Commit 2 JT 031119 (5fff1893) · Commits · 郑智淋 / lammps

examples/SPIN/gneb_bfo/Si.sw

deleted100644 → 0

+0 −18

Original line number	Diff line number	Diff line
		# DATE: 2007-06-11 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Stillinger and Weber, Phys Rev B, 31, 5262, (1985)
		# Stillinger-Weber parameters for various elements and mixtures
		# multiple entries can be added to this file, LAMMPS reads the ones it needs
		# these entries are in LAMMPS "metal" units:
		# epsilon = eV; sigma = Angstroms
		# other quantities are unitless

		# format of a single entry (one or more lines):
		# element 1, element 2, element 3,
		# epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol

		# Here are the original parameters in metal units, for Silicon from:
		#
		# Stillinger and Weber, Phys. Rev. B, v. 31, p. 5262, (1985)
		#

		Si Si Si 2.1683 2.0951 1.80 21.0 1.20 -0.333333333333
		7.049556277 0.6022245584 4.0 0.0 0.0

examples/SPIN/gneb_bfo/final.hop1

deleted100644 → 0

+0 −2

Original line number	Diff line number	Diff line
		1
		412 14.0 20.5 0

examples/SPIN/gneb_bfo/final.iron_spin_data

deleted100644 → 0

+0 −82

Original line number	Diff line number	Diff line
		LAMMPS data file via write_data, version 4 Jan 2019, timestep = 0

		32 atoms
		1 atom types

		0.0000000000000000e+00 1.1465999999999999e+01 xlo xhi
		0.0000000000000000e+00 1.1465999999999999e+01 ylo yhi
		0.0000000000000000e+00 2.8664999999999998e+00 zlo zhi

		Masses

		1 55.845

		Atoms # spin

		1 1 2.2000000000000002e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		2 1 2.2000000000000002e+00 1.4332499999999999e+00 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		3 1 2.2000000000000002e+00 2.8664999999999998e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		4 1 2.2000000000000002e+00 4.2997499999999995e+00 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		5 1 2.2000000000000002e+00 5.7329999999999997e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		6 1 2.2000000000000002e+00 7.1662499999999998e+00 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		7 1 2.2000000000000002e+00 8.5994999999999990e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		8 1 2.2000000000000002e+00 1.0032750000000000e+01 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		9 1 2.2000000000000002e+00 0.0000000000000000e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		11 1 2.2000000000000002e+00 2.8664999999999998e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		13 1 2.2000000000000002e+00 5.7329999999999997e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		15 1 2.2000000000000002e+00 8.5994999999999990e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		10 1 2.2000000000000002e+00 1.4332499999999999e+00 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		12 1 2.2000000000000002e+00 4.2997499999999995e+00 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		14 1 2.2000000000000002e+00 7.1662499999999998e+00 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		16 1 2.2000000000000002e+00 1.0032750000000000e+01 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		17 1 2.2000000000000002e+00 0.0000000000000000e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		18 1 2.2000000000000002e+00 1.4332499999999999e+00 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		19 1 2.2000000000000002e+00 2.8664999999999998e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		20 1 2.2000000000000002e+00 4.2997499999999995e+00 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		21 1 2.2000000000000002e+00 5.7329999999999997e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		22 1 2.2000000000000002e+00 7.1662499999999998e+00 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		23 1 2.2000000000000002e+00 8.5994999999999990e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		24 1 2.2000000000000002e+00 1.0032750000000000e+01 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		25 1 2.2000000000000002e+00 0.0000000000000000e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		27 1 2.2000000000000002e+00 2.8664999999999998e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		29 1 2.2000000000000002e+00 5.7329999999999997e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		31 1 2.2000000000000002e+00 8.5994999999999990e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		26 1 2.2000000000000002e+00 1.4332499999999999e+00 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		28 1 2.2000000000000002e+00 4.2997499999999995e+00 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		30 1 2.2000000000000002e+00 7.1662499999999998e+00 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0
		32 1 2.2000000000000002e+00 1.0032750000000000e+01 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0

		Velocities

		1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		11 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		13 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		15 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		12 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		14 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		16 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		17 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		31 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		30 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		32 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00

examples/SPIN/gneb_bfo/in.neb.spin_iron→examples/SPIN/gneb_bfo/in.gneb.iron

+0 −0

File moved.

View file

examples/SPIN/gneb_bfo/in.neb.hop1

deleted100644 → 0

+0 −67

Original line number	Diff line number	Diff line
		# 2d NEB surface simulation, hop from surface to become adatom
		print "Test 1"

		dimension 2
		boundary p s p

		atom_style atomic
		neighbor 0.3 bin
		neigh_modify delay 5
		atom_modify map array sort 0 0.0

		variable u uloop 20

		# create geometry with flat surface

		lattice hex 0.9
		region box block 0 20 0 10 -0.25 0.25

		#create_box 3 box
		#create_atoms 1 box
		#mass * 1.0
		#write_data initial.hop1

		read_data ../examples/SPIN/gneb_bfo/initial.hop1

		# LJ potentials

		pair_style lj/cut 2.5
		pair_coeff * * 1.0 1.0 2.5
		pair_modify shift yes

		# initial minimization to relax surface

		minimize 1.0e-6 1.0e-4 1000 10000
		reset_timestep 0

		# define groups

		region 1 block INF INF INF 1.25 INF INF
		group lower region 1
		group mobile subtract all lower
		set group lower type 2

		timestep 0.05

		# group of NEB atoms - either block or single atom ID 412

		region surround block 10 18 17 20 0 0 units box
		group nebatoms region surround
		#group nebatoms id 412
		set group nebatoms type 3
		group nonneb subtract all nebatoms

		fix 1 lower setforce 0.0 0.0 0.0
		fix 2 nebatoms neb 1.0 parallel ideal
		fix 3 all enforce2d

		thermo 100

		#dump 1 nebatoms atom 10 dump.neb.$u
		#dump 2 nonneb atom 10 dump.nonneb.$u

		# run NEB for 2000 steps or to force tolerance

		min_style quickmin

		neb 0.0 0.1 1000 1000 100 final ../examples/SPIN/gneb_bfo/final.hop1

Admin message