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David L Parkhurst 660042da0e Changed variable from max to max_cells. 
Added variable all_cells to be able to initialize new cell_data.
moved old_cells, max_cells, all_cells to phreeqc class.

initialized old_cells, max_cells, all_cells in init of phreeqc class. 
Added to copy constructor.

changed logic for switching to numerical derivatives by adding && numerical_fixed_volume == false
if (iterations > 99 && numerical_fixed_volume == false)

Added 
			gammas_pz();
			jacobian_sums();
For restart in pitzer.cpp

Added 
			gammas_sit();
			jacobian_sums();
for restart in sit.cpp.

git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8835 1feff8c3-07ed-0310-ac33-dd36852eb9cd
2014-07-11 20:05:09 +00:00
advection.cpp
moved phreeqc files into src
2013-01-10 06:04:12 +00:00
basicsubs.cpp
Changed calc_logk_s to use original equation.
2014-05-20 20:12:05 +00:00
chart_icon.gif
moved phreeqc files into src
2013-01-10 06:04:12 +00:00
ChartHandler.cpp
updated to allow charts to stay open in phreeqci
2013-08-30 04:29:19 +00:00
ChartHandler.h
Added active_charts to ChartHandler.
2012-12-20 23:22:16 +00:00
ChartObject.cpp
Tony's change to connecting graphs
2014-02-07 23:25:04 +00:00
ChartObject.h
Added second logical in batch. First is color, second is grid.
2012-08-01 20:03:47 +00:00
cl1.cpp
Avoid overlapping memcpy in cl1.cpp
2014-07-09 16:19:57 +00:00
cl1mp.cpp
Fixed leaks:
2014-07-08 19:05:54 +00:00
class_main.cpp
Fixed leaks:
2014-07-08 19:05:54 +00:00
CurveObject.cpp
fixed all System::Threading::Interlocked::CompareExchange and added some debugging code
2012-12-13 22:20:53 +00:00
CurveObject.h
Merged ErrorHandling 6119-6268 changes.
2012-03-06 23:42:49 +00:00
cvdense.cpp
Fixed leaks:
2014-07-08 19:05:54 +00:00
cvdense.h
added LICENSE to cvode files
2014-05-08 02:23:14 +00:00
cvode.cpp
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
cvode.h
added LICENSE to cvode files
2014-05-08 02:23:14 +00:00
cxxKinetics.cxx
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
cxxKinetics.h
PHREEQC should now have no USE_MPI
2012-10-29 23:16:27 +00:00
cxxMix.cxx
Use MIX_RAW in dump to read negative numbered mixes.
2014-01-27 22:04:45 +00:00
cxxMix.h
const static vopts
2012-07-17 17:12:50 +00:00
dense.cpp
added LICENSE to cvode files
2014-05-08 02:23:14 +00:00
dense.h
added LICENSE to cvode files
2014-05-08 02:23:14 +00:00
distribution.checklist
Copying new classes (cxx) and cpp files to src
2006-02-16 00:21:39 +00:00
distribution.mk
working on 3.0 dist
2013-01-15 21:46:19 +00:00
dumper.cpp
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
dumper.h
added Set_append
2013-05-31 05:39:52 +00:00
dw.cpp
moved phreeqc files into src
2013-01-10 06:04:12 +00:00
Exchange.cxx
fixed uninitialized values
2014-07-10 20:12:14 +00:00
Exchange.h
PHREEQC should now have no USE_MPI
2012-10-29 23:16:27 +00:00
ExchComp.cxx
PHREEQC should now have no USE_MPI
2012-10-29 23:16:27 +00:00
ExchComp.h
PHREEQC should now have no USE_MPI
2012-10-29 23:16:27 +00:00
Form1.h
Removed yellow for graphing.
2014-01-16 15:54:30 +00:00
Form1.resX
moved phreeqc files into src
2013-01-10 06:04:12 +00:00
GasComp.cxx
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
GasComp.h
const static vopts
2012-07-17 17:12:50 +00:00
gases.cpp
Tony's changes for gases.
2013-04-26 16:57:25 +00:00
GasPhase.cxx
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
GasPhase.h
PHREEQC should now have no USE_MPI
2012-10-29 23:16:27 +00:00
global_structures.h
Had timing reversed in PhreeqcRM.cpp for heterogeneous case.
2014-06-04 17:05:57 +00:00
input.cpp
moved phreeqc files into src
2013-01-10 06:04:12 +00:00
integrate.cpp
valgrind changes/set-but-unused vars
2014-07-08 19:53:00 +00:00
inverse.cpp
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
ISolution.cxx
Removed Phreeqc_class.h.
2012-04-19 18:35:14 +00:00
ISolution.h
Default_pe is now const char *, saves some string_hsave in clear in prep.
2013-05-15 20:46:20 +00:00
ISolutionComp.cxx
Bugs fixes noted by Marco De-Vroed
2014-01-14 20:42:12 +00:00
ISolutionComp.h
updated for linux (added headers)
2012-04-20 05:18:15 +00:00
isotopes.cpp
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
Keywords.cpp
Fixed bugs with mixing calculations (keywords not set up right).
2012-07-24 18:19:29 +00:00
Keywords.h
Added new keywords to mix SOLUTION, EXCHANGE, GAS_PHASE, KINETICS, EQUILIBRIUM_PHASES, SOLID_SOLUTIONS, SURFACE
2012-07-24 16:51:26 +00:00
kinetics.cpp
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
KineticsComp.cxx
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
KineticsComp.h
Added logic for rate limiter, but not used.
2013-04-30 16:41:40 +00:00
mainsubs.cpp
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
Makefile
Tony's vm revisions, phreeqc.dat gfw for N redox states
2013-11-18 20:58:12 +00:00
Makefile.am
added SelectedOutput and UserPunch to automake
2013-11-05 00:05:13 +00:00
Makefile.old
remove R_SO from class_release_64
2014-07-10 14:15:18 +00:00
model.cpp
Changed variable from max to max_cells.
2014-07-11 20:05:09 +00:00
NA.h
moved phreeqc files into src
2013-01-10 06:04:12 +00:00
NameDouble.cxx
NameDouble dump failed with string greater than 21 characters.
2013-04-02 20:05:34 +00:00
NameDouble.h
PHREEQC should now have no USE_MPI
2012-10-29 23:16:27 +00:00
newiso.dat
moved phreeqc files into src
2013-01-10 06:04:12 +00:00
NumKeyword.cxx
Allow negative numbers on entity mixes.
2012-07-24 18:52:15 +00:00
NumKeyword.h
Merged ErrorHandling 6119-6268 changes.
2012-03-06 23:42:49 +00:00
nvector_serial.cpp
fixed if R_SO not set
2014-07-09 19:46:08 +00:00
nvector_serial.h
added LICENSE to cvode files
2014-05-08 02:23:14 +00:00
nvector.cpp
added LICENSE to cvode files
2014-05-08 02:23:14 +00:00
nvector.h
added LICENSE to cvode files
2014-05-08 02:23:14 +00:00
parse.cpp
moved phreeqc files into src
2013-01-10 06:04:12 +00:00
Parser.cxx
first pass @ removing std::cerr, std::cout, exit, stderr, stdout from R version.
2014-04-05 04:14:16 +00:00
Parser.h
has _DEBUG #defines for extended ascii/ANSI character set to avoid assert.
2013-02-07 16:08:13 +00:00
PBasic.cpp
Fixed leaks:
2014-07-08 19:05:54 +00:00
PBasic.h
Added a Fortran callback.
2013-08-05 18:56:31 +00:00
phast.xsd
eol
2009-12-03 01:06:34 +00:00
phqalloc.cpp
moved phreeqc files into src
2013-01-10 06:04:12 +00:00
phqalloc.h
moved phreeqc files into src
2013-01-10 06:04:12 +00:00
Phreeqc.cpp
Changed variable from max to max_cells.
2014-07-11 20:05:09 +00:00
phreeqc.dat
Copying new classes (cxx) and cpp files to src
2006-02-16 00:21:39 +00:00
phreeqc.distribution.checklist
moved phreeqc files into src
2013-01-10 06:04:12 +00:00
Phreeqc.h
Changed variable from max to max_cells.
2014-07-11 20:05:09 +00:00
phreeqc.Makefile
moved phreeqc files into src
2013-01-10 06:04:12 +00:00
phreeqc.rev
Copying new classes (cxx) and cpp files to src
2006-02-16 00:21:39 +00:00
phreex.ico
moved phreeqc files into src
2013-01-10 06:04:12 +00:00
PHRQ_base.cxx
first pass @ removing std::cerr, std::cout, exit, stderr, stdout from R version.
2014-04-05 04:14:16 +00:00
PHRQ_base.h
roughed in cxxPressure class. A lot more to do.
2011-11-30 16:50:52 +00:00
PHRQ_io_output.cpp
moved Phreeqc methods process_file_names, open_input_stream,
2014-05-02 03:36:26 +00:00
PHRQ_io.cpp
init ctor; changed success to include 0; fixed delete[]
2014-07-09 23:56:56 +00:00
PHRQ_io.h
all tests passing for one selected_output file;
2013-08-12 22:24:18 +00:00
phrqtype.h
moved phreeqc files into src
2013-01-10 06:04:12 +00:00
pitzer_structures.cpp
Fixed bug with redefinition of sit parameters
2014-04-08 15:06:20 +00:00
pitzer.cpp
Changed variable from max to max_cells.
2014-07-11 20:05:09 +00:00
PPassemblage.cxx
added pointers for solid solution and ss component in unknown struct to speed calculations, all test cases run
2013-05-16 20:42:28 +00:00
PPassemblage.h
PHREEQC should now have no USE_MPI
2012-10-29 23:16:27 +00:00
PPassemblageComp.cxx
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
PPassemblageComp.h
PHREEQC should now have no USE_MPI
2012-10-29 23:16:27 +00:00
prep.cpp
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
Pressure.cxx
Changed read _modify to warning if entity not found.
2014-02-06 18:28:24 +00:00
Pressure.h
Changed read _modify to warning if entity not found.
2014-02-06 18:28:24 +00:00
print.cpp
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
Reaction.cxx
const static vopts
2012-07-17 17:12:50 +00:00
Reaction.h
const static vopts
2012-07-17 17:12:50 +00:00
read.cpp
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
ReadClass.cxx
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
readtr.cpp
Changed variable from max to max_cells.
2014-07-11 20:05:09 +00:00
runner.cpp
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
runner.h
added Setters for time params
2013-03-07 05:42:24 +00:00
SelectedOutput.cpp
changed EOL to native
2014-01-23 01:31:19 +00:00
SelectedOutput.h
changed EOL to native
2014-01-23 01:31:19 +00:00
sit.cpp
Changed variable from max to max_cells.
2014-07-11 20:05:09 +00:00
smalldense.cpp
fixed if R_SO not set
2014-07-09 19:46:08 +00:00
smalldense.h
added LICENSE to cvode files
2014-05-08 02:23:14 +00:00
Solution.cxx
Got all Tests working with MPI except the units tester.
2014-03-13 01:06:32 +00:00
Solution.h
Roughing in mcd capability.
2014-02-28 21:29:53 +00:00
SolutionIsotope.cxx
const static vopts
2012-07-17 17:12:50 +00:00
SolutionIsotope.h
const static vopts
2012-07-17 17:12:50 +00:00
spread.cpp
memory error on units line
2014-07-10 18:08:02 +00:00
SS.cxx
LDBLEs
2013-03-29 17:42:27 +00:00
SS.h
PHREEQC should now have no USE_MPI
2012-10-29 23:16:27 +00:00
SSassemblage.cxx
more testing of copy operator.
2013-02-11 19:04:35 +00:00
SSassemblage.h
PHREEQC should now have no USE_MPI
2012-10-29 23:16:27 +00:00
SScomp.cxx
LDBLE for SScomp
2013-04-03 22:06:01 +00:00
SScomp.h
LDBLE for SScomp
2013-04-03 22:06:01 +00:00
step.cpp
Modification to use REACTION_PRESSURE for a
2014-02-28 15:33:20 +00:00
StorageBin.cxx
Moved uz_bin to workers to avoid possible data conflicts.
2014-04-15 22:55:59 +00:00
StorageBin.h
Moved uz_bin to workers to avoid possible data conflicts.
2014-04-15 22:55:59 +00:00
StorageBinList.cpp
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
StorageBinList.h
added some const and added cell for use in phreeqci
2013-05-29 23:38:00 +00:00
structures.cpp
fixed memory leaks.
2014-06-10 23:51:13 +00:00
sundialsmath.cpp
added LICENSE to cvode files
2014-05-08 02:23:14 +00:00
sundialsmath.h
added LICENSE to cvode files
2014-05-08 02:23:14 +00:00
sundialstypes.h
added LICENSE to cvode files
2014-05-08 02:23:14 +00:00
Surface.cxx
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
Surface.h
PHREEQC should now have no USE_MPI
2012-10-29 23:16:27 +00:00
SurfaceCharge.cxx
PHREEQC should now have no USE_MPI
2012-10-29 23:16:27 +00:00
SurfaceCharge.h
PHREEQC should now have no USE_MPI
2012-10-29 23:16:27 +00:00
SurfaceComp.cxx
PHREEQC should now have no USE_MPI
2012-10-29 23:16:27 +00:00
SurfaceComp.h
PHREEQC should now have no USE_MPI
2012-10-29 23:16:27 +00:00
System.cxx
Removed Phreeqc_class.h.
2012-04-19 18:35:14 +00:00
System.h
Removed Phreeqc_class.h.
2012-04-19 18:35:14 +00:00
tally.cpp
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
Temperature.cxx
Changed read _modify to warning if entity not found.
2014-02-06 18:28:24 +00:00
Temperature.h
Changed read _modify to warning if entity not found.
2014-02-06 18:28:24 +00:00
test.xml
eol
2009-12-03 01:06:34 +00:00
tidy.cpp
latest, fixed bug from R with relative dielectric
2014-05-20 20:42:32 +00:00
transport.cpp
removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable]
2014-07-09 01:46:43 +00:00
Use.cpp
Linux Makefile
2012-01-11 16:46:37 +00:00
Use.h
Merged ErrorHandling 6119-6268 changes.
2012-03-06 23:42:49 +00:00
UserPunch.cpp
changed EOL to native
2014-01-23 01:31:19 +00:00
UserPunch.h
changed EOL to native
2014-01-23 01:31:19 +00:00
utilities.cpp
Got a request for interacting sites, such as this surface complex.
2013-09-05 17:06:20 +00:00
Utils.cxx
LDBLEs
2013-03-29 17:42:27 +00:00
Utils.h
LDBLEs
2013-03-29 17:42:27 +00:00
ZedGraph.dll
moved phreeqc files into src
2013-01-10 06:04:12 +00:00
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C++ 81.6%
Makefile 9.2%
C 4.8%
Fortran 1.8%
R 1%
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