Diffusion SpecMiCP / ReactMiCP (cython) History

History
cythonf96d0f24dfe0b924de68d66…

Dec 9 2014

start implementation of EquilibriumCurve approad to reactive transport
f96d0f24dfe0
·fabien on Dec 9 2014, 05:15.
add specmicp/adimensional/equilibrium_curve.cpp example
44a03c6fdab1
·fabien on Dec 9 2014, 05:09.
correct examples files to use the dfpm/mesh module
8fd901c33698
·fabien on Dec 9 2014, 05:07.
remove const keyword for the output member
110e0d72687e
·fabien on Dec 9 2014, 05:06.
add src/dfpm/types.hpp in sources
8caac4f45779
·fabien on Dec 9 2014, 05:00.
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 a thermodynamic modeling of carbonation using AdimensionalSystem
88a1b28269f2
·fabien on Dec 5 2014, 22:24.
update AdimensionalSystem tests
4baa74b5ad51
·fabien on Dec 5 2014, 22:19.
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 4 2014

add new example to test diffusion program
1756ece2bb85
·fabien on Dec 4 2014, 17:49.

Dec 3 2014

initialize gas fugacity using previous solution
49676e6dff97
·branch: adim
·fabien on Dec 3 2014, 20:34.
add tests to test fixed activity/fugacity in AdimensionalSystem
50ed2ee880c0
·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.
update tests/adim to handle new BC
8524c7fb6b09
·fabien on Dec 3 2014, 17:00.
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.
update tests to use the new Adimensional system options
1978388f2d69
·fabien on Dec 2 2014, 19:47.
add AdimensionalSystemOptions, like ReducedSystemOptions
0b629aa5b824
·fabien on Dec 2 2014, 19:47.
update leaching and carbonation example
758ac6e99658
·fabien on Dec 2 2014, 19:13.
add options for enabling/disabling solution of purely aqueous problem
7cf040dc468d
·fabien on Dec 2 2014, 19:13.

Dec 1 2014

update leaching
e8034b61a600
·fabien on Dec 1 2014, 17:40.
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

update leaching example
698b0df1c91e
·fabien on Nov 25 2014, 15:24.
try improving convergence
32ec38c717c2
·fabien on Nov 25 2014, 15:23.

Nov 24 2014

update leaching example
6075784701c3
·fabien on Nov 24 2014, 17:37.
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

update leaching to match latest improvements in reactive transport solver
bad60df63f6f
·fabien on Nov 23 2014, 22:05.
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.
Merged master into kinetics
b72295e4c0ac
·georget on Nov 22 2014, 19:36.
update leaching example
98988b02e071
·georget on Nov 22 2014, 19:32.
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

add more tests for adimensional system
522419257276
·fabien on Nov 21 2014, 16:49.
include decimeter into computation, + better restarting guess
225e2990dde6
·fabien on Nov 21 2014, 16:48.
remove jsoncpp from the library we link too, it is already included
87334ca27afe
·fabien on Nov 21 2014, 16:43.
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.
set porosity to the good value
c247cad865b6
·fabien on Nov 18 2014, 15:13.

Nov 17 2014

update leaching example
c37a53cf2ee0
·fabien on Nov 17 2014, 21:01.
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

update carbonation and leaching example to use the latest developments
dc0a7d7b0a80
·fabien on Nov 13 2014, 00:57.
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.
correct boost include dir varaibles in CMakelist.txt
8d8999e139be
·fabien on Nov 13 2014, 00:47.
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

update examples for reactmicp
5246c20b3234
·fabien on Nov 11 2014, 22:04.
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 cemdata database for new version of jsoncpp
d36d2c5a0a89
·fabien on Nov 11 2014, 22:00.
update database reader to use the 3d party jsoncpp lib
71533d2f738a
·fabien on Nov 11 2014, 21:59.
Update Cmakelist, easier to compile in ohter system (i.e. denali)
2763d88b9342
·fabien on Nov 11 2014, 21:58.

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.

Oct 26 2014

update cython interface to use the licit charge conservation equation
0b9e18fb7d56
·fabien on Oct 26 2014, 19:45.
add explicit charge conservation in ReducedSystem
bbb049d91863
·fabien on Oct 26 2014, 19:16.
undef INFO macro, specmicp logger's INFO is the correct one, not the one by…
29fe36a29e5a
·fabien on Oct 26 2014, 00:32.
move and try improving sparse solver tools
b86528d727b5
·fabien on Oct 26 2014, 00:03.