# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 273.15*${_u_temperature} variable temp_converted equal 273.15*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 273.15 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 273.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "273.15 - 1.0" variable T_up equal "273.15 + 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 -43748.71 -43748.71 -43819.289 -43819.289 273.15 273.15 38208.068 38208.068 1973.1365 1973.1365 1000 -44570.615 -44570.615 -44646.143 -44646.143 292.30182 292.30182 37905.225 37905.225 -1121.3647 -1121.3647 Loop time of 15.1368 on 1 procs for 1000 steps with 2000 atoms Performance: 5.708 ns/day, 4.205 hours/ns, 66.064 timesteps/s, 132.128 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 | 14.775 | 14.775 | 14.775 | 0.0 | 97.61 Neigh | 0.20791 | 0.20791 | 0.20791 | 0.0 | 1.37 Comm | 0.072125 | 0.072125 | 0.072125 | 0.0 | 0.48 Output | 6.2407e-05 | 6.2407e-05 | 6.2407e-05 | 0.0 | 0.00 Modify | 0.065931 | 0.065931 | 0.065931 | 0.0 | 0.44 Other | | 0.01593 | | | 0.11 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20050 ave 20050 max 20050 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: 3.8297e+06 ave 3.8297e+06 max 3.8297e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3829700 Ave neighs/atom = 1914.85 Neighbor list builds = 3 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 = ${P}" flag: Temp = 267.963874071346, Press = 30.0935456466016 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 21.44 | 21.44 | 21.44 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -44570.615 -44570.615 -44646.143 -44646.143 292.30182 292.30182 37905.225 37905.225 -1121.3647 -1121.3647 2000 -44650.581 -44650.581 -44718.14 -44718.14 261.45894 261.45894 37857.605 37857.605 3195.6975 3195.6975 Loop time of 14.9754 on 1 procs for 1000 steps with 2000 atoms Performance: 5.769 ns/day, 4.160 hours/ns, 66.776 timesteps/s, 133.552 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.752 | 14.752 | 14.752 | 0.0 | 98.51 Neigh | 0.068405 | 0.068405 | 0.068405 | 0.0 | 0.46 Comm | 0.069032 | 0.069032 | 0.069032 | 0.0 | 0.46 Output | 5.5204e-05 | 5.5204e-05 | 5.5204e-05 | 0.0 | 0.00 Modify | 0.070369 | 0.070369 | 0.070369 | 0.0 | 0.47 Other | | 0.01539 | | | 0.10 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20062 ave 20062 max 20062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3.83417e+06 ave 3.83417e+06 max 3.83417e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3834170 Ave neighs/atom = 1917.085 Neighbor list builds = 1 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 273.567943042277, Press = 6.26152282212112 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 21.44 | 21.44 | 21.44 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -44650.581 -44650.581 -44718.14 -44718.14 261.45894 261.45894 37857.605 37857.605 3195.6975 3195.6975 3000 -44642.533 -44642.533 -44712.669 -44712.669 271.43406 271.43406 37879.785 37879.785 -3494.2814 -3494.2814 Loop time of 14.7521 on 1 procs for 1000 steps with 2000 atoms Performance: 5.857 ns/day, 4.098 hours/ns, 67.787 timesteps/s, 135.574 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.598 | 14.598 | 14.598 | 0.0 | 98.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.068638 | 0.068638 | 0.068638 | 0.0 | 0.47 Output | 5.6526e-05 | 5.6526e-05 | 5.6526e-05 | 0.0 | 0.00 Modify | 0.069635 | 0.069635 | 0.069635 | 0.0 | 0.47 Other | | 0.01542 | | | 0.10 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20074 ave 20074 max 20074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3.83298e+06 ave 3.83298e+06 max 3.83298e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3832982 Ave neighs/atom = 1916.491 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 273.140571995, Press = -8.4336139684757 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 21.44 | 21.44 | 21.44 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -44642.533 -44642.533 -44712.669 -44712.669 271.43406 271.43406 37879.785 37879.785 -3494.2814 -3494.2814 4000 -44645.057 -44645.057 -44713.244 -44713.244 263.89122 263.89122 37889.755 37889.755 -7826.9825 -7826.9825 Loop time of 14.6553 on 1 procs for 1000 steps with 2000 atoms Performance: 5.895 ns/day, 4.071 hours/ns, 68.234 timesteps/s, 136.469 katom-step/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.505 | 14.505 | 14.505 | 0.0 | 98.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.067961 | 0.067961 | 0.067961 | 0.0 | 0.46 Output | 5.6436e-05 | 5.6436e-05 | 5.6436e-05 | 0.0 | 0.00 Modify | 0.06812 | 0.06812 | 0.06812 | 0.0 | 0.46 Other | | 0.01459 | | | 0.10 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20041 ave 20041 max 20041 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3.83055e+06 ave 3.83055e+06 max 3.83055e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3830546 Ave neighs/atom = 1915.273 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T273.15.out" else "print 'not_converged' file output/vol_T273.15.out" print '${V}' file output/vol_T273.15.out 37872.4579297368 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0