Merge pull request #2511 from samueljmcameron/fix_bd_sphere
Add USER-BROWNIAN package
This commit is contained in:
Axel Kohlmeyer
86
unittest/force-styles/tests/data.brownian
Normal file
86
unittest/force-styles/tests/data.brownian
Normal file
@ -0,0 +1,86 @@
|
||||
LAMMPS data file via write_data, version 30 Nov 2020, timestep = 120000
|
||||
|
||||
32 atoms
|
||||
1 atom types
|
||||
|
||||
-2.7144176165949063 2.7144176165949063 xlo xhi
|
||||
-2.7144176165949063 2.7144176165949063 ylo yhi
|
||||
-1.3572088082974532 1.3572088082974532 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1
|
||||
|
||||
Pair Coeffs # zero
|
||||
|
||||
1
|
||||
|
||||
Atoms # hybrid
|
||||
|
||||
1 1 0.8174385639059338 -1.5010271964354949 1.0637924298773633 0 0.6257069940596588 -0.111108944542851 -0.7721046302331049 1 1 -1 0 -1
|
||||
2 1 -1.5885878110813303 2.2401728691740113 0.47068930278928994 0 -0.5102593570021903 0.8585717488647711 -0.049899305035241655 1 1 0 -1 -1
|
||||
3 1 -1.1818944957014061 -2.6848623178033457 -1.1800939297629425 0 -0.004166477179696561 0.19766436575888424 0.9802609035236738 1 1 0 0 0
|
||||
4 1 0.1720589621174558 1.3643946759490944 -1.1522506184595422 0 0.11721568749368932 0.2990753541702089 -0.9470028590945996 1 1 0 -1 0
|
||||
5 1 -2.5038595242428823 -1.624930716630223 -1.1484315973168586 0 -0.3868419197154481 -0.6136739748888413 0.6883005024660352 1 1 0 0 0
|
||||
6 1 -1.2345478646498314 -0.3224402671532977 0.5533955773621407 0 0.24969915142093102 -0.15640101573329426 -0.9556092590893315 1 1 0 0 -1
|
||||
7 1 1.1946150666115714 0.4921384424233923 -0.516829526742452 0 0.0036359783326705107 -0.4590891155800383 -0.8883827798969893 1 1 0 0 -1
|
||||
8 1 1.8342027600045443 1.516095010832566 0.043843911607852545 0 -0.8435468778359277 0.11782686457134713 -0.5239708912511688 1 1 0 -1 -1
|
||||
9 1 -0.5406701027756321 2.23952568921304 0.5241488585364904 0 0.045872039042421424 0.13268297551853248 -0.9900964518882184 1 1 0 0 -1
|
||||
10 1 -0.3972258497968314 0.7566024687022016 -0.2323435643206888 0 0.655171514572036 -0.43050189344470563 0.6208207520966965 1 1 0 0 -1
|
||||
11 1 -0.7183933447005026 1.1587411649504586 0.20950093049531074 0 0.22933670283280452 -0.6843477395075139 -0.6921508854034168 1 1 0 0 -1
|
||||
12 1 1.022524253197315 0.17877446802634833 0.29899480569943504 0 0.6711103355965887 -0.41621190608313047 -0.6134969981100816 1 1 0 0 -2
|
||||
13 1 -1.4250800612966135 -2.4056565408365356 0.21801121763465003 0 -0.5029961497078136 0.46126362983367525 -0.7309108955076378 1 1 0 1 0
|
||||
14 1 -1.7432369014700662 1.621196939810902 0.07955801420882219 0 -0.7988534279257005 0.3194109740977685 -0.5097154405325315 1 1 0 0 -1
|
||||
15 1 -0.9908151496097626 -2.6488792381485773 -1.1948117198271224 0 0.5516163133238324 -0.6234158094772195 0.5541409309633126 1 1 0 1 0
|
||||
16 1 2.6948716697156523 0.41280900513864877 0.1548529904178103 0 -0.8512724888069316 0.23988291811633639 0.4666811924605956 1 1 0 0 -1
|
||||
17 1 -1.5494542712095147 -0.53420074244155 -0.6250925146711168 0 -0.07678144567993991 -0.03950496198488684 0.9962650087089635 1 1 0 0 0
|
||||
18 1 -2.3151948315996678 -2.6221617748715036 -0.1899804833264763 0 -0.7569384929404162 -0.33315612552157964 -0.562184234866597 1 1 0 0 0
|
||||
19 1 2.1590179665621467 1.6095466091914918 -1.2253859221608403 0 0.20879037375649698 -0.06905534931949565 0.9755193173674137 1 1 0 -1 0
|
||||
20 1 2.202409043221526 0.14395355359028536 1.335860415061412 0 -0.14984238844204667 -0.9847320173066201 0.08860086183112265 1 1 0 -1 -1
|
||||
21 1 -1.4500395490531754 -1.5281375693866057 0.00020797713894412338 0 -0.9915462127271186 0.08451237717795997 0.09845692525281326 1 1 0 0 0
|
||||
22 1 -1.0657362106538344 0.6350242518491277 -0.7513800843604899 0 -0.6569043427466144 -0.07223746743273625 0.7505054515321944 1 1 0 -1 0
|
||||
23 1 -0.5619632776222234 1.8699713384517294 -0.9467270322768698 0 0.7911745431454184 0.5177930983571434 -0.3254737310019788 1 1 0 0 0
|
||||
24 1 -2.1040517028343215 -2.247249268720423 0.11322260281322279 0 -0.04193441020358475 0.2313330374822751 -0.9719704373128341 1 1 1 0 -1
|
||||
25 1 -0.868354233492487 -0.14640654973697223 -0.9035771863161228 0 -0.15652971300701132 0.0848859275832726 -0.9840187133608133 1 1 0 0 0
|
||||
26 1 -0.4652717213714348 0.12334049868763304 -0.3826888902964762 0 0.6487662426744875 0.7578954080882759 0.06853402632804934 1 1 -1 0 -1
|
||||
27 1 -1.0478542019398558 2.3814414358320106 1.2039965288246885 0 0.10846325104076994 -0.6457073741173193 -0.7558423844851409 1 1 0 0 -1
|
||||
28 1 2.500698605198214 -0.728008572758278 0.48410831318342695 0 -0.3622892345018212 0.911584495321123 0.19431988692415955 1 1 0 0 -1
|
||||
29 1 -1.416084269787537 -1.7066588654378656 0.8328319180724224 0 -0.08971242415920104 -0.44687722085944426 0.8900856309526737 1 1 0 1 -1
|
||||
30 1 -0.6370519124977301 0.47113373856505564 -0.08549434306971403 0 -0.6030496979424049 -0.7976847581640081 -0.0054852898193420265 1 1 0 0 0
|
||||
31 1 0.8225325721319097 -0.441545584269452 0.3381678086542899 0 -0.6909877678544062 -0.7162885851668209 0.09729628685258002 1 1 0 0 0
|
||||
32 1 2.1861742760925518 1.5740929150306235 -0.01693950575830974 0 0.890366016527044 0.3247001065794207 0.3190896385047258 1 1 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 -524.6769664299819 215.42199277006424 -112.27005568908588 -462.03530876082846 -551.9512642384534 -196.46403300264745
|
||||
2 391.3416799472542 48.7957761872576 -623.1311508507263 489.33832403519347 -260.3072072833973 -529.7105564646685
|
||||
3 109.86388293585976 665.5499875054874 -583.4371492475789 -678.3137468561738 622.6210695594215 37.427168579931944
|
||||
4 398.4814329387423 -117.47798197974335 -376.25882363220865 44.966011242133156 -720.7197483734453 654.1933839835833
|
||||
5 584.5314601424474 159.82839534760055 -199.69054648577074 298.5492685852273 657.8565691587017 -616.4449676099423
|
||||
6 609.4975570025578 738.2439586459146 284.06966373218285 143.74329023895925 256.75048911205783 -57.96098774586574
|
||||
7 -27.968041606728725 752.3634409363073 223.6145040530379 -496.9033910070852 198.22198514310026 -81.32767873220877
|
||||
8 -451.1189781565461 -759.642533657806 547.0603381420482 316.5054412546416 669.7302717449263 -447.9786170711034
|
||||
9 -54.531235862640735 -115.1466962517251 -610.7279757582849 -731.9703465871636 -735.0301879611621 -584.8114323501295
|
||||
10 748.6292469789635 701.8693636792311 -498.1997398935133 208.99011146198362 -538.4269075676226 130.16593091403558
|
||||
11 -174.9453247974202 153.40962619436522 390.8158086666639 -381.20607659097726 548.6301954978544 225.4382939850729
|
||||
12 -393.58450479962613 562.7494007708912 -512.2495061493412 425.83486537187855 260.1521699032197 -605.409242525273
|
||||
13 294.0485676041469 -416.4803586200817 -678.9550420350499 284.48925268723156 -67.2753269810592 559.4386740115784
|
||||
14 -764.1287373972617 733.8169442814999 720.6030317274988 357.0913464046234 521.8205481343224 173.7714175822938
|
||||
15 -91.18940426263303 224.9036504882129 284.4326488075122 -207.62866349692237 501.5282881027212 445.99895870682315
|
||||
16 179.07740801693492 -535.4403834538152 -318.55850921823156 266.7175735768374 444.97898080245074 -381.12832705309194
|
||||
17 -428.2045641732463 -491.50884735767914 -270.6175162521197 727.5062118970601 128.20058511314278 270.88345291377027
|
||||
18 395.0795674693432 306.1681692632796 -13.216405710204159 671.3857274637012 102.79070644890297 322.4136674209789
|
||||
19 -203.6409986589429 -54.701509197392014 581.0635722032287 -186.75568274826543 476.4083542709755 -601.0363388843747
|
||||
20 -115.92502268264624 -762.0000436955148 -223.1167962036293 489.85643882981896 -247.41158767130918 -365.8330907652003
|
||||
21 658.7418242889948 586.715926671846 -624.8573383343708 -10.66175165422313 359.69577124554525 -340.2786090411881
|
||||
22 56.13036471905219 261.41167548131494 373.8653013382346 673.5607754029996 -245.8613985477709 353.0482780954667
|
||||
23 -252.99394908800596 -466.09490577221976 -670.846651689147 -616.9981712696467 -541.8114132827196 -369.70154580103025
|
||||
24 -627.059810991902 278.53716543954556 457.18418082455213 -101.65170342061822 225.64771910612274 649.9004460194175
|
||||
25 -542.388717452386 -105.31239543953356 69.1170307021082 -204.78231016519337 -522.3497436231834 -357.49930063072486
|
||||
26 -213.4605252121538 -534.3449644895232 244.1099101456221 275.4530388773477 212.2684271906576 -165.97485643999994
|
||||
27 595.2153731851414 626.5401264322599 -736.723964414168 -188.93350086112284 -459.44316502268424 -484.4606024327521
|
||||
28 -400.55444615195614 606.638183855102 121.6628831751137 359.49918126198475 668.2849798601502 -135.04633035091715
|
||||
29 -347.6624143232117 -365.7917228400548 -541.6372617049859 160.0398519292602 -624.5129134218859 -448.13097661684066
|
||||
30 -104.98117502101249 500.1388613847156 731.4317325082025 -481.0858846642298 -574.8809141763269 122.21267028742885
|
||||
31 754.8558584263326 -34.937336585228245 -726.0948084688208 -103.81133072710576 431.8053281041717 -479.89267857331
|
||||
32 140.02839515740888 643.0847109951975 -535.5893264521633 -373.10470401809016 -661.5529040774077 37.5722333352976
|
||||
80
unittest/force-styles/tests/fix-timestep-brownian.yaml
Normal file
80
unittest/force-styles/tests/fix-timestep-brownian.yaml
Normal file
@ -0,0 +1,80 @@
|
||||
---
|
||||
lammps_version: 24 Aug 2020
|
||||
date_generated: Tue Dec 08 12:28:40 2020
|
||||
epsilon: 1e-12
|
||||
prerequisites: ! |
|
||||
atom hybrid dipole sphere
|
||||
fix brownian/sphere
|
||||
pre_commands: ! ""
|
||||
post_commands: ! |
|
||||
fix test solute brownian/sphere 1.0 1.0 1.0 1.0 1049270 dipole
|
||||
fix_modify test virial yes
|
||||
input_file: in.brownian
|
||||
natoms: 32
|
||||
run_pos: ! |2
|
||||
1 0.8198132185477983 -1.5120221815010249 1.069236010215717
|
||||
2 -1.583657719347759 2.2448791290372445 0.48185576252150486
|
||||
3 -1.1880610036164596 -2.678219122115848 -1.1824396130063375
|
||||
4 0.1908794667962731 1.3593710068293134 -1.1524405138570022
|
||||
5 -2.502067366922716 -1.6291621715156412 -1.155308629818198
|
||||
6 -1.214213515524568 -0.33667539680264325 0.5468489960944642
|
||||
7 1.2020658999364164 0.5045561046001554 -0.5265404283266816
|
||||
8 1.8138899397447894 1.5212405777462397 0.04943268689972926
|
||||
9 -0.547736141448719 2.2385521615789026 0.5146647473679599
|
||||
10 -0.38821952892982114 0.7570899758491753 -0.23554333362488367
|
||||
11 -0.7101567507222957 1.1587573566149103 0.19674801175715137
|
||||
12 1.0217947252204158 0.1732739652383159 0.3064332055619567
|
||||
13 -1.43254480550968 -2.4145346257525504 0.22508495277327453
|
||||
14 -1.7469141674373843 1.605802890508775 0.07604534549063337
|
||||
15 -0.9840165887382163 -2.631709004347024 -1.1933270065258215
|
||||
16 2.6947076505094056 0.4027838910781582 0.16197472527708037
|
||||
17 -1.553343026077184 -0.5326249015108566 -0.6372569894483383
|
||||
18 -2.32697929027452 -2.6229660088889384 -0.1908463010722981
|
||||
19 2.161025566743724 1.613342829181601 -1.2185964188334404
|
||||
20 2.200299550516107 0.13388691832171218 1.3492239308384593
|
||||
21 -1.444652156145116 -1.5251851082502694 -0.01486082239207267
|
||||
22 -1.069098522661769 0.6345737477571621 -0.7476592232484849
|
||||
23 -0.5530156382651018 1.8581482829486815 -0.9359906503001887
|
||||
24 -2.1057002294256346 -2.2411635326026076 0.1027461222133986
|
||||
25 -0.846470575235486 -0.16100145290710122 -0.8945542130124591
|
||||
26 -0.4600833044897612 0.1168099650353831 -0.3780372490219117
|
||||
27 -1.0507601010756238 2.380597031527799 1.2042435415073673
|
||||
28 2.4951223446270854 -0.7272384746662179 0.49148118274363145
|
||||
29 -1.4227701815513125 -1.7103131555856865 0.8522428843219197
|
||||
30 -0.6362527497446904 0.4809930863631752 -0.09023977411046079
|
||||
31 0.8307577317570568 -0.43366523738108803 0.3435388363003548
|
||||
32 2.193071783870056 1.5720818983016567 -0.002617308630618007
|
||||
run_vel: ! |2
|
||||
1 -199.33264006196603 -425.90458140644324 687.4446082626521
|
||||
2 -437.96841023792416 91.79431782876951 428.57844526457393
|
||||
3 256.4136360073004 753.6546188320922 -477.2093961250793
|
||||
4 566.9823183079484 -598.4626629699561 -572.6010613373849
|
||||
5 193.3673483203161 517.2757090545375 86.71381952181962
|
||||
6 330.2395000638781 -14.096120493379578 -736.8264608358458
|
||||
7 772.6058378438489 335.4342218605717 -492.47120565202727
|
||||
8 -379.69346948872095 328.07026948905315 212.8907928502149
|
||||
9 -32.22616772317161 520.1349898628745 -354.5179475075607
|
||||
10 1.0828608441585152 -152.03654350035677 -287.63229160711455
|
||||
11 -8.398427517515586 462.54972999070884 -696.8949630195855
|
||||
12 -35.97938353895289 590.1362599649709 750.3193298672243
|
||||
13 -738.0063700936831 2.1036698005985586 521.0581963709241
|
||||
14 734.7145728536893 -576.3310076952716 -212.8973489276375
|
||||
15 462.14962458969075 517.8011186395346 582.1970348843957
|
||||
16 579.8864331189503 -723.7080269305067 -397.93358494791835
|
||||
17 -74.75036331228799 -271.6937286797369 318.88308122021147
|
||||
18 -390.80278885093725 -625.5459111419849 -678.090840223804
|
||||
19 -598.6933260882906 41.7579655827356 750.013779723682
|
||||
20 158.9763823000137 310.0053213378944 226.83667759758563
|
||||
21 -578.1763126419472 755.241466585726 -387.1851268613029
|
||||
22 -686.649568451259 496.2326396493665 -392.30182210275524
|
||||
23 139.72339904857833 686.4901911325059 460.94182891802774
|
||||
24 625.6387119562066 -178.79780516572728 194.63377933230842
|
||||
25 761.5753760889415 -550.6374632586046 -355.3666363468769
|
||||
26 -167.9925585211552 -748.0176849962858 537.6949353742531
|
||||
27 -687.973065038564 -637.3675344653028 -231.07938308121751
|
||||
28 -480.2313784604401 372.9809695991278 24.972745276651647
|
||||
29 67.21410614540838 54.58636231646205 639.3712010004265
|
||||
30 -469.9090654062959 715.7242943947524 -386.21519675922724
|
||||
31 -380.59017466972404 487.7214660680053 177.24466119039292
|
||||
32 138.31144158562722 31.005629253137737 621.8772779588675
|
||||
...
|
||||
16
unittest/force-styles/tests/in.brownian
Normal file
16
unittest/force-styles/tests/in.brownian
Normal file
@ -0,0 +1,16 @@
|
||||
variable newton_pair index on
|
||||
variable newton_bond index on
|
||||
variable units index lj
|
||||
variable input_dir index .
|
||||
variable data_file index ${input_dir}/data.brownian
|
||||
variable pair_style index 'zero 8.0'
|
||||
|
||||
atom_style hybrid dipole sphere
|
||||
atom_modify map array
|
||||
neigh_modify delay 2 every 2 check no
|
||||
units ${units}
|
||||
timestep 0.00001
|
||||
newton ${newton_pair} ${newton_bond}
|
||||
|
||||
pair_style ${pair_style}
|
||||
read_data ${data_file}
|
||||
Reference in New Issue
Block a user