# periodic boundary conditions along all three dimensions boundary p p p # Set neighbor skin variable neigh_skin equal 2.0*${_u_distance} variable neigh_skin equal 2.0*1 neighbor ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 6.429567344486713*${_u_distance} variable latticeconst_converted equal 6.429567344486713*1 lattice diamond ${latticeconst_converted} lattice diamond 6.42956734448671 Lattice spacing in x,y,z = 6.4295673 6.4295673 6.4295673 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (64.295673 64.295673 64.295673) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 8000 atoms create_atoms CPU = 0.003 seconds variable mass_converted equal 118.71*${_u_mass} variable mass_converted equal 118.71*1 kim_interactions Sn #=== BEGIN kim_interactions ================================== pair_style kim MEAM_LAMMPS_EtesamiBaskesLaradji_2018_PbSn__MO_162736908871_000 pair_coeff * * Sn #=== END kim_interactions ==================================== mass 1 ${mass_converted} mass 1 118.71 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 265794.046314035 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 265794.046314035/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 265794.046314035/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 265794.046314035/(1*1*${_u_distance}) variable V0_metal equal 265794.046314035/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 265794.046314035*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 265794.046314035 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 313.15*${_u_temperature} variable temp_converted equal 313.15*1 variable Tdamp_converted equal 0.1*${_u_time} variable Tdamp_converted equal 0.1*1 variable press_converted equal 0.0*${_u_pressure} variable press_converted equal 0.0*1 variable Pdamp_converted equal 1*${_u_time} variable Pdamp_converted equal 1*1 # create initial velocities consistent with the chosen temperature velocity all create ${temp_converted} 17 mom yes rot yes velocity all create 313.15 17 mom yes rot yes # set NPT ensemble for all atoms fix ensemble all npt temp ${temp_converted} ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.1 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.1 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.1 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.1 iso 0 0 1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_u_energy} variable etotal_metal equal etotal/1 variable pe_metal equal pe/${_u_energy} variable pe_metal equal pe/1 variable T_metal equal temp/${_u_temperature} variable T_metal equal temp/1 variable V_metal equal vol/(${_u_distance}*${_u_distance}*${_u_distance}) variable V_metal equal vol/(1*${_u_distance}*${_u_distance}) variable V_metal equal vol/(1*1*${_u_distance}) variable V_metal equal vol/(1*1*1) variable P_metal equal press/${_u_pressure} variable P_metal equal press/1 fix avgmyTemp all ave/time 5 20 100 v_T_metal ave running start 5000 fix avgmyPress all ave/time 5 20 100 v_P_metal ave running start 5000 fix avgmyVol all ave/time 5 20 100 v_V_metal ave running start 5000 # extract fix quantities into variables so they can be used in if-else logic later. variable T equal f_avgmyTemp variable P equal f_avgmyPress variable V equal f_avgmyVol # set error bounds for temperature and pressure in original metal units (K and bar) variable T_low equal "313.15 - 0.2" variable T_up equal "313.15 + 0.2" variable P_low equal "0.0 - 0.2" variable P_up equal "0.0 + 0.2" # print to logfile every 1000 timesteps thermo_style custom step etotal v_etotal_metal pe v_pe_metal temp v_T_metal vol v_V_metal press v_P_metal thermo 1000 # Run a simulation for at most 2000*1000 timesteps. At each 1000th time step, check # whether the temperature and pressure have converged. If yes, break. label top variable a loop 2000 run 1000 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 18 18 18 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.683 | 4.683 | 4.683 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -25348.389 -25348.389 -25672.171 -25672.171 313.15 313.15 265794.05 265794.05 1301.1502 1301.1502 1000 -24989.857 -24989.857 -25326.461 -25326.461 325.55092 325.55092 269682.67 269682.67 382.8414 382.8414 Loop time of 266.5 on 1 procs for 1000 steps with 8000 atoms Performance: 0.324 ns/day, 74.028 hours/ns, 3.752 timesteps/s 50.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 265.81 | 265.81 | 265.81 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.089424 | 0.089424 | 0.089424 | 0.0 | 0.03 Output | 6.33e-05 | 6.33e-05 | 6.33e-05 | 0.0 | 0.00 Modify | 0.47764 | 0.47764 | 0.47764 | 0.0 | 0.18 Other | | 0.1191 | | | 0.04 Nlocal: 8000.00 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 368000.0 ave 368000 max 368000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 368000 Ave neighs/atom = 46.000000 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.684 | 4.684 | 4.684 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -24989.857 -24989.857 -25326.461 -25326.461 325.55092 325.55092 269682.67 269682.67 382.8414 382.8414 2000 -25027.587 -25027.587 -25344.556 -25344.556 306.56065 306.56065 269796.69 269796.69 -133.24571 -133.24571 Loop time of 280.419 on 1 procs for 1000 steps with 8000 atoms Performance: 0.308 ns/day, 77.894 hours/ns, 3.566 timesteps/s 48.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 279.68 | 279.68 | 279.68 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.1533 | 0.1533 | 0.1533 | 0.0 | 0.05 Output | 5.85e-05 | 5.85e-05 | 5.85e-05 | 0.0 | 0.00 Modify | 0.49926 | 0.49926 | 0.49926 | 0.0 | 0.18 Other | | 0.08455 | | | 0.03 Nlocal: 8000.00 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 368000.0 ave 368000 max 368000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 368000 Ave neighs/atom = 46.000000 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.684 | 4.684 | 4.684 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -25027.587 -25027.587 -25344.556 -25344.556 306.56065 306.56065 269796.69 269796.69 -133.24571 -133.24571 3000 -25008.423 -25008.423 -25341.113 -25341.113 321.76525 321.76525 270013.85 270013.85 -363.73207 -363.73207 Loop time of 274.996 on 1 procs for 1000 steps with 8000 atoms Performance: 0.314 ns/day, 76.388 hours/ns, 3.636 timesteps/s 49.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 274.24 | 274.24 | 274.24 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12167 | 0.12167 | 0.12167 | 0.0 | 0.04 Output | 5.96e-05 | 5.96e-05 | 5.96e-05 | 0.0 | 0.00 Modify | 0.59493 | 0.59493 | 0.59493 | 0.0 | 0.22 Other | | 0.04139 | | | 0.02 Nlocal: 8000.00 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 368000.0 ave 368000 max 368000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 368000 Ave neighs/atom = 46.000000 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.684 | 4.684 | 4.684 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -25008.423 -25008.423 -25341.113 -25341.113 321.76525 321.76525 270013.85 270013.85 -363.73207 -363.73207 4000 -25020.57 -25020.57 -25341.983 -25341.983 310.85929 310.85929 269735.32 269735.32 18.484422 18.484422 Loop time of 266.33 on 1 procs for 1000 steps with 8000 atoms Performance: 0.324 ns/day, 73.981 hours/ns, 3.755 timesteps/s 50.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 265.63 | 265.63 | 265.63 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.097885 | 0.097885 | 0.097885 | 0.0 | 0.04 Output | 4.54e-05 | 4.54e-05 | 4.54e-05 | 0.0 | 0.00 Modify | 0.56826 | 0.56826 | 0.56826 | 0.0 | 0.21 Other | | 0.03402 | | | 0.01 Nlocal: 8000.00 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 368000.0 ave 368000 max 368000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 368000 Ave neighs/atom = 46.000000 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.684 | 4.684 | 4.684 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -25020.57 -25020.57 -25341.983 -25341.983 310.85929 310.85929 269735.32 269735.32 18.484422 18.484422 5000 -25012.58 -25012.58 -25334.483 -25334.483 311.33283 311.33283 269771.4 269771.4 73.525169 73.525169 Loop time of 266.549 on 1 procs for 1000 steps with 8000 atoms Performance: 0.324 ns/day, 74.041 hours/ns, 3.752 timesteps/s 51.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 265.7 | 265.7 | 265.7 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.089554 | 0.089554 | 0.089554 | 0.0 | 0.03 Output | 4.5e-05 | 4.5e-05 | 4.5e-05 | 0.0 | 0.00 Modify | 0.72508 | 0.72508 | 0.72508 | 0.0 | 0.27 Other | | 0.03411 | | | 0.01 Nlocal: 8000.00 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 368000.0 ave 368000 max 368000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 368000 Ave neighs/atom = 46.000000 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 316.316465252237, Press = 81.1940344200481 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.684 | 4.684 | 4.684 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -25012.58 -25012.58 -25334.483 -25334.483 311.33283 311.33283 269771.4 269771.4 73.525169 73.525169 6000 -25018.996 -25018.996 -25341.415 -25341.415 311.83191 311.83191 269514.55 269514.55 369.56535 369.56535 Loop time of 259.861 on 1 procs for 1000 steps with 8000 atoms Performance: 0.332 ns/day, 72.184 hours/ns, 3.848 timesteps/s 52.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 259.22 | 259.22 | 259.22 | 0.0 | 99.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.069724 | 0.069724 | 0.069724 | 0.0 | 0.03 Output | 4.66e-05 | 4.66e-05 | 4.66e-05 | 0.0 | 0.00 Modify | 0.51778 | 0.51778 | 0.51778 | 0.0 | 0.20 Other | | 0.05421 | | | 0.02 Nlocal: 8000.00 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 368000.0 ave 368000 max 368000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 368000 Ave neighs/atom = 46.000000 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 313.415959265816, Press = 14.4326956643602 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.684 | 4.684 | 4.684 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 6000 -25018.996 -25018.996 -25341.415 -25341.415 311.83191 311.83191 269514.55 269514.55 369.56535 369.56535 7000 -25015.882 -25015.882 -25334.783 -25334.783 308.42985 308.42985 269707.05 269707.05 161.33591 161.33591 Loop time of 244.576 on 1 procs for 1000 steps with 8000 atoms Performance: 0.353 ns/day, 67.938 hours/ns, 4.089 timesteps/s 55.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 243.95 | 243.95 | 243.95 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.066781 | 0.066781 | 0.066781 | 0.0 | 0.03 Output | 4.75e-05 | 4.75e-05 | 4.75e-05 | 0.0 | 0.00 Modify | 0.50804 | 0.50804 | 0.50804 | 0.0 | 0.21 Other | | 0.0541 | | | 0.02 Nlocal: 8000.00 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 368000.0 ave 368000 max 368000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 368000 Ave neighs/atom = 46.000000 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" print "flag: Temp = ${T}, Press = ${P}" flag: Temp = 313.090167717384, Press = 5.45656458540684 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.684 | 4.684 | 4.684 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 7000 -25015.882 -25015.882 -25334.783 -25334.783 308.42985 308.42985 269707.05 269707.05 161.33591 161.33591 8000 -25019.908 -25019.908 -25341.488 -25341.488 311.02041 311.02041 269716.33 269716.33 55.566347 55.566347 Loop time of 218.036 on 1 procs for 1000 steps with 8000 atoms Performance: 0.396 ns/day, 60.566 hours/ns, 4.586 timesteps/s 62.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 217.33 | 217.33 | 217.33 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.08939 | 0.08939 | 0.08939 | 0.0 | 0.04 Output | 4.67e-05 | 4.67e-05 | 4.67e-05 | 0.0 | 0.00 Modify | 0.52184 | 0.52184 | 0.52184 | 0.0 | 0.24 Other | | 0.09397 | | | 0.04 Nlocal: 8000.00 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 368000.0 ave 368000 max 368000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 368000 Ave neighs/atom = 46.000000 Neighbor list builds = 0 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break" jump SELF break # Write final averaged volume to file if temperature and volume have converged; otherwise wirte a # flag to indicate non-convergence. variable myStep equal step if "${myStep} < 2000000" then "print '${V}' file output/vol_T313.15.out" else "print 'not_converged' file output/vol_T313.15.out" print '${V}' file output/vol_T313.15.out 269770.15484603 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0