Diffusion SpecMiCP / ReactMiCP (master) History

History
master7c8016b56303ad01af31d7f…

Feb 23 2015

Do not compute speciation for a component if the total concentration is <1e-10
7c8016b56303
·fabien on Feb 23 2015, 20:17.
Solve the advection problem with the upstream scheme
912b33a4f6ec
·fabien on Feb 23 2015, 20:17.
Add the possibility to add slave nodes to the problem in saturated_react. Slave…
3013f5ef096c
·fabien on Feb 23 2015, 20:17.
Prepare the saturated_react system to solve advection problem
8c6fd9361771
·fabien on Feb 23 2015, 20:17.
Initialise the reactive transport solver Preformance struct
a162fe6f75cd
·fabien on Feb 23 2015, 20:17.
add an error message when linesearch cannot find a step bigger than the minimum…
6773a29706c7
·fabien on Feb 23 2015, 20:17.
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.
correct tests for AdimensionalSystem &co, add test for the PCFM method
aa478c67960b
·fabien on Feb 23 2015, 04:21.
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

add relevant citations in the doxygen citation.bib file
5428e191095b
·fabien on Feb 17 2015, 04:53.
add the pcfm methods in the CMakeList.txt file
7ce05df64442
·fabien on Feb 17 2015, 04:51.
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

Update test and examples of AdimensionalSystem to agree with commit 987ce30
60c8038a6ab2
·fabien on Feb 13 2015, 16:20.
Modify sorped species calculation, add a specific equation. Free sorption sites…
987ce3089fb7
·fabien on Feb 13 2015, 16:18.
update MoMas benchmark database to agree with commit a8c4203
e19767784417
·fabien on Feb 13 2015, 16:14.
Free sorption sites is no longer a component
a8c4203fea6b
·fabien on Feb 13 2015, 16:13.

Feb 11 2015

add some simple tests for AdimKinetics, will add more in the future
9a4089e18a62
·branch: kinetics
·fabien on Feb 11 2015, 15:01.
add a AdimensionalSolver examples / with kinetics
8c94dee2ed89
·fabien on Feb 11 2015, 15:00.
Add the database for the MoMas benchmark, maybe use for other test too
965036a9c569
·fabien on Feb 11 2015, 14:56.
No Ca/Al/SO2 at the boundary, seems to work much better
5b397acac2a4
·fabien on Feb 11 2015, 14:50.
reduce maximum step lenght in adim tests/to match others, remove a cycling…
f683d9d25c24
·fabien on Feb 11 2015, 14:39.
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.
start updating the cython interface
9be560f1edb0
·fabien on Feb 6 2015, 14:46.
update ex_reactmicp_leaching
9ea6b8ee2396
·fabien on Feb 6 2015, 14:32.
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 4 2015

update examples
7a9771634f6a
·fabien on Feb 4 2015, 14:16.

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

move test of ODEint solvers from the Cxxtest to the Catch framework, fixes…
78be35d16fbe
·fabien on Jan 19 2015, 19:14.
move micpsolver tests to the Catch framework, instead of the CxxTest framework
8f33b9c54fdb
·fabien on Jan 19 2015, 18:51.
issue #8, all tests compiles
a4ba90c69915
·fabien on Jan 19 2015, 17:22.
all the examples compile correctly
e10c1ed3491b
·fabien on Jan 19 2015, 16:55.
Documentation for specmicp::AdimensionalSystem
19d5b16cc3f1
·fabien on Jan 19 2015, 16:44.
issue #4, change MULTILINE_CPP_BRIEF to NO in the doxygen configuration file
070e54dc9d24
·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

Recode database test to use the Catch framework instead of CxxTest
bb1015b50ad5
·fabien on Jan 16 2015, 23:03.
Remove test for the OneStepImplicit saturated diffusion system
b7869e7de918
·fabien on Jan 16 2015, 21:37.
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.
Improve/clean cmakelist, list requirements/options in INSTALL
4bf2553e54f6
·fabien on Jan 16 2015, 16:34.
Improve leaching example for the new reactive transport solver
f22e7d5e8694
·fabien on Jan 16 2015, 16:18.
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

add Leaching example for the new system/reactive transport solver
7237ac8fa937
·fabien on Jan 14 2015, 00:27.
Improvements/bug correction in the saturated react system
d4ae324ea89d
·fabien on Jan 14 2015, 00:26.
add test equilibrium stagger in the git history / small correction in…
cd1fb73b0dac
·fabien on Jan 14 2015, 00:20.
Add AdimensionalSystemSolutionModificator, to modify (scaling, removing solid…
26ecea65a83b
·fabien on Jan 14 2015, 00:18.

Jan 12 2015

add test for the equilibrium stagger in saturated_react
a3c35a95c9f4
·fabien on Jan 12 2015, 23:45.
add more test for saturated_react system, correct bugs
0bedb6497e35
·fabien on Jan 12 2015, 22:52.
add some tests for the saturated_react systems, more to come
2408f52593d3
·fabien on Jan 12 2015, 20:55.
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

add tests for the new flexible reactive transport solver, proof of concept
092c377c7c2a
·fabien on Jan 9 2015, 22:06.
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.
modify examples
2c7e1c431676
·fabien on Jan 9 2015, 15:20.

Dec 19 2014

update reactmicp/equilibrium_curve to agree with commit 030defd, rename BC to…
1bd7817be013
·fabien on Dec 19 2014, 21:29.

Historymaster7c8016b56303ad01af31d7f…

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 4 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

History
master7c8016b56303ad01af31d7f…