# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.299560785293579*${_u_distance} variable latticeconst_converted equal 4.299560785293579*1 lattice fcc ${latticeconst_converted} lattice fcc 4.29956078529358 Lattice spacing in x,y,z = 4.2995608 4.2995608 4.2995608 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (42.995608 42.995608 42.995608) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (42.995608 42.995608 42.995608) create_atoms CPU = 0.001 seconds variable mass_converted equal 20.1797*${_u_mass} variable mass_converted equal 20.1797*1 kim interactions Ne #=== BEGIN kim interactions ================================== pair_style kim Morse_Shifted_Glyde_1970_Ne__MO_169434419764_004 pair_coeff * * Ne #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 20.1797 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 79482.6392486835 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 79482.6392486835/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 79482.6392486835/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 79482.6392486835/(1*1*${_u_distance}) variable V0_metal equal 79482.6392486835/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 79482.6392486835*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 79482.6392486835 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 253.15*${_u_temperature} variable temp_converted equal 253.15*1 variable Tdamp_converted equal 0.01*${_u_time} variable Tdamp_converted equal 0.01*1 variable press_converted equal 0.0*${_u_pressure} variable press_converted equal 0.0*1 variable Pdamp_converted equal 0.1*${_u_time} variable Pdamp_converted equal 0.1*1 # create initial velocities consistent with the chosen temperature velocity all create ${temp_converted} 17 mom yes rot yes velocity all create 253.15 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 253.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 1000 fix avgmyPress all ave/time 5 20 100 v_P_metal ave running start 1000 fix avgmyVol all ave/time 5 20 100 v_V_metal ave running start 1000 # 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 "253.15 - 1.0" variable T_up equal "253.15 + 1.0" variable P_low equal "0.0 - 5.0" variable P_up equal "0.0 + 5.0" # 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 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM Project: doi:10.1007/s11837-011-0102-6 @Article{tadmor:elliott:2011, author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker}, title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels}, journal = {{JOM}}, year = 2011, volume = 63, number = 17, pages = {17}, doi = {10.1007/s11837-011-0102-6} } - OpenKIM potential: https://openkim.org/cite/MO_169434419764_004#item-citation CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.005 | 7.005 | 7.005 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 19.232283 19.232283 -111.62382 -111.62382 253.15 253.15 79482.639 79482.639 1758.4939 1758.4939 1000 121.8207 121.8207 -8.169074 -8.169074 251.47404 251.47404 621635.63 621635.63 223.90698 223.90698 Loop time of 6.85008 on 1 procs for 1000 steps with 4000 atoms Performance: 12.613 ns/day, 1.903 hours/ns, 145.984 timesteps/s, 583.935 katom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7021 | 5.7021 | 5.7021 | 0.0 | 83.24 Neigh | 0.95716 | 0.95716 | 0.95716 | 0.0 | 13.97 Comm | 0.033389 | 0.033389 | 0.033389 | 0.0 | 0.49 Output | 0.00011239 | 0.00011239 | 0.00011239 | 0.0 | 0.00 Modify | 0.1386 | 0.1386 | 0.1386 | 0.0 | 2.02 Other | | 0.01876 | | | 0.27 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3559 ave 3559 max 3559 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: 114524 ave 114524 max 114524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114524 Ave neighs/atom = 28.631 Neighbor list builds = 75 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 = ${P}" flag: Temp = 251.547408542536, Press = 246.840908244413 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.948 | 3.948 | 3.948 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 121.8207 121.8207 -8.169074 -8.169074 251.47404 251.47404 621635.63 621635.63 223.90698 223.90698 2000 128.55052 128.55052 -1.5709312 -1.5709312 251.72877 251.72877 3395847.8 3395847.8 41.034261 41.034261 Loop time of 1.83864 on 1 procs for 1000 steps with 4000 atoms Performance: 46.991 ns/day, 0.511 hours/ns, 543.879 timesteps/s, 2.176 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1464 | 1.1464 | 1.1464 | 0.0 | 62.35 Neigh | 0.51687 | 0.51687 | 0.51687 | 0.0 | 28.11 Comm | 0.021802 | 0.021802 | 0.021802 | 0.0 | 1.19 Output | 5.5604e-05 | 5.5604e-05 | 5.5604e-05 | 0.0 | 0.00 Modify | 0.13918 | 0.13918 | 0.13918 | 0.0 | 7.57 Other | | 0.01431 | | | 0.78 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1803 ave 1803 max 1803 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 21354 ave 21354 max 21354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21354 Ave neighs/atom = 5.3385 Neighbor list builds = 110 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 251.63397578175, Press = 120.224632431116 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 30 30 30 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.676 | 3.676 | 3.676 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 128.55052 128.55052 -1.5709312 -1.5709312 251.72877 251.72877 3395847.8 3395847.8 41.034261 41.034261 3000 129.83917 129.83917 -0.31440444 -0.31440444 251.79092 251.79092 17402871 17402871 7.9889081 7.9889081 Loop time of 0.945846 on 1 procs for 1000 steps with 4000 atoms Performance: 91.347 ns/day, 0.263 hours/ns, 1057.254 timesteps/s, 4.229 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42794 | 0.42794 | 0.42794 | 0.0 | 45.24 Neigh | 0.34893 | 0.34893 | 0.34893 | 0.0 | 36.89 Comm | 0.017644 | 0.017644 | 0.017644 | 0.0 | 1.87 Output | 7.1374e-05 | 7.1374e-05 | 7.1374e-05 | 0.0 | 0.01 Modify | 0.13717 | 0.13717 | 0.13717 | 0.0 | 14.50 Other | | 0.01409 | | | 1.49 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 961 ave 961 max 961 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4198 ave 4198 max 4198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4198 Ave neighs/atom = 1.0495 Neighbor list builds = 172 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 251.690744557362, Press = 72.5582592971335 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 52 52 52 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.212 | 4.212 | 4.212 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 129.83917 129.83917 -0.31440444 -0.31440444 251.79092 251.79092 17402871 17402871 7.9889081 7.9889081 4000 130.1115 130.1115 -0.045848199 -0.045848199 251.79821 251.79821 85352033 85352033 1.6294873 1.6294873 Loop time of 0.87723 on 1 procs for 1000 steps with 4000 atoms Performance: 98.492 ns/day, 0.244 hours/ns, 1139.952 timesteps/s, 4.560 Matom-step/s 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27708 | 0.27708 | 0.27708 | 0.0 | 31.59 Neigh | 0.42773 | 0.42773 | 0.42773 | 0.0 | 48.76 Comm | 0.019294 | 0.019294 | 0.019294 | 0.0 | 2.20 Output | 5.2399e-05 | 5.2399e-05 | 5.2399e-05 | 0.0 | 0.01 Modify | 0.13708 | 0.13708 | 0.13708 | 0.0 | 15.63 Other | | 0.01599 | | | 1.82 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 536 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 896 Ave neighs/atom = 0.224 Neighbor list builds = 272 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" jump SELF unstable print "ERROR: System volume ${V_metal} A^3 has become larger than ${V0_metal_times1000} A^3. Aborting calculation." ERROR: System volume 85352032.9372103 A^3 has become larger than 79482639.2486835 A^3. Aborting calculation. Total wall time: 0:00:10