Diffusion SpecMiCP / ReactMiCP (cython) History

specmicp/src
cython522d1d188e48b9155a250f3…

Mar 31 2015

Refactor residual and jacobian in specmicp
8d287d0302ef
·fabien on Mar 31 2015, 16:00.
Correct include in micpsolver.inl
4438bed8f0a6
·fabien on Mar 31 2015, 15:59.

Mar 27 2015

Small changes in micpsolver
a915d2a00af6
·fabien on Mar 27 2015, 19:02.
fixes commit 0174eeb
665b1c9415f6
·fabien on Mar 27 2015, 16:10.
Optimize the semismooth reformulation
3f78fff02e69
·fabien on Mar 27 2015, 16:04.

Mar 26 2015

Udpdate license text in database module
b264515ec25e
·fabien on Mar 26 2015, 20:31.
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 ReactMiCP for the new databse module
3240263f41a0
·fabien on Mar 25 2015, 20:22.
Minor changes/bug fixes in the database module
1cd97637d904
·fabien on Mar 25 2015, 20:20.
Small correction to allow compilation with gcc 4.8.3
ac7ea29f1b9b
·georget on Mar 25 2015, 16:18.
The timer is started when initialized
cdb78898dc90
·fabien on Mar 25 2015, 14:55.
Update the adimensional system for the new database module
c6b716588c1d
·fabien on Mar 25 2015, 14:45.
Bug fixes and minor improvements in the database module
87fc4962ea72
·fabien on Mar 25 2015, 14:38.
remove import of database::Database in src/database.hpp
3db25ff1295e
·fabien on Mar 25 2015, 14:34.
The index_t and EIGEN_DEFAULT_DENSE_INDEX_TYPE is now consistent
c2ae9df66c89
·fabien on Mar 25 2015, 14:13.

Mar 24 2015

Remove all the old code in the reactmicp folder
dfd04be5d63c
·fabien on Mar 24 2015, 19:06.
Remove the ReducedSystem
7f9de8ece968
·fabien on Mar 24 2015, 19:04.
Improves the database
c2a8ab6f9a8e
·fabien on Mar 24 2015, 18:38.

Mar 19 2015

include half-cells reaction in the database
ce7cf38633f9
·fabien on Mar 19 2015, 19:39.
improve signature of functions in the physics module
aa2cfcd016e3
·fabien on Mar 19 2015, 19:39.
Add NOEXCEPT macor, noexcept if not in debug mode
82d0adb9bd56
·fabien on Mar 19 2015, 19:39.
Improve the OpenMP section
cb15e034fead
·tag: 0.0.2
·fabien on Mar 19 2015, 19:16.

Mar 17 2015

add a convenience function in specmicp adimensional solver to solve a system
f952caf0c318
·fabien on Mar 17 2015, 15:46.
Add a runner class for the reactive transport solver
a1bb082f067b
·fabien on Mar 17 2015, 15:45.
In reactive transpor solver, return a reference to the timer instead of a copy
c9a42d8c3f55
·fabien on Mar 17 2015, 15:44.
Add the member reset_main_variables in reactmicp::solver::VariablesBase
e5adba3b79c0
·fabien on Mar 17 2015, 15:42.
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.

specmicp/srccython522d1d188e48b9155a250f3…

Mar 31 2015

Mar 27 2015

Mar 26 2015

Mar 25 2015

Mar 24 2015

Mar 19 2015

Mar 17 2015

Mar 13 2015

Mar 6 2015

Mar 4 2015

Mar 2 2015

Feb 28 2015

Feb 27 2015

Feb 26 2015

Feb 25 2015

Feb 24 2015

Feb 23 2015

Feb 22 2015

Feb 17 2015

Feb 16 2015

Feb 13 2015

Feb 11 2015

Feb 10 2015

specmicp/src
cython522d1d188e48b9155a250f3…