# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.368100389838219*${_u_distance} variable latticeconst_converted equal 3.368100389838219*1 lattice bcc ${latticeconst_converted} lattice bcc 3.36810038983822 Lattice spacing in x,y,z = 3.3681004 3.3681004 3.3681004 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (33.681004 33.681004 33.681004) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (33.681004 33.681004 33.681004) create_atoms CPU = 0.000 seconds variable mass_converted equal 50.9415*${_u_mass} variable mass_converted equal 50.9415*1 kim interactions V #=== BEGIN kim interactions ================================== pair_style kim LJ_ElliottAkerson_2015_Universal__MO_959249795837_003 pair_coeff * * V #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 50.9415 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 38208.068427331 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 38208.068427331/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 38208.068427331/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 38208.068427331/(1*1*${_u_distance}) variable V0_metal equal 38208.068427331/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 38208.068427331*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 38208.068427331 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_959249795837_003#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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 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) = 21.19 | 21.19 | 21.19 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -43743.542 -43743.542 -43819.289 -43819.289 293.15 293.15 38208.068 38208.068 2117.6044 2117.6044 1000 -44569.923 -44569.923 -44647.939 -44647.939 301.93053 301.93053 37901.987 37901.987 -312.49864 -312.49864 Loop time of 15.2026 on 1 procs for 1000 steps with 2000 atoms Performance: 5.683 ns/day, 4.223 hours/ns, 65.778 timesteps/s, 131.557 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 | 14.752 | 14.752 | 14.752 | 0.0 | 97.04 Neigh | 0.29141 | 0.29141 | 0.29141 | 0.0 | 1.92 Comm | 0.073353 | 0.073353 | 0.073353 | 0.0 | 0.48 Output | 9.8335e-05 | 9.8335e-05 | 9.8335e-05 | 0.0 | 0.00 Modify | 0.068759 | 0.068759 | 0.068759 | 0.0 | 0.45 Other | | 0.01651 | | | 0.11 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20052 ave 20052 max 20052 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: 3.82787e+06 ave 3.82787e+06 max 3.82787e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3827874 Ave neighs/atom = 1913.937 Neighbor list builds = 4 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 = ${P}" flag: Temp = 287.329745773601, Press = -27.1250582109263 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 21.44 | 21.44 | 21.44 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -44569.923 -44569.923 -44647.939 -44647.939 301.93053 301.93053 37901.987 37901.987 -312.49864 -312.49864 2000 -44584.458 -44584.458 -44657.654 -44657.654 283.2738 283.2738 37906.643 37906.643 -3542.5034 -3542.5034 Loop time of 14.767 on 1 procs for 1000 steps with 2000 atoms Performance: 5.851 ns/day, 4.102 hours/ns, 67.719 timesteps/s, 135.437 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.61 | 14.61 | 14.61 | 0.0 | 98.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.069205 | 0.069205 | 0.069205 | 0.0 | 0.47 Output | 6.1595e-05 | 6.1595e-05 | 6.1595e-05 | 0.0 | 0.00 Modify | 0.071728 | 0.071728 | 0.071728 | 0.0 | 0.49 Other | | 0.01551 | | | 0.11 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19998 ave 19998 max 19998 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3.83026e+06 ave 3.83026e+06 max 3.83026e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3830262 Ave neighs/atom = 1915.131 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 291.809471555437, Press = -3.72340108263587 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 21.44 | 21.44 | 21.44 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -44584.458 -44584.458 -44657.654 -44657.654 283.2738 283.2738 37906.643 37906.643 -3542.5034 -3542.5034 3000 -44579.338 -44579.338 -44657.522 -44657.522 302.57862 302.57862 37924.795 37924.795 -8215.4654 -8215.4654 Loop time of 14.6913 on 1 procs for 1000 steps with 2000 atoms Performance: 5.881 ns/day, 4.081 hours/ns, 68.067 timesteps/s, 136.135 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.536 | 14.536 | 14.536 | 0.0 | 98.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.068769 | 0.068769 | 0.068769 | 0.0 | 0.47 Output | 5.0354e-05 | 5.0354e-05 | 5.0354e-05 | 0.0 | 0.00 Modify | 0.070741 | 0.070741 | 0.070741 | 0.0 | 0.48 Other | | 0.01533 | | | 0.10 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20049 ave 20049 max 20049 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3.82869e+06 ave 3.82869e+06 max 3.82869e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3828692 Ave neighs/atom = 1914.346 Neighbor list builds = 0 Dangerous builds = 0 if "${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" jump SELF break # Write final averaged volume to file if temperature and volume have converged; otherwise wirte a # flag to indicate non-convergence. variable myStep equal step if "${myStep} < 2000000" then "print '${V}' file output/vol_T293.15.out" else "print 'not_converged' file output/vol_T293.15.out" print '${V}' file output/vol_T293.15.out 37902.6393105217 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0