# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.147414512932301*${_u_distance} variable latticeconst_converted equal 3.147414512932301*1 lattice bcc ${latticeconst_converted} lattice bcc 3.1474145129323 Lattice spacing in x,y,z = 3.1474145 3.1474145 3.1474145 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (31.474145 31.474145 31.474145) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (31.474145 31.474145 31.474145) create_atoms CPU = 0.000 seconds variable mass_converted equal 95.94*${_u_mass} variable mass_converted equal 95.94*1 kim interactions Mo #=== BEGIN kim interactions ================================== pair_style kim EAM_Dynamo_SmirnovaKuskinStarikov_2013_UMoXe__MO_679329885632_005 pair_coeff * * Mo #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 95.94 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 31178.9746672538 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 31178.9746672538/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 31178.9746672538/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 31178.9746672538/(1*1*${_u_distance}) variable V0_metal equal 31178.9746672538/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 31178.9746672538*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 31178.9746672538 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_679329885632_005#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 = 8.1960961 ghost atom cutoff = 8.1960961 binsize = 4.098048, 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) = 4.577 | 4.577 | 4.577 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -13793.33 -13793.33 -13858.742 -13858.742 253.15 253.15 31178.975 31178.975 2240.8545 2240.8545 1000 -13723.817 -13723.817 -13790.315 -13790.315 257.3529 257.3529 31278.823 31278.823 -1208.8337 -1208.8337 Loop time of 4.70583 on 1 procs for 1000 steps with 2000 atoms Performance: 18.360 ns/day, 1.307 hours/ns, 212.502 timesteps/s, 425.005 katom-step/s 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6178 | 4.6178 | 4.6178 | 0.0 | 98.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.019791 | 0.019791 | 0.019791 | 0.0 | 0.42 Output | 6.8879e-05 | 6.8879e-05 | 6.8879e-05 | 0.0 | 0.00 Modify | 0.061714 | 0.061714 | 0.061714 | 0.0 | 1.31 Other | | 0.006416 | | | 0.14 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5471 ave 5471 max 5471 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: 336000 ave 336000 max 336000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 336000 Ave neighs/atom = 168 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 = ${P}" flag: Temp = 253.061813448683, Press = 28.5166910314925 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1960961 ghost atom cutoff = 8.1960961 binsize = 4.098048, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.577 | 4.577 | 4.577 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -13723.817 -13723.817 -13790.315 -13790.315 257.3529 257.3529 31278.823 31278.823 -1208.8337 -1208.8337 2000 -13726.898 -13726.898 -13792.887 -13792.887 255.38499 255.38499 31271.079 31271.079 -460.14801 -460.14801 Loop time of 5.25228 on 1 procs for 1000 steps with 2000 atoms Performance: 16.450 ns/day, 1.459 hours/ns, 190.394 timesteps/s, 380.787 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1612 | 5.1612 | 5.1612 | 0.0 | 98.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.019606 | 0.019606 | 0.019606 | 0.0 | 0.37 Output | 3.3513e-05 | 3.3513e-05 | 3.3513e-05 | 0.0 | 0.00 Modify | 0.064956 | 0.064956 | 0.064956 | 0.0 | 1.24 Other | | 0.006455 | | | 0.12 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5471 ave 5471 max 5471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 307652 ave 307652 max 307652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 307652 Ave neighs/atom = 153.826 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 253.082095343624, Press = 6.60858285974311 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1960961 ghost atom cutoff = 8.1960961 binsize = 4.098048, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.577 | 4.577 | 4.577 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -13726.898 -13726.898 -13792.887 -13792.887 255.38499 255.38499 31271.079 31271.079 -460.14801 -460.14801 3000 -13722.379 -13722.379 -13790.382 -13790.382 263.1795 263.1795 31232.683 31232.683 4155.1596 4155.1596 Loop time of 5.31834 on 1 procs for 1000 steps with 2000 atoms Performance: 16.246 ns/day, 1.477 hours/ns, 188.028 timesteps/s, 376.057 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2279 | 5.2279 | 5.2279 | 0.0 | 98.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01968 | 0.01968 | 0.01968 | 0.0 | 0.37 Output | 4.8121e-05 | 4.8121e-05 | 4.8121e-05 | 0.0 | 0.00 Modify | 0.064291 | 0.064291 | 0.064291 | 0.0 | 1.21 Other | | 0.006419 | | | 0.12 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5471 ave 5471 max 5471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 308096 ave 308096 max 308096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 308096 Ave neighs/atom = 154.048 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.962075674231, Press = 7.94959864420982 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1960961 ghost atom cutoff = 8.1960961 binsize = 4.098048, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.577 | 4.577 | 4.577 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -13722.379 -13722.379 -13790.382 -13790.382 263.1795 263.1795 31232.683 31232.683 4155.1596 4155.1596 4000 -13731.288 -13731.288 -13797.376 -13797.376 255.76731 255.76731 31283.934 31283.934 -2299.502 -2299.502 Loop time of 5.37706 on 1 procs for 1000 steps with 2000 atoms Performance: 16.068 ns/day, 1.494 hours/ns, 185.975 timesteps/s, 371.951 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2864 | 5.2864 | 5.2864 | 0.0 | 98.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.019862 | 0.019862 | 0.019862 | 0.0 | 0.37 Output | 4.5625e-05 | 4.5625e-05 | 4.5625e-05 | 0.0 | 0.00 Modify | 0.064348 | 0.064348 | 0.064348 | 0.0 | 1.20 Other | | 0.006421 | | | 0.12 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5471 ave 5471 max 5471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 308870 ave 308870 max 308870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 308870 Ave neighs/atom = 154.435 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T253.15.out" else "print 'not_converged' file output/vol_T253.15.out" print '${V}' file output/vol_T253.15.out 31267.684117181 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0