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Author SHA1 Message Date
David L Parkhurst
95133f2b54 Tony's changes. 
Added porosities.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10737 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-26 21:39:37 +00:00
David L Parkhurst
8dc42fee7e Tony fixed the memory problem. 
Will rerun Valgrind one more time.

Revised Amm.dat

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10736 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-25 17:40:40 +00:00
David L Parkhurst
96e537f08d Initialization, memory leak. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10732 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-22 15:42:59 +00:00
David L Parkhurst
891e33bf47 More initialization 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10731 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-22 01:34:20 +00:00
David L Parkhurst
24dd5ede7a Working on valgrind uninitialized variables. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10730 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-22 00:07:22 +00:00
David L Parkhurst
1fcb85d634 use space for cell_data 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10729 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-21 17:45:57 +00:00
David L Parkhurst
964b1665eb Initialize sol_D[l_cell_no].spec 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10728 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-21 17:32:09 +00:00
David L Parkhurst
7f842da63e removed MPI. 
Fixed memory leak.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10727 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-21 16:29:14 +00:00
David L Parkhurst
7fbf8779ce Removed parallelization. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10726 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-21 00:20:02 +00:00
David L Parkhurst
41bb948377 fix for linux, but Cl has NaN 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10723 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-20 22:02:20 +00:00
David L Parkhurst
dbaabe0180 initialize variables 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10722 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-20 21:30:24 +00:00
David L Parkhurst
9644278e49 added Dictionary and Serializer 
Deleted unused files.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10720 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-20 18:19:12 +00:00
David L Parkhurst
174c739d26 Updated concrete source from concrete_parallel source (not using parallel). 
Now going to run test cases on Linux.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10719 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-20 18:12:15 +00:00
David L Parkhurst
5af5488477 Switching back to diagonal_scale false for default. No obvious advantage in test cases to change, and it 
could break someone's runs.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10711 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-20 16:01:03 +00:00
David L Parkhurst
716a978be0 Made diagonal_scale true by default. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10703 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-19 23:06:50 +00:00
David L Parkhurst
516d6937ee Another check for null pointers. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10664 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-11 21:47:58 +00:00
David L Parkhurst
6f7a2e50dd Fixed segvs from Kinniburgh. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10663 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-11 21:01:54 +00:00
David L Parkhurst
a94659326b Fixed formatting for temperature of Specific Conductance. 
Added test cases missing_surf_related_equi, missing_surf_related_kin, and SC_temp.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10641 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2016-01-04 17:17:15 +00:00
David L Parkhurst
8f51d9279b Need to set new_def to trap error with surface related to rate. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10634 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-30 21:25:06 +00:00
David L Parkhurst
dec66bb848 tweak if tidy_min_surface is invoked on a _raw definition. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10633 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-30 18:23:01 +00:00
David L Parkhurst
ae2286eb41 Added serializer for rebalance by cell. 
Made fix to tidy_min_surface, same as tidy_kin_surface; skip if not new def.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10632 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-30 18:14:48 +00:00
David L Parkhurst
a702035139 totals of surface comp set incorrectly after read_raw. Skipping tidy for these cases. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10630 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-30 17:39:12 +00:00
Scott R Charlton
6ae25495c5 added ifdef for R (R_SO) 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10618 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-29 05:17:03 +00:00
Scott R Charlton
6ecc3a10d2 added Dictionary/Serializer 
git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@10612 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-29 02:11:34 +00:00
David L Parkhurst
b33a28fa91 fgets warning 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10610 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-29 00:27:52 +00:00
David L Parkhurst
b88bd3f955 more Linux warnings 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10609 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-29 00:10:20 +00:00
David L Parkhurst
eb7e91ebad fixed Makefile.old, Linux warnings 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10608 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-29 00:02:35 +00:00
David L Parkhurst
af2dbfdce2 Added changes for serializing. 
Copied files from concrete_parallel, without merging or svn_copy.
Added Dictionary.cpp and Serializer.cxx + header files.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10607 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-28 23:35:36 +00:00
David L Parkhurst
4dc54757e6 Bug showed up in PHAST. Errors in definition of surface related to mineral or kinetics were not detected. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10606 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-28 22:12:48 +00:00
David L Parkhurst
c6f09779a8 added equi_delay to the convergence sets 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10585 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-16 18:01:29 +00:00
David L Parkhurst
5476982186 roughed in equi_delay 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10582 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-16 00:53:27 +00:00
David L Parkhurst
ca4c8f9e55 delay removing phases in ineq, should be unchanged until delay is > 0 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10575 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-15 19:42:49 +00:00
David L Parkhurst
0970c44067 using old viscosity 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10570 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-14 21:18:25 +00:00
David L Parkhurst
301d2d009c transport.cpp, ifdefd old viscosity, initialized variables; basicsubs call viscosity();phreeqc, revert ineq_tol 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10569 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-14 20:35:26 +00:00
David L Parkhurst
c15e56ad5b -potential not defined for solution read_raw. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/branches/concrete@10567 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-14 20:09:32 +00:00
David L Parkhurst
a719b57921 First cut at parallelization. 
Runs with PhreeqcRM, but I don't think answers are right yet.

git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@10561 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-10 20:56:20 +00:00
David L Parkhurst
e4fa262155 Removed phreeqcpp/ from include statement. 
Added ifdef for PHREEQC_PARALLEL

git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@10557 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-12-09 16:50:33 +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
David L Parkhurst
2fe6313f47 Avoid a null pointer. Not really sure what causes it, combination of charge balance, pe constraint, alkalinity, and C(4). 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10432 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-10-26 20:05:47 +00:00
David L Parkhurst
bef66de3c3 Fixed formula for pressure dependence of B1, B2, F1, F2. Previously had a limit of -10C, otherwise produced a floating point exception. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10385 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-10-15 20:04:36 +00:00
David L Parkhurst
218f4f5fab Avoid negative moles of equilibrium phase. 
Typo in RELEASE

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10368 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-10-09 13:29:30 +00:00
David L Parkhurst
a51e899fdc Activated argument for number of threads. 
Typo in print.
Revised ASSERT to avoid asserting with std::cerr.


git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@10364 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-10-08 15:20:42 +00:00
Scott R Charlton
33b4ae373e fixed BUILD_SHARED_LIBS build on windows 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10347 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-10-06 03:15:13 +00:00
Scott R Charlton
34f7921371 fixed BUILD_SHARED_LIBS build on windows 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10347 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-10-06 03:15:13 +00:00
David L Parkhurst
f997d62a13 [ not handled as upper for solution_spread in copy_token_tab. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10327 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-10-01 17:07:17 +00:00
David L Parkhurst
e8553de46e Debug prints for Peter de Moel. 
Possible null reference in tidy_solution.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10325 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-10-01 15:46:09 +00:00
David L Parkhurst
3f332d180b Trap null pointer missing gas components. 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10317 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-09-29 19:33:39 +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
Scott R Charlton
190128c155 updated for R 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10310 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-09-25 06:18:48 +00:00
Scott R Charlton
6e752e26c4 windows java working with callback 
git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@10300 1feff8c3-07ed-0310-ac33-dd36852eb9cd
 2015-09-24 06:10:03 +00:00