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log.lammps
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LAMMPS (17 Nov 2016)
# 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))
# -n the number of successive cutting
#variable respath string ${v}x100_m_s-1_Groove${grooveDepth}T${grooveTan}_SiC_${potential}
variable respath string ${v}x100_m_s-1_SiC_${potential}_${n}
variable respath string 4.00x100_m_s-1_SiC_${potential}_${n}
variable respath string 4.00x100_m_s-1_SiC_EA_${n}
variable respath string 4.00x100_m_s-1_SiC_EA_7
print "${respath}"
4.00x100_m_s-1_SiC_EA_7
shell mkdir ${respath}
shell mkdir 4.00x100_m_s-1_SiC_EA_7
WARNING: Shell command 'mkdir' failed with error 'File exists' (../input.cpp:1264)
shell mkdir ${respath}/log_files
shell mkdir 4.00x100_m_s-1_SiC_EA_7/log_files
WARNING: Shell command 'mkdir' failed with error 'File exists' (../input.cpp:1264)
shell mkdir ${respath}/restart_files
shell mkdir 4.00x100_m_s-1_SiC_EA_7/restart_files
WARNING: Shell command 'mkdir' failed with error 'File exists' (../input.cpp:1264)
shell mkdir ${respath}/ovito_analysis-results
shell mkdir 4.00x100_m_s-1_SiC_EA_7/ovito_analysis-results
WARNING: Shell command 'mkdir' failed with error 'File exists' (../input.cpp:1264)
shell chmod 774 ${respath}
shell chmod 774 4.00x100_m_s-1_SiC_EA_7
shell chmod 774 ${respath}/log_files
shell chmod 774 4.00x100_m_s-1_SiC_EA_7/log_files
shell chmod 774 ${respath}/restart_files
shell chmod 774 4.00x100_m_s-1_SiC_EA_7/restart_files
shell chmod 777 ${respath}/ovito_analysis_results
shell chmod 777 4.00x100_m_s-1_SiC_EA_7/ovito_analysis_results
WARNING: Shell command returned with non-zero status (../input.cpp:1336)
#package cuda gpu/node 1 0
#package omp 2 force/neigh
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary s s p
atom_style atomic
variable a equal 4.3667
variable b equal 3.571
variable c equal $a/$b
variable c equal 4.3667/$b
variable c equal 4.3667/3.571
lattice fcc $a
lattice fcc 4.3667
Lattice spacing in x,y,z = 4.3667 4.3667 4.3667
region whole block 0 99 0 47 0 9
create_box 3 whole
Created orthogonal box = (0 0 0) to (432.303 205.235 39.3003)
2 by 1 by 1 MPI processor grid
read_data dia_mol1_$n.dat add append group gpCTmob #extra/atom/types 1
read_data dia_mol1_7.dat add append group gpCTmob
orthogonal box = (-306.938 -52.0232 0) to (990.21 205.255 39.3003)
2 by 1 by 1 MPI processor grid
reading atoms ...
79853 atoms
reading velocities ...
79853 velocities
#group gpCTmob type 1
print "read1"
read1
read_data dia_mol2_$n.dat add append group gpCTtsbd
read_data dia_mol2_7.dat add append group gpCTtsbd
orthogonal box = (-306.938 -52.0232 0) to (990.21 190.467 39.3003)
2 by 1 by 1 MPI processor grid
reading atoms ...
4785 atoms
reading velocities ...
4785 velocities
#group gpCTtsbd subtract all gpCTmob
print "read2"
read2
read_data dia_mol3_$n.dat add append group gpCTbd
read_data dia_mol3_7.dat add append group gpCTbd
orthogonal box = (-306.938 -52.0232 0) to (990.21 190.467 39.3003)
2 by 1 by 1 MPI processor grid
reading atoms ...
4950 atoms
reading velocities ...
4950 velocities
#group gpCTbd subtract all gpCTmob gpCTtsbd
#print "read3"
group gpDia type 1
89588 atoms in group gpDia
print "diamond tool created"
diamond tool created
read_data 0_mol4_$n.dat add append group gpWPmob0 shift -100 0 0
read_data 0_mol4_7.dat add append group gpWPmob0 shift -100 0 0
orthogonal box = (-100.042 -0.0132843 0) to (417.116 133.939 39.3003)
2 by 1 by 1 MPI processor grid
reading atoms ...
25192 atoms
reading velocities ...
25192 velocities
#group gpWPmob0 subtract all gpDia gpSiCX
read_data 0_mol5_$n.dat add append group gpWPtsbd0 shift -100 0 0
read_data 0_mol5_7.dat add append group gpWPtsbd0 shift -100 0 0
orthogonal box = (-100.042 -0.0132843 0) to (417.038 133.928 39.3003)
2 by 1 by 1 MPI processor grid
reading atoms ...
3798 atoms
reading velocities ...
3798 velocities
#group gpWPtsbd0 subtract all gpDia gpSiCX gpWPmob0
read_data 0_mol6_$n.dat add append group gpWPbd0 shift -100 0 0
read_data 0_mol6_7.dat add append group gpWPbd0 shift -100 0 0
orthogonal box = (-100.042 -0.0132843 0) to (417.038 133.928 39.3003)
2 by 1 by 1 MPI processor grid
reading atoms ...
4950 atoms
reading velocities ...
4950 velocities
#group gpWPbd0 subtract all gpDia gpSiCX gpWPmob0 gpWPtsbd0
group gpSiC0 union gpWPmob0 gpWPtsbd0 gpWPbd0
33940 atoms in group gpSiC0
read_data wp_mol4_$n.dat add append group gpWPmobX #extra/atom/types 2 3
read_data wp_mol4_7.dat add append group gpWPmobX
orthogonal box = (-306.938 -52.0232 0) to (990.21 190.467 39.3003)
2 by 1 by 1 MPI processor grid
reading atoms ...
41407 atoms
reading velocities ...
41407 velocities
#group gpWPmobX type 2 3
read_data wp_mol5_$n.dat add append group gpWPtsbdX
read_data wp_mol5_7.dat add append group gpWPtsbdX
orthogonal box = (-306.938 -52.0232 0) to (990.21 190.467 39.3003)
2 by 1 by 1 MPI processor grid
reading atoms ...
2596 atoms
reading velocities ...
2596 velocities
#group gpWPtsbdX subtract all gpDia gpWPmobX
read_data wp_mol6_$n.dat add append group gpWPbdX
read_data wp_mol6_7.dat add append group gpWPbdX
orthogonal box = (-306.938 -52.0232 0) to (990.21 190.467 39.3003)
2 by 1 by 1 MPI processor grid
reading atoms ...
4482 atoms
reading velocities ...
4482 velocities
#group gpWPbdX subtract all gpDia gpWPmobX gpWPtsbdX
group gpSiCX union gpWPmobX gpWPtsbdX gpWPbdX
48485 atoms in group gpSiCX
group gpWPmobE union gpWPmob0 gpWPtsbd0
28990 atoms in group gpWPmobE
# groups atoms
group gpSiC type 2 3
82425 atoms in group gpSiC
group gpWPbd union gpWPbd0 gpWPbdX
9432 atoms in group gpWPbd
group gpWPtsbd union gpWPtsbd0 gpWPtsbdX
6394 atoms in group gpWPtsbd
group gpWPmob union gpWPmob0 gpWPmobX
66599 atoms in group gpWPmob
group mobile union gpWPmob gpCTmob
146452 atoms in group mobile
print "Workpiece created"
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)
group Si type 2
42447 atoms in group Si
group C type 1 3
129566 atoms in group C
lattice fcc 4.3667 origin 0 0 0
Lattice spacing in x,y,z = 4.3667 4.3667 4.3667
# ------------------------ FORCE FIELDS ------------------------------
if "${potential} == TersoffScr" then "pair_style atomistica TersoffScr" else "pair_style tersoff"
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
pair_coeff * * SiC_Erhart-Albe.tersoff C Si C
# ------------------------- SETTINGS ---------------------------------
######################################
# EQUILIBRATION
# set temperature at 300 K
#compute myCTtemp gpCTmob0 temp
compute myWPtemp0 gpWPtsbd0 temp
compute myWPtemp gpWPmob0 temp
fix 2 gpWPtsbd0 nvt temp 300.0 300.0 0.05 #iso 1.0 1.0 0.5
fix_modify 2 temp myWPtemp0
WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1389)
reset_timestep 0
timestep 0.0005 # set 1 femtosecond per step
fix 3 gpWPbd move linear 0 0 0
fix 4 gpCTbd move linear 0 0 0
fix 5 gpWPmob0 nve
fix 6 gpWPmob0 temp/rescale 5 300.0 300.0 10 0.8
fix 10 all balance 100 0.9 shift xy 10 1.05 out tmp.balance.log
fix 13 all property/atom mol
WARNING: Fix property/atom mol or charge or rmass w/out ghost communication (../fix_property_atom.cpp:123)
set group gpCTmob mol 1
79853 settings made for mol
set group gpCTtsbd mol 2
4785 settings made for mol
set group gpCTbd mol 3
4950 settings made for mol
set group gpWPmob mol 4
66599 settings made for mol
set group gpWPtsbd mol 5
6394 settings made for mol
set group gpWPbd mol 6
9432 settings made for mol
# Display thermo
thermo 100
#compute eCSP all centro/atom fcc
#compute atomke all ke/atom
dump e0dumpCSP all custom 1 ${respath}/dump.cutsic_eq.*.lammpstrj id type mol element x y z vx vy vz # c_atomke
dump e0dumpCSP all custom 1 4.00x100_m_s-1_SiC_EA_7/dump.cutsic_eq.*.lammpstrj id type mol element x y z vx vy vz
dump_modify e0dumpCSP element C Si C
# backup initial state and every 1000 steps
write_restart ${respath}/restart_files/cut_sic_eq.restart.0000
write_restart 4.00x100_m_s-1_SiC_EA_7/restart_files/cut_sic_eq.restart.0000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.96
ghost atom cutoff = 4.96
binsize = 2.48 -> bins = 210 55 16
restart 1000 ${respath}/restart_files/cut_sic_eq.restart
restart 1000 4.00x100_m_s-1_SiC_EA_7/restart_files/cut_sic_eq.restart
# Run for at least 10 picosecond
print "start run equilibration"
start run equilibration
#minimize 1.0e-4 1.0e-6 100 1000
run 1000
Memory usage per processor = 56.4129 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 904.95858 -1110069.8 0 -1089948.7 86800.709 2771993.2
100 895.73784 -1110238.5 0 -1090322.4 86393.284 2771993.2
200 895.88646 -1110247.4 0 -1090327.9 86131.872 2771993.2
300 894.9635 -1110259.5 0 -1090360.6 85794.081 2771993.2
400 895.26105 -1110261.5 0 -1090356 85479.851 2771993.2
500 895.00128 -1110250.3 0 -1090350.6 84915.379 2771993.2
600 894.89452 -1110243.5 0 -1090346.2 84576.614 2771993.2
700 895.4974 -1110253.1 0 -1090342.4 84325.714 2771993.2
800 894.92831 -1110237.4 0 -1090339.3 84089.368 2771993.2
900 894.85595 -1110232.4 0 -1090335.9 84021.941 2771993.2
1000 895.5115 -1110245 0 -1090334 84109.063 2771993.2
Loop time of 1068.75 on 2 procs for 1000 steps with 172013 atoms
Performance: 0.040 ns/day, 593.749 hours/ns, 0.936 timesteps/s
89.6% CPU use with 2 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 540.33 | 603.37 | 666.42 | 256.6 | 56.46
Neigh | 3.3393 | 3.8163 | 4.2933 | 24.4 | 0.36
Comm | 4.2755 | 67.193 | 130.11 | 767.6 | 6.29
Output | 377.49 | 382.35 | 387.21 | 24.9 | 35.78
Modify | 2.9277 | 3.9034 | 4.8791 | 49.4 | 0.37
Other | | 8.111 | | | 0.76
Nlocal: 86006.5 ave 86007 max 86006 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 27130 ave 27181 max 27079 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
FullNghs: 5.68761e+06 ave 7.06294e+06 max 4.31229e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 11375226
Ave neighs/atom = 66.13
Neighbor list builds = 10
Dangerous builds = 0
#run 400000
######################################
# # DEFORMATION
#
#
# unfix 2
# undump e0dumpCSP
#
# compute myCTtemp gpCTmob temp
# 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 units box
# 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
#
# #fix 14 gpDia wall/reflect xlo 800.0 xhi 850.0 units box
#
# 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 3
# fix 3 gpWPbd 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 1 ${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"
jump ../in.senddone.lmp
### copy the following line to the end of your lammps script
##
## jump ../in.senddone.lmp
##
###
######################################
# SIMULATION DONE
print "All done"
All done
## Send notification via email
# shell echo "Cutting simulation has completed -- cut_sic_eq" | mail -s "LAMMPS - simulation done" ***REMOVED***
# Send notification via pushbullet
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"
Total wall time: 0:17:55