# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.292160376906395*${_u_distance} variable latticeconst_converted equal 5.292160376906395*1 lattice fcc ${latticeconst_converted} lattice fcc 5.29216037690639 Lattice spacing in x,y,z = 5.2921604 5.2921604 5.2921604 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.921604 52.921604 52.921604) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.921604 52.921604 52.921604) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Smoothed_Bernardes_1958_Ar__MO_764178710049_001 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 148217.331689156 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 148217.331689156/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 148217.331689156/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 148217.331689156/(1*1*${_u_distance}) variable V0_metal equal 148217.331689156/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 148217.331689156*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 148217.331689156 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 253.15*${_u_temperature} variable temp_converted equal 253.15*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 253.15 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 253.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "253.15 - 1.0" variable T_up equal "253.15 + 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_764178710049_001#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 = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, 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 -152.17465 -152.17465 -283.03075 -283.03075 253.15 253.15 148217.33 148217.33 943.00496 943.00496 1000 70.174054 70.174054 -58.743908 -58.743908 249.40054 249.40054 549409.49 549409.49 113.50089 113.50089 Loop time of 7.34833 on 1 procs for 1000 steps with 4000 atoms Performance: 11.758 ns/day, 2.041 hours/ns, 136.085 timesteps/s, 544.341 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 | 6.4436 | 6.4436 | 6.4436 | 0.0 | 87.69 Neigh | 0.69778 | 0.69778 | 0.69778 | 0.0 | 9.50 Comm | 0.031687 | 0.031687 | 0.031687 | 0.0 | 0.43 Output | 0.00011049 | 0.00011049 | 0.00011049 | 0.0 | 0.00 Modify | 0.16001 | 0.16001 | 0.16001 | 0.0 | 2.18 Other | | 0.01519 | | | 0.21 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3960 ave 3960 max 3960 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: 142014 ave 142014 max 142014 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142014 Ave neighs/atom = 35.5035 Neighbor list builds = 51 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 = ${P}" flag: Temp = 253.065206010749, Press = 114.840420254581 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 16 16 16 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.849 | 3.849 | 3.849 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 70.174054 70.174054 -58.743908 -58.743908 249.40054 249.40054 549409.49 549409.49 113.50089 113.50089 2000 113.87456 113.87456 -14.71694 -14.71694 248.76897 248.76897 2502749.9 2502749.9 47.056804 47.056804 Loop time of 2.62156 on 1 procs for 1000 steps with 4000 atoms Performance: 32.957 ns/day, 0.728 hours/ns, 381.452 timesteps/s, 1.526 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8956 | 1.8956 | 1.8956 | 0.0 | 72.31 Neigh | 0.54143 | 0.54143 | 0.54143 | 0.0 | 20.65 Comm | 0.022426 | 0.022426 | 0.022426 | 0.0 | 0.86 Output | 6.2037e-05 | 6.2037e-05 | 6.2037e-05 | 0.0 | 0.00 Modify | 0.14861 | 0.14861 | 0.14861 | 0.0 | 5.67 Other | | 0.01341 | | | 0.51 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2130 ave 2130 max 2130 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32680 ave 32680 max 32680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32680 Ave neighs/atom = 8.17 Neighbor list builds = 92 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.610909945922, Press = 87.3992138156428 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 26 26 26 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.532 | 3.532 | 3.532 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 113.87456 113.87456 -14.71694 -14.71694 248.76897 248.76897 2502749.9 2502749.9 47.056804 47.056804 3000 128.69637 128.69637 -3.9249369 -3.9249369 256.56492 256.56492 13488058 13488058 10.061217 10.061217 Loop time of 1.17156 on 1 procs for 1000 steps with 4000 atoms Performance: 73.748 ns/day, 0.325 hours/ns, 853.562 timesteps/s, 3.414 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63123 | 0.63123 | 0.63123 | 0.0 | 53.88 Neigh | 0.36479 | 0.36479 | 0.36479 | 0.0 | 31.14 Comm | 0.017207 | 0.017207 | 0.017207 | 0.0 | 1.47 Output | 5.9401e-05 | 5.9401e-05 | 5.9401e-05 | 0.0 | 0.01 Modify | 0.14467 | 0.14467 | 0.14467 | 0.0 | 12.35 Other | | 0.0136 | | | 1.16 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1143 ave 1143 max 1143 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 7318 ave 7318 max 7318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7318 Ave neighs/atom = 1.8295 Neighbor list builds = 161 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.673672741869, Press = 57.4417349593417 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 46 46 46 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.917 | 3.917 | 3.917 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 128.69637 128.69637 -3.9249369 -3.9249369 256.56492 256.56492 13488058 13488058 10.061217 10.061217 4000 129.4959 129.4959 -0.9996045 -0.9996045 252.45239 252.45239 70563421 70563421 1.952236 1.952236 Loop time of 0.939115 on 1 procs for 1000 steps with 4000 atoms Performance: 92.002 ns/day, 0.261 hours/ns, 1064.832 timesteps/s, 4.259 Matom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33541 | 0.33541 | 0.33541 | 0.0 | 35.72 Neigh | 0.4261 | 0.4261 | 0.4261 | 0.0 | 45.37 Comm | 0.016866 | 0.016866 | 0.016866 | 0.0 | 1.80 Output | 5.7016e-05 | 5.7016e-05 | 5.7016e-05 | 0.0 | 0.01 Modify | 0.14561 | 0.14561 | 0.14561 | 0.0 | 15.51 Other | | 0.01507 | | | 1.60 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 615 ave 615 max 615 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1792 ave 1792 max 1792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1792 Ave neighs/atom = 0.448 Neighbor list builds = 261 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.759038249547, Press = 40.4876491106912 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 79 79 79 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.668 | 5.668 | 5.668 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 129.4959 129.4959 -0.9996045 -0.9996045 252.45239 252.45239 70563421 70563421 1.952236 1.952236 5000 130.81314 130.81314 -0.21503686 -0.21503686 253.4829 253.4829 3.5604462e+08 3.5604462e+08 0.39190313 0.39190313 Loop time of 1.2683 on 1 procs for 1000 steps with 4000 atoms Performance: 68.123 ns/day, 0.352 hours/ns, 788.455 timesteps/s, 3.154 Matom-step/s 97.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20917 | 0.20917 | 0.20917 | 0.0 | 16.49 Neigh | 0.89437 | 0.89437 | 0.89437 | 0.0 | 70.52 Comm | 0.017584 | 0.017584 | 0.017584 | 0.0 | 1.39 Output | 3.9093e-05 | 3.9093e-05 | 3.9093e-05 | 0.0 | 0.00 Modify | 0.13078 | 0.13078 | 0.13078 | 0.0 | 10.31 Other | | 0.01635 | | | 1.29 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 350 ave 350 max 350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 458 Ave neighs/atom = 0.1145 Neighbor list builds = 412 Dangerous builds = 0 if "${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 356044617.74239 A^3 has become larger than 148217331.689156 A^3. Aborting calculation. Total wall time: 0:00:13