Diffusion SpecMiCP / ReactMiCP (fixpoint) History

specmicp/src
fixpointfe4a3c6ffe370f142f579af…

Sep 10 2014

Merge branch 'reactivetransport'
fe4a3c6ffe37
·fabien on Sep 10 2014, 03:39.
remove thermodata.hpp, use DataContainer in reduced solver
8d16e3a0c811
·fabien on Sep 10 2014, 03:35.
add the main diffusion system
d01a0c53637d
·fabien on Sep 10 2014, 02:12.
introducing DiffusionSecondary for activity coefficient and concentration of…
f1b23f04d9ad
·fabien on Sep 10 2014, 02:12.
move and improve equation numbering for diffusion reactive transport system
e0f20360e06e
·fabien on Sep 10 2014, 02:12.
jacobian and residuals computation - not tested
43a8958938af
·fabien on Sep 10 2014, 02:12.
add range support in database::DataContainer
4873112352b5
·fabien on Sep 10 2014, 02:12.
bug correction for diffusion system
54f4e1c465c9
·fabien on Sep 10 2014, 02:12.
first commit on branch reactivetransport
b1dec92efd3e
·fabien on Sep 10 2014, 02:12.

Sep 9 2014

The python interface is able to solve the first step of thermocarbo
f89b95873e65
·fabien on Sep 9 2014, 17:25.

Sep 8 2014

Starting the work on the reaction path solver
5d71ccc1da23
·fabien on Sep 8 2014, 23:29.

Sep 5 2014

reintroduce the old solver, for a ~working min solver
54f50e62ff4b
·fabien on Sep 5 2014, 19:25.
check if mineral species contribute to total concentration
b9fd53649f8f
·fabien on Sep 5 2014, 19:20.
try helping convergence of min-FB linesearch algorithm - does not work
bcbf5078d653
·fabien on Sep 5 2014, 19:18.

Sep 1 2014

use the activity for the pH, not the molality
07a62349e37e
·fabien on Sep 1 2014, 16:06.

Aug 19 2014

comment and docs for database modules
d08941d1b3b4
·fabien on Aug 19 2014, 17:33.
comments and doc, correctition of bug in micpsolver no_scaling
cdf13a8c9cff
·fabien on Aug 19 2014, 15:07.
comments and doc for reduced system solver
879414fa334f
·fabien on Aug 19 2014, 14:33.
correct and add comments EquilibriumState
510760a8471f
·fabien on Aug 19 2014, 04:37.
comment and small refactoring for ReactionPathDriver
a583a91abe36
·fabien on Aug 19 2014, 04:19.

Aug 18 2014

simplify initialisation of reaction path driver
e9f68b0250c3
·fabien on Aug 18 2014, 19:35.
change copyright
be84b355a07d
·fabien on Aug 18 2014, 16:50.
cleaning not working gasphase in reduce_system
2555d4790cc7
·fabien on Aug 18 2014, 16:23.
after a long absence, start cleaning
768489c0ad3e
·fabien on Aug 18 2014, 16:07.

Jun 20 2014

more small corrections and preparations for the gas phase
fbc3b1f9f7c0
·georget on Jun 20 2014, 16:31.

Jun 19 2014

correct wrong activity coefficients in solution when ther is inactive components
881a9cd5b582
·branch: gasphase
·georget on Jun 19 2014, 16:22.

Jun 18 2014

Use 'full' warmstart to improve computation
e4061f7461ed
·georget on Jun 18 2014, 23:04.
Make sure that the activity coefficients are computed correctly - They are not !
54afcac13afc
·georget on Jun 18 2014, 23:00.

Jun 17 2014

start implementing the fixed volume problem
9320d65b0bd7
·georget on Jun 17 2014, 22:31.
separate common laws, constant and unit conversion in their own files
191e81a7b47a
·georget on Jun 17 2014, 22:29.
add some constants and trivial laws
4d7d50dc1a4f
·georget on Jun 17 2014, 15:47.

Jun 16 2014

start support of gas phase in database
392b50f45f16
·georget on Jun 16 2014, 21:36.
correct initialization of eigen solver - valgrind output is now ok
2fba35c488d9
·georget on Jun 16 2014, 21:34.

Jun 5 2014

add source file for data_container...
f5ff5181ce69
·georget on Jun 5 2014, 20:43.
everything compiles and run
b53f240bd6a4
·georget on Jun 5 2014, 20:15.
add support for molar volume of minerals
9bb9fb95bbcf
·georget on Jun 5 2014, 17:24.
add support for molar mass
bfff495f16bd
·georget on Jun 5 2014, 05:15.

Jun 4 2014

clean directory before merging branch
583c1a0f5574
·georget on Jun 4 2014, 23:59.
Improve EquilibriumState, use it in examples
35b1899b35ba
·georget on Jun 4 2014, 23:46.
add EquilibriumState to store and manage solution of equilibrium computation
36b376748b48
·georget on Jun 4 2014, 19:40.

Jun 3 2014

correct bug in database - allow selection of components
063a9f5832a7
·georget on Jun 3 2014, 16:05.

Jun 2 2014

adaptative step for embedded runge kutta
f41982d51b13
·georget on Jun 2 2014, 19:07.

May 29 2014

change template parameter - less confusing
0c026352549a
·georget on May 29 2014, 21:46.
add support for DormandPrince method
563cc0253cc5
·georget on May 29 2014, 21:09.
start inplementing ode integrator
f71ccdc1dc33
·georget on May 29 2014, 20:09.

May 20 2014

start works on kinetic
f5c48f3f547f
·georget on May 20 2014, 15:58.
compute logIAP of a mineral - maybe to simplified
1592526f1247
·georget on May 20 2014, 15:41.

May 16 2014

also select the correct minerals governed by kinetics
e25bc4143ef5
·georget on May 16 2014, 19:57.

May 3 2014

remove extended system and min function support in micpsolver
843229b1b8a7
·georget on May 3 2014, 22:34.
documentation
7faccfcacb59
·tag: 0.0.1
·georget on May 3 2014, 21:21.

May 1 2014

add test when reading database, check for consistency of charges
6e931682987f
·georget on May 1 2014, 00:19.

Apr 30 2014

improve convergence ?
f55c50218084
·georget on Apr 30 2014, 20:07.
use last development in databases modules
c0c6efecc588
·georget on Apr 30 2014, 20:00.
Add database module to keep only some minerals in equilibrium computation
68d4d285bf5e
·georget on Apr 30 2014, 19:59.
add base class for database modules
fe85b199d55b
·georget on Apr 30 2014, 17:44.

Apr 29 2014

allow dissolution of minerals and aqueous species
07e0e8497a80
·georget on Apr 29 2014, 22:04.
add support for kinetically governed minerals
2c2e886f02ce
·georget on Apr 29 2014, 21:29.
add min-FB linesearch arlgorithm - does not work
98612e6c3e19
·georget on Apr 29 2014, 19:54.

Apr 25 2014

Prepare the new min micpsolver
9ae71fb529cc
·georget on Apr 25 2014, 18:44.

Apr 18 2014

modify the restarting strategy
c69b6bbe42b8
·georget on Apr 18 2014, 23:24.
correct computation of total aquoues concentration in the case where one…
96cb0e494d88
·georget on Apr 18 2014, 23:23.
use the max_factorization option in the no_Scaling solution
a5a27e272923
·georget on Apr 18 2014, 23:21.

Apr 15 2014

reduce number of variables to the active set when the min function is used
3f9089b77fc2
·georget on Apr 15 2014, 02:40.
add an option to disallow automatic restart
c361bc90119b
·georget on Apr 15 2014, 02:38.

Apr 14 2014

start working on a global algorithm for reaction path modeling
e9fae70e5055
·georget on Apr 14 2014, 19:53.
initialisation
ce5e17f2cd94
·georget on Apr 14 2014, 19:48.
initialize variables
cfc0b7deec27
·georget on Apr 14 2014, 19:45.

Apr 12 2014

add 2 performance object together
89b65baa7e9a
·georget on Apr 12 2014, 17:55.

Apr 11 2014

easier way to change a basis
4c6dfeae96da
·georget on Apr 11 2014, 22:49.
correct bug, enhance errors
3e40c915ae53
·georget on Apr 11 2014, 22:01.
correct bugs
be6d4801e493
·georget on Apr 11 2014, 22:01.
also select aqueous parameters
2ceac1e74674
·georget on Apr 11 2014, 22:01.
manage options a little better
7a6b209cf0ce
·georget on Apr 11 2014, 15:47.
add options to limit the number of factorization step
a14a8bf5ce2c
·georget on Apr 11 2014, 15:45.

Apr 10 2014

Choose the NCP-function to use
99cf67ee7b3c
·georget on Apr 10 2014, 21:06.
add support for using min as a NCP-function
a8ca288cc7f5
·georget on Apr 10 2014, 20:49.
works but slow
16a46eb4411f
·georget on Apr 10 2014, 16:24.
better handling of non existing component
bebc0a28d0df
·georget on Apr 10 2014, 15:17.
correction of perturbation and detection of stationary point (issue #3)
b75af9fe6fdc
·georget on Apr 10 2014, 15:13.
move canonicalization and basis_switching to their own class, Database call…
2a2c40048cee
·georget on Apr 10 2014, 00:16.
database : add invalid_database exception, move definition of exceptions in…
5d310946ccfe
·georget on Apr 10 2014, 00:13.

Apr 9 2014

add ReactionPathDriver - able to run
98ef97febe79
·georget on Apr 9 2014, 23:12.
add a defautl constructor
d38dc8a3264e
·georget on Apr 9 2014, 23:11.
change default value, best for our problems
9e86c2755aa3
·georget on Apr 9 2014, 23:10.
different way to initialize a database
bf4aba0306f5
·georget on Apr 9 2014, 23:09.
Add the class ReducedSystemSolver, interface to solve a ReducedSystem
26d44083fef7
·georget on Apr 9 2014, 21:16.
Add a method to return the list of non active components
b2b3619c1e93
·georget on Apr 9 2014, 21:13.
Database can now remove some components (and the corresponding species) from…
cc06c8c7b905
·georget on Apr 9 2014, 21:10.
Thermodata may need to return the raw database
a17e5379d078
·georget on Apr 9 2014, 21:08.
Set options in bulk
fac9d726710f
·georget on Apr 9 2014, 21:07.
optimize reformulation of jacobian
3001d89b9660
·georget on Apr 9 2014, 20:55.
separate struct and enum used by MiCPSolver in a different header
50a966577063
·georget on Apr 9 2014, 20:08.
database selector - remove components from the basis
a293c41b2539
·georget on Apr 9 2014, 16:55.

Apr 8 2014

allow the desactivation of a component
0e5c208d1044
·georget on Apr 8 2014, 23:55.
add access to labels for debug
e4df9145f105
·georget on Apr 8 2014, 23:55.
a new reduced system, don't solve explicitely for secodnary aqueous…
a19cea4818a7
·georget on Apr 8 2014, 21:15.
adapt extended system to new hook_start_iteration method
918d946487c3
·georget on Apr 8 2014, 21:14.
improve convergence, tune linesearch to accept a max lambda
c344ec429965
·georget on Apr 8 2014, 21:13.

Apr 7 2014

move specmicp to extended_system
a29e40517129
·georget on Apr 7 2014, 19:47.
be careful of numerical issue when computing loggamma
c3557baf079a
·georget on Apr 7 2014, 03:26.

specmicp/srcfixpointfe4a3c6ffe370f142f579af…

Sep 10 2014

Sep 9 2014

Sep 8 2014

Sep 5 2014

Sep 1 2014

Aug 19 2014

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Apr 7 2014

specmicp/src
fixpointfe4a3c6ffe370f142f579af…