Diffusion SpecMiCP / ReactMiCP (cython) History

specmicp/src
cythonc99feaa019032b9f165ddca…

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.
add options for reduced system
96b7b4f73361
·fabien on Dec 1 2014, 17:38.
add a class to compute exponential moving average
bc007865d143
·fabien on Dec 1 2014, 17:33.

Nov 25 2014

try improving convergence
32ec38c717c2
·fabien on Nov 25 2014, 15:23.

Nov 24 2014

improve convergence for reactive transport
03a6ee9fa3fe
·fabien on Nov 24 2014, 17:36.
Correct unit problem (again) in transport update
3406a6d82549
·fabien on Nov 24 2014, 17:34.

Nov 23 2014

improve algorithm
276009d19c18
·fabien on Nov 23 2014, 22:04.
add a method to check if there is any solid in the speciation solution
fd81222c02eb
·fabien on Nov 23 2014, 22:03.

Nov 22 2014

correct compilation error link to namespace
0d2b686c39c7
·fabien on Nov 22 2014, 19:46.
Merge branch 'kinetics'
01a5614ae626
·fabien on Nov 22 2014, 19:38.
correct reactive transport solver
bdfe852fa9b2
·georget on Nov 22 2014, 19:32.
Allow for truncated axisymmetric mesh
9d76e2cc297d
·georget on Nov 22 2014, 19:30.
small corrections in specmicp ReducedSystem and associate
3a8861713bdf
·fabien on Nov 22 2014, 19:25.
Add AdimensionnalSystemSolutionExtractor
1449c5f7ed20
·fabien on Nov 22 2014, 19:24.
add density of water function (to improve) and use scalar_t for the real type
8acca7ec6e52
·fabien on Nov 22 2014, 01:28.
add more methods to the database which can take units as argument
81a129921f3f
·fabien on Nov 22 2014, 01:27.

Nov 21 2014

include decimeter into computation, + better restarting guess
225e2990dde6
·fabien on Nov 21 2014, 16:48.
perturb jacobian if it cannot be factorized when no scaling is used - same as…
dd32bf844e0c
·fabien on Nov 21 2014, 16:41.
improve problem solver
7976b7effc36
·fabien on Nov 21 2014, 16:12.
add missing dependancy for src/utils/log.hpp, order of include does not matter…
d4534f7eaf1e
·fabien on Nov 21 2014, 16:11.
add decimeter as a length unit (for liter)
101e1e70dfc5
·fabien on Nov 21 2014, 16:08.

Nov 20 2014

add solver for Adimensional system and Dissolver, to set up problem
d1998e3678d3
·fabien on Nov 20 2014, 02:41.
add a molar_mass_basis function adjustable to the unit in the database
c1d916f6a6a8
·fabien on Nov 20 2014, 02:37.

Nov 19 2014

rename adim into adimensional system
e2078e2d32ae
·fabien on Nov 19 2014, 16:42.
Remove unused header file in Reduced system
9192af49fe62
·fabien on Nov 19 2014, 16:24.
add support for units in adimensional system
99eb486901e6
·fabien on Nov 19 2014, 16:21.
add support for units in database
a80d7faccc53
·fabien on Nov 19 2014, 16:19.
add supports for units
55250fbca69d
·fabien on Nov 19 2014, 16:18.

Nov 18 2014

implementation of adimensional system and test
477470dc6bc8
·fabien on Nov 18 2014, 23:54.

Nov 17 2014

correct naming in uniform mesh 1D
4905ca8043ef
·fabien on Nov 17 2014, 20:58.
improve reactive solver
ab9678d714b1
·fabien on Nov 17 2014, 20:56.
style
811727685964
·fabien on Nov 17 2014, 20:56.

Nov 16 2014

Correct/improve equilibrium data
6da64e226377
·fabien on Nov 16 2014, 19:55.

Nov 13 2014

use temporary variables for the computation
75e069a6735b
·fabien on Nov 13 2014, 00:56.
add support for gmres in sparse_solver module
f67b525bf55f
·fabien on Nov 13 2014, 00:55.
use new Performance Structure/ PErformance handler and Options handler in…
d9b9320c1f9b
·fabien on Nov 13 2014, 00:54.
add options to reset the options in Options handler
736804e88863
·fabien on Nov 13 2014, 00:48.
Add PerformanceHandler on the model of OptionsHandler
a4f20df9b49f
·fabien on Nov 13 2014, 00:46.
rename file containing the reactive transport solver options
25b4a7a686ca
·fabien on Nov 13 2014, 00:45.

Nov 11 2014

improve reactmicp
e1f224c238f0
·fabien on Nov 11 2014, 22:04.
improve kinetic system
86887f7bc2f2
·fabien on Nov 11 2014, 22:03.
add computation of total concentrations in equilibrium data
05109a387e26
·fabien on Nov 11 2014, 22:02.
correct strang linesearch
89ad784609cf
·fabien on Nov 11 2014, 22:01.
update database reader to use the 3d party jsoncpp lib
71533d2f738a
·fabien on Nov 11 2014, 21:59.

Nov 7 2014

add kinetic solver - to be improved
bc9b1984b554
·fabien on Nov 7 2014, 19:07.
update/improve Runge-Kutta solver
76335401d226
·fabien on Nov 7 2014, 19:06.
options to enable/disable nonmonotone linesearch
f6de050d917e
·fabien on Nov 7 2014, 18:59.
add base class to handle options
d6ddcf0a9bd2
·fabien on Nov 7 2014, 18:58.

Oct 28 2014

start implementing kinetics solver
2f65d5a63c08
·fabien on Oct 28 2014, 20:44.
clean ode integrator
250e37bca411
·fabien on Oct 28 2014, 15:28.