Commit Graph

884 Commits

Author SHA1 Message Date
James McClure
e421406788 fix wide halo bug in list memory 2021-02-09 15:25:20 -05:00
Rex Zhe Li
9ddf949a9e save the work; to be compiled and tested 2021-02-07 23:37:26 -05:00
Rex Zhe Li
2ed34592d0 Merge branch 'FOM' into FOM_dev 2021-02-01 00:19:55 -05:00
Rex Zhe Li
ac06cd3428 build pass; continue model debugging 2021-02-01 00:14:24 -05:00
Rex Zhe Li
3a6edc365d build pass; ongoing model validation 2021-01-31 21:26:03 -05:00
Mark Berrill
90ba7ed65a Fixing bug with analysis 2021-01-22 10:05:16 -05:00
James McClure
c350e2b45e demo for performance in MRT model 2021-01-20 18:25:29 -05:00
James McClure
e63b471260 added performance estimator to scalbl 2021-01-20 16:50:25 -05:00
Rex Zhe Li
fef81a0e47 resolve merge conflicts 2021-01-18 22:51:16 -05:00
James McClure
9051753f4c wide halo updates 2021-01-17 12:37:13 -05:00
James McClure
9bc8100a1d debugging wide halo 2021-01-15 16:33:57 -05:00
JamesEMcclure
1d85db88ed adding Lee model to FOM 2021-01-15 15:38:15 -05:00
Rex Zhe Li
e0416a676c merge with electrokinetic and resolve merge conflicts 2021-01-14 05:20:47 -05:00
JamesEMcclure
0fe3125833 merging multi-halo 2021-01-13 21:44:23 -05:00
James McClure
64b49f720e merge complete / cpu tests 2021-01-06 11:58:43 -05:00
James McClure
7644a8288e refactor Domain to include electorchem grey and FOM 2021-01-05 12:38:28 -05:00
James McClure
74e8c5e75f update barrier in ScaLBL / color model 2021-01-05 00:04:59 -05:00
James McClure
0983e63fbf merging FOM with new functions 2021-01-04 23:29:02 -05:00
James McClure
c998cc24b0 update to ScaLBL 2021-01-04 23:10:21 -05:00
James McClure
2f5fc9ead1 merging with FOM 2021-01-04 22:16:58 -05:00
James McClure
81953c2fce files match direct from FOM 2021-01-04 21:49:54 -05:00
James McClure
20800ed7eb partial merge 2021-01-04 19:33:27 -05:00
James McClure
2fc85dead8 merging electrokinetic & greyscale 2021-01-04 14:00:44 -05:00
Rex Zhe Li
d02eff3017 done: add restart and write visfiles for greyscale Color 2020-12-14 01:08:59 -05:00
JamesEMcclure
5e70189b16 merge read from file 2020-12-07 13:25:07 -05:00
Rex Zhe Li
e93b941d9e save the work; fluxBC for Ion solver still does not fully agree COMSOL 2020-11-19 13:17:31 -05:00
Rex Zhe Li
69f319ab5c work in progress; add CPU ion flux BC 2020-11-05 21:51:29 -05:00
JamesEMcclure
c479402256 Merge branch 'master' of github.com:JamesEMcClure/LBPM-WIA 2020-10-13 14:19:35 -04:00
JamesEMcclure
7071804bfd Merge branch 'Greyscale-Analysis' into Greyscale_stable 2020-10-12 15:08:15 -04:00
JamesEMcclure
1c4f4801b3 fix uncommented copyright 2020-10-12 09:35:55 -04:00
JamesEMcclure
56dc55a14d added equinor copyright statement 2020-10-12 06:08:29 -04:00
JamesEMcclure
35447181df merging multi-halo with electrokinetic 2020-10-09 15:19:59 -04:00
James McClure
5dfd2de344 Merge branch 'LeeModel' of github.com:JamesEMcClure/LBPM-WIA into LeeModel 2020-10-09 15:05:54 -04:00
James McClure
7244258135 merging greyscale and electrokinetic in ScaLBL 2020-10-09 15:05:14 -04:00
Rex Zhe Li
8b3a2a3ff0 post-polish; make greyscaleColor analysis consistent with normal color;build test passed 2020-10-09 13:07:06 -04:00
JamesEMcclure
9b8dd50f78 wide halo compiles 2020-10-08 13:17:15 -04:00
Mark Berrill
34b75e2ccf Getting HIP compiling on Summit 2020-10-07 13:36:42 -04:00
JamesEMcclure
af07ddb099 fixing build 2020-10-05 14:36:50 -04:00
James McClure
c232f076dc adding wide halo gradient test 2020-10-01 16:41:17 -04:00
James McClure
cc654bb54b adding wide halo gradient test 2020-10-01 16:36:16 -04:00
Rex Zhe Li
88063edb97 save the work;upgrade output data writing by writing single file instead of decomposed data 2020-10-01 16:27:46 -04:00
JamesEMcclure
f3c74bc89f update Memory Optimized Layout -tests passing 2020-09-30 15:22:37 -04:00
James McClure
1c1155d3b7 debug halo width 2020-09-30 15:15:57 -04:00
James McClure
5ed82a54f4 fix failing commm test 2020-09-30 15:14:28 -04:00
JamesEMcclure
624ec5a145 memory optimized layout with halo width 2020-09-30 15:10:18 -04:00
James McClure
0c594fa33d add halo to memory optimized layout 2020-09-30 14:45:51 -04:00
James McClure
e69f2db777 add map to widehalo 2020-09-30 09:06:15 -04:00
James McClure
3126318900 building wide halo class 2020-09-29 16:35:09 -04:00
James McClure
229accee9c fixing compile bugs 2020-09-29 11:00:42 -04:00
James McClure
c722aeb1bb fixing compile bugs 2020-09-29 10:58:33 -04:00
James McClure
afa9dac22a fixing compile bugs 2020-09-29 10:56:01 -04:00
James McClure
bfcd85af84 fixing compile bugs 2020-09-29 10:48:54 -04:00
James McClure
23f6c089f0 fix name of function 2020-09-29 10:43:31 -04:00
James McClure
6b335eaf28 add wide halo class 2020-09-29 10:39:05 -04:00
James McClure
a69504f96a fixed weird type in ScaLBL (revert) 2020-09-29 09:43:38 -04:00
Rex Zhe Li
4657adbc94 add routine for ion model to read from file 2020-09-28 17:08:49 -04:00
James McClure
0b94f29d58 fixed weird type in ScaLBL 2020-09-28 15:44:22 -04:00
Rex Zhe Li
33fdfeb29d add a routine for single-fluid greyscale to read from file - voxel porosity and perm 2020-09-24 21:57:04 -04:00
Rex Zhe Li
471f71d690 save the work; untested; add a routine of read from file for greyscale simulator 2020-09-23 22:15:05 -04:00
Rex Zhe Li
f9d3376951 Merge branch 'Greyscale_stable_dev' of github.com:JamesEMcClure/LBPM-WIA into Greyscale_stable_dev 2020-09-23 17:47:12 -04:00
Rex Zhe Li
226147a498 save the work of read from user-input file 2020-09-23 17:47:02 -04:00
James McClure
85844ec8e3 template for read from file 2020-09-23 15:21:15 -04:00
James McClure
fd27b3138a tweak BC conventions 2020-09-23 14:53:46 -04:00
James McClure
11be793575 use periodic BC in ScaLBL (model specific BC possible) 2020-09-23 12:30:22 -04:00
Rex Zhe Li
039978cc81 GPU version is available now 2020-09-20 11:00:36 -04:00
JamesEMcclure
64f1bfd37d Merge branch 'master' of github.com:JamesEMcClure/LBPM-WIA 2020-09-16 11:28:13 -04:00
Rex Zhe Li
11e9af54b6 CPU only;finish preliminary work on testing Poisson and Ion models and their coupling 2020-09-11 22:56:00 -04:00
Rex Zhe Li
20c8cc9c3b update PoissonSolver and fix numerous bugs 2020-09-02 11:37:23 -04:00
Rex Zhe Li
ae9e7a0408 fix integer index bug in AggregateLabels in morphdrain 2020-08-29 13:11:56 -04:00
Rex Zhe Li
0a7b1c331b further clean up the code 2020-08-28 21:53:41 -04:00
Rex Zhe Li
aa26fcafda fix miscellaneous bugs and update the data structure of electric potential 2020-08-28 11:15:55 -04:00
Rex Zhe Li
d8a1837ba0 save the work; to be continued to clean up the code 2020-08-19 11:31:32 -04:00
Rex Zhe Li
2180f7b2bf resolve merge conflict 2020-08-18 18:02:28 -04:00
Rex Zhe Li
5756d6f138 fix a few trivial bugs; add some checkpoint print; still debugging 2020-08-18 12:40:41 -04:00
Rex Zhe Li
771f679f5c add output; CPU version compiled; to be tested 2020-08-17 09:59:22 -04:00
Rex Zhe Li
85fc59190c save the work;CPU version compiled; to be tested 2020-08-16 11:20:11 -04:00
James McClure
30014a49c0 add zeta potential to Poisson 2020-08-11 16:52:56 -04:00
JamesEMcclure
6ff5a9a8ae fixed bugs in bounceback list 2020-08-11 15:34:12 -04:00
James McClure
e0b0e05664 added bounce-back interaction capability 2020-08-11 15:16:40 -04:00
James McClure
3592ac7562 distinguish parallel comm / bounceback sites at halo 2020-08-11 14:35:46 -04:00
Rex Zhe Li
dff4e3d536 save the work;to be continued 2020-08-07 17:44:02 -04:00
JamesEMcclure
fcdb84b2ad electro skeleton compiles 2020-08-06 16:06:52 -04:00
James McClure
5e6a9f552c Adding skeleton for electrokinetic LBM 2020-08-06 15:41:40 -04:00
Rex Zhe Li
80c7afc27c save the work; make several greynode wettability models available; need more validation and tests 2020-07-23 10:44:43 -04:00
Mark Berrill
8c5dd2e43a Adding MPI test 2020-07-20 13:41:48 -04:00
Rex Zhe Li
b0d6f7cd04 1. add color grad for debug;2. fix bug for calculating greyscale solid gradient 2020-07-08 22:24:37 -04:00
JamesEMcclure
8aa36c69c8 Merge branch 'master' of github.com:JamesEMcClure/LBPM-WIA 2020-06-24 23:56:31 -04:00
JamesEMcclure
0d292a52b2 fix volume bug 2020-06-24 23:33:36 -04:00
Rex Zhe Li
9a599b504f fix typo 2020-06-24 21:45:08 -04:00
Rex Zhe Li
4434bfe282 GPU only, make greyscaleColor equivalent single-phase model available 2020-06-22 13:39:51 -04:00
Rex Zhe Li
2621a7718f Greyscale Color model; both CPU and GPU versions are ready 2020-06-15 22:41:01 -04:00
Rex Zhe Li
16cc9cb5aa GreyscaleSC: save the work; pressureBC does not work 2020-05-20 22:57:42 -04:00
Mark Berrill
85cc3363da Adding function to reorder ranks based on load balancing 2020-05-15 13:39:36 -04:00
JamesEMcclure
49f5ec07a6 Merge branch 'master' of github.com:JamesEMcClure/LBPM-WIA 2020-05-07 14:03:11 -04:00
Rex Zhe Li
e83e794021 GreyscaleSC model;BGK works but MRT doesnt;save the work 2020-05-04 23:36:27 -04:00
James McClure
7b731e327b update pseudo-reflection 2020-05-04 15:26:41 -04:00
James McClure
d424771849 fix scope in Domain inlet/outlet 2020-05-04 15:12:50 -04:00
James McClure
16e187e1dc add pseudo-reflection 2020-05-04 14:50:23 -04:00
Rex Zhe Li
9f8af47d2b continue GreyscaleSC debugging;save the work 2020-05-03 18:03:44 -04:00
Rex Zhe Li
8e2efa8f05 GreyscaleSC model;GPU only;save the work;model does not function correctly 2020-04-30 23:42:17 -04:00
Rex Zhe Li
4c84ab8eb9 GPU ONLY; clean up the two-phase greyscale code; rename the old greyscaleColor to greyscaleFE 2020-04-25 17:01:01 -04:00
Rex Zhe Li
eaf9e828ea GPU only; save the work; greyscaleFE works only conditionally; 2020-04-24 16:20:52 -04:00
Rex Zhe Li
389c60a06f GPU version; save the work; mass is not conserved 2020-04-19 22:21:43 -04:00
Rex Zhe Li
dd3c177dee change the mass transport formulation;no longer solve Aq and Bq, only solve for phase field 2020-04-18 22:46:44 -04:00
Rex Zhe Li
67f5076fa3 fix bug in recvGrad 2020-04-17 16:32:09 -04:00
Rex Zhe Li
297ea4cb63 update the chemical potential approach and save work 2020-04-17 16:23:06 -04:00
Rex Zhe Li
984e7b504e GPU: save the work; mass transport using chemical potential 2020-04-12 23:38:24 -04:00
James McClure
bdf8539f40 debugging strange mass conservation issue 2020-04-10 15:03:15 -04:00
Rex Zhe Li
cc14324c33 GPU version ONLY; two-phase greyscale model; save the work 2020-04-07 15:29:33 -04:00
James McClure
3b006fbc3c reflect BC for D3Q7 2020-04-07 10:38:21 -04:00
James McClure
a82c8995fe make sure not to remove solid for reflection BC 2020-04-07 09:27:32 -04:00
James McClure
91f42ab74f condition unpack routines on BC for halo 2020-04-07 08:45:06 -04:00
James McClure
735b3f5d3e fix argfs 2020-04-03 20:29:37 -04:00
James McClure
e1e603b25f add reflection condition for color grad 2020-04-03 20:26:32 -04:00
James McClure
e4d836e7fc add reflection condition for color grad 2020-04-03 20:24:29 -04:00
James McClure
10b630662a fix reflection name 2020-04-03 10:00:17 -04:00
James McClure
e62208caaa add reflection BC to MRT / Color 2020-04-03 09:52:23 -04:00
James McClure
81f2548633 fix a few warnings 2020-04-03 09:34:35 -04:00
James McClure
e64d44e438 added D3Q19 reflection BVC 2020-04-03 09:30:55 -04:00
James McClure
e641e2e3ed remove old comments 2020-04-03 08:26:48 -04:00
James McClure
32f1bae784 don't unpack distributions when external BC are applied (D3Q7/D3Q19) 2020-04-03 08:24:28 -04:00
James McClure
2c554fc89a Merge branch 'Greyscale' into bugfix 2020-04-02 10:32:18 -04:00
James McClure
64a19a718b make ScaLBL communicator public for 2020-04-01 12:26:55 -04:00
James McClure
b47f11a395 Merge branch 'bugfix' of github.com:JamesEMcClure/LBPM-WIA into bugfix 2020-03-31 13:30:26 -04:00
JamesEMcclure
05cafcb525 fix failed merge 2020-03-17 21:44:45 -04:00
JamesEMcclure
9f5b44dfe4 Revert "Moving more MPI calls to the wrapper"
This reverts commit 0f91767b6c.
2020-03-17 21:23:18 -04:00
JamesEMcclure
7bb01557d8 updated bugfix with old ScaLBL 2020-03-17 13:45:51 -04:00
Mark Berrill
94156e066e Trying to fix bug with MPI communication 2020-03-12 10:26:17 -04:00
Rex Zhe Li
c11cfcf069 Merge branch 'morphLBM' into Greyscale 2020-02-21 21:25:25 -05:00
James McClure
0246577a9c Merge branch 'FOM' 2020-02-10 13:25:29 -05:00
Mark Berrill
57156d16fc Fixing build issue 2020-02-05 07:35:13 -05:00
Rex Zhe Li
72ab9f803e merge with morphLBM to incorporate the newest backend updates 2020-02-04 13:28:57 -05:00
JamesEMcclure
c426aa7d1d remove deprecated pressure BC routines 2020-02-03 15:13:45 -05:00
JamesEMcclure
79669b30d0 merging with morphLBM (may be some problems still) 2020-02-03 14:30:03 -05:00
Mark Berrill
8751fa245b Fixing minor issues with some operating systems 2020-02-03 12:41:09 -05:00
Rex Zhe Li
50e4b5a9ba add the greyscale effective viscosity back, but by default it is set equal to the normal viscosity 2020-02-01 14:04:39 -05:00
Rex Zhe Li
69ee9f79cb Some updates:(1)add different fq initialization for BGK and IMRT;(2)user can choose collision model 2020-01-31 15:15:26 -05:00
Rex Zhe Li
34c5b223b0 fix printf bug 2020-01-30 17:57:56 -05:00
Rex Zhe Li
25df1e0f35 add a few print-out to make the program output more verbose 2020-01-30 13:23:27 -05:00
Rex Zhe Li
6e7cb83254 add pressure to output data 2020-01-29 23:49:36 -05:00
Mark Berrill
0f91767b6c Moving more MPI calls to the wrapper 2020-01-28 12:33:36 -05:00
Mark Berrill
d1f714a82e Adding MPI wrapper class 2020-01-28 08:51:32 -05:00
Mark Berrill
78c2e710b9 Fixing compile warnings 2020-01-22 12:01:29 -05:00
Mark Berrill
3c854fd002 Updating StackTrace and improving performance converting uCT data 2020-01-22 11:00:25 -05:00
Rex Zhe Li
9fa091a49d save the work, CPU versions seem to work, but need non-unity porosity test 2020-01-17 18:46:28 -05:00
JamesEMcclure
c80b74a754 Merge branch 'master' of github.com:JamesEMcClure/LBPM-WIA 2020-01-17 09:40:34 -05:00
Rex Zhe Li
12c0d42d36 change specifier of printf to correct the output for very large image 2020-01-14 12:01:33 -05:00
Rex Zhe Li
9c48b3de70 enable single phase abs-perm simulator to read medium from Filename 2019-12-09 15:17:27 -05:00
Rex Zhe Li
a67d3f8b69 calculate the medium porosity if read domain from Filename 2019-12-09 14:44:58 -05:00
Rex Zhe Li
86beafab8a save the work for cpu version 2019-11-21 13:43:32 -05:00
JamesEMcclure
cf28b2794b created skeleton for greyscale model 2019-11-20 13:20:11 -05:00
JamesEMcclure
4878557e20 update labels in loop 2019-11-20 09:53:44 -05:00
JamesEMcclure
26cac9060a fix bug with relabel 2019-11-19 12:35:24 -05:00
JamesEMcclure
9efd6461a0 enable grid reader for color simulation 2019-11-15 10:37:26 -05:00
JamesEMcclure
1acae53d82 Merge branch 'morphLBM' of github.com:JamesEMcClure/LBPM-WIA 2019-11-14 11:30:58 -05:00
Mark Berrill
b5ee28f044 Adding reader for compressed uCT data 2019-11-08 10:06:07 -05:00
JamesEMcclure
ddf08413c2 Merge branch 'morphLBM' of github.com:JamesEMcClure/LBPM-WIA into morphLBM 2019-10-16 16:06:51 -04:00
JamesEMcclure
89f523cb19 fix small bug 2019-10-14 16:05:08 -04:00
JamesEMcclure
55b93e6cac Merge branch 'morphLBM' of github.com:JamesEMcClure/LBPM-WIA into morphLBM 2019-10-10 09:53:18 -04:00
James McClure
d8f2344739 resolve conflict between voxel length / domain length 2019-10-10 09:30:33 -04:00
JamesEMcclure
cc0f04a3d3 Merge branch 'morphLBM' of github.com:JamesEMcClure/LBPM-WIA into morphLBM 2019-10-01 14:27:07 -04:00
JamesEMcclure
c52ff20519 fix relable bug 2019-10-01 14:26:48 -04:00
James E McClure
eb66dcaed6 Aggregate labels is public 2019-09-30 22:15:35 -04:00
James E McClure
a539bf28db move label aggregate to Domain 2019-09-30 22:07:57 -04:00
JamesEMcclure
017f06039e Merge branch 'morphLBM' of github.com:JamesEMcClure/LBPM-WIA into morphLBM 2019-09-30 21:25:14 -04:00
Rex Zhe Li
084d009286 Merge branch 'morphLBM' of github.com:JamesEMcClure/LBPM-WIA into morphLBM 2019-09-24 15:23:50 -04:00
Rex Zhe Li
06ecaa61c4 add options to select what phase (e.g. nw or w phase) to be put in the inlet/outlet buffer layers 2019-09-24 15:23:41 -04:00
JamesEMcclure
a948506e7a Merge branch 'morphLBM' of github.com:JamesEMcClure/LBPM-WIA into morphLBM 2019-09-24 14:56:25 -04:00
JamesEMcclure
5ea0b2278c fix label / checker bug 2019-09-24 14:54:49 -04:00
JamesEMcclure
8210b4c0bd Merge branch 'morphLBM' of github.com:JamesEMcClure/LBPM-WIA into morphLBM 2019-08-21 10:02:50 -04:00
JamesEMcclure
87f3d6b96e refactor Domain/color for reading input file sequence 2019-08-16 10:28:00 -04:00
JamesEMcclure
e049fa4482 Merge branch 'morphLBM' of github.com:JamesEMcClure/LBPM-WIA into morphLBM 2019-08-07 16:38:12 -04:00
JamesEMcclure
d4806cef20 Domain has parallel decomp function to test 2019-08-06 13:36:04 -04:00
James E McClure
b23af91d98 refactor Domain for decomp parallel 2019-08-06 13:34:22 -04:00
James E McClure
5892f82f00 refactor Decomp for parallel 2019-08-06 13:29:04 -04:00
James E McClure
f434404cb2 trying not to gum up rank 2019-08-06 13:07:33 -04:00
James E McClure
ed6853345c refactor lbpm_serial_decomp 2019-08-06 13:02:24 -04:00
JamesEMcclure
9663b13ffb Domain decomp function 2019-08-06 12:48:16 -04:00
James E McClure
d74aec8493 decomp in Domain 2019-08-06 12:33:02 -04:00
JamesEMcclure
089b53f800 Merge branch 'morphLBM' of github.com:JamesEMcClure/LBPM-WIA into morphLBM 2019-05-09 08:43:45 -04:00
JamesEMcclure
fd713ba3af fix voxel length 2019-05-02 15:25:43 -04:00
JamesEMcclure
869695cb5c Merge branch 'morphLBM' of github.com:JamesEMcClure/LBPM-WIA into morphLBM 2019-05-01 16:48:26 -04:00
JamesEMcclure
e2a7cca884 fix domain voxel length bug 2019-05-01 16:37:17 -04:00
JamesEMcclure
d26b25278a Merge branch 'morphLBM' of github.com:JamesEMcClure/LBPM-WIA into morphLBM 2019-05-01 13:16:17 -04:00
JamesEMcclure
18d0affaaa print voxel length when specified 2019-05-01 13:15:53 -04:00
JamesEMcclure
4090aa975a print voxel length 2019-05-01 12:36:57 -04:00
James E McClure
aaeab20884 Merge branch 'morphLBM' of github.com:JamesEMcClure/LBPM-WIA into morphLBM 2019-04-23 17:26:09 -04:00
James E McClure
8e4169cb83 updated color model with default parameters 2019-04-19 10:49:55 -04:00
James E McClure
10f3865fb1 added voxel length to domain 2019-04-19 10:48:18 -04:00
James E McClure
e169e1a089 Merge branch 'morphLBM' of github.com:JamesEMcClure/LBPM-WIA into morphLBM 2019-04-04 20:25:50 -04:00
James E McClure
ace0c78ff3 fixed bug in permeability calculation 2019-04-04 20:22:48 -04:00
James E McClure
a0fabd4b32 make signed char explicit 2019-03-29 06:46:48 -04:00
James E McClure
79c3b0d173 added outlet layers to domain 2019-03-26 15:42:26 -04:00
James E McClure
2eddcfd8cd increased default inlet/outlet layers to 10 2019-03-26 15:30:34 -04:00
James E McClure
23e221d84e combined updates 2019-03-22 21:33:05 -04:00
Mark Berrill
0a49f9ce77 Updating threadpool / StackTrace 2019-03-18 09:42:44 -04:00
James E McClure
252fddac79 update domain structure to know about inlet 2019-03-06 07:04:17 -05:00
James E McClure
69818bacf2 Merge branch 'morphLBM' of github.com:JamesEMcClure/LBPM-WIA 2019-02-20 08:02:10 -05:00
Mark Berrill
ca82036c03 Fixing OS detection issue on Summit 2018-12-03 14:37:59 -05:00
James E McClure
c7566c3d4f Merge branch 'master' of github.com:JamesEMcClure/LBPM-WIA 2018-11-25 20:55:58 -05:00