Diffusion SpecMiCP / ReactMiCP (yaml/safe) History

safe08dbc2f3e9123a3d3c40df2…

Mar 17 2015

import reactive transport timestepper
08dbc2f3e912
·fabien on Mar 17 2015, 15:38.
add more access to the starting and ending point of a timer, aslo correct const…
719661d3e345
·fabien on Mar 17 2015, 15:34.
Add and improve functions in the io library
941766fc8a67
·fabien on Mar 17 2015, 15:33.

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.
Remove the check for Total concentration too small in the reactive transport…
2ab1f72f9891
·fabien on Mar 13 2015, 04:14.
Add member functions in MiCPSolverOptions to help set the options
746e385268f2
·fabien on Mar 13 2015, 04:13.
Bypass the descent condition if the factor is negative in the MiCPsolver
136d82ff2ccb
·fabien on Mar 13 2015, 04:11.
Remove the cut-off for including a component in the total concentration; the…
d16ed536054f
·fabien on Mar 13 2015, 02:55.
Add a threshold for including the component in the computation in…
f5f97272d811
·fabien on Mar 13 2015, 02:53.

Mar 6 2015

add member function is SaturatedVariables to access main variables directly
331aa30110ba
·fabien on Mar 6 2015, 14:42.

Mar 4 2015

Minor enhancements in the Timestepper
f26e0452c13c
·fabien on Mar 4 2015, 19:47.
correct generic 1D mesh
64fa3c732f53
·fabien on Mar 4 2015, 19:44.

Mar 2 2015

Add new ReactiveTransportSolverReturnCode in the IO library
d4f8837fe33a
·fabien on Mar 2 2015, 21:30.
improve detection of problems in the ReactiveTransportSolver
5acd30632a6a
·fabien on Mar 2 2015, 21:29.
Change the message for ErrorMinimized in MiCPSolver
9873b241a642
·fabien on Mar 2 2015, 21:25.
Add a absolute tolerance test for the residuals in the parabolic driver
aa631431a161
·fabien on Mar 2 2015, 21:22.

Feb 28 2015

add more output function
f2a40262416b
·fabien on Feb 28 2015, 23:37.
Add more information about time in ReactiveTransportPerformance
abe3dbcbe88d
·fabien on Feb 28 2015, 23:36.
Add a member in SaturatedReact::Variables to reset the main variables
67e8b2d9680e
·fabien on Feb 28 2015, 23:33.
Randomize the restarting guess in AdimensionalSystem.
9cf41f6dfb45
·fabien on Feb 28 2015, 23:31.

Feb 27 2015

Add a simple io library to output data
bf7a37fc71e9
·fabien on Feb 27 2015, 17:36.
Use the new timer class in the reactive transport solver
39c9426c395d
·fabien on Feb 27 2015, 17:34.
Add a simple timer class
10ab4cafbaa0
·fabien on Feb 27 2015, 17:32.
Add a validity check (just print warning and or error for the PCFM method…
bddaf0d936da
·fabien on Feb 27 2015, 16:02.

Feb 26 2015

When possible only factorize the matrix, without analysing the pattern again…
38a97fbd2242
·fabien on Feb 26 2015, 16:21.
Separate the analysePattern and factorization part of the sparse matrix…
53237ab864d3
·fabien on Feb 26 2015, 16:10.
save the ndf in the transport program and set inline
f7c3cd7d6b9b
·fabien on Feb 26 2015, 15:21.
Add a generic 1D mesh, issue #13
339c6d31875f
·fabien on Feb 26 2015, 04:09.
add a timer in the reactive transport solver to obtain more information about…
9417b8aab783
·fabien on Feb 26 2015, 04:06.

Feb 25 2015

Correct the AdimensionalSystem jacobian, fixes issue #29
0b1682bb59f9
·fabien on Feb 25 2015, 23:46.
Add a member to update the parameter in ExponentialMovingAverage:
5cde60cd6d35
·fabien on Feb 25 2015, 22:11.
add a variadic template for custom initialization of the opn class in Option…
327e2020bb5c
·fabien on Feb 25 2015, 22:10.
obtain chemistry error in reactive transport solver, fixes issue #16
7ea49ff12a15
·fabien on Feb 25 2015, 22:07.
add an adaptative timestepper algorithm
e403516d3274
·fabien on Feb 25 2015, 22:05.
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

Use the immobile concentration instead of the solid concentration, include the…
602cfb4f2886
·fabien on Feb 23 2015, 20:17.
Add the possibility to use a different constraints for each node
6a53d7d1a970
·fabien on Feb 23 2015, 20:17.
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.
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.

specmicp/srcyaml/safe08dbc2f3e9123a3d3c40df2…

Mar 17 2015

Mar 13 2015

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Mar 2 2015

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Feb 17 2015

Feb 16 2015

Feb 13 2015

Feb 11 2015

Feb 10 2015

Feb 6 2015

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Feb 3 2015

Jan 20 2015

Jan 19 2015

Jan 18 2015

Jan 17 2015

Jan 16 2015

Jan 15 2015

specmicp/src
yaml/safe08dbc2f3e9123a3d3c40df2…