Examples and docs
This commit is contained in:
julient31
@ -36,6 +36,7 @@ fix 3 all integration/spin lattice yes
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timestep 0.0001
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# compute and output options
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compute out_mag all compute/spin
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compute out_pe all pe
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File diff suppressed because it is too large
Load Diff
@ -1,95 +0,0 @@
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#!/usr/bin/env python
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# This file reads in the file log.lammps generated by the script ELASTIC/in.elastic
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# It prints out the 6x6 tensor of elastic constants Cij
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# followed by the 6x6 tensor of compliance constants Sij
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# It uses the same conventions as described in:
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# Sprik, Impey and Klein PRB (1984).
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# The units of Cij are whatever was used in log.lammps (usually GPa)
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# The units of Sij are the inverse of that (usually 1/GPa)
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from numpy import zeros
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from numpy.linalg import inv
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# define logfile layout
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nvals = 21
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valpos = 4
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valstr = '\nElastic Constant C'
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# define order of Cij in logfile
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cindices = [0]*nvals
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cindices[0] = (0,0)
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cindices[1] = (1,1)
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cindices[2] = (2,2)
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cindices[3] = (0,1)
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cindices[4] = (0,2)
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cindices[5] = (1,2)
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cindices[6] = (3,3)
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cindices[7] = (4,4)
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cindices[8] = (5,5)
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cindices[9] = (0,3)
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cindices[10] = (0,4)
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cindices[11] = (0,5)
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cindices[12] = (1,3)
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cindices[13] = (1,4)
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cindices[14] = (1,5)
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cindices[15] = (2,3)
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cindices[16] = (2,4)
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cindices[17] = (2,5)
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cindices[18] = (3,4)
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cindices[19] = (3,5)
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cindices[20] = (4,5)
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# open logfile
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logfile = open("log.lammps",'r')
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txt = logfile.read()
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# search for 21 elastic constants
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c = zeros((6,6))
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s2 = 0
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for ival in range(nvals):
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s1 = txt.find(valstr,s2)
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if (s1 == -1):
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print "Failed to find elastic constants in log file"
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exit(1)
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s1 += 1
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s2 = txt.find("\n",s1)
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line = txt[s1:s2]
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# print line
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words = line.split()
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(i1,i2) = cindices[ival]
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c[i1,i2] = float(words[valpos])
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c[i2,i1] = c[i1,i2]
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print "C tensor [GPa]"
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for i in range(6):
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for j in range(6):
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print "%10.8g " % c[i][j],
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print
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# apply factor of 2 to columns of off-diagonal elements
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for i in range(6):
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for j in range(3,6):
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c[i][j] *= 2.0
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s = inv(c)
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# apply factor of 1/2 to columns of off-diagonal elements
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for i in range(6):
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for j in range(3,6):
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s[i][j] *= 0.5
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print "S tensor [1/GPa]"
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for i in range(6):
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for j in range(6):
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print "%10.8g " % s[i][j],
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print
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@ -1,142 +0,0 @@
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# NOTE: This script should not need to be
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# modified. See in.elastic for more info.
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#
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# Find which reference length to use
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if "${dir} == 1" then &
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"variable len0 equal ${lx0}"
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if "${dir} == 2" then &
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"variable len0 equal ${ly0}"
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if "${dir} == 3" then &
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"variable len0 equal ${lz0}"
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if "${dir} == 4" then &
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"variable len0 equal ${lz0}"
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if "${dir} == 5" then &
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"variable len0 equal ${lz0}"
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if "${dir} == 6" then &
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"variable len0 equal ${ly0}"
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# Reset box and simulation parameters
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clear
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box tilt large
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read_restart restart.equil
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include potential.mod
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# Negative deformation
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variable delta equal -${up}*${len0}
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variable deltaxy equal -${up}*xy
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variable deltaxz equal -${up}*xz
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variable deltayz equal -${up}*yz
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if "${dir} == 1" then &
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"change_box all x delta 0 ${delta} xy delta ${deltaxy} xz delta ${deltaxz} remap units box"
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if "${dir} == 2" then &
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"change_box all y delta 0 ${delta} yz delta ${deltayz} remap units box"
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if "${dir} == 3" then &
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"change_box all z delta 0 ${delta} remap units box"
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if "${dir} == 4" then &
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"change_box all yz delta ${delta} remap units box"
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if "${dir} == 5" then &
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"change_box all xz delta ${delta} remap units box"
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if "${dir} == 6" then &
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"change_box all xy delta ${delta} remap units box"
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# Relax atoms positions
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minimize ${etol} ${ftol} ${maxiter} ${maxeval}
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# Obtain new stress tensor
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variable tmp equal pxx
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variable pxx1 equal ${tmp}
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variable tmp equal pyy
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variable pyy1 equal ${tmp}
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variable tmp equal pzz
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variable pzz1 equal ${tmp}
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variable tmp equal pxy
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variable pxy1 equal ${tmp}
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variable tmp equal pxz
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variable pxz1 equal ${tmp}
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variable tmp equal pyz
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variable pyz1 equal ${tmp}
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# Compute elastic constant from pressure tensor
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variable C1neg equal ${d1}
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variable C2neg equal ${d2}
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variable C3neg equal ${d3}
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variable C4neg equal ${d4}
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variable C5neg equal ${d5}
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variable C6neg equal ${d6}
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# Reset box and simulation parameters
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clear
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box tilt large
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read_restart restart.equil
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include potential.mod
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# Positive deformation
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variable delta equal ${up}*${len0}
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variable deltaxy equal ${up}*xy
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variable deltaxz equal ${up}*xz
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variable deltayz equal ${up}*yz
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if "${dir} == 1" then &
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"change_box all x delta 0 ${delta} xy delta ${deltaxy} xz delta ${deltaxz} remap units box"
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if "${dir} == 2" then &
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"change_box all y delta 0 ${delta} yz delta ${deltayz} remap units box"
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if "${dir} == 3" then &
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"change_box all z delta 0 ${delta} remap units box"
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if "${dir} == 4" then &
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"change_box all yz delta ${delta} remap units box"
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if "${dir} == 5" then &
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"change_box all xz delta ${delta} remap units box"
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if "${dir} == 6" then &
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"change_box all xy delta ${delta} remap units box"
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# Relax atoms positions
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minimize ${etol} ${ftol} ${maxiter} ${maxeval}
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# Obtain new stress tensor
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variable tmp equal pe
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variable e1 equal ${tmp}
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variable tmp equal press
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variable p1 equal ${tmp}
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variable tmp equal pxx
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variable pxx1 equal ${tmp}
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variable tmp equal pyy
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variable pyy1 equal ${tmp}
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variable tmp equal pzz
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variable pzz1 equal ${tmp}
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variable tmp equal pxy
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variable pxy1 equal ${tmp}
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variable tmp equal pxz
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variable pxz1 equal ${tmp}
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variable tmp equal pyz
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variable pyz1 equal ${tmp}
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# Compute elastic constant from pressure tensor
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variable C1pos equal ${d1}
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variable C2pos equal ${d2}
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variable C3pos equal ${d3}
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variable C4pos equal ${d4}
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variable C5pos equal ${d5}
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variable C6pos equal ${d6}
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# Combine positive and negative
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variable C1${dir} equal 0.5*(${C1neg}+${C1pos})
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variable C2${dir} equal 0.5*(${C2neg}+${C2pos})
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variable C3${dir} equal 0.5*(${C3neg}+${C3pos})
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variable C4${dir} equal 0.5*(${C4neg}+${C4pos})
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variable C5${dir} equal 0.5*(${C5neg}+${C5pos})
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variable C6${dir} equal 0.5*(${C6neg}+${C6pos})
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# Delete dir to make sure it is not reused
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variable dir delete
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@ -1,59 +0,0 @@
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# fcc cobalt in a 3d periodic box
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clear
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units metal
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atom_style spin
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dimension 3
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boundary p p p
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# check why?
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atom_modify map array
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lattice fcc 3.54
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region box block 0.0 5.0 0.0 5.0 0.0 5.0
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create_box 1 box
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create_atoms 1 box
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# setting mass, mag. moments, and interactions for cobalt
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mass 1 58.93
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set group all spin/random 31 1.72
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velocity all create 100 4928459 rot yes dist gaussian
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#pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
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pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0
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pair_coeff * * eam/alloy ../examples/SPIN/cobalt/Co_PurjaPun_2012.eam.alloy Co
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pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
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#pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731
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neighbor 0.1 bin
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neigh_modify every 10 check yes delay 20
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fix 1 all force/spin zeeman 0.1 0.0 0.0 1.0
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fix 2 all langevin/spin 0.0 0.1 21
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fix 3 all integration/spin lattice yes
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timestep 0.0001
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compute out_mag all compute/spin
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compute out_pe all pe
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compute out_ke all ke
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compute out_temp all temp
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variable magz equal c_out_mag[3]
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variable magnorm equal c_out_mag[4]
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variable emag equal c_out_mag[5]
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variable tmag equal c_out_mag[6]
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variable mag_force equal f_1
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thermo_style custom step time v_magnorm v_emag temp etotal
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thermo 10
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#dump 1 all custom 50 dump_cobalt.lammpstrj type x y z spx spy spz
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run 1000
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@ -1,204 +0,0 @@
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# Compute elastic constant tensor for a crystal
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#
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# Written by Aidan Thompson (Sandia, athomps@sandia.gov)
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#
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# This script uses the following three include files.
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#
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# init.mod (must be modified for different crystal structures)
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# Define units, deformation parameters and initial
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# configuration of the atoms and simulation cell.
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#
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#
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# potential.mod (must be modified for different pair styles)
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# Define pair style and other attributes
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# not stored in restart file
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#
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#
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# displace.mod (displace.mod should not need to be modified)
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# Perform positive and negative box displacements
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# in direction ${dir} and size ${up}.
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# It uses the resultant changes
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# in stress to compute one
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# row of the elastic stiffness tensor
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#
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# Inputs variables:
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# dir = the Voigt deformation component
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# (1,2,3,4,5,6)
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# Global constants:
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# up = the deformation magnitude (strain units)
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# cfac = conversion from LAMMPS pressure units to
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# output units for elastic constants
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#
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#
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# To run this on a different system, it should only be necessary to
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# modify the files init.mod and potential.mod. In order to calculate
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# the elastic constants correctly, care must be taken to specify
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# the correct units in init.mod (units, cfac and cunits). It is also
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# important to verify that the minimization of energy w.r.t atom
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# positions in the deformed cell is fully converged.
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# One indication of this is that the elastic constants are insensitive
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# to the choice of the variable ${up} in init.mod. Another is to check
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# the final max and two-norm forces reported in the log file. If you know
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# that minimization is not required, you can set maxiter = 0.0 in
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# init.mod.
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#
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include init.mod
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include potential.mod
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# Compute initial state
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fix 3 all box/relax aniso 0.0
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minimize ${etol} ${ftol} ${maxiter} ${maxeval}
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variable tmp equal pxx
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variable pxx0 equal ${tmp}
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variable tmp equal pyy
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variable pyy0 equal ${tmp}
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variable tmp equal pzz
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variable pzz0 equal ${tmp}
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variable tmp equal pyz
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variable pyz0 equal ${tmp}
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variable tmp equal pxz
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variable pxz0 equal ${tmp}
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variable tmp equal pxy
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variable pxy0 equal ${tmp}
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variable tmp equal lx
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variable lx0 equal ${tmp}
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variable tmp equal ly
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variable ly0 equal ${tmp}
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variable tmp equal lz
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variable lz0 equal ${tmp}
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# These formulas define the derivatives w.r.t. strain components
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# Constants uses $, variables use v_
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variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
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variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
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variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
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variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
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variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
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variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}
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displace_atoms all random ${atomjiggle} ${atomjiggle} ${atomjiggle} 87287 units box
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# Write restart
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unfix 3
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write_restart restart.equil
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# uxx Perturbation
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variable dir equal 1
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include displace.mod
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# uyy Perturbation
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variable dir equal 2
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include displace.mod
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# uzz Perturbation
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variable dir equal 3
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include displace.mod
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# uyz Perturbation
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variable dir equal 4
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include displace.mod
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# uxz Perturbation
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variable dir equal 5
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include displace.mod
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# uxy Perturbation
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variable dir equal 6
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include displace.mod
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# Output final values
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variable C11all equal ${C11}
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variable C22all equal ${C22}
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variable C33all equal ${C33}
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variable C12all equal 0.5*(${C12}+${C21})
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variable C13all equal 0.5*(${C13}+${C31})
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variable C23all equal 0.5*(${C23}+${C32})
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variable C44all equal ${C44}
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variable C55all equal ${C55}
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variable C66all equal ${C66}
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variable C14all equal 0.5*(${C14}+${C41})
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variable C15all equal 0.5*(${C15}+${C51})
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variable C16all equal 0.5*(${C16}+${C61})
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variable C24all equal 0.5*(${C24}+${C42})
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variable C25all equal 0.5*(${C25}+${C52})
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variable C26all equal 0.5*(${C26}+${C62})
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variable C34all equal 0.5*(${C34}+${C43})
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variable C35all equal 0.5*(${C35}+${C53})
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variable C36all equal 0.5*(${C36}+${C63})
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variable C45all equal 0.5*(${C45}+${C54})
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variable C46all equal 0.5*(${C46}+${C64})
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variable C56all equal 0.5*(${C56}+${C65})
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# Average moduli for cubic crystals
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variable C11cubic equal (${C11all}+${C22all}+${C33all})/3.0
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variable C12cubic equal (${C12all}+${C13all}+${C23all})/3.0
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variable C44cubic equal (${C44all}+${C55all}+${C66all})/3.0
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variable bulkmodulus equal (${C11cubic}+2*${C12cubic})/3.0
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variable shearmodulus1 equal ${C44cubic}
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variable shearmodulus2 equal (${C11cubic}-${C12cubic})/2.0
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variable poissonratio equal 1.0/(1.0+${C11cubic}/${C12cubic})
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# For Stillinger-Weber silicon, the analytical results
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# are known to be (E. R. Cowley, 1988):
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# C11 = 151.4 GPa
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# C12 = 76.4 GPa
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# C44 = 56.4 GPa
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print "========================================="
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print "Components of the Elastic Constant Tensor"
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print "========================================="
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print "Elastic Constant C11all = ${C11all} ${cunits}"
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print "Elastic Constant C22all = ${C22all} ${cunits}"
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print "Elastic Constant C33all = ${C33all} ${cunits}"
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print "Elastic Constant C12all = ${C12all} ${cunits}"
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print "Elastic Constant C13all = ${C13all} ${cunits}"
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print "Elastic Constant C23all = ${C23all} ${cunits}"
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print "Elastic Constant C44all = ${C44all} ${cunits}"
|
||||
print "Elastic Constant C55all = ${C55all} ${cunits}"
|
||||
print "Elastic Constant C66all = ${C66all} ${cunits}"
|
||||
|
||||
print "Elastic Constant C14all = ${C14all} ${cunits}"
|
||||
print "Elastic Constant C15all = ${C15all} ${cunits}"
|
||||
print "Elastic Constant C16all = ${C16all} ${cunits}"
|
||||
|
||||
print "Elastic Constant C24all = ${C24all} ${cunits}"
|
||||
print "Elastic Constant C25all = ${C25all} ${cunits}"
|
||||
print "Elastic Constant C26all = ${C26all} ${cunits}"
|
||||
|
||||
print "Elastic Constant C34all = ${C34all} ${cunits}"
|
||||
print "Elastic Constant C35all = ${C35all} ${cunits}"
|
||||
print "Elastic Constant C36all = ${C36all} ${cunits}"
|
||||
|
||||
print "Elastic Constant C45all = ${C45all} ${cunits}"
|
||||
print "Elastic Constant C46all = ${C46all} ${cunits}"
|
||||
print "Elastic Constant C56all = ${C56all} ${cunits}"
|
||||
|
||||
print "========================================="
|
||||
print "Average properties for a cubic crystal"
|
||||
print "========================================="
|
||||
|
||||
print "Bulk Modulus = ${bulkmodulus} ${cunits}"
|
||||
print "Shear Modulus 1 = ${shearmodulus1} ${cunits}"
|
||||
print "Shear Modulus 2 = ${shearmodulus2} ${cunits}"
|
||||
print "Poisson Ratio = ${poissonratio}"
|
||||
@ -1,55 +0,0 @@
|
||||
# NOTE: This script can be modified for different atomic structures,
|
||||
# units, etc. See in.spin.curie_temperature for more info.
|
||||
#
|
||||
|
||||
# Define the finite deformation size. Try several values of this
|
||||
# variable to verify that results do not depend on it.
|
||||
variable up equal 1.0e-6
|
||||
|
||||
# Define the amount of random jiggle for atoms
|
||||
# This prevents atoms from staying on saddle points
|
||||
variable atomjiggle equal 1.0e-5
|
||||
|
||||
# Uncomment one of these blocks, depending on what units
|
||||
# you are using in LAMMPS and for output
|
||||
|
||||
# metal units, elastic constants in eV/A^3
|
||||
#units metal
|
||||
#variable cfac equal 6.2414e-7
|
||||
#variable cunits string eV/A^3
|
||||
|
||||
# metal units, elastic constants in GPa
|
||||
units metal
|
||||
variable cfac equal 1.0e-4
|
||||
variable cunits string GPa
|
||||
|
||||
# real units, elastic constants in GPa
|
||||
#units real
|
||||
#variable cfac equal 1.01325e-4
|
||||
#variable cunits string GPa
|
||||
|
||||
# Define minimization parameters
|
||||
variable etol equal 0.0
|
||||
variable ftol equal 1.0e-10
|
||||
variable maxiter equal 100
|
||||
variable maxeval equal 1000
|
||||
variable dmax equal 1.0e-2
|
||||
|
||||
# generate the box and atom positions using a diamond lattice
|
||||
variable a equal 5.43
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice fcc 3.54
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
#lattice diamond $a
|
||||
#region box prism 0 2.0 0 3.0 0 4.0 0.0 0.0 0.0
|
||||
#create_box 1 box
|
||||
#create_atoms 1 box
|
||||
|
||||
# Need to set mass (even for fixed lattice calculation, just to satisfy LAMMPS)
|
||||
mass 1 58.93
|
||||
|
||||
@ -1,30 +0,0 @@
|
||||
# NOTE: This script can be modified for different pair styles
|
||||
# See in.elastic for more info.
|
||||
|
||||
# Choose potentials (spin or spin-lattice)
|
||||
pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy ../examples/SPIN/cobalt/Co_PurjaPun_2012.eam.alloy Co
|
||||
air_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
|
||||
# Setup neighbor style
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
# Setup minimization style
|
||||
min_style cg
|
||||
min_modify dmax ${dmax} line quadratic
|
||||
|
||||
# Setup output
|
||||
compute out_mag all compute/spin
|
||||
compute out_temp all temp
|
||||
|
||||
variable magnorm equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[7]
|
||||
|
||||
thermo_style custom step time v_magnorm v_tmag temp
|
||||
thermo 1
|
||||
|
||||
|
||||
#thermo 1
|
||||
#thermo_style custom step temp pe press pxx pyy pzz pxy pxz pyz lx ly lz vol
|
||||
#thermo_modify norm no
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,129 +0,0 @@
|
||||
###################
|
||||
#######Init########
|
||||
###################
|
||||
|
||||
clear
|
||||
units metal
|
||||
dimension 3
|
||||
#boundary p p p
|
||||
boundary p p p
|
||||
|
||||
#newton off
|
||||
|
||||
#setting atom_style to spin:
|
||||
atom_style spin
|
||||
|
||||
#Define sort for paramagnetic simulations (if no pair interaction)
|
||||
#atom_modify sort 1000 4.0
|
||||
|
||||
atom_modify map array
|
||||
|
||||
###########################
|
||||
#######Create atoms########
|
||||
###########################
|
||||
|
||||
lattice fcc 3.54
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
#######################
|
||||
#######Settings########
|
||||
#######################
|
||||
|
||||
#isolating 1 atom into a group
|
||||
group single_spin id 10
|
||||
|
||||
#Setting one or more properties of one or more atoms.
|
||||
mass 1 58.93
|
||||
|
||||
#Setting spins orientation and moment
|
||||
set group all spin/random 31 1.72
|
||||
#set group all spin 1.72 0.0 0.0 1.0
|
||||
#set group single_spin spin/random 11 1.72
|
||||
|
||||
#velocity all create 200 4928459 rot yes dist gaussian
|
||||
velocity all create 200 4928459 rot yes dist gaussian
|
||||
|
||||
#Magneto-mechanic interactions for bulk fcc Cobalt
|
||||
#pair_style pair/spin/exchange 4.0
|
||||
#pair_style eam/alloy
|
||||
pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
|
||||
#pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0
|
||||
|
||||
pair_coeff * * eam/alloy ../examples/SPIN/dev/Co_PurjaPun_2012.eam.alloy Co
|
||||
#pair_coeff * * ../Co_PurjaPun_2012.eam.alloy Co
|
||||
|
||||
#pair_style pair/spin/exchange 4.0
|
||||
#type i and j | interaction type | cutoff | J1 (eV) | J2 (adim) | J3 (Ang) (for Exchange)
|
||||
#pair_coeff * * exchange 4.0 -0.0446928 0.003496 1.4885
|
||||
#pair_coeff * * exchange 4.0 0.0 0.003496 1.4885
|
||||
pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
#pair_coeff * * pair/spin/exchange exchange 2.5 0.0446928 0.003496 1.4885
|
||||
#pair_coeff * * pair/spin/exchange exchange 4.0 0.0 0.003496 1.4885
|
||||
|
||||
#type i and j | interaction type | cutoff | Int (eV) | [dx,dy,dz] (for DMI and ME)
|
||||
#pair_coeff * * dmi 2.6 0.001 0.0 0.0 1.0
|
||||
#pair_coeff * * me 2.6 0.01 1.0 1.0 1.0
|
||||
|
||||
#type i and j | interaction type | cutoff | K1 (eV) | K2 (adim) | K3 (Ang) (for SOC)
|
||||
#pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731
|
||||
|
||||
pair_coeff * * pair/spin/soc/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
|
||||
|
||||
#pair_coeff * * pair/spin/soc/neel neel 4.0 0.0 0.864159 2.13731
|
||||
|
||||
#Define a skin distance, update neigh list every
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
#neighbor 1.0 bin
|
||||
#neigh_modify every 1 check no delay 0
|
||||
|
||||
#Magnetic field fix
|
||||
#Type | Intensity (T or eV) | Direction
|
||||
fix 1 all force/spin zeeman 0.0 0.0 0.0 1.0
|
||||
#fix 1 all force/spin anisotropy 0.01 0.0 0.0 1.0
|
||||
|
||||
#Fix Langevin spins (merging damping and temperature)
|
||||
#Temp | Alpha_trans | Alpha_long | Seed
|
||||
#fix 2 all langevin/spin 0.0 0.1 21
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
#Magnetic integration fix
|
||||
fix 3 all integration/spin lattice yes
|
||||
#fix 3 all integration/spin lattice no
|
||||
|
||||
#compute real time, total magnetization, magnetic energy, and spin temperature
|
||||
#Iteration | Time | Mx | My | Mz | |M| | Em | Tm
|
||||
|
||||
#Setting the timestep for the simulation (in ps)
|
||||
timestep 0.0001
|
||||
|
||||
##################
|
||||
#######run########
|
||||
##################
|
||||
|
||||
compute out_mag all compute/spin
|
||||
compute out_pe all pe
|
||||
compute out_ke all ke
|
||||
compute out_temp all temp
|
||||
|
||||
variable magx equal c_out_mag[1]
|
||||
variable magy equal c_out_mag[2]
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
|
||||
thermo 50
|
||||
#thermo_style custom step time v_magx v_magy v_magy v_magnorm v_emag v_tmag
|
||||
thermo_style custom step time pe ke v_emag etotal
|
||||
thermo_modify format float %20.15g
|
||||
|
||||
#Dump the positions and spin directions of magnetic particles (vmd format)
|
||||
#dump 1 all custom 50 dump_cobalt.lammpstrj type x y z spx spy spz
|
||||
|
||||
#Running the simulations for N timesteps
|
||||
#run 10
|
||||
run 20000
|
||||
|
||||
@ -1,126 +0,0 @@
|
||||
###################
|
||||
#######Init########
|
||||
###################
|
||||
|
||||
clear
|
||||
#setting units to metal (Ang, picosecs, eV, ...):
|
||||
units metal
|
||||
|
||||
#setting dimension of the system (N=2 or 3):
|
||||
dimension 3
|
||||
|
||||
#setting boundary conditions. (p for periodic, f for fixed, ...)
|
||||
boundary p p p
|
||||
#boundary f f f
|
||||
|
||||
#setting atom_style to spin:
|
||||
atom_style spin
|
||||
|
||||
#Define sort for paramagnetic simulations (if no pair interaction)
|
||||
#atom_modify sort 1000 4.0
|
||||
|
||||
#why?
|
||||
atom_modify map array
|
||||
|
||||
#newton off for pair spin in SEQNEI
|
||||
#newton off off
|
||||
|
||||
###########################
|
||||
#######Create atoms########
|
||||
###########################
|
||||
|
||||
#Lattice constant of fcc Cobalt
|
||||
lattice fcc 3.54
|
||||
#lattice sc 2.50
|
||||
|
||||
#Test Kagome
|
||||
#variable a equal sqrt(3.0)/8.0
|
||||
#variable b equal 3.0*sqrt(3.0)/8.0
|
||||
#variable c equal sqrt(3.0)/4.0
|
||||
|
||||
#lattice custom 2.5 a1 1.0 0.0 0.0 &
|
||||
# a2 0.0 1.0 0.0 &
|
||||
# a3 0.0 0.0 1.0 &
|
||||
# basis 0.0 $a 0.0 &
|
||||
# basis 0.25 $a 0.0 &
|
||||
# basis 0.375 0.0 0.0 &
|
||||
# basis 0.25 $b 0.0 &
|
||||
# basis 0.5 $b 0.0 &
|
||||
# basis 0.625 $c 0.0
|
||||
|
||||
#Defining a geometric region of space. Sets ID(user's choice), style(block, sphere, ...), then, args depends on the style chosen
|
||||
#(for block, one has x0, xf, y0, yf, z0, zf, in distance units)
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
|
||||
#Creating a simulation box based on the specified region. Entries: number of atom types and box ref.
|
||||
create_box 1 box
|
||||
|
||||
#Creating atoms (or molecules) on a lattice, or a single atom (or molecule), ...
|
||||
#Entries: atom type,
|
||||
create_atoms 1 box
|
||||
|
||||
#Replicating NxNxN the entire set of atoms
|
||||
#replicate 1 1 1
|
||||
|
||||
|
||||
#######################
|
||||
#######Settings########
|
||||
#######################
|
||||
|
||||
#Setting one or more properties of one or more atoms.
|
||||
#Setting mass
|
||||
mass 1 1.0
|
||||
#set group all mass 1.0
|
||||
#Setting spins orientation and moment
|
||||
#set group all spin/random 11 1.72
|
||||
set group all spin 1.72 1.0 0.0 0.0
|
||||
|
||||
#Magnetic exchange interaction coefficient for bulk fcc Cobalt
|
||||
pair_style pair/spin 4.0
|
||||
#type i and j | interaction type | cutoff | J1 (eV) | J2 (adim) | J3 (Ang) (for Exchange)
|
||||
pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885
|
||||
#type i and j | interaction type | cutoff | Int (eV) | [dx,dy,dz] (for DMI and ME)
|
||||
#pair_coeff * * dmi 2.6 0.001 0.0 0.0 1.0
|
||||
#pair_coeff * * me 2.6 0.01 1.0 1.0 1.0
|
||||
|
||||
#Define a skin distance, update neigh list every
|
||||
#neighbor 1.0 bin
|
||||
#neigh_modify every 10 check yes delay 20
|
||||
neighbor 0.0 bin
|
||||
neigh_modify every 1 check no delay 0
|
||||
|
||||
#Magnetic field fix
|
||||
#Type | Intensity (T or eV) | Direction
|
||||
fix 1 all force/spin zeeman 1.0 0.0 0.0 1.0
|
||||
#fix 1 all force/spin anisotropy 0.001 0.0 0.0 1.0
|
||||
#fix 1 all force/spin anisotropy -0.1 0.0 0.0 1.0
|
||||
#fix 1 all force/spin anisotropy 0.1 0.0 1.0 0.0
|
||||
|
||||
#Fix Langevin spins (merging damping and temperature)
|
||||
#Temp | Alpha_trans | Alpha_long | Seed
|
||||
#fix 2 all langevin/spin 0.0 0.1 0.0 21
|
||||
fix 2 all langevin/spin 1.0 0.1 0.0 21
|
||||
#fix 2 all langevin/spin 0.0 0.0 0.0 21
|
||||
|
||||
#Magnetic integration fix
|
||||
fix 3 all nve/spin mpi
|
||||
|
||||
#compute real time, total magnetization, magnetic energy, and spin temperature
|
||||
#Iteration | Time | Mx | My | Mz | |M| | Em | Tm
|
||||
compute mag all compute/spin
|
||||
fix outmag all ave/time 1 1 10 c_mag[1] c_mag[2] c_mag[3] c_mag[4] c_mag[5] c_mag[6] c_mag[7] file mag_Co_nodamp.dat format %20.16g
|
||||
|
||||
#Setting the timestep for the simulation (in ps)
|
||||
timestep 0.0001
|
||||
|
||||
##################
|
||||
#######run########
|
||||
##################
|
||||
|
||||
#Dump the positions and spin directions of magnetic particles (vmd format)
|
||||
dump 1 all custom 100 dump_spin_T100.lammpstrj type x y z spx spy spz
|
||||
|
||||
#Running the simulations for N timesteps
|
||||
run 2000
|
||||
#run 1
|
||||
|
||||
@ -0,0 +1,5 @@
|
||||
2.492 2.803
|
||||
3.524 0.0816
|
||||
4.316 0.35
|
||||
4.983 0.16
|
||||
5.572 0.0408
|
||||
32
examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fit.py
Normal file
32
examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fit.py
Normal file
@ -0,0 +1,32 @@
|
||||
# program fitting the exchange interaction
|
||||
# model curve: Bethe-Slater function
|
||||
import numpy as np, pylab, tkinter
|
||||
import matplotlib.pyplot as plt
|
||||
from scipy.optimize import curve_fit
|
||||
from decimal import *
|
||||
|
||||
print("Loop begin")
|
||||
|
||||
# definition of the Bethe-Slater function
|
||||
def func(x,a,b,c):
|
||||
return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2)
|
||||
|
||||
# exchange coeff table (data to fit)
|
||||
rdata, Jdata = np.loadtxt('exchange_fcc_ni.dat', usecols=(0,1), unpack=True)
|
||||
plt.plot(rdata, Jdata, 'b-', label='data')
|
||||
|
||||
# perform the fit
|
||||
popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.]))
|
||||
plt.plot(rdata, func(rdata, *popt), 'r--', label='fit')
|
||||
|
||||
# print the fitted parameters
|
||||
print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt))
|
||||
|
||||
# ploting the result
|
||||
plt.xlabel('r_ij')
|
||||
pylab.xlim([0,6.5])
|
||||
plt.ylabel('J_ij')
|
||||
plt.legend()
|
||||
plt.show()
|
||||
|
||||
print("Loop end")
|
||||
@ -10,29 +10,29 @@ boundary p p p
|
||||
# check why?
|
||||
atom_modify map array
|
||||
|
||||
lattice fcc 3.54
|
||||
lattice fcc 3.524
|
||||
region box block 0.0 5.0 0.0 5.0 0.0 5.0
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
# setting mass, mag. moments, and interactions for cobalt
|
||||
|
||||
mass 1 58.93
|
||||
mass 1 58.69
|
||||
|
||||
set group all spin/random 31 1.72
|
||||
set group all spin/random 31 0.6
|
||||
velocity all create 100 4928459 rot yes dist gaussian
|
||||
|
||||
#pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
|
||||
pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0
|
||||
pair_coeff * * eam/alloy ../examples/SPIN/cobalt/Co_PurjaPun_2012.eam.alloy Co
|
||||
pair_coeff * * pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
pair_coeff * * eam/alloy ../examples/SPIN/nickel/Ni99.eam.alloy Ni
|
||||
pair_coeff * * pair/spin/exchange exchange 4.0 0.009718152197 0.000153 1.243
|
||||
#pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 all force/spin zeeman 0.1 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.1 21
|
||||
fix 1 all force/spin zeeman 0.0 0.0 0.0 1.0
|
||||
fix 2 all langevin/spin 0.0 0.0 21
|
||||
|
||||
fix 3 all integration/spin lattice yes
|
||||
|
||||
|
||||
@ -1,81 +0,0 @@
|
||||
# initial variables
|
||||
|
||||
# dimensions of the box and of each layer
|
||||
variable box_size equal 50.0
|
||||
variable ir_thick equal 4.0
|
||||
variable fe_thick equal 0.5
|
||||
variable pd_thick equal 0.5
|
||||
|
||||
variable fe_hi equal ${ir_thick}+${fe_thick}
|
||||
variable pd_hi equal ${ir_thick}+${fe_thick}+${pd_thick}
|
||||
|
||||
|
||||
units metal
|
||||
atom_style spin
|
||||
|
||||
dimension 3
|
||||
boundary p p f
|
||||
|
||||
# check why?
|
||||
atom_modify map array
|
||||
|
||||
lattice fcc 3.839 orient x 1 -1 0 orient y 1 1 -2 orient z 1 1 1
|
||||
region box block 0.0 ${box_size} 0.0 ${box_size} 0.0 ${pd_hi}
|
||||
region box_ir block 0.0 ${box_size} 0.0 ${box_size} 0.0 ${ir_thick}
|
||||
region box_fe block 0.0 ${box_size} 0.0 ${box_size} ${ir_thick} ${fe_hi}
|
||||
region box_pd block 0.0 ${box_size} 0.0 ${box_size} ${fe_hi} ${pd_hi}
|
||||
|
||||
create_box 3 box
|
||||
|
||||
create_atoms 1 region box_ir
|
||||
create_atoms 2 region box_fe
|
||||
create_atoms 3 region box_pd
|
||||
|
||||
group ir_atoms region box_ir
|
||||
group fe_atoms region box_fe
|
||||
group pd_atoms region box_pd
|
||||
|
||||
# setting mass, mag. moments, and interactions for cobalt
|
||||
|
||||
mass 1 192.217 # mass of Ir atoms
|
||||
mass 2 55.845 # mass of Fe atoms
|
||||
mass 3 106.42 # mass of Pd atoms
|
||||
|
||||
set group ir_atoms spin/random 31 0.01 # has to set a length for LAMMPS to be happy
|
||||
set group fe_atoms spin/random 89 2.7
|
||||
set group pd_atoms spin/random 55 0.3
|
||||
|
||||
#pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
|
||||
pair_style hybrid/overlay pair/spin/exchange 4.0
|
||||
#pair_style hybrid/overlay pair/spin/exchange 4.0 pair/spin/soc/dmi 2.6
|
||||
pair_coeff * * pair/spin/exchange exchange 4.0 0.0 0.003496 1.4885
|
||||
pair_coeff 2 2 pair/spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
|
||||
#pair_coeff * * pair/spin/soc/dmi dmi 2.6 0.01 0.0 0.0 1.0
|
||||
#pair_coeff * * pair/spin/soc/neel neel 4.0 0.003330282 0.864159 2.13731
|
||||
|
||||
neighbor 0.1 bin
|
||||
neigh_modify every 10 check yes delay 20
|
||||
|
||||
fix 1 fe_atoms force/spin anisotropy 0.0001 0.0 0.0 1.0
|
||||
fix 2 all force/spin zeeman 0.1 0.0 0.0 1.0
|
||||
fix 3 all langevin/spin 0.0 0.1 21
|
||||
fix 4 all integration/spin lattice no
|
||||
|
||||
timestep 0.0002
|
||||
|
||||
# define output and run
|
||||
|
||||
compute out_mag all compute/spin
|
||||
variable magz equal c_out_mag[3]
|
||||
variable magnorm equal c_out_mag[4]
|
||||
variable emag equal c_out_mag[5]
|
||||
variable tmag equal c_out_mag[6]
|
||||
variable mag_force equal f_1
|
||||
|
||||
thermo_style custom step time v_magnorm v_emag etotal
|
||||
thermo 10
|
||||
|
||||
dump 1 all custom 50 dump_skyrmion.lammpstrj type x y z spx spy spz
|
||||
|
||||
run 1000
|
||||
|
||||
Reference in New Issue
Block a user