Diffusion SpecMiCP / ReactMiCP (adim) History

History
adim736804e888631ea9c867dca…

Nov 13 2014

add options to reset the options in Options handler
736804e88863
·fabien on Nov 13 2014, 00:48.
correct boost include dir varaibles in CMakelist.txt
8d8999e139be
·fabien on Nov 13 2014, 00:47.
Add PerformanceHandler on the model of OptionsHandler
a4f20df9b49f
·fabien on Nov 13 2014, 00:46.
rename file containing the reactive transport solver options
25b4a7a686ca
·fabien on Nov 13 2014, 00:45.

Nov 11 2014

update examples for reactmicp
5246c20b3234
·fabien on Nov 11 2014, 22:04.
improve reactmicp
e1f224c238f0
·fabien on Nov 11 2014, 22:04.
improve kinetic system
86887f7bc2f2
·fabien on Nov 11 2014, 22:03.
add computation of total concentrations in equilibrium data
05109a387e26
·fabien on Nov 11 2014, 22:02.
correct strang linesearch
89ad784609cf
·fabien on Nov 11 2014, 22:01.
update cemdata database for new version of jsoncpp
d36d2c5a0a89
·fabien on Nov 11 2014, 22:00.
update database reader to use the 3d party jsoncpp lib
71533d2f738a
·fabien on Nov 11 2014, 21:59.
Update Cmakelist, easier to compile in ohter system (i.e. denali)
2763d88b9342
·fabien on Nov 11 2014, 21:58.

Nov 7 2014

add kinetic solver - to be improved
bc9b1984b554
·fabien on Nov 7 2014, 19:07.
update/improve Runge-Kutta solver
76335401d226
·fabien on Nov 7 2014, 19:06.
options to enable/disable nonmonotone linesearch
f6de050d917e
·fabien on Nov 7 2014, 18:59.
add base class to handle options
d6ddcf0a9bd2
·fabien on Nov 7 2014, 18:58.

Oct 28 2014

start implementing kinetics solver
2f65d5a63c08
·fabien on Oct 28 2014, 20:44.
clean ode integrator
250e37bca411
·fabien on Oct 28 2014, 15:28.

Oct 26 2014

update cython interface to use the licit charge conservation equation
0b9e18fb7d56
·fabien on Oct 26 2014, 19:45.
add explicit charge conservation in ReducedSystem
bbb049d91863
·fabien on Oct 26 2014, 19:16.
undef INFO macro, specmicp logger's INFO is the correct one, not the one by…
29fe36a29e5a
·fabien on Oct 26 2014, 00:32.
move and try improving sparse solver tools
b86528d727b5
·fabien on Oct 26 2014, 00:03.

Oct 25 2014

add reactive transport neutrality solver, and update transport program and the…
6d08d8744732
·fabien on Oct 25 2014, 22:31.
add transport_parameters_base, to share porosity and have only one variables
745d2292fc54
·fabien on Oct 25 2014, 22:29.
set update check to be at machine epsilon in secondary variables computation
8ce74ad5e3d5
·fabien on Oct 25 2014, 22:24.
improve drivers
849e20a62100
·fabien on Oct 25 2014, 22:22.

Oct 22 2014

correct equilibrium_date (int -> index_t)
7135b65ac516
·fabien on Oct 22 2014, 17:43.
update program, coupler tests and examples to use new features of dfpm solver
6c35d421db39
·fabien on Oct 22 2014, 17:41.
better scaling and velocity handling
a2c41c6968cc
·fabien on Oct 22 2014, 17:39.

Oct 21 2014

lots of small corrections
7009d71a1296
·fabien on Oct 21 2014, 21:38.
modify jacobian computation in electroneutrality program
0e24a03b71fa
·fabien on Oct 21 2014, 21:35.
add scaling to dfpmsolver
6bc8e317a3ae
·fabien on Oct 21 2014, 21:33.

Oct 20 2014

add electroneutrality transport program
ab2944bc8002
·fabien on Oct 20 2014, 23:03.
add minimal support for quasi Newton iterations in parabolic solver
dd35febf8e48
·fabien on Oct 20 2014, 22:54.
add strang linesearch into parabolic driver
e64992a2bc6c
·fabien on Oct 20 2014, 16:28.

Oct 15 2014

start work on a the transport oslver with neutrality
e882181496b7
·fabien on Oct 15 2014, 23:16.

Oct 10 2014

adapt reduce_system_Solver to allow minerals that can't dissolve
f42f76860daf
·fabien on Oct 10 2014, 20:07.
add support for not dissolving/not precipitating minerals in database
4607780abc35
·fabien on Oct 10 2014, 19:51.

Oct 9 2014

reduce header dependancy
9ac10ec69a99
·fabien on Oct 9 2014, 04:39.
add again the contribution of the descent step direction, change dection of…
e72e464ed90b
·fabien on Oct 9 2014, 03:31.
use typedef
69f1f340a8f5
·fabien on Oct 9 2014, 02:43.

Oct 8 2014

add example directory
da3d68efcce0
·fabien on Oct 8 2014, 22:06.
correct name of reactmicp test folder to tests/reactmicp
afebadac83de
·fabien on Oct 8 2014, 20:21.
add axissymmetric mesh 1d, one file per mesh, add reactmicp/mesh.hpp
a3fe40ba7210
·fabien on Oct 8 2014, 20:19.
correct type in safeguard
d7e3744afdfe
·fabien on Oct 8 2014, 16:57.
Prepare mesh module for asymmetric mesh
a82ae4d34189
·fabien on Oct 8 2014, 16:57.
add transport options into reactive transport options
dbcf1c3de1b8
·fabien on Oct 8 2014, 16:45.
detect linesearch failure in MiCPSolver, which allow restart in…
e5216c0292f7
·fabien on Oct 8 2014, 16:34.

Oct 6 2014

delete previous files added by mistake
a70d03795fe6
·fabien on Oct 6 2014, 21:17.
Merge branch 'reactivetransport' of bitbucket.org:fabieng/specmicp into…
48eb4f5d4263
·fabien on Oct 6 2014, 21:14.
update database, micpsolver and specmicp to use common.hpp
c7ac0a493911
·fabien on Oct 6 2014, 21:13.
update database, micpsolver and specmicp to use common.hpp
032d87790f74
·fabien on Oct 6 2014, 21:11.
modify reactmicp and dfpmsolver to use common.hpp
c46a22fd727b
·fabien on Oct 6 2014, 19:19.
modify equilibrium data so it uses the new common.hpp
a04acf96600a
·fabien on Oct 6 2014, 15:31.
add common.hpp, modify database module to use it
eb7779e20fdf
·fabien on Oct 6 2014, 15:30.

Oct 3 2014

add cmakefile in directory test
191d56f41074
·fabien on Oct 3 2014, 16:28.
remove unecessary files
e5484eae1665
·fabien on Oct 3 2014, 00:36.
improve fixed-point iteration solver
1461da1319e9
·fabien on Oct 3 2014, 00:30.

Oct 1 2014

SIA reactive transport start to work
83e1af765087
·fabien on Oct 1 2014, 19:37.
add scaling method in EquilibriumState
f0bae6f199e0
·fabien on Oct 1 2014, 19:34.
add method to compute residuals from outside, and adjust logging message
48743d675901
·fabien on Oct 1 2014, 19:33.

Sep 28 2014

start working on BCs and ther applications
49aeec52193c
·fabien on Sep 28 2014, 23:38.
update and coupling utils in SIASaturatedVariables
a68894083238
·fabien on Sep 28 2014, 20:16.

Sep 26 2014

add residuals and update norms in performance for parabolic solver
eebb86eba7d7
·fabien on Sep 26 2014, 19:40.
add residual and update norm in performance for micpsolver
35e7d8aacfae
·fabien on Sep 26 2014, 19:39.
allow the non-conservation of water in reaction_path/reduce_system
6110aa030886
·fabien on Sep 26 2014, 16:44.
dfpmsolver, and saturated_diffusion program can be solved
8342bd67907c
·fabien on Sep 26 2014, 02:27.

Sep 25 2014

start working on SIA solver
b5fde6377526
·fabien on Sep 25 2014, 05:00.
reactive transport - fully implicit ... does not work
f1c39bf54729
·fabien on Sep 25 2014, 01:31.

Sep 24 2014

towards a correct code ?
90597818e3ba
·fabien on Sep 24 2014, 15:23.

Sep 21 2014

it works \o/
68b7dab0dd3d
·fabien on Sep 21 2014, 21:01.
add a few methods to EquilibriumState
26456e9e2cd2
·fabien on Sep 21 2014, 21:00.
Correct bug in ionic strength computation in Reducedsystem
8a4ab92c89b3
·fabien on Sep 21 2014, 20:54.

Sep 11 2014

MiCPParabolicSolver runs, does not solve anything
8659642b7a98
·fabien on Sep 11 2014, 22:49.

Sep 10 2014

correction of bugs due to merging, also use new database range_* function in…
141e6db490b4
·fabien on Sep 10 2014, 03:54.
Merge branch 'reactivetransport'
fe4a3c6ffe37
·fabien on Sep 10 2014, 03:39.
remove thermodata.hpp, use DataContainer in reduced solver
8d16e3a0c811
·fabien on Sep 10 2014, 03:35.
add the main diffusion system
d01a0c53637d
·fabien on Sep 10 2014, 02:12.
introducing DiffusionSecondary for activity coefficient and concentration of…
f1b23f04d9ad
·fabien on Sep 10 2014, 02:12.
move and improve equation numbering for diffusion reactive transport system
e0f20360e06e
·fabien on Sep 10 2014, 02:12.
jacobian and residuals computation - not tested
43a8958938af
·fabien on Sep 10 2014, 02:12.
add range support in database::DataContainer
4873112352b5
·fabien on Sep 10 2014, 02:12.
bug correction for diffusion system
54f4e1c465c9
·fabien on Sep 10 2014, 02:12.
first commit on branch reactivetransport
b1dec92efd3e
·fabien on Sep 10 2014, 02:12.

Sep 9 2014

improving the CMake file to compile the python interface
f19180e3b265
·fabien on Sep 9 2014, 21:26.
thermocarbo.py is running ok
f401e32a96d2
·fabien on Sep 9 2014, 20:54.
The python interface is able to solve the first step of thermocarbo
f89b95873e65
·fabien on Sep 9 2014, 17:25.
use shared_ptr instead of raw ptr in database module
5ece8356c796
·fabien on Sep 9 2014, 16:06.
Wrapper for ReducedSystemSolverOptions
ba25334b0c65
·fabien on Sep 9 2014, 05:04.
complete ReactionPathSimulation
5d8bdeedf9e7
·fabien on Sep 9 2014, 00:14.

Sep 8 2014

Starting the work on the reaction path solver
5d71ccc1da23
·fabien on Sep 8 2014, 23:29.
comments and documentation
3dbb26cb459b
·fabien on Sep 8 2014, 21:28.
create module specmicp and add unit tests
41ba8a2a83cb
·fabien on Sep 8 2014, 21:05.
swapping components and removing minerals is now possible in python
84dc444f1a49
·fabien on Sep 8 2014, 19:10.

Sep 7 2014

first commit to cython branch, start interface for database
cc762abbb0d9
·fabien on Sep 7 2014, 05:20.

Sep 5 2014

improve thermocarbo and carboalu test
02c100013be0
·fabien on Sep 5 2014, 19:26.
reintroduce the old solver, for a ~working min solver
54f50e62ff4b
·fabien on Sep 5 2014, 19:25.
check if mineral species contribute to total concentration
b9fd53649f8f
·fabien on Sep 5 2014, 19:20.
try helping convergence of min-FB linesearch algorithm - does not work
bcbf5078d653
·fabien on Sep 5 2014, 19:18.
correction of C3S,C2S dissolution
8da8a817bca6
·fabien on Sep 5 2014, 19:17.

Historyadim736804e888631ea9c867dca…

Nov 13 2014

Nov 11 2014

Nov 7 2014

Oct 28 2014

Oct 26 2014

Oct 25 2014

Oct 22 2014

Oct 21 2014

Oct 20 2014

Oct 15 2014

Oct 10 2014

Oct 9 2014

Oct 8 2014

Oct 6 2014

Oct 3 2014

Oct 1 2014

Sep 28 2014

Sep 26 2014

Sep 25 2014

Sep 24 2014

Sep 21 2014

Sep 11 2014

Sep 10 2014

Sep 9 2014

Sep 8 2014

Sep 7 2014

Sep 5 2014

History
adim736804e888631ea9c867dca…