Include LAMMPS tables (bd54b30a) · Commits · Moreland, Ken / psi-bubble-finding

lammps_vtk/CMakeLists.txt

+17 −0

Original line number	Diff line number	Diff line
		@@ -16,3 +16,20 @@ if(NOT MPI_FOUND)
		PRIVATE LAMMPS::mpi_stubs
		)
		endif()

		# Copy LAMMPS potentials tables to binary directory next to executable so that
		# they are easier for LAMMPS to find.
		set(lammps_potentials
		He-Beck1968_modified.table
		W-He-Juslin2013.table
		W_Juslin2010_AT_mod.eam.fs
		)
		foreach(potential IN LISTS lammps_potentials)
		set(src ${CMAKE_CURRENT_SOURCE_DIR}/${potential})
		set(dest $<TARGET_FILE_DIR:lammps_vtk>/${potential})
		add_custom_target(copy_potential_${potential} ALL
		COMMAND ${CMAKE_COMMAND} -E copy ${src} ${dest}
		SOURCES ${src}
		COMMENT "Copying LAMMPS potential ${potential} to binary directory."
		)
		endforeach()

lammps_vtk/He-Beck1968_modified.table

0 → 100644

+5006 −0

File added.

Preview size limit exceeded, changes collapsed.

lammps_vtk/LammpsVtkSerial.cpp

+17 −16

Original line number	Diff line number	Diff line
		@@ -474,15 +474,13 @@ void loadDumpFile(const LAMMPS &rLammps, char *filename, std::string timestep,
		<< " x y z box yes scaled yes purge yes replace no add yes";
		std::string str = oss.str();
		rLammps.input->one(str.c_str());
		rLammps.input->one("variable pots string '/global/lammps/potentials'");
		rLammps.input->one("pair_style hybrid eam/fs table linear 10000");
		rLammps.input->one(
		"pair_coeff * * eam/fs ${pots}/W_Juslin2010_AT_mod.eam.fs W NULL");
		rLammps.input->one("pair_coeff 1 2 table ${pots}/W-He-Juslin2013.table WHe");
		rLammps.input->one(
		"pair_coeff 2 2 table ${pots}/He-Beck1968_modified.table HeHe");
		rLammps.input->one("pair_coeff * * eam/fs W_Juslin2010_AT_mod.eam.fs W NULL");
		rLammps.input->one("pair_coeff 1 2 table W-He-Juslin2013.table WHe");
		rLammps.input->one("pair_coeff 2 2 table He-Beck1968_modified.table HeHe");
		rLammps.input->one("mass 1 183.84");
		rLammps.input->one("mass 2 4.002602");
		#if 0
		rLammps.input->one("compute tensor all stress/atom");
		rLammps.input->one(
		"variable omega atom -(c_tensor[1]+c_tensor[2]+c_tensor[3])/3");
		@@ -491,6 +489,7 @@ void loadDumpFile(const LAMMPS &rLammps, char *filename, std::string timestep,
		rLammps.input->one("dump 1 all custom 1 dump.PV-temp id v_omega");
		rLammps.input->one("run 0 post no");
		rLammps.input->one("fix 1 all nve");
		#endif
		}

		// Loads .restart file using the given input details
		@@ -1054,7 +1053,9 @@ struct ColorScheme PickColors(int SimColors, float HeOpacity, float WOpacity,
		return colors;
		break;
		case 15: // MU colors
		colors = ColorScheme(Color(1.0f, 1.0f, 1.0f, AtomOpacity), // helium atoms
		colors = ColorScheme(
		Color(1.0f, 1.0f, 1.0f,
		AtomOpacity), // helium atoms
		// Color(241,184,45, HeOpacity), // helium bubbles
		Color(0, 0, 0, HeOpacity), // voids
		Color(0.0f, 0.0f, 0.0f, AtomOpacity), // tungsten atoms

lammps_vtk/W-He-Juslin2013.table

0 → 100644

+331 −0

Original line number	Diff line number	Diff line
		#-> LAMMPS Potential File in tabular format. <-#
		# N. Juslin and B.D. Wirth, J. Nucl. Mater. 432: 61-66 (2013). #
		# Implemented by K.D. Hammond (2013) karlh@utk.edu
		WHe
		N 325

		1 0.01 193967.941432641 21165142.7035409
		2 0.02 88781.7058271842 5199760.86773195
		3 0.03 54461.7226844158 2255783.27652381
		4 0.04 37754.4525147374 1233285.07338825
		5 0.05 28027.0551422937 765154.791685769
		6 0.06 21746.7711436002 514318.047209743
		7 0.07 17407.2122555268 365457.111099578
		8 0.08 14260.380890756 270524.172812057
		9 0.09 11894.315375388 206649.630589727
		10 0.1 10064.3593879466 161847.200920021
		11 0.11 8616.61401638085 129358.142417815
		12 0.12 7449.7679909506 105145.917230655
		13 0.13 6494.61875555217 86685.1834957916
		14 0.14 5702.42313976808 72334.2424211515
		15 0.15 5037.94580316996 60990.8171175998
		16 0.16 4475.14199778904 51894.0939422829
		17 0.17 3994.38401078788 44506.229619365
		18 0.18 3580.62666819885 38438.9489608325
		19 0.19 3222.16279673461 33406.7013437966
		20 0.2 2909.75986785247 29195.976537891
		21 0.21 2636.04908399207 25644.7364933058
		22 0.22 2395.08534986163 22628.3414553063
		23 0.23 2182.02521022247 20049.740107058
		24 0.24 1992.88767473625 17832.5164484929
		25 0.25 1824.374223221 15915.8858113167
		26 0.26 1673.73168801722 14251.0430039002
		27 0.27 1538.64662154286 12798.4627755747
		28 0.28 1417.16307190682 11525.8804272463
		29 0.29 1307.61796220838 10406.7644777657
		30 0.3 1208.58985019291 9419.14958758174
		31 0.31 1118.8579596074 8544.73619272459
		32 0.32 1037.36917029033 7768.18965475981
		33 0.33 963.211228625566 7076.59012069084
		34 0.34 895.590859433663 6458.9972713357
		35 0.35 833.815769676712 5906.10340798657
		36 0.36 777.27976462076 5409.9550164674
		37 0.37 725.450370074705 4963.72782166695
		38 0.38 677.858485369477 4561.54392990095
		39 0.39 634.089691821654 4198.3223154716
		40 0.4 593.776918443069 3869.65589682796
		41 0.41 556.594226358163 3571.70994736531
		42 0.42 522.251519987548 3301.13772506169
		43 0.43 490.490029664824 3055.01007668961
		44 0.44 461.07843929567 2830.75644369566
		45 0.45 433.809555685745 2626.11521737135
		46 0.46 408.497434574275 2439.09179705296
		47 0.47 384.974893215623 2267.92302383156
		48 0.48 363.091351319355 2111.04691385653
		49 0.49 342.710951882019 1967.07681501168
		50 0.5 323.710921379843 1834.77927007332
		51 0.51 305.980135298364 1713.05499722693
		52 0.52 289.417860333203 1600.9225017701
		53 0.53 273.932649026687 1497.50391617084
		54 0.54 259.44136628296 1402.0127334168
		55 0.55 245.86833026895 1313.74315392891
		56 0.56 233.144552771494 1232.06081168718
		57 0.57 221.207066231741 1156.3946825672
		58 0.58 209.998326488761 1086.23000874818
		59 0.59 199.465681793803 1021.10209864685
		60 0.6 189.560899952328 960.590883129588
		61 0.61 180.239746551915 904.316126537919
		62 0.62 171.461608172096 851.933205957983
		63 0.63 163.189155273495 803.129384679904
		64 0.64 155.388040149985 757.62051633995
		65 0.65 148.026625916815 715.148125151611
		66 0.66 141.075743014823 675.476815185188
		67 0.67 134.508470148273 638.391968073426
		68 0.68 128.299936952045 603.697693987706
		69 0.69 122.427146011509 571.215005397664
		70 0.7 116.868812142757 540.780187122909
		71 0.71 111.605217088269 512.243339613345
		72 0.72 106.618077998551 485.467075341772
		73 0.73 101.890428258492 460.32535073159
		74 0.74 97.4065093817089 436.702418234594
		75 0.75 93.1516728402801 414.491885070093
		76 0.76 89.1122908237631 393.595866780115
		77 0.77 85.2756750325343 373.92422518237
		78 0.78 81.6300027083206 355.393881543952
		79 0.79 78.1642491910339 337.928196880203
		80 0.8 74.8681263671512 321.456412227117
		81 0.81 71.7320264421784 305.913142560798
		82 0.82 68.7469705293107 291.237918759986
		83 0.83 65.9045615992059 277.374772641144
		84 0.84 63.1969413826496 264.271860652001
		85 0.85 60.6167508595336 251.881122298665
		86 0.86 58.1570940046202 240.157969812335
		87 0.87 55.8115044935616 229.061005941579
		88 0.88 53.5739151020755 218.551767091662
		89 0.89 51.4386295574478 208.594489329042
		90 0.9 49.400296625012 199.15589503172
		91 0.91 47.4538862332645 190.204998198848
		92 0.92 45.5946674600827 181.712926639528
		93 0.93 43.818188219384 173.652759444123
		94 0.94 42.1202565026948 165.999378304597
		95 0.95 40.4969230436942 158.729331395598
		96 0.96 38.944465286023 151.820708657476
		97 0.97 37.4593725456438 145.253027437895
		98 0.98 36.03833226895 139.00712755184
		99 0.99 34.6782172967515 133.065074912029
		100 1 33.3760740523261 127.410072964226
		101 1.01 32.1291115790037 122.026381235854
		102 1.02 30.9346913593292 116.899240372539
		103 1.03 29.7903178538011 112.014803096661
		104 1.04 28.6936297025718 107.360070575369
		105 1.05 27.6423915383737 102.922833733498
		106 1.06 26.6344863633652 98.69161908997
		107 1.07 25.6679084466039 94.6556387351718
		108 1.08 24.7407567025028 90.804744101767
		109 1.09 23.8272933774771 87.0424919424945
		110 1.1 22.9746938084833 83.501083250349
		111 1.11 22.1568053467682 80.0995862713648
		112 1.12 21.372249301539 76.8339257499533
		113 1.13 20.6196874341871 73.7000865054019
		114 1.14 19.8978213575361 70.6941134318681
		115 1.15 19.2053919350916 67.8121114983956
		116 1.16 18.5411786802966 65.0502457488983
		117 1.17 17.9039991557794 62.4047413021631
		118 1.18 17.2927083726064 59.8718833518619
		119 1.19 16.7061981895337 57.4480171665332
		120 1.2 16.1433967122567 55.1295480895992
		121 1.21 15.6032676926612 52.9129415393513
		122 1.22 15.0848099280771 50.7947230089626
		123 1.23 14.5870566605305 48.7714780664787
		124 1.24 14.1090749759875 46.8398523548244
		125 1.25 13.6499652036138 44.9965515917961
		126 1.26 13.2088603150229 43.2383415700692
		127 1.27 12.784925323525 41.5620481571964
		128 1.28 12.3773566833817 39.9645572956038
		129 1.29 11.9853816890583 38.4428150025965
		130 1.3 11.60825787447 36.9938273703497
		131 1.31 11.2452724122346 35.6146605659201
		132 1.32 10.8957415129272 34.3024408312399
		133 1.33 10.5590098243284 33.0543544831148
		134 1.34 10.234449830679 31.8676479132323
		135 1.35 9.92146125192414 30.739627588146
		136 1.36 9.61947044297006 29.6676600492951
		137 1.37 9.32792979293674 28.6491719129885
		138 1.38 9.04631712440562 27.6816498704143
		139 1.39 8.77413509267092 26.7626406876384
		140 1.4 8.51091058499253 25.8897512055996
		141 1.41 8.25619411984519 25.0606483401084
		142 1.42 8.00955924617449 24.2730590818669
		143 1.43 7.77060194264106 23.524770496429
		144 1.44 7.53894001687615 22.8136297242495
		145 1.45 7.31421250473534 22.1375439806457
		146 1.46 7.09607906954318 21.4944805558102
		147 1.47 6.88421940134788 20.8824668148159
		148 1.48 6.678332616175 20.2995901976151
		149 1.49 6.47813665527576 19.743998219024
		150 1.5 6.28336768437487 19.2138984687485
		151 1.51 6.09377949293196 18.7075586113629
		152 1.52 5.90914289338127 18.2233063863173
		153 1.53 5.72924512039265 17.759529607943
		154 1.54 5.55388923011117 17.3146761654411
		155 1.55 5.38289349942409 16.8872540228954
		156 1.56 5.21609082520001 16.4758312192575
		157 1.57 5.05332812353902 16.0790358683639
		158 1.58 4.89446572903546 15.6955561589207
		159 1.59 4.73937679401809 15.3241403545121
		160 1.6 4.58794668780786 14.9635967935988
		161 1.61 4.44007239596442 14.6127938895147
		162 1.62 4.29566191954302 14.2706601304803
		163 1.63 4.15463367433779 13.9361840795741
		164 1.64 4.01691589014092 13.6084143747644
		165 1.65 3.88244600998598 13.2864597288958
		166 1.66 3.75117008941481 12.9694889296766
		167 1.67 3.62304219570535 12.6567308397093
		168 1.68 3.49802380713948 12.3474743964548
		169 1.69 3.37608321225264 12.04106861226
		170 1.7 3.25719490908079 11.7369225743464
		171 1.71 3.14133900441368 11.4345054448136
		172 1.72 3.02850061304264 11.1333464606264
		173 1.73 2.91866925702027 10.8330349336425
		174 1.74 2.81183826489826 10.533220250582
		175 1.75 2.70800417099883 10.233611873045
		176 1.76 2.60716611463897 9.93397933750975
		177 1.77 2.50932523941003 9.63415225533254
		178 1.78 2.41448409240832 9.3340203127359
		179 1.79 2.3226460234938 9.03353327083141
		180 1.8 2.23381458454253 8.732700965596
		181 1.81 2.14799292869986 8.43159330788831
		182 1.82 2.06518320961743 8.13034028344418
		183 1.83 1.98538598072548 7.82913195286937
		184 1.84 1.90859959447164 7.52821845164772
		185 1.85 1.83481960157053 7.2279099901466
		186 1.86 1.7640381502589 6.92857685359786
		187 1.87 1.69624338555161 6.63064940211416
		188 1.88 1.63141884849222 6.33461807069079
		189 1.89 1.56954287538349 6.04103336918388
		190 1.9 1.51058799706618 5.75050588234672
		191 1.91 1.45452033816503 5.46370626978796
		192 1.92 1.40129901631838 5.18136526601165
		193 1.93 1.35087554145878 4.90427368037354
		194 1.94 1.30319321504351 4.63328239712837
		195 1.95 1.25818652931969 4.36930237539354
		196 1.96 1.21578056655756 4.11330464916909
		197 1.97 1.17589039832831 3.86632032733041
		198 1.98 1.13842048472736 3.62944059362462
		199 1.99 1.10326407363948 3.4038167066833
		200 2 1.07030260000113 3.19065999999702
		201 2.01 1.03940508502285 2.99124188195356
		202 2.02 1.01042753546074 2.80689383580147
		203 2.03 0.98321234287971 2.63900741967382
		204 2.04 0.957587682867711 2.48903426657353
		205 2.05 0.93336691431989 2.35848608439528
		206 2.06 0.910347978676441 2.24893465587638
		207 2.07 0.888312799175878 2.16201183866769
		208 2.08 0.867026680100139 2.09940956527362
		209 2.09 0.846311972535292 2.0501194750481
		210 2.1 0.826052090711088 2.00205155230487
		211 2.11 0.806267097861257 1.95513674544071
		212 2.12 0.786945609506685 1.90934585391834
		213 2.13 0.7680765291529 1.86465047725327
		214 2.14 0.749649040410966 1.82102299086693
		215 2.15 0.731652599355765 1.77843652275056
		216 2.16 0.714076927113717 1.73686493090964
		217 2.17 0.696912002672274 1.69628278155967
		218 2.18 0.680148055903811 1.65666532804561
		219 2.19 0.663775560796824 1.61798849045792
		220 2.2 0.647785228887586 1.5802288359199
		221 2.21 0.632168002885678 1.54336355952145
		222 2.22 0.616915050487049 1.50737046587586
		223 2.23 0.602017758368489 1.47222795127685
		224 2.24 0.587467726357617 1.43791498643425
		225 2.25 0.573256761772716 1.40441109976729
		226 2.26 0.559376873926913 1.37169636123572
		227 2.27 0.54582026879146 1.33975136668933
		228 2.28 0.532579343812991 1.30855722271748
		229 2.29 0.519646682879861 1.27809553198093
		230 2.3 0.507015051432831 1.24834837900889
		231 2.31 0.494677391715517 1.21929831644497
		232 2.32 0.482626818160208 1.19092835172618
		233 2.33 0.470856612904789 1.16322193418007
		234 2.34 0.459360221436662 1.1361629425252
		235 2.35 0.448131248359705 1.10973567276124
		236 2.36 0.437163453280438 1.08392482643501
		237 2.37 0.426450746809703 1.05871549926971
		238 2.38 0.415987186676291 1.0340931701448
		239 2.39 0.405766973949056 1.01004369041464
		240 2.4 0.395784449364215 0.986553273554313
		241 2.41 0.38603408975458 0.963608485121541
		242 2.42 0.376510504577652 0.941196233024116
		243 2.43 0.367208432539548 0.919303758082476
		244 2.44 0.358122738311864 0.897918624877599
		245 2.45 0.349248409338683 0.877028712874665
		246 2.46 0.340580552730998 0.85662220781334
		247 2.47 0.332114392245936 0.83668759335581
		248 2.48 0.323845265348255 0.8172136429841
		249 2.49 0.315768620351645 0.798189412138432
		250 2.5 0.307880013637488 0.779604230588763
		251 2.51 0.300175106948751 0.761447695031842
		252 2.52 0.292649664756829 0.743709661906479
		253 2.53 0.285299551699157 0.726380240419923
		254 2.54 0.278120730085547 0.70944978577854
		255 2.55 0.271109257471214 0.69290889261619
		256 2.56 0.264149883217677 0.704309455966822
		257 2.57 0.257023670963235 0.720548414483017
		258 2.58 0.249746544950963 0.73449858053557
		259 2.59 0.242341191411443 0.746201328856265
		260 2.6 0.234829852474346 0.755704032488528
		261 2.61 0.227234268357011 0.763059628544665
		262 2.62 0.219575623890343 0.768326185205915
		263 2.63 0.211874499363033 0.771566471270733
		264 2.64 0.204150825652343 0.772847529495918
		265 2.65 0.196423843597567 0.772240254912945
		266 2.66 0.188712067560753 0.769818979238484
		267 2.67 0.181033253108439 0.765661062433794
		268 2.68 0.17340436873789 0.759846492402718
		269 2.69 0.165841571561793 0.752457493752577
		270 2.7 0.158360186856416 0.743578146476553
		271 2.71 0.150974691370005 0.733294015350452
		272 2.72 0.14369870028059 0.721691790771177
		273 2.73 0.136544957685405 0.708858941699004
		274 2.74 0.129525330497857 0.69488338130108
		275 2.75 0.122650805622294 0.679853145829612
		276 2.76 0.115931490271846 0.663856087205069
		277 2.77 0.10937661529017 0.646979579712699
		278 2.78 0.102994541334199 0.629310241159726
		279 2.79 0.0967927677717845 0.610933668781077
		280 2.8 0.0907779441455664 0.591934190123306
		281 2.81 0.0849558840523623 0.572394629079895
		282 2.82 0.0793315812859323 0.552396087196204
		283 2.83 0.0739092280900552 0.532017740309284
		284 2.84 0.0686922353684514 0.51133665053656
		285 2.85 0.0636832546982004 0.490427593578163
		286 2.86 0.058884201993894 0.469362901250494
		287 2.87 0.0542962826708072 0.448212319123508
		288 2.88 0.0499200181568738 0.427042879091302
		289 2.89 0.04575527360515 0.405918786664859
		290 2.9 0.0418012866607671 0.384901322737369
		291 2.91 0.0380566971390415 0.364048759536354
		292 2.92 0.0345195774744505 0.343416290443013
		293 2.93 0.0311874638035265 0.323055973327595
		294 2.94 0.0280573875483925 0.303016687020528
		295 2.95 0.0251259073715924 0.283344100512051
		296 2.96 0.0223891413770724 0.264080654448684
		297 2.97 0.0198427994365954 0.245265554472591
		298 2.98 0.017482215525515 0.226934775930029
		299 2.99 0.0153023799566589 0.20912107945741
		300 3 0.0132979714060716 0.191854036938167
		301 3.01 0.0114633886294948 0.175160067310366
		302 3.02 0.009792781773727 0.159062481694054
		303 3.03 0.00828008319235769 0.143581537298372
		304 3.04 0.00691903768080766 0.128734499561665
		305 3.05 0.00570323205109961 0.114535711972949
		306 3.06 0.0046261239723178 0.100996673020243
		307 3.07 0.00368107000826405 0.088126119710232
		308 3.08 0.00286135278937321 0.0759301171045549
		309 3.09 0.00216020726148435 0.0644121533205429
		310 3.1 0.00157084595956787 0.0535732394484653
		311 3.11 0.00108648325995938 0.0434120138431347
		312 3.12 0.000700358570037423 0.0339248502550448
		313 3.13 0.000405758419588332 0.0251059692749879
		314 3.14 0.000196037423311657 0.0169475525761798
		315 3.15 6.46380890244662E-05 0.00943985944932857
		316 3.16 5.1094511057313E-06 0.00257134513861945
		317 3.17 0 0
		318 3.18 0 0
		319 3.19 0 0
		320 3.2 0 0
		321 3.21 0 0
		322 3.22 0 0
		323 3.23 0 0
		324 3.24 0 0
		325 3.25 0 0

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