# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.262299403548241*${_u_distance} variable latticeconst_converted equal 5.262299403548241*1 lattice fcc ${latticeconst_converted} lattice fcc 5.26229940354824 Lattice spacing in x,y,z = 5.2622994 5.2622994 5.2622994 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.622994 52.622994 52.622994) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.622994 52.622994 52.622994) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim Morse_SigmoidalSmoothed_Jelinek_1972_Ar__MO_071460865933_002 WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1127) pair_coeff * * Ar #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 39.948 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 145722.516377902 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 145722.516377902/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 145722.516377902/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 145722.516377902/(1*1*${_u_distance}) variable V0_metal equal 145722.516377902/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 145722.516377902*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 145722.516377902 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 273.15*${_u_temperature} variable temp_converted equal 273.15*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 273.15 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 273.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "273.15 - 1.0" variable T_up equal "273.15 + 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_071460865933_002#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 = 11 11 11 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) = 5.37 | 5.37 | 5.37 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 140.96757 140.96757 -0.2267577 -0.2267577 273.15 273.15 145722.52 145722.52 1034.9269 1034.9269 1000 141.49575 141.49575 1.1502823 1.1502823 271.50782 271.50782 1055746.2 1055746.2 144.93039 144.93039 Loop time of 5.07432 on 1 procs for 1000 steps with 4000 atoms Performance: 17.027 ns/day, 1.410 hours/ns, 197.071 timesteps/s, 788.283 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 | 4.1774 | 4.1774 | 4.1774 | 0.0 | 82.32 Neigh | 0.71836 | 0.71836 | 0.71836 | 0.0 | 14.16 Comm | 0.027356 | 0.027356 | 0.027356 | 0.0 | 0.54 Output | 9.9758e-05 | 9.9758e-05 | 9.9758e-05 | 0.0 | 0.00 Modify | 0.1343 | 0.1343 | 0.1343 | 0.0 | 2.65 Other | | 0.01677 | | | 0.33 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2908 ave 2908 max 2908 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: 63182 ave 63182 max 63182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63182 Ave neighs/atom = 15.7955 Neighbor list builds = 82 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 = ${P}" flag: Temp = 271.483056221511, Press = 158.2125537444 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 21 21 21 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.491 | 3.491 | 3.491 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 141.49575 141.49575 1.1502823 1.1502823 271.50782 271.50782 1055746.2 1055746.2 144.93039 144.93039 2000 140.57466 140.57466 0.16787669 0.16787669 271.62644 271.62644 5926215.9 5926215.9 25.389443 25.389443 Loop time of 1.38443 on 1 procs for 1000 steps with 4000 atoms Performance: 62.408 ns/day, 0.385 hours/ns, 722.319 timesteps/s, 2.889 Matom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.82191 | 0.82191 | 0.82191 | 0.0 | 59.37 Neigh | 0.39816 | 0.39816 | 0.39816 | 0.0 | 28.76 Comm | 0.018594 | 0.018594 | 0.018594 | 0.0 | 1.34 Output | 7.9409e-05 | 7.9409e-05 | 7.9409e-05 | 0.0 | 0.01 Modify | 0.13275 | 0.13275 | 0.13275 | 0.0 | 9.59 Other | | 0.01295 | | | 0.94 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1437 ave 1437 max 1437 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11468 ave 11468 max 11468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11468 Ave neighs/atom = 2.867 Neighbor list builds = 127 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 271.566581861733, Press = 75.8072870513049 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 36 36 36 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.676 | 3.676 | 3.676 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 140.57466 140.57466 0.16787669 0.16787669 271.62644 271.62644 5926215.9 5926215.9 25.389443 25.389443 3000 140.44255 140.44255 0.010404513 0.010404513 271.6755 271.6755 30717696 30717696 4.8844744 4.8844744 Loop time of 0.820722 on 1 procs for 1000 steps with 4000 atoms Performance: 105.273 ns/day, 0.228 hours/ns, 1218.440 timesteps/s, 4.874 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34345 | 0.34345 | 0.34345 | 0.0 | 41.85 Neigh | 0.31391 | 0.31391 | 0.31391 | 0.0 | 38.25 Comm | 0.016558 | 0.016558 | 0.016558 | 0.0 | 2.02 Output | 5.4903e-05 | 5.4903e-05 | 5.4903e-05 | 0.0 | 0.01 Modify | 0.13265 | 0.13265 | 0.13265 | 0.0 | 16.16 Other | | 0.0141 | | | 1.72 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 839 ave 839 max 839 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2248 ave 2248 max 2248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2248 Ave neighs/atom = 0.562 Neighbor list builds = 203 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 271.607367213429, Press = 45.5795201726143 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 62 62 62 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.556 | 4.556 | 4.556 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 140.44255 140.44255 0.010404513 0.010404513 271.6755 271.6755 30717696 30717696 4.8844744 4.8844744 4000 140.45865 140.45865 0.010223977 0.010223977 271.70699 271.70699 1.5233393e+08 1.5233393e+08 0.9849896 0.9849896 Loop time of 0.937691 on 1 procs for 1000 steps with 4000 atoms Performance: 92.141 ns/day, 0.260 hours/ns, 1066.450 timesteps/s, 4.266 Matom-step/s 97.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24323 | 0.24323 | 0.24323 | 0.0 | 25.94 Neigh | 0.52098 | 0.52098 | 0.52098 | 0.0 | 55.56 Comm | 0.020933 | 0.020933 | 0.020933 | 0.0 | 2.23 Output | 5.3871e-05 | 5.3871e-05 | 5.3871e-05 | 0.0 | 0.01 Modify | 0.13596 | 0.13596 | 0.13596 | 0.0 | 14.50 Other | | 0.01654 | | | 1.76 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 474 ave 474 max 474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 490 ave 490 max 490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 490 Ave neighs/atom = 0.1225 Neighbor list builds = 309 Dangerous builds = 0 if "${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 152333930.132217 A^3 has become larger than 145722516.377902 A^3. Aborting calculation. Total wall time: 0:00:08