# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.252865672111511*${_u_distance} variable latticeconst_converted equal 5.252865672111511*1 lattice fcc ${latticeconst_converted} lattice fcc 5.25286567211151 Lattice spacing in x,y,z = 5.2528657 5.2528657 5.2528657 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.528657 52.528657 52.528657) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.528657 52.528657 52.528657) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim Morse_QuinticSmoothed_Jelinek_1972_Ar__MO_908645784389_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 144940.209626461 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144940.209626461/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144940.209626461/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 144940.209626461/(1*1*${_u_distance}) variable V0_metal equal 144940.209626461/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 144940.209626461*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 144940.209626461 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_908645784389_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 -223.09762 -223.09762 -374.63018 -374.63018 293.15 293.15 144940.21 144940.21 1116.6992 1116.6992 1000 62.050325 62.050325 -90.233564 -90.233564 294.60351 294.60351 465988.87 465988.87 128.97411 128.97411 Loop time of 4.68363 on 1 procs for 1000 steps with 4000 atoms Performance: 18.447 ns/day, 1.301 hours/ns, 213.509 timesteps/s, 854.038 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 | 4.026 | 4.026 | 4.026 | 0.0 | 85.96 Neigh | 0.49869 | 0.49869 | 0.49869 | 0.0 | 10.65 Comm | 0.02395 | 0.02395 | 0.02395 | 0.0 | 0.51 Output | 7.994e-05 | 7.994e-05 | 7.994e-05 | 0.0 | 0.00 Modify | 0.12331 | 0.12331 | 0.12331 | 0.0 | 2.63 Other | | 0.01158 | | | 0.25 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4027 ave 4027 max 4027 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: 149612 ave 149612 max 149612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149612 Ave neighs/atom = 37.403 Neighbor list builds = 46 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 = ${P}" flag: Temp = 291.696516297869, Press = 121.930888109935 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 16 16 16 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.85 | 3.85 | 3.85 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 62.050325 62.050325 -90.233564 -90.233564 294.60351 294.60351 465988.87 465988.87 128.97411 128.97411 2000 124.98504 124.98504 -26.462862 -26.462862 292.98623 292.98623 1948762.5 1948762.5 65.119496 65.119496 Loop time of 1.81404 on 1 procs for 1000 steps with 4000 atoms Performance: 47.628 ns/day, 0.504 hours/ns, 551.255 timesteps/s, 2.205 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2682 | 1.2682 | 1.2682 | 0.0 | 69.91 Neigh | 0.40212 | 0.40212 | 0.40212 | 0.0 | 22.17 Comm | 0.017047 | 0.017047 | 0.017047 | 0.0 | 0.94 Output | 4.8962e-05 | 4.8962e-05 | 4.8962e-05 | 0.0 | 0.00 Modify | 0.11657 | 0.11657 | 0.11657 | 0.0 | 6.43 Other | | 0.01003 | | | 0.55 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2258 ave 2258 max 2258 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 38252 ave 38252 max 38252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38252 Ave neighs/atom = 9.563 Neighbor list builds = 81 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.800797285184, Press = 103.803211953588 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 25 25 25 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.522 | 3.522 | 3.522 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 124.98504 124.98504 -26.462862 -26.462862 292.98623 292.98623 1948762.5 1948762.5 65.119496 65.119496 3000 146.18815 146.18815 -7.5459026 -7.5459026 297.40895 297.40895 10372621 10372621 14.900353 14.900353 Loop time of 0.854859 on 1 procs for 1000 steps with 4000 atoms Performance: 101.069 ns/day, 0.237 hours/ns, 1169.784 timesteps/s, 4.679 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41937 | 0.41937 | 0.41937 | 0.0 | 49.06 Neigh | 0.2939 | 0.2939 | 0.2939 | 0.0 | 34.38 Comm | 0.013964 | 0.013964 | 0.013964 | 0.0 | 1.63 Output | 3.78e-05 | 3.78e-05 | 3.78e-05 | 0.0 | 0.00 Modify | 0.11699 | 0.11699 | 0.11699 | 0.0 | 13.69 Other | | 0.01059 | | | 1.24 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1203 ave 1203 max 1203 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 9244 ave 9244 max 9244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9244 Ave neighs/atom = 2.311 Neighbor list builds = 148 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.890231816581, Press = 70.9306760352534 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 43 43 43 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.833 | 3.833 | 3.833 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 146.18815 146.18815 -7.5459026 -7.5459026 297.40895 297.40895 10372621 10372621 14.900353 14.900353 4000 150.08136 150.08136 -1.7977775 -1.7977775 293.8205 293.8205 54624376 54624376 2.9224677 2.9224677 Loop time of 0.684585 on 1 procs for 1000 steps with 4000 atoms Performance: 126.208 ns/day, 0.190 hours/ns, 1460.738 timesteps/s, 5.843 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2168 | 0.2168 | 0.2168 | 0.0 | 31.67 Neigh | 0.32489 | 0.32489 | 0.32489 | 0.0 | 47.46 Comm | 0.013807 | 0.013807 | 0.013807 | 0.0 | 2.02 Output | 4.5235e-05 | 4.5235e-05 | 4.5235e-05 | 0.0 | 0.01 Modify | 0.11689 | 0.11689 | 0.11689 | 0.0 | 17.07 Other | | 0.01215 | | | 1.77 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 651 ave 651 max 651 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2416 ave 2416 max 2416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2416 Ave neighs/atom = 0.604 Neighbor list builds = 241 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.8136501213, Press = 50.3813743394576 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 75 75 75 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.36 | 5.36 | 5.36 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 150.08136 150.08136 -1.7977775 -1.7977775 293.8205 293.8205 54624376 54624376 2.9224677 2.9224677 5000 151.19331 151.19331 -0.38257322 -0.38257322 293.23383 293.23383 2.7864923e+08 2.7864923e+08 0.5782677 0.5782677 Loop time of 1.07804 on 1 procs for 1000 steps with 4000 atoms Performance: 80.145 ns/day, 0.299 hours/ns, 927.608 timesteps/s, 3.710 Matom-step/s 96.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15102 | 0.15102 | 0.15102 | 0.0 | 14.01 Neigh | 0.77821 | 0.77821 | 0.77821 | 0.0 | 72.19 Comm | 0.01566 | 0.01566 | 0.01566 | 0.0 | 1.45 Output | 3.8492e-05 | 3.8492e-05 | 3.8492e-05 | 0.0 | 0.00 Modify | 0.11788 | 0.11788 | 0.11788 | 0.0 | 10.94 Other | | 0.01523 | | | 1.41 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 368 ave 368 max 368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 574 ave 574 max 574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 574 Ave neighs/atom = 0.1435 Neighbor list builds = 390 Dangerous builds = 0 if "${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 278649230.122041 A^3 has become larger than 144940209.626461 A^3. Aborting calculation. Total wall time: 0:00:09