# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.235186479985714*${_u_distance} variable latticeconst_converted equal 5.235186479985714*1 lattice fcc ${latticeconst_converted} lattice fcc 5.23518647998571 Lattice spacing in x,y,z = 5.2351865 5.2351865 5.2351865 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.351865 52.351865 52.351865) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.351865 52.351865 52.351865) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim Exp6_KongChakrabarty_1973_ArNe__MO_946046425752_002 WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1122) 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 143481.684999044 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 143481.684999044/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 143481.684999044/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 143481.684999044/(1*1*${_u_distance}) variable V0_metal equal 143481.684999044/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 143481.684999044*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 143481.684999044 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_946046425752_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 -179.38679 -179.38679 -341.25757 -341.25757 313.15 313.15 143481.68 143481.68 1205.0112 1205.0112 1000 99.645489 99.645489 -62.629941 -62.629941 313.93282 313.93282 587624.38 587624.38 163.61047 163.61047 Loop time of 6.26888 on 1 procs for 1000 steps with 4000 atoms Performance: 13.782 ns/day, 1.741 hours/ns, 159.518 timesteps/s, 638.073 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5379 | 5.5379 | 5.5379 | 0.0 | 88.34 Neigh | 0.56806 | 0.56806 | 0.56806 | 0.0 | 9.06 Comm | 0.025046 | 0.025046 | 0.025046 | 0.0 | 0.40 Output | 8.5812e-05 | 8.5812e-05 | 8.5812e-05 | 0.0 | 0.00 Modify | 0.12476 | 0.12476 | 0.12476 | 0.0 | 1.99 Other | | 0.01307 | | | 0.21 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3691 ave 3691 max 3691 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: 119716 ave 119716 max 119716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119716 Ave neighs/atom = 29.929 Neighbor list builds = 56 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 = ${P}" flag: Temp = 312.927339787702, Press = 165.440070907526 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.852 | 3.852 | 3.852 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 99.645489 99.645489 -62.629941 -62.629941 313.93282 313.93282 587624.38 587624.38 163.61047 163.61047 2000 146.74615 146.74615 -15.517399 -15.517399 313.90985 313.90985 2839562.8 2839562.8 53.181318 53.181318 Loop time of 1.98231 on 1 procs for 1000 steps with 4000 atoms Performance: 43.586 ns/day, 0.551 hours/ns, 504.463 timesteps/s, 2.018 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4319 | 1.4319 | 1.4319 | 0.0 | 72.24 Neigh | 0.40406 | 0.40406 | 0.40406 | 0.0 | 20.38 Comm | 0.016909 | 0.016909 | 0.016909 | 0.0 | 0.85 Output | 3.3363e-05 | 3.3363e-05 | 3.3363e-05 | 0.0 | 0.00 Modify | 0.11796 | 0.11796 | 0.11796 | 0.0 | 5.95 Other | | 0.0114 | | | 0.57 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1960 ave 1960 max 1960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26796 ave 26796 max 26796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26796 Ave neighs/atom = 6.699 Neighbor list builds = 97 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.925388213052, Press = 111.61412762526 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 28 28 28 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.554 | 3.554 | 3.554 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 146.74615 146.74615 -15.517399 -15.517399 313.90985 313.90985 2839562.8 2839562.8 53.181318 53.181318 3000 152.12501 152.12501 -4.2378439 -4.2378439 302.49455 302.49455 15214852 15214852 10.619356 10.619356 Loop time of 0.902487 on 1 procs for 1000 steps with 4000 atoms Performance: 95.735 ns/day, 0.251 hours/ns, 1108.050 timesteps/s, 4.432 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48288 | 0.48288 | 0.48288 | 0.0 | 53.51 Neigh | 0.27593 | 0.27593 | 0.27593 | 0.0 | 30.57 Comm | 0.013852 | 0.013852 | 0.013852 | 0.0 | 1.53 Output | 3.4494e-05 | 3.4494e-05 | 3.4494e-05 | 0.0 | 0.00 Modify | 0.11774 | 0.11774 | 0.11774 | 0.0 | 13.05 Other | | 0.01205 | | | 1.34 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1047 ave 1047 max 1047 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 6168 ave 6168 max 6168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6168 Ave neighs/atom = 1.542 Neighbor list builds = 165 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.904324560215, Press = 71.415884172227 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 49 49 49 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.011 | 4.011 | 4.011 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 152.12501 152.12501 -4.2378439 -4.2378439 302.49455 302.49455 15214852 15214852 10.619356 10.619356 4000 163.68509 163.68509 -1.0865642 -1.0865642 318.76193 318.76193 79061967 79061967 2.2066494 2.2066494 Loop time of 0.750347 on 1 procs for 1000 steps with 4000 atoms Performance: 115.147 ns/day, 0.208 hours/ns, 1332.717 timesteps/s, 5.331 Matom-step/s 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24127 | 0.24127 | 0.24127 | 0.0 | 32.15 Neigh | 0.36492 | 0.36492 | 0.36492 | 0.0 | 48.63 Comm | 0.013598 | 0.013598 | 0.013598 | 0.0 | 1.81 Output | 4.4474e-05 | 4.4474e-05 | 4.4474e-05 | 0.0 | 0.01 Modify | 0.11757 | 0.11757 | 0.11757 | 0.0 | 15.67 Other | | 0.01295 | | | 1.73 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 580 ave 580 max 580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1498 ave 1498 max 1498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1498 Ave neighs/atom = 0.3745 Neighbor list builds = 270 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.925318639982, Press = 50.1239825376625 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 85 85 85 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.188 | 6.188 | 6.188 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 163.68509 163.68509 -1.0865642 -1.0865642 318.76193 318.76193 79061967 79061967 2.2066494 2.2066494 5000 165.46233 165.46233 -0.22536615 -0.22536615 320.53408 320.53408 3.9688633e+08 3.9688633e+08 0.44475193 0.44475193 Loop time of 1.46327 on 1 procs for 1000 steps with 4000 atoms Performance: 59.046 ns/day, 0.406 hours/ns, 683.400 timesteps/s, 2.734 Matom-step/s 90.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1678 | 0.1678 | 0.1678 | 0.0 | 11.47 Neigh | 1.1377 | 1.1377 | 1.1377 | 0.0 | 77.75 Comm | 0.022373 | 0.022373 | 0.022373 | 0.0 | 1.53 Output | 4.9653e-05 | 4.9653e-05 | 4.9653e-05 | 0.0 | 0.00 Modify | 0.11878 | 0.11878 | 0.11878 | 0.0 | 8.12 Other | | 0.01655 | | | 1.13 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 321 ave 321 max 321 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 396 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 396 Ave neighs/atom = 0.099 Neighbor list builds = 426 Dangerous builds = 0 if "${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 396886326.407593 A^3 has become larger than 143481684.999044 A^3. Aborting calculation. Total wall time: 0:00:11