_sum add photoelectric and bound compton heating by H2, H2+, and H3+

mole_h_step usee Yun et al. photoionization cross section for H2, for H2+ had used 2*H0 photo rate, change to just H0 rate since this is a one-electron system

opacity_addtotal.c use Yun et al photo cs for H2 opacity, had been 2H0, include H2 in bound compton opacity, had not been included
39 Directory Listing
Modified 16 years, 7 months ago
Sun Nov 27 14:30:28 2005 UTC
gary
Original Path: trunk/source
Log:
update to do list
38 Directory Listing
Modified 16 years, 7 months ago
Sat Nov 26 21:18:19 2005 UTC
gary
Original Path: trunk/source
Log:
small formatting  changes
34 Directory Listing
Modified 16 years, 7 months ago
Sat Nov 26 17:34:22 2005 UTC
gary
Original Path: trunk/source
Log:
work on H2 photo cross sections - photo rate and opacity in but not yet heating
33 Directory Listing
Modified 16 years, 7 months ago
Sat Nov 26 01:16:27 2005 UTC
gary
Original Path: trunk/source
Log:
update limit_recoil_ion.out column density
31 Directory Listing
Modified 16 years, 7 months ago
Fri Nov 25 19:26:40 2005 UTC
gary
Original Path: trunk/source
Log:
partially add Dalgarno cs for H2 photoionization - only in for rate, not opacity or heating
28 Directory Listing
Modified 16 years, 7 months ago
Fri Nov 25 00:37:26 2005 UTC
gary
Original Path: trunk/source
Log:
changes in punch output file names in slow test suit
27 Directory Listing
Modified 16 years, 7 months ago
Fri Nov 25 00:28:16 2005 UTC
gary
Original Path: trunk/source
Log:
two new routines written by Terry Yun brought into source but not called.

Fe_10_11_13_cs in cool_iron.c - evaluate Fe 10, 11, and 13 collision strengths - has array bounds problems

Yan_H2_CS in opacity_createall.c - has defects present in original Dalgarno paper
23 Directory Listing
Modified 16 years, 7 months ago
Thu Nov 24 02:38:00 2005 UTC
gary
Original Path: trunk/source
Log:
test
21 Directory Listing
Modified 16 years, 7 months ago
Wed Nov 23 21:39:50 2005 UTC
gary
Original Path: trunk/source
Log:
fix bug in iter_end_chk.c where div by zero occurred in oxygen in grains check
16 Directory Listing
Modified 16 years, 7 months ago
Wed Nov 23 15:01:36 2005 UTC
peter
Original Path: trunk/source
Log:
Changed eol-style property to native on various *.dat files in data/uta and
  tsuite/auto.

optimize_input.c: bug-fix
  variable limit exceeded was handled incorrectly by optimizer.
grid_input.c: bug-fix
  same problem, same fix.

14 Directory Listing
Modified 16 years, 7 months ago
Wed Nov 23 14:12:43 2005 UTC
gary
Original Path: trunk/source
Log:
small changes in punch output file names for test suite

remove some stellar atmosphere data from repos
13 Directory Listing
Modified 16 years, 7 months ago
Wed Nov 23 02:50:16 2005 UTC
gary
Original Path: trunk/source
Log:
adjust file properties for ascii and perl files - no source change
11 Directory Listing
Modified 16 years, 7 months ago
Wed Nov 23 00:01:34 2005 UTC
gary
Original Path: trunk/source
Log:
change source files svn:eol-style to native
10 Directory Listing
Modified 16 years, 7 months ago
Tue Nov 22 23:41:53 2005 UTC
gary
Original Path: trunk/source
Log:
NA add stop if too many molecules on grains

revise input scripts for molecule freeze out 
9 Directory Listing
Modified 16 years, 7 months ago
Tue Nov 22 16:27:38 2005 UTC
gary
Original Path: trunk/source
Log:
minor changes to input scripts
7 Directory Listing
Modified 16 years, 7 months ago
Tue Nov 22 00:20:25 2005 UTC
gary
Original Path: trunk/source
Log:
NA minor changes in molecular condensation onto grains, change path to point to trunk not current
5 Directory Listing
Modified 16 years, 7 months ago
Mon Nov 21 03:59:52 2005 UTC
gary
Original Path: trunk/source
Log:

3 Directory Listing
Modified 16 years, 7 months ago
Mon Nov 21 02:39:10 2005 UTC
gary
Original Path: trunk/source
Log:

1 Directory Listing
Added 16 years, 7 months ago
Mon Nov 21 01:32:37 2005 UTC
gary
Original Path: trunk/source
Log:


gary@uky.edu
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