80 Commits

Author SHA1 Message Date
David L Parkhurst
9bf1411f42 Updated to PHREEQC3 12386
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@12387 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2017-02-09 16:41:47 +00:00
David L Parkhurst
4405e60e4e Merged source up to phreeqc3-trunk SVN 10892
copied files from trunk and merged changes manually.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10893 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2016-03-04 18:13:43 +00:00
David L Parkhurst
626d678296 Added setdiff_c method.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10891 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2016-03-04 16:38:33 +00:00
David L Parkhurst
fb18be24e2 Tony's implementation of electric current.
Test case current1.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10550 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2015-12-08 16:54:38 +00:00
Scott R Charlton
64703778f0 updated for R
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10311 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2015-09-25 06:30:33 +00:00
David L Parkhurst
e7915af7ac Test case edl_species tests the function.
Works, but maybe questions on thickness for Debye length calculation.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@9916 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2015-06-30 18:01:55 +00:00
David L Parkhurst
49ba8bca71 Working on edl for PHREEQCRM
Adding edl_species for PHREEQC.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@9915 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2015-06-30 17:06:53 +00:00
David L Parkhurst
678fd85c15 Debugged Basic callback for PHAST mpi.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@9458 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2015-04-02 20:34:05 +00:00
David L Parkhurst
76e16420f5 Added METHOD_REGISTERBASICCALLBACK for MPI.
CALL register_basic_callback_fortran() in InitializeRM
CALL register_basic_callback_fortran() in mpi_methods
phast_manager my_basic_fortran_callback and register_basic_callback_fortran
PBasic defined tokcell_pore_volume, tokcell_volume, tokcell_porosity, and tokcell_saturation

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@9457 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2015-04-02 19:07:59 +00:00
David L Parkhurst
a9906af5f6 Fixing VS static checker warnings.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@9300 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2015-02-24 19:22:09 +00:00
David L Parkhurst
8e104d5463 Roughed in surface area calculation by DeClercq (sa_declercq for now).
Fixed bug where H+ was missing from list of aqueous species generated by SYS.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@9230 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2015-02-03 15:58:09 +00:00
David L Parkhurst
8262d5f224 Added diff_c function to basic.
Added test case diff_c to mytest.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@9072 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-11-18 18:29:27 +00:00
David L Parkhurst
4f60c8774e PBasicStop accidently changed to PhreeqcStop at version 8906.
test negexp_totmol failed.
Switched back to PBasicStop.


git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8911 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-08-05 15:49:15 +00:00
Scott R Charlton
9f77e000d5 fixed some of the easier clang++ scan-build bugs
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8908 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-08-05 05:51:47 +00:00
Scott R Charlton
f1438518eb fixed some of the easier clang++ scan-build bugs
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8907 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-08-05 02:51:35 +00:00
Scott R Charlton
fbb95d10b0 made catch(...) always rethrow;
changed catches to const references


git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8906 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-08-05 02:49:22 +00:00
David L Parkhurst
86a2b0461d Clean up PBasic memory on syntax error.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8847 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-07-15 15:37:53 +00:00
David L Parkhurst
b93eda4643 Fixed leaks:
SELECTED_OUTPUT redefinition, read_selected_output
zero in cl1mp.cpp
leak in eq_frac Basic function
if file open failed, leaked ofstream pointer


Don't close files in class_main.cpp
cvdense and cvode changed to allow use of MS memory debugging


git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8815 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-07-08 19:05:54 +00:00
David L Parkhurst
caf7554690 Added solution number method.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8754 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-05-20 20:07:04 +00:00
David L Parkhurst
9b9e34a241 git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8721 1feff8c3-07ed-0310-ac33-dd36852eb9cd 2014-05-07 15:32:19 +00:00
David L Parkhurst
3945c0d78e bug in writing error, loop limit used wrong counter. (PhreeqcRM.cpp)
Saturation was not set correctly (phast_manager.F90)
Added OLD_STYLE_XYZ to configuration for debug (phreeqcpp.vcxproj)
Basic function equiv_frac was not handled.


git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8653 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-11 14:43:24 +00:00
Scott R Charlton
0030e8dafd replaced printf(...) with output_msg(PhreeqcPtr->sformatf(...)) req'd for R.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8622 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-05 05:23:11 +00:00
Scott R Charlton
3abc37a82d replaced putchar('\n') with output_msg("\n") in PBasic.cpp (reqd for R)
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8621 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-04-05 04:50:54 +00:00
Scott R Charlton
01a54bdb7d added assert header file for MINGW-R
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8490 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-02-14 07:15:24 +00:00
Scott R Charlton
adf7d98498 Merged revision(s) 7863-7986 from phreeqc3/branches/multi_punch:
Branching at 7862 for multiple SELECTED_OUTPUT, USER_PUNCH
........
Have multiple SELECTED_OUTPUT working.

Need to have multiple USER_PUNCH.
........
Think multiple instances of both SELECTED_OUTPUT and USER_PUNCH are working.
........
Fixed up inverse.cpp a bit.
........
Fixed missing -pressure in solution dump_raw and read_raw.
........
Merging revisedfandg back into trunk. Makes Excel spreadsheet for carbon-14 dating.

OK by Niel. Has Revised_Fontes_ and_Garnier_ in_NetpathXL.docx to add for documentation.
........
Added Revised_Fontes_ and_Garnier_ in_NetpathXL.docx to installation
Fixed bug that wouldn't allow uninstall
........
updated ftp targets
........
NetpathXL 1.4
........
checkin from make
........
latest test with change in Pitzer pressure, -pressure in SOLUTION_RAW, runs modify_test, has error
........
bugs linux caught, something different about when to print headings
........
Working on multipunch
........
working on high_precision, using SELECTED_OUTPUT 1
........
dump precision
........
Added basic functions:
EQ_FRAC
KIN_TIME
SPECIES_FORMULA
STR_F
STR_E
Added //{{NEW BASIC HERE}} for updating BASIC routines

........
Making backward compatible.

Copying all but lists.

Revised tidy_punch logic.
........
Still working to make backward compatible.

Think there will be one diff, headings will not be rewritten (ddl_flux).
........
updated dump tests (new -pressure line)
........
multi_punch branch

........
Added a Fortran callback.

Will try to revise so that the same callback works for Fortran and C.
........
Revised name to BasicFortran

Added methods for C call SetBasicCallback.

Need to check C side and documentation.
........


git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7987 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-08-28 23:11:07 +00:00
David L Parkhurst
346cf2239b Added a Fortran callback.
Will try to revise so that the same callback works for Fortran and C.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7883 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-08-05 18:56:31 +00:00
David L Parkhurst
ce4284a561 working on high_precision, using SELECTED_OUTPUT 1
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/multi_punch@7876 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-08-01 22:48:14 +00:00
David L Parkhurst
27b3c05684 Working on multipunch
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/multi_punch@7875 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-08-01 21:00:50 +00:00
David L Parkhurst
d436c9cf4f bugs linux caught, something different about when to print headings
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/multi_punch@7874 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-08-01 20:35:33 +00:00
David L Parkhurst
276322a936 Have multiple SELECTED_OUTPUT working.
Need to have multiple USER_PUNCH.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/multi_punch@7864 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-07-31 19:26:34 +00:00
David L Parkhurst
7848242e28 Fixed error for malloc introduced in recent Basic function.
Fixed error with Pitzer paramenters that were not recalculated with
a change in pressure. Parameters depend on density of water I think.
Also changed SIT, although I am not sure the parameters have a pressure
dependence.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7837 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-07-17 21:15:01 +00:00
David L Parkhurst
a03d2ae87e Added f = EQ_FRAC("AlX3", eq, x$)
Also added synonyms PHASE_FORMULA$ and SPECIES_FORMULA$.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7829 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-07-16 19:25:14 +00:00
David L Parkhurst
4b643b866b Finishing touches on species_formula.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7828 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-07-16 17:10:07 +00:00
David L Parkhurst
ff764f3fe5 Added species_formula("CaOH+", count, elt$, coef)
returns
Ca 1
O  1
H  1
charge 1 
in elt$ and coef.
count is 4.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7827 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-07-16 16:37:19 +00:00
Scott R Charlton
6a0b9146b8 change req'd to compile in MinGW
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7822 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-07-16 04:38:44 +00:00
David L Parkhurst
6b36a70531 Lost break after tokstr_ case
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7783 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-07-01 19:51:24 +00:00
David L Parkhurst
102ce31980 Revised manual: Figure 8 had part B twice and was missing part A.
Fixed in Version 3 in previous check in.
Fixed in doc.
Fixed in HTMLversion examples.fm, and reset cross refs so all .fm files changed.
Replaced phreeqc3-232.gif with revised figure.

Fixed system_total_si to return max SI, returned zero if max SI was less than zero.
Added Basic function tokstr_e$ to format a number in exponential form.
log10 not checked for positive argument, probably will print NaN if result is printed.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7782 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-07-01 19:04:05 +00:00
David L Parkhurst
f1a98f8c3f Decided to widen fields if necessary rather than print *** for STR_F$.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7766 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-06-14 22:49:02 +00:00
David L Parkhurst
56ca1c2c0e Added Basic function STR_F$(x, w, d), where x is the number to format, w is the field width, and d is the number of decimal places.
PRINT STR_F$(1/3, 10, 2) produces "     0.33"

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7765 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-06-14 22:35:45 +00:00
David L Parkhurst
47d0c62fc3 Added new Basic function kin_time, which is the time interval for the current kinetic integration.
kin_delta/kin_time is the average rate over the time interval.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7676 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-05-01 16:14:16 +00:00
David L Parkhurst
24ed8b5cc0 Tony's changes for gases.
Removes some more 's.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7653 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-04-26 16:57:25 +00:00
David L Parkhurst
c42bd89280 LDBLEs
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7588 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-03-29 17:42:27 +00:00
David L Parkhurst
a2a1aafe9d PBasic use phreeqc_ptr warning msg instead of default phrq_io warning msg.
Fixed bug in s_s assemblage print

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7495 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-02-22 19:15:42 +00:00
David L Parkhurst
d23bd01f38 Changes for Kinniburgh's underflow and overflow problems.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7319 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2013-01-11 17:00:38 +00:00
David L Parkhurst
65c2d5288b Tony change of numtostr.
Removed assert for surf_total.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7179 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2012-12-06 22:00:39 +00:00
David L Parkhurst
d7b2ab1ba5 Fixed spacing for PRINT command high precision.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7072 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2012-11-09 20:25:56 +00:00
David L Parkhurst
98baecfe0d Added two new functions.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@7038 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2012-10-26 21:55:04 +00:00
Scott R Charlton
475cf8f1a0 added some (parse_all) logic to avoid crashes in phreeqci
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@6944 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2012-08-30 22:28:13 +00:00
David L Parkhurst
ad3e78e2f5 Added Basic functions GFW and SOLN_VOL.
Added test case gfw in mytest and added to Makefile

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@6796 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2012-07-18 19:15:04 +00:00
David L Parkhurst
8823f0ff2f Added STATIC_VOPTS to make vopts static, not static unless defined.
Guy had problems with static variables with OpenMP.

Also removed other static variables fpunchf_user s_warning and buffer, spread length, utilities spinner. Put in Phreeqc.h.

Removed static fnbuf from Pbasic.cpp, put in Pbasic.h.

I think only static variables are in Keywords.h and are necessary for initialization.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@6770 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2012-07-11 16:23:02 +00:00