add a couple of simple example single/multi-elment inputs for meam/spline pair styles (d0da0639) · Commits · 郑智淋 / lammps

examples/USER/misc/meam_spline/Si_1.meam.spline

0 → 100644

+63 −0

Original line number	Diff line number	Diff line
		DATE: 2012-02-01 CONTRIBUTOR: Alexander Stukowski, stukowski@mm.tu-darmstadt.de CITATION: Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter and Kress, Modell Simul Mater Sci Eng, 8, 825 (2000) COMMENT: Spline-based MEAM potential for Si. Reference: T. J. Lenosky, B. Sadigh, E. Alonso, V. V. Bulatov, T. D. de la Rubia, J. Kim, A. F. Voter, and J. D. Kress, Modell. Simul. Mater. Sci. Eng. 8, 825 (2000)
		10
		-4.266966781858503300e+01 0.000000000000000000e+00
		1 0 1 0
		1.500000000000000000e+00 6.929943430771341000e+00 1.653321602557917600e+02
		1.833333333333333300e+00 -4.399503747408950400e-01 3.941543472528634600e+01
		2.166666666666666500e+00 -1.701233725061446700e+00 6.871065423413908100e+00
		2.500000000000000000e+00 -1.624732919215791800e+00 5.340648014033163800e+00
		2.833333333333333000e+00 -9.969641728342462100e-01 1.534811309391571000e+00
		3.166666666666667000e+00 -2.739141845072665100e-01 -6.334706186546093900e+00
		3.500000000000000000e+00 -2.499156963774082700e-02 -1.798864729909626500e+00
		3.833333333333333500e+00 -1.784331481529976400e-02 4.743496636420091500e-01
		4.166666666666666100e+00 -9.612303290166881000e-03 -4.006506271304824400e-02
		4.500000000000000000e+00 0.000000000000000000e+00 -2.394996574779807200e-01
		11
		-1.000000000000000000e+00 0.000000000000000000e+00
		1 0 0 0
		1.500000000000000000e+00 1.374674212682983900e-01 -3.227795813279568500e+00
		1.700000000000000000e+00 -1.483141815327918000e-01 -6.411648793604404900e+00
		1.899999999999999900e+00 -5.597204896096039700e-01 1.003068519633888300e+01
		2.100000000000000100e+00 -7.310964379372824100e-01 2.293461970618954700e+00
		2.299999999999999800e+00 -7.628287071954063000e-01 1.742018781618444500e+00
		2.500000000000000000e+00 -7.291769685066557000e-01 5.460640949384478700e-01
		2.700000000000000200e+00 -6.662022220044453400e-01 4.721760106467195500e-01
		2.899999999999999900e+00 -5.732830582550895200e-01 2.056894449546524200e+00
		3.100000000000000100e+00 -4.069014309729406300e-01 2.319615721086100800e+00
		3.299999999999999800e+00 -1.666155295956388300e-01 -2.497162196179187900e-01
		3.500000000000000000e+00 0.000000000000000000e+00 -1.237130660986393100e+01
		8
		7.351364478015182100e-01 6.165217237728655200e-01
		1 1 1 1
		-1.770934559908718700e+00 -1.074925682941420000e+00 -1.482768170233858500e-01
		-3.881557649503457600e-01 -2.004503493658201000e-01 -1.492100354067345500e-01
		9.946230300080272100e-01 4.142241371345077300e-01 -7.012475119623896900e-02
		2.377401824966400000e+00 8.793892953828742500e-01 -3.944355024164965900e-02
		3.760180619924772900e+00 1.266888024536562100e+00 -1.581431192239436000e-02
		5.142959414883146800e+00 1.629979548834614900e+00 2.611224310900800400e-02
		6.525738209841518900e+00 1.977379549636293600e+00 -1.378738550324104500e-01
		7.908517004799891800e+00 2.396177220616657200e+00 7.494253977092666400e-01
		10
		-3.618936018538757300e+00 0.000000000000000000e+00
		1 0 1 0
		1.500000000000000000e+00 1.250311510312851300e+00 2.790400588857243500e+01
		1.722222222222222300e+00 8.682060369372680600e-01 -4.522554291731776900e+00
		1.944444444444444400e+00 6.084604017544847900e-01 5.052931618779816800e+00
		2.166666666666666500e+00 4.875624808097850400e-01 1.180825096539679600e+00
		2.388888888888888800e+00 4.416345603457190700e-01 -6.673769465415171400e-01
		2.611111111111111200e+00 3.760976313325982700e-01 -8.938118490837722000e-01
		2.833333333333333000e+00 2.714524157414608400e-01 -5.090324763524399800e-01
		3.055555555555555400e+00 1.481440300150710900e-01 6.623665830603995300e-01
		3.277777777777777700e+00 4.854596610856590900e-02 7.403702452268122700e-01
		3.500000000000000000e+00 0.000000000000000000e+00 2.578982318481970500e+00
		8
		-1.395041572145673000e+01 1.134616739799360700e+00
		1 1 1 1
		-1.000000000000000900e+00 5.254163992149617700e+00 1.582685381253900500e+01
		-7.428367052748285900e-01 2.359149452448745100e+00 3.117611233789983400e+01
		-4.856734105496561800e-01 1.195946960915646100e+00 1.658962813584905800e+01
		-2.285101158244838800e-01 1.229952028074150000e+00 1.108360928564026400e+01
		2.865317890068852500e-02 2.035650777568434500e+00 9.088861456447702400e+00
		2.858164736258610400e-01 3.424741418405580000e+00 5.489943377538379500e+00
		5.429797683510331200e-01 4.948585892304984100e+00 -1.882291580187675700e+01
		8.001430630762056400e-01 5.617988713941801200e+00 -7.718625571850646200e+00

examples/USER/misc/meam_spline/TiO.meam.spline

0 → 100644

+130 −0

Original line number	Diff line number	Diff line
		# Ti-O cubic spline potential where O is in the dilute limit. DATE: 2016-06-05 CONTRIBUTOR: Pinchao Zhang, Dallas R. Trinkle
		meam/spline 2 Ti O
		spline3eq
		13
		-20 0
		1.742692837 3.744277175966 99.4865081627958
		2.05580176725 0.910839730906 10.8702523265355
		2.3689106975 0.388045896634 -1.55322418749562
		2.68201962775 -0.018840906533 2.43630041329215
		2.995128558 -0.248098929639 2.67912713976835
		3.30823748825 -0.264489550297 -0.125056384603077
		3.6213464185 -0.227196189283 1.10662555360438
		3.93445534875 -0.129293090176 -0.592053676745914
		4.247564279 -0.059685366933 -0.470123414607672
		4.56067320925 -0.031100025561 -0.0380739973059663
		4.8737821395 -0.013847363202 -0.0711547960695406
		5.18689106975 -0.003203412728 -0.081768292420175
		5.5 0 -0.0571422964883619
		spline3eq
		5
		0.155001355787331 0
		1.9 0.533321679606674 0
		2.8 0.456402081843862 -1.60311717015859
		3.7 -0.324281383502201 1.19940299483249
		4.6 -0.474029826906675 1.47909794595154
		5.5 0 -2.49521499855605
		spline3eq
		13
		0 0
		1.742692837 0 0
		2.05580176725 0 0
		2.3689106975 0 0
		2.68201962775 0 0
		2.995128558 0 0
		3.30823748825 0 0
		3.6213464185 0 0
		3.93445534875 0 0
		4.247564279 0 0
		4.56067320925 0 0
		4.8737821395 0 0
		5.18689106975 0 0
		5.5 0 0
		spline3eq
		11
		-1 0
		2.055801767 1.7475279661 -525.869786904802
		2.2912215903 -5.8677963945 252.796316927755
		2.5266414136 -8.3376288737 71.7318388721015
		2.7620612369 -5.8398712842 -1.93587742753693
		2.9974810602 -3.1140648231 -39.2999192667503
		3.2329008835 -1.7257245065 14.3424136002004
		3.4683207068 -0.4428977017 -29.4925534559498
		3.7037405301 -0.1466643003 -3.18010534572236
		3.9391603534 -0.2095507945 3.33490838803603
		4.1745801767 -0.1442384563 3.71918691359508
		4.41 0 -9.66717019857564
		spline3eq
		5
		-61.9827585211652 0
		1.9 11.2293641315584 0
		2.8 -27.9976343076148 122.648031332411
		3.7 -8.32979773113248 -54.3340881766381
		4.6 -1.00863195297399 3.23150064581724
		5.5 0 -5.3514242228123
		spline3eq
		4
		0.00776934946045395 0.105197706160344
		-55.14233165 -0.29745568008 0.00152870603877451
		-44.7409899033333 -0.15449458722 0.00038933722543571
		-34.3396481566667 0.05098657168 0.00038124926922248
		-23.93830641 0.57342694704 0.0156639264890892
		spline3eq
		5
		-0.00676745157022662 -0.0159520381982146
		-23.9928 0.297607384684645 0
		-15.9241175 0.216691597077105 -0.0024248755353942
		-7.855435 0.0637598673719069 0.00306245895013358
		0.213247499999998 -0.00183450621970427 -0.00177588407633909
		8.28193 -0.111277018874367 0
		spline3eq
		10
		2.77327511656661 0
		2.055801767 -0.1485215264 72.2010867146919
		2.31737934844444 1.6845304918 -47.2744689053404
		2.57895692988889 2.0113365977 -15.1859578405326
		2.84053451133333 1.1444092747 3.33978204841873
		3.10211209277778 0.2861606803 2.587867603808
		3.36368967422222 -0.3459281126 6.14070694084556
		3.62526725566667 -0.6257480601 3.7397696717154
		3.88684483711111 -0.6119510826 4.64749084871402
		4.14842241855556 -0.3112059651 2.83275746415936
		4.41 0 -15.0612086827734
		spline3eq
		5
		12.3315547862781 0
		1.9 2.62105440156724 0
		2.8 10.2850803058354 -25.439802988016
		3.7 3.23933763743897 -7.20203673434025
		4.6 -5.79049355858613 39.5509978688682
		5.5 0 -41.221771373642
		spline3eq
		8
		8.33642274810572 -60.4024574736564
		-1 0.07651409193 -110.652321293778
		-0.724509054371429 0.14155824541 44.8853405500508
		-0.449018108742857 0.75788697341 -25.3065115342002
		-0.173527163114286 0.63011570378 -2.48510144915082
		0.101963782514286 0.09049597305 2.68769386908235
		0.377454728142857 -0.35741586657 -1.01558570129633
		0.652945673771428 -0.65293217647 13.4224786001212
		0.9284366194 -6.00912190653 -452.752542694929
		spline3eq
		5
		0.137191606537625 -1.55094230968985
		-1 0.0513843442016519 0
		-0.5 0.0179024412245673 -2.44986494990154
		0 -0.260650876879273 3.91774583656401
		0.5 -0.190163791764901 -4.84414871911743
		1 -0.763795416646599 0
		spline3eq
		8
		0 0
		-1 0 0
		-0.724509054371429 0 0
		-0.449018108742857 0 0
		-0.173527163114286 0 0
		0.101963782514286 0 0
		0.377454728142857 0 0
		0.652945673771428 0 0
		0.9284366194 0 0

examples/USER/misc/meam_spline/in.meam-spline.Si

0 → 100644

+22 −0

Original line number	Diff line number	Diff line
		# Si fcc phase

		units metal
		boundary p p p

		atom_style atomic
		lattice fcc 3.98
		region box block 0 5 0 5 0 5
		create_box 1 box
		create_atoms 1 box

		pair_style meam/spline
		pair_coeff * * Si_1.meam.spline Si
		mass * 28.085

		velocity all create 500.0 44226611

		fix 1 all nvt temp 500.0 500.0 1.0

		thermo 50
		run 500

examples/USER/misc/meam_spline/in.meam-spline.TiO2

0 → 100644

+92 −0

Original line number	Diff line number	Diff line
		#

		variable T_depart equal 300

		variable dt equal 0.0002

		variable a equal 4.5937
		variable c equal 2.9587
		variable ca equal ${c}/${a}

		variable nx equal 6
		variable ny equal 6
		variable nz equal 11

		variable bx equal ${a}*${nx}
		variable by equal ${a}*${ny}
		variable bz equal ${c}*${nz}
		# =======================================================================

		units metal
		atom_style atomic
		dimension 3
		boundary p p p


		lattice sc 1.0
		region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
		create_box 2 box_vide

		#lattice sc 1.0
		#region box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz}

		# titanium atoms
		lattice custom ${a} origin 0.0 0.0 0.0 &
		orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 &
		a1 1.0 0.0 0.0 &
		a2 0.0 1.0 0.0 &
		a3 0.0 0.0 ${ca} &
		basis 0.0 0.0 0.0 &
		basis 0.5 0.5 0.5

		create_atoms 2 region box_vide

		# Oxygen atoms
		lattice custom ${a} origin 0.0 0.0 0.0 &
		orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 &
		a1 1.0 0.0 0.0 &
		a2 0.0 1.0 0.0 &
		a3 0.0 0.0 ${ca} &
		basis 0.30478 0.30478 0.0 &
		basis 0.69522 0.69522 0.0 &
		basis 0.19522 0.80478 0.5 &
		basis 0.80478 0.19522 0.5

		create_atoms 1 region box_vide


		mass 1 16.00
		group Oxy type 1

		mass 2 47.867
		group Ti type 2

		velocity all create ${T_depart} 277387

		pair_style meam/spline
		pair_coeff * * TiO.meam.spline O Ti

		neighbor 0.5 bin
		neigh_modify every 2 delay 0 check yes

		timestep ${dt}

		thermo_style custom step temp press pe ke etotal lx ly lz vol
		thermo 10


		#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z

		fix 3 all nve
		run 100

		unfix 3
		fix 1 all box/relax tri 0.0 vmax 0.001
		minimize 1.0e-3 1.0e-5 1000 10000

		unfix 1
		reset_timestep 0
		thermo 50
		fix 3 all npt temp 300 300 0.1 aniso 1.0 1.0 1.0
		run 500

examples/USER/misc/meam_spline/log.4May2017.meam-spline.Si.g++.1

0 → 100644

+88 −0

Original line number	Diff line number	Diff line
		LAMMPS (13 Apr 2017)
		using 1 OpenMP thread(s) per MPI task
		# Si fcc phase

		units metal
		boundary p p p

		atom_style atomic
		lattice fcc 3.98
		Lattice spacing in x,y,z = 3.98 3.98 3.98
		region box block 0 5 0 5 0 5
		create_box 1 box
		Created orthogonal box = (0 0 0) to (19.9 19.9 19.9)
		1 by 1 by 1 MPI processor grid
		create_atoms 1 box
		Created 500 atoms

		pair_style meam/spline
		pair_coeff * * Si_1.meam.spline Si
		Reading potential file Si_1.meam.spline with DATE: 2012-02-01
		mass * 28.085

		velocity all create 500.0 44226611

		fix 1 all nvt temp 500.0 500.0 1.0

		thermo 50
		run 500
		Neighbor list info ...
		update every 1 steps, delay 10 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 6.5
		ghost atom cutoff = 6.5
		binsize = 3.25, bins = 7 7 7
		2 neighbor lists, perpetual/occasional/extra = 2 0 0
		(1) pair meam/spline, perpetual
		attributes: full, newton on
		pair build: full/bin/atomonly
		stencil: full/bin/3d
		bin: standard
		(2) pair meam/spline, perpetual, half/full from (1)
		attributes: half, newton on
		pair build: halffull/newton
		stencil: none
		bin: none
		Per MPI rank memory allocation (min/avg/max) = 3.892 \| 3.892 \| 3.892 Mbytes
		Step Temp E_pair E_mol TotEng Press
		0 500 -1847.729 0 -1815.4786 1813162.7
		50 1934.0932 -1940.8016 0 -1816.051 -48657.676
		100 2570.1286 -1984.8725 0 -1819.0971 8002.4248
		150 2566.7917 -1990.2724 0 -1824.7123 16819.447
		200 2555.1319 -1995.2233 0 -1830.4152 5891.5313
		250 2487.2881 -1995.8302 0 -1835.3981 -4339.7172
		300 2381.4836 -1994.2492 0 -1840.6415 16508.04
		350 2330.8663 -1996.6588 0 -1846.3161 24194.447
		400 2212.6035 -1994.9278 0 -1852.2131 -9856.3709
		450 2257.7531 -2003.8187 0 -1858.1918 -8029.6019
		500 2211.4385 -2006.9846 0 -1864.345 4152.4867
		Loop time of 5.13837 on 1 procs for 500 steps with 500 atoms

		Performance: 8.407 ns/day, 2.855 hours/ns, 97.307 timesteps/s
		99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 5.0952 \| 5.0952 \| 5.0952 \| 0.0 \| 99.16
		Neigh \| 0.026447 \| 0.026447 \| 0.026447 \| 0.0 \| 0.51
		Comm \| 0.0063307 \| 0.0063307 \| 0.0063307 \| 0.0 \| 0.12
		Output \| 0.0001905 \| 0.0001905 \| 0.0001905 \| 0.0 \| 0.00
		Modify \| 0.0082877 \| 0.0082877 \| 0.0082877 \| 0.0 \| 0.16
		Other \| \| 0.00187 \| \| \| 0.04

		Nlocal: 500 ave 500 max 500 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 1767 ave 1767 max 1767 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 18059 ave 18059 max 18059 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		FullNghs: 36118 ave 36118 max 36118 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 36118
		Ave neighs/atom = 72.236
		Neighbor list builds = 14
		Dangerous builds = 0

		Total wall time: 0:00:05

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