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1
examples/README
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@ -27,6 +27,7 @@ These are the sample problems in the various sub-directories:
couple: code example of how to link to LAMMPS as a library
colloid: big colloid particles in a small particle solvent, 2d system
comb: models using the COMB potential
crack: crack propagation in a 2d solid
dipole: point dipolar particles, 2d system
elastic: zero temperature elastic constant tensor of silicon

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This folder contains examples of using LAMMPS COMB potential
Created by Tzu-Ray Shan (UF, rayshan@ufl.edu), Apr 2010
All examples contains:
1. input script: in.comb.*
2. log file: log.lammps.*
3. output cfg file: out.*.cfg (use with AtomEye)
4. some examples include a structure file data.*
Note: thse is also a F90 program, elastic.f90, which can be used to
generate elastic constants.
Examples:
1. in.comb.Si: Pure Si crystal, structure created by LAMMPS, qeq off
2. in.comb.Si.elastic: Pure Si crystal, qeq off, calculates
stress-strain, no out.*.cfg.
3. in.comb.Cu: Pure Cu crystal, structure created by LAMMPS, qeq off
4. in.comb.Cu2O.elastic: Cu2O crystal, qeq on, minimizes, then calculates
elastic constants
5. in.comb.HfO2: HfO2 polymorphs: Monoclinic HfO2 NVT @ 300K

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! This program calculates elastic constants
! Must be used with in.comb-elastic script, and reads output log.lammps
! Written by T-R Shan, MSE, UF, Feb 2010
program main
implicit none
integer :: i,j,k,l
real*8 :: box(6,11),force(6,11),vol(11),eps(11),strbox(6,11)
real*8 :: sumx,sumx2,sumy,sumxy,c11,c12,c13,c14,c15,c16,c33,c44,c66,bulk,shear
character*7 :: header1
open(5,status='old',file='log.lammps')
do i=1,500
read(5,'(a7)') header1
if(header1.eq.'Step Lx')then
do j=1,11
read(5,*) k,(box(l,j),l=1,6),(force(l,j),l=1,6)
vol(j)=box(1,j)*box(2,j)*box(3,j)*dsqrt(1-(box(4,j)/box(1,j))*(box(4,j)/box(1,j))-(box(6,j)/box(3,j))*(box(6,j)/box(3,j)-(box(5,j)/box(3,j))*(box(5,j)/box(3,j))))
eps(j)=(box(1,j)-box(1,1))/box(1,1)
do l=1,6
strbox(l,j)=force(l,j)/vol(j)/1.0d4
enddo
enddo
exit
endif
enddo
!! C11
sumx = 0.0; sumx2 = 0.0; sumy = 0.0; sumxy = 0.0
do j=2,11
sumx = sumx + eps(j)
sumx2= sumx2+ eps(j)*eps(j)
sumy = sumy + strbox(1,j)
sumxy= sumxy+ strbox(1,j)*eps(j)
enddo
c11 = (sumxy-sumx*sumy/10.0)/(sumx2-sumx*sumx/10.0)
!! C12
sumy = 0.0; sumxy = 0.0
do j=2,11
sumy = sumy + strbox(2,j)
sumxy= sumxy+ strbox(2,j)*eps(j)
enddo
c12 = (sumxy-sumx*sumy/10.0)/(sumx2-sumx*sumx/10.0)
!! C13
sumy = 0.0; sumxy = 0.0
do j=2,11
sumy = sumy + strbox(3,j)
sumxy= sumxy+ strbox(3,j)*eps(j)
enddo
c13 = (sumxy-sumx*sumy/10.0)/(sumx2-sumx*sumx/10.0)
!! C14
sumy = 0.0; sumxy = 0.0
do j=2,11
sumy = sumy + strbox(4,j)
sumxy= sumxy+ strbox(4,j)*eps(j)
enddo
c14 = (sumxy-sumx*sumy/10.0)/(sumx2-sumx*sumx/10.0)
!! C15
sumy = 0.0; sumxy = 0.0
do j=2,11
sumy = sumy + strbox(5,j)
sumxy= sumxy+ strbox(5,j)*eps(j)
enddo
c15 = (sumxy-sumx*sumy/10.0)/(sumx2-sumx*sumx/10.0)
!! C16
sumy = 0.0; sumxy = 0.0
do j=2,11
sumy = sumy + strbox(6,j)
sumxy= sumxy+ strbox(6,j)*eps(j)
enddo
c16 = (sumxy-sumx*sumy/10.0)/(sumx2-sumx*sumx/10.0)
!! C33
do i=1,500
read(5,'(a7)') header1
if(header1.eq.'Step Lx')then
do j=1,11
read(5,*) k,(box(l,j),l=1,6),(force(l,j),l=1,6)
vol(j)=box(1,j)*box(2,j)*box(3,j)*dsqrt(1-(box(4,j)/box(1,j))*(box(4,j)/box(1,j))-(box(6,j)/box(3,j))*(box(6,j)/box(3,j)-(box(5,j)/box(3,j))*(box(5,j)/box(3,j))))
eps(j)=(box(3,j)-box(3,1))/box(3,1)
do l=1,6
strbox(l,j)=force(l,j)/vol(j)/1.0d4
enddo
enddo
exit
endif
enddo
sumx = 0.0; sumx2 = 0.0; sumy = 0.0; sumxy = 0.0
do j=2,11
sumx = sumx + eps(j)
sumx2= sumx2+ eps(j)*eps(j)
sumy = sumy + strbox(3,j)
sumxy= sumxy+ strbox(3,j)*eps(j)
enddo
c33 = (sumxy-sumx*sumy/10.0)/(sumx2-sumx*sumx/10.0)
!! C44
do i=1,500
read(5,'(a7)') header1
if(header1.eq.'Step Lx')then
do j=1,11
read(5,*) k,(box(l,j),l=1,6),(force(l,j),l=1,6)
vol(j)=box(1,j)*box(2,j)*box(3,j)*dsqrt(1.0-(box(4,j)/box(1,j))*(box(4,j)/box(1,j))-(box(6,j)/box(3,j))*(box(6,j)/box(3,j)-(box(5,j)/box(3,j))*(box(5,j)/box(3,j))))
do l=1,6
strbox(l,j)=force(l,j)/vol(j)/1.0d4
enddo
enddo
exit
endif
enddo
sumx = 0.0; sumx2 = 0.0; sumy = 0.0; sumxy = 0.0
do j=2,11
eps(j)=asin(box(6,j)/box(3,j))
sumx = sumx + eps(j)
sumx2= sumx2+ eps(j)*eps(j)
sumy = sumy + strbox(6,j)
sumxy= sumxy+ strbox(6,j)*eps(j)
enddo
c44 = (sumxy-sumx*sumy/10.0)/(sumx2-sumx*sumx/10.0)
!! C66
do i=1,500
read(5,'(a7)') header1
if(header1.eq.'Step Lx')then
do j=1,11
read(5,*) k,(box(l,j),l=1,6),(force(l,j),l=1,6)
vol(j)=box(1,j)*box(2,j)*box(3,j)*dsqrt(1.0-(box(4,j)/box(1,j))*(box(4,j)/box(1,j))-(box(6,j)/box(3,j))*(box(6,j)/box(3,j)-(box(5,j)/box(3,j))*(box(5,j)/box(3,j))))
do l=1,6
strbox(l,j)=force(l,j)/vol(j)/1.0d4
enddo
enddo
exit
endif
enddo
sumx = 0.0; sumx2 = 0.0; sumy = 0.0; sumxy = 0.0
do j=2,11
eps(j)=asin(box(4,j)/box(1,j))
sumx = sumx + eps(j)
sumx2= sumx2+ eps(j)*eps(j)
sumy = sumy + strbox(4,j)
sumxy= sumxy+ strbox(4,j)*eps(j)
enddo
c66 = (sumxy-sumx*sumy/10.0)/(sumx2-sumx*sumx/10.0)
bulk=(c11*2.0+c33)/9.0+2.0*(c12+c13*2.0)/9.0
shear=(2.*c11+c33-c12-2.*c13)/15.+(2.*c44+c66)/5.
write(*,*)
write(*,*)'Elastic constants (GPa):'
write(*,101) 'C11 = ',c11
write(*,101) 'C12 = ',c12
write(*,101) 'C13 = ',c13
write(*,101) 'C14 = ',c14
write(*,101) 'C15 = ',c15
write(*,101) 'C16 = ',c16
write(*,101) 'C33 = ',c33
write(*,101) 'C44 = ',c44
write(*,101) 'C66 = ',c66
write(*,101) 'B = ',bulk
write(*,101) 'G = ',shear
write(5,*)
write(5,*)'Elastic constants (GPa):'
write(5,101) 'C11 = ',c11
write(5,101) 'C12 = ',c12
write(5,101) 'C13 = ',c13
write(5,101) 'C14 = ',c14
write(5,101) 'C15 = ',c15
write(5,101) 'C16 = ',c16
write(5,101) 'C33 = ',c33
write(5,101) 'C44 = ',c44
write(5,101) 'C66 = ',c66
write(5,101) 'B = ',bulk
write(5,101) 'G = ',shear
101 format(a6,f11.3)
stop
end

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# COMB parameters for various elements (Si, Cu, Hf, Ti, Zr, U, O) and mixtures (their oxides and alloys)
# Edited by Tzu-Ray Shan from MSE, Univ. FL in Apr 2010
#
# Elements currently available: Si, Cu, Hf, Ti, Zr, U, O
# Oxides currently available: Si-O, Cu-O, Hf-O, Ti-O
#
# Si parameter set from (JG Yu, SB Sinnott, SR Phillpot, Phys. Rev. B 75 085311 2007)
# ,and (TR Shan, BD Devine, SR Phillpot, SB Sinnott, to be sub to Phys. Rev. B)
# O parameter set from (TR Shan, BD Devine, SB Sinnott, SR Phillpot, Phys. Rev. B 81 125328 2010)
# Cu parameter set from (BD Devine, TR Shan, SB Sinnott, SR Phillpot, to be sub to Phys. Rev. B)
# Hf parameter set from (TR Shan, BD Devine, SB Sinnott, SR Phillpot, Phys. Rev. B 81 125328 2010)
# Ti parameter set from (TR Shan, SR Phillpot, SB Sinnott, in preparation)
# U parameter set from (Y Li, TR Shan, SB Sinnott, SR Phillpot, in preparation)
# Zr parameter set from (T Iwasaki, J. Mater. Res. 20 5 1300 2005)
#
# Multiple entries can be added to this file, LAMMPS reads the ones it needs
# Only M-O are added in the potential table, using mixing rules to generate desired alloy (A-B) parameters
# 8 entries for a desired A-B type: AAA, BBB, AAB, ABA, ABB, BAA, BBA, BBA
# 27 entries for a system containing three elements A, B and C
# These entries are in LAMMPS "metal" units
#
Hf Hf Hf 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.90 0.10 2.069563 2.069563 707.53 707.53 0 0 0.008 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12 0.0
Ti Ti Ti 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 3.45 0.10 2.082408 2.082408 546.386 546.386 0 0 0.0015 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 2.46820415900968 0 0.151351003255176 0 0.873685 0.392632 0.392632 1.78349 1.78349 12 0.0
O O O 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.8 0.2 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0.0
Cu Cu Cu 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.90 0.05 2.794608 2.794608 952.693 952.693 0.077 0.0095 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.72571 0.72571 12 -2.0
Si Si Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.80 0.20 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0.0
Zr Zr Zr 1 0 1 0 1 0 0.929 0.929 39.9454 39.9454 3.8 0.31 1.857 1.857 382.6 382.6 0 0 0 0 0 0 1 1 1 1 -4 4 1.64 -1.5 -4 4 1.64 -1.5 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12 0.0
U U U 1 0 1 0 4.346966 0.77617 0.832 0.832 162.6 162.6 3.9 0.15 1.835 1.835 795.6 795.6 0 0 0 0 0 0 1 1 1 1 -4 4 2 -2 -4 4 2 -2 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12 0.0
#
Si O O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.20 2.4799 5.36 1830.8 3326.69 0 0 0 109.47 0.3122 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
O Si Si 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 2.80 0.20 5.36 2.4799 3326.69 1830.8 0 0 0 143.73 2.6 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
Si O Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.20 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
O Si O 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 3.20 0.10 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
Si Si O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.80 0.20 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0
O O Si 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.80 0.20 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0
#
Si Cu Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 2.80 0.110 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -6 2 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12 0
Cu Si Si 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 2.80 0.110 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12 0
Si Cu Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 2.80 0.110 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -6 2 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12 0
Cu Si Cu 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 2.80 0.110 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12 0
Si Si Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.80 0.11 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0
Cu Cu Si 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.80 0.11 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12 0
#
Si O Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.20 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
Cu O Si 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.30 0.11 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12 0
Si Cu O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 2.80 0.110 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -6 2 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12 0
Cu Si O 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 2.80 0.110 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12 0
O Si Cu 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 2.80 0.20 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
O Cu Si 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.30 0.11 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12 0
#
Cu O O 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.30 0.1150 2.794608 5.36 952.693 3326.69 0 0 0 360 1.0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12 -1.0
O Cu Cu 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.30 0.1150 5.36 2.794608 3326.69 952.693 0 0 0 109.47 0.38 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12 0
Cu O Cu 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.30 0.1150 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12 0
O Cu O 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.30 0.1150 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12 0
Cu Cu O 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.30 0.115 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12 0
O O Cu 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.30 0.115 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0
#
Si Hf Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.21 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0
Hf Si Si 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.21 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0
Si Hf Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.21 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0
Hf Si Hf 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.21 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0
Si Si Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 3.21 0.15 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0
Hf Hf Si 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.21 0.15 2.069563 2.069563 707.53 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.13952 0 0.00941 0 0.719131 -3.92875 -3.92875 4.83958 4.83958 12 0
#
Si O Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.20 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0
Hf O Si 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.18 0.15 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.14 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.719131 -3.92875 -3.922011 4.83958 0.971086 12 0.29
Si Hf O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.21 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0
Hf Si O 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.21 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0
O Si Hf 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 2.80 0.20 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0
O Hf Si 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.18 0.15 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.14 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12 0
#
Hf O O 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.29 0.12 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.14 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.922011 4.83958 0.971086 12 0.29
O Hf Hf 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.29 0.12 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.14 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12 0.29
Hf O Hf 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.29 0.12 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.14 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.922011 4.83958 0.971086 12 0.29
O Hf O 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.29 0.12 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.14 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12 0.29
Hf Hf O 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.29 0.12 2.069563 2.069563 707.53 707.53 0 0 0 0 0 0.0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12 0.29
O O Hf 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 3.29 0.12 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0.0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0.29
#
Ti O O 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 3.11 0.24 2.082408 5.36 546.386 3326.69 0 0 0 90 0.603105 9.50 0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12 0.0
O Ti Ti 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 3.11 0.24 5.36 2.082408 3326.69 546.386 0 0 0 130.54 0.202777 9.50 0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12 0.0
Ti O Ti 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 4.20 0.15 2.082408 5.36 546.386 3326.69 0 0 0 0 0 9.50 0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12 0.0
O Ti O 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 4.20 0.15 5.36 2.082408 3326.69 546.386 0 0 0 0 0 9.50 0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12 0.0
Ti Ti O 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 4.20 0.15 2.082408 2.082408 546.386 546.386 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.392632 1.78349 1.78349 12 0.0
O O Ti 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 4.20 0.15 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0.0
#
Ti Cu Cu 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 3.162411 0.118976 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -6 2 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0
Cu Ti Ti 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 3.162411 0.118976 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0
Ti Cu Ti 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 3.162411 0.118976 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -6 2 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0
Cu Ti Cu 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 3.162411 0.118976 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0
Ti Ti Cu 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 2.80 0.20 2.082408 2.082408 546.386 546.386 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.392632 1.78349 1.78349 12 0
Cu Cu Ti 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 2.90 0.05 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12 0
#
Ti O Cu 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 3.11 0.24 2.082408 5.36 546.386 3326.69 0 0 0 0 0 9.50 0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12 0
Cu O Ti 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.30 0.10 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12 0
Ti Cu O 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 2.849074 0.150926 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -6 2 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0
Cu Ti O 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 2.849074 0.150926 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0
O Ti Cu 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 3.11 0.24 5.36 2.082408 3326.69 546.386 0 0 0 0 0 9.50 0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12 0
O Cu Ti 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.30 0.10 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 0.15867 1.106214 0.533319 1.857837 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12 0

30
examples/comb/in.comb.Cu Normal file
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# Pure Cu crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice fcc 3.615
region box block 0 4 0 4 0 4
create_box 1 box
create_atoms 1 box
mass 1 63.54
pair_style comb
pair_coeff * * ffield.comb Cu
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Cu
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10

98
examples/comb/in.comb.Cu2O.elastic Normal file
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# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Cu2O
mass 1 63.5
mass 2 16.0
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Cu O
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul lx ly lz vol
thermo_modify norm yes
thermo 1
fix 1 all nve
fix 2 all qeq/comb 1 0.0001
dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
dump_modify 1 append yes element Cu O
run 2
thermo_style custom step temp etotal pe evdwl ecoul lx ly lz vol
thermo_modify norm yes
thermo 1
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.001
minimize 1.0e-14 1.0e-20 1000 10000
min_modify dmax 0.2 line quadratic
thermo_style custom step temp etotal pe evdwl ecoul lx ly lz vol
thermo_modify norm yes
thermo 1
unfix 1
fix 1 all nve
run 1
unfix 1
unfix 2
undump 1
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum &
c_perfx[1] c_perfx[2] c_perfx[3] &
c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz &
c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
run 10
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum &
c_perfz[1] c_perfz[2] c_perfz[3] &
c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz &
c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum &
c_perfyz[1] c_perfyz[2] c_perfyz[3] &
c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz &
c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum &
c_perfxy[1] c_perfxy[2] c_perfxy[3] &
c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz &
c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10

32
examples/comb/in.comb.HfO2 Normal file
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# HfO2 polymorphs: Monoclinic HfO2 NVT @ 300K
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.m-HfO2
#read_data data.t-HfO2
#read_data data.c-HfO2
mass 1 178.0
mass 2 16.0
pair_style comb
pair_coeff * * ffield.comb Hf O
neighbor 0.5 bin
neigh_modify every 10 delay 10 check yes
timestep 0.00020
fix 1 all nvt temp 300.0 300.0 0.1
fix 2 all qeq/comb 1 0.003
dump 1 all cfg 100 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
dump_modify 1 append yes element Hf O
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 300.1 2398378
thermo 1
run 10

30
examples/comb/in.comb.Si Normal file
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# Pure Si crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.43
region box block 0 4 0 4 0 4
create_box 1 box
create_atoms 1 box
mass 1 29.0
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
dump_modify 1 append yes element Si
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10

81
examples/comb/in.comb.Si.elastic Normal file
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# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.431
region box block 0 4 0 4 0 4
create_box 1 box
create_atoms 1 box
mass 1 29.0
change_box triclinic
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
fix 1 all box/relax aniso 0.0 vmax 0.001
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul &
#lx ly lz vol pxx pyy pzz
thermo_modify norm yes
thermo 1
minimize 1.0e-14 1.0e-20 1000 10000
min_modify dmax 0.2 line quadratic
unfix 1
run 1
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum &
c_perfx[1] c_perfx[2] c_perfx[3] &
c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz &
c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
run 10
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum &
c_perfz[1] c_perfz[2] c_perfz[3] &
c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz &
c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum &
c_perfyz[1] c_perfyz[2] c_perfyz[3] &
c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz &
c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum &
c_perfxy[1] c_perfxy[2] c_perfxy[3] &
c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz &
c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10

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LAMMPS (20 Aug 2010)
# Pure Cu crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
1 by 1 by 1 processor grid
create_atoms 1 box
Created 256 atoms
mass 1 63.54
pair_style comb
pair_coeff * * ffield.comb Cu
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Cu
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10
Memory usage per processor = 2.55348 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0
1 10.099643 -3.5063151 -3.5076155 -3.5076155 0 27.512983 3023.4645 14.46 14.46 14.46 0
2 10.098572 -3.5063151 -3.5076153 -3.5076153 0 27.563765 3023.4645 14.46 14.46 14.46 0
3 10.096788 -3.5063151 -3.5076151 -3.5076151 0 27.64839 3023.4645 14.46 14.46 14.46 0
4 10.094291 -3.5063151 -3.5076148 -3.5076148 0 27.766843 3023.4645 14.46 14.46 14.46 0
5 10.09108 -3.5063151 -3.5076144 -3.5076144 0 27.919101 3023.4645 14.46 14.46 14.46 0
6 10.087158 -3.5063151 -3.5076139 -3.5076139 0 28.105138 3023.4645 14.46 14.46 14.46 0
7 10.082524 -3.5063151 -3.5076133 -3.5076133 0 28.324919 3023.4645 14.46 14.46 14.46 0
8 10.077179 -3.5063151 -3.5076126 -3.5076126 0 28.578403 3023.4645 14.46 14.46 14.46 0
9 10.071123 -3.5063151 -3.5076118 -3.5076118 0 28.865545 3023.4645 14.46 14.46 14.46 0
10 10.06436 -3.5063151 -3.5076109 -3.5076109 0 29.186292 3023.4645 14.46 14.46 14.46 0
Loop time of 0.796709 on 1 procs for 10 steps with 256 atoms
Pair time (%) = 0.794205 (99.6857)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00052619 (0.0660454)
Outpt time (%) = 0.00174093 (0.218515)
Other time (%) = 0.00023675 (0.0297159)
Nlocal: 256 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4375 ave 4375 max 4375 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: 172544 ave 172544 max 172544 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 172544
Ave neighs/atom = 674
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (20 Aug 2010)
# Pure Cu crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
1 by 2 by 2 processor grid
create_atoms 1 box
Created 256 atoms
mass 1 63.54
pair_style comb
pair_coeff * * ffield.comb Cu
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Cu
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10
Memory usage per processor = 2.02958 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0
1 10.099638 -3.5063151 -3.5076155 -3.5076155 0 27.513531 3023.4645 14.46 14.46 14.46 0
2 10.098553 -3.5063151 -3.5076153 -3.5076153 0 27.565957 3023.4645 14.46 14.46 14.46 0
3 10.096744 -3.5063151 -3.5076151 -3.5076151 0 27.653322 3023.4645 14.46 14.46 14.46 0
4 10.094212 -3.5063151 -3.5076148 -3.5076148 0 27.775611 3023.4645 14.46 14.46 14.46 0
5 10.090958 -3.5063151 -3.5076144 -3.5076144 0 27.932801 3023.4645 14.46 14.46 14.46 0
6 10.086981 -3.5063151 -3.5076139 -3.5076139 0 28.124863 3023.4645 14.46 14.46 14.46 0
7 10.082283 -3.5063151 -3.5076132 -3.5076132 0 28.351761 3023.4645 14.46 14.46 14.46 0
8 10.076864 -3.5063151 -3.5076125 -3.5076125 0 28.613454 3023.4645 14.46 14.46 14.46 0
9 10.070725 -3.5063151 -3.5076118 -3.5076118 0 28.909893 3023.4645 14.46 14.46 14.46 0
10 10.063868 -3.5063151 -3.5076109 -3.5076109 0 29.241022 3023.4645 14.46 14.46 14.46 0
Loop time of 0.213216 on 4 procs for 10 steps with 256 atoms
Pair time (%) = 0.198187 (92.951)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00896907 (4.20656)
Outpt time (%) = 0.00509757 (2.3908)
Other time (%) = 0.000962973 (0.451641)
Nlocal: 64 ave 64 max 64 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2971 ave 2971 max 2971 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 43136 ave 43136 max 43136 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 172544
Ave neighs/atom = 674
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (20 Aug 2010)
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Cu2O
triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
1 by 1 by 1 processor grid
1296 atoms
mass 1 63.5
mass 2 16.0
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Cu O
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul lx ly lz vol
thermo_modify norm yes
thermo 1
fix 1 all nve
fix 2 all qeq/comb 1 0.0001
dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
dump_modify 1 append yes element Cu O
run 2
Memory usage per processor = 5.52723 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Lx Ly Lz Volume
0 1 -3.829214 -3.8293431 -1.1478494 -2.6814937 25.62 25.62 25.62 16816.568
1 0.99910949 -3.8288107 -3.8289397 -0.98919398 -2.8397458 25.62 25.62 25.62 16816.568
2 0.99716052 -3.8288117 -3.8289405 -0.98918925 -2.8397512 25.62 25.62 25.62 16816.568
Loop time of 1.06923 on 1 procs for 2 steps with 1296 atoms
Pair time (%) = 0.313538 (29.3238)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000249863 (0.0233685)
Outpt time (%) = 0.0164599 (1.53942)
Other time (%) = 0.73898 (69.1134)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
thermo_style custom step temp etotal pe evdwl ecoul lx ly lz vol
thermo_modify norm yes
thermo 1
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.001
minimize 1.0e-14 1.0e-20 1000 10000
Memory usage per processor = 6.5657 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Lx Ly Lz Volume
2 0.99716052 -3.8353061 -3.8354349 -0.98078011 -2.8546548 25.62 25.62 25.62 16816.568
3 0.99716052 -3.8353061 -3.8354349 -0.98078011 -2.8546548 25.62 25.62 25.62 16816.568
Loop time of 2.25395 on 1 procs for 1 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3.83543488693 -3.83543488693 -3.83543488693
Force two-norm initial, final = 23.8394 23.8394
Force max component initial, final = 13.7501 13.7501
Final line search alpha, max atom move = 1.77556e-08 2.44141e-07
Iterations, force evaluations = 1 13
Pair time (%) = 2.23947 (99.3578)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00154233 (0.0684279)
Outpt time (%) = 0 (0)
Other time (%) = 0.0129333 (0.573804)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
thermo_style custom step temp etotal pe evdwl ecoul lx ly lz vol
thermo_modify norm yes
thermo 1
unfix 1
fix 1 all nve
run 1
Memory usage per processor = 5.53152 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Lx Ly Lz Volume
3 0.99716052 -3.8353061 -3.8354349 -0.98078011 -2.8546548 25.62 25.62 25.62 16816.568
4 0.99496464 -3.8321571 -3.8322856 -0.99348579 -2.8387999 25.62 25.62 25.62 16816.568
Loop time of 0.483416 on 1 procs for 1 steps with 1296 atoms
Pair time (%) = 0.158201 (32.7257)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000115871 (0.0239693)
Outpt time (%) = 0.00830197 (1.71736)
Other time (%) = 0.316797 (65.533)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
unfix 2
undump 1
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
run 10
Memory usage per processor = 5.53225 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
4 25.62 25.62 25.62 0 0 0 -21726041 -21723954 -21725372 -83549.539 -87604.182 -73307.259
5 25.620256 25.62 25.62 0 0 0 -21726041 -21723954 -21725372 -83549.539 -87604.182 -73307.259
6 25.620512 25.62 25.62 0 0 0 -21482181 -21660885 -21662304 -83548.124 -87602.629 -73302.267
7 25.620769 25.62 25.62 0 0 0 -21238323 -21597822 -21599240 -83546.708 -87601.076 -73297.276
8 25.621025 25.62 25.62 0 0 0 -20994465 -21534763 -21536182 -83545.293 -87599.524 -73292.284
9 25.621281 25.62 25.62 0 0 0 -20750609 -21471710 -21473129 -83543.878 -87597.971 -73287.293
10 25.621537 25.62 25.62 0 0 0 -20506753 -21408662 -21410080 -83542.462 -87596.419 -73282.303
11 25.621793 25.62 25.62 0 0 0 -20262899 -21345619 -21347037 -83541.046 -87594.868 -73277.312
12 25.62205 25.62 25.62 0 0 0 -20019045 -21282580 -21283999 -83539.631 -87593.316 -73272.322
13 25.622306 25.62 25.62 0 0 0 -19775193 -21219547 -21220966 -83538.215 -87591.764 -73267.332
14 25.622562 25.62 25.62 0 0 0 -19531341 -21156519 -21157938 -83536.8 -87590.211 -73262.342
Loop time of 1.71503 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.70735 (99.5524)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00122905 (0.0716634)
Outpt time (%) = 0.00573516 (0.334406)
Other time (%) = 0.000711918 (0.0415105)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 6.04934 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
14 25.622562 25.62 25.62 0 0 0 -19287491 -21093496 -21094915 -83535.385 -87588.659 -73257.353
15 25.622562 25.62 25.620256 0 0 0 -19287491 -21093496 -21094915 -83535.385 -87588.659 -73257.353
16 25.622562 25.62 25.620512 0 0 0 -19224467 -21030439 -20851099 -83529.627 -87587.105 -73256.13
17 25.622562 25.62 25.620769 0 0 0 -19161448 -20967388 -20607285 -83523.869 -87585.551 -73254.908
18 25.622562 25.62 25.621025 0 0 0 -19098433 -20904341 -20363471 -83518.112 -87583.996 -73253.685
19 25.622562 25.62 25.621281 0 0 0 -19035424 -20841299 -20119659 -83512.355 -87582.442 -73252.462
20 25.622562 25.62 25.621537 0 0 0 -18972420 -20778263 -19875848 -83506.599 -87580.887 -73251.24
21 25.622562 25.62 25.621793 0 0 0 -18909421 -20715231 -19632037 -83500.844 -87579.333 -73250.017
22 25.622562 25.62 25.62205 0 0 0 -18846427 -20652205 -19388228 -83495.088 -87577.778 -73248.794
23 25.622562 25.62 25.622306 0 0 0 -18783438 -20589183 -19144420 -83489.334 -87576.223 -73247.571
24 25.622562 25.62 25.622562 0 0 0 -18720454 -20526167 -18900613 -83483.579 -87574.668 -73246.348
Loop time of 1.71457 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.70702 (99.5597)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00125837 (0.073393)
Outpt time (%) = 0.00560689 (0.327015)
Other time (%) = 0.0006845 (0.0399226)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 6.56643 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
24 25.622562 25.62 25.622562 0 0 0 -18657475 -20463156 -18656806 -83477.825 -87573.114 -73245.125
25 25.622562 25.62 25.622562 0 0 5.1245124e-07 -18657475 -20463156 -18656806 -83477.825 -87573.114 -73245.125
26 25.622562 25.62 25.622562 0 0 1.0249025e-06 -18657475 -20463156 -18656806 -83477.821 -87573.108 -73010.392
27 25.622562 25.62 25.622562 0 0 1.5373537e-06 -18657475 -20463156 -18656806 -83477.816 -87573.103 -72775.659
28 25.622562 25.62 25.622562 0 0 2.049805e-06 -18657475 -20463156 -18656806 -83477.812 -87573.097 -72540.926
29 25.622562 25.62 25.622562 0 0 2.5622562e-06 -18657475 -20463156 -18656806 -83477.808 -87573.092 -72306.193
30 25.622562 25.62 25.622562 0 0 3.0747074e-06 -18657475 -20463156 -18656806 -83477.804 -87573.086 -72071.46
31 25.622562 25.62 25.622562 0 0 3.5871587e-06 -18657475 -20463156 -18656806 -83477.8 -87573.08 -71836.727
32 25.622562 25.62 25.622562 0 0 4.0996099e-06 -18657475 -20463156 -18656806 -83477.795 -87573.075 -71601.994
33 25.622562 25.62 25.622562 0 0 4.6120612e-06 -18657475 -20463156 -18656806 -83477.791 -87573.069 -71367.261
34 25.622562 25.62 25.622562 0 0 5.1245124e-06 -18657475 -20463156 -18656806 -83477.787 -87573.064 -71132.528
Loop time of 1.71546 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.70773 (99.5491)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00118756 (0.0692271)
Outpt time (%) = 0.00583315 (0.340034)
Other time (%) = 0.000713587 (0.0415974)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 7.08352 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
34 25.622562 25.62 25.622562 0 0 5.1245124e-06 -18657475 -20463156 -18656806 -83477.783 -87573.058 -70897.795
35 25.622562 25.62 25.622562 5.124e-07 0 5.1245124e-06 -18657475 -20463156 -18656806 -83477.783 -87573.058 -70897.795
36 25.622562 25.62 25.622562 1.0248e-06 0 5.1245124e-06 -18657475 -20463156 -18656806 -83243.086 -87573.055 -70897.789
37 25.622562 25.62 25.622562 1.5372e-06 0 5.1245124e-06 -18657475 -20463156 -18656806 -83008.389 -87573.052 -70897.783
38 25.622562 25.62 25.622562 2.0496e-06 0 5.1245124e-06 -18657475 -20463156 -18656806 -82773.692 -87573.048 -70897.777
39 25.622562 25.62 25.622562 2.562e-06 0 5.1245124e-06 -18657475 -20463156 -18656806 -82538.995 -87573.045 -70897.771
40 25.622562 25.62 25.622562 3.0744e-06 0 5.1245124e-06 -18657475 -20463156 -18656806 -82304.298 -87573.042 -70897.765
41 25.622562 25.62 25.622562 3.5868e-06 0 5.1245124e-06 -18657475 -20463156 -18656806 -82069.601 -87573.039 -70897.759
42 25.622562 25.62 25.622562 4.0992e-06 0 5.1245124e-06 -18657475 -20463156 -18656806 -81834.904 -87573.035 -70897.753
43 25.622562 25.62 25.622562 4.6116e-06 0 5.1245124e-06 -18657475 -20463156 -18656806 -81600.207 -87573.032 -70897.747
44 25.622562 25.62 25.622562 5.124e-06 0 5.1245124e-06 -18657475 -20463156 -18656806 -81365.51 -87573.029 -70897.741
Loop time of 1.71539 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.70771 (99.5524)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00123024 (0.0717178)
Outpt time (%) = 0.00571179 (0.332973)
Other time (%) = 0.000736237 (0.0429195)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0

311
examples/comb/log.comb.Cu2O.elastic.linux.4 Normal file
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LAMMPS (20 Aug 2010)
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Cu2O
triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
1 by 2 by 2 processor grid
1296 atoms
mass 1 63.5
mass 2 16.0
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Cu O
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul lx ly lz vol
thermo_modify norm yes
thermo 1
fix 1 all nve
fix 2 all qeq/comb 1 0.0001
dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
dump_modify 1 append yes element Cu O
run 2
Memory usage per processor = 2.89174 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Lx Ly Lz Volume
0 1 -3.829214 -3.8293431 -1.1478494 -2.6814937 25.62 25.62 25.62 16816.568
1 0.99856549 -3.8247839 -3.8249129 -0.98856777 -2.8363451 25.62 25.62 25.62 16816.568
2 0.99567536 -3.8247849 -3.8249135 -0.98856242 -2.8363511 25.62 25.62 25.62 16816.568
Loop time of 0.283128 on 4 procs for 2 steps with 1296 atoms
Pair time (%) = 0.0761476 (26.8951)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00257343 (0.908929)
Outpt time (%) = 0.017866 (6.31021)
Other time (%) = 0.186541 (65.8857)
Nlocal: 324 ave 324 max 324 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4943 ave 4943 max 4943 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 202608 max 202608 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
thermo_style custom step temp etotal pe evdwl ecoul lx ly lz vol
thermo_modify norm yes
thermo 1
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.001
minimize 1.0e-14 1.0e-20 1000 10000
Memory usage per processor = 3.83986 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Lx Ly Lz Volume
2 0.99567536 -3.8351396 -3.8352682 -0.97470326 -2.860565 25.62 25.62 25.62 16816.568
3 0.99567536 -3.8351396 -3.8352682 -0.97470326 -2.860565 25.62 25.62 25.62 16816.568
Loop time of 0.582395 on 4 procs for 1 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3.83526822048 -3.83526822048 -3.83526822048
Force two-norm initial, final = 24.0512 24.0512
Force max component initial, final = 13.892 13.892
Final line search alpha, max atom move = 1.75742e-08 2.44141e-07
Iterations, force evaluations = 1 13
Pair time (%) = 0.543527 (93.3262)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0210947 (3.62207)
Outpt time (%) = 0 (0)
Other time (%) = 0.0177733 (3.05175)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
thermo_style custom step temp etotal pe evdwl ecoul lx ly lz vol
thermo_modify norm yes
thermo 1
unfix 1
fix 1 all nve
run 1
Memory usage per processor = 2.89244 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Lx Ly Lz Volume
3 0.99567536 -3.8351396 -3.8352682 -0.97470326 -2.860565 25.62 25.62 25.62 16816.568
4 0.99345143 -3.8298017 -3.82993 -0.99430003 -2.83563 25.62 25.62 25.62 16816.568
Loop time of 0.131975 on 4 procs for 1 steps with 1296 atoms
Pair time (%) = 0.0390449 (29.5852)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0017758 (1.34556)
Outpt time (%) = 0.00901824 (6.83332)
Other time (%) = 0.0821356 (62.2359)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
unfix 2
undump 1
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
run 10
Memory usage per processor = 2.97812 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
4 25.62 25.62 25.62 0 0 0 -21746646 -21740667 -21741827 -70786.767 -93074.742 -74160.519
5 25.620256 25.62 25.62 0 0 0 -21746646 -21740667 -21741827 -70786.767 -93074.742 -74160.519
6 25.620512 25.62 25.62 0 0 0 -21502725 -21677635 -21678795 -70785.42 -93073.091 -74155.594
7 25.620769 25.62 25.62 0 0 0 -21258805 -21614609 -21615768 -70784.073 -93071.441 -74150.67
8 25.621025 25.62 25.62 0 0 0 -21014886 -21551587 -21552747 -70782.726 -93069.792 -74145.746
9 25.621281 25.62 25.62 0 0 0 -20770968 -21488571 -21489730 -70781.379 -93068.143 -74140.823
10 25.621537 25.62 25.62 0 0 0 -20527050 -21425559 -21426719 -70780.032 -93066.493 -74135.901
11 25.621793 25.62 25.62 0 0 0 -20283134 -21362553 -21363712 -70778.685 -93064.844 -74130.978
12 25.62205 25.62 25.62 0 0 0 -20039219 -21299551 -21300711 -70777.338 -93063.196 -74126.055
13 25.622306 25.62 25.62 0 0 0 -19795305 -21236555 -21237715 -70775.991 -93061.546 -74121.133
14 25.622562 25.62 25.62 0 0 0 -19551392 -21173564 -21174723 -70774.644 -93059.897 -74116.211
Loop time of 0.454987 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.417214 (91.6981)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0204811 (4.50146)
Outpt time (%) = 0.0166161 (3.652)
Other time (%) = 0.000675619 (0.148492)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 3.45218 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
14 25.622562 25.62 25.62 0 0 0 -19307480 -21110577 -21111737 -70773.297 -93058.247 -74111.289
15 25.622562 25.62 25.620256 0 0 0 -19307480 -21110577 -21111737 -70773.297 -93058.247 -74111.289
16 25.622562 25.62 25.620512 0 0 0 -19244493 -21047558 -20867860 -70767.49 -93056.598 -74110.079
17 25.622562 25.62 25.620769 0 0 0 -19181510 -20984543 -20623984 -70761.684 -93054.948 -74108.869
18 25.622562 25.62 25.621025 0 0 0 -19118533 -20921533 -20380109 -70755.878 -93053.298 -74107.659
19 25.622562 25.62 25.621281 0 0 0 -19055560 -20858528 -20136235 -70750.072 -93051.649 -74106.449
20 25.622562 25.62 25.621537 0 0 0 -18992593 -20795528 -19892363 -70744.267 -93049.999 -74105.239
21 25.622562 25.62 25.621793 0 0 0 -18929631 -20732534 -19648491 -70738.463 -93048.348 -74104.029
22 25.622562 25.62 25.62205 0 0 0 -18866674 -20669544 -19404620 -70732.659 -93046.698 -74102.819
23 25.622562 25.62 25.622306 0 0 0 -18803721 -20606559 -19160750 -70726.855 -93045.048 -74101.609
24 25.622562 25.62 25.622562 0 0 0 -18740774 -20543580 -18916881 -70721.052 -93043.398 -74100.398
Loop time of 0.45449 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.417112 (91.7759)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0202234 (4.44969)
Outpt time (%) = 0.0165236 (3.63564)
Other time (%) = 0.000630558 (0.13874)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 3.92624 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
24 25.622562 25.62 25.622562 0 0 0 -18677832 -20480605 -18673014 -70715.249 -93041.748 -74099.188
25 25.622562 25.62 25.622562 0 0 5.1245124e-07 -18677832 -20480605 -18673014 -70715.249 -93041.748 -74099.188
26 25.622562 25.62 25.622562 0 0 1.0249025e-06 -18677832 -20480605 -18673014 -70715.244 -93041.743 -73864.49
27 25.622562 25.62 25.622562 0 0 1.5373537e-06 -18677832 -20480605 -18673014 -70715.24 -93041.738 -73629.792
28 25.622562 25.62 25.622562 0 0 2.049805e-06 -18677832 -20480605 -18673014 -70715.235 -93041.733 -73395.093
29 25.622562 25.62 25.622562 0 0 2.5622562e-06 -18677832 -20480605 -18673014 -70715.231 -93041.728 -73160.395
30 25.622562 25.62 25.622562 0 0 3.0747074e-06 -18677832 -20480605 -18673014 -70715.226 -93041.723 -72925.696
31 25.622562 25.62 25.622562 0 0 3.5871587e-06 -18677832 -20480605 -18673014 -70715.222 -93041.718 -72690.998
32 25.622562 25.62 25.622562 0 0 4.0996099e-06 -18677832 -20480605 -18673014 -70715.217 -93041.713 -72456.3
33 25.622562 25.62 25.622562 0 0 4.6120612e-06 -18677832 -20480605 -18673014 -70715.213 -93041.708 -72221.601
34 25.622562 25.62 25.622562 0 0 5.1245124e-06 -18677832 -20480605 -18673014 -70715.208 -93041.702 -71986.903
Loop time of 0.453631 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.416858 (91.8936)
Neigh time (%) = 0 (0)
Comm time (%) = 0.020052 (4.42033)
Outpt time (%) = 0.0161096 (3.55125)
Other time (%) = 0.000611365 (0.134771)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 4.4003 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
34 25.622562 25.62 25.622562 0 0 5.1245124e-06 -18677832 -20480605 -18673014 -70715.204 -93041.697 -71752.205
35 25.622562 25.62 25.622562 5.124e-07 0 5.1245124e-06 -18677832 -20480605 -18673014 -70715.204 -93041.697 -71752.205
36 25.622562 25.62 25.622562 1.0248e-06 0 5.1245124e-06 -18677832 -20480605 -18673014 -70480.541 -93041.694 -71752.198
37 25.622562 25.62 25.622562 1.5372e-06 0 5.1245124e-06 -18677832 -20480605 -18673014 -70245.879 -93041.691 -71752.192
38 25.622562 25.62 25.622562 2.0496e-06 0 5.1245124e-06 -18677832 -20480605 -18673014 -70011.217 -93041.688 -71752.186
39 25.622562 25.62 25.622562 2.562e-06 0 5.1245124e-06 -18677832 -20480605 -18673014 -69776.555 -93041.684 -71752.179
40 25.622562 25.62 25.622562 3.0744e-06 0 5.1245124e-06 -18677832 -20480605 -18673014 -69541.892 -93041.681 -71752.173
41 25.622562 25.62 25.622562 3.5868e-06 0 5.1245124e-06 -18677832 -20480605 -18673014 -69307.23 -93041.678 -71752.166
42 25.622562 25.62 25.622562 4.0992e-06 0 5.1245124e-06 -18677832 -20480605 -18673014 -69072.568 -93041.675 -71752.16
43 25.622562 25.62 25.622562 4.6116e-06 0 5.1245124e-06 -18677832 -20480605 -18673014 -68837.906 -93041.671 -71752.154
44 25.622562 25.62 25.622562 5.124e-06 0 5.1245124e-06 -18677832 -20480605 -18673014 -68603.243 -93041.668 -71752.147
Loop time of 0.454455 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.416851 (91.7254)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0202795 (4.46238)
Outpt time (%) = 0.0167049 (3.6758)
Other time (%) = 0.000620067 (0.136442)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (20 Aug 2010)
# HfO2 polymorphs: Monoclinic HfO2 NVT @ 300K
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.m-HfO2
triclinic box = (0 0 0) to (30.7704 25.957 26.4845) with tilt (0 -4.46691 0)
1 by 1 by 1 processor grid
1800 atoms
#read_data data.t-HfO2
#read_data data.c-HfO2
mass 1 178.0
mass 2 16.0
pair_style comb
pair_coeff * * ffield.comb Hf O
neighbor 0.5 bin
neigh_modify every 10 delay 10 check yes
timestep 0.00020
fix 1 all nvt temp 300.0 300.0 0.1
fix 2 all qeq/comb 1 0.003
dump 1 all cfg 100 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
dump_modify 1 append yes element Hf O
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 300.1 2398378
thermo 1
run 10
Memory usage per processor = 8.67517 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 300.1 -10.137558 -10.176327 2.41206 -12.588387 -416223.6 21153.363 30.7704 25.957 26.4845 -4.46691
1 300.08959 -10.141034 -10.179802 2.5355907 -12.715392 -404486.56 21153.363 30.7704 25.957 26.4845 -4.46691
2 300.24619 -10.141052 -10.179841 2.5359652 -12.715806 -404168.46 21153.363 30.7704 25.957 26.4845 -4.46691
3 300.57503 -10.141091 -10.179922 2.5364593 -12.716381 -403610.71 21153.363 30.7704 25.957 26.4845 -4.46691
4 301.07546 -10.14112 -10.180016 2.5366768 -12.716692 -402851.34 21153.363 30.7704 25.957 26.4845 -4.46691
5 301.74489 -10.141145 -10.180127 2.5366919 -12.716819 -401887.86 21153.363 30.7704 25.957 26.4845 -4.46691
6 302.58008 -10.141164 -10.180253 2.5365678 -12.716821 -400713.79 21153.363 30.7704 25.957 26.4845 -4.46691
7 303.57705 -10.141182 -10.180401 2.5363422 -12.716743 -399322.96 21153.363 30.7704 25.957 26.4845 -4.46691
8 304.73109 -10.141205 -10.180573 2.5360367 -12.716609 -397713.35 21153.363 30.7704 25.957 26.4845 -4.46691
9 306.03674 -10.141224 -10.18076 2.5356698 -12.71643 -395881.68 21153.363 30.7704 25.957 26.4845 -4.46691
10 307.48774 -10.141243 -10.180967 2.5352504 -12.716218 -393822.27 21153.363 30.7704 25.957 26.4845 -4.46691
Loop time of 15.392 on 1 procs for 10 steps with 1800 atoms
Pair time (%) = 6.52695 (42.4048)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00162959 (0.0105873)
Outpt time (%) = 0.00065732 (0.00427053)
Other time (%) = 8.86276 (57.5803)
Nlocal: 1800 ave 1800 max 1800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10960 ave 10960 max 10960 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: 1.245e+06 ave 1.245e+06 max 1.245e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1245000
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0

70
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LAMMPS (20 Aug 2010)
# HfO2 polymorphs: Monoclinic HfO2 NVT @ 300K
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.m-HfO2
triclinic box = (0 0 0) to (30.7704 25.957 26.4845) with tilt (0 -4.46691 0)
2 by 1 by 2 processor grid
1800 atoms
#read_data data.t-HfO2
#read_data data.c-HfO2
mass 1 178.0
mass 2 16.0
pair_style comb
pair_coeff * * ffield.comb Hf O
neighbor 0.5 bin
neigh_modify every 10 delay 10 check yes
timestep 0.00020
fix 1 all nvt temp 300.0 300.0 0.1
fix 2 all qeq/comb 1 0.003
dump 1 all cfg 100 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
dump_modify 1 append yes element Hf O
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 300.1 2398378
thermo 1
run 10
Memory usage per processor = 3.40015 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 300.1 -10.137558 -10.176327 2.41206 -12.588387 -416223.6 21153.363 30.7704 25.957 26.4845 -4.46691
1 300.08824 -10.14208 -10.180848 2.5381551 -12.719003 -404888.72 21153.363 30.7704 25.957 26.4845 -4.46691
2 300.2422 -10.142108 -10.180896 2.5385179 -12.719413 -404575.01 21153.363 30.7704 25.957 26.4845 -4.46691
3 300.56846 -10.14215 -10.18098 2.5390086 -12.719988 -404021.29 21153.363 30.7704 25.957 26.4845 -4.46691
4 301.06641 -10.142179 -10.181073 2.539236 -12.720309 -403262.75 21153.363 30.7704 25.957 26.4845 -4.46691
5 301.73344 -10.142206 -10.181186 2.5392647 -12.720451 -402298.69 21153.363 30.7704 25.957 26.4845 -4.46691
6 302.56634 -10.142224 -10.181312 2.539154 -12.720466 -401123.13 21153.363 30.7704 25.957 26.4845 -4.46691
7 303.5611 -10.142241 -10.181457 2.5389412 -12.720398 -399730.1 21153.363 30.7704 25.957 26.4845 -4.46691
8 304.71301 -10.142258 -10.181623 2.5386467 -12.72027 -398117.54 21153.363 30.7704 25.957 26.4845 -4.46691
9 306.01661 -10.142271 -10.181804 2.5382886 -12.720093 -396282.69 21153.363 30.7704 25.957 26.4845 -4.46691
10 307.46565 -10.142283 -10.182004 2.5378762 -12.719881 -394219.71 21153.363 30.7704 25.957 26.4845 -4.46691
Loop time of 3.81594 on 4 procs for 10 steps with 1800 atoms
Pair time (%) = 1.58554 (41.5506)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0347861 (0.9116)
Outpt time (%) = 0.00457448 (0.119878)
Other time (%) = 2.19103 (57.418)
Nlocal: 450 ave 450 max 450 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6470 ave 6470 max 6470 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 311250 ave 311250 max 311250 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1245000
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (20 Aug 2010)
# Pure Si crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.43
Lattice spacing in x,y,z = 5.43 5.43 5.43
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
1 by 1 by 1 processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
dump_modify 1 append yes element Si
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10
Memory usage per processor = 2.95744 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0
1 10.097843 -4.6284152 -4.6297179 -4.6297179 0 1140.8131 10246.592 21.72 21.72 21.72 0
2 10.091376 -4.6284152 -4.6297171 -4.6297171 0 1140.8972 10246.592 21.72 21.72 21.72 0
3 10.080606 -4.6284152 -4.6297157 -4.6297157 0 1141.0373 10246.592 21.72 21.72 21.72 0
4 10.065546 -4.6284152 -4.6297137 -4.6297137 0 1141.233 10246.592 21.72 21.72 21.72 0
5 10.046214 -4.6284152 -4.6297113 -4.6297113 0 1141.4842 10246.592 21.72 21.72 21.72 0
6 10.022634 -4.6284152 -4.6297082 -4.6297082 0 1141.7906 10246.592 21.72 21.72 21.72 0
7 9.9948348 -4.6284152 -4.6297046 -4.6297046 0 1142.1515 10246.592 21.72 21.72 21.72 0
8 9.9628496 -4.6284152 -4.6297005 -4.6297005 0 1142.5666 10246.592 21.72 21.72 21.72 0
9 9.9267173 -4.6284152 -4.6296958 -4.6296958 0 1143.0353 10246.592 21.72 21.72 21.72 0
10 9.8864817 -4.6284152 -4.6296906 -4.6296906 0 1143.5568 10246.592 21.72 21.72 21.72 0
Loop time of 0.451024 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.447055 (99.12)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000573397 (0.127132)
Outpt time (%) = 0.00299764 (0.664629)
Other time (%) = 0.000398159 (0.0882789)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 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: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (20 Aug 2010)
# Pure Si crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.43
Lattice spacing in x,y,z = 5.43 5.43 5.43
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
1 by 2 by 2 processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
dump_modify 1 append yes element Si
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
run 10
Memory usage per processor = 2.07331 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0
1 10.097841 -4.6284152 -4.6297179 -4.6297179 0 1140.8134 10246.592 21.72 21.72 21.72 0
2 10.091367 -4.6284152 -4.6297171 -4.6297171 0 1140.8983 10246.592 21.72 21.72 21.72 0
3 10.080586 -4.6284152 -4.6297157 -4.6297157 0 1141.0397 10246.592 21.72 21.72 21.72 0
4 10.065511 -4.6284152 -4.6297137 -4.6297137 0 1141.2373 10246.592 21.72 21.72 21.72 0
5 10.046161 -4.6284152 -4.6297112 -4.6297112 0 1141.4909 10246.592 21.72 21.72 21.72 0
6 10.02256 -4.6284152 -4.6297082 -4.6297082 0 1141.8001 10246.592 21.72 21.72 21.72 0
7 9.9947353 -4.6284152 -4.6297046 -4.6297046 0 1142.1645 10246.592 21.72 21.72 21.72 0
8 9.9627224 -4.6284152 -4.6297005 -4.6297005 0 1142.5835 10246.592 21.72 21.72 21.72 0
9 9.9265602 -4.6284152 -4.6296958 -4.6296958 0 1143.0565 10246.592 21.72 21.72 21.72 0
10 9.8862927 -4.6284152 -4.6296906 -4.6296906 0 1143.5829 10246.592 21.72 21.72 21.72 0
Loop time of 0.128749 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.111608 (86.6863)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0089699 (6.96697)
Outpt time (%) = 0.00725859 (5.63779)
Other time (%) = 0.000912726 (0.708919)
Nlocal: 128 ave 128 max 128 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3073 ave 3073 max 3073 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 53248 max 53248 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (20 Aug 2010)
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
change_box triclinic
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
fix 1 all box/relax aniso 0.0 vmax 0.001
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
thermo_modify norm yes
thermo 1
minimize 1.0e-14 1.0e-20 1000 10000
Memory usage per processor = 3.48277 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -4.6295947 -4.6297237 -4.6297237 0
1 1 -4.6295963 -4.6297253 -4.6297253 0
2 1 -4.6295965 -4.6297255 -4.6297255 0
3 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.763644 on 1 procs for 3 steps with 512 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-4.62972371535 -4.62972550036 -4.62972550036
Force two-norm initial, final = 5.86582 0.235602
Force max component initial, final = 3.38663 0.136025
Final line search alpha, max atom move = 0.000114869 1.5625e-05
Iterations, force evaluations = 3 16
Pair time (%) = 0.759505 (99.458)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000995398 (0.130348)
Outpt time (%) = 3.48091e-05 (0.00455829)
Other time (%) = 0.00310874 (0.407093)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 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: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
run 1
Memory usage per processor = 2.56725 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
3 1 -4.6295965 -4.6297255 -4.6297255 0
4 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.044728 on 1 procs for 1 steps with 512 atoms
Pair time (%) = 0.0446391 (99.8012)
Neigh time (%) = 0 (0)
Comm time (%) = 5.79357e-05 (0.129529)
Outpt time (%) = 1.50204e-05 (0.0335816)
Other time (%) = 1.5974e-05 (0.0357137)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 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: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
run 10
Memory usage per processor = 3.02501 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
4 21.728073 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 1.9450404e-06 2.4752556e-06 -1.6071587e-06
5 21.728291 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 1.8110987e-06 2.6015226e-06 -1.1358357e-06
6 21.728508 21.728073 21.728073 0 0 0 364177.1 295296.39 295296.39 -4.4966424e-06 1.848553e-07 -2.2958737e-06
7 21.728725 21.728073 21.728073 0 0 0 510377.09 372612.85 372612.85 2.4287963e-06 2.6615821e-06 -1.9832618e-06
8 21.728942 21.728073 21.728073 0 0 0 656576.36 449925.76 449925.76 2.4447348e-06 2.4469323e-06 -8.4990897e-07
9 21.72916 21.728073 21.728073 0 0 0 802774.92 527235.13 527235.13 4.0363922e-06 -5.9982754e-06 -2.3201799e-06
10 21.729377 21.728073 21.728073 0 0 0 948972.76 604540.97 604540.97 2.8253812e-06 2.5964234e-06 -8.931554e-07
11 21.729594 21.728073 21.728073 0 0 0 1095169.9 681843.26 681843.26 2.3933505e-06 2.283704e-06 -3.9266049e-07
12 21.729811 21.728073 21.728073 0 0 0 1241366.3 759142.02 759142.02 2.2037259e-06 2.6987214e-06 3.737462e-07
13 21.730029 21.728073 21.728073 0 0 0 1387562 836437.23 836437.23 2.6802555e-06 2.9969439e-06 1.7521287e-07
14 21.730246 21.728073 21.728073 0 0 0 1533757 913728.91 913728.91 4.4634386e-06 -4.2738918e-06 3.2367003e-07
Loop time of 0.482373 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.478604 (99.2187)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000607967 (0.126037)
Outpt time (%) = 0.00288773 (0.59865)
Other time (%) = 0.000273228 (0.0566424)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 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: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 3.48277 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
14 21.730246 21.728073 21.728073 0 0 0 1679951.2 991017.05 991017.05 1.3848713e-06 1.8198295e-06 -3.1488289e-06
15 21.730246 21.728073 21.728291 0 0 0 1679951.2 991017.05 991017.05 1.4477769e-06 2.1276907e-06 -2.7563351e-06
16 21.730246 21.728073 21.728508 0 0 0 1757243.6 1068312.4 1137190.1 2.1162843e-06 -3.0681281e-06 -1.8698946e-06
17 21.730246 21.728073 21.728725 0 0 0 1834532.4 1145604.2 1283362.4 1.5226892e-06 3.1081802e-06 -2.6821714e-06
18 21.730246 21.728073 21.728942 0 0 0 1911817.6 1222892.5 1429534 -7.5700513e-07 1.7188656e-06 4.1051196e-06
19 21.730246 21.728073 21.72916 0 0 0 1989099.3 1300177.3 1575704.9 -1.4391091e-06 2.0797417e-06 3.9123487e-06
20 21.730246 21.728073 21.729377 0 0 0 2066377.5 1377458.5 1721875.1 -1.5213551e-06 1.9181068e-06 -2.1773741e-06
21 21.730246 21.728073 21.729594 0 0 0 2143652.1 1454736.2 1868044.5 -1.4238005e-06 1.7984361e-06 -2.0333083e-06
22 21.730246 21.728073 21.729811 0 0 0 2220923.2 1532010.3 2014213.3 4.4088785e-06 2.5805071e-06 -2.1480169e-06
23 21.730246 21.728073 21.730029 0 0 0 2298190.7 1609280.9 2160381.3 -9.3407459e-07 2.1740278e-06 -1.3082692e-06
24 21.730246 21.728073 21.730246 0 0 0 2375454.8 1686547.9 2306548.6 -1.7972725e-06 2.108669e-06 -1.6910019e-06
Loop time of 0.481719 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.478137 (99.2564)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000609636 (0.126554)
Outpt time (%) = 0.00270128 (0.560759)
Other time (%) = 0.00027132 (0.0563234)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 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: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 3.94054 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
24 21.730246 21.728073 21.730246 0 0 0 2452715.2 1763811.4 2452715.2 -1.7548117e-06 3.6087566e-06 -3.6198628e-06
25 21.730246 21.728073 21.730246 0 0 4.3460492e-07 2452715.2 1763811.4 2452715.2 -1.7167978e-06 3.4304272e-06 -2.9804569e-06
26 21.730246 21.728073 21.730246 0 0 8.6920984e-07 2452715.2 1763811.4 2452715.2 -1.8729445e-06 4.5840765e-06 243.65136
27 21.730246 21.728073 21.730246 0 0 1.3038148e-06 2452715.2 1763811.4 2452715.2 -1.2316967e-06 2.6286266e-06 487.30276
28 21.730246 21.728073 21.730246 0 0 1.7384197e-06 2452715.2 1763811.4 2452715.2 -1.3251453e-06 2.7225014e-06 730.95419
29 21.730246 21.728073 21.730246 0 0 2.1730246e-06 2452715.2 1763811.4 2452715.2 -8.5464495e-07 -6.3592996e-07 974.60551
30 21.730246 21.728073 21.730246 0 0 2.6076295e-06 2452715.2 1763811.4 2452715.2 -1.7272259e-06 2.0497545e-06 1218.2569
31 21.730246 21.728073 21.730246 0 0 3.0422344e-06 2452715.2 1763811.4 2452715.2 -4.6626464e-07 2.1955509e-06 1461.9083
32 21.730246 21.728073 21.730246 0 0 3.4768394e-06 2452715.2 1763811.4 2452715.2 -1.1296433e-06 2.2397275e-06 1705.5598
33 21.730246 21.728073 21.730246 0 0 3.9114443e-06 2452715.2 1763811.4 2452715.2 -1.388603e-06 1.2425658e-06 1949.2111
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -1.1793341e-06 1.7092936e-06 2192.8625
Loop time of 0.4816 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.477913 (99.2343)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000584126 (0.121289)
Outpt time (%) = 0.00282931 (0.587482)
Other time (%) = 0.000273943 (0.0568818)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 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: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 4.3983 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -1.7294679e-06 4.8293026e-06 2436.5139
35 21.730246 21.728073 21.730246 4.3456146e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -1.4630595e-06 4.5052213e-06 2436.5139
36 21.730246 21.728073 21.730246 8.6912293e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 243.63758 -0.00012576585 2436.5139
37 21.730246 21.728073 21.730246 1.3036844e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 487.27522 -0.00025542614 2436.5139
38 21.730246 21.728073 21.730246 1.7382459e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 730.91286 -0.00038565598 2436.5139
39 21.730246 21.728073 21.730246 2.1728073e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 974.55045 -0.00051669611 2436.5138
40 21.730246 21.728073 21.730246 2.6073688e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1218.188 -0.00064706412 2436.5139
41 21.730246 21.728073 21.730246 3.0419303e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1461.8257 -0.0007779958 2436.5139
42 21.730246 21.728073 21.730246 3.4764917e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1705.4633 -0.00090716273 2436.5138
43 21.730246 21.728073 21.730246 3.9110532e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1949.1009 -0.001038008 2436.5138
44 21.730246 21.728073 21.730246 4.3456146e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2192.7385 -0.0011663311 2436.5138
Loop time of 0.482365 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.478748 (99.2501)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00061512 (0.127522)
Outpt time (%) = 0.00275278 (0.570684)
Other time (%) = 0.000249386 (0.0517006)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 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: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

270
examples/comb/log.comb.Si.elastic.15Jan10.linux.4 Normal file
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LAMMPS (20 Aug 2010)
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 2 by 2 processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
change_box triclinic
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
fix 1 all box/relax aniso 0.0 vmax 0.001
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
thermo_modify norm yes
thermo 1
minimize 1.0e-14 1.0e-20 1000 10000
Memory usage per processor = 2.6376 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -4.6295947 -4.6297237 -4.6297237 0
1 1 -4.6295963 -4.6297253 -4.6297253 0
2 1 -4.6295965 -4.6297255 -4.6297255 0
3 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.269178 on 4 procs for 3 steps with 512 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-4.62972371535 -4.62972550036 -4.62972550036
Force two-norm initial, final = 5.86582 0.235602
Force max component initial, final = 3.38663 0.136025
Final line search alpha, max atom move = 0.000114869 1.5625e-05
Iterations, force evaluations = 3 16
Pair time (%) = 0.19249 (71.5101)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0661291 (24.567)
Outpt time (%) = 0.000723839 (0.268907)
Other time (%) = 0.00983572 (3.65398)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
run 1
Memory usage per processor = 1.72207 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
3 1 -4.6295965 -4.6297255 -4.6297255 0
4 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.0159932 on 4 procs for 1 steps with 512 atoms
Pair time (%) = 0.0113423 (70.9195)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00383902 (24.0041)
Outpt time (%) = 0.000667989 (4.17671)
Other time (%) = 0.000143886 (0.899669)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
run 10
Memory usage per processor = 2.17984 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
4 21.728073 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 -5.331517e-06 3.0239293e-06 -4.7684649e-06
5 21.728291 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 -4.2797025e-06 2.0730342e-06 -3.2414474e-06
6 21.728508 21.728073 21.728073 0 0 0 364177.1 295296.39 295296.39 6.7462199e-07 1.6210516e-06 -2.8184106e-06
7 21.728725 21.728073 21.728073 0 0 0 510377.09 372612.85 372612.85 -3.9337607e-06 2.4599063e-06 -4.2531358e-06
8 21.728942 21.728073 21.728073 0 0 0 656576.36 449925.76 449925.76 -3.6805931e-06 3.0030584e-06 -2.6648247e-06
9 21.72916 21.728073 21.728073 0 0 0 802774.92 527235.13 527235.13 1.0867248e-05 -8.1694237e-06 -1.7161938e-06
10 21.729377 21.728073 21.728073 0 0 0 948972.76 604540.97 604540.97 -3.2850644e-06 1.3204575e-06 -1.5057612e-06
11 21.729594 21.728073 21.728073 0 0 0 1095169.9 681843.26 681843.26 -3.6006336e-06 2.4158409e-06 -2.7959314e-06
12 21.729811 21.728073 21.728073 0 0 0 1241366.3 759142.02 759142.02 -3.3313125e-06 1.4697892e-06 -2.7046099e-06
13 21.730029 21.728073 21.728073 0 0 0 1387562 836437.23 836437.23 -4.1963855e-06 1.8017491e-06 -2.3957259e-06
14 21.730246 21.728073 21.728073 0 0 0 1533757 913728.91 913728.91 8.2405636e-06 -9.2080568e-06 -2.6979061e-06
Loop time of 0.177429 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.121605 (68.5369)
Neigh time (%) = 0 (0)
Comm time (%) = 0.041932 (23.6331)
Outpt time (%) = 0.0134844 (7.59985)
Other time (%) = 0.000408351 (0.230149)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 2.6376 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
14 21.730246 21.728073 21.728073 0 0 0 1679951.2 991017.05 991017.05 -4.8604756e-06 3.7251477e-06 -2.9550019e-06
15 21.730246 21.728073 21.728291 0 0 0 1679951.2 991017.05 991017.05 -3.8939866e-06 2.9223391e-06 -2.2819697e-06
16 21.730246 21.728073 21.728508 0 0 0 1757243.6 1068312.4 1137190.1 -3.6671782e-06 -3.9050298e-06 -2.216407e-06
17 21.730246 21.728073 21.728725 0 0 0 1834532.4 1145604.2 1283362.4 -3.9258267e-06 2.221206e-06 -2.1819285e-06
18 21.730246 21.728073 21.728942 0 0 0 1911817.6 1222892.5 1429534 -3.1570557e-06 8.2160424e-07 4.7018758e-06
19 21.730246 21.728073 21.72916 0 0 0 1989099.3 1300177.3 1575704.9 -3.572314e-06 1.2809206e-06 4.3456208e-06
20 21.730246 21.728073 21.729377 0 0 0 2066377.5 1377458.5 1721875.1 -2.6839761e-06 1.8703615e-06 -2.1448559e-06
21 21.730246 21.728073 21.729594 0 0 0 2143652.1 1454736.2 1868044.5 -2.7199703e-06 1.6784208e-06 -2.426873e-06
22 21.730246 21.728073 21.729811 0 0 0 2220923.2 1532010.3 2014213.3 -2.5654468e-06 2.0648963e-06 -1.6998995e-06
23 21.730246 21.728073 21.730029 0 0 0 2298190.7 1609280.9 2160381.3 -3.3044419e-06 2.6103683e-06 -2.5246759e-06
24 21.730246 21.728073 21.730246 0 0 0 2375454.8 1686547.9 2306548.6 -3.5025824e-06 1.2024729e-06 -1.5524318e-06
Loop time of 0.177355 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.121552 (68.5361)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0417938 (23.565)
Outpt time (%) = 0.0136406 (7.69114)
Other time (%) = 0.000368536 (0.207795)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 3.09536 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
24 21.730246 21.728073 21.730246 0 0 0 2452715.2 1763811.4 2452715.2 -2.4048644e-06 3.3513607e-06 -2.8722185e-06
25 21.730246 21.728073 21.730246 0 0 4.3460492e-07 2452715.2 1763811.4 2452715.2 -2.481322e-06 3.6480379e-06 -3.1092437e-06
26 21.730246 21.728073 21.730246 0 0 8.6920984e-07 2452715.2 1763811.4 2452715.2 -3.0751506e-06 5.8376744e-06 243.65136
27 21.730246 21.728073 21.730246 0 0 1.3038148e-06 2452715.2 1763811.4 2452715.2 -2.7247323e-06 2.3340173e-06 487.30277
28 21.730246 21.728073 21.730246 0 0 1.7384197e-06 2452715.2 1763811.4 2452715.2 -2.8719517e-06 4.5249397e-06 730.95419
29 21.730246 21.728073 21.730246 0 0 2.1730246e-06 2452715.2 1763811.4 2452715.2 -2.6310243e-06 -6.3464035e-07 974.60551
30 21.730246 21.728073 21.730246 0 0 2.6076295e-06 2452715.2 1763811.4 2452715.2 -2.5635976e-06 3.5771871e-06 1218.2569
31 21.730246 21.728073 21.730246 0 0 3.0422344e-06 2452715.2 1763811.4 2452715.2 -3.2260573e-06 2.5233788e-06 1461.9083
32 21.730246 21.728073 21.730246 0 0 3.4768394e-06 2452715.2 1763811.4 2452715.2 -3.0611909e-06 3.1329051e-06 1705.5598
33 21.730246 21.728073 21.730246 0 0 3.9114443e-06 2452715.2 1763811.4 2452715.2 -2.6095826e-06 1.3805022e-06 1949.2111
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -2.8236839e-06 1.8352159e-06 2192.8625
Loop time of 0.177727 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.12163 (68.4366)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0418997 (23.5754)
Outpt time (%) = 0.013804 (7.76697)
Other time (%) = 0.000392795 (0.221011)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 3.55313 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -2.4937771e-06 4.8352356e-06 2436.5139
35 21.730246 21.728073 21.730246 4.3456146e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -2.6268441e-06 5.4186954e-06 2436.5139
36 21.730246 21.728073 21.730246 8.6912293e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 243.63758 -0.00012459169 2436.5139
37 21.730246 21.728073 21.730246 1.3036844e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 487.27522 -0.00025416174 2436.5139
38 21.730246 21.728073 21.730246 1.7382459e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 730.91286 -0.00038484627 2436.5139
39 21.730246 21.728073 21.730246 2.1728073e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 974.55045 -0.00051633193 2436.5138
40 21.730246 21.728073 21.730246 2.6073688e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1218.188 -0.00064696028 2436.5138
41 21.730246 21.728073 21.730246 3.0419303e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1461.8257 -0.00077648633 2436.5139
42 21.730246 21.728073 21.730246 3.4764917e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1705.4633 -0.00090632398 2436.5138
43 21.730246 21.728073 21.730246 3.9110532e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1949.1009 -0.0010366567 2436.5138
44 21.730246 21.728073 21.730246 4.3456146e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2192.7385 -0.0011656542 2436.5138
Loop time of 0.165732 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.121818 (73.5031)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0296696 (17.9022)
Outpt time (%) = 0.0138543 (8.35943)
Other time (%) = 0.000389934 (0.235279)
Nlocal: 128 ave 152 max 112 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 3073 ave 3089 max 3049 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 63232 max 46592 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0