112 Commits

Author SHA1 Message Date
David L Parkhurst
9f7e982ffe eol
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3842 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-12-03 00:56:22 +00:00
David L Parkhurst
a4bac119db eol for system.cxx
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3841 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-12-03 00:54:28 +00:00
David L Parkhurst
3fe2fcd3bb Modified to run_cells if solution exists, even with no reactants.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3824 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-12-02 15:45:49 +00:00
Scott R Charlton
303864120a updated for COM object
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3749 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-11-03 23:39:32 +00:00
David L Parkhurst
5de5c6f307 Needed to turn of echo when rereading components.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3743 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-11-03 19:41:47 +00:00
David L Parkhurst
ff19c86d65 The tellg and seekg did not work for gz files because the
methods are not implemented.

Modified the parser to accumulate lines so that they
could be turned into a stream and reread. Modified
kinetics, exchange, ppassemblage, ssassemblage, and surface to use the new way to reread lines for component values. 

git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3742 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-11-03 17:55:36 +00:00
David L Parkhurst
e35673205b Typo of file instead of stream for setting echo to file.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3739 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-11-02 20:43:37 +00:00
David L Parkhurst
c73fc4b2e9 Modifications for Linux.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3736 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-11-02 15:34:29 +00:00
David L Parkhurst
b3b22f3fd5 New class
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3735 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-11-02 15:25:39 +00:00
David L Parkhurst
259c0839f0 Added new class runner.
Finished new keyword RUN_CELLS.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3730 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-10-30 22:27:43 +00:00
David L Parkhurst
5f9cf78f01 Modified for parallel version. Had some lists
in the pack and unpack routines that now are 
maps.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3728 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-10-29 20:08:56 +00:00
David L Parkhurst
cd38a8036d Have done preliminary testing with all MODIFY keywords.
Added brief documentation in revisions.

Fixed dump feature of TRANSPORT to work with
dump_raw of C++.

ppdump now has testing for DUMP, DELETE, and MODIFY.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3727 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-10-29 19:53:35 +00:00
David L Parkhurst
d54c04039a Have converted std::list to std::map for all entities.
surface is completed but needs testing.

SS and kinetics need to have reread of components implemented for MODIFY option.

gas_phase may be done, needs to be tested.



git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3726 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-10-28 19:15:17 +00:00
David L Parkhurst
f015759286 exchange_modify is working.
changed list of comps to map of comps.

made sure that description changes were captured for solution, equilibrium_phases, and exchange.

surface is next.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3725 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-10-27 22:57:49 +00:00
David L Parkhurst
b9e38f4da8 Updated phreeqcpp to have examples from phreeqc.
equilibrium_phases_read_raw has duplicate lines.




git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3724 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-10-27 20:29:04 +00:00
David L Parkhurst
cbfb768381 Initial testing of SOLUTION_MODIFY and EQUILIBRIUM_PHASES_MODIFY.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3721 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-10-27 16:38:25 +00:00
David L Parkhurst
2fd35ce463 Delete, Dump seem to work.
SOLUTION_MODIFY seems to work, but need to check all features.

EQUILIBRIUM_PHASES_MODIFY fails. Need to use maps to allow update I think. 

git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3719 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-10-23 00:03:23 +00:00
David L Parkhurst
74bb0bc5d0 For dump and delete, added StorageBinList
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3718 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-10-22 19:26:38 +00:00
David L Parkhurst
79092e94b4 Have added delete, but parser is not working correctly. Am going back to 3705 to see if it worked correctly then.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3716 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-10-22 19:24:31 +00:00
David L Parkhurst
6ca3a6d3b2 Added the suite of modify keywords:
SOLUTION_MODIFY
	EQUILIBRIUM_PHASES_MODIFY
	EXCHANGE_MODIFY
	SURFACE_MODIFY
	SOLID_SOLUTIONS_MODIFY
	GAS_PHASE_MODIFY
	KINETICS_MODIFY

May now revisit dump to add a delete capability.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3714 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-10-21 19:40:43 +00:00
David L Parkhurst
c3d4c1c462 Subsequent simulation wiped out dump file even though there was no dump. Check to see if dump file is needed before opening file in dump_entities.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3705 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-10-07 16:19:39 +00:00
David L Parkhurst
4d71795183 Added dump files.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3701 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-10-06 23:00:51 +00:00
David L Parkhurst
a81cd945b3 Added dump datablock for phreeqcpp
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3700 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-10-06 22:55:15 +00:00
David L Parkhurst
ccd310298d SOLUTION_RAW: c++ version used in PHAST misinterpreted the
element Tc as the temperature identifier and crashed
	when additional elements followed in -totals or 
	-activity_coefficients.
	
	Removed "tc" as an identifier for temperature.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3613 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-08-12 16:55:42 +00:00
David L Parkhurst
45d120f629 Fixed bug with reallocation for Read_raw for storage bin. Was allocating space for a pointer array instead of structure arrays for exchange, surface, etc. ReadClass.cxx.
Commented delay_free for debugging in main.c

down and dirty dump for transport using dump_raw StorageBin. (readtr.c)

Changed definitions for sit.c to use variables in pitzer.c. Defined with extern in sit.c.







git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3459 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2009-04-20 20:40:12 +00:00
David L Parkhurst
ff282a405f Missed one line for struct to class conversion of
ppassemblage for precipitate_only.




git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3227 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2008-12-09 22:39:51 +00:00
David L Parkhurst
e398c418f0 Updated PHREEQCPP to have precipitate_only option for pp_assemblage.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3200 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2008-11-24 17:44:38 +00:00
David L Parkhurst
cefe071f17 Reindented, fixed errors, ran test cases.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3176 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2008-10-31 19:09:45 +00:00
David L Parkhurst
d37ed2c6ae indented header files.
removed ^M from System.h





git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3169 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2008-10-31 15:32:53 +00:00
David L Parkhurst
3313c814a9 Ran indent program on phreeqcpp
indent -bli0 -i4 -ts4 -npcs -nbc *.cxx




git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3168 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2008-10-31 15:19:39 +00:00
David L Parkhurst
60d57c5062 Delete kinetics.h at PhreeqcPP src level. Duplicate I assume
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@3099 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2008-09-18 15:46:01 +00:00
David L Parkhurst
193e8ef865 Bug with adding mixing solution when already in list. Replaced old fraction with new
fraction. Now adds the two fractions. 

This created a bug with rivers when mixing with the same solution. The mass fraction
was calculated incorrectly because only the second part of the solution was used (solution, frac 2).


git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2888 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2008-04-24 23:59:55 +00:00
David L Parkhurst
7a60bb9877 Write around assert.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2746 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2008-03-11 22:04:33 +00:00
David L Parkhurst
d106dbea5c Added missing tests from phreeqc/mytest and related files:
netpathxl
      eq_EC
      salt_ec

Fixed Makefile to include gmp library and fix typo on INVERSE_CL1MP definition.



git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2713 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2008-02-19 23:28:29 +00:00
David L Parkhurst
25666df97c Used new gcc on srv2rcolkr.
Cleaned up all the const errors when using constant string in 
arguments to functions.

removed ex1.

Modified makefile to include/exclude cl1mp.



git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2712 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2008-02-19 22:05:11 +00:00
David L Parkhurst
b9520a207f Worked on dependencies for Makefile.
Made dependencies the same for serial and parallel,
can check with make depends and make depends_parallel, 
dependencies and dependencies_parallel should be the same.

Modified fortran with -I/usr/include for gfortran compiler
to find mpif.h.

Now use mpif.h in mpimod.F90 to define MPI_COMM_WORLD.

Dictionary.h moved in cxx files to make serial and parallel
dependencies the same.

Ifdef'd mpimod to exclude everything in module for serial version. 



git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2707 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2008-02-14 17:56:32 +00:00
David L Parkhurst
bfec3cc7c7 Missing break in kinetics_read_raw switch.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2693 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2008-02-07 23:14:24 +00:00
David L Parkhurst
3f9693c68c Updated C++ to have new variables for KINETICS
cvode_steps, cvode_order.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2684 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2008-02-05 21:41:45 +00:00
Scott R Charlton
f630dd8377 added linker option to check for --hash-style availability
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2531 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2008-01-15 01:20:44 +00:00
David L Parkhurst
711f5f948e Fixed syntax for bash
cat file > xxx 2>&1;

Weird.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2414 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2007-11-20 21:34:23 +00:00
David L Parkhurst
5764f894ad Simplified get_total_element a bit
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2378 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2007-11-08 00:08:45 +00:00
David L Parkhurst
f4777a194b Fixed bug, and streamlined.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2376 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2007-11-07 22:23:47 +00:00
David L Parkhurst
3f93ab5a1c Tried optimizing get_total_element using std::strings
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2374 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2007-11-07 18:28:25 +00:00
David L Parkhurst
e7ec5c7691 Removed echo that was always true. Made huge string that crashed
restart. Results are same without the removed lines.




git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2276 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2007-09-21 19:01:46 +00:00
David L Parkhurst
8d475282bf Added read_raw_keyword.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2271 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2007-09-20 19:09:38 +00:00
David L Parkhurst
75255ea2f2 No memory leak check in output files.
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2205 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2007-08-30 16:36:35 +00:00
David L Parkhurst
e3859a08c3 reordering mpi.h
git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2189 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2007-08-28 20:45:29 +00:00
David L Parkhurst
37b1add946 Ifdef'd ORCHESTRA.
Added lines at end of files.

Ran test cases, a few had changes from format and Tony.





git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2182 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2007-08-16 19:49:38 +00:00
David L Parkhurst
7ab1e21ce7 Works with reaction calculation of pure phase equilibrium.
Worked out relation between phreeqc components H,O,charge and Orchestra H+, e-, H2O.

It's a lot of code and still have not implemented SURFACE, EXCHANGE, GAS_PHASE,

much les KINETICS.

Convergence problem when including pyrite.

Also have REACTION (REQCTION_TEMP?);

git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2181 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2007-08-16 18:51:35 +00:00
David L Parkhurst
c78dd87daf Have version working that formats an input file for Orchestra, runs Orchestra with a system call to a batch file, reads results from Orchestra, stores results in global phreeqc storage, and prints results.
Works only for initial solution calculation.

Still some problems with the solver. Ex1 fails.

Cleaned up organization a little. Ready to start on "reaction" calculation.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@2176 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2007-08-07 15:04:13 +00:00