Diffusion SpecMiCP / ReactMiCP (cython) History

specmicp/src
cythonaa478c67960bf48c1051bb6…

Feb 23 2015

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 22 2015

Add a memebr to the meshes to obtain the position of a node
fc5372845077
·fabien on Feb 22 2015, 22:27.
Add two functions in DatabaseSelector : - Remove all minerals in the…
dd2b91d3795d
·fabien on Feb 22 2015, 22:18.

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.

Feb 16 2015

add a check in database reader to ensure the the number of sites occupied by a…
5546ccd49e01
·fabien on Feb 16 2015, 18:28.
add numbering of secodnary species and activity coefficients in…
08d31233017d
·fabien on Feb 16 2015, 16:10.
Add functions for custom initialisation of the main variables
2e391aab5671
·fabien on Feb 16 2015, 15:57.
reuse already defined function to compute the total solid concentration of a…
78836305e4b0
·fabien on Feb 16 2015, 15:56.
Use the new AdimensionalSystemNumbering Base clase in the…
680ccde7e3f4
·fabien on Feb 16 2015, 15:52.
externalize the dof numberign of the AdimensionalSystem, so it can be used by…
31d88c30dde8
·fabien on Feb 16 2015, 15:46.
The main variable for the free surface concentration is now a the log_10 of the…
5e7f42ca25c3
·fabien on Feb 16 2015, 15:18.
Modify debug information messages so they also give the expected value
422798ba5085
·fabien on Feb 16 2015, 15:16.

Feb 13 2015

Modify sorped species calculation, add a specific equation. Free sorption sites…
987ce3089fb7
·fabien on Feb 13 2015, 16:18.
Free sorption sites is no longer a component
a8c4203fea6b
·fabien on Feb 13 2015, 16:13.

Feb 11 2015

improve AdimKinetic(Euler)Solver, choose DormandPrince as the ODE integrator
26182c883bf1
·fabien on Feb 11 2015, 14:37.

Feb 10 2015

small corrections for the adimensional system with the new sorbed species
8ec8f50ef0fa
·fabien on Feb 10 2015, 21:01.
modification in units::convert_pressure to avoir compiler warning
7ac65cc8ee32
·fabien on Feb 10 2015, 20:53.
add support for sorbed species in AdmiensionalSystem
1af9208c7a4c
·fabien on Feb 10 2015, 17:11.
correct jacobian for the water equation in AdimensionalSystem, fixes issue #25
513ba6bd0ef3
·fabien on Feb 10 2015, 17:09.
add support for sorped species in the database
298190351669
·fabien on Feb 10 2015, 15:22.
small enhancements of specmicp
9290bd437d11
·fabien on Feb 10 2015, 03:12.
add a boolean to check that the solution has been initialized
835f7071e071
·fabien on Feb 10 2015, 03:08.
allow custom initialisation
c0917faf9b6a
·fabien on Feb 10 2015, 03:06.
add kinetics solver for the AdimensionalSystem (issue #15), TO TEST
a388607362fe
·fabien on Feb 10 2015, 02:18.

Feb 6 2015

remove unused struct from saturated_react
a0d7a916d1a1
·fabien on Feb 6 2015, 20:45.
correct AdimensionalSystemSolutionExtractor::log_molality_component for water
47a6cfb7136d
·fabien on Feb 6 2015, 14:28.

Feb 5 2015

add a generic Axisymmetric 1D mesh class, in process of resolving issue #13
113faa16267a
·fabien on Feb 5 2015, 21:11.

Feb 3 2015

correct typo in residual water in AdimensionalSystem, fixes bug #20
cd36fb74436f
·fabien on Feb 3 2015, 21:47.
add scaling for the AdimensionalSystem, fixes issue #23
86c34c364f68
·fabien on Feb 3 2015, 17:39.
correct pressure contribution in specmicp, fixes issue #24
50b53a239634
·fabien on Feb 3 2015, 17:35.

Jan 20 2015

Correct complaints of valgrind-memcheck abount non-initialized values
c0560e3c1407
·fabien on Jan 20 2015, 22:56.
fixes issue #19, The desctructor of SparseSolverBase was not virtual
f494edc15db3
·fabien on Jan 20 2015, 22:06.
fixes bug introduced by commit 64b3616, get_performance was removed from…
29b3278d5651
·fabien on Jan 20 2015, 20:07.
Documentation for the adimensionalsystem and associates
056dfbdf23b9
·fabien on Jan 20 2015, 19:34.
documentation and test for the MiCP solver
64b3616eea48
·fabien on Jan 20 2015, 16:37.
Update/improve documentation for the reactmicp::solver namespace and its members
ecc0663ea7ef
·fabien on Jan 20 2015, 15:46.

Jan 19 2015

issue #8, all tests compiles
a4ba90c69915
·fabien on Jan 19 2015, 17:22.
Documentation for specmicp::AdimensionalSystem
19d5b16cc3f1
·fabien on Jan 19 2015, 16:44.

Jan 18 2015

include <iostream> for the GMRES solver,m issue #17
14f16a9d1764
·fabien on Jan 18 2015, 00:04.

Jan 17 2015

update dfpmsolver::ParabolicDriver to use the new SparseSolvers of commit…
ef2d31ec34ae
·fabien on Jan 17 2015, 22:35.
modify the sparse solver module to resolve issue #11
a247fbc100c4
·fabien on Jan 17 2015, 22:34.

Jan 16 2015

documentation
b2bda1a419fd
·fabien on Jan 16 2015, 18:50.
Remove the one step reactive transport system - don't work, don't compile
b9a808db21fb
·branch: fixpoint
·fabien on Jan 16 2015, 16:38.
Do not update variables if EquilibriumSolver has not converged
9fc5d580b72b
·fabien on Jan 16 2015, 16:18.

Jan 15 2015

Prepare AdimensionalSystem environment for kinetics
c99feaa01903
·fabien on Jan 15 2015, 22:18.
add member function in database::Database to keep only certain minerals (given…
c4a87185190b
·fabien on Jan 15 2015, 22:15.
Restart values for the concentration in AdimensionalSystem is now an…
a3c945176de8
·fabien on Jan 15 2015, 19:16.

Jan 14 2015

Improvements/bug correction in the saturated react system
d4ae324ea89d
·fabien on Jan 14 2015, 00:26.
Add AdimensionalSystemSolutionModificator, to modify (scaling, removing solid…
26ecea65a83b
·fabien on Jan 14 2015, 00:18.

Jan 12 2015

add more test for saturated_react system, correct bugs
0bedb6497e35
·fabien on Jan 12 2015, 22:52.
Minor\ corrections in SaturatedReact systems
1d57790e5b76
·fabien on Jan 12 2015, 20:53.
A return code was missing in ReactiveTransportSolver::solve_one_iteration
55b82d2b1e21
·fabien on Jan 12 2015, 20:52.
use correct mmember functions in assert in AdimensionalSystem
cefbc702655c
·fabien on Jan 12 2015, 20:49.
Set the return code to the correct value if linesearch has failed in MiCPsolver
87604b01bf0d
·fabien on Jan 12 2015, 20:47.
Start the work on the new SaturatedDiffusion systems for the new reactive…
3c484d96fa9b
·fabien on Jan 12 2015, 17:05.
Correct typo in reactmicp::solver::StaggerReturnCode
edab8e64cbc6
·fabien on Jan 12 2015, 15:21.

Jan 10 2015

improve reactive transport solver
17ac62383dd7
·fabien on Jan 10 2015, 02:29.

Jan 9 2015

Improve reactive transport solver
6f21451dd340
·fabien on Jan 9 2015, 22:05.
add foundations of the flexible reactive transport solver
a19ce13e1a11
·fabien on Jan 9 2015, 17:45.

Dec 19 2014

update reactmicp/equilibrium_curve to agree with commit 030defd, rename BC to…
1bd7817be013
·fabien on Dec 19 2014, 21:29.
rename BC to constraints in AdimensionalSystem
030defdf3929
·fabien on Dec 19 2014, 20:04.
do not copy the solution in the solution extractor
681e327723b8
·fabien on Dec 19 2014, 19:31.

Dec 16 2014

use previous flux in reactive transport - do not work
6dd908c529b8
·fabien on Dec 16 2014, 15:15.
use correct density at 25C
2898b6821462
·fabien on Dec 16 2014, 15:10.

Dec 15 2014

improve documentation of AdimensionalSystem
6203177d8b3f
·fabien on Dec 15 2014, 19:57.
add WaterEquationType to the AdimensionalSystem
067602901bfb
·fabien on Dec 15 2014, 17:59.
improve MiCPsolver, making it possible to disable condition estimation
2c8f021cdfeb
·fabien on Dec 15 2014, 17:53.

Dec 12 2014

add coupler, extractor for equilibrium
4adc6181a531
·fabien on Dec 12 2014, 19:42.
correct size management of the array in Chemictry equilibrium curve
bde740772827
·fabien on Dec 12 2014, 19:33.
improve transport program of reactive transport
3a5d25312f42
·fabien on Dec 12 2014, 19:25.
improve 1D diffusion problem
e1c6af4f4f1b
·fabien on Dec 12 2014, 19:15.

Dec 11 2014

add member to compute volume of a cell inside an element
2c221cb0eb9a
·fabien on Dec 11 2014, 22:10.
correct includes in dfpm/types.hpp header
ad85c18048cb
·fabien on Dec 11 2014, 22:09.

Dec 9 2014

start implementation of EquilibriumCurve approad to reactive transport
f96d0f24dfe0
·fabien on Dec 9 2014, 05:15.
remove const keyword for the output member
110e0d72687e
·fabien on Dec 9 2014, 05:06.
correct coupling, update water in speciation solver to keep saturation at 1
44f3acfa1b25
·fabien on Dec 9 2014, 04:59.
start implementation of 1d diffusion
cc470b429ffa
·fabien on Dec 9 2014, 04:58.
defaults value for epsilon_jacobian in src/common.hpp
f1765f058b94
·fabien on Dec 9 2014, 04:56.
correct AdimensionalSystemSolver : now, works with 2 or more non active…
c3c6d4e7ad1c
·fabien on Dec 9 2014, 04:46.
correct AdimensionalSystemSolver : now, works with 2 or more non active…
481fe8a4b959
·fabien on Dec 9 2014, 04:40.
add member 'get_units' in units::UnitsBaseClass
2f7ca0ac5ea7
·fabien on Dec 9 2014, 04:38.

Dec 7 2014

add the dfpm module, generic finite volume module, move meshes to dfpm
511a07d7f37c
·fabien on Dec 7 2014, 20:50.

Dec 5 2014

Add EquilibriumCurve, base class to create ReactionPath model
d442c9ff39a3
·fabien on Dec 5 2014, 22:16.
add member to compute contribution to total concentration
3eec16ab89ba
·fabien on Dec 5 2014, 21:53.

Dec 3 2014

initialize gas fugacity using previous solution
49676e6dff97
·branch: adim
·fabien on Dec 3 2014, 20:34.
solve fix activity/fix fugacity problems
4492a6f8382a
·fabien on Dec 3 2014, 20:29.
add handling of fugacity in AdimensionalSystemSolution
c714d768185e
·fabien on Dec 3 2014, 20:28.
add member 'gas_label_to_id' in DatabaseModule to retrieve id of a gas
670db7099f20
·fabien on Dec 3 2014, 20:21.
Add better handling of boundary conditions, toward the inclusion of fixed…
32144b0c32f5
·fabien on Dec 3 2014, 16:59.

Dec 2 2014

More flexible struct to choose equation type for aqueous type in the…
f5fae35bcbf9
·fabien on Dec 2 2014, 23:38.
add non fixed fugacity gas
3cd1304c75d9
·fabien on Dec 2 2014, 22:42.
Add a method to remove all gases in the SelectorDatabase module
56e9b0f63246
·fabien on Dec 2 2014, 22:41.
add AdimensionalSystemOptions, like ReducedSystemOptions
0b629aa5b824
·fabien on Dec 2 2014, 19:47.
add options for enabling/disabling solution of purely aqueous problem
7cf040dc468d
·fabien on Dec 2 2014, 19:13.

Dec 1 2014

don't compute speciation if there is no more mineral
e2bd2e54f5c5
·fabien on Dec 1 2014, 17:40.

specmicp/srccythonaa478c67960bf48c1051bb6…

Feb 23 2015

Feb 22 2015

Feb 17 2015

Feb 16 2015

Feb 13 2015

Feb 11 2015

Feb 10 2015

Feb 6 2015

Feb 5 2015

Feb 3 2015

Jan 20 2015

Jan 19 2015

Jan 18 2015

Jan 17 2015

Jan 16 2015

Jan 15 2015

Jan 14 2015

Jan 12 2015

Jan 10 2015

Jan 9 2015

Dec 19 2014

Dec 16 2014

Dec 15 2014

Dec 12 2014

Dec 11 2014

Dec 9 2014

Dec 7 2014

Dec 5 2014

Dec 3 2014

Dec 2 2014

Dec 1 2014

specmicp/src
cythonaa478c67960bf48c1051bb6…