# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.24417295455933*${_u_distance} variable latticeconst_converted equal 5.24417295455933*1 lattice fcc ${latticeconst_converted} lattice fcc 5.24417295455933 Lattice spacing in x,y,z = 5.244173 5.244173 5.244173 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.44173 52.44173 52.44173) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.44173 52.44173 52.44173) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958HighCutoff_Ar__MO_242741380554_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 144221.835764993 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144221.835764993/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144221.835764993/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 144221.835764993/(1*1*${_u_distance}) variable V0_metal equal 144221.835764993/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 144221.835764993*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 144221.835764993 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_242741380554_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 = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 5 5 5 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) = 24.97 | 24.97 | 24.97 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -192.52791 -192.52791 -354.39869 -354.39869 313.15 313.15 144221.84 144221.84 1198.8265 1198.8265 1000 90.072339 90.072339 -72.328325 -72.328325 314.1751 314.1751 572730.83 572730.83 155.08682 155.08682 Loop time of 57.3389 on 1 procs for 1000 steps with 4000 atoms Performance: 1.507 ns/day, 15.927 hours/ns, 17.440 timesteps/s, 69.761 katom-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 | 53.727 | 53.727 | 53.727 | 0.0 | 93.70 Neigh | 3.3511 | 3.3511 | 3.3511 | 0.0 | 5.84 Comm | 0.07506 | 0.07506 | 0.07506 | 0.0 | 0.13 Output | 0.00016211 | 0.00016211 | 0.00016211 | 0.0 | 0.00 Modify | 0.15718 | 0.15718 | 0.15718 | 0.0 | 0.27 Other | | 0.02808 | | | 0.05 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10369 ave 10369 max 10369 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: 1.22823e+06 ave 1.22823e+06 max 1.22823e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1228228 Ave neighs/atom = 307.057 Neighbor list builds = 55 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 = ${P}" flag: Temp = 312.295667899521, Press = 155.123856443404 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 11.41 | 11.41 | 11.41 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 90.072339 90.072339 -72.328325 -72.328325 314.1751 314.1751 572730.83 572730.83 155.08682 155.08682 2000 144.20491 144.20491 -17.076784 -17.076784 312.01038 312.01038 2687606.2 2687606.2 55.094441 55.094441 Loop time of 16.6484 on 1 procs for 1000 steps with 4000 atoms Performance: 5.190 ns/day, 4.625 hours/ns, 60.066 timesteps/s, 240.263 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.539 | 14.539 | 14.539 | 0.0 | 87.33 Neigh | 1.8746 | 1.8746 | 1.8746 | 0.0 | 11.26 Comm | 0.04818 | 0.04818 | 0.04818 | 0.0 | 0.29 Output | 8.521e-05 | 8.521e-05 | 8.521e-05 | 0.0 | 0.00 Modify | 0.16173 | 0.16173 | 0.16173 | 0.0 | 0.97 Other | | 0.02454 | | | 0.15 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5104 ave 5104 max 5104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 265390 ave 265390 max 265390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 265390 Ave neighs/atom = 66.3475 Neighbor list builds = 95 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.693315920749, Press = 109.973077335025 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 13 13 13 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.571 | 7.571 | 7.571 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 144.20491 144.20491 -17.076784 -17.076784 312.01038 312.01038 2687606.2 2687606.2 55.094441 55.094441 3000 159.9141 159.9141 -4.1325858 -4.1325858 317.35944 317.35944 14458189 14458189 11.748271 11.748271 Loop time of 4.60201 on 1 procs for 1000 steps with 4000 atoms Performance: 18.774 ns/day, 1.278 hours/ns, 217.297 timesteps/s, 869.186 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.14 | 3.14 | 3.14 | 0.0 | 68.23 Neigh | 1.2631 | 1.2631 | 1.2631 | 0.0 | 27.45 Comm | 0.032537 | 0.032537 | 0.032537 | 0.0 | 0.71 Output | 5.2539e-05 | 5.2539e-05 | 5.2539e-05 | 0.0 | 0.00 Modify | 0.14758 | 0.14758 | 0.14758 | 0.0 | 3.21 Other | | 0.01876 | | | 0.41 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2527 ave 2527 max 2527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52902 ave 52902 max 52902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52902 Ave neighs/atom = 13.2255 Neighbor list builds = 163 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.875994859654, Press = 71.2216400789237 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 23 23 23 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.85 | 6.85 | 6.85 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 159.9141 159.9141 -4.1325858 -4.1325858 317.35944 317.35944 14458189 14458189 11.748271 11.748271 4000 161.33574 161.33574 -1.0199362 -1.0199362 314.08806 314.08806 75283619 75283619 2.2953488 2.2953488 Loop time of 1.90913 on 1 procs for 1000 steps with 4000 atoms Performance: 45.256 ns/day, 0.530 hours/ns, 523.799 timesteps/s, 2.095 Matom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.91408 | 0.91408 | 0.91408 | 0.0 | 47.88 Neigh | 0.80759 | 0.80759 | 0.80759 | 0.0 | 42.30 Comm | 0.028355 | 0.028355 | 0.028355 | 0.0 | 1.49 Output | 4.6027e-05 | 4.6027e-05 | 4.6027e-05 | 0.0 | 0.00 Modify | 0.14176 | 0.14176 | 0.14176 | 0.0 | 7.43 Other | | 0.0173 | | | 0.91 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1373 ave 1373 max 1373 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11284 ave 11284 max 11284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11284 Ave neighs/atom = 2.821 Neighbor list builds = 264 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.730024692469, Press = 50.0774623171604 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 39 39 39 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.082 | 7.082 | 7.082 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 161.33574 161.33574 -1.0199362 -1.0199362 314.08806 314.08806 75283619 75283619 2.2953488 2.2953488 5000 162.94558 162.94558 -0.24226005 -0.24226005 315.69794 315.69794 3.7920645e+08 3.7920645e+08 0.45905706 0.45905706 Loop time of 1.34592 on 1 procs for 1000 steps with 4000 atoms Performance: 64.194 ns/day, 0.374 hours/ns, 742.985 timesteps/s, 2.972 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4425 | 0.4425 | 0.4425 | 0.0 | 32.88 Neigh | 0.71488 | 0.71488 | 0.71488 | 0.0 | 53.11 Comm | 0.028694 | 0.028694 | 0.028694 | 0.0 | 2.13 Output | 4.7569e-05 | 4.7569e-05 | 4.7569e-05 | 0.0 | 0.00 Modify | 0.14049 | 0.14049 | 0.14049 | 0.0 | 10.44 Other | | 0.0193 | | | 1.43 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 778 ave 778 max 778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2580 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2580 Ave neighs/atom = 0.645 Neighbor list builds = 417 Dangerous builds = 0 if "${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 379206446.847352 A^3 has become larger than 144221835.764993 A^3. Aborting calculation. Total wall time: 0:01:22