# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.253563612699509*${_u_distance} variable latticeconst_converted equal 5.253563612699509*1 lattice fcc ${latticeconst_converted} lattice fcc 5.25356361269951 Lattice spacing in x,y,z = 5.2535636 5.2535636 5.2535636 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.535636 52.535636 52.535636) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.535636 52.535636 52.535636) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim Morse_Shifted_Jelinek_1972_Ar__MO_831902330215_004 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 144997.99128488 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144997.99128488/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144997.99128488/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 144997.99128488/(1*1*${_u_distance}) variable V0_metal equal 144997.99128488/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 144997.99128488*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 144997.99128488 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 333.15*${_u_temperature} variable temp_converted equal 333.15*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 333.15 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 333.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "333.15 - 1.0" variable T_up equal "333.15 + 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_831902330215_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 = 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 -199.00363 -199.00363 -371.21264 -371.21264 333.15 333.15 144997.99 144997.99 1268.5656 1268.5656 1000 103.68679 103.68679 -71.403244 -71.403244 338.72354 338.72354 570919 570919 175.66994 175.66994 Loop time of 4.43789 on 1 procs for 1000 steps with 4000 atoms Performance: 19.469 ns/day, 1.233 hours/ns, 225.332 timesteps/s, 901.329 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 | 3.6857 | 3.6857 | 3.6857 | 0.0 | 83.05 Neigh | 0.58767 | 0.58767 | 0.58767 | 0.0 | 13.24 Comm | 0.024681 | 0.024681 | 0.024681 | 0.0 | 0.56 Output | 7.0913e-05 | 7.0913e-05 | 7.0913e-05 | 0.0 | 0.00 Modify | 0.1277 | 0.1277 | 0.1277 | 0.0 | 2.88 Other | | 0.01202 | | | 0.27 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3744 ave 3744 max 3744 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: 124650 ave 124650 max 124650 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124650 Ave neighs/atom = 31.1625 Neighbor list builds = 54 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 = ${P}" flag: Temp = 333.766929452944, Press = 175.210579344278 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.853 | 3.853 | 3.853 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 103.68679 103.68679 -71.403244 -71.403244 338.72354 338.72354 570919 570919 175.66994 175.66994 2000 152.78533 152.78533 -18.928723 -18.928723 332.19248 332.19248 2723880.2 2723880.2 57.509715 57.509715 Loop time of 1.47402 on 1 procs for 1000 steps with 4000 atoms Performance: 58.615 ns/day, 0.409 hours/ns, 678.416 timesteps/s, 2.714 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.92838 | 0.92838 | 0.92838 | 0.0 | 62.98 Neigh | 0.40336 | 0.40336 | 0.40336 | 0.0 | 27.36 Comm | 0.016268 | 0.016268 | 0.016268 | 0.0 | 1.10 Output | 4.1868e-05 | 4.1868e-05 | 4.1868e-05 | 0.0 | 0.00 Modify | 0.1157 | 0.1157 | 0.1157 | 0.0 | 7.85 Other | | 0.01027 | | | 0.70 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2023 ave 2023 max 2023 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 28102 ave 28102 max 28102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28102 Ave neighs/atom = 7.0255 Neighbor list builds = 95 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.969305818594, Press = 119.153058882317 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 28 28 28 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.555 | 3.555 | 3.555 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 152.78533 152.78533 -18.928723 -18.928723 332.19248 332.19248 2723880.2 2723880.2 57.509715 57.509715 3000 164.41693 164.41693 -5.0218949 -5.0218949 327.7909 327.7909 14540540 14540540 11.981285 11.981285 Loop time of 0.75412 on 1 procs for 1000 steps with 4000 atoms Performance: 114.571 ns/day, 0.209 hours/ns, 1326.049 timesteps/s, 5.304 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33643 | 0.33643 | 0.33643 | 0.0 | 44.61 Neigh | 0.27747 | 0.27747 | 0.27747 | 0.0 | 36.79 Comm | 0.013672 | 0.013672 | 0.013672 | 0.0 | 1.81 Output | 2.8043e-05 | 2.8043e-05 | 2.8043e-05 | 0.0 | 0.00 Modify | 0.11575 | 0.11575 | 0.11575 | 0.0 | 15.35 Other | | 0.01076 | | | 1.43 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1066 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 6494 ave 6494 max 6494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6494 Ave neighs/atom = 1.6235 Neighbor list builds = 163 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.742248458478, Press = 76.6222595293487 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 49 49 49 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.011 | 4.011 | 4.011 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 164.41693 164.41693 -5.0218949 -5.0218949 327.7909 327.7909 14540540 14540540 11.981285 11.981285 4000 171.98807 171.98807 -1.2109136 -1.2109136 335.06518 335.06518 75772929 75772929 2.4167057 2.4167057 Loop time of 0.752421 on 1 procs for 1000 steps with 4000 atoms Performance: 114.829 ns/day, 0.209 hours/ns, 1329.043 timesteps/s, 5.316 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20997 | 0.20997 | 0.20997 | 0.0 | 27.91 Neigh | 0.39029 | 0.39029 | 0.39029 | 0.0 | 51.87 Comm | 0.014441 | 0.014441 | 0.014441 | 0.0 | 1.92 Output | 4.5927e-05 | 4.5927e-05 | 4.5927e-05 | 0.0 | 0.01 Modify | 0.12443 | 0.12443 | 0.12443 | 0.0 | 16.54 Other | | 0.01324 | | | 1.76 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 607 ave 607 max 607 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1610 ave 1610 max 1610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1610 Ave neighs/atom = 0.4025 Neighbor list builds = 266 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.851890000513, Press = 53.8406258505014 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 84 84 84 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.096 | 6.096 | 6.096 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 171.98807 171.98807 -1.2109136 -1.2109136 335.06518 335.06518 75772929 75772929 2.4167057 2.4167057 5000 174.05459 174.05459 -0.20976197 -0.20976197 337.12621 337.12621 3.8152521e+08 3.8152521e+08 0.48669226 0.48669226 Loop time of 1.51999 on 1 procs for 1000 steps with 4000 atoms Performance: 56.842 ns/day, 0.422 hours/ns, 657.898 timesteps/s, 2.632 Matom-step/s 98.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18265 | 0.18265 | 0.18265 | 0.0 | 12.02 Neigh | 1.1479 | 1.1479 | 1.1479 | 0.0 | 75.52 Comm | 0.024416 | 0.024416 | 0.024416 | 0.0 | 1.61 Output | 4.8912e-05 | 4.8912e-05 | 4.8912e-05 | 0.0 | 0.00 Modify | 0.14619 | 0.14619 | 0.14619 | 0.0 | 9.62 Other | | 0.01876 | | | 1.23 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 354 ave 354 max 354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 328 ave 328 max 328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328 Ave neighs/atom = 0.082 Neighbor list builds = 419 Dangerous builds = 0 if "${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 381525205.86715 A^3 has become larger than 144997991.28488 A^3. Aborting calculation. Total wall time: 0:00:09