Diffusion SpecMiCP / ReactMiCP (master) History

specmicp/src
masterd242af75fe4834829db5cb2…

Apr 16 2015

Documentation
d242af75fe48
·fabien on Apr 16 2015, 05:32.

Apr 15 2015

License update before release
b174f1ddf352
·tag: 0.0.3
·fabien on Apr 15 2015, 22:11.
Documentation for the database/species module
94f086f45381
·fabien on Apr 15 2015, 04:29.
The hashing fn does not be to be in every list
9641dcf37708
·fabien on Apr 15 2015, 04:02.

Apr 13 2015

Continue refactoring of Database reader
cfebef7a040e
·fabien on Apr 13 2015, 04:36.
Refactor database reader
14493d59dde5
·fabien on Apr 13 2015, 00:05.

Apr 12 2015

Improve consistency of function naming
d4be19a55956
·fabien on Apr 12 2015, 22:40.

Apr 11 2015

Minor fixes in the c++ SpecMiCP API
a5a9ab80bdf3
·fabien on Apr 11 2015, 22:29.

Apr 10 2015

Add helper function to initialize the solver
9c778f32ba82
·fabien on Apr 10 2015, 05:14.
Solution can return the vector of main solution
698bdbf6176e
·fabien on Apr 10 2015, 03:59.

Apr 8 2015

correct function naming in micpsolver structs
ffb470e98818
·fabien on Apr 8 2015, 22:44.
Add helper meber functions
824f90062e79
·fabien on Apr 8 2015, 15:31.
Add member function to set options in MiCPSolverOptions
0510c2d1f2b1
·fabien on Apr 8 2015, 15:24.

Apr 6 2015

Reader : Move implementation details into the cpp file
4cf2a40df164
·fabien on Apr 6 2015, 15:35.

Apr 2 2015

Fixes strange allocation bug in ReactiveTransportRunner
cdf89e2fd60f
·fabien on Apr 2 2015, 05:25.
Add end user include
56a3baf15614
·fabien on Apr 2 2015, 03:56.
Documentation in src/common.hpp
affc03129ce6
·fabien on Apr 2 2015, 03:40.
Update licence
ed9f62bffad3
·fabien on Apr 2 2015, 02:56.
No diffusion of the electron
d8b65021bdf9
·branch: oxydoreduc
·fabien on Apr 2 2015, 02:34.

Apr 1 2015

Add the ability to solve oxydoreduction system
ea534669b0e6
·fabien on Apr 1 2015, 23:05.
Add the Faraday constants to the list of constants
9a83589563ca
·fabien on Apr 1 2015, 23:03.
Add AqueousSelector and OxydoSelector
cb51196a93d4
·fabien on Apr 1 2015, 23:02.

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.

specmicp/srcmasterd242af75fe4834829db5cb2…

Apr 16 2015

Apr 15 2015

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Feb 23 2015

specmicp/src
masterd242af75fe4834829db5cb2…