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in.cutsic_cont_201407201atomistica.lmp
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in.cutsic_cont_201407201atomistica.lmp
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# Input file for nanocutting of Cubic SiC with a diamond tool
# Chris Fung, April 2013
# input variables
# -potential (choose the version of Tersoff potential used, options=y94/EA/TersoffScr)
# -v (cutting velocity = v * 100 (m s^-1 in x-direction))
#x -grooveDepth (choose a value in the range from 0.0 to 9.0 angstroms)
#x -grooveTan (half angle of the groove in tangent = half width/depth)
#variable respath string ${v}x100_m_s-1_Groove${grooveDepth}T${grooveTan}_SiC_${potential}
variable respath string ${v}x100_m_s-1_SiC_${potential}
print "${respath}"
shell mkdir ${respath}
shell mkdir ${respath}/log_files
shell mkdir ${respath}/restart_files
shell mkdir ${respath}/ovito_analysis-results
shell chmod 774 ${respath}
shell chmod 774 ${respath}/log_files
shell chmod 774 ${respath}/restart_files
shell chmod 777 ${respath}/ovito_analysis_results
package cuda gpu/node 1 0
package omp 2 force/neigh
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary s s p
atom_style atomic
read_restart cut_sic_eq.restart.10000
reset_timestep 0
fix 13 all property/atom mol
#dump 0dumpCSP all custom 500 dump.cutsic.*.lammpstrj id type mol x y z vx vy vz
#run 0
group gpDia type 1
group gpCTbd molecule 3
group gpCTtsbd molecule 2
group gpCTmob molecule 1
print "diamond tool created"
#------------------------------------------------------------
# define the lattice of cubic SiC (two atom types form two interpenetrating face-centered cubic lattices)
# groups atoms
group gpSiC type 2 3
group gpWPbd molecule 6
group gpWPtsbd molecule 5
group gpWPmob molecule 4
group mobile subtract all gpCTtsbd gpWPtsbd
print "Workpiece created"
#-------------------------------------------------
# define the mass of atoms
mass 1 12 #.0107 # C (g/mol)
mass 2 28 #.0855 # Si (g/mol)
mass 3 12 #.0107 # C (g/mol)
variable a equal 4.3667
variable b equal 3.571
variable c equal $a/$b
variable dx equal 70*$c
variable dy equal 5*$c
variable lx equal 31
variable ly equal 31
variable dx1 equal ${dx}+${lx}
variable dy1 equal ${dy}+${ly}
variable lr equal 4
variable rx equal ${dx}+${lr}
variable ry equal ${dy}+${lr}
variable tx1 equal ${dx}+${lr}+2.35
variable tx2 equal ${dx1}+${lr}+2.35
variable ty2 equal ${dy}+${lx}*tan(10/180*PI)
variable bx1 equal ${dx1}-1
variable bx2 equal ${bx1}-1
variable by1 equal ${dy1}-1
variable by2 equal ${by1}-1
#lattice diamond $b
#variable gy equal ${grooveDepth}+3.2226178427343
#variable gy1 equal ${gy}+1.0
#variable gz1 equal ${grooveTan}*18+1.5
#region groove4 block ${dx} ${dx1} ${gy} ${gy1} 2.5 ${gz1}
#variable gy1 equal ${gy1}+1.0
#variable gz0 equal 2.5+${grooveTan}
#variable gz1 equal ${gz1}-${grooveTan}
#region groove5 block ${dx} ${dx1} ${gy} ${gy1} ${gz0} ${gz1}
#variable gy1 equal ${gy1}+1.0
#variable gz0 equal ${gz0}+${grooveTan}
#variable gz1 equal ${gz1}-${grooveTan}
#region groove6 block ${dx} ${dx1} ${gy} ${gy1} ${gz0} ${gz1}
#variable gy1 equal ${gy1}+1.0
#variable gz0 equal ${gz0}+${grooveTan}
#variable gz1 equal ${gz1}-${grooveTan}
#region groove7 block ${dx} ${dx1} ${gy} ${gy1} ${gz0} ${gz1}
#variable gy1 equal ${gy1}+1.0
#variable gz0 equal ${gz0}+${grooveTan}
#variable gz1 equal ${gz1}-${grooveTan}
#region groove8 block ${dx} ${dx1} ${gy} ${gy1} ${gz0} ${gz1}
#variable gy1 equal ${gy1}+1.0
#variable gz0 equal ${gz0}+${grooveTan}
#variable gz1 equal ${gz1}-${grooveTan}
#region groove9 block ${dx} ${dx1} ${gy} ${gy1} ${gz0} ${gz1}
#variable gy1 equal ${gy1}+1.0
#variable gz0 equal ${gz0}+${grooveTan}
#variable gz1 equal ${gz1}-${grooveTan}
#region groove10 block ${dx} ${dx1} ${gy} ${gy1} ${gz0} ${gz1}
#variable gy1 equal ${gy1}+1.0
#variable gz0 equal ${gz0}+${grooveTan}
#variable gz1 equal ${gz1}-${grooveTan}
#region groove11 block ${dx} ${dx1} ${gy} ${gy1} ${gz0} ${gz1}
#variable gy1 equal ${gy1}+1.0
#variable gz0 equal ${gz0}+${grooveTan}
#variable gz1 equal ${gz1}-${grooveTan}
#region groove12 block ${dx} ${dx1} ${gy} ${gy1} ${gz0} ${gz1}
#delete_atoms #region groove4
#delete_atoms #region groove5
#delete_atoms #region groove6
#delete_atoms #region groove7
#delete_atoms #region groove8
#delete_atoms #region groove9
#delete_atoms #region groove10
#delete_atoms #region groove11
#delete_atoms #region groove12
#lattice fcc 4.3596 origin 0 0 0
# ------------------------ FORCE FIELDS ------------------------------
if "${potential} == TersoffScr" then "pair_style atomistica TersoffScr" &
else "pair_style tersoff"
#variable index string ${potential}
if "${potential} == EA" then "pair_coeff * * SiC_Erhart-Albe.tersoff C Si C" &
elif "${potential} == y94" "pair_coeff * * SiC_1994.tersoff C Si C" &
elif "${potential} == TersoffScr" "pair_coeff * * C Si C" &
else "print 'choose the variable -potential to be y94 or EA'" & quit
# ------------------------- SETTINGS ---------------------------------######################################
# DEFORMATION
fix 1 gpWPall nvt temp 300.0 300.0 0.05 #iso 1.0 1.0 0.5
fix 2 gpCTall nvt temp 300.0 300.0 0.05 #iso 1.0 1.0 0.5
unfix 1
unfix 2
compute myCTtemp gpCTmob temp/partial 0 1 1
compute myWPtemp gpWPmob temp/partial 0 1 1
compute myCTTStemp gpCTtsbd temp
compute myWPTStemp gpWPtsbd temp/partial 0 1 1
#compute myCTpress gpCTmob pressure myCTtemp
#compute myWPpress gpWPmob pressure myWPtemp
timestep 0.0005 # set 1 femtosecond per step
fix 1 gpWPtsbd nvt temp 300.0 300.0 0.05 #iso 1.0 1.0 0.5
fix_modify 1 temp myWPTStemp
fix 2 gpCTtsbd nvt temp 300.0 300.0 0.05 #iso 1.0 1.0 0.5
fix_modify 2 temp myCTTStemp
#unfix 3
#unfix 4
#fix 3 gpWPbd setforce 0.0 0.0 0.0 #move linear 0 0 0
#fix 4 gpCTbd setforce 0.0 0.0 0.0 # units box sum no
#velocity gpCTbd set -1.0 0.0 0.0 units box
fix 3 gpWPbd move linear 0 0 0
fix 4 gpCTbd move linear 0 0 0 units box # cutting speed = v * 100 (m s^-1 in the x-direction)
fix 5 mobile nve
fix 10 all balance 10 1.05 shift xy 100 1.05 out ${respath}/log_files/tmp.balance.log
compute ke all ke/atom
fix 12 all ave/atom 10 50 500 c_ke
#fix 13 all property/atom mol
#set group gpCTmob mol 1
#set group gpCTtsbd mol 2
#set group gpCTbd mol 3
#set group gpWPmob mol 4
#set group gpWPtsbd mol 5
#set group gpWPbd mol 6
shell cp log.lammps ${respath}/log_files/
log ${respath}/log_files/cut_sic_re_eq.log
# Re-equilibrium
thermo 500
thermo_style custom step c_myCTtemp c_myWPtemp press etotal fmax fnorm
run 0 # 20 ps
print "Complete re-equilibrium"
# start cutting
log ${respath}/log_files/cut_sic_cut.log
reset_timestep 0
unfix 4
fix 4 gpCTbd move linear -$v 0 0 units box # cutting speed = v * 100 (m s^-1 in the x-direction)
# Output strain and stress info to file
# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa]
# p2, p3, p4 are in GPa
dump 0dumpCSP all custom 500 ${respath}/dump.cutsic.*.lammpstrj id type mol x y z vx vy vz f_12
#c_atomdisp[4] c_atomstres[1] c_atomstres[2] c_atomstres[3] c_atomstres[4] c_atomstres[5] c_atomstres[6]
dump_modify 0dumpCSP element C Si C
write_restart cut_sic_re_eq.0000.restart
restart 10000 ${respath}/restart_files/cut_sic.*.restart
# For the cutting advancement of 20 nm
variable Nstep equal ceil(400000/$v)
run ${Nstep}
#run 133333 # if vx = -3.0
#run 200000 # if vx = -2.0
#run 400000 # if vx = -1.0
######################################
# SIMULATION DONE
shell echo "Cutting simulation has completed -- ${respath}" | mail -s "LAMMPS - simulation done" ***REMOVED***
shell curl -u ***REMOVED***: https://api.pushbullet.com/v2/pushes -d type=note -d device_iden="***REMOVED***" -d title="Push from KhrisU" -d body="LAMMPS -- Simulation is finish"
print "All done"