# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 313.15*${_u_temperature} variable temp_converted equal 313.15*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 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 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "313.15 - 1.0" variable T_up equal "313.15 + 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 50.246962 50.246962 -111.62382 -111.62382 313.15 313.15 79482.639 79482.639 2175.2808 2175.2808 1000 154.82727 154.82727 -6.1315503 -6.1315503 311.38574 311.38574 661748.35 661748.35 278.25013 278.25013 Loop time of 6.74715 on 1 procs for 1000 steps with 4000 atoms Performance: 12.805 ns/day, 1.874 hours/ns, 148.211 timesteps/s, 592.843 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 | 5.5672 | 5.5672 | 5.5672 | 0.0 | 82.51 Neigh | 0.98561 | 0.98561 | 0.98561 | 0.0 | 14.61 Comm | 0.034068 | 0.034068 | 0.034068 | 0.0 | 0.50 Output | 0.00011291 | 0.00011291 | 0.00011291 | 0.0 | 0.00 Modify | 0.14083 | 0.14083 | 0.14083 | 0.0 | 2.09 Other | | 0.0193 | | | 0.29 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3488 ave 3488 max 3488 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: 105958 ave 105958 max 105958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105958 Ave neighs/atom = 26.4895 Neighbor list builds = 79 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 = ${P}" flag: Temp = 310.984781721171, Press = 303.539963171028 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 18 18 18 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.953 | 3.953 | 3.953 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 154.82727 154.82727 -6.1315503 -6.1315503 311.38574 311.38574 661748.35 661748.35 278.25013 278.25013 2000 159.64348 159.64348 -1.2904018 -1.2904018 311.33752 311.33752 3620282.6 3620282.6 47.717749 47.717749 Loop time of 1.75625 on 1 procs for 1000 steps with 4000 atoms Performance: 49.196 ns/day, 0.488 hours/ns, 569.396 timesteps/s, 2.278 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0808 | 1.0808 | 1.0808 | 0.0 | 61.54 Neigh | 0.50348 | 0.50348 | 0.50348 | 0.0 | 28.67 Comm | 0.020623 | 0.020623 | 0.020623 | 0.0 | 1.17 Output | 5.5173e-05 | 5.5173e-05 | 5.5173e-05 | 0.0 | 0.00 Modify | 0.13741 | 0.13741 | 0.13741 | 0.0 | 7.82 Other | | 0.01383 | | | 0.79 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1734 ave 1734 max 1734 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 19842 ave 19842 max 19842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19842 Ave neighs/atom = 4.9605 Neighbor list builds = 112 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 311.259447876424, Press = 143.254212918119 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 31 31 31 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.69 | 3.69 | 3.69 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 159.64348 159.64348 -1.2904018 -1.2904018 311.33752 311.33752 3620282.6 3620282.6 47.717749 47.717749 3000 160.75051 160.75051 -0.28057279 -0.28057279 311.52555 311.52555 18375881 18375881 9.3626834 9.3626834 Loop time of 0.896117 on 1 procs for 1000 steps with 4000 atoms Performance: 96.416 ns/day, 0.249 hours/ns, 1115.925 timesteps/s, 4.464 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40836 | 0.40836 | 0.40836 | 0.0 | 45.57 Neigh | 0.32159 | 0.32159 | 0.32159 | 0.0 | 35.89 Comm | 0.016468 | 0.016468 | 0.016468 | 0.0 | 1.84 Output | 8.0511e-05 | 8.0511e-05 | 8.0511e-05 | 0.0 | 0.01 Modify | 0.13601 | 0.13601 | 0.13601 | 0.0 | 15.18 Other | | 0.01361 | | | 1.52 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 951 ave 951 max 951 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3922 ave 3922 max 3922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3922 Ave neighs/atom = 0.9805 Neighbor list builds = 172 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 311.344823854864, Press = 86.2071466808314 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 52 52 52 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.212 | 4.212 | 4.212 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 160.75051 160.75051 -0.28057279 -0.28057279 311.52555 311.52555 18375881 18375881 9.3626834 9.3626834 4000 161.00403 161.00403 0.003987254 0.003987254 311.46551 311.46551 89561329 89561329 1.924108 1.924108 Loop time of 0.875359 on 1 procs for 1000 steps with 4000 atoms Performance: 98.702 ns/day, 0.243 hours/ns, 1142.388 timesteps/s, 4.570 Matom-step/s 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27023 | 0.27023 | 0.27023 | 0.0 | 30.87 Neigh | 0.4343 | 0.4343 | 0.4343 | 0.0 | 49.61 Comm | 0.019161 | 0.019161 | 0.019161 | 0.0 | 2.19 Output | 5.3991e-05 | 5.3991e-05 | 5.3991e-05 | 0.0 | 0.01 Modify | 0.13579 | 0.13579 | 0.13579 | 0.0 | 15.51 Other | | 0.01582 | | | 1.81 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 577 ave 577 max 577 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 762 ave 762 max 762 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 762 Ave neighs/atom = 0.1905 Neighbor list builds = 276 Dangerous builds = 0 if "${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 89561329.147532 A^3 has become larger than 79482639.2486835 A^3. Aborting calculation. Total wall time: 0:00:10