Diffusion SpecMiCP / ReactMiCP (yaml/safe) History

safe4dbbf9cd6a1963ffb05dcca…

Dec 19 2015

impr: fix compilation warning (gcc and clang)
61a1e89e1271
·fabien on Dec 19 2015, 21:11.

Dec 16 2015

doc: remove lots of warning in doc generation
9d4326f47013
·fabien on Dec 16 2015, 17:49.

Nov 25 2015

fix: fix hdf5 cmake include dirs/definitions, yes again...
f77af9a60aa4
·fabieng on Nov 25 2015, 05:24.
fix: fix include dir hdf5 (second)
82934be6a211
·fabien on Nov 25 2015, 04:26.
fix: correct include directories for HDF5
6c0ef321bcf9
·fabien on Nov 25 2015, 04:11.

Nov 15 2015

fix: export symbols of hdf5 functions
307c69a60f2b
·fabien on Nov 15 2015, 22:36.
fix: consistent API, name is before section in save_*() in HDF5 format
7d858caaf955
·fabien on Nov 15 2015, 21:43.
Fix : HDF5 : Hide implementation symbols
9f2a62399b3d
·fabien on Nov 15 2015, 21:43.
feat: save adimensional system solution in hdf5
28a4bc161e9f
·fabien on Nov 15 2015, 21:43.

Nov 11 2015

impr: AdimensionalExtractor can now return a copy of the solution
f0a961c3d86d
·fabien on Nov 11 2015, 21:54.

Sep 29 2015

refactor: separe residual water in 2 functions
8eea5f44bc3c
·fabien on Sep 29 2015, 18:08.
fix: re-compute gas scaling factor
bc2979556f46
·fabien on Sep 29 2015, 18:08.
refactor: rename saturation_ -> volume_fraction_ in AdimensionalSystem
fcd797321b23
·fabien on Sep 29 2015, 18:08.
refactor: remove AdimensionalSystem header inclusion in solver
4e562635f94b
·fabien on Sep 29 2015, 16:16.
fix: correct functions for volume fraction gas
4f8c2e8a5fc2
·fabien on Sep 29 2015, 16:16.
feature: add water pressure model in specmicp
4bb92b2d2b3f
·fabien on Sep 29 2015, 16:16.

Sep 26 2015

impr: padding in adimensional_system_solution
e1d44a9d9d81
·fabien on Sep 26 2015, 23:53.

Sep 14 2015

refactor: hide default options of AdimensinalSystemOptions
24ef8eadfa0f
·fabien on Sep 14 2015, 23:30.
refactor: adim default options are now in config_*.h file
f0fd4a5cd0ff
·fabien on Sep 14 2015, 23:04.
refactor: move configuration solution output in config_<> file
8f3676bf7899
·fabien on Sep 14 2015, 22:11.
output: add comment in solution files of SpecMiCP
3fe35fdcbd16
·fabien on Sep 14 2015, 21:55.

Sep 9 2015

fix: correct initialisation of variables in AdimensionalSolver
390c23c8aaee
·fabien on Sep 9 2015, 21:35.
fix: correct parsing of a fix fugacity constraint
e8d5bb01032b
·fabien on Sep 9 2015, 21:34.

Aug 11 2015

impr: abort solution parsing if metadata are not correct
db7f20a8c8a1
·fabien on Aug 11 2015, 20:55.
cosmetic: remove old code in comment
f75db11b41df
·fabien on Aug 11 2015, 20:54.

Jul 20 2015

fix: correct assertions in adimensional system numbering
1c251fa879ac
·fabien on Jul 20 2015, 23:00.

Jul 17 2015

fix: Correct saturation index sum
5d8f161fb9ba
·fabien on Jul 17 2015, 19:34.

Jul 13 2015

fix: modificator.set_minerals_kinetic
cee2d2898673
·fabien on Jul 13 2015, 20:56.

Jun 25 2015

Use the new format class info in output.
7d9e3901a22c
·fabien on Jun 25 2015, 19:24.

Jun 22 2015

Modify signature of AdimensionalSystemSolver constructors
1212aabdfff4
·fabien on Jun 22 2015, 20:58.
Remove print statement
84f2ee511d2e
·fabien on Jun 22 2015, 20:55.
Add a function to print the constraints
0a4a5f442443
·fabien on Jun 22 2015, 20:30.
Fix bug in SpecMiCP configuration
a01084ae1afa
·fabien on Jun 22 2015, 20:26.

Jun 19 2015

Do not remove H[+]/HO[-] when dissolving system
28fbffc41fa8
·fabien on Jun 19 2015, 23:06.

Jun 10 2015

Correct includes in io files
7fee7928fda3
·fabien on Jun 10 2015, 16:21.
Fix, minor improvements in SpecMiCP module
1d81493e610c
·fabien on Jun 10 2015, 16:20.

Jun 9 2015

Documentation
f9d6ee556023
·fabien on Jun 9 2015, 14:44.
Move AdimensionalSystemSolverSaver to YAML formatting
f28c1c458a8b
·fabien on Jun 9 2015, 05:53.

Jun 8 2015

Update configurations to use the new updates in YAML module
35f1ce4a8720
·fabien on Jun 8 2015, 19:44.

Jun 5 2015

Add more constraints configuration
e809292d7440
·branch: configuration
·fabien on Jun 5 2015, 16:47.
Start implementing constraints configuration in SpecMiCP
88a299bc1607
·fabien on Jun 5 2015, 04:15.
Add Configuration for formulation
7178ca623984
·fabien on Jun 5 2015, 03:38.

Jun 2 2015

Modify molar_mass_<species> in DataContainer
7d1722d5bb0f
·fabien on Jun 2 2015, 16:30.

May 29 2015

Add an option to not modify the database in the dissolver
202e336d65a6
·fabien on May 29 2015, 05:01.

May 28 2015

Use the compounds in the dissolver
fd28a36ed4a4
·fabien on May 28 2015, 22:57.

May 18 2015

Add lto flags
a4fe4c3a589a
·fabien on May 18 2015, 00:39.

May 13 2015

Namespace documentation
ef44ef6723d3
·fabien on May 13 2015, 15:36.
Use macro to define default options for SpecMiCP
8b7823715ed7
·fabien on May 13 2015, 01:02.

May 5 2015

I forgot the secondary aqueous species in the solution saver....
bdda0cd099d0
·fabien on May 5 2015, 15:00.

May 3 2015

Add the specmicp_common library
ff0d0fbcfe7b
·fabien on May 3 2015, 22:19.

May 1 2015

Corret symbol export in serializer
7e7e298a6160
·fabien on May 1 2015, 00:15.
Add a serializer for AdimensionalSystemSolution
583eb2cd10a4
·fabien on May 1 2015, 00:09.

Apr 30 2015

Minor fixes/documentation in Specmicp
8dd3dcc176c6
·fabien on Apr 30 2015, 04:03.
Add a fixed molality constraints in AdimensionalSystem
eee5a564c204
·fabien on Apr 30 2015, 00:29.

Apr 28 2015

CmakeLists fixes/enhancements
3d80bf60e333
·fabien on Apr 28 2015, 16:19.
Set the visibility flags for the Specmicp library
7df477fd05e4
·fabien on Apr 28 2015, 04:53.
Fixes to compile with Clang (3.6.0)
9c9d231a7dfd
·fabien on Apr 28 2015, 01:27.

Apr 27 2015

Fixes suggested by Cppcheck
da87eb82fc39
·fabien on Apr 27 2015, 22:41.

Apr 23 2015

Fixes minor problems found with the new SANITIZER build type
ecc68045c31e
·fabien on Apr 23 2015, 05:34.
Use small step by default in AdimensionalSystemSolver
9f4ca7e6c456
·fabien on Apr 23 2015, 00:23.

Apr 22 2015

Minor fixes in Cmake files
40a28cb7668f
·fabien on Apr 22 2015, 01:49.

Apr 21 2015

correct inclusion of headers
4dde22e2e8fc
·fabien on Apr 21 2015, 21:58.
Proper installation of cython/databases/doc
d05c342d7b8f
·fabien on Apr 21 2015, 17:23.
finally, SpecMiCP/ReactMiCP can be installed
367d9d550e9d
·fabien on Apr 21 2015, 05:24.

Apr 20 2015

Deprecate the total_saturation_{mineral,water}
9cc89d2d9dc1
·fabien on Apr 20 2015, 03:10.

Apr 16 2015

Morning doc welcomes duck
d204ff482220
·fabien on Apr 16 2015, 15:15.
Documentation
d242af75fe48
·fabien on Apr 16 2015, 05:32.

Apr 15 2015

License update before release
b174f1ddf352
·tag: 0.0.3
·fabien on Apr 15 2015, 22:11.

Apr 12 2015

Improve consistency of function naming
d4be19a55956
·fabien on Apr 12 2015, 22:40.

Apr 11 2015

Minor fixes in the c++ SpecMiCP API
a5a9ab80bdf3
·fabien on Apr 11 2015, 22:29.

Apr 10 2015

Solution can return the vector of main solution
698bdbf6176e
·fabien on Apr 10 2015, 03:59.

Apr 8 2015

Add helper meber functions
824f90062e79
·fabien on Apr 8 2015, 15:31.

Apr 2 2015

Update licence
ed9f62bffad3
·fabien on Apr 2 2015, 02:56.

Apr 1 2015

Add the ability to solve oxydoreduction system
ea534669b0e6
·fabien on Apr 1 2015, 23:05.

Mar 31 2015

Refactor residual and jacobian in specmicp
8d287d0302ef
·fabien on Mar 31 2015, 16:00.

Mar 27 2015

fixes commit 0174eeb
665b1c9415f6
·fabien on Mar 27 2015, 16:10.

Mar 26 2015

Small optimization, avoid checking and scaling the molar volumes too many times…
0174eeb1cf69
·fabien on Mar 26 2015, 18:43.
Intern refactoring of AdimensionalSystem
33d3d8b8a771
·fabien on Mar 26 2015, 15:30.

Mar 25 2015

Disable bulk copy of variables for now - to fix
fa87e6334e88
·fabien on Mar 25 2015, 20:38.
Update the adimensional system for the new database module
c6b716588c1d
·fabien on Mar 25 2015, 14:45.

Mar 24 2015

Remove the ReducedSystem
7f9de8ece968
·fabien on Mar 24 2015, 19:04.

Mar 17 2015

add a convenience function in specmicp adimensional solver to solve a system
f952caf0c318
·fabien on Mar 17 2015, 15:46.

Mar 13 2015

Update headers in the src/specmicp/adimensional files
e94e903fe893
·fabien on Mar 13 2015, 04:22.
Disable the descent condition in the AdimensionalSystemSolver.
8e74befa1920
·fabien on Mar 13 2015, 04:21.
Add a return value (boolean) in the AdimensionalSystemPCFM::check_validity
5e764b31a7c6
·fabien on Mar 13 2015, 04:18.
Add a threshold for including the component in the computation in…
f5f97272d811
·fabien on Mar 13 2015, 02:53.

Feb 28 2015

Randomize the restarting guess in AdimensionalSystem.
9cf41f6dfb45
·fabien on Feb 28 2015, 23:31.

Feb 27 2015

Add a validity check (just print warning and or error for the PCFM method…
bddaf0d936da
·fabien on Feb 27 2015, 16:02.

Feb 25 2015

Correct the AdimensionalSystem jacobian, fixes issue #29
0b1682bb59f9
·fabien on Feb 25 2015, 23:46.
Correct the surface model, so the activity are defined with respect to the…
ac9b4eb735f4
·fabien on Feb 25 2015, 14:53.

Feb 24 2015

Correct porosity computation, minerals offset
a4055a6a6783
·fabien on Feb 24 2015, 16:07.

Feb 23 2015

Improve AdimensionalSystemSolver, initialisation of pcfm solver, debug messages…
d76c3f21bd38
·fabien on Feb 23 2015, 20:17.
Correct jacobian computation (both analytical and finite difference) in…
8b5357988ba5
·fabien on Feb 23 2015, 20:17.
Improve initialisation of surface model in AdimensionalSystemConstraints
d39cf3d5d38a
·fabien on Feb 23 2015, 04:18.
AdimensionalSystemSolver variable initalization : change…
59f0bfff78d5
·fabien on Feb 23 2015, 04:13.
documentation fixes for AdimensionalSystemNumbering
69652eb35705
·fabien on Feb 23 2015, 04:10.
Add a function in AdimensionalSystem that return the surface sorption model
4338212826c9
·fabien on Feb 23 2015, 04:09.

Feb 17 2015

include the pcfm method to the AdimensionalSystemSolver
2d49c2d3302a
·fabien on Feb 17 2015, 04:45.
Add AdimensionalSystemPCFM, a class to precondition an aqeous solver using the…
c7608a0ce239
·fabien on Feb 17 2015, 04:44.
Documentation for AdimensionalSystem
8ecff9b7f967
·fabien on Feb 17 2015, 04:42.

specmicp/src/specmicpyaml/safe4dbbf9cd6a1963ffb05dcca…

Dec 19 2015

Dec 16 2015

Nov 25 2015

Nov 15 2015

Nov 11 2015

Sep 29 2015

Sep 26 2015

Sep 14 2015

Sep 9 2015

Aug 11 2015

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Jul 17 2015

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Jun 25 2015

Jun 22 2015

Jun 19 2015

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May 1 2015

Apr 30 2015

Apr 28 2015

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Apr 23 2015

Apr 22 2015

Apr 21 2015

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Apr 16 2015

Apr 15 2015

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Apr 1 2015

Mar 31 2015

Mar 27 2015

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Mar 24 2015

Mar 17 2015

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Feb 28 2015

Feb 27 2015

Feb 25 2015

Feb 24 2015

Feb 23 2015

Feb 17 2015

specmicp/src/specmicp
yaml/safe4dbbf9cd6a1963ffb05dcca…