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Author SHA1 Message Date
Scott R Charlton
48ec1a3837 added LICENSE to cvode files 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8727 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-05-08 02:23:14 +00:00
David L Parkhurst
8e81c17eb2 Next try on DELETE; -all 
Fixed warnings for MAC lion operating system

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8724 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-05-07 21:27:47 +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
Scott R Charlton
b2a5ed444e added undef SS suggested by Ripley for x86 Solaris 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8708 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-05-06 23:12:44 +00:00
David L Parkhurst
8b2c1a8d07 R problem for ex16. 
memcpy was overwriting the same space if i = row.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8703 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-05-05 21:49:38 +00:00
Scott R Charlton
c343330920 removed no longer needed R_SO ifdefs 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8702 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-05-02 03:41:04 +00:00
Scott R Charlton
f92afa36fb moved Phreeqc methods process_file_names, open_input_stream, 
open_output_stream, and open_output_file 
from PHRQ_io_output.cpp to class_main.cpp

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8701 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-05-02 03:36:26 +00:00
David L Parkhurst
504bcf6dd0 Gentisic problem. H2O was defined as a SURFACE_SPECIES. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8700 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-05-01 22:11:48 +00:00
Scott R Charlton
cfa58371fe changes req'd for R 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8684 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-04-29 23:29:04 +00:00
David L Parkhurst
d77460e672 Added error print after each worker RunString. 
Fixed uninitialized variables when cxxKinetics was constructed from a mix.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8682 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-04-29 21:35:06 +00:00
David L Parkhurst
112feb81b9 Delete all before filling module. 
multithreaded debug dll in project

gas phase create from mix had a bug.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8677 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-04-25 18:55:19 +00:00
David L Parkhurst
53e3bd59e6 Moved uz_bin to workers to avoid possible data conflicts. 
PartitionUZ updated
Added TransferCellsUZ
Added Add(src_bin, n) to StorageBin

Need to document partitioning.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8658 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-04-15 22:55:59 +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
David L Parkhurst
de0ec2ad75 Fixed bug with redefinition of sit parameters 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8627 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-04-08 15:06:20 +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
7c0b1106aa first pass @ removing std::cerr, std::cout, exit, stderr, stdout from R version. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8619 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-04-05 04:14:16 +00:00
David L Parkhurst
7359b9dcb6 changed input_units_* to units_*. 
thru GetMpiTasks
Changed GetIPhreeqcId to GetIPhreeqcPointer
added to tests RM_GetIPhreeqcId

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8586 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-03-21 00:00:00 +00:00
David L Parkhurst
47eec62e40 Redefinition of Pitzer parameter was bad wrong. 
First exchange and surface species were included in lists.
Second, a map used to lookup the pitzer parameter number got out of date when tidy_pitzer was called.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8576 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-03-19 21:19:11 +00:00
Scott R Charlton
78a273ebe2 All IPhreeqc checks passing on windows 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8564 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-03-17 22:34:03 +00:00
David L Parkhurst
c843de8fb0 Got all Tests working with MPI except the units tester. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8556 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-03-13 01:06:32 +00:00
David L Parkhurst
f10f513716 Save only aqueous species in phreeqc species_map. 
Added species_map to copy operator
made mg/L default for Solution.cxx
default species_save_on is false.
Added some defaults to documentation
added species_cpp test.

bug in species_utility_cpp.txt

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8543 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-03-04 20:08:26 +00:00
Scott R Charlton
3f0cd06d6e Added Peng/Robinson gas parameters and molar volume for solids to keyword PHASES 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8538 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-03-01 07:31:56 +00:00
David L Parkhurst
c43019c496 Roughing in mcd capability. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8536 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-02-28 21:29:53 +00:00
David L Parkhurst
38bfd3328b Modification to use REACTION_PRESSURE for a 
fixed-pressure gas phase.

Fixed Basic function GAS_VM for a fixed-pressure gas phase.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8532 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-02-28 15:33:20 +00:00
David L Parkhurst
e284f1167e Next fix for MCD 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8520 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-02-24 19:35:03 +00:00
David L Parkhurst
a59b8b7abf Tony's fix for MCD after unequal cell lengths for diffusion. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8518 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-02-24 15:41:21 +00:00
David L Parkhurst
b5e86c636e Do not dump negative entities. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8502 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-02-19 16:57:35 +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
David L Parkhurst
4922f9efe0 Tony's fix for unequal cells in diffusion. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8484 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-02-12 17:26:54 +00:00
David L Parkhurst
c9fb95a0d6 Tony's change to connecting graphs 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8469 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-02-07 23:25:04 +00:00
David L Parkhurst
aee604b56e Changed read _modify to warning if entity not found. 
Tony's bug in phrq_io. punch_ostream was deleted twice.

roughed in REACTION_TEMPERATURE_MODIFY and REACTION_PRESSURE_MODIFY. Think they work, and 
added to test case modify_ignore.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8453 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-02-06 18:28:24 +00:00
David L Parkhurst
063ba6202a Tony's punch_stream error when Basic error. 
Test case punch_stream added.

run_cell_range adjusted to account for including MIX in RUN_CELLS

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8452 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-02-06 16:57:39 +00:00
Scott R Charlton
63a9c36ad8 changed so that 'dist' and 'time' are always doubles for R 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8446 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-02-06 00:40:58 +00:00
David L Parkhurst
5bbe7db623 changes to Tests and 
include mix in RUN_CELLS

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8419 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-02-04 00:01:04 +00:00
David L Parkhurst
b6f962428e guarded gzstream in FileHandler.cpp 
rewrote WriteRestart to use DumpModule
Don't call DumpModule from manager/worker, now only in WriteFils
fixed DumpModule to work for serial and parallel. Uses dump_file_name with no adjustments to extensions.
added LastInitialPhreeqc2Module(vector<int> cell_numbers).
Changed args in RunFile and RunString in PhreeqcRM to bools, affected
   RM_interface.cpp, RM_interface_C.cpp, Tests/advection_cpp.cpp
In Copy for cxxStorageBin, check if destination == source.



git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8411 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-01-30 01:36:11 +00:00
David L Parkhurst
7cad09da67 Only solutions, not mix in run_cells 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8409 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-01-29 20:12:37 +00:00
David L Parkhurst
5e788df195 modifications to STORAGEBIN, added Copy. 
Check for missing solution in run_cells.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8408 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-01-29 19:53:57 +00:00
David L Parkhurst
f9eff4b835 Use MIX_RAW in dump to read negative numbered mixes. 
Added testcase negative_user_number

Tony's fix for start time units

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8403 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-01-27 22:04:45 +00:00
Scott R Charlton
473ea39b19 Added additional check to LoadDatabase 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8399 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-01-24 03:46:46 +00:00
David L Parkhurst
9d9e86f875 Added next_user_number to Phreeqc. 
Added a template function Rxn_next_user_number.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8397 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-01-24 00:34:03 +00:00
Scott R Charlton
aab6347c98 changed EOL to native 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8391 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-01-23 01:31:19 +00:00
David L Parkhurst
ab9b2ddd28 ex4 works with old flow from 8056. Will now try to keep all other changes, but go back to updated flow calculation. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8380 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-01-16 17:20:14 +00:00
David L Parkhurst
aee342676b Removed yellow for graphing. 
Changed Li molar volume in Pitzer, Amm, phreeqc.dat
Added test case Vm_LiCl_sol

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8378 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-01-16 15:54:30 +00:00
David L Parkhurst
1e48b85c86 Removed error trap in write_mass_action_eqn_x 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8375 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-01-15 17:11:46 +00:00
David L Parkhurst
6f849b215f More changes for Marco. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8374 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-01-15 15:59:50 +00:00
David L Parkhurst
2a37e80674 Do not set master_bsearch[i]->total = 0.0 in clear() for now. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8372 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-01-14 22:07:42 +00:00
David L Parkhurst
9048a9be86 Bugs fixes noted by Marco De-Vroed 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8371 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-01-14 20:42:12 +00:00
David L Parkhurst
e9b05399a5 Clean up initial_data 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8369 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-01-13 23:09:50 +00:00
David L Parkhurst
4ec2784a6b Tony's fix to solution volume. 
Added test case, updated Makefile
Added comment to Release.txt

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8356 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2014-01-07 16:11:24 +00:00