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add example for fix pimd/langevin with reduced units

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Yifan Li
2023-03-27 22:21:38 -04:00
parent 4e4ae34de6
commit 561f80ccc7
4 changed files with 465 additions and 0 deletions
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219
examples/PACKAGES/pimd/lj_reduced_units/data.lj01 Normal file
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LAMMPS data file via write_data, version 8 Feb 2023, timestep = 2000
200 atoms
1 atom types
-3.4945130603740377 3.4945130603740377 xlo xhi
-3.4945130603740377 3.4945130603740377 ylo yhi
-3.4945130603740377 3.4945130603740377 zlo zhi
Masses
1 1
Pair Coeffs # lj/cut
1 1 1
Atoms # atomic
108 1 -2.7795690566068996 -2.0367677788080942 3.4238258338844894 2 1 -1
102 1 -2.609481280743025 -1.8912619121268304 -2.399753092988466 1 -1 -1
141 1 -3.140749645549514 -2.8903241627869427 -2.7071762462261537 2 0 0
49 1 -2.3658136681990007 -3.088812044820056 3.4760124445890623 0 1 -1
88 1 -1.6158710173914035 -2.3369020600614756 3.233517474511907 0 1 -1
192 1 -1.2960228223928079 -3.237522585981233 -3.1506262911155765 1 1 2
113 1 -0.5058112539671865 -2.175265580488635 -2.895948573481031 -1 0 0
147 1 -0.22721902013037146 -3.2095321965856187 -2.5444416457809185 0 1 0
55 1 0.6250447384071113 -2.6446349401275255 -2.959767417439857 -1 0 -1
63 1 1.6783992808137906 -3.22203513406057 -3.1652676844989256 -1 1 1
95 1 1.3579478870419064 -2.684729254303277 -2.052496056604152 0 2 -1
105 1 1.4496281787006915 -1.9673030959679096 -3.332658945278261 0 0 0
84 1 2.4045875426768606 -1.8297724699275564 -2.7874627893944544 0 0 0
65 1 -2.68682939849047 -0.8114540186440395 -3.126687818057689 0 -1 0
112 1 -1.7203801180145006 -0.8038481618523634 -2.0163240721427838 0 0 0
174 1 -1.4968933339977661 -1.3290620346554367 -3.064010040861048 -1 0 -1
189 1 -0.6249709402997541 -1.252931712435372 -1.9882716349469658 0 0 2
9 1 -0.23886293275872486 -1.0612344376875333 -3.025432389188406 0 0 1
146 1 -0.9802936024515303 -0.3953988402073487 -2.8364522494017708 2 1 2
171 1 0.39730078560778914 -1.7846492070113664 -2.443607407553737 0 2 -1
140 1 0.5573788374911133 -0.5990036144148324 -2.402963062521378 -1 0 0
152 1 3.4379847727225346 -1.3055938268830742 -2.4905074589410936 -2 -1 0
11 1 3.1992117767992068 -1.191883736793153 -3.4723419170834338 -1 2 1
69 1 2.6376153053668867 -0.2845436411244765 -2.788279844473203 0 -2 0
173 1 -1.967038944001471 0.06098718735032446 -2.58940519609616 1 0 1
190 1 -2.8711350478349926 0.9129034739862979 -3.477848194666021 0 0 0
164 1 -2.8409776961511124 1.1599509265598786 -2.2464830240939375 0 0 1
161 1 -1.6469671018177567 0.9360204597700993 -3.3491365145788827 1 0 2
74 1 -0.028453987680887038 0.3739399392930446 -2.9891764409930484 1 -1 1
162 1 -0.9152119867762214 1.8538003710645874 -2.0787458665529313 0 0 1
165 1 0.20472499231506947 0.41157279287578097 -1.7804952487691292 0 0 0
28 1 0.9556568956317052 0.9070586383550882 -3.051580171737043 0 -1 -1
107 1 0.27101548210140264 1.6697625775553313 3.256398876364515 -1 1 0
53 1 -2.2768986954542476 1.9520208666344268 -2.905899876141582 -1 -1 1
60 1 -2.3748565234893153 3.1415519659534046 -2.6903226937570888 1 1 0
172 1 -1.3831407623603917 2.6439383680022495 -2.988114399273657 0 0 2
35 1 -1.9040946957475922 2.4850230251463294 -1.8238074088896814 1 -1 0
90 1 -0.6407155002729499 2.891205873820353 -2.184576201275668 0 -1 1
183 1 -0.7452468270399182 1.6958511415691964 -3.2646018242495516 1 0 0
46 1 -0.22701759376730096 2.672935498985858 -3.2296828094464414 1 -1 -1
26 1 0.3607641531328818 1.9915770180932266 -2.4322620664253045 0 -1 1
41 1 0.6373758855225722 3.1576967379383136 -2.2076729513672273 0 0 1
62 1 1.2599715479139464 2.4637352645229535 -2.996655642771261 0 0 1
114 1 0.7095094175128512 3.3529225376529834 -3.446569928809617 0 -1 1
29 1 -3.4441516076858747 3.186682881361427 -3.164290558791177 1 -1 0
120 1 -2.7699397214807666 -3.0679149510930377 -1.4586405778286127 2 1 1
166 1 -2.9639598123456348 -1.8230569851379879 -1.1336421298957986 0 1 0
19 1 -2.219481001384856 -2.718720936926987 -0.17152653954078959 1 1 -1
143 1 -3.3367462911096637 -2.646710289319255 -0.08639804580378332 1 1 0
14 1 -0.8080539703460301 -3.3138674801902015 -1.5513416052298858 -1 0 1
17 1 -1.2519028473371163 -1.9834151764617522 -0.4751925051419198 -2 0 0
7 1 -0.6422036076119758 -2.1822637849150257 -1.309964136714573 -1 0 1
76 1 0.002896678458885543 -2.2620445897063184 -0.2330303144789453 0 0 0
25 1 0.3195487317939559 -2.5915964162672633 -1.6847661018972104 -1 0 1
122 1 0.9437732996524034 -3.076308154774796 -1.0301951566376644 1 0 -1
188 1 1.3149323047475332 -2.0202232851439175 -0.9332517483120624 -1 0 0
196 1 2.4252816482051065 -2.9991133261256717 -0.2915609413585816 0 2 1
154 1 1.617010887740887 -2.199305270305938 0.15712874770371849 -1 2 0
64 1 2.934967635633404 -1.92620475221537 -0.7077313528493354 0 1 0
79 1 -2.8111804533557017 -0.5176533778232942 -2.0486672107634094 0 1 0
80 1 -2.079807139196039 -1.2506968999173758 -0.6878784167189951 0 0 1
12 1 -2.996784469690298 -1.494057160171672 -0.09378065633433766 0 0 1
87 1 -1.4786937501974577 -0.24572242955022147 -1.0411298155891553 0 -1 1
118 1 -1.5219571471797697 -0.6469152337096267 0.07790607124041445 0 1 0
106 1 1.1039107347748043 -0.9982945968846851 -1.4358613477546331 -1 0 0
6 1 0.2994229743009 -1.5755502164022743 -1.1025451212735877 2 0 0
98 1 0.14422647245316755 -0.4562748967814887 -1.1288823927075846 -1 0 0
36 1 1.117403260546369 -0.6258611972204157 -0.45746732579129296 1 -1 0
133 1 0.859517194013173 -1.4579095853876511 0.2223121798831755 1 1 1
1 1 1.9750704226304612 -1.2226584851722493 -0.5050391499153623 0 -1 0
91 1 2.930212504963826 -0.8900603772487206 0.31326990070574257 0 -1 -1
135 1 -1.8704119131145511 1.4151617424236407 -2.0299493395071555 1 0 0
145 1 -2.5978280185456044 0.23771261564216897 -0.6973478660383656 0 -2 -1
194 1 -0.802106175542123 1.5380363524561962 -1.0014646333327863 0 1 -1
177 1 -0.4209642163497379 1.4081511815239465 0.048786606404428355 0 1 -1
56 1 0.1655081354187105 0.488612868229853 -0.6685586469118172 0 0 1
137 1 1.0403444543974962 0.29392106264506496 -1.157047853549803 -1 1 -1
3 1 1.426791637331859 1.1994824011018168 -0.7391487398561316 0 -1 1
125 1 0.6384933993980926 1.4087406696008793 -0.04513978672724809 0 1 0
85 1 3.492386221258323 -0.022918569575539983 -0.18415289757087 1 0 1
37 1 1.9446560065460998 0.32690249887078415 -1.557848909197346 1 0 1
157 1 2.2693311785439514 1.4234672203444076 -1.3950756204319474 -1 -1 1
81 1 2.2043144165939133 0.7734976358785483 -0.1443989261496442 -1 0 1
193 1 -2.800913203549158 3.3913795040038752 -0.3002902442199323 1 0 0
127 1 -1.832485514575906 -3.475177695698571 -1.0143919033965547 0 0 0
104 1 -0.9864189902172598 -3.128510029811542 -0.3946109581791233 0 0 -1
72 1 -1.091863924309645 2.651695772194485 -1.1525574140711645 1 -1 0
99 1 -1.376188772302252 2.1367308970905112 -0.22414000562735564 0 -1 0
24 1 1.0798151658945965 1.8088284522753606 -1.611839691529319 1 -1 0
42 1 3.3099578488331143 2.7636832208891664 -0.11775790598994411 -1 1 -1
38 1 -2.6469918571054945 -2.446265188540552 0.8006326688775777 1 0 1
86 1 -3.3982593364606077 -1.9911707046121028 1.4129412590921573 -1 0 0
116 1 -3.3782151164102614 3.3939134790192074 0.6418244028431277 1 0 0
144 1 -2.152212571536467 -2.8119708535854224 1.6778364082976118 0 1 0
179 1 -0.8263021362457004 -1.7214596406733806 0.6812305480127513 -1 3 1
151 1 -1.5217298498042864 -2.5933593936403763 0.7963122225368328 0 1 2
130 1 -0.41366866285633624 -2.851509016203123 0.6773665297002652 -1 1 0
149 1 -0.8196954968551895 -2.4620140380344058 1.6681749543249536 1 1 0
123 1 0.42149982032625755 -2.3318080821151144 1.1400194349387576 -1 1 -1
142 1 1.7676090653529768 -2.7694388971884765 1.0411093428968425 1 1 0
43 1 1.2651581412723922 -1.7350310325188918 1.2119129817343088 -1 -1 1
156 1 2.796603060966876 -1.975811297437484 0.5269881248554414 0 -1 0
30 1 -2.572197786362113 -0.5211520888332514 0.06478473226429171 1 -1 0
200 1 -2.796037525463158 -1.2242406753887405 0.9147806710233006 -1 0 0
75 1 -3.264195451754593 -0.2758623474229462 0.8501703715118789 1 -1 0
199 1 -1.8606891200301348 -0.81109530705794 1.234068196576104 1 -1 1
119 1 -1.8952925629684365 -1.6742391291961565 0.3056526633582653 0 -1 0
153 1 -0.6179778569135823 -0.6812551828045249 0.8822634033092613 1 1 0
31 1 0.1434804396367878 -0.5352374975985325 0.00065681711961239 0 -1 0
8 1 0.9896949675708329 -0.5825805499366115 0.8390036708294969 0 0 0
198 1 0.20957042666083733 -1.2300305579788615 1.1505092305231928 0 0 1
22 1 0.11282413745771128 -0.029722367543426716 1.1299864513218787 -1 0 -1
195 1 2.9662277270739343 -0.9097471611972223 1.378968815531931 1 0 2
32 1 1.9176581701385829 -1.0963885598161285 0.612637989357651 1 0 -1
139 1 2.2034635745403706 -0.09403988556633318 0.8645554281632429 -1 2 0
77 1 1.7035877859699526 -0.8133688575022073 1.6318409740615665 0 -1 1
111 1 -3.223221512681343 0.8515794477136406 0.5304444380887284 1 1 1
138 1 -2.102339643808083 0.3205080511040257 0.6397061187151873 0 1 -1
103 1 -2.8441279458234914 0.5800051690180812 1.512417106043963 -1 1 0
184 1 -2.4512811422970944 1.4407376078485292 1.024840909070544 0 0 1
73 1 -1.2083083753201984 0.16913042396249212 1.31830897028215 0 -2 0
89 1 -0.622943103836138 0.15695545887374523 0.03344907944561345 0 0 -1
93 1 -0.6871612783719626 1.4782545941619265 1.7130745398216136 0 -1 0
94 1 -1.209899480419889 1.1419050120740204 0.768566708093127 0 0 0
181 1 0.8338139283938067 0.2955625473112081 0.1708175991674893 -1 1 -1
129 1 1.1355758059362249 0.3630461551808931 1.290797674214222 -1 0 0
182 1 0.08831527814343061 0.9709201913937692 0.9217855950625892 0 1 -1
158 1 1.4062820374169525 1.1517166598840343 0.6269036353613398 0 0 0
100 1 2.8360458941172935 1.5280995172170748 0.62642849190607 0 1 0
59 1 3.120666407088228 0.49773318717092796 1.2390797462592613 0 -1 1
40 1 2.1784673001300465 0.9493086808156442 1.37690657576216 0 0 0
110 1 3.092811420136352 1.457598231264991 1.8333488137634408 0 0 -2
71 1 -2.704068160468349 3.198799130983575 1.5420861670955985 0 -1 -1
187 1 -3.3809787804159894 2.339193447924602 0.9253127201661663 1 1 0
58 1 -1.8161128905276918 3.295453805825648 0.4419286058239596 0 -1 0
39 1 -1.9288855291902436 2.399541640622866 1.1856795461879515 0 -2 0
115 1 -1.3188418056778684 -3.426962627878111 1.3071043811339145 1 1 0
109 1 0.7422148102651713 1.9772692916114134 0.8946623229549697 -1 1 0
48 1 1.212990075236676 2.7637861839630933 1.668138216427735 0 0 -1
44 1 1.8875283020177747 2.01954806585405 0.15097670327664356 -1 -1 1
16 1 2.5088486436667465 3.2867062332187165 0.5352876678637931 0 -2 1
150 1 2.339993315563226 2.225227215494749 1.201791196292386 0 -1 1
101 1 -2.7232595674410254 -2.5310321070553594 2.520173028347837 1 3 1
121 1 -0.1371595891679715 -2.734037361783574 3.2547541081110136 -1 1 -1
131 1 -1.616105025949218 -1.97873290984862 2.2250110182725185 1 0 0
50 1 -0.9774458776093428 -3.080336575399165 2.647294574069851 0 1 0
78 1 -0.6388640381972747 -1.8358994538797384 3.0793625374288474 1 -1 1
126 1 0.2617829860592282 -3.185635897887874 2.046978007125428 0 1 -1
185 1 0.3910180046792306 -1.7476201774885758 3.460179487049301 -2 1 -1
27 1 0.9216706073777299 -2.620009754961919 2.980059759810019 0 0 1
5 1 0.14805884420723833 -2.060999311749248 2.194803632818035 0 -1 -1
10 1 1.3885697256222325 -2.5811721069430047 1.960299612344295 0 0 1
68 1 1.2305537223759786 3.452417391198064 2.5060768204562396 0 0 1
92 1 3.2579931163558924 -3.0623298587917547 1.8252693484803535 0 2 -1
178 1 2.26419751848874 -1.7585846281228215 1.7123805014943867 1 1 0
96 1 2.599921016729558 -2.6427367710738228 3.4145177684858803 -2 2 -1
57 1 3.2402592062064213 -1.9899576048001384 2.7907002699370937 1 0 0
155 1 2.209613988042176 -1.7162524781709796 2.7271827572979834 0 0 -1
168 1 3.477326382335708 -3.4068959852573992 2.821891114170504 -1 1 -2
175 1 -3.1260125076640937 -0.1261845495956751 3.231607373653429 0 0 0
117 1 -2.5082381499858095 -1.6201356456498082 1.916360867966056 0 0 0
4 1 -3.1142920073981517 -0.7023062901592412 1.8555906719306698 0 0 -1
51 1 -1.9626772134484154 -1.4010881760394245 3.033958867461655 0 0 -1
148 1 -3.011516485433896 -1.1469037793442038 2.7610753028279933 0 0 0
197 1 -2.0048159662329326 -0.6749211621392989 2.344679442661877 0 -1 -1
70 1 -1.8654941392471802 -0.3319695813423535 3.329224742630753 0 1 1
23 1 -1.0720302561208543 -0.8796307974060223 2.9652586368172633 0 0 -2
134 1 -0.9769774773292339 -1.023866537972646 1.8133872200496586 -1 0 0
66 1 0.0812156007450339 -1.0967406204476347 2.677696992399577 -1 -1 -1
33 1 -0.42833987516917704 0.2127920276630183 3.0504271041557827 0 -1 -1
18 1 0.8738459806171345 -0.7301638515378504 3.451151027750579 0 -1 -2
167 1 1.1687036142366616 -1.4517802174625138 2.5014340704062015 0 1 -1
136 1 1.795137560517328 -0.5623222017058748 2.761148573575212 0 -1 -2
176 1 0.8667263057428289 -0.39855552371320657 2.157386135628261 0 0 0
132 1 2.7791570748849397 -0.1854473725861777 3.06331164881256 0 0 -1
163 1 2.861161516036147 -0.9653887253660198 2.3742914745631665 -1 -1 0
159 1 -1.638440405488927 1.040992844593558 1.6945368306541542 0 0 0
34 1 -2.319980614869211 0.615010700172925 2.607891496520952 1 0 -1
67 1 -1.8758084270870021 1.7856292006021222 2.9794597615239873 1 0 0
82 1 3.450078342208421 0.43347862445962865 2.3965330453749276 -1 -1 -1
20 1 -0.3345634991984191 0.4474749361055883 2.021125197093307 1 0 -1
160 1 -1.337826167757788 0.19507650189296638 2.4559469377176044 0 0 0
191 1 -0.9433598322448645 1.0765639185970945 2.7978676989244713 1 -1 0
97 1 1.4995074975439164 1.4827775589636611 2.8582397165142885 0 -1 -1
83 1 0.7440931705195399 0.28485269404070884 2.8824261695219513 0 -2 0
186 1 0.4501325900005473 1.1817617584793225 2.171005382838285 1 1 0
21 1 1.5799209373811796 0.5165927484280916 2.197344395644513 1 0 -1
170 1 1.781383760665039 0.4589516263468447 3.2606047972968697 -1 1 -1
15 1 2.5264882009659457 -0.10271458568953422 1.9429509270634897 -1 0 -1
54 1 2.4907565610148112 1.0443458588262453 2.659572052524602 0 -1 -1
45 1 -2.3851170089162586 2.7278135027281576 3.2923683043438063 1 0 -1
47 1 -2.417816843075144 1.911767591397239 2.070179319067279 0 1 0
52 1 -3.4931268842957652 2.50155605132379 2.127865658713496 0 -1 0
180 1 -1.9509177290095516 3.309670529089689 2.349688492929276 1 -1 1
13 1 -0.12240867021598209 3.2141258686958913 2.833411182871058 -1 -1 1
2 1 -1.340442106022601 2.2849149851767008 2.069093746173476 1 -2 -1
124 1 -0.41265942682553436 2.1334074442091007 2.592421577863454 1 -1 -1
61 1 0.7799049336891462 2.500510040165389 2.633457440959517 -1 -2 0
128 1 2.8514020342376654 2.399755896897204 3.251183881976271 0 0 -2
169 1 2.1185477137097575 2.27540363851787 2.3296903855745934 0 0 0

219
examples/PACKAGES/pimd/lj_reduced_units/data.lj02 Normal file
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LAMMPS data file via write_data, version 8 Feb 2023, timestep = 8000
200 atoms
1 atom types
-3.4945130603740377 3.4945130603740377 xlo xhi
-3.4945130603740377 3.4945130603740377 ylo yhi
-3.4945130603740377 3.4945130603740377 zlo zhi
Masses
1 1
Pair Coeffs # lj/cut
1 1 1
Atoms # atomic
141 1 -1.763209980389579 -2.6156484242195064 -2.931843780833984 2 0 0
152 1 -1.5928871542954757 3.3501884422702433 -1.8656866405706811 -1 -2 0
49 1 -2.7539752553137182 -3.2181862303090325 -3.2982185001231508 0 1 0
113 1 -0.7003027892165357 -2.1799819378730754 -2.999588953057854 -1 0 0
147 1 -0.9066147762335637 -3.0721536393085946 -3.451497569202878 0 1 0
25 1 -0.8348129272923334 -3.2010555139777104 -2.4342714727995403 -1 0 1
7 1 -1.155032969500839 -2.109409697780318 -2.01960214884411 -1 0 1
122 1 -0.11210230788570166 -2.6275713274626975 -1.900506384406081 1 0 -1
55 1 0.23346664931542635 -2.573966195106371 -3.0437128589517024 -1 0 -1
95 1 0.716981854784511 -1.7560064219465084 -1.6999612600924723 0 2 -1
105 1 1.1248014998718883 -1.7403082354703703 -3.356758018801178 0 0 0
84 1 2.225043764737794 -2.1031554472806464 -3.42558560520243 0 0 0
65 1 -2.8977942390562763 -2.1977837904725823 -3.370623324950664 0 -1 0
175 1 -3.151432241251456 -0.37515180280237564 3.4437485581764316 0 0 0
173 1 -2.3157350741156972 -0.12943144237356516 -2.753320161369244 1 0 1
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26
examples/PACKAGES/pimd/lj_reduced_units/in.lmp Normal file
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@ -0,0 +1,26 @@
variable ibead uloop 32 pad
units lj
atom_style atomic
atom_modify map yes
boundary p p p
pair_style lj/cut 2.8015
read_data data.lj${ibead}
pair_coeff * * 1.0 1.0
pair_modify shift yes
mass 1 1.0
timestep 0.00044905847
fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 lj 0.00965188 3.4 39.948 4.135667403e-3 1.03646168908e-4 thermostat PILE_L ${ibead}
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no format line "%d %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f"
dump dcd all custom 1 ${ibead}.xyz id type x y z vx vy vz ix iy iz fx fy fz
dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
run 1000

1
examples/PACKAGES/pimd/lj_reduced_units/run.sh Normal file
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mpirun -np 2 $LMP -in in.lmp -p 2x1 -log log -screen screen