1138 Commits

Author SHA1 Message Date
Darth Vader
5e9815843e Squashed 'phreeqcpp/' changes from 455b49c..ccb9ba3
ccb9ba3 Fixed uninitialized memory errors

git-subtree-dir: phreeqcpp
git-subtree-split: ccb9ba3c63b17166035f42586010bb43f217220b
2024-10-22 23:29:47 +00:00
Darth Vader
301276613d Squashed 'phreeqcpp/' changes from 8c0d001..455b49c
455b49c Tony's tweak to transport, updated RELEASE.TXT
7233c29 fixed viscos_0 as new datum in solution class.
9f438c1 Tony's changes for viscosity and heat in transport. ex13_impl failed in Release.

git-subtree-dir: phreeqcpp
git-subtree-split: 455b49c2a7e20aef296e2cbd08348391c1e8d9e5
2024-10-22 01:04:23 +00:00
Darth Vader
9172a45eb2 Squashed 'phreeqcpp/' changes from ead498a..8c0d001
8c0d001 Changed Lamda to Lambda, but retained backward compatibility

git-subtree-dir: phreeqcpp
git-subtree-split: 8c0d00166b66af612f75b87eebc47f0badc6ce37
2024-10-11 19:12:45 +00:00
Darth Vader
792cdda060 Squashed 'phreeqcpp/' changes from c876219..ead498a
ead498a Merge pull request #79 from dlparkhurst/mix_error
4409349 fixed error with MIX that Scott found on merge.

git-subtree-dir: phreeqcpp
git-subtree-split: ead498ab60e71b7175c0e4bc6468a0804851ac20
2024-10-08 22:02:03 +00:00
Darth Vader
4e80a54467 Squashed 'phreeqcpp/' changes from 7c7fafd..c876219
c876219 Merge commit '64310ada821d1cc387af4507db7029fe3326784b'
64310ad Squashed 'common/' changes from 399aba2..648db22

git-subtree-dir: phreeqcpp
git-subtree-split: c876219b1b064ab7c17e0bc4ad8bff13e0aeb108
2024-10-08 20:05:00 +00:00
Darth Vader
b537589773 Squashed 'phreeqcpp/' changes from e317dd0..7c7fafd
7c7fafd Merge pull request #78 from dlparkhurst/mix_error
eb0591c Merge pull request #74 from mwtoews/fix-typos
334df5e Tony's fix in heat transport
bf897a2 Marked old error in mix. Updated test case.
58566a6 Fix ah2o in adding a solution. Fixed bad_graph database.
75effd0 Merge branch 'viscosity' into mix_error
f4708df account for water mass in addition to mixing fractions
70954c6 mixing by water mass times mixing fraction
84b59ab Fix typos

git-subtree-dir: phreeqcpp
git-subtree-split: 7c7fafd686d7c41753132a978a1d55d4d25b601b
2024-10-08 20:04:33 +00:00
Darth Vader
c155685f63 Squashed 'phreeqcpp/' changes from fdc0bb5..e317dd0
e317dd0 Guarded case with no points in curves for log axes. Added bad_graph test case.

git-subtree-dir: phreeqcpp
git-subtree-split: e317dd0e41bbfd18abd2255ab5f2cf3933cd4c69
2024-09-24 22:02:30 +00:00
Darth Vader
8f7d206a80 Squashed 'phreeqcpp/' changes from c477ba1..fdc0bb5
fdc0bb5 fixed nullptr for pre-c++11

git-subtree-dir: phreeqcpp
git-subtree-split: fdc0bb51869877771df528f727fe577f58877c7d
2024-08-29 21:04:42 +00:00
Darth Vader
45befa7108 Squashed 'phreeqcpp/' changes from faf8144..c477ba1
c477ba1 Converted to utf-8
53b14b4 Tony fixed latest viscosity bug in surface calculations
2375f7b fixed mismatched ifdef
84ad1ce Tony's changes. [200~Added variable viscos_DDL in EDL(viscos_DDL, surface_name) to give the viscosity of a Donnan layer on a surface in BASIC. Note that the surface_name should not contain an underscore _, the Donnan properties are for the surface, not for surface charge, thus use the surface name Hfo, not Hfo_w. If surface_name is omitted, the viscosity is given for the first surface in the alphabetical order.

git-subtree-dir: phreeqcpp
git-subtree-split: c477ba119a0ecfa4361b88f0b49523847a1a03bc
2024-08-29 19:02:04 +00:00
Darth Vader
c1c1f286b6 Squashed 'phreeqcpp/' changes from b6a23a2..faf8144
faf8144 50 apple clang 15 with c++11 or higher reports warnings wwritable strings in pbasiccpp (#57)

git-subtree-dir: phreeqcpp
git-subtree-split: faf81447ee82e86ce3b2cb9d71fd81316cccfd9f
2024-08-15 17:08:49 +00:00
Darth Vader
88d5ec2035 Squashed 'phreeqcpp/' changes from 587223f..b6a23a2
b6a23a2 reorder classes in global_structures.h to avoid incomplete definitions

git-subtree-dir: phreeqcpp
git-subtree-split: b6a23a2457530f9ca6e13fe4f0c226db3bba48af
2024-08-14 21:44:26 +00:00
Darth Vader
9a4caf7def Squashed 'phreeqcpp/' changes from e4c4cf3..587223f
587223f Extra check to not dump negative user numbers

git-subtree-dir: phreeqcpp
git-subtree-split: 587223f4d35ddca5105498f1f0ef31638f748562
2024-07-11 17:08:34 +00:00
Darth Vader
2abb0b0bcd Squashed 'phreeqcpp/' changes from 798f8f9..e4c4cf3
e4c4cf3 Added functions SPECIES_EQUATION and PHASE_EQUATION, and species_equation test case.

git-subtree-dir: phreeqcpp
git-subtree-split: e4c4cf31fb54a3546e6bdbb1fda762952803fd82
2024-06-20 21:52:29 +00:00
Darth Vader
a9c4ef8324 Squashed 'phreeqcpp/' changes from ceab9a1..798f8f9
798f8f9 Merge commit '3eaa057b5d2bbc9327f2ab3adfd52577c687cfca'
3eaa057 Squashed 'common/' changes from 6abe004..399aba2
4cad3d5 [iphreeqc] Fixed for R

git-subtree-dir: phreeqcpp
git-subtree-split: 798f8f9d827d6ba7cf6a6d0c9a1fd3c7e806c72c
2024-06-11 00:58:17 +00:00
Darth Vader
8024ee1289 Squashed 'phreeqcpp/' changes from e2f4d06..ceab9a1
ceab9a1 Tony's change to Sr and NH4, SC_Ohm and rate_xmpls, basicsubs.cpp error

git-subtree-dir: phreeqcpp
git-subtree-split: ceab9a1033d2046c72a6bcf19c2c2244e8b23f97
2024-06-07 21:56:13 +00:00
Darth Vader
067a8b1aaa Squashed 'phreeqcpp/' changes from 3d5242f..e2f4d06
e2f4d06 updated InternalCopy
d8abe83 Fixed problem with N vs NO3, for example, converting units with calculated density. Now gives same result for N or NO3.

git-subtree-dir: phreeqcpp
git-subtree-split: e2f4d060cd01b0b9912f0da7aa6c7cc20f77a9c5
2024-05-29 19:05:39 +00:00
Darth Vader
09af2d5b12 Squashed 'phreeqcpp/' changes from cb6d9f4..3d5242f
3d5242f bug in processing ISOTOPE_RATIOS
034e921 added commented code to check e- in non-master species.

git-subtree-dir: phreeqcpp
git-subtree-split: 3d5242f5ccaf56cbcad48d33caee0340fb97da65
2024-05-27 19:31:40 +00:00
Darth Vader
0b3f349ad3 Squashed 'phreeqcpp/' changes from 07c887a..cb6d9f4
cb6d9f4 [phreeqci] Fixed phreeqci memory leaks
77df73c [phreeqci] Fixed memory leak for phreeqci
38a34f7 [phreeqci] Removed trailing whitespace

git-subtree-dir: phreeqcpp
git-subtree-split: cb6d9f49b0957bc431c0eca2c21711bfde4411e7
2024-05-16 01:04:33 +00:00
Darth Vader
1efeb35669 Squashed 'phreeqcpp/' changes from 8f6cb45..07c887a
07c887a [phreeqci] Removed assert since svn -r8264(3.1.0 -- 2013-11-27) fails opening ex6

git-subtree-dir: phreeqcpp
git-subtree-split: 07c887a02026b1c0bfc6019d09b8ed45e22bb678
2024-05-13 18:45:27 +00:00
Darth Vader
97a4237601 Squashed 'phreeqcpp/' changes from c035d9c..8f6cb45
8f6cb45 Pad needed a free. Ran all test cases.
56ba680 Freed result from strexpr

git-subtree-dir: phreeqcpp
git-subtree-split: 8f6cb45a04ca40ea253c0f3ca90f52427d99592d
2024-05-10 20:36:07 +00:00
Darth Vader
bacfb0ea50 Squashed 'phreeqcpp/' changes from 60ccbf8..c035d9c
c035d9c Tony updates to phreeqc_rates.dat. Added albite_rates. Copy/paste error in read.cpp
fcec621 basicsubs.cpp fix from Tony
e5b4b11 Fixed some HTML, still a problem with colors of links.

git-subtree-dir: phreeqcpp
git-subtree-split: c035d9c3b76f807db7d87066c235c9f6867e5497
2024-05-09 19:46:42 +00:00
Darth Vader
4a24a89572 Squashed 'phreeqcpp/' changes from 0243c90..60ccbf8
60ccbf8 Removed CALCULATE_VALUES, added MEAN_GAMMAS, made phreeqc_rates.dat, updated CMakeLists, ran all examples, added test case ss_kinetics
baa0eee Added a little error checking to tokrate_pk
50d999b Tony added table numbers, kinetic_rates_plus has complete tables.
bf054e3 Finished up mean_gammas keyword and test case. Tony has some new changes I need to add.
8c561f0 Implemented rate parameters PK, SVD, Hermanska
5998b71 Added Basic function RATE_PK and RATE_SVERDRUP
c881283 added put$ and get$ Basic functions. Added test cases get_put_ to test get$ and put$. Added kinetic_rates_carbfix to use new database kinec.v2.dat. Fixed pad$ to use strexpr.

git-subtree-dir: phreeqcpp
git-subtree-split: 60ccbf83563b6f60011e37200b0357361e9e6379
2024-05-07 22:41:18 +00:00
Darth Vader
f100f492a5 Squashed 'phreeqcpp/' changes from 89d028d..0243c90
0243c90 Updated to build in vs2005

git-subtree-dir: phreeqcpp
git-subtree-split: 0243c905af6767a3777640ad6b89de56ec5ab4b7
2024-04-18 21:17:18 +00:00
Darth Vader
c378c74d7f Squashed 'phreeqcpp/' changes from 7284fed..89d028d
89d028d Tony's fix for Valgrind error in Debye1.
9716b89 fix for new Valgrind problem. Added a newer CEMDATA database for the database collection.
eee3969 Merge branch 'master' into viscosity
b575463 Merge branch 'master' into viscosity
b74423e Issue resolution to be tested: Valgrind-Conditional jump or move depends on uninitialised value (SC) #48
67a69ae Tony changes 20240414, with correction to CH4 Vm. Changes to src. seaw_SC expanded.
34b880c Merge branch 'master' into viscosity
1819d3a Merge branch 'master' into viscosity

git-subtree-dir: phreeqcpp
git-subtree-split: 89d028d8321339d90539869f46da1143f23d4025
2024-04-18 18:16:55 +00:00
Darth Vader
1ebe8191c2 Squashed 'phreeqcpp/' changes from 87919a0..7284fed
7284fed Fixed alignment for some of the utf-8
7babc4b Changed sprintf to snprintf
0d90285 Changed encoding to utf-8
3e00b23 Merge pull request #45 from dlparkhurst/viscosity
4aa8034 merged master into viscosity
166aec1 Tony tweak of t3 in transport.cpp
6a4443d used density_x. Added xsoln_visc test case
4ad0613 removed viscos_x and density_x
269d107 Tony's changes Mar 15, 2024
f50111a Tony's changes with added test cases. All test cases run

git-subtree-dir: phreeqcpp
git-subtree-split: 7284fed50f48610d24dc565cb530f6444940b4a3
2024-04-17 00:16:57 +00:00
Darth Vader
0ebad0eedc Squashed 'phreeqcpp/' changes from 9925ceb..87919a0
87919a0 Merge commit 'b397d9d56c7985fddac5b7dbe8cd3c63152bf033'
b397d9d Squashed 'common/' changes from 11183a1..6abe004
a25b00d Try this to fix warning on Darwin
a2f6386 fixed ‘nullptr’ was not declared in this scope on ubuntu-16.04

git-subtree-dir: phreeqcpp
git-subtree-split: 87919a001bdcde90d6559f597b06586d0d5015fd
2024-03-05 15:42:26 +00:00
Darth Vader
488c119ac8 Squashed 'phreeqcpp/' changes from f975e17..9925ceb
9925ceb Updated for more visual studios tested on vs2005 vs2012 vs2013 vs2015 vs2019

git-subtree-dir: phreeqcpp
git-subtree-split: 9925ceb3d2afa5ed8686dbc781b857e6f1b45314
2023-11-18 03:54:34 +00:00
Darth Vader
a5b8a03fd7 Squashed 'phreeqcpp/' changes from ff1cc7a..f975e17
f975e17 Merge commit 'f82d3a73538ba56c8ed81977b0d26d46ebcb7f98'
f82d3a7 Squashed 'common/' changes from 740bdd5..11183a1

git-subtree-dir: phreeqcpp
git-subtree-split: f975e17ccce7eca010a391898d91c25e6e10990b
2023-11-18 01:35:08 +00:00
Darth Vader
589ec40c7c Squashed 'phreeqcpp/' changes from 3e6c2e9..ff1cc7a
ff1cc7a [phreeqci] Updated to compile on vs2005

git-subtree-dir: phreeqcpp
git-subtree-split: ff1cc7aa82e0ec1145f593a84025ff174af18463
2023-11-18 01:30:46 +00:00
Darth Vader
deb497735e Squashed 'phreeqcpp/' changes from 625f6f1..3e6c2e9
3e6c2e9 Merge commit 'c4958bb740964f1804a6a4e6ae5d8df52c5c64ad'
c4958bb Squashed 'common/' changes from b9af572..740bdd5

git-subtree-dir: phreeqcpp
git-subtree-split: 3e6c2e94e308d95c2be3b98e50cf0f253f327a29
2023-11-16 05:11:36 +00:00
Darth Vader
ed1fbe9491 Squashed 'phreeqcpp/' changes from bd2e2b6..625f6f1
625f6f1 Fixed bugs in inverse
ea9e0ef strcpy_safe and strcat_safe
9b06157 trying different header files
e890269 added <cstring>
c370c7b warnings, strcat, strcpy
14ed59f Try using goto(s)
d2d31d2 Try updated logical expression
d2a3eac Turn off optimizing on k_temp

git-subtree-dir: phreeqcpp
git-subtree-split: 625f6f14905e41a1130a3d0a217b8de478631aca
2023-11-16 05:06:27 +00:00
Darth Vader
6ea0442d45 Squashed 'phreeqcpp/' changes from 8dade82..bd2e2b6
bd2e2b6 Merge remote-tracking branch 'usgs-coupled/master'
f170ab5 Merge branch 'usgs-coupled:master' into phreeqc-1-working
4cbc303 bug fix on Basic functions; minor update to Release.txt

git-subtree-dir: phreeqcpp
git-subtree-split: bd2e2b68ccf277552f19c498e9ef0b972c6d8b7e
2023-08-25 15:29:27 +00:00
Darth Vader
99b1030598 Squashed 'phreeqcpp/' changes from 3b5f98c..8dade82
8dade82 Merge commit '64c9761e116474c4c9e673976f02111fbec32caf'
64c9761 Squashed 'common/' changes from a088e29..b9af572

git-subtree-dir: phreeqcpp
git-subtree-split: 8dade82c963a39f50ceeaab4d2d7b9700b53822f
2023-08-25 03:34:17 +00:00
Darth Vader
e902474819 Squashed 'phreeqcpp/' changes from 8fa568f..3b5f98c
3b5f98c No memory leaks; Still need to turn-on Fortran

git-subtree-dir: phreeqcpp
git-subtree-split: 3b5f98c838520da9638d08384186b2c85103ff30
2023-08-25 03:29:16 +00:00
Darth Vader
322a40bb3a Squashed 'phreeqcpp/' changes from 6dade54..8fa568f
8fa568f removed src/print.cpp.utf8
d140c3f End of Run after

git-subtree-dir: phreeqcpp
git-subtree-split: 8fa568f0b446527445c0601dc860cfeab5626212
2023-05-28 19:59:33 +00:00
Darth Vader
dd7aa46600 Squashed 'phreeqcpp/' changes from 82515f7..6dade54
6dade54 Merge commit '4f698833b1b758cefb3440762b18bec08bb945b9'
4f69883 Squashed 'common/' changes from 7c31f5b..a088e29

git-subtree-dir: phreeqcpp
git-subtree-split: 6dade54926bd93a4c9a2bcbd792a41b525784929
2023-05-26 04:32:50 +00:00
Darth Vader
050663209b Squashed 'phreeqcpp/' changes from 93ab5c9..82515f7
82515f7 Merge remote-tracking branch 'origin/master'
1cc4fa0 fix phi for water at high TP. Tony May, 2023
275b340 Tony's changes May 5 and 7.
0fb2509 cleaned up compiler warnings. removed math.h. cleaned up NAN

git-subtree-dir: phreeqcpp
git-subtree-split: 82515f7fecada9be373fd832dd0c5cdf53c79da7
2023-05-26 04:27:58 +00:00
Darth Vader
dc26aa2a8f Squashed 'phreeqcpp/' changes from b12de1f..93ab5c9
93ab5c9 Merge commit '2841329ea39783ebc402e2644413de9e72904213'
2841329 Squashed 'common/' changes from 6e625e5..7c31f5b

git-subtree-dir: phreeqcpp
git-subtree-split: 93ab5c94e48156a2792207f284e9413df097c82f
2023-05-26 02:36:52 +00:00
Darth Vader
35dec7bafc Squashed 'phreeqcpp/' changes from e7c12e1..b12de1f
b12de1f Added sleeps after curl -X POST
fb55642 working on SelectedOutput for BMI
a050758 Closes #48 -- Illegal character encoding in string literal (#49)

git-subtree-dir: phreeqcpp
git-subtree-split: b12de1f7f0eadb7b6153bffca9d0412801d2e132
2023-05-26 02:32:21 +00:00
Darth Vader
aff166b184 Squashed 'phreeqcpp/' changes from 97a0327..e7c12e1
e7c12e1 Merge commit '823f839bc515d692be4dba290f43673b3c0493ab'
823f839 Squashed 'common/' changes from 04cb71a..6e625e5
c0c3f59 Merge remote-tracking branch 'github/master'
6a30753 changed math.h to cmath.
171ff7f ifdef for NAN
f0839d1 fixed warnings from Intel C++ 2023 compiler
49d0a56 fixed surface.cxx correct_gc. tweaked P_Vm, but it is not too stable.
f2b8caa added viscosity to solution.h, solution.cpp, and xsolution_save
7ff51aa Tony's viscosity with many examples

git-subtree-dir: phreeqcpp
git-subtree-split: e7c12e191414a87ddcedcf73f17d7765702cb75b
2023-04-10 18:27:31 +00:00
Darth Vader
0a7874068e Squashed 'phreeqcpp/' changes from e1de8e8..97a0327
97a0327 fixed compiler warnings except NAN
ee1acc4 changed all double precision to real(kind=8) in all files. Compiles and runs test cases.

git-subtree-dir: phreeqcpp
git-subtree-split: 97a0327aa6a4017dcd2e0298f44d5e672b05288a
2023-04-10 03:21:02 +00:00
Darth Vader
cb707ac2b7 Squashed 'phreeqcpp/' changes from 11d588e..e1de8e8
e1de8e8 Closes usgs-coupled/phast3#2 (#3)

git-subtree-dir: phreeqcpp
git-subtree-split: e1de8e819060ecaf6d402694b29d70ffd0a3bf10
2023-03-08 19:58:39 +00:00
Darth Vader
eeee6d3cce Squashed 'phreeqcpp/' changes from eb35357..11d588e
11d588e Merge commit '84dc8253eb8498cc204cacb6b24ee3b92f0a58b3'
84dc825 Squashed 'common/' changes from fb03f6a..04cb71a

git-subtree-dir: phreeqcpp
git-subtree-split: 11d588edde138d4961072f7b55c9bebc666189db
2023-03-07 02:49:49 +00:00
Darth Vader
772c30924f Squashed 'phreeqcpp/' changes from f8cd55c..eb35357
eb35357 Merge pull request #17 from scharlton2/bmi-working
26a26c1 pre-commit changes use $ pre-commit run --all-files

git-subtree-dir: phreeqcpp
git-subtree-split: eb35357c1291b425b97f8bae8a62d5a888a6d4e3
2023-03-07 02:48:23 +00:00
Darth Vader
bc9ab58d16 Squashed 'phreeqcpp/' changes from 0b60d1a..f8cd55c
f8cd55c Merge branch 'master' of code.chs.usgs.gov:coupled/phreeqc3
56731ea updated RELEASE.TXT, revised PR_P and PR_PHI functions and the test case PR_error_incremental
35190be added Thermoddem database. Fixed error in PR_P and PR_PHI. Added test case to check PR_P and PR_PHI are fixed.

git-subtree-dir: phreeqcpp
git-subtree-split: f8cd55c27c133f195a16f21cb6e07a46d280b2f3
2023-03-07 01:00:20 +00:00
Darth Vader
c85a9cde6d Squashed 'phreeqcpp/' changes from e9db33b..0b60d1a
0b60d1a Closes usgs-coupled/phreeqcrm#12 (#13)

git-subtree-dir: phreeqcpp
git-subtree-split: 0b60d1aeccfdbd9d0f0c4959ee6a04e99d7725e4
2023-03-07 00:42:18 +00:00
Darth Vader
a4eba15e3b Squashed 'phreeqcpp/' changes from bbd2543..e9db33b
e9db33b Added replacement code for snprintf for vs versions before vs2015 (#30)

git-subtree-dir: phreeqcpp
git-subtree-split: e9db33b14235f3d9018e1205ae05895dd2eb3e2e
2023-02-11 17:25:04 +00:00
Darth Vader
fb59ec8b19 Squashed 'phreeqcpp/' changes from feaa432..bbd2543
bbd2543 [phreeqc] fixes what iphreeqc/issue-8 broke

git-subtree-dir: phreeqcpp
git-subtree-split: bbd2543978c857c8e46ff6f553231f188c5cb32c
2023-01-17 03:32:29 +00:00
Darth Vader
be9e230efb Squashed 'phreeqcpp/' changes from 8715a91..feaa432
feaa432 [iphreeqc] Issue 8 -- change sprintf to snprintf for CRAN (#9)

git-subtree-dir: phreeqcpp
git-subtree-split: feaa4321a63ece0f205ce12795d6553261c74f7d
2023-01-15 06:04:23 +00:00
Darth Vader
e0b04393ed Squashed 'phreeqcpp/' changes from ba27ef1..8715a91
8715a91 fixed MacInnes in warning msg

git-subtree-dir: phreeqcpp
git-subtree-split: 8715a91e401b61cf8ab5e3482e97ae26becf114b
2022-03-25 16:36:54 +00:00