8 Commits

Author	SHA1	Message	Date
Darth Vader	d7222e4f0b	Squashed 'src/' changes from 2bcb24a8..f627828f ... f627828f Merge commit 'c1c1f286b61ca73ae3204c7fa4831bb2e3066070' c1c1f286 Squashed 'phreeqcpp/' changes from b6a23a2..faf8144 d051e14c Merge remote-tracking branch 'usgs-coupled/master' 7ad5a592 50 apple clang 15 with c++11 or higher reports warnings wwritable strings in pbasiccpp (#57) git-subtree-dir: src git-subtree-split: f627828fb52a2880ff95d7c341dc335b856fd8c5	2024-08-15 17:09:44 +00:00
Darth Vader	09d8fe4783	Squashed 'src/' changes from ba5f2ba8..f715edb5 ... f715edb5 Merge commit '2243d25babbc524e7875b3d591bb6b91c4399a95' 2243d25b Merge commit '013c822f76e5dc2e4fc19e87c6e5777aea6151d2' f8b289df Merge commit 'c1af6f3585142e84fc40ec2c74914ef4a3b5da8b' c1af6f35 added newlines for CRAN 013c822f added newlines for CRAN d3bdd8b5 added newlines for CRAN 60ad724c Merge commit 'e4bd9bafb40c82bff5ef275528ca3dd2836672e5' e4bd9baf [phreeqc3] fixes -Wclass-memaccess warnings for CRAN 33f5157d Merge commit '29f06d269c189449f230e15761d01381cfd51de2' 29f06d26 fixed alignment in Description of solution ae41a1ff Merge commit '09a2680a6ec98cfd9d59e5b40b1594edfd6b4eff' 09a2680a guarded write_banner with NO_UTF8_ENCODING 082edbb5 changed src/print.cpp back to windows-1252 encoding; updated check_utf.sh fd78a499 Merge commit '8d7c1fce37a929778a2c34ee19c29933529f46bc' 8d7c1fce adding mcd_Jtot and mcd_Jconc 9f0f6225 Merge branch 'master' of github.com:usgs-coupled/phreeqc3 47a8b4e3 Merge commit '1040066da8c5dea10f0b29ece9e43082cd745fd8' 1040066d Merge remote-tracking branch 'usgs-coupled/master' d19961bf Merge remote-tracking branch 'usgs-coupled/master' d4dfe590 Merge commit '07a864d1a6ed582ddfae5e1c3bf5b0620c3dd75c' 2a946443 cleaned up to eliminate some prints 07a864d1 all jacobians are consistent. Looks pretty good. 56975a7e Saved surface for numerical derivatives df0d68b9 Runs all the test cases. Numerical derivatives work, but still some changes in residuals before and after jacobian calculations. 6bd936e0 Fixed numerical derivative (non-pitzer) 0dde2b01 removed comments aef51fa3 Finally have derivatives right, I think 20281a0e always reset gases 13ec2fcd best I could do for H2S while maintaining old tests. Used INCREMENTAL reactions 8be1ba83 revised jacobian_pz with new logic. Works with fixed_pressure examples H2S, H2S_pz, H2S_pz_appt, H2S_NaCl_Na2SO4. 71cf2a97 still produces different residuals 9022ded8 Tony H2S. Amm.dat, phreeqc.dat, pitzer.dat, utf8, updated test cases afff58ff Merge commit '48cb5e8969285f6d6e54955b6b7f8db76b2ec99f' cb1f9afc Finished up C, Fortran, documentation. Need to check DOxygen 524bfc46 Finished up C, Fortran, documentation. Need to check DOxygen 9dad4471 Merge remote-tracking branch 'origin/master' into state 26c71a35 Merge remote-tracking branch 'origin/master' into state d647eec2 Added StateSave, StateApply, StateDelete with documentation for C++. Need testing, Fortran, and C c22cbb7b Added StateSave, StateApply, StateDelete with documentation for C++. Need testing, Fortran, and C 48cb5e89 Including OH- in converting units. Revised calculated density for H+ and OH-. Makes a difference in several test cases. Removed timing at end of .out in test cases. Checking in all test cases and selected output. 47e1ce5d added OH in density iteration calculation, test case NaOH_density 4aefb066 allow Fe(+3), equivalent to Fe(3), in TOT and TOTMOL. Previously fixed in SELECTED_OUTPUT -total 9b94f8be Merge commit 'bea0ad10a02659d9964f6c88e0ca4e415a2c0aca' bea0ad10 unused variable, punch Fe(+3) 37de8fa9 Merge commit 'eaf788b473321914e188d3afd7ff0df1500665fb' eaf788b4 fixed add_constant, undefined surface null pointer, added test cases 5b7cf2f8 Merge commit '2212f9ccb1ed55b463746d524ace70e78258d5bc' 2212f9cc fixed bug in reprep when sit had surface species. Added capability of sit + edl, have not tested it 2e334cb4 Merge commit '79956e3d9ffcae4885bb46b893d01f311100dca1' 79956e3d made tally_table a vector of class tally 7a2f8916 made tally_table a vector of class tally aa62814a Merge commit '58b0d1fccfc6763e569bee30f4ab5e4122963ede' 58b0d1fc Merge commit 'd77c11ec700085f19b76af6543013e23ee0739d3' d77c11ec [phreeqci] fixed header error with phast 63175ab7 [phreeqci] fixed header error with phast 2efc7423 Merge commit '0feb71507f3a246e8021a2c4781ab6c814c73e71' 0feb7150 [phreeqci] fixed WINDOWS.H already included error on windows builds 4ae64944 Merge commit '123cc8a5f5b095cfebea092a1e49a8872fc676d4' 123cc8a5 [phreeqci] fixed _ASSERTE error on linux builds 4a848dcc Merge commit '22c4a624a98244cf2706842b9d989e0edc3b91e2' 22c4a624 [phreeqci] struct to class changes 8080cbce Merge commit '4cee19d768863d8f09b3629ee36a11e1a6030f33' 4cee19d7 Merge commit '2d8ca2d0f37d13ad67be582208a4e65edfcf702f' 2d8ca2d0 [phreeqci] added 'new' debugging d0c82123 [phreeqci] added 'new' debugging abacccd0 Merge commit '9661feab0a6da6876e32a18565ac4e79eaec2634' 9661feab tokadd_heading leak 2537a2c3 Merge commit '4565c5d894d2a9f58577183783ba1969cbc680ea' 4565c5d8 catching upMerge remote-tracking branch 'origin/master' into classify c22d792c fix notab leak 4b9b9926 Merge commit '6d2b45a8e168aa9e55ee677afe52367857e8140d' 6d2b45a8 Merge remote-tracking branch 'usgs-coupled/master' 38cfe186 memory leak user_print, pitz/sit store, add uphill_NPa, remove TESTINT bd096259 Merge commit '24f9bf72f092f0c9edcb18d959cb174f74f96c10' 24f9bf72 removed TESTING definition d77dff57 removed TESTING definition 35ea7ef7 updated for classify branch 2697dc95 Merge commit 'e2ce92882c5f21ac206e180cf38812d976025717' e2ce9288 Tony agreed with change for all_cells, new test case 0479fc1a Merge commit 'd2a5d63f30d0e3e2fddfeba7058caf8e8401de78' d2a5d63f reset all_cells in all cases 0aa30d21 Merge commit 'e3c0d61bc7acc87be515f9923da3a68e14e20880' e3c0d61b initialize aphi c960e059 builds on vs2005; still needs to initialize class pitz_param* aphi 71dc944c cl1mp, bad initialization 639490d0 Merge commit '2e5f255c794096790125293dcc3af274bed7a61a' 2e5f255c fixed errors/warnings from ming and intel 369733e9 converted to classes b1efa4f2 Merge commit '7961b1686b4e064ec4ec886e76543074d060129f' 7961b168 release.txt, couple size_t 5d76f825 copy operator works well enough 7ce89470 updated InternalCopy for operator equal 7bd13ffa new/delete theta params, pitz_param_copy 50e8903e new/delete pitz_params 87d67929 reverting changes to sit_params and theta_params. Will consider using new and delet dcb9efe0 sit_params ac3335ed theta_params 88782320 delete rate, unused cptr 492df61d descriptions 25e06210 cell_data 051ddba2 stag_data 33157a20 fixed more size_t and initialized all structs f86f4304 back to original set of files I think af1b7616 removing CReaction and Classes files 006d1de9 reorganizing 287f81cd elt_list vectorized 7228bd0d move struct rxn_token 28de8b5c more size_t d2e3a4e5 Removed cxxChemRxn ce647201 cleaned up, removed struct reaction 028e9089 moving to CReaction dc2dc531 vectorized token 9fd3f2a2 save_values rewritten with map 8a6cef51 vectorized save_values 86852254 fixed clang errors, needed .c_str 318e267c (size_t) max and count 1547d91b finished up spread b5c7ba4a going to work on warnings 4c848b4e all inverse structures vectorized. Starting on solver workspace 980d58eb finished vectorizing struct inverse. Need to do sub structs d13bb764 removed count_elts 89ab28d7 vector inverse elts d575ade3 tidy.cpp, title_x 16fd18fe removed string_duplicate from prep.cpp 82a10d6e revised get_elt and get_token d7e3be4c cleaned up some string_duplicate 76366a6a fixed processing file names 157a4584 description_x 51fec193 class_main c748922b added const qualifier for all the parsing 380a6eaf methods set to const, variables need to follow 6d67e22e copier and dash 48e6b939 fixed a new master, advection punch_temp and print_temp, some tidying 5f21dafa unknown->master now a vector. Using size instead of a null to end list. 3c432d05 user_graph commands, alk_list 2b14f809 last_model 4ca2e4e1 Merge commit '885a2f77289ac2738f6e8e02c8039f7e26ee7828' 7a6b8b6d Merge branch 'warnings_redux' into vectorize_2 885a2f77 Fix memory bug in ex13_impl, tweak Makefile. 6907bb06 base, sit arrays 90e84120 starting on pitzer bd0cad94 vector kinetics arrays 1850c32c basic commands are now std::string 78a83eda c,d in polint d82d5d61 vector llnl parameters, removed hash references 7c538b62 Revert "delete s[i]" 97bcfd73 Merge branch 'warnings_redux' into vectorize 15a8991e delete s[i] 0b194040 master new/delete b100f853 more new/delete. Fixed str_tolower for ming fd93f846 needed to new/delete species and phase structs 7b0c2df0 Merge commit '1986e00a933549022abb335d82f40c65abf2a292' 1986e00a alphabetize tokens ee6fa533 bool analytic cc614e64 add_logk for logk, species, phases 67447c5a Removed hashtable, all hashes have been replaced with maps. ee7d2c57 replaced hash for isotope_ratio, isotope_alpha, calculate_value with maps. Fixed some case errors with new maps. 52e06225 replase master_isotope_hash_table with master_isotope_map c01c8d66 replace logk_hash_table with logk_map. Added str_tolower(std::string) 3e69461c replaced phases_hash_table with phases_map effafe0a replace species_hash_table with species_map 8bff6d36 removed HASH code. replaced elements_hash_table with elements_map 90e9ee02 removed ineq_init. Vector advection_print, advection_punch 2f380479 size_t for subscripts de884e4e Merge commit '5161ea7563e7ed51be9ed623611762890c785858' 5161ea75 Merged origin/master, Alphabetized Basic toks 0c581ea4 Merge commit 'f8e05c176fd6c469ae6c54f21450d48ef52778be' f8e05c17 only call qsort with more than one element 8e9c5b35 only call qsort with more than one element c1c08f2f Merge commit '1ab86414f0b25f986c14a55bdb967dfdef3af2ae' 1ab86414 remove _v, use std::vector only, alloc at least 1 scratch 9732a1c5 cannot qsort size 0 vector 3770354f Merge commit '67fc478a2f7873db5a2cf6306b433fa07fd58575' 67fc478a one more .data 2f0f5e16 Some replacements of .data() were incorrect ecbb26c3 Merge commit 'ba9813a43c6d087851bf5c2ea86a658cc785060c' ba9813a4 remove .data() 43765f86 need <struct xxx> 5688f837 Merge commit '0feb20dead731b8dedf3e86d5ef664bc24733127' 0feb20de after merging origin/master, one fix needed f136feb6 Merging origin/master. Merge remote-tracking branch 'origin/master' into warnings_redux 71aa5b9f bug count_sys not incremented e43550cd vector inverse d4cc14ef vector x 6c0edef0 vector rates e3cc46ad vector save_values 41b99655 vector species_list 449a54f6 vector mb_unknowns 51514eb1 vector delta, sum_jacobx f0707aa0 vector sum_mb1, sum_mb2 7d303de1 vector trxn.token 83cfb298 elt_list, moved qsort to elt_list_combine e8c90279 vector elt_list 0957a528 vector theta_params b1af156b vector pitz_params e3ea0100 vector sit_params b87d0cdd vector my_array, residual, delta e43471a7 vector s_x 622d3618 vector s_x 3d41ef82 vector logk e8dd2083 vector sys 3c9f5946 vector master de1ba623 vector s e7c78a88 vector phases f2c64fef vector elements e8af689a vector isotope_alpha ba2601a3 vector isotope_ratio 76da4f89 finished master_isotope 4bb1c800 vector master_isotope 97e574d2 vector calculate_value** 9d9fbfb8 cl1 variables converted to std::vector 1e0d4105 using memset 54b0d4d1 starting on space 8c8f6fd1 Merge commit '5a649c2b485a02008d5bfa3763c25dca41358e67' 5a649c2b Merge pull request #2 from usgs-coupled/gasphasepressures d6e6d11b Merge pull request #2 from usgs-coupled/gasphasepressures a9925376 (void)sscanf, removed SKIP, removed PHREEQ98 710d0096 Merge commit '6a5bb8aba56d568bd139bc3aed7363d929397790' 6a5bb8ab Merge pull request #1 from usgs-coupled/mar10 d9ced82f Fixed uninitialized constructors and couple of other warnings 6b19edba Fixed uninitialized constructors and couple of other warnings c79d2c23 working on UTF-8 fcee4d5d Added delta_h_species, delta_h_phase, dh_a0, dh_bdot Basic functions 81e862db Tonys changes Mar 10. SIs in inverse calulations 62c51bb4 Merge commit '9e8b3828595be0339d3c63b5707412e34a4e5007' 9e8b3828 Merge remote-tracking branch 'usgs-coupled/master' 4473286a Merge commit '053b4c6fb3cb778f08377b932745643472888aa5' 053b4c6f Merge remote-tracking branch 'origin/master' b9f44da2 Merge remote-tracking branch 'origin/master' 20091aa5 Merge branch 'log10molalities' into gasphasepressures c4f9d291 Merge branch 'log10molalities' into gasphasepressures 41e1112f Last of changes for GetGasPhasePressures and GetGasPhasePhi, openmp and mpi. MPI fortrans not tested. 18158db3 Last of changes for GetGasPhasePressures and GetGasPhasePhi, openmp and mpi. MPI fortrans not tested. e1f9cb1c more checking in. Should be down to tweaks for SetGasPhaseMoles. e1554d99 more checking in. Should be down to tweaks for SetGasPhaseMoles. 00ee6e36 C++ is working with OpenMP and MPI for Get/SetGasPhaseMoles. Need to add c and F90. 0a633289 C++ is working with OpenMP and MPI for Get/SetGasPhaseMoles. Need to add c and F90. c3a3153f Added GetSpeciesLog10Molalities. Tested OpenMP with VS. Tested MPI with MinGW. Fortran, C, and C++ seem to work. 566bfbce Added GetSpeciesLog10Molalities. Tested OpenMP with VS. Tested MPI with MinGW. Fortran, C, and C++ seem to work. e8b11f34 added optional 6th argument to Basic function sys to change sort order from molality or moles to the name. Added synonym PAD$. Added new mytest/sys_sort. 20ab4be9 Merge commit '3e4fc7ea18da750b2746422898dc100d74271b34' 3e4fc7ea cleanup commented lines 54b992f5 working on tabs and no newline 21818473 Merge branch 'master' of https://github.com/usgs-coupled/phreeqc3 deeecb0c needed strexpr in ADD_HEADING to allow expressions 2d2f55ad Merge commit '9b7785f0730513093816cfbd1c24fbf068e4f2ca' 9b7785f0 [iphreeqccom] updated date 33f58989 [iphreeqccom] updated date e224625f Merge commit '711b1d061cba1005f028d1b17b0bb34e2b2d9162' 711b1d06 Merge commit '608e74f5d3c55a4d91a4e08d86f2fd6df0ce0a05' 608e74f5 [wphast] updated date 50016849 Merge commit '5128e1337b2edd39ac3d16d2a5ce1c7f1e5f0773' 73d356aa [iphreeqc] updated image location 5128e133 [phreeqc3] updated image location fba8ae2a [phreeqc3] updated image location 43988f06 initialize punch_newline 176fb029 Moved initialization from header to constructor, special characters in As.out c9f796a0 added ADD_HEADING for IPhreeqc 1362f0ff Added EOL_NOTAB$ and NO_NEWLINE$, updated release notes 055ebf5c Merge commit '2b4dbbdb167b77809e7c89bbec406810aa28162a' 2b4dbbdb Merge commit 'cd51d8aeed46909e5f028a19089acfef43d6ede9' 589d88ff Merge commit 'f2023c4d83f55cbf4598ae8e308df3ef06b8f08c' f2023c4d Merge branch 'gtest' into 'master' f4bf55d7 Merge branch 'gtest' into 'master' cd51d8ae reset for dlls 54161f4a reset for dlls a28c2414 reset for dlls e904f5b7 Merge commit '01c99a70a5baf72d53ae8e8f6db53948ddcd990c' 01c99a70 Merge remote-tracking branch 'github/master' 23f39174 Merge remote-tracking branch 'scharlton2/master' f6644e6e check for null pointer. Encoding for .out file e562e09e Merge commit '9319c9daf8fe76ef24cf4d262081e8cd0c8fc3fe' 9319c9da Merge commit '5b816fa1fd82eb94e2702b6bd9df6066fb71267b' ea2c663c Merge commit '07717b1e931b4526f3c33921cd872577599410b6' 5b816fa1 added src/phreeqcpp/common/PHRQ_exports.h 07717b1e added src/phreeqcpp/common/PHRQ_exports.h 0b0fced3 added src/phreeqcpp/common/PHRQ_exports.h d8c638fb Merge remote-tracking branch 'origin/master' into gtest c8be5dae Merge remote-tracking branch 'origin/master' into gtest 18e137ff Merge commit '87bbb6a6f08a3f6cf0e4122e9c080db4ef000344' 87bbb6a6 adjusted alignment for utf-8 strings 3782d442 Merge commit '03bda166155a6b2ce652e4ad6aceaf807c3bc041' 03bda166 added write_banner to non-DOS and added UTF8 define 995de526 converted to utf-8 d4261840 Merge commit 'fc8fe3e98fb3f1e42482636938537ed6028b3ee6' fc8fe3e9 re-added src/ZedGraph.dll 6e7023f8 Merge commit 'fbae3e92947cf79c1d615e657192eb8d5c78b9e9' fbae3e92 code change for extending porosity definition. Change to TonyLitharge2a 46257e73 added googletest and fixed some minor bugs 13ca0551 added googletest and fixed some minor bugs 2760ad0c added googletest and fixed some minor bugs dd058e3b implemented Get/SetErrorOn f1dda6c5 Fixed problem with exchange-related when exchanger is defined as CaX2 b138ed20 Merge commit '20daad41c8999670f933430f1c705384cdfa6947' 20daad41 I guess cxxSurface::NO_EDL is correct 5631ce1e Merge commit '801812ded3961b37ed264997211694bd0563d554' 801812de Tony's changes to implicit Nernst-Planck calculation 6b4892cf added Basic function DEBYE_LENGTH and test case zeta 921ab106 Changed tidy_exchange_min and tidy_exchange_kin to tidy only for new_def and n_user >= 0. Fixed bug if surf_charge not defined for NO_EDL. Added test MoreExchMix 9d480bc1 Merge commit '2aef60aa6f00411ac4491e868c3cf2b6beab11ab' 2aef60aa Finished up surface and exchange related for cases where related phase or kinetic reaction was modified. Proportionality should now be maintained. Added test cases. 569e1e13 Exchange related. Needed to update in case the related entity changed. ea54e02a Free str in callback in PBasic ea21e58a Remove SetErrorFileOn from RunCellsNoPrint, RunStringThread, RunFileThread. Remove Set_error_on from IPreeqc::SetErrorFileOn. 9029c2bc added changes from email dated 2020-07-15 74b541d4 Merge commit 'a87cd1fee89cf0076aa06b9018e8ad3b44566516' a87cd1fe Merge commit '1871b026ca8487c23a025415dbc0b2eca01f9af4' 1871b026 fixed some c2011 warnings, added more info for -formula errors, fixed pressure llnl examples aa4d0234 fixed some c2011 warnings, added more info for -formula errors, fixed pressure llnl examples 1c3edaa7 Merge commit 'e1465e33228a3f867bd822405fb100614d5f6d0c' e1465e33 Commit from David's Email 2020-05-22; Implementing llnl-type databases with higher temperature nad pressure 89ca3d27 Merge commit 'e18e1ec6be5107e051f99e41103638c907b1eaf5' e18e1ec6 Tony bug fix for TRANSPORT. Harmonic mean for boundary? Added Cub example. a208e394 [phast3] Testing subtree merges a4c58264 Merge commit '44f077e8893ba3434c5a0feccfe42be7e9aa83db' 44f077e8 Merge commit 'e68934133fc9cd45e7cccc397c55e13f7ee92e5b' 090f5e68 Merge commit '4f34fd04ff34668494863eab5312157ce746d862' e6893413 [phreeqci] Testing subtree merges 4f34fd04 [phreeqci] Testing subtree merges 9bcc875c [phast3] Testing subtree merges 8e901d06 Merge commit '69c0bb3e62a7d3759d685b37652cac80373a58e7' 69c0bb3e fixed conflict on merge bb5bcbf1 fixed conflict on merge 55c4dbad Merge commit 'b25fc5bdd48b6d3ab8d677f7d38ad3a462789500' b25fc5bd fixed conflict on merge ca80be6e fixed conflict on merge 49a74a6a [phreeqc3] Testing subtree merges aec6f90b [phreeqc3] Testing subtree merges c4c224ad Merge commit '84865ad5ac30a9edb86c89ced4194d127ee896fd' 10875555 Merge commit '0bf4138d63cd63d9cb3cd2081c16e706b8c867d2' 0bf4138d Merge commit '4a8727cecd9fefd1587485820e913c0e666b77d9' 92807718 Merge commit '4a8727cecd9fefd1587485820e913c0e666b77d9' 4a8727ce Merge commit '553875fa3799217dc937ee3ef6e9d874e545ccf5' 553875fa Merge commit 'aab8bc12ea8be8aec5943e1c77a54b19d28168cb' efbddbf6 Merge commit 'aab8bc12ea8be8aec5943e1c77a54b19d28168cb' aab8bc12 Merge commit '84865ad5ac30a9edb86c89ced4194d127ee896fd' 7bd02ff8 Fixed bug with more porosities than cells in TRANSPORT. Added silica sorption to databases. Revised CalPortDiff 84865ad5 Added .gitlab-ci.yml d3981950 Added .gitlab-ci.yml eed9de90 Added .gitlab-ci.yml 40c2787c Added .gitlab-ci.yml b6921025 Added .gitlab-ci.yml 3b6ce6c1 Added .gitlab-ci.yml daf64a14 Added .gitlab-ci.yml 757927da Merge commit 'ae06f3533db376699e82c3b0b183fb2bdd43721a' ae06f353 Fixed GFW bug on new elements in TRANSPORT aa963a9c Merge commit '9cc783b02f8bc437a0572eb32d523f69344724bf' 9cc783b0 added Basic functions for PHAST: velocity_x, velocity_y, velocity_z, transport_cell_no 0366caf1 added Basic functions for PHAST: velocity_x, velocity_y, velocity_z, transport_cell_no d97736a3 Merge commit '79f768a7bd6c88e064ba25a33880cb84cfd1489f' 79f768a7 Merge branch 'master' into 'master' bd7634a8 removed j = j in loop d0e5bac5 Merge commit '542394c95add8bc99c697c8dc33887efe2b1ae20' 542394c9 IPhreeqc: ifdef'd out references to std::cerr and std::cout 6fe5c0e2 IPhreeqc: ifdef'd out references to std::cerr and std::cout e5bf8b0a Merge commit '6067ce8ce599b9cbfaf012c0abc377f20e616b42' 6067ce8c Merge branch 'implicit3' into 'master' 21bd20f5 Fixed more compile warnings. Removed andra_kin_ss from testing, results are inconsistent between Linux and Windows, presumably the ifs in RATES fd242bd3 Merge commit '97b9c5848ee2b8ae6413ffa09e0b79be7d739ef8' 97b9c584 Merge branch 'implicit3' into 'master' 45db5cf0 Another Linux warning, lower tol on andra_kin_ss. 3049467b Merge commit '443be1cdb1adce5a8da310d883bf4d97fc661576' 443be1cd Merge branch 'implicit3' into 'master' 9a29aaf8 Last Linux compile warnings. Added more precision to andra_kin_ss. d7188d25 Merge commit '6dafd7d75e3dc4b97ed0b5efa7424bf0630829e0' 6dafd7d7 Merge branch 'implicit3' into 'master' fbde6338 Fixing Linux compiler warnings, checking in new regression test files. 679c637e Merge commit '22077113d63c5f086de917486dcf4df678a9c464' 22077113 Merge branch 'implicit3' into 'master' 77e36a23 Tony fixed some transport, revised colloid_U. New cases added to Makefile. f07caf97 Changed back print to allow incremental_reactions to work correctly d8ba4ac6 Merge commit 'beadd0738b548a8bebe9934e5de2497cd6e3a7e0' beadd073 Merge commit '5947da90657d1cb8f832152b4573dca0bbefb49e' 63108ac7 Merge commit '6a49d41253c7705c0273262d0290389b18643d32' 6a49d412 changes to make related and mixing items independent of case. surface_mix test case. 5947da90 initial Tony changes 8089c102 initial Tony changes 86888c46 Merge commit '009aec74d1cae1a8fc361a5560d89f44173fd7ee' 009aec74 Merge remote-tracking branch 'coupled/master' 4676ee4d added more P-R gas paramteters 26c751fd Merge commit 'c07314c7e58a9e3fda0d3157863a3a8634864f02' c07314c7 Merge commit '492a4d257f300b7a9e0b5dc7e212c8f85ecb7f6e' d9a6717e Merge commit '81ca6334dc10ebd6f24a7f6a76358751524a7f0f' 492a4d25 Merge remote-tracking branch 'coupled/master' 81ca6334 Merge remote-tracking branch 'coupled/master' 86c54339 Merge remote-tracking branch 'coupled/master' 950fca24 CRAN: replaced deprecated std::ptr_fun with lambda function 597bcd76 CRAN: replaced deprecated std::ptr_fun with lambda function 1b13e09d CRAN: replaced deprecated std::ptr_fun with lambda function 5b3379b9 Merge commit '044e0ea2c0337ab4d175f3303e1d6d192a451782' 044e0ea2 phreeqc_ptr bug in internal copy 67342a4d Merge commit '59342977ed27c7b504432da94511229f5998437a' 59342977 Merge commit '5c53fb207238bc0e846123a7e0d71a48bd9976ab' 84128239 Merge commit '5c53fb207238bc0e846123a7e0d71a48bd9976ab' 5c53fb20 Merge commit '1327e93127e40e7a55ec629dcc9dd91ec29e77fe' c117e182 Tony fix of index error b90ddb56 Fixed Tony's fix, added implicit_as example 03acc3f7 changed abs to fabs 1fef40e1 added implicit, max_mixf to internal copy 5a46f0d7 Merge commit '32939bae4bdfa4b8c6c448688524bc35d5ce6baa' 32939bae Merge commit '1327e93127e40e7a55ec629dcc9dd91ec29e77fe' aa34ac11 Merge commit 'b3bf691b4964b3eedbaf04d6ee9bd35f98afb113' b3bf691b fixed > > in templates for gcc c9291134 Tony fix May 31 1327e931 Implicit seems to be working with Tony's latest changes 55ea163d Implicit seems to be working with Tony's latest changes c7111f77 Sort of works, still bugs and serious errors compared to explicit 79c28e50 Merge commit '600c7ee5728aa23c963828df22b6e0c94038a3ed' 600c7ee5 Fixed some bugs with iso.dat inverse modeling, added test case. Still does not generate [13C](4) and [13C](-4) from SOLUTION 94155a63 Merge commit '2291700eebddc4374b8cd88d19fc0978ee84c7e9' 2291700e Fixed gas_phase_mix bug, added test case 51fbb3d5 Merge commit '035a4e0f7db61f7256e63659b0e7853dd299263e' 035a4e0f Tony tweak to transport.cpp 1e4a2941 Merge commit 'bd4fc256a6f168e127f6d2b783653c890c23a231' bd4fc256 Merge branch 'tony20190117' into 'master' 71c994b6 skipping restart 3b730866 Merge commit '1257f8c7c984818ead2402595470f93d96db76ca' 1257f8c7 Merge branch 'issue-3' into 'master' f0c3701b Merge branch 'issue-3' into 'master' fbde6453 Merge branch 'issue-2' into 'master' ce33478c Fixed -Wcatch-value warnings reported by CRAN c88ff034 Fixed -Wcatch-value warnings reported by CRAN 548aead5 Merge commit '040fd95fadbc2cd62df3c056ef7a41e10c8b7a29' 040fd95f include restart, remove ex20_debug 12df06b3 Merge commit 'd57264d9733b6f5687d8b7d87f5e9a8aad7e7d71' d57264d9 2. changes to solid solution numerical method 43386a0b Merge commit '3fd8155d566798e121a1f54418f901cdd0db5e6c' 3fd8155d changes to solid solution numerical method f90fc5af Merge commit '2b14a9475c1cb0c64d3adaf67a907b63ea454c9c' 2b14a947 Tony's changes 20190117 9d51f5cf Added code to record git commit hash 1a4422b8 Merge commit 'ae6e8b05440ea1db35226a479daf5d3b4a05690a' 1bfc9f49 Merge branch 'master' into 'master' ae6e8b05 added modify methods for restart files fa7776b8 added modify methods for restart files 749c3e09 Merge commit 'b500c5448b613a20c48a08237460c3b495d3d390' b500c544 changed restart file to include UZ 1150a4a2 changed restart file to include UZ c2dada99 Merge commit 'fffac6d359c01544c617aae6717678f0fd884193' fffac6d3 another try for ex20_debug 4235170d Merge commit 'fa5ee5049432867a5161fcd97aebe475854fffdb' fa5ee504 fix problem with ex20_debug 65dbd2c1 Merge commit 'd99390113028519f41895af04cedba4a43258336' d9939011 encoding, limit.h 6e92ecf9 Merge commit '92c81f9fdd43f175d302028b56e7edbab81a7d06' 92c81f9f Revised logic for nmix dbefc44f Merge commit '3cc84da8ceac5d4a819fc0a6779b7ca361c17226' 3cc84da8 Merge remote-tracking branch 'coupled/master' into ss_trans c83e4bf7 Merge commit '56b5bf3f438e0b99c7a35b79ad169be36c2fa352' 56b5bf3f create valid ranges when sscanf doesn't return 2 c43c9af3 tweaked ss, changed surf function per Kinniburgh b10df16b Corrected syntax of integer limit, previous commit actually changed ss convergence parameter, used to multiply by 0.99 d74c8ff5 Corrected syntax of integer limit 906cfd49 Check value of nmix 058375c2 removed check of ss when sum of components is small c4fa021e Merge commit '2977db4424a04e3643bb02d356984c7aa78d1fde' 2977db44 Tonys fix to diffusion bug with porosity change ec4ec0a3 Merge commit 'f90446715b85306f1c8489219316d4c962fd4659' f9044671 revised lists to be cumulative for eq, gas, kin, ss 3a0292c6 revised lists to be cumulative for eq, gas, kin, ss 7b836dd6 Merge commit '9285985dc0222cf6fde33c32625027d376159b3b' 9285985d merging coupled/master into copy 7c23b625 Fixed string_duplicate memory error 2d5551a3 fixed sc7 for copy and initial time 4842d9ef inverse iter 100000; finished copy operator; a bit more testing to go 4eefe43a ex20_debug fix 78e39cde still debugging copy cee10e7a fixing bugs in copy operator ebab4bce fixing bugs in copy operator 5a35e027 Fixed Linux warnings, memory errors b86f7938 Beginning to test copy operator b3e7b2ec Merge commit '5d40e69cc7fcc5bca0037ee70d9d64e4c370e5dd' ae05e0a6 Merge branch 'cran-warnings' into 'master' 5d40e69c [IPhreeqc] added parens for clang++ -Wlogical-op-parentheses 67d807cc [IPhreeqc] added parens for clang++ -Wlogical-op-parentheses 113fd9aa Merge commit '936de384743fe782f702ed0ab96e4a549ca3dd2e' 6894b4a7 Merge commit 'd96f386211ad5fbace94d550ca371d9eacb3262f' d96f3862 Merge commit 'ebeddcde9d54e3e79c8923496a0b7573432d9388' 936de384 removed register keywords and updated for misc clang warnings af408f7c removed register keywords and updated for misc clang warnings ec9de4cf beginning of checking copy operation b447434d [iphreeqc] Changes for CRAN 3.4.7 ebeddcde [iphreeqc] Changes for CRAN 3.4.7 b4894423 Merge commit '9592d6e8015707da5eb033f136590ba40015da61' 9592d6e8 Merge branch 'dlpark-phreeqc3-TonyApr2018' into 'master' 7c0fb65b [phreeqc3] needed to check gas phase type for same model, added test case ca5e069a Closes #1 98d075d4 Merge commit '9152ca292e2ea2a042a654b6393b6fcd9160e0d4' 9152ca29 Closes #1 78b05b07 Merge commit 'ebc4f69cd45b414f2fce86455cd025a2eb762134' ebc4f69c Merge branch 'dlpark-phreeqc3-TonyApr2018' into 'master' 97a0cec3 Fixed bug where 1W was interpreted as an isotope 2deb4edc added option -ddl to surface. Added test case 9e316ab6 Merge commit 'df7d5debc6ce37c341b48ad123e4839ab409da38' df7d5deb Merge branch 'gammas' into 'master' 35d8d926 Merge branch 'gammas' into 'master' cf35bf3b fixed some bugs in the reaction lists and got to the point that data is now all available in the phreeqcrm object once FindComponents is called. 34abb5b0 gammas finished, working on reactants e8ae8322 gammas finished, working on reactants 311fa04f Merge commit '53148278fc5456fddfcffc2d46aa7ccb7fff0ee9' 53148278 Tony's changes; diffuse layer with pitzer 83e3b8c0 Merge commit '4271ca42adb6957392c22a564d82baf99933b166' 4271ca42 Tonys corrections, added balonis test ae5624d5 Merge commit '2e390fd5ab713c0c135208931dd015935da01f19' 2e390fd5 commit fix for Mtg 1d5c59a1 Add 'phreeqcpp/' from commit 'da9d06b423a87ed5eae503c0faf779ac11c96027' da9d06b4 Split 'common/' into commit '077abe0106b2c1d44d8e996d62ae3e8b2c23bf62' 114cea67 minor memory leak in fail2 7d044e79 Tony fixed error with sc2 and aquia 86a55b5b Tony's changes from 20180305 b0fdcc41 Added Mtg(g) in calc_PR 6c9e9843 One more compiler warning 8e121390 Fixed bug from Shell. Segv because s_list.size differed from count_s_x. fa7a3c71 Tony's changes and bug fixes d801026f moved concrete-2005 and renamed to trunk 800f2345 added Form1.2005.resX to configure dist db60ab0e fixed to compile in vs2005 a46a85a9 Making consistent 077abe01 Tony's changes. b5ef46d0 Tony's changes. 299188f3 Fixed dist_x function for transport. bdd21cd1 Tony's fix for LG function for exchange. 29a5848d Tony's fix for LG function for exchange. 5812e211 Synced to PHREEQC3 12702 e6a13b70 Error when reading PHASES and -no_check was read instead of equation. 92aa19a4 Synced with concrete 12683. 2c1f1b33 Synced with PHREEQC 12683. bdef01ca Expanded error report for equation balancing. e3bac3db Updated to svn 12361 on trunk 73a34a99 Added "calculate" capability to density in SOLUTION_SPREAD. bf6dcd08 Iterate to calculate density in initial solution calculation. 6190fb36 New Basic function TITLE 43ecf1e3 New Basic function TITLE 66481ea6 added tokequiv_frac to tokeq_frac 5f165e7e Duplicate tok fixed up some of the new features. 8421d08e Updated to phreeqc3-trunk 21475 Adds some pr h2o tests. Adds Aphi calculation for Jonathon Toner Latest Tony tweak on PR. 6a6e07e0 Tony's tweak. b121ec3b Added tests for PR calculations with water ex7_T_P pr_h2o. Added to Makefile Tony's change to prep.cpp to keep phi(H2O) in a good range. Changes to allow Jonathon Toner to define A(phi). 739dfeb9 Tony's fix for potential null pointer. a15efe53 Minor updates to databases. Tony fixed potential null pointer. 63ac5f3c Fixed null check, also needs elements > 0. Added more test files that were missing. 4df098a2 comment check for null after find_J. Don't know how it works. 62286ff4 Commented out check for null. Not sure how it works for Clogging, will investigate on Linux. Checking in new SC values! 9d2762b1 Merge to trunk 12441. cff3ae90 Wrote tranport_cleanup. 873b98ff Caught error I think caused by defining X as a SURFACE and an EXCHANGEr. Added test case. Initialized unknown structure variables. Caught null pointer in Tony's multi_D. 6a60c92f Need to set Dw 35458cd0 Initialize correct_Dw to 0. e9fe756b updated Makefile? fixed compiler warnings in transport.cpp cf4a14f0 no gmp 025d2a1e Merged in Tony's changes for electro diffusion. 9bf1411f Updated to PHREEQC3 12386 d1cf5f96 Running tester on Windows. It's been a while since the test cases have been checked in. With lobo gone, will do primary checks on Windows. 8d624a7f fixed compilation for linux c++11 424c0703 fixed compilation for linux c++11 80f143a6 changed macros for unique_ptr b06b4f2c replace auto_ptr with unique_ptr 9a6ec5b1 Error in sys("equi",...). Returned the values from the phases structure rather than from the unknown structure. So, the value from the beginning of the simulation was given rather than the reacted amount. 52ea7271 Had a problem with mismatch between mass_water (1e-6) and total_o (~55.5) from Colman phast run. Now set mass_water based on total_o. 53fade44 Bug when related to surface related to kinetics and proportion was zero. Think there was a bug anyway trying to identify the right surface total. Hopefully fixed. baf36d4a fix memcpy overwrite 85021963 removing shrink for pitzer c6e27337 shrink_array for pitzer in model.cpp 32b2b166 removed dw.cpp 51974df3 removed dw.cpp 22fa4499 Moved mpi.h to beginning of each file. Conflict with stdio? Fixed TestRM.vcxproj to have zlib defined correctly. 9cf105c9 Kinniburgh problem with P(O2) = 10^-51 e8aa08af Tony's latest. f65078e9 added function phase_vm and test case. 06e41e92 Tony's changes for advection/diffusion with irregular grid. He was not able to get a robust result. edf7f8f6 Added Basic functions for KINETICS_FORMULA$ and SYS("kin" 96839072 Needed to write around signbit. 03c9d56c Tony's updates to allow fixed current. fe3f36ea Need to zero moles in tally struct in addition to zeroing totals. ad55ede3 fixed selected_output missing headers when SelectedOutputFileOn == true c02d598b wrong format in read 394f918e changed preprocessor guard for windows _set_output_format call e37e06ad fixed selected output missing headers given the following input: solution selected_output end e9837bb0 fixed bug that overwrote selected output files when (re-)opening a .pqi file d918a52d switch back to 1e-25 79a49656 Change MIN_TOTAL to 1e-18 MIN_TOTAL added to KNOBS. 8604336e Update from phreeqc3 through 10983. d2dba8c2 Tony's latest changes. New test case SC_Ohm, added to Makefile. 48b4d870 Added asserts to inverse.cpp (had -1 for a row number). Ensure that master species for an element contains the element. Fixed memory leaks if problems detected in read_master_species. d5e7aa0a Tony's changes. Call calc_delta_v always. 810f51a2 two changes for vm_tc, always calc_delta_v 4405e60e Merged source up to phreeqc3-trunk SVN 10892 626d6782 Added setdiff_c method. 8bc58627 Switch back for now. Tony will fix later. ed231a91 calc_logk_s, removed if (s_ptr->logk[vm_tc]) at line 489. 78c5daa0 Negative mass of water bug. 2a9ab265 For concrete, this is correct. For phreeqc-trunk without the new transport changes, previous is needed. 81525819 Needed for old test cases. bde722c2 Another try on porosities. 7c77eda9 Forgot to remove testing code for differences in porosity between old and new version. 320aef18 Merged Tony's 2/3/16 changes for setting porosities. 998f194b To read multiple lines of porosities. 2c3cd3e3 To read multiple lines of porosities. 38322728 Tony's fixes 0bd85c16 reverting to old porosity definition. 279acc25 Merging Tony's changes for reading porosity. 72991f1a First fix of day. b8ee7f64 Another temporary fix. 4cd0224e Temporary fix for Jenkins. Need Tony's fix for porosity of stagnant zone if porosity defined for mobile zone. a6390ed8 free pors 7c56b919 free pors. f5ea53e0 Added porosities. 95133f2b Tony's changes. Added porosities. 8dc42fee Tony fixed the memory problem. Will rerun Valgrind one more time. 96e537f0 Initialization, memory leak. 891e33bf More initialization 24dd5ede Working on valgrind uninitialized variables. 1fcb85d6 use space for cell_data 964b1665 Initialize sol_D[l_cell_no].spec 7f842da6 removed MPI. Fixed memory leak. 7fbf8779 Removed parallelization. 41bb9483 fix for linux, but Cl has NaN dbaabe01 initialize variables 9644278e added Dictionary and Serializer Deleted unused files. 174c739d Updated concrete source from concrete_parallel source (not using parallel). Now going to run test cases on Linux. 5af54884 Switching back to diagonal_scale false for default. No obvious advantage in test cases to change, and it could break someone's runs. 716a978b Made diagonal_scale true by default. 516d6937 Another check for null pointers. 6f7a2e50 Fixed segvs from Kinniburgh. a9465932 Fixed formatting for temperature of Specific Conductance. Added test cases missing_surf_related_equi, missing_surf_related_kin, and SC_temp. 8f51d927 Need to set new_def to trap error with surface related to rate. dec66bb8 tweak if tidy_min_surface is invoked on a _raw definition. ae2286eb Added serializer for rebalance by cell. Made fix to tidy_min_surface, same as tidy_kin_surface; skip if not new def. a7020351 totals of surface comp set incorrectly after read_raw. Skipping tidy for these cases. 6ae25495 added ifdef for R (R_SO) b33a28fa fgets warning b88bd3f9 more Linux warnings eb7e91eb fixed Makefile.old, Linux warnings af2dbfdc Added changes for serializing. Copied files from concrete_parallel, without merging or svn_copy. Added Dictionary.cpp and Serializer.cxx + header files. 4dc54757 Bug showed up in PHAST. Errors in definition of surface related to mineral or kinetics were not detected. c6f09779 added equi_delay to the convergence sets 54769821 roughed in equi_delay ca4c8f9e delay removing phases in ineq, should be unchanged until delay is > 0 0970c440 using old viscosity 301d2d00 transport.cpp, ifdefd old viscosity, initialized variables; basicsubs call viscosity();phreeqc, revert ineq_tol c15e56ad -potential not defined for solution read_raw. fb18be24 Tony's implementation of electric current. Test case current1. 2fe6313f Avoid a null pointer. Not really sure what causes it, combination of charge balance, pe constraint, alkalinity, and C(4). bef66de3 Fixed formula for pressure dependence of B1, B2, F1, F2. Previously had a limit of -10C, otherwise produced a floating point exception. 218f4f5f Avoid negative moles of equilibrium phase. Typo in RELEASE 33b4ae37 fixed BUILD_SHARED_LIBS build on windows 34f79213 fixed BUILD_SHARED_LIBS build on windows f997d62a [ not handled as upper for solution_spread in copy_token_tab. e8553de4 Debug prints for Peter de Moel. Possible null reference in tidy_solution. 3f332d18 Trap null pointer missing gas components. 64703778 updated for R 190128c1 updated for R 6e752e26 windows java working with callback fbaeb7dc working on swig callback 8f1eb25c Added SetScreenOn to C++, C, and Fortran. Updated PhreeqcRM tests to include a call to the new methods. Set minimum concentration (moles) to 1e-18 in Solution.cxx. 560306e0 reran test cases. Diffs caused by CO2 changes in database e6d44638 Extra print for Donnan Layer psi from Tony. caecf8b8 added common directory for Parser/PHRQ_base/PHRQ_io/phrqtype/Utils adbe4d66 added common directory for Parser/PHRQ_base/PHRQ_io/phrqtype/Utils eef31c95 Iterator bug. 1b4a3076 Null pointer if K-Cl interaction parameters (b0, b1, c0) were not defined. 2dd34675 Tony's fix for erm (enrichment factors). New test case erm. 72352f53 mu=0 in one of Kinniburgh's problems. 2fcfd8e7 Hack for bug with pressure, caused ternary to have low pressure result. e7915af7 Test case edl_species tests the function. Works, but maybe questions on thickness for Debye length calculation. 49ba8bca Working on edl for PHREEQCRM Adding edl_species for PHREEQC. f15d9155 GetSpeciesLogGammas GetSurfaceDiffuseLayerConcentrations GetSurfaceDiffuseLayerNames 37b8b3f4 Have surface species data saved in the charge class. Now need to expose it with PhreeqcRM e5a96004 Removed dead code from pitzer b9b84141 Tweaking lists. 7e2a34cc Make sure MacInnis pitzer parameters are calculated. 6de09799 Trying Pitzer lists again. c319dc83 reverted Pitzer optimization. Not sure what goes wrong. 4e07ab28 Optimizations for pitzer.cpp Change in PTEMP did not work for unknown reasons. 0e78b172 memory leak when chart was closed before it plotting was finished. ex15b was used for debugging. 7b75b1c9 removed building of 32-bit and 64-bit linux versions; added missing CMake files 51db3a15 Shrink array for SIT b157d11a Reading a dumped SURFACE was processed as a new surface, which caused a problem. 3e1e2bae created IPHREEQC_ENABLE_MODULE option ef8611e0 Switch bases for SIT. ca572ee9 Revised Basic function surf. I broke some functionality when I modified to get correct values for H and O. Reverted, but check for H and O, which uses another method (surf_total_no_redox). 383cc7f2 Estimate activities in PhreeqcRM 75cce6a2 Do not use full pitzer for all retries in run_wrapper only number 4. 9779f907 Revised sit to use lists. Runs maybe 2-3 times faster. 413fa2a7 fixed g++ warnings 8e9134e3 fixed crash that occurred when sit.dat was loaded twice 371548b5 added initializing to pitz_param ba6f7f7b fixed crash that occurred when pitzer.dat was loaded twice c6671809 Bad input for SURFACE_SPECIES and SURFACE_MASTER_SPECIES generated a NULL pointer. Added additional error checks. 18f0512b len=l for callback fortran string. 678fd85c Debugged Basic callback for PHAST mpi. 76e16420 Added METHOD_REGISTERBASICCALLBACK for MPI. CALL register_basic_callback_fortran() in InitializeRM CALL register_basic_callback_fortran() in mpi_methods phast_manager my_basic_fortran_callback and register_basic_callback_fortran PBasic defined tokcell_pore_volume, tokcell_volume, tokcell_porosity, and tokcell_saturation b255de16 length argument needed for callback. 9ca23025 worked on pressure dependence in lk_phase ab440058 Working on IPhreeqc Basic callback. Compiles with ISO_C_BINDING, but may need some more debugging. 793df0c2 error check for Pitzer parameter was wrong a6d63e33 Commented dead code related to density of water in Pitzer. 4d47ed13 limit on eps_r in utilities.cpp. ffd459c6 Added SYS("equi", count, name$, type$, moles). Equi option was never implemented. 66f047f9 default initial solution for the reaction calculation was not defined properly when using only SOLUTION_SPREAD. 544db5a2 Tony fixed problem with Peng Robinson SO2 (Marc Parmentier). Added test case peng_SO2, which should test for fix. eafa16d0 CCM only for NO_DL (not donnan or diffuse_layer). 6309425a First try at constant capacitance model. 8914d2c5 needed to check sum_fractions for zero cfa5f98e Fixed bug in SURF(O/H,surf). H and O not counted correctly. Went back to old method before it was changed to account for redox master species (Fe(2)), for example. H(0) H(+1), O(-2) and O(0) probably do not work correctly, but I think everything else will. a67f52b8 Bug with quick_setup, pp_assemblage did not compare without case. Failed in transport when one cell had Ferrihydrite and the other had ferrihydrite. c3defbf4 Fixing VS static checker warnings. 4a2f590f fixed for Keyword a9906af5 Fixing VS static checker warnings. c4bf48e6 updated for PhreeqcKeywords 82d57719 moved keywords to PhreeqcKeywords directory 8e104d54 Roughed in surface area calculation by DeClercq (sa_declercq for now). cf9fa724 added initialization code for cxxPPassemblage 1d876f55 Initialize type in NameDouble.cpp f6931e58 removed USE_GMP fcff4cc3 Fixed left shift operator error and null pointer error for R UBSAN check; Added INVERSE_CL1MP guard to cl1mp.cpp; Added test for ex10 3ad52ff7 Fixed bug, H+ was missing from SYS("AQ", ... 8262d5f2 Added diff_c function to basic. Added test case diff_c to mytest. 77aa5ae5 latest test cases, minor changes except for .pat file, which were wrong bbd0d318 Bryant Jurgens, bug with pat file for Netpath. dff3691e Made native a28ca9a3 changed all fortran string length parameters to be size_t simplified fortran wrappers for windows eb41112a Looks like kinetic names were not saved with string_hsave. Need to check again. e04d2539 Added andsurfcomplex4, USER_PUNCH was redefined without commands, caused a segv. e036c2c4 Added logic to run only one step in RunCells 8945b19b Another bug in mixing gas phase. e62cc9cb try/catch in class_main.cpp 4f60c877 PBasicStop accidently changed to PhreeqcStop at version 8906. test negexp_totmol failed. Switched back to PBasicStop. 0eb0264b fixed for bug that occurred when elt_ptr was NULL a2c90e9e changed : to ; 9f77e000 fixed some of the easier clang++ scan-build bugs f1438518 fixed some of the easier clang++ scan-build bugs fbb95d10 made catch(...) always rethrow; changed catches to const references f2a25dac copy/paste error for surface in totalize system. db91bf07 ready for next release 88c8cbee initialized local_database_file and local_output_stream 0236d42a memset not used for NDEBUG e1686910 Another try to speed up rates. 98741bbe finalizing compute_gfw using map for rates 685a4d45 Optimizing compute_gfw 9f0ee021 Trying to optimize compute_gfw. 87ad7693 Working with gas phase. Bug in calculation of total pressure of mix. Other issues when element of a gas component was not present in the system. 1c3b3965 r-found error in type mismatch of conditional 76bd0c29 Fixes for dumped no_edl SURFACE. cf02876f after Valgrind fixes 86a2b046 Clean up PBasic memory on syntax error. 9689a12d no need to check for null with delete. 660042da 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. 96f839e1 fixed uninitialized values 8b6631a0 memory error on units line fd1e3265 remove R_SO from class_release_64 ccfac52c init ctor; changed success to include 0; fixed delete[] be4e769e fixed if R_SO not set c7d153e7 unused variables 04ecf346 Avoid overlapping memcpy in cl1.cpp 25508288 removed set but not used variables using gcc 4.8.2[-Wunused-but-set-variable] 38ded3b2 valgrind changes/set-but-unused vars b93eda46 Fixed leaks: SELECTED_OUTPUT redefinition, read_selected_output zero in cl1mp.cpp leak in eq_frac Basic function if file open failed, leaked ofstream pointer e4229340 fixed memory leaks. commented lines are directives for visual studio _CRTDBG_MAP_ALLOC, _CrtSetDbgFlag VarClear in GetSelectedOutputHeading. RebalanceLoadPerCell fixed for serial version, clear clock times. delete out stream and punch stream before new, RunCells also set streams to NULL after deleted. also serial version. VarClear in RunCellsThreadNoPrint timing only if rebalance cell, RunCellsThreadNoPrint VarClear in RunCellsThread. changed methods to return pointer instead of reference, Get_out_stream ~IPhreeqcPhast, delete streams if necessary. phast_manager did not delete module for flow-only. phast_worker did not delete module for flow-only. ab43d75b Had timing reversed in PhreeqcRM.cpp for heterogeneous case. 1c495583 Revised error message to give solution number, mainsubs.cpp. aa40f2e7 latest, fixed bug from R with relative dielectric 6a75a7f3 Changed calc_logk_s to use original equation. Checking for 0 gfws caf75546 Added solution number method. 0ff6f481 Fixed bug with 18O, redox states not defined in default. Also, the logic for using -isotopes data was changed so that the last defined applies to all remaining solutions. 9d05f14c removed extra comma 48ec1a38 added LICENSE to cvode files 8e81c17e Next try on DELETE; -all Fixed warnings for MAC lion operating system 9b9e34a2 git-svn-id: svn://136.177.114.72/svn_GW/phreeqc3/trunk@8721 1feff8c3-07ed-0310-ac33-dd36852eb9cd b2a5ed44 added undef SS suggested by Ripley for x86 Solaris 8b2c1a8d R problem for ex16. memcpy was overwriting the same space if i = row. c3433309 removed no longer needed R_SO ifdefs f92afa36 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 504bcf6d Gentisic problem. H2O was defined as a SURFACE_SPECIES. cfa58371 changes req'd for R d77460e6 Added error print after each worker RunString. 112feb81 Delete all before filling module. 53e3bd59 Moved uz_bin to workers to avoid possible data conflicts. PartitionUZ updated Added TransferCellsUZ Added Add(src_bin, n) to StorageBin 3945c0d7 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. de0ec2ad Fixed bug with redefinition of sit parameters 0030e8da replaced printf(...) with output_msg(PhreeqcPtr->sformatf(...)) req'd for R. 3abc37a8 replaced putchar('\n') with output_msg("\n") in PBasic.cpp (reqd for R) 7c0b1106 first pass @ removing std::cerr, std::cout, exit, stderr, stdout from R version. 7359b9dc changed input_units_* to units_*. thru GetMpiTasks Changed GetIPhreeqcId to GetIPhreeqcPointer added to tests RM_GetIPhreeqcId 47eec62e 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. 78a273eb All IPhreeqc checks passing on windows c843de8f Got all Tests working with MPI except the units tester. f10f5137 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. 3f0cd06d Added Peng/Robinson gas parameters and molar volume for solids to keyword PHASES c43019c4 Roughing in mcd capability. 38bfd332 Modification to use REACTION_PRESSURE for a fixed-pressure gas phase. e284f116 Next fix for MCD a59b8b7a Tony's fix for MCD after unequal cell lengths for diffusion. b5e86c63 Do not dump negative entities. 01a54bdb added assert header file for MINGW-R 4922f9ef Tony's fix for unequal cells in diffusion. c9fb95a0 Tony's change to connecting graphs aee604b5 Changed read _modify to warning if entity not found. Tony's bug in phrq_io. punch_ostream was deleted twice. 063ba620 Tony's punch_stream error when Basic error. 63a9c36a changed so that 'dist' and 'time' are always doubles for R 5bbe7db6 changes to Tests and include mix in RUN_CELLS b6f96242 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. 7cad09da Only solutions, not mix in run_cells 5e788df1 modifications to STORAGEBIN, added Copy. Check for missing solution in run_cells. f9eff4b8 Use MIX_RAW in dump to read negative numbered mixes. 473ea39b Added additional check to LoadDatabase 9d9e86f8 Added next_user_number to Phreeqc. Added a template function Rxn_next_user_number. aab6347c changed EOL to native ab9b2ddd ex4 works with old flow from 8056. Will now try to keep all other changes, but go back to updated flow calculation. aee34267 Removed yellow for graphing. Changed Li molar volume in Pitzer, Amm, phreeqc.dat Added test case Vm_LiCl_sol 1e48b85c Removed error trap in write_mass_action_eqn_x 6f849b21 More changes for Marco. 2a37e806 Do not set master_bsearch[i]->total = 0.0 in clear() for now. 9048a9be Bugs fixes noted by Marco De-Vroed e9b05399 Clean up initial_data 4ec2784a Tony's fix to solution volume. Added test case, updated Makefile Added comment to Release.txt 7c40b44e removed all refs to MERGE_FILE, MPICH_NAME, GZIP_RESTART, and HDF5_CREATE ifdefs (except HDF5.props). 57014d0f Renamed Reaction_module to PhreeqcRM 23deef14 Revised GetDensity to retrieve from workers. Also, density was not saved correctly with the solution (mainsubs.cpp updated). InitialPhreeqc2Module had an id argument which was not needed. a3110d47 Should zero soln_vol And missed calculation of patm (pressure). 11de0894 removed unnecessary erase to fix bug in IPhreeqc a191ef4b Still working on selected output. 70482839 Added GetMpiTasks ab5384de Tony's vm revisions, phreeqc.dat gfw for N redox states c80ebbc6 added soln_vol to cxxSolution. 634211a2 added SelectedOutput and UserPunch to automake be614498 added const routines fda47b4b recovering tortoisesvn deletion of UserPunch.h (i think it's a problem with externals (was working on iphreeqc)) 8c78708f added const versions for Get_headings and Get_rate 257b2805 fixed reset now acts like setting as-is vars 314db2a5 rearranged vars and added code to track changes 5edcc20b added assert for phreeqci b956c837 fixed memory leak 9d1f0e34 set unknown state just in case. b3d02ae5 Added river turning into drain in IPhreeqc version of PHAST c1687e21 updates reqd for vs2010 4983afc6 Got a request for interacting sites, such as this surface complex. d3ed6904 updated to allow charts to stay open in phreeqci 7c66a50b changed back to using high_precision bool for diffc and disp in dump_cpp 39abad33 makefile's to run test cases 92a78618 Added -high_precision to PRINT for USER_PRINT. adf7d984 Merged revision(s) 7863-7986 from phreeqc3/branches/multi_punch: Branching at 7862 for multiple SELECTED_OUTPUT, USER_PUNCH ........ Have multiple SELECTED_OUTPUT working. b88c4901 fixed for phreeqc3-multi-punch; passes all unit tests ab6875b5 solid_solutions had extra s in selected_output headings 32b9285d changes req'd for multi_punch a99ef8b3 changes req'd for multi_punch 43f5baf0 Tony's latest changes, including F1 and F2. 695d6d4e Tony trying to fix v_m in model.cpp 2c6f8c22 working on multi_punch tests for IPhreeqc ec4fa77c changed print.cpp for Molar volume when not PR 25a99075 Tony's rewrite of tidy_gas_phase, still pretty ugly. a6f82d99 minor reformatting 9069b4a8 logic for headings of selected_output 1; logic of opening selected_output file 1773d7e5 removed inline from Set_file_name 9faaee66 fixes compile error on linux; changes made for TestIPhreeqc::case2 ee4cd5ec Next try on tidy_gas_phase 2abb2f22 Revised tidy_gases. Structure was wrong and j was used in two loops. 6eaca680 all tests passing for one selected_output file; may still need additional tests for TestIPhreeqc case1 and case2 59b456bd Change in store_tally_table to try to line up with Fortran. b18d2ff0 Guard namespace. 8609b3df Added row ntally_row + 1 that contains the moles of each reactant. a49f540e Tony's wording for fugacity 30164dc7 functions are fcn ca3e1128 Initialize basic_callback_ptr 1e8a8c03 Update RELEASE.TXT Added print about fugacity for SI. 88742cdb Fixed post-build in project 3682cff0 use reset -false by default for SELECTED_OUTPUT n != 1 305cd863 Revised name to BasicFortran 346cf223 Added a Fortran callback. 04141a30 Still working to make backward compatible. 62feec3f Making backward compatible. 8474b535 dump precision ce4284a5 working on high_precision, using SELECTED_OUTPUT 1 27b3c056 Working on multipunch d436c9cf bugs linux caught, something different about when to print headings 6fd2cc8b Fixed missing -pressure in solution dump_raw and read_raw. 1afe3e43 Fixed up inverse.cpp a bit. 38934142 Think multiple instances of both SELECTED_OUTPUT and USER_PUNCH are working. 276322a9 Have multiple SELECTED_OUTPUT working. e9202575 Caught SS definition errors if 2 components not defined. d26571fb Tony cleaned up XI in Pitzer. 79698b01 Tony's fixes for Pitzer, High Pressure is still not right, will require more fitting. 7da9c7b1 Merge Tony's changes. 6b8ccd82 latest tests 7837; some Linux warnings in src 7848242e Fixed error for malloc introduced in recent Basic function. Fixed error with Pitzer paramenters that were not recalculated with a change in pressure. Parameters depend on density of water I think. Also changed SIT, although I am not sure the parameters have a pressure dependence. a03d2ae8 Added f = EQ_FRAC("AlX3", eq, x$) 4b643b86 Finishing touches on species_formula. ff764f3f Added species_formula("CaOH+", count, elt$, coef) returns Ca 1 O 1 H 1 charge 1 in elt$ and coef. count is 4. 7d90df4e Pointers for MacInnis scaling were not reset when -B0 was redefined with Cl- K+ order. Now check for either order. 6a0b9146 change req'd to compile in MinGW 6b36a705 Lost break after tokstr_ case 102ce319 Revised manual: Figure 8 had part B twice and was missing part A. Fixed in Version 3 in previous check in. Fixed in doc. Fixed in HTMLversion examples.fm, and reset cross refs so all .fm files changed. Replaced phreeqc3-232.gif with revised figure. f1a98f8c Decided to widen fields if necessary rather than print *** for STR_F$. 56ca1c2c Added Basic function STR_F$(x, w, d), where x is the number to format, w is the field width, and d is the number of decimal places. f2cccb00 Isotopes moles and molalities were not correct when mass of water was not equal to 1. Added test case 14C_isotopes; added to Makefile. 87fea869 Tony's changes 6/1 for pr. Set gas volume to zero if fixed pressure and no moles of gas. Add test cases low_t (minimum mu), modify_zero (set total to zero in SOLUTION_MODIFY), and volume-zero (no moles of gas in fixed pressure gas phase, volume should be zero). 8fdb7313 fixed bug in DELETE reported by laurin.wissmeier@web.de 2013-06-01 037b2bb8 added Set_append 6ab5932f Removed lower limit on mu. At low T, Kwater can be much smaller and pure water has lower ionic strength. 6c4f7253 added some const and added cell for use in phreeqci 145fcc00 vcxproj has some change. 701878af If total set to zero in Solution_modify, took log of zero to update la and failed to converge. Added check not to update la unless both old and new totals are greater than zero. a52fc625 added get/set StorageBinList method 26614f70 minor optimizations of tidy_model 0b7b5f7c added pointers for solid solution and ss component in unknown struct to speed calculations, all test cases run 11ef24eb replaced Find with pp_assemblage_comp_ptr stored in struct unknown f127add4 Default_pe is now const char *, saves some string_hsave in clear in prep. d7321bd3 skip inverse in no inverse defined. 96285f22 put back piece in molalities that was necessary after all ba25fabd optimizing surface references in molalities. ed46140f Remove strcmp from calc_vm, calc_delta_v, calc_lk_phase c176fe3b Cleaning up code. c9c8a7ac Fixed volume print for -gas in SELECTED_OUTPUT. Added Gas_FixVolume test case. 47d0c62f Added new Basic function kin_time, which is the time interval for the current kinetic integration. d71ea17a Added logic for rate limiter, but not used. 8e3394ca fixed checks for successful opening of std::ofstream 28d649ab fixed for input file having spaces b23fb304 still working on print of saturation indices for gases 0607e086 Fix print of PR gases in saturation_indices. 69112597 CLOCKS_PER_SEC 24ed8b5c Tony's changes for gases. e60d708c Some of Tony's changes that I missed. f73a156b revised cvode is working I think. Had to be careful when updating m_temp and use the saved solutions. 0cb1337f added patch from tmishima@jcity.maeda.co.jp for multi-threaded IPhreeqc 2c9611d0 tony fix to print 20130425 ce037cb2 Fixed gas_phase problem. total_p was reset for fixed pressure in a couple of places (prep and tidy). 4cb5d32f Added phi to gas_phase print. Test case gas_phase_pressure 40e97fd9 Fix to the incremental updating. f uses saved pp_assemblage and ss_assemblage. 6917e9be Error, used last_good_y instead of kinetic_y at final step. 4733f935 Working on REVISED_CVODE ifdef. 5330549e Revising cvode dc977aee LDBLE for SScomp Changed sundials to use LDBLE d5fa02a7 a little rearranging of global_structures and under da493bbb One more fix for gas_phase (new_def) 8696224a Bug with gas_phase_modify. 28e082bc NameDouble dump failed with string greater than 21 characters. 31ebd3d3 LDBLE fix c3bd2eca LDBLE fix 0d6e0bc8 used small activity water step for pizter, sit 6a9624d2 ah2o_x should be set to zero. ah2o is then summed from solution or mix. c42bd892 LDBLEs 7bb4d371 cvode MAX_ITERS 40 hnew = hg predict_fail CVMEM cvode_error == TRUE || predict_fail after CVnls if (CVMEM cvode_error == TRUE) after CVNewtonIteration CVDoErrorTest exit(4); 2ba41a62 More fixes to saturation index. 82fc3b7e Reverting from Tony's fix to my fix for saturation index of pure phases with pressure. acd7d32d Fixed bug in SI of pure phase assemblage that did not account for pressure (Tony's version). 6899bc4b fixes bug with cd_psi in model.cpp. 9849ed1a added Setters for time params ebe3cbf7 SOLUTION_MASTER_SPECIES was not defined correctly. Fixed Null pointer. Abort if input_error in build_model. a2a1aafe PBasic use phreeqc_ptr warning msg instead of default phrq_io warning msg. Fixed bug in s_s assemblage print 1342a5c5 Alternate method for sum_species 3461797c Copied Advection and Transport data in InternalCopy. 27e3f75c Optimized sum_species. Keeps lists of species in a map <std::string, std::vector<std::string> > sum_species_map. c6261d5f added GetAllItems method - with fixed history 342bf39f trying to fix history dd104e8d trying to fix history b44c54f9 for some reason TortoiseSVN deleted StorageBinList.h on checkin bdadfbeb added GetAllItems method deace44a make IPhreeqcPhast and Reaction_module a friend of Phreeqc. 85528955 more testing of copy operator. 916ccdaf Working on copy operator. 6412a827 Forgot to copy sit_param f38caf06 Lost revisions to model.cpp in reorg. fc1c2b11 class main to test copy. 04741427 Working on Phreeqc copy Running ion association model with equilibrium phases Running Pitzer. b3e59d93 has _DEBUG #defines for extended ascii/ANSI character set to avoid assert. c9380090 There was a long gap before this was checked in. a1d93167 Tony's changes to the status timer. 4cb54559 added some UNREFERENCED_PARAMETER; removed g_spread_sheet 2628e3aa added NOTICE to configure c8c26e81 Tony's new Pitzer test cases 67c08b44 Fixed activity and gamma Basic functions to include EX and SURF 1199a003 merged branches/reorg -r7307-7330 into the trunk ea2bd445 working on 3.0 dist d759535c check for zero before log10 11b00551 tweaked changes to make zn.test run on linux 801d7ed3 Linux changes d23bd01f Changes for Kinniburgh's underflow and overflow problems. 7ef536ff working on linux dist 662894ff renamed GNUmakefile to Makefile bb2ea3d7 updated dependencies 9976920f updated dependencies 709e1176 modified source files for rearranged directories 564a0f8a moved phreeqc files into src 0daf341e Use PHR_ISFINITE b1241f43 check exp for isfinite 2832b3ad Flushing error file. a42ef3aa updated for COM 2109cc8f Added active_charts to ChartHandler. Incremented when form starts, decremented when form ends. e765dc43 Updated makefiles for parallel testing. bd446838 accidently checked in 2-digit exponent bd10ce02 Fixed memory leak for CD_MUSIC af148da6 Freed s_x by mistake 6f221185 Changed Rxn_new from vector to set. f74bc444 Solution_spread did not set Rxn_new_solution b75ce1b7 Fixed bug with _modify. Did not get correct n_user! c2f8b3bb Saved list of newly read entities (including _raw and _modify). c0a8627f fixed all System::Threading::Interlocked::CompareExchange and added some debugging code 65c2d528 Tony change of numtostr. 5852b6a3 added check for gmp.h and -lgmp 21801d62 added stdio.h 58fdf968 stdarg for fpunchf_helper 1f52fff8 Kinniburgh found bug in surf_total. Made a mistake when allowing redox states. Added test case surf_check.out ed6ad167 fixed hidden var declaration 378f2ff7 fixed buffer overwrite in fpunchf; updated unit tests for phreeqc3 31efde46 working on configure f6498fee DELETE; -cells #no list of cells Causes all reactants to be deleted, same as DELETE; -all cfdbf58d new def removed for raw Gas Phase and Surface. 6ac877e7 Step, problem mu requires ah2o to be 1.0. d7b2ab1b Fixed spacing for PRINT command high precision. 283ff2df Tony turned off PR in mainsubs.cpp af6f13be changed read_delete to reuse StorageBinList for each call 03b0b884 Remove Dictionary, Linux changes 9d4bb2e1 PHREEQC should now have no USE_MPI 63a1879a Finished zone flow chemistry write for MPI. 98baecfe Added two new functions. e13a4d80 Think rewrite of rebalance is working, need to fix zone chemistry file for mpi. d4721e49 Wrote rebalance_load for MPI_Bcast ed73e17f Working on copy constructor. Roughed in Pitzer, need to do Sit and TRANSPORT. Test e3638b34 Revised phreeqc constructor, init, and initialize. All data members are now initialized in init. Almost all allocation is in initialize. There is a little bit of duplication in initialize, but not much. 03d70eeb Set pr.headings true in class_main.cpp pr.headings not reset in do_status. pr.headings not changed for IPhreeqc call to do_status. d13ffaa6 Fixed Dieke's Viet Nam problem, la was limited to -300, now can go lower. 4c2e8c33 Modified to tidy exchange, gas_phase, ppassemblage, solution, ssassemblage, and surface when _raw or _modify are read. Set new_def for each. Had problem with equilibrium_phases as shown in eq_phase_mod test case. Probably will add amdtreat test case from which it was derived. d0d48fca added additional initializing code to g_spread_sheet 475cf8f1 added some (parse_all) logic to avoid crashes in phreeqci 83f7c0c4 Adjusted convergence for small numbers. 3503962f bug with saturaation curve pressure. e1ef00c5 Tony's changes for dates 3b42a98f (int) c352283a Updated to Tony's latest. Amm.dat and Pitzer.dat have extra terms. d96dc80f Runs ex4 correctly. fb36b693 Deleted dead code in reaction module. 5e62aeb2 Runs, getting xyz file right, checking results. 881ca8f2 debugging and optimizing 8b0481a1 Working on efficiency of updating Solution.cxx Need to revise solution_modify. 31c1ae86 Optimizing activity update e5177c60 void null pointer for master 1a1950c4 Added total_h and total_o to tally table. 545dbd10 Added some status_on = true in status. 1f8d8608 fixed location, resizing, tab order. baf45663 Added second logical in batch. First is color, second is grid. 54ec7c4a Removed toggle hints and toggle background Added Chart options... a7acb6ff added trys between System::Threading::Interlocked::CompareExchange and System::Threading::Interlocked::Exchange d3a8fab5 added const version of Get_pressures; added reaction_pressure to error_msg list; 0440b0c7 Think restart files should work, but cannot test yet. 1f52826b Have initial conditions working. c0463f6f Does initial conditions, but is really slow. c6c27b03 Allow negative numbers on entity mixes. 60151014 Fixed bugs with mixing calculations (keywords not set up right). 06cc39e8 Added new keywords to mix SOLUTION, EXCHANGE, GAS_PHASE, KINETICS, EQUILIBRIUM_PHASES, SOLID_SOLUTIONS, SURFACE e20fd6af modified to use auto_ptr for early termination memory cleanup aa903967 bug in totmol(water) ad3e78e2 Added Basic functions GFW and SOLN_VOL. Added test case gfw in mytest and added to Makefile b0b007ca const static vopts 065f7ea3 BUG FIX: runs that threw didn't close the input file(s) and do_status was never called. a826fa57 Added Update method, removed unused prototypes. 87c00324 Avoiding null pointer. 64024732 Don't print chart detached unless there are charts. 81521287 Tony's fix for reaction in transport.cpp Used Sleep(5) instead of Sleep(1) throughout. Removed timeout on detaching charts. It will just hang if something goes wrong. 3295cd5b Deleted ifdef skips f069c8e5 renamed c files. b664e431 Removed unneeded declaration. 0ca96543 Reversed logic to NO_STATIC_VOPTS, default is now static vopts. No changes to Makefile or project needed now. 8823f0ff Added STATIC_VOPTS to make vopts static, not static unless defined. 66f3b9b8 PHRQ_io::error_msg now throws on STOP 01495bfb changes reqd for merge version 782106e4 Tony's changes 232bb18f Added time unit to advection, kinetics, transport, and run_cells fc2d4425 Added SOLUTION_MIX m-n keyword that mixes solutions without doing a full reaction calculation. Results of mix are stored as SOLUTION m-n. 77b082d0 Fixed handling of pressure for solution_spread. 7413759a csv to tsv 2222bd96 Added check on residual > MIN_TOTAL for MB equations. 5c551753 MMS friend added f45f490e Trying to optimize calculate values. With isotopes, all the isotope ratios and isotope alphas are kind of slow. bd328e58 Revised method of calculating equiv for EX and SURF in tity_species dcc27441 Calculate equiv for surface and exchange in tidy. a8b09b7a tsv updated in code. 50907986 Updated tally table to include Alkalinity and secondary master species (solutions only). e55ff96b Tony's latest water properties in utilities.cpp. c1886eb2 fixed for phreeqci (basic renumber) modified listtokens to put single quotes around strings containing double quotes d369d0f7 added __cplusplus_cli defines for methods that require CLR for faster linkage with USER_GRAPH editing in phreeqci 692cd611 added const methods c9dfe616 Rewrote -batch of USER_GRAPH to handle filenames with spaces. 0fcfb42a Cleanup of temporary code 4a8e2ca9 fixed heap error: 6dd55677 Added -batch option to USER_GRAPH. b984ef5a Tony added function DH and Qbrn. 1510698e Write image without red hints in boxes. 94460826 Added toggle background. 693e36ce Tony's changes through May 16. 0eef1187 Modified for new handling of surf related to phase. 3f982ac5 Don't check zero charge for CD_MUSIC master species in surface related to charge. d07b45cc Revised logic for surf related to phase 204108a6 Latest examples 07e9545f clearloops after basic_run to avoid memory leak. PBasic.cpp. cbba2c24 added const versions for ChartHandler/ChartObject made ExtractCurveInfo static in order to use in phreeqci 6a865f65 fixed minor assert 2e6e2bc3 re-added malloc_dbg for string_duplicate 54c328a3 equal_increments synonym in Kinetics. Increased max_tries in mainsubs for responding thread. removed extra calc_dielectrics in prep f1e2ecdd Tony's changes 20120423. 2ca408ed updated for linux (added headers) added build dirs to ignore list fbe3108b removed Phreeqc_class.h from dependencies 74c97b0e removed dependencies Phreeqc.h and Parser.h from Utils.h aa8047e1 minor formatting a4d8672a made get_line and get_logical_line virtual eace3df0 removed Utils.h dependency 59016d1c added GNUmakefile which rebuilds dependencies during each compile the dependencies are stored in each configurations .deps directory 3eb956bd removed dependency on phrqtype.h by using a template for addPair removed unnecessary Phreeqc.h 3d2e4ae4 Removed Phreeqc_class.h. 8e0844ed Fixed memory all memory leaks from mytest. bf96306c output file was closed before free_all, no messages appeared. 9c1a63dc Bug with key in pitzer parameters. Needed type, in addition to ions to make the key unique. a718706e fixed string_duplicate leaks 67b089f8 changed ifdefs for string_duplicate 2f10f2e7 fix for level 4 warning level 495a2200 merged in http://internalbrr.cr.usgs.gov/svn_GW/phreeqcpp/branches/ErrorHandling 6269-6445 e972c511 trying to recover Phreeqc.h w/ history this should have been -r 6391 969e5df5 trying to recover Phreeqc.h w/ history cce0fe25 fix for level 4 warning level 07fdb2cb added memory cleanup code 4d8f7893 added memory cleanup code ac861bde replaced WaitForSingleObject w/ PhreeqcIWait; 4309bd45 minor cleanup of reading code 6167acc9 sped up pitz_param/sit_param reading; added memory debug code for string_duplicate a512faaf setup for ERROR_OSTREAM ae27e8a3 added init code ae7c893c added initialization code 6a921663 const modifications 828eaf16 const modifications 0e640f45 const modifications 733d093f const modifications 8e9a4e0c made istream_getc static; made some routines virtual; added virtual getc method; 8ea8082f added const version of Get_pp_assemblage_comps 7347290a const modifications d2577f8b const modifications 82d49974 const modifications 02460252 added const version of Get_SSs 0574952b added const version of Get_temps 33eabd03 SOLUTION_SPREAD 7c3f0b5b changed implementation of trim_left trim_right and trim. see http://stackoverflow.com/questions/216823/whats-the-best-way-to-trim-stdstring 69711a42 made iso_defaults public and static 96294247 trying to fix loss of history with Phreeqc.h c98ac9ac trying to fix loss of history with Phreeqc.h c8c82a99 resurrected Phreeqc.h; Don't know how it was deleted 3df08dd0 made iso_defaults public and static 1ad10142 added serializing code for selected_output file name 54d517d4 added const versions 4f70c394 added const versions 4b5f2692 updated to use windows malloc debug c892ae27 BasicObj fd26a7ed fixed memory leak caused by duplicate numbered solutions (see ex12 -- solution 0) (previous fix was just a band-aid) a35fb059 fixed memory leak caused by duplicate numbered solutions (see ex12 -- solution 0) 91f650a5 Merged ErrorHandling 6119-6268 changes. All reactant structs have been removed. Tony's pressure uses mu in pressure term of log_k. Test cases run, discriminant check at 1e-8. 20b360fe modified for warnings in 2010 50ba9dbe Made minor class of valrec 5f058aec memory initialization for cvode 23121d78 Initialize PBasic structures. 02f2e253 Fixed bug in jacobian calculation for Cvode dd06c2ea Runs most kinetics, kinsurf is a problem. 18906cdd Removed skipped code. ea54bb8f reworked logic for using previously read line from parser. 82bd21f4 Running Linux with new SS bcdeaf22 Tony's 17Jan2012 changes to gases, prep, read.cpp 02ece436 New format for SOLID_SOLUTION_RAW. d051a777 compiles and runs solid_solution test case. 2673f81b Working on ss 6bd23b9b Rename item from http://internalbrr.cr.usgs.gov/svn_GW/phreeqcpp/branches/ErrorHandling/src/rename_cpp to http://internalbrr.cr.usgs.gov/svn_GW/phreeqcpp/branches/ErrorHandling/src/phreeqc f5b51e1d moved -r6061 http://internalbrr.cr.usgs.gov/svn_GW/phreeqc/branches/rename_cpp to http://internalbrr.cr.usgs.gov/svn_GW/phreeqcpp/branches/ErrorHandling/src/rename_cpp 549ba5c2 Jonathan Toner changes for low temperature pitzer included as comments. Change when his paper is published. 875a5f1a floating point exceptions on Linux. f108e75a long double mismatch 76839828 changed all double to LDBLE 9aef1acf out of range subscript in get_line 93aa3317 n_mix_user_orig setter bug. 765f7b8d Linux Makefile 765d5413 first bug with use 568a2ab7 classified struct use 4f0fb6c9 Finished ss_assemblage rename. cbd736da Renaming SSassemblageSS to SS and cxxSS f0855460 Renaming SSassemblageSS 619e7824 Tony's 1/10/12 changes 89153db8 turn off warnings for dll linkage for std::list 3458661f bug with case for phase name in surf_related_pz 2590f549 Bug fixes for pp_assemblage 48639132 pp_assemblage is mostly working. Need final checking ff5fc98a removed extra qualification cxxGasComp:: on member multiply 1ed24bf1 added GasComp.cxx to unit project; fixed typo in GasPhase.cxx e295db8b New files d0c049ed windows log functions passed 67eb8271 Tony's updates relative to 5941. 9758c574 Last of SKIPs 7257281b Fixed bug in read_gas_phase_modify, appended components already in list. 18eba6bd cleaning up bugs with exchange 90934690 started removing SKIP 16e00762 eof handling in cleanup_after_parser. 15dbbaa3 New Makefile. acf62c78 gas_phase and irrev removed. ddafdd17 Added missing members to dump/read _raw 97a38235 Made const char * b52ab4df Exchange changes have been made, but need to debug. 02839d60 Removed struct mix. 4bb72929 Change count in dump_raw for temperature. b5c652e2 Removed struct temperature. Uses only cxxTemperature. a05de5e5 Removed old hash for strings and replaced with standard map. a8ad8258 hsave_string returns const char *. 2095c5bf Linux changes e0ef4941 changed error_string to const char *. 70eb5e27 Revisions from Tony. 84644301 added force_numerical_jacobian 28534b50 removed REVISED_GASES from Makefile. 9fa2b74b Removed gas_pressure unknown. f7518987 Modified to run all fixed volume calculations through REVISED_GASES code. 8107f787 have old activity of water and correct tanh version of activity of water. 267b5934 Incorporated Tony's changes for -vm fe15de34 Fixed long heading problem from Kinniburgh 8a8547be Think fixed volume P-R gases are working correctly with numerical derivatives. c46e4876 Added pr_in to C++ gas_phase class. 4ed743d0 added Set_file_name method for use in IPhreeqc 36bf6b7f Compiles with and without REVISED_GASES. 1715e7b4 Numerical derivatives with REVISED_GASES works with the P_Vm test case. 877f19e6 define bool slack to allow a slack variable in array (default false). 88dc8b96 Changed activity of water equation to use tanh to allow activity of water to approach zero smoothly. 57620590 sync'd warning_msg with error_msg 2211621f istreams moved to phrq_io a4c8e993 moved istreams from Phreeqc class to PHRQ_io class changed modes std::ifstream:: to std::ios_base:: deleted some #ifdef SKIP c3d019a0 Fixed action of dumper. Retains information until next read, only changes what is read. A DUMP keyword with no body will repeat current definitions. 8cbaba8e Converted output to streams. b260023b replaced dump_file with dump_ostream 1f7e4e16 added IPQ_DLL_EXPORT for IPhreeqc dll versions 6fb5faa2 added PHRQ_io member 23f209d9 added guards for phrq_io 6bca2105 Linux version of all examples for version 3. 2e64a171 Minor fix to REACTION_PRESSURE e803c8db Fixed but in TRIM. 2887acf8 my bug in read dumper 0a98983f Think reaction_pressure is done. 23a80097 updated for g++ 4a7158c4 Getting there with adding REACTION_PRESSURE capabilities. 8a678fa9 removed ../ from include 99b8eac5 Have read_reaction_pressure and read_reaction_pressure_raw working. Dump reaction_pressure raw also works. 0f6547cc IPhreeqc passes all unit tests on VS2005 ae868f0a Got reader for reaction_pressure working. 90f30845 Added erase basic function. 2c80bb5f Needed header file on Linux? 278ce5a9 New keywords files 17a4c844 Moved keywords to separate class 584b79bd roughed in cxxPressure class. A lot more to do. 041db991 Removed keyword hash. Added enum for unique keywords, static map of phreeqc keywords, map of keyword names. 02119ae8 Fixed but for David Kinniburg. 03bc3d38 Going to try checking cl1 results for inverse modeling. c552aab8 updated reading for istream cookies removed PFN_READ_CALLBACK 14ef22ef reordered calls to calc_PR in prep.c. c5a5c33d printing out pressure in examples. aa77b78d Tony's changes to gases. 5ec591a0 Update to VS2010. b160c3da Header file change 06ef90e5 initialize basic_interpreter 79b256e4 added code to handle IDS_* added code for HANDLE #ifdef'd the WaitForSingleObject 4268bd93 Merging Basic1. 2a8089a8 Merging Basic1 from PhreeqcI into Basic. 9d1dc096 Made PBasic commands static, initialized only once. 46b50f49 Made NameDouble use LDBLE eb2fab2e Indented last try/catch. 97caf60b Indented Phreeqc.h, read_delta_v_only 9c73b964 Needed to merge two read_delta_v_only 4c938e63 Crapsi changes 29276b98 More cleanup of PBasic.cpp Removed PASCAL_MAIN. Removed Anyptr. 7271b9d5 Replaced TRY/RECOVER with try/catch c20d3ca2 Latest version (5757) with fixed up PBasic (std::map). 122f2b87 Cleaned up PBasic some. f8d1baf0 deleted obsolete QBasic directory ff2d48f1 Going with new PBasic. 5930d762 Changes to set_pz and set_sit. Avoids setting lg = 0 for the first attempt in set_and_run_wrapper, but then sets = 0 for additional attempts. 579d5a3f Fixed up PBasic for Linux. 27168dbe Has PR calculations. 40f0539e PBasic files. 516bd2ea Added PBasic with #ifdef PBASIC. 7f18c67b fixed bug in phqalloc.cpp. f8887170 Implemented Tony's Peng-Robinson changes. Need to run his test cases. d2c28c17 safe_close now takes pointer to file pointer fdd1cee2 Phreeqc_class.h case in #include statements. Fixed warnings and errors in Unix. Updated Makefile for class only versions. 2efc1ee2 Rearranged header files. 7e0ae150 Fixed up eol for error messaging. cc03f8d1 QBasic 21da7bae Renamed output_temp_ to output_. 38373629 phreeqc_class header needed. 980e6802 removed setjmp except in Basic. 95aa3278 Removed phrqproto.h from project and svn deleted. be8d41f2 removed MERGE_INCLUDE_FILES some static and extern unused static maps de377b66 CLASS_STATIC replaced with static STATIC replaced with empty 9eb1ba4e Removed EXTERNAL, PITZER_EXTERNAL, and kinetics.h. e0cbcff7 CLASS_QUALIFIER is gone, svnid gone removed dead code from PHRQ_io.cpp f1e5f4c7 About to do CLASS_QUALIFIER 7e26eec1 Last checkin svn deleted obsolete files output.h, output.cpp, phreeqc_files, main.cpp. 601d8515 Removed PHREEQC_CPP and some PHREEQC_CLASS. 05495494 Removed output.h throughout. 53a00d4a Finished fpunchf. 6c2f0b5b Did OUTPUT_PUNCH. ccc05114 Accidently had wrong PHRQ_io.cpp on checkin. d57af053 OUTPUT_MESSAGE removed, need to check a bit. 92d8a3b9 OUTPUT_CHECKLINE and OUTPUT_ECHO done. efe04692 OUTPUT_SCREEN and OUTPUT_LOG are done. fbaa4906 Done with OUTPUT_WARNING 3630733e Will not compile non-class versions! c0cc6d8b Removed OUTPUT_DUMP. e2e3ba09 Renamed methods and added _msg to output (_temp for now), punch, error, log, dump. ab425548 Beginning to remove enum OUTPUT_MESSAGE, OUTPUT_ERROR, etc. ecd1d9c6 Working on interface for run_reactions. 53400537 Cleaned up kinetics.cpp. Changed io in Parser.cxx a little. 1fb2150c Removed OUTPUT_CVODE, OUTPUT_STDERR, OUTPUT_BASIC, and commented OUTPUT_SEND_MESSAGE. 79541da6 Removing struct system. Not used. cbc2c210 Added ptr_to_user for mix, irrev, and temperature. ee9dcce4 writing cxxStorageBin2phreeqc. 6e4445fa Working on reaction module and RM_interface. 03dcbf8e Added Simplify_totals method and Update method to aid in PHAST implementation. 7ccdb161 removed dead code, mostly P_INSTANCE and PHREEQC_PTR 58c0e3f7 Added optional argument to dump_raw to a different user number. fe9f3144 Replaced modify_activities so that PHREEQC instance is not needed. 5b39b2f7 NumKeyword reads negative user numbers. a7aed179 Fixed segv with GAS_PHASE that had gas component with element not in system. d0075d7c Converted phrq_io to pointer rather than an instance. e89dd593 Removed SKIP code in PHRQ_io and Parser. 6fa41ac0 Rewrote PHRQ_io. Removed handlers. 4d323147 Changed longjmp to throw for PHREEQC_CLASS 9201846c Added isopen_handler 9fe532ea Cleaned up Get_ and Set_ except for parser. bf84746d Converted last StorageBin to remove P_INSTANCE. b18bda26 Working on StorageBin. Moved 3 routines to structures to eliminate P_INSTANCEs. 6acf05a1 Removed ORCHESTRA 4d728afc Removed MOVE_TO_STRUCTURES ifdefs. 9efcd6ec Finished all but loose ends with P_INSTANCEs. 9561576a Finished SSassemblage.cxx Cleaned up other files some. e42590e5 Cleaned up NameDouble, still need to remove elt_list. 62a55134 Worked through solution removing PHREEQC_PTR_ARG. 02ab5c20 Finished PPassemblage and Reaction P_INSTANCE removal. 2dab6f8e Removed PHREEQC_PTR_ARG from gas phase and temperature. 06f4e08e Finished with Exchange removing all P_INSTANCE I think. 7c991319 Worked through kinetics to remove PHREEQC_PTR. 12d62e8e Removed P_INSTANCE for error_msg, which removed entirely from some methods. c2987e2d Think ErrorHandling reproduces original results. b7729cf2 Changed all check of input_error to get_input_errors for phreeqc. 0cf22bd9 Class_release and Release compare with phreeqcpp-trunk. 40bb6533 Fixed bugs with end of lines for status, warning msg count. 50b369a2 Compiles all configurations of phreeqcpp.vcproj 11da9fec Worked on output. Added output_string to PHRQ_io. 7eeeab45 all classes inherit from PHRQ_base, except f6ed50af Added base to kinetics, mix, and exchange. aba47964 Added file_on variables to PHRQ_io. 02797e69 Added PHRQ_base and PHRQ_io to project. a57c89d7 New version of parser 70d290b5 Removed headers from header files where possible. 79e978a7 reverting Tony's change. 978f1515 Removed unnecessary header file ISolution.h 00430524 Modified for "+" sign; makes Fe(+3) synonymous with Fe(3), for example. 3be93e8f Renaming Form2 to Form1. ae170dc3 Removing CHART compile option, replaced by MULTICHART. dc45fa36 Tony changed csv symbols. 3d989d5f fixed compile error in g++ 4.4.3 7d523c89 fixed compile error in g++ 4.4.3 c43921fa fixed compile error in g++ 4.4.3 68b9c041 Sorted results for list_s_s c9b1781f new sit.dat database. cd41ca95 Removed some header files from phreeqc.h. 4e02d925 Guarded ChartHandler.h in Phreeqc.h. 865cdad9 missed list_s_s prototype for class 2da02dd0 Updated revisions for revisions and PHREEQCPP-RELEASE.txt 646207fa Added phase_formula function. 2c906a06 Fixed missing reaction_modify in Class version a36a7924 Worked on bug with DUMP and read_raw of isotopes. 67258ef6 reading with parser differed from reading from stream, and did not handle missing id number correctly (NumKeyword.cxx) 2b117727 Rewrote run_cells to do all of the calculations that would be done if a series of USE and SAVE. 41a6354f Added example 20 to examples.fm. db5f8e6a Removed dead code and dead logic for adding series. 72298ad6 Simplified logic, but left old commented. c3230634 Trying modification of logic of user_graph 1ac4976f Latest output for test cases. 24eabcb5 Couple errors in parsing chart parameters. 1238db91 Made fixes for Tony's 5/06/11 zedgraph tests. f2fcaea1 Revised for Tony's comments. CSV colors have separate default_color_csv. Added -active. If csv for graph_y or graph_sy, no symbols. 2d59bd8c Worked on logic for Tony. If headings are defined, don't remove Basic code. If no definitions in USER_GRAPH, remove Basic code. 5af51e0c May need to free rate even if Form has not started. 99f7eab6 Had duplicate chart_start code. 2a491b71 merged MULTICHART branch back to trunk 8060c065 Removed chart files that were accidently checked in. eb2227ac Before reloading from home. cd87eed3 Added some LDBLE, particularly for pow(). c5fc6bef Added version/date replacement strings 13910c9b moved and renamed revisions to src/PHREEQCPP-RELEASE.txt 27bc1114 removed old revisions from phreeqcpp/src 16c2689a Fixed adjustments of activities after solution_modify. Better treatment of redox states; bug in get_total_element. 1e8147c0 Added note on automatic modification of activities after SOLUTION_MODIFY. e746bb8e Added code to adjust activities of master species in solution when totals are adjusted by SOLUTION_MODIFY. 4419cb42 Changed output to output_file. cb4073bb Added Tony's ceil and floor Basic Functions. 8ad0987b Added ndiff option 89f399c2 fixed uninitialized variables punch.new_def, status_timer, count_strings; Changed #include "time.h" to #include <time.h> 5ac33b0f Cleaned up some more memory leaks reported by Intel Inspector XE 2011 (Kinneburgh) e3ec792a Tony's changes. e2c2949e latest phreeqcpp f3f50f02 Added EOL$ function. 6f9a13b1 Redid include as include$. e0ed0a61 Updated project to include chart icon in managed resources. 3e8e7927 Some spec cond diffs. d6d3c223 Initialized solid solution in read.c 75e0df6e Through REACTION_MODIFY and REACTION_RAW. 7a46255d Eliminated requirement for equal_steps in kinetics_raw read. Thought this would make it more backward compatible. 8b69f05f Added missing -dw parameters for MgCO3, MgHCO3, and MgSO4 aqueous species. 61580e15 added equal_steps to cxxKinetics. Had not implemented the "in steps" option for the Kinetics class. 3c280751 exchange_modify, recalculate formula_totals after redefinition. 11b0315d Made pitzer_exchange_gammas true the default. 5aafb6d5 Added some identifier synonyms for DUMP and DELETE. 8e65d00c Fixed duplicate lines in echoing output at end of file Streamify checks for OPTION_KEYWORD; check_line is KEYWORD. aa5cafea Use OPTION_KEYWORD for stremify KEYWORD for check_line. d34b328b Added -cell to dump, copy, delete. f41c9446 Redid capability to include input files using #include fn. 619dc25c Modified merging #include files to use file pointer instead of stream. fd55082c wrote code to allow files to be included recursively in the main input file. b1fca87a Added -mix, -reaction, -temperature, -cells to DUMP. 8ff9cd79 Fixed negative exponent problem. 2034b500 Moved some initialization from initialize to class. 1b6f05cd Works for class, need to split up initialization for static variables. 20cf5c40 Fixed uninitialized variable in V_M structure in transport.c, which caused sc7 to fail under Class_release configuration (NDEBUG). 4de8e60e Changed phqalloc to allow 3 cases: 89090c46 added stdlib.h for exit on SunOS 4b311977 Redid modifications for hidden variables using l_ prefix. 053c817d added stdlib.h for exit prototype on SunOS 579a2837 Fixing hidden variables in 261bc011 fixed p_instance bug for raw and ppdump 778c7b05 changed p_instance to p_instance1 hiding variables ba762e6d fixed hiding variables bf1e9bff fixed hiding variables 1e9f6e57 Fixed up charting changes for class version. 98e6f469 Modified class version to detect end of USER_GRAPH thread. 24f5a295 Added code to allow phreeqc_instance to stay in scope until the thread count drops to 8. Don't know if this will always work. 31eafb92 Sortof works on class clr version, but need to be able to detect when chart thread ends. 0b4092e1 Still need to work on Form1 to pass a phreeqc instance. 5b8e7fdf added output_message prototype to output.h removed prototype from phreeqcpp/Phreeqc.h and phreeqcpp/phreeqc/print.c e1b52e15 reworking output_message prototype 09bf8787 deleted unused variables sit_remove_unstable_phases and pitzer_remove_unstable_phases. 4940d97f combined src/Makefile.am src/phreeqcpp/Makefile.am src/phreecpp/phreeqc/Makefile.am into one file cba7d11b modified Makefile.am's to handle each src dir independently e3888e1f added newline at end of files 0833d79e changed svn:eol-style to native for many files 7ca9917f Remove from unit: TestInterface.cpp TestInterface.h IPhreeqc.hpp IPhreeqc.h IPhreeqc.cpp module_output.cpp module_files.cpp fwrap.cpp fwrap2.cpp fwrap3.cpp IPhreeqc.cpp CVar.hxx ErrorReporter.hxx OutputFiles.hxx Phreeqc.hxx PhreeqcParser.hxx SelectedOutput.hxx Var.h Remove from IPhreeqc IPhreeqc.cpp IPhreeqc.h IPhreeqc.hpp module_output.cpp module_files.cpp adcd4447 passes all tests on win32; before changing to multiple instances 8db3c1ac Added prototypes to class for Basic functions: total_mole iso_value iso_unit 4d050487 added prototypes for dump routines; added ostream header 7e52b0c3 Did not pick up redox species from solution. ffb8ee86 moved list_components from class_main.cpp to Phreeqc.cpp 4eb0dbc9 list_components method to extract complete list of elements in all solutions, equilibrium_phases, etc that are currently defined within the object. a22a6db0 need to test on linux 9ed87e33 std header files added. e245f8af Updated for IPhreeqc to use PHREEQC_CPP and PHREEQC_CLASS. Currently doesn't include gmp. MemDebug project still needs work. Needs to be tested on linux. 4ddc8358 Added equilibrium_phase keyword to Phreeqc.cpp constructor 81717e18 Removing zero editing. ef4a5b53 Before modification to use standard database files, shorten run times, and limit output. 5e23f440 Made pressurs a synonym of total_p in gas_phase_modify. 7b777201 Added viscosity function for SC at temperature. ef46b2f3 Fixed remove_unstable_phases for class 694c0748 Bugs with kinetics in PHAST. 490fd2be Added options to the UNITS keyword to allow moles of solid reactants to be interpreted as moles per liter of WATER or moles per liter of ROCK: d8506413 mpi.h needs to be defined first because of a conflict with stdio (SEEK_SET ifdef). 7dbc8d06 PHREEQC runs as class. b4544293 Fixed error with callback. Had not saved the phreeqc pointer in the parser constructor. 65ff0a94 Fixed Makefile on Linux to make class version. 3131740c Compiles as class, debug, and Release. 9f4eefd2 Made all the changes to add phreeqc pointer as argument to Phreeqcpp class methods. 157e5cc7 Slowly adding arguments and qualifiers to pass phreeqc class instance to routines that need it. 6859605b Debug and release compile. 2b76f04a Cleaned up header files to remove unnecessary includes of .h files. Moved includes to source code where possible. e65ab2ea cleaned up storagebin headers. 0a91aa5b phreeqcpp (nonclass) compiles. b33830cc Moving class_main, phreeqc.cpp and phreeqc.h into phreeqcpp.sln 07d5fa74 merged 3750-3846 of plusify; system.cxx and system.h need to be formated removed char * and used std::string's and std::map's dd1c83ed eol 51183867 eol 9f7e982f eol a4bac119 eol for system.cxx 3fe2fcd3 Modified to run_cells if solution exists, even with no reactants. 30386412 updated for COM object 5de5c6f3 Needed to turn of echo when rereading components. ff19c86d The tellg and seekg did not work for gz files because the methods are not implemented. e3567320 Typo of file instead of stream for setting echo to file. c73fc4b2 Modifications for Linux. b3b22f3f New class 259c0839 Added new class runner. 5f9cf78f Modified for parallel version. Had some lists in the pack and unpack routines that now are maps. cd38a803 Have done preliminary testing with all MODIFY keywords. d54c0403 Have converted std::list to std::map for all entities. f0157592 exchange_modify is working. b9e38f4d Updated phreeqcpp to have examples from phreeqc. cbfb7683 Initial testing of SOLUTION_MODIFY and EQUILIBRIUM_PHASES_MODIFY. 2fd35ce4 Delete, Dump seem to work. 74bb0bc5 For dump and delete, added StorageBinList 79092e94 Have added delete, but parser is not working correctly. Am going back to 3705 to see if it worked correctly then. 6ca3a6d3 Added the suite of modify keywords: SOLUTION_MODIFY EQUILIBRIUM_PHASES_MODIFY EXCHANGE_MODIFY SURFACE_MODIFY SOLID_SOLUTIONS_MODIFY GAS_PHASE_MODIFY KINETICS_MODIFY c3d4c1c4 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. 4d717951 Added dump files. a81cd945 Added dump datablock for phreeqcpp ccd31029 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. 45d120f6 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. ff282a40 Missed one line for struct to class conversion of ppassemblage for precipitate_only. e398c418 Updated PHREEQCPP to have precipitate_only option for pp_assemblage. cefe071f Reindented, fixed errors, ran test cases. d37ed2c6 indented header files. 3313c814 Ran indent program on phreeqcpp 60d57c50 Delete kinetics.h at PhreeqcPP src level. Duplicate I assume 193e8ef8 Bug with adding mixing solution when already in list. Replaced old fraction with new fraction. Now adds the two fractions. 7a60bb98 Write around assert. d106dbea Added missing tests from phreeqc/mytest and related files: netpathxl eq_EC salt_ec 25666df9 Used new gcc on srv2rcolkr. b9520a20 Worked on dependencies for Makefile. bfec3cc7 Missing break in kinetics_read_raw switch. 3f9693c6 Updated C++ to have new variables for KINETICS cvode_steps, cvode_order. f630dd83 added linker option to check for --hash-style availability 711f5f94 Fixed syntax for bash 5764f894 Simplified get_total_element a bit f4777a19 Fixed bug, and streamlined. 3f93ab5a Tried optimizing get_total_element using std::strings e7ec5c76 Removed echo that was always true. Made huge string that crashed restart. Results are same without the removed lines. 8d475282 Added read_raw_keyword. 75255ea2 No memory leak check in output files. e3859a08 reordering mpi.h 37b1add9 Ifdef'd ORCHESTRA. 7ab1e21c Works with reaction calculation of pure phase equilibrium. c78dd87d 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. 0f2ef116 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. ea61d055 Can read a solution result from Orchestra.cxx 1848045b Added new functions to allow multiply. c5d2d6d8 Fixed some warnings found by Studio (casts) b2dd9ad8 Simplified test for missing solution. 0bebfae5 Fixed bug in get_total_element 4145b60e Fixes for cxx version of xsolution_save (constructor(n_user)) 8a84d795 End of line for now, have solution and exchange saving from c storage after calculation. a7a19e57 Still has problems, but roughed in xsolution_save and xexchange_save as constructor methods for Solution and Exchange. Takes c storage and makes C++ objects after a calculation. 7830f46d Merged 1727 through 2055 from orchestra/phreeqcpp_for_orch into phreeeqcpp trunk 4a5bbef3 New compiler, lots of diffs in test cases. 546c3e8e Had extra :: qualifiers, not needed in header file. 2b442eef git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/trunk@1723 1feff8c3-07ed-0310-ac33-dd36852eb9cd 93a7759e Beginning to revise cpp classes. bd852de5 removed extraneous cxxDictionary:: from int2char method 4f7eec29 gcc did not like comma at end of enumeration 07f03ea2 Fixed echo in parser for ReadClass.cxx. 2dc33fb7 Working on echoing for CParser 3320ef3c removed error increment in get_option. Logic allows a missing option in component reads, which bubble up to keyword reads. 888140c4 Updated with phreeqc files. eb5b9511 Stray debug print removed from StorageBin. 42300692 fixed warn again. f8c7968c Fixed incorrect casts. 52ab13ec Fixed some bugs in C++ classes. 812bb1ad Updated with Tony's MCD additions to Surface and SurfaceComp classes. e4ca1d77 Forgot to include force_equality in PPassemblageComp 7953591e Working through changes to surface structure 119b0325 Had not included formula_totals and formula_z in structure. 89c12ec0 using type and dl_type in Surface 217bdd77 Converted to VS2005. cb46a1de Removed warning messages from compiler 309d3d7b Fixed cast warnings in c++ a524c461 Updated to latest PHAST cpp files. 382075cc Couple changes for exchange mixing 1e28de64 changed automatic arrays to dynamic arrays 6df20749 Added mix_cxxExchange to storage bin with assorted routines and changes to make it work. d8a1b2d7 Renaming some files 764d31c7 Added Dictionary to svn 11431ae2 packing and unpacking cxx classes for mpi is running need to check result. 297744ea Updated for VS7.Net a38caf49 Serial version is working for Linux with restart option. 8356664d workds on serial and parallel using StorageBin for uz, sz, and phreeqc cb5ccd55 Works with szBin on serial and parallel. a372f9a8 Simplified mix with add(int, factor) method 88e3ff60 Initialize default NumKeyword n_user = 1. 8c747cbb Almost working on unsaturated zone serial version. b3028f79 Roughed in some printing for debugging phast c41fb4e5 phastpp works on linear_ic in debug mode. 574da9a1 Working on phast driver to use classes for main storage 3261c998 Added class SolutionIsotopeList 957551d0 Updates e2b5a470 Dump_raw for storage bin works, but have not tested. bc119814 Adding StorageBin 90a787e4 Changed name to ISolutionComp. 2fe8f7d4 Working on saving state. c42d9855 Moved Isotope to SolutionIsotope 39494b02 Renamed SolutionComp to ISolutionComp because it is not used in cxxSolution. 75b28d81 Moved Conc to SolutionComp 0d1acff7 removed classes and headers that are in phreeqc directory. 3da5643a Makefile is working. dff0e345 House cleaning for phreeqcpp 60a15440 Copying new classes (cxx) and cpp files to src git-subtree-dir: src git-subtree-split: f715edb5897985acf0692d2b0bde4ab34379469f	2021-10-30 22:54:22 +00:00
David L Parkhurst	6c199ffc46	len=l for callback fortran string. ... Made basic callback string a "const" in 8 places. git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@9463 1feff8c3-07ed-0310-ac33-dd36852eb9cd	2015-04-02 22:59:33 +00:00
David L Parkhurst	81d91ff357	length argument needed for callback. ... git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@9435 1feff8c3-07ed-0310-ac33-dd36852eb9cd	2015-03-30 18:38:56 +00:00
David L Parkhurst	b66d8cf775	Working on IPhreeqc Basic callback. Compiles with ISO_C_BINDING, but may need some more debugging. ... Need to merge this change with PhreeqcRM-trunk. git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@9424 1feff8c3-07ed-0310-ac33-dd36852eb9cd	2015-03-27 22:03:36 +00:00
Scott R Charlton	f1dcd36005	working on fortran/test integration ... git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@9360 1feff8c3-07ed-0310-ac33-dd36852eb9cd	2015-03-14 01:17:56 +00:00
David L Parkhurst	6c002b22d8	removed FC_FUNC from IPhreeqc_interface_F.h, fixed padfstring to use int sofar ... git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@9357 1feff8c3-07ed-0310-ac33-dd36852eb9cd	2015-03-13 18:34:10 +00:00
David L Parkhurst	548bf128e2	Made IPhreeqc a Fortran module when IPHREEQC_MODULE is defined. ... fwrap routines are used if IPHREEQC_MODULE is not defined. If IPHREEQC_MODULE is defined, then IPhreeqc_interface.F90 defines the Fortran Module. compile it with the user Fortran code. IPhreeqc_interface_F.cpp is a modification of fwrap.cpp, which the Fortran Module functions call. IPhreeqc_interface_F.h is a modification of fwrap.h used only by IPhreeqc_interface_F.cpp. git-svn-id: svn://136.177.114.72/svn_GW/IPhreeqc/trunk@9347 1feff8c3-07ed-0310-ac33-dd36852eb9cd	2015-03-11 16:18:41 +00:00