Merge pull request brucefan1983#1354 from brucefan1983/neighbor_skin

Neighbor skin

Author: brucefan1983

examples/gpumd_static_qnep/check_force.m

@@ -0,0 +1,10 @@
+clear; close all;
+load force.out; f_gpumd=force;
+load ../qnep_train/force_train.out; f_nep=force_train(end-250+1:end,1:3);
+
+% The difference should be of the order of 1.0e-5 (used float32)
+figure;
+plot(f_gpumd-f_nep);
+xlabel('force components');
+ylabel('force difference (eV/A)');
+

examples/gpumd_static_qnep/force.out

@@ -0,0 +1,252 @@
+250
+energy=-930.7339 config_type=nep2xyz pbc="T T T" Lattice="0.0 16.42598 16.42598 16.42598 0.0 16.42598 16.42598 16.42598 0.0" Properties=species:S:1:pos:R:3:force:R:3
+Te 3.271619 3.093816 3.354722 0.4178623 -0.03671069 -0.04290853
+Te 3.726119 6.524911 6.853489 -1.835852 -0.5027356 -0.4577284
+Te 3.062335 9.854356 9.655031 0.9576747 0.1414655 0.03138862
+Te 3.113253 13.23199 13.04023 0.3957994 0.3373227 -0.4825681
+Te 3.151938 16.45746 16.58453 0.4619781 -0.3557196 1.073658
+Te 6.61597 3.406539 6.56348 -0.5119107 -0.309184 -0.1483855
+Te 6.818419 6.396775 9.446898 -0.172662 0.3738411 1.341981
+Te 6.58936 9.750887 13.12029 -0.6761609 -0.2965099 -0.193118
+Te 6.509181 12.90718 16.0896 -0.07672233 0.0629147 0.4893807
+Te 6.795459 16.01639 20.01796 -0.4616477 0.7669315 -0.4298059
+Te 9.799578 3.213685 9.695748 -0.2964724 0.3111931 0.5021567
+Te 10.25448 6.746473 13.23286 -0.2369433 -0.6828483 -0.369616
+Te 10.06031 10.00271 16.2163 -0.2623187 -0.8411739 0.6022076
+Te 10.08539 13.25318 19.50965 -0.4481792 -0.2830888 0.528738
+Te 9.840529 16.49882 22.82711 0.08347789 -0.05744876 0.2549964
+Te 12.92435 3.214646 13.18038 0.5564087 0.5415148 -0.4445723
+Te 13.65254 6.808584 16.38037 -0.7309651 -0.3045799 0.1410419
+Te 13.19434 9.88329 19.98644 -0.6555074 -0.1026289 -0.3467572
+Te 13.08389 13.2721 23.07105 0.5007784 0.01250488 -0.1009295
+Te 12.94047 16.23888 26.64511 0.2856781 0.2614301 -1.342086
+Te 16.50385 3.484317 16.89154 0.1983468 -0.2825685 -1.2957
+Te 16.42666 6.364239 19.88528 0.02872045 0.7237774 0.3953798
+Te 16.34348 10.02925 22.96552 0.2320294 -0.1884236 -0.6261373
+Te 16.6657 13.23955 26.68232 -0.6276999 -0.08495966 -0.6826707
+Te 16.32071 16.42075 29.4197 0.130578 -0.06857815 1.24198
+Te 6.653993 6.200308 3.37074 -0.1380501 0.4812093 -0.6276657
+Te 6.715292 9.865942 6.458605 -0.3030834 0.2484845 0.2623713
+Te 6.522793 13.16659 9.714314 0.09823397 0.08949508 0.1505688
+Te 6.376528 16.3824 13.20978 0.1326017 0.1228017 -0.3079168
+Te 7.016444 19.50251 16.40108 -1.348899 0.02520408 0.06015767
+Te 9.843024 6.478901 6.815334 0.3329155 -0.1649574 -0.4896913
+Te 10.09985 9.936726 9.932042 -0.8080412 -0.2060245 0.4087245
+Te 9.833313 13.1322 13.30761 -0.02024022 0.03962487 -0.9381703
+Te 9.765676 16.28636 16.25086 -0.4155767 0.1373126 1.215676
+Te 10.14753 19.40495 19.82298 -0.8619866 1.710019 -0.09218778
+Te 13.03418 6.364902 10.00673 0.4646212 0.1179495 -0.3013794
+Te 12.84195 9.806069 13.013 0.444393 0.2942519 0.1589155
+Te 12.83186 13.10297 16.07298 1.404882 0.2557028 0.1972959
+Te 13.06883 16.51057 19.53538 0.279159 -0.5649678 1.014018
+Te 13.30587 20.00114 23.13237 -0.06226308 -1.462515 0.02610864
+Te 16.5526 6.578258 12.95772 0.6250243 -0.7390754 0.2887572
+Te 16.45025 9.781472 16.46165 0.04031036 0.02456321 0.2496806
+Te 16.17805 13.61743 19.71222 0.6063068 -1.064941 0.02198587
+Te 16.56738 16.19983 23.10549 -0.2232278 1.056379 -0.1448011
+Te 16.20464 19.82877 26.28801 0.3085634 0.2077757 0.3939086
+Te 19.85517 6.608617 16.38447 0.4686427 -0.283312 0.1500215
+Te 20.01787 9.713969 19.5051 -1.044881 0.1032558 0.2604769
+Te 19.52284 12.7906 22.91347 0.4649547 0.4325998 0.01323022
+Te 19.68557 16.33484 26.32861 -0.1058113 0.5840195 -0.2634257
+Te 19.60017 19.94678 29.52157 0.0341643 -0.8876624 0.1776707
+Te 9.752102 9.631653 3.21619 0.5651868 -0.04843566 0.1797296
+Te 10.17266 13.12713 6.298129 -0.9070545 0.08358381 0.9555175
+Te 9.647569 16.19221 9.845938 0.4611896 0.9552449 -0.1677078
+Te 9.739165 19.62242 12.9631 0.1049626 0.9108093 -0.05449078
+Te 9.668087 22.73405 16.2236 1.046418 0.9585665 0.03525393
+Te 13.15035 9.964495 6.451198 0.09504678 0.01513465 0.7439503
+Te 12.93371 12.87214 9.596161 0.07971778 0.6038511 0.4345798
+Te 12.78712 16.49645 13.51108 0.7078491 -0.3700581 -1.332965
+Te 13.11617 19.59238 16.6097 0.5984583 0.3332274 -0.2975208
+Te 13.04055 23.15966 19.97637 0.3212137 -0.2311452 -0.4860329
+Te 16.26494 9.953267 10.23873 0.6986035 -0.2995097 -0.5554386
+Te 16.15845 12.99397 12.93615 0.6025555 0.5360302 0.2379038
+Te 16.19623 16.08619 16.45401 0.07462887 0.7342525 -0.40692
+Te 16.34217 19.91963 19.94488 0.2365406 -0.1019782 -0.2924877
+Te 16.57676 23.18063 23.21917 -0.1224732 -0.2331979 -0.03241153
+Te 19.72765 9.668235 13.14587 0.1059227 0.7529546 -0.1939959
+Te 19.51579 13.15856 16.24165 0.354252 0.1286236 0.02886121
+Te 19.42775 16.44608 19.28568 0.3782406 0.09320807 0.3753693
+Te 19.97098 19.93138 23.07382 -0.3803166 -0.4596229 -0.3343343
+Te 19.59941 22.82606 26.18738 -0.1718882 0.1365622 0.0598887
+Te 22.84377 9.742506 16.55719 0.3969737 0.1889196 -1.273697
+Te 23.19012 12.86294 19.80729 -0.392519 0.2592839 -0.2840821
+Te 22.98495 16.59922 22.50676 0.09615732 -0.3441186 0.5537661
+Te 23.0413 19.79295 26.33442 -0.2198644 -0.2677602 1.095605
+Te 22.93291 23.02847 29.41573 0.1560279 -0.2603299 -0.08434326
+Te 13.49315 13.29685 3.191847 -0.5561757 -0.04502978 0.1620968
+Te 13.10399 16.8922 6.782936 -0.02619075 -0.3291844 -0.2963825
+Te 13.17212 19.70593 9.666586 0.1980778 0.02301659 0.216726
+Te 13.12841 22.60864 13.19792 -0.2113059 0.541669 0.1193137
+Te 13.43609 26.2835 16.26833 -0.5939187 -0.3026222 0.3561308
+Te 16.36711 13.35355 6.555164 0.142872 0.04830603 -0.1540305
+Te 16.4587 16.88677 9.41268 -0.449064 -0.9250133 0.6704662
+Te 16.63699 19.81113 13.18397 -0.6391712 -1.060792 -0.04569551
+Te 17.09441 22.96167 16.31496 -1.079916 -0.07479181 0.1792029
+Te 16.24122 26.2487 19.63076 0.1366179 -0.9683704 0.1218345
+Te 19.81702 13.22891 9.634319 0.2619817 -0.5605295 0.3699209
+Te 19.83018 16.8145 12.70389 -0.3711576 -0.6543218 0.7377583
+Te 19.54711 20.02282 16.35082 1.234444 -0.6816143 0.129164
+Te 19.65816 23.09867 19.49372 0.1138861 -0.08349364 0.5369375
+Te 19.59114 26.40206 23.01524 1.146714 0.7202297 0.02806017
+Te 22.99628 13.07312 13.29928 -0.557681 -0.4217914 -0.2875785
+Te 22.68905 16.595 16.13783 0.2966849 -0.2595265 0.6125215
+Te 23.00432 19.52895 19.80219 -0.00771327 0.254186 -0.2815232
+Te 22.80952 22.91463 22.51089 0.7953683 0.843891 0.341168
+Te 22.99666 26.09775 26.51839 -0.01797682 -0.1121758 -0.09464158
+Te 26.55801 12.76718 16.5486 -0.4176666 0.5193005 -0.3459772
+Te 26.28996 16.13355 19.51889 -0.1191773 0.7080027 0.7579734
+Te 26.44108 19.83296 22.83472 0.3804671 -0.3241681 0.09484598
+Te 26.36981 23.06605 25.86473 -0.216101 -0.433407 0.7215093
+Te 26.33588 26.09245 29.48707 -0.3824567 0.1966021 -0.1320356
+Te 16.30581 16.1198 3.207095 0.1762601 0.2374005 -0.3618564
+Te 16.60908 20.14057 6.706967 0.1285667 -0.2467724 -0.4864591
+Te 16.73828 23.15942 9.988163 -0.4322052 0.05406187 -0.3111791
+Te 16.00778 25.95506 12.68563 1.429248 0.5211037 0.5952873
+Te 16.50287 29.4319 16.53595 -0.02610361 0.08460394 -0.08429304
+Te 19.64282 16.49554 6.536366 0.079586 0.5427508 -0.4255004
+Te 19.60305 19.7774 9.939389 0.5655909 -0.04102947 0.03817765
+Te 20.03185 23.38647 13.13093 -0.3300069 0.00508344 0.2603405
+Te 19.56777 26.26793 16.2745 0.7502346 0.3120122 -0.0106814
+Te 19.98792 29.58167 19.56572 -0.1452311 -0.233717 -0.03519835
+Te 22.91222 16.43406 9.769725 -0.09810562 -0.1168843 0.3946648
+Te 22.91675 19.41143 13.08919 0.05315387 0.5665113 -0.1945502
+Te 23.53007 23.12869 15.69246 -0.07279816 0.07115629 1.958474
+Te 22.70245 26.28953 19.96822 0.3418579 -0.4197184 -0.4207875
+Te 22.7301 29.63234 23.08503 0.7390414 -0.186939 -0.2568269
+Te 26.29256 16.31056 13.17398 -0.1420594 0.0990279 0.129362
+Te 26.05219 19.60529 16.22146 -0.2409526 -0.02813591 0.1592126
+Te 26.00763 23.10161 19.64653 0.1703689 -0.1625375 -0.5382918
+Te 26.29527 26.46534 22.57284 -0.07916441 -0.2006908 0.8064147
+Te 26.36312 29.81318 26.38093 0.5389042 -0.5922257 -0.265708
+Te 29.63839 16.43856 16.37616 -0.2972888 0.1975511 0.3307215
+Te 29.70753 19.9619 19.36755 -0.2810625 -0.1042271 0.4756591
+Te 29.66368 23.14297 23.14656 0.03606841 0.06289943 -0.4319156
+Te 29.68859 26.2336 26.5819 -0.5343883 -0.05862129 -1.577152
+Te 29.71768 29.43496 29.5237 -0.9631964 0.02077338 0.2085259
+Pb 16.47114 0.4236777 16.57017 -0.4552497 -0.3012434 0.00967641
+Pb 0.1505992 3.331709 3.417618 -0.07930008 -0.5178978 0.2889917
+Pb 0.3682952 6.908693 6.802916 -0.2294214 -0.1697576 0.05395334
+Pb 16.46376 10.02862 26.01018 -0.2008672 0.1942918 0.281638
+Pb 16.21912 29.38144 13.39268 0.35449 -0.1078183 -0.3755942
+Pb 19.42357 16.12292 3.333082 0.2033474 0.3509803 0.1825591
+Pb 19.80419 19.84949 6.839192 0.08989513 -0.1790542 -0.2660138
+Pb 19.83872 23.02259 10.10324 0.1793011 0.1005776 -0.2739763
+Pb 2.798711 10.25272 12.68271 0.09819595 -0.748346 0.3356297
+Pb 3.08343 13.15923 15.95781 0.6543095 -0.3498453 1.136109
+Pb 22.91224 16.58842 6.798641 0.1959809 -0.04400631 -0.2869491
+Pb 22.81701 19.72375 9.897097 0.08696858 -0.1528902 0.0296456
+Pb 23.06904 22.70706 12.96962 0.07714704 -0.08020815 -1.576178
+Pb 22.91337 26.15014 16.65898 -0.1310284 0.4959097 0.05107187
+Pb 6.874417 12.97518 19.71235 -0.2144171 -0.2581765 -0.01496118
+Pb 26.04549 16.46861 10.12116 0.04914492 -0.1785714 -0.2811877
+Pb 9.843035 3.294036 12.81705 -0.4541946 -0.01714358 0.7711135
+Pb 10.25246 6.702556 16.27314 0.1665738 -0.09288058 0.2662945
+Pb 25.86911 26.35393 19.52441 -0.1199253 0.05309357 0.0207392
+Pb 10.1404 13.25738 22.97017 -0.8469818 -0.03029087 0.0673749
+Pb 13.04288 0.207372 13.18027 0.08345558 -0.5963219 0.5292234
+Pb 29.00363 19.75063 16.20347 0.655498 0.05869543 0.3808134
+Pb 29.04578 23.20373 19.65942 0.6213053 -0.4605318 -0.157831
+Pb 29.67852 26.25068 23.21341 -0.3553272 0.1778558 0.2044311
+Pb 29.74109 29.46094 26.47524 0.1155771 0.06495349 -0.04715816
+Pb 3.465951 19.48524 16.54462 -0.04793568 0.729939 0.04425291
+Pb 3.165605 6.169866 3.353108 0.3197958 0.3799439 0.06732748
+Pb 3.324785 9.49879 6.427485 0.2397809 0.9857993 -0.325551
+Pb 19.75686 13.33541 26.30086 -0.3487237 -0.4194981 -0.4140215
+Pb 3.260894 16.35882 13.77251 0.1557122 0.3500332 -1.937363
+Pb 6.96865 19.63297 19.72224 -0.4551898 -0.3660643 -0.0562896
+Pb 6.534764 6.759867 6.580843 1.39826 0.06596352 -0.6749625
+Pb 6.671526 10.14949 9.843002 -0.01209092 -0.913911 -0.1555436
+Pb 6.816282 12.77251 12.93811 -0.2955361 0.6604922 0.5025176
+Pb 6.719262 16.00495 16.90762 -0.2755926 0.1885617 -0.323533
+Pb 9.573784 3.276565 6.753419 0.7105202 -0.04090249 -0.5827534
+Pb 10.01424 6.599314 10.07908 -0.662405 0.1230771 -0.1107269
+Pb 9.588059 9.794149 13.23024 0.2777287 0.2787613 -0.3005793
+Pb 9.967723 13.03467 16.43261 -0.95117 0.3022127 0.09294478
+Pb 9.845206 16.57604 19.62049 -0.1013729 -1.424786 0.1395914
+Pb 12.84383 3.076767 9.951634 0.5273625 -0.00878279 -0.1249406
+Pb 13.58805 6.823465 13.04111 -1.157203 -0.6047291 0.5591815
+Pb 13.28683 10.06864 16.57396 -0.4283134 -0.3459605 -0.1665637
+Pb 13.13798 12.96 19.8843 -0.2477424 0.5258024 -0.1008084
+Pb 13.00745 16.53741 23.22361 0.1038187 -0.00550744 0.0197309
+Pb 16.50055 19.53585 29.62247 -0.1416334 0.2523016 0.03329608
+Pb 16.90296 6.613087 16.93248 -0.7561127 0.02328146 -0.4342833
+Pb 16.07146 10.22046 19.60028 1.019029 -0.1061481 0.2644084
+Pb 16.34152 13.25764 22.86181 0.3153713 -0.2371158 0.2812737
+Pb 16.3798 16.77656 26.5599 -0.01386222 -0.6235293 -1.031657
+Pb 23.11883 23.01951 32.73967 -0.6774963 -0.4213539 0.5396778
+Pb 23.0164 9.663747 19.46929 0.3104188 0.01846432 1.134738
+Pb 6.660604 13.12648 6.627982 -0.0469092 0.2073687 -0.6260284
+Pb 6.427621 16.28586 9.892939 -0.2661854 0.570339 0.3542586
+Pb 22.90958 19.99388 29.68692 0.2911062 -1.141999 -0.04305036
+Pb 9.826208 22.78215 19.64381 0.07833469 0.3564284 0.2513719
+Pb 10.00322 9.501995 7.004243 -0.07905021 0.501907 -0.8620366
+Pb 9.706674 13.30971 10.02183 0.4996683 -1.1014 0.1403172
+Pb 9.645476 16.73622 13.43491 -0.5359885 -0.7315449 -1.115166
+Pb 9.97193 19.83553 16.59385 0.5198737 -0.8762301 -0.1713316
+Pb 13.10553 6.448529 6.756917 -0.1139646 1.142514 -0.1707036
+Pb 13.19601 9.837274 9.604901 0.01931025 -0.231087 0.08278512
+Pb 13.10088 13.0013 12.67615 -0.06320368 0.1125173 0.5037073
+Pb 12.78625 16.35561 16.52695 0.7581846 -0.0270756 0.1031366
+Pb 13.10697 19.48722 19.98199 0.6619269 0.6202042 -0.1576915
+Pb 16.11869 6.742069 9.871807 0.2582889 -0.1283871 0.07669078
+Pb 15.91887 9.443044 13.34942 0.432611 1.206046 -0.0680839
+Pb 16.33068 13.0238 16.65139 -0.0379842 0.238402 -0.5360035
+Pb 16.28881 16.65586 19.87974 -0.1055606 0.3019105 0.02243742
+Pb 16.63065 19.81613 23.15092 0.1210274 0.03676146 0.0222794
+Pb 19.72281 6.591162 13.20406 -0.2004019 -0.0157837 0.03759349
+Pb 19.5683 9.864079 16.22829 0.1884777 0.1600121 0.4560643
+Pb 19.89572 12.92453 19.76836 0.05124101 -0.08989451 -0.02583272
+Pb 19.79675 16.55528 22.61969 -0.03775303 0.06822538 0.2918857
+Pb 19.63721 19.55222 26.24767 0.06498454 -0.1533157 0.07792047
+Pb 9.812574 9.703303 0.1809424 0.1393287 -0.1579687 -0.1069064
+Pb 9.995788 13.0941 3.345598 0.1177294 -0.5404144 -0.2939503
+Pb 26.13128 16.34557 23.05954 0.01881255 -0.118833 -0.1609591
+Pb 10.13586 19.23787 9.71984 -0.3110856 0.5651088 0.2679084
+Pb 26.15048 22.96608 29.27835 0.3316525 -0.349567 -0.06628326
+Pb 13.11283 9.949235 3.543946 -0.4690019 -0.06430194 -0.8068692
+Pb 13.11689 13.75228 6.742264 0.5084562 -0.1614625 -0.7054194
+Pb 13.12563 16.5672 10.02238 0.1841281 -0.06485438 -0.1802444
+Pb 13.71818 19.50061 13.35254 -1.13839 0.1609118 0.1500806
+Pb 13.01987 23.02747 16.62962 0.05582305 3.58e-05 -0.00651712
+Pb 16.72952 10.22167 6.598318 -1.267876 -0.1995301 -0.01666824
+Pb 16.80728 12.95207 9.751488 -0.5050027 0.4389297 0.1274429
+Pb 16.00908 16.34847 12.90175 0.2886186 -0.4223795 0.3254676
+Pb 16.72817 19.73346 16.75752 -1.473874 0.00767551 -0.02989843
+Pb 16.4991 23.08094 20.261 -0.334917 -0.00493688 -0.7109595
+Pb 19.6331 25.8897 26.53902 -0.3010659 0.5245229 -0.3203811
+Pb 19.79365 13.30568 12.95709 -0.3078111 0.14431 0.1207613
+Pb 19.33216 16.6418 15.99988 0.1439152 -0.2795729 -0.064258
+Pb 19.56865 19.81657 19.82475 0.3477235 -0.07460461 0.1580026
+Pb 19.84296 23.48977 22.96939 -0.4773512 -0.9081029 -0.1704594
+Pb 23.10437 25.97894 29.53879 -0.1663912 0.9683847 0.751643
+Pb 22.88789 12.97927 16.51435 -0.07897714 0.2450064 0.09121716
+Pb 22.59992 16.52049 19.32695 0.08635618 -0.2216374 0.1910302
+Pb 23.38601 20.16633 23.50789 -0.415478 -0.9638194 -1.381787
+Pb 22.61355 22.95115 26.12954 0.4948719 -0.3037977 -0.1189824
+Pb 13.41539 29.63791 16.41939 -0.3110632 -0.1593982 0.1182934
+Pb 29.46922 16.48082 19.6076 0.1298439 -0.07431568 0.01121289
+Pb 29.99494 20.11561 22.67822 -0.6087404 -0.3253704 0.1234005
+Pb 13.04939 22.93309 9.897104 0.1490305 0.03725854 0.1449523
+Pb 13.08746 26.0651 13.06542 -0.5973291 0.08646698 1.204235
+Pb 16.62114 29.09356 19.65227 0.02960563 1.390549 0.2642678
+Pb 16.43315 16.82818 6.222935 -0.2083256 -0.1580895 0.4978938
+Pb 16.59573 19.92096 9.696522 -0.5359686 0.1896113 0.6111418
+Pb 16.2802 22.78407 13.26779 -0.0046312 0.6312124 -0.0176184
+Pb 16.50345 26.04562 15.8261 -0.3319387 0.08394059 0.2763738
+Pb 19.63921 13.49488 6.457866 -0.1983318 -0.6763413 -0.1612323
+Pb 19.53714 16.25107 9.671512 0.1287282 0.3538035 0.3259786
+Pb 19.42241 20.32228 13.21737 1.556869 -0.2974837 -0.152519
+Pb 20.10479 23.1004 16.4136 0.06987589 0.4033801 -0.1687026
+Pb 19.36351 26.47421 19.42703 0.4799813 -0.262866 0.1282122
+Pb 23.52347 29.08843 26.06517 -0.7226603 1.037316 0.4438153
+Pb 23.00029 16.19638 13.2181 -0.1011865 0.2484128 -0.5521249
+Pb 22.80281 20.10308 16.11823 0.3387706 -0.6022585 0.4076155
+Pb 22.88064 22.53929 19.31565 -0.1700167 0.2577152 0.1553445
+Pb 23.12234 26.53024 23.55448 -0.03643381 -0.2162895 -1.430733
+Pb 25.95353 12.92549 13.48482 0.879704 0.1376883 -0.3309284
+Pb 26.14225 16.07482 16.57886 -0.04536396 0.2990848 -0.7703942
+Pb 26.60045 19.41816 19.73334 -0.4216853 0.1327813 -0.2883173
+Pb 26.22585 22.9084 22.71694 -0.02867495 0.4824893 0.2037399
+Pb 26.32996 26.05282 26.20213 0.3392269 0.4091293 0.09732578

examples/gpumd_static_qnep/model.xyz

@@ -0,0 +1,2 @@
+Neighbor info at step 0: radial(max=92,actual=72), angular(max=10,actual=8).
+Neighbor info at step 0: radial(max=92,actual=72), angular(max=10,actual=8).

examples/gpumd_static_qnep/neighbor.out

@@ -0,0 +1,7 @@
+potential   ../qnep_train/nep.txt
+velocity    1
+
+ensemble nve
+time_step 0
+dump_force 1
+run 1