# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.226186460256581*${_u_distance} variable latticeconst_converted equal 4.226186460256581*1 lattice fcc ${latticeconst_converted} lattice fcc 4.22618646025658 Lattice spacing in x,y,z = 4.2261865 4.2261865 4.2261865 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (42.261865 42.261865 42.261865) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (42.261865 42.261865 42.261865) create_atoms CPU = 0.001 seconds variable mass_converted equal 20.1797*${_u_mass} variable mass_converted equal 20.1797*1 kim interactions Ne #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958HighCutoff_Ne__MO_966254629593_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 75482.4456404676 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 75482.4456404676/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 75482.4456404676/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 75482.4456404676/(1*1*${_u_distance}) variable V0_metal equal 75482.4456404676/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 75482.4456404676*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 75482.4456404676 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 293.15*${_u_temperature} variable temp_converted equal 293.15*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 293.15 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 293.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "293.15 - 1.0" variable T_up equal "293.15 + 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_966254629593_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 = 18 ghost atom cutoff = 18 binsize = 9, bins = 5 5 5 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) = 26.12 | 26.12 | 26.12 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 45.902535 45.902535 -105.63002 -105.63002 293.15 293.15 75482.446 75482.446 2144.2675 2144.2675 1000 143.24194 143.24194 -7.4426043 -7.4426043 291.50947 291.50947 624775.26 624775.26 274.95989 274.95989 Loop time of 43.1693 on 1 procs for 1000 steps with 4000 atoms Performance: 2.001 ns/day, 11.991 hours/ns, 23.165 timesteps/s, 92.658 katom-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 | 39.415 | 39.415 | 39.415 | 0.0 | 91.30 Neigh | 3.5247 | 3.5247 | 3.5247 | 0.0 | 8.16 Comm | 0.066797 | 0.066797 | 0.066797 | 0.0 | 0.15 Output | 9.044e-05 | 9.044e-05 | 9.044e-05 | 0.0 | 0.00 Modify | 0.14019 | 0.14019 | 0.14019 | 0.0 | 0.32 Other | | 0.02225 | | | 0.05 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7566 ave 7566 max 7566 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: 632096 ave 632096 max 632096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 632096 Ave neighs/atom = 158.024 Neighbor list builds = 77 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 = ${P}" flag: Temp = 291.085361732559, Press = 296.657559756448 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 9.106 | 9.106 | 9.106 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 143.24194 143.24194 -7.4426043 -7.4426043 291.50947 291.50947 624775.26 624775.26 274.95989 274.95989 2000 149.29838 149.29838 -1.4040926 -1.4040926 291.54415 291.54415 3394880.4 3394880.4 48.091491 48.091491 Loop time of 7.39365 on 1 procs for 1000 steps with 4000 atoms Performance: 11.686 ns/day, 2.054 hours/ns, 135.251 timesteps/s, 541.005 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0051 | 6.0051 | 6.0051 | 0.0 | 81.22 Neigh | 1.2078 | 1.2078 | 1.2078 | 0.0 | 16.34 Comm | 0.031679 | 0.031679 | 0.031679 | 0.0 | 0.43 Output | 4.2169e-05 | 4.2169e-05 | 4.2169e-05 | 0.0 | 0.00 Modify | 0.13488 | 0.13488 | 0.13488 | 0.0 | 1.82 Other | | 0.01417 | | | 0.19 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3612 ave 3612 max 3612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117680 ave 117680 max 117680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117680 Ave neighs/atom = 29.42 Neighbor list builds = 110 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 291.384036420854, Press = 141.096671614258 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.197 | 7.197 | 7.197 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 149.29838 149.29838 -1.4040926 -1.4040926 291.54415 291.54415 3394880.4 3394880.4 48.091491 48.091491 3000 150.41748 150.41748 -0.30082452 -0.30082452 291.57478 291.57478 17178574 17178574 9.3768262 9.3768262 Loop time of 2.34342 on 1 procs for 1000 steps with 4000 atoms Performance: 36.869 ns/day, 0.651 hours/ns, 426.728 timesteps/s, 1.707 Matom-step/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4103 | 1.4103 | 1.4103 | 0.0 | 60.18 Neigh | 0.76599 | 0.76599 | 0.76599 | 0.0 | 32.69 Comm | 0.022926 | 0.022926 | 0.022926 | 0.0 | 0.98 Output | 3.0898e-05 | 3.0898e-05 | 3.0898e-05 | 0.0 | 0.00 Modify | 0.13072 | 0.13072 | 0.13072 | 0.0 | 5.58 Other | | 0.01348 | | | 0.58 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1867 ave 1867 max 1867 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23276 ave 23276 max 23276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23276 Ave neighs/atom = 5.819 Neighbor list builds = 169 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 291.465506282031, Press = 85.0280179329112 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 29 29 29 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.911 | 6.911 | 6.911 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 150.41748 150.41748 -0.30082452 -0.30082452 291.57478 291.57478 17178574 17178574 9.3768262 9.3768262 4000 150.68133 150.68133 0.017029118 0.017029118 291.4703 291.4703 83825190 83825190 1.9282252 1.9282252 Loop time of 1.20973 on 1 procs for 1000 steps with 4000 atoms Performance: 71.421 ns/day, 0.336 hours/ns, 826.630 timesteps/s, 3.307 Matom-step/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52771 | 0.52771 | 0.52771 | 0.0 | 43.62 Neigh | 0.51639 | 0.51639 | 0.51639 | 0.0 | 42.69 Comm | 0.020909 | 0.020909 | 0.020909 | 0.0 | 1.73 Output | 3.0908e-05 | 3.0908e-05 | 3.0908e-05 | 0.0 | 0.00 Modify | 0.12914 | 0.12914 | 0.12914 | 0.0 | 10.68 Other | | 0.01555 | | | 1.29 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1056 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4888 ave 4888 max 4888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4888 Ave neighs/atom = 1.222 Neighbor list builds = 271 Dangerous builds = 0 if "${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 83825189.7834289 A^3 has become larger than 75482445.6404676 A^3. Aborting calculation. Total wall time: 0:00:54