add adatom and vacancy examples for AGNI pair style (b9770766) · Commits · 郑智淋 / lammps

examples/USER/misc/agni/Al_prb.agni

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File added.

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examples/USER/misc/agni/adatom.data

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Original line number	Diff line number	Diff line
		Data File created from VASP POSCAR

		181 atoms
		1 atom types

		0 17.121440767 xlo xhi
		0 14.8276026536 ylo yhi
		0 39.3197318979 zlo zhi

		Masses

		1 26.982

		Atoms

		1 1 0.0 1.64751140595 15.0
		2 1 2.85357346116 1.64751140595 15.0
		3 1 5.70714692232 1.64751140595 15.0
		4 1 8.56072038348 1.64751140595 15.0
		5 1 11.4142938446 1.64751140595 15.0
		6 1 14.2678673058 1.64751140595 15.0
		7 1 1.42678673058 4.11877851488 15.0
		8 1 4.28036019174 4.11877851488 15.0
		9 1 7.1339336529 4.11877851488 15.0
		10 1 9.98750711406 4.11877851488 15.0
		11 1 12.8410805752 4.11877851488 15.0
		12 1 15.6946540364 4.11877851488 15.0
		13 1 0.0 6.59004562381 15.0
		14 1 2.85357346116 6.59004562381 15.0
		15 1 5.70714692232 6.59004562381 15.0
		16 1 8.56072038348 6.59004562381 15.0
		17 1 11.4142938446 6.59004562381 15.0
		18 1 14.2678673058 6.59004562381 15.0
		19 1 1.42678673058 9.06131273274 15.0
		20 1 4.28036019174 9.06131273274 15.0
		21 1 7.1339336529 9.06131273274 15.0
		22 1 9.98750711406 9.06131273274 15.0
		23 1 12.8410805752 9.06131273274 15.0
		24 1 15.6946540364 9.06131273274 15.0
		25 1 0.0 11.5325798417 15.0
		26 1 2.85357346116 11.5325798417 15.0
		27 1 5.70714692232 11.5325798417 15.0
		28 1 8.56072038348 11.5325798417 15.0
		29 1 11.4142938446 11.5325798417 15.0
		30 1 14.2678673058 11.5325798417 15.0
		31 1 1.42678673058 14.0038469506 15.0
		32 1 4.28036019174 14.0038469506 15.0
		33 1 7.1339336529 14.0038469506 15.0
		34 1 9.98750711406 14.0038469506 15.0
		35 1 12.8410805752 14.0038469506 15.0
		36 1 15.6946540364 14.0038469506 15.0
		37 1 0.0 0.0 17.3299329745
		38 1 2.85357346116 0.0 17.3299329745
		39 1 5.70714692232 0.0 17.3299329745
		40 1 8.56072038348 0.0 17.3299329745
		41 1 11.4142938446 0.0 17.3299329745
		42 1 14.2678673058 0.0 17.3299329745
		43 1 1.42678673058 2.47126710893 17.3299329745
		44 1 4.28036019174 2.47126710893 17.3299329745
		45 1 7.1339336529 2.47126710893 17.3299329745
		46 1 9.98750711406 2.47126710893 17.3299329745
		47 1 12.8410805752 2.47126710893 17.3299329745
		48 1 15.6946540364 2.47126710893 17.3299329745
		49 1 0.0 4.94253421786 17.3299329745
		50 1 2.85357346116 4.94253421786 17.3299329745
		51 1 5.70714692232 4.94253421786 17.3299329745
		52 1 8.56072038348 4.94253421786 17.3299329745
		53 1 11.4142938446 4.94253421786 17.3299329745
		54 1 14.2678673058 4.94253421786 17.3299329745
		55 1 1.42678673058 7.41380132679 17.3299329745
		56 1 4.28036019174 7.41380132679 17.3299329745
		57 1 7.1339336529 7.41380132679 17.3299329745
		58 1 9.98750711406 7.41380132679 17.3299329745
		59 1 12.8410805752 7.41380132679 17.3299329745
		60 1 15.6946540364 7.41380132679 17.3299329745
		61 1 0.0 9.88506843572 17.3299329745
		62 1 2.85357346116 9.88506843572 17.3299329745
		63 1 5.70714692232 9.88506843572 17.3299329745
		64 1 8.56072038348 9.88506843572 17.3299329745
		65 1 11.4142938446 9.88506843572 17.3299329745
		66 1 14.2678673058 9.88506843572 17.3299329745
		67 1 1.42678673058 12.3563355446 17.3299329745
		68 1 4.28036019174 12.3563355446 17.3299329745
		69 1 7.1339336529 12.3563355446 17.3299329745
		70 1 9.98750711406 12.3563355446 17.3299329745
		71 1 12.8410805752 12.3563355446 17.3299329745
		72 1 15.6946540364 12.3563355446 17.3299329745
		73 1 1.42678673058 0.823755702976 19.6598659489
		74 1 4.28036019174 0.823755702976 19.6598659489
		75 1 7.1339336529 0.823755702976 19.6598659489
		76 1 9.98750711406 0.823755702976 19.6598659489
		77 1 12.8410805752 0.823755702976 19.6598659489
		78 1 15.6946540364 0.823755702976 19.6598659489
		79 1 0.0 3.29502281191 19.6598659489
		80 1 2.85357346116 3.29502281191 19.6598659489
		81 1 5.70714692232 3.29502281191 19.6598659489
		82 1 8.56072038348 3.29502281191 19.6598659489
		83 1 11.4142938446 3.29502281191 19.6598659489
		84 1 14.2678673058 3.29502281191 19.6598659489
		85 1 1.42678673058 5.76628992084 19.6598659489
		86 1 4.28036019174 5.76628992084 19.6598659489
		87 1 7.1339336529 5.76628992084 19.6598659489
		88 1 9.98750711406 5.76628992084 19.6598659489
		89 1 12.8410805752 5.76628992084 19.6598659489
		90 1 15.6946540364 5.76628992084 19.6598659489
		91 1 0.0 8.23755702976 19.6598659489
		92 1 2.85357346116 8.23755702976 19.6598659489
		93 1 5.70714692232 8.23755702976 19.6598659489
		94 1 8.56072038348 8.23755702976 19.6598659489
		95 1 11.4142938446 8.23755702976 19.6598659489
		96 1 14.2678673058 8.23755702976 19.6598659489
		97 1 1.42678673058 10.7088241387 19.6598659489
		98 1 4.28036019174 10.7088241387 19.6598659489
		99 1 7.1339336529 10.7088241387 19.6598659489
		100 1 9.98750711406 10.7088241387 19.6598659489
		101 1 12.8410805752 10.7088241387 19.6598659489
		102 1 15.6946540364 10.7088241387 19.6598659489
		103 1 0.0 13.1800912476 19.6598659489
		104 1 2.85357346116 13.1800912476 19.6598659489
		105 1 5.70714692232 13.1800912476 19.6598659489
		106 1 8.56072038348 13.1800912476 19.6598659489
		107 1 11.4142938446 13.1800912476 19.6598659489
		108 1 14.2678673058 13.1800912476 19.6598659489
		109 1 0.0 1.64751140595 21.9897989234
		110 1 2.85357346116 1.64751140595 21.9897989234
		111 1 5.70714692232 1.64751140595 21.9897989234
		112 1 8.56072038348 1.64751140595 21.9897989234
		113 1 11.4142938446 1.64751140595 21.9897989234
		114 1 14.2678673058 1.64751140595 21.9897989234
		115 1 1.42678673058 4.11877851488 21.9897989234
		116 1 4.28036019174 4.11877851488 21.9897989234
		117 1 7.1339336529 4.11877851488 21.9897989234
		118 1 9.98750711406 4.11877851488 21.9897989234
		119 1 12.8410805752 4.11877851488 21.9897989234
		120 1 15.6946540364 4.11877851488 21.9897989234
		121 1 0.0 6.59004562381 21.9897989234
		122 1 2.85357346116 6.59004562381 21.9897989234
		123 1 5.70714692232 6.59004562381 21.9897989234
		124 1 8.56072038348 6.59004562381 21.9897989234
		125 1 11.4142938446 6.59004562381 21.9897989234
		126 1 14.2678673058 6.59004562381 21.9897989234
		127 1 1.42678673058 9.06131273274 21.9897989234
		128 1 4.28036019174 9.06131273274 21.9897989234
		129 1 7.1339336529 9.06131273274 21.9897989234
		130 1 9.98750711406 9.06131273274 21.9897989234
		131 1 12.8410805752 9.06131273274 21.9897989234
		132 1 15.6946540364 9.06131273274 21.9897989234
		133 1 0.0 11.5325798417 21.9897989234
		134 1 2.85357346116 11.5325798417 21.9897989234
		135 1 5.70714692232 11.5325798417 21.9897989234
		136 1 8.56072038348 11.5325798417 21.9897989234
		137 1 11.4142938446 11.5325798417 21.9897989234
		138 1 14.2678673058 11.5325798417 21.9897989234
		139 1 1.42678673058 14.0038469506 21.9897989234
		140 1 4.28036019174 14.0038469506 21.9897989234
		141 1 7.1339336529 14.0038469506 21.9897989234
		142 1 9.98750711406 14.0038469506 21.9897989234
		143 1 12.8410805752 14.0038469506 21.9897989234
		144 1 15.6946540364 14.0038469506 21.9897989234
		145 1 0.0 0.0 24.3197318979
		146 1 2.85357346116 0.0 24.3197318979
		147 1 5.70714692232 0.0 24.3197318979
		148 1 8.56072038348 0.0 24.3197318979
		149 1 11.4142938446 0.0 24.3197318979
		150 1 14.2678673058 0.0 24.3197318979
		151 1 1.42678673058 2.47126710893 24.3197318979
		152 1 4.28036019174 2.47126710893 24.3197318979
		153 1 7.1339336529 2.47126710893 24.3197318979
		154 1 9.98750711406 2.47126710893 24.3197318979
		155 1 12.8410805752 2.47126710893 24.3197318979
		156 1 15.6946540364 2.47126710893 24.3197318979
		157 1 0.0 4.94253421786 24.3197318979
		158 1 2.85357346116 4.94253421786 24.3197318979
		159 1 5.70714692232 4.94253421786 24.3197318979
		160 1 8.56072038348 4.94253421786 24.3197318979
		161 1 11.4142938446 4.94253421786 24.3197318979
		162 1 14.2678673058 4.94253421786 24.3197318979
		163 1 1.42678673058 7.41380132679 24.3197318979
		164 1 4.28036019174 7.41380132679 24.3197318979
		165 1 7.1339336529 7.41380132679 24.3197318979
		166 1 9.98750711406 7.41380132679 24.3197318979
		167 1 12.8410805752 7.41380132679 24.3197318979
		168 1 15.6946540364 7.41380132679 24.3197318979
		169 1 0.0 9.88506843572 24.3197318979
		170 1 2.85357346116 9.88506843572 24.3197318979
		171 1 5.70714692232 9.88506843572 24.3197318979
		172 1 8.56072038348 9.88506843572 24.3197318979
		173 1 11.4142938446 9.88506843572 24.3197318979
		174 1 14.2678673058 9.88506843572 24.3197318979
		175 1 1.42678673058 12.3563355446 24.3197318979
		176 1 4.28036019174 12.3563355446 24.3197318979
		177 1 7.1339336529 12.3563355446 24.3197318979
		178 1 9.98750711406 12.3563355446 24.3197318979
		179 1 12.8410805752 12.3563355446 24.3197318979
		180 1 15.6946540364 12.3563355446 24.3197318979
		181 1 7.1339336529 4.11877851488 26.7197318979

examples/USER/misc/agni/in.adatom

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Original line number	Diff line number	Diff line

		processors * * 1
		units metal
		boundary p p f
		read_data adatom.data

		pair_style agni
		pair_coeff * * Al_prb.agni Al

		neighbor 0.3 bin
		neigh_modify delay 2 check yes

		timestep 0.0005
		velocity all create 500 12345
		fix 1 all nvt temp 250 250 0.2
		fix 5 all momentum 1 linear 1 1 1

		thermo 100
		thermo_style custom step ke temp

		# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz

		run 1000

examples/USER/misc/agni/in.vacancy

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Original line number	Diff line number	Diff line

		units metal
		boundary p p p
		read_data vacancy.data

		pair_style agni
		pair_coeff * * Al_prb.agni Al
		neighbor 0.3 bin
		neigh_modify delay 2 check yes


		timestep 0.0005
		velocity all create 1000 12345
		fix 1 all nvt temp 900 900 200
		fix 5 all momentum 1 linear 1 1 1


		thermo 100
		thermo_style custom step ke etotal temp

		# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz

		run 1000

examples/USER/misc/agni/log.9Nov16.adatom.g++.1

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Original line number	Diff line number	Diff line
		LAMMPS (9 Nov 2016)
		using 1 OpenMP thread(s) per MPI task

		processors * * 1
		units metal
		boundary p p f
		read_data adatom.data
		orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
		1 by 1 by 1 MPI processor grid
		reading atoms ...
		181 atoms

		pair_style agni
		pair_coeff * * Al_prb.agni Al
		Reading potential file Al_prb.agni with DATE: 2016-11-11

		neighbor 0.3 bin
		neigh_modify delay 2 check yes

		timestep 0.0005
		velocity all create 500 12345
		fix 1 all nvt temp 250 250 0.2
		fix 5 all momentum 1 linear 1 1 1

		thermo 100
		thermo_style custom step ke temp

		# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz

		run 1000
		Neighbor list info ...
		1 neighbor list requests
		update every 1 steps, delay 2 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 8.3
		ghost atom cutoff = 8.3
		binsize = 4.15 -> bins = 5 4 10
		Memory usage per processor = 2.37049 Mbytes
		Step KinEng Temp
		0 11.633413 500
		100 4.049974 174.06646
		200 5.8983472 253.50889
		300 5.3667309 230.66021
		400 4.9343935 212.0785
		500 5.4054496 232.32432
		600 6.1779127 265.52452
		700 6.3749266 273.9921
		800 6.0701481 260.89283
		900 6.4582394 277.57286
		1000 6.4047444 275.27366
		Loop time of 20.8273 on 1 procs for 1000 steps with 181 atoms

		Performance: 2.074 ns/day, 11.571 hours/ns, 48.014 timesteps/s
		100.0% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 20.79 \| 20.79 \| 20.79 \| 0.0 \| 99.82
		Neigh \| 0.022742 \| 0.022742 \| 0.022742 \| 0.0 \| 0.11
		Comm \| 0.0040836 \| 0.0040836 \| 0.0040836 \| 0.0 \| 0.02
		Output \| 0.00011086 \| 0.00011086 \| 0.00011086 \| 0.0 \| 0.00
		Modify \| 0.0089345 \| 0.0089345 \| 0.0089345 \| 0.0 \| 0.04
		Other \| \| 0.001819 \| \| \| 0.01

		Nlocal: 181 ave 181 max 181 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 562 ave 562 max 562 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 0 ave 0 max 0 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		FullNghs: 18810 ave 18810 max 18810 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 18810
		Ave neighs/atom = 103.923
		Neighbor list builds = 33
		Dangerous builds = 0

		Please see the log.cite file for references relevant to this simulation

		Total wall time: 0:00:20

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