# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 313.15*${_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_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 -209.34186 -209.34186 -371.21264 -371.21264 313.15 313.15 144997.99 144997.99 1192.4098 1192.4098 1000 85.787104 85.787104 -78.790976 -78.790976 318.38746 318.38746 521731.93 521731.93 157.6934 157.6934 Loop time of 4.8557 on 1 procs for 1000 steps with 4000 atoms Performance: 17.794 ns/day, 1.349 hours/ns, 205.944 timesteps/s, 823.774 katom-step/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0539 | 4.0539 | 4.0539 | 0.0 | 83.49 Neigh | 0.61083 | 0.61083 | 0.61083 | 0.0 | 12.58 Comm | 0.028457 | 0.028457 | 0.028457 | 0.0 | 0.59 Output | 9.029e-05 | 9.029e-05 | 9.029e-05 | 0.0 | 0.00 Modify | 0.14918 | 0.14918 | 0.14918 | 0.0 | 3.07 Other | | 0.01319 | | | 0.27 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3851 ave 3851 max 3851 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: 133594 ave 133594 max 133594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133594 Ave neighs/atom = 33.3985 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 = ${P}" flag: Temp = 313.597329255243, Press = 151.810897532875 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 16 16 16 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.848 | 3.848 | 3.848 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 85.787104 85.787104 -78.790976 -78.790976 318.38746 318.38746 521731.93 521731.93 157.6934 157.6934 2000 141.91709 141.91709 -21.236026 -21.236026 315.63076 315.63076 2370259.6 2370259.6 62.042367 62.042367 Loop time of 1.96819 on 1 procs for 1000 steps with 4000 atoms Performance: 43.898 ns/day, 0.547 hours/ns, 508.081 timesteps/s, 2.032 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2823 | 1.2823 | 1.2823 | 0.0 | 65.15 Neigh | 0.50739 | 0.50739 | 0.50739 | 0.0 | 25.78 Comm | 0.020898 | 0.020898 | 0.020898 | 0.0 | 1.06 Output | 6.3629e-05 | 6.3629e-05 | 6.3629e-05 | 0.0 | 0.00 Modify | 0.14491 | 0.14491 | 0.14491 | 0.0 | 7.36 Other | | 0.01261 | | | 0.64 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2082 ave 2082 max 2082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31934 ave 31934 max 31934 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31934 Ave neighs/atom = 7.9835 Neighbor list builds = 89 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.497965715243, Press = 112.753641182116 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 27 27 27 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.543 | 3.543 | 3.543 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 141.91709 141.91709 -21.236026 -21.236026 315.63076 315.63076 2370259.6 2370259.6 62.042367 62.042367 3000 155.67891 155.67891 -5.6278399 -5.6278399 312.05885 312.05885 12665295 12665295 12.953709 12.953709 Loop time of 0.859328 on 1 procs for 1000 steps with 4000 atoms Performance: 100.544 ns/day, 0.239 hours/ns, 1163.700 timesteps/s, 4.655 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39871 | 0.39871 | 0.39871 | 0.0 | 46.40 Neigh | 0.30806 | 0.30806 | 0.30806 | 0.0 | 35.85 Comm | 0.014806 | 0.014806 | 0.014806 | 0.0 | 1.72 Output | 5.872e-05 | 5.872e-05 | 5.872e-05 | 0.0 | 0.01 Modify | 0.12594 | 0.12594 | 0.12594 | 0.0 | 14.66 Other | | 0.01175 | | | 1.37 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1127 ave 1127 max 1127 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 7550 ave 7550 max 7550 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7550 Ave neighs/atom = 1.8875 Neighbor list builds = 157 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.753548132598, Press = 74.0962357689942 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 46 46 46 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.917 | 3.917 | 3.917 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 155.67891 155.67891 -5.6278399 -5.6278399 312.05885 312.05885 12665295 12665295 12.953709 12.953709 4000 159.8697 159.8697 -1.5706512 -1.5706512 312.31731 312.31731 66541587 66541587 2.5576328 2.5576328 Loop time of 0.697063 on 1 procs for 1000 steps with 4000 atoms Performance: 123.949 ns/day, 0.194 hours/ns, 1434.590 timesteps/s, 5.738 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20703 | 0.20703 | 0.20703 | 0.0 | 29.70 Neigh | 0.34558 | 0.34558 | 0.34558 | 0.0 | 49.58 Comm | 0.01467 | 0.01467 | 0.01467 | 0.0 | 2.10 Output | 6.4811e-05 | 6.4811e-05 | 6.4811e-05 | 0.0 | 0.01 Modify | 0.11713 | 0.11713 | 0.11713 | 0.0 | 16.80 Other | | 0.01259 | | | 1.81 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 621 ave 621 max 621 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1884 ave 1884 max 1884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1884 Ave neighs/atom = 0.471 Neighbor list builds = 259 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.850657656394, Press = 52.2673393282693 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 80 80 80 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.75 | 5.75 | 5.75 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 159.8697 159.8697 -1.5706512 -1.5706512 312.31731 312.31731 66541587 66541587 2.5576328 2.5576328 5000 160.32281 160.32281 -0.29833751 -0.29833751 310.7325 310.7325 3.364784e+08 3.364784e+08 0.50802109 0.50802109 Loop time of 1.17671 on 1 procs for 1000 steps with 4000 atoms Performance: 73.425 ns/day, 0.327 hours/ns, 849.826 timesteps/s, 3.399 Matom-step/s 96.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15151 | 0.15151 | 0.15151 | 0.0 | 12.88 Neigh | 0.87715 | 0.87715 | 0.87715 | 0.0 | 74.54 Comm | 0.016074 | 0.016074 | 0.016074 | 0.0 | 1.37 Output | 4.5596e-05 | 4.5596e-05 | 4.5596e-05 | 0.0 | 0.00 Modify | 0.11683 | 0.11683 | 0.11683 | 0.0 | 9.93 Other | | 0.01511 | | | 1.28 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 352 ave 352 max 352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 464 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 464 Ave neighs/atom = 0.116 Neighbor list builds = 413 Dangerous builds = 0 if "${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 336478401.176083 A^3 has become larger than 144997991.28488 A^3. Aborting calculation. Total wall time: 0:00:09