# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.029959537088871*${_u_distance} variable latticeconst_converted equal 3.029959537088871*1 lattice bcc ${latticeconst_converted} lattice bcc 3.02995953708887 Lattice spacing in x,y,z = 3.0299595 3.0299595 3.0299595 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (30.299595 30.299595 30.299595) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (30.299595 30.299595 30.299595) create_atoms CPU = 0.001 seconds variable mass_converted equal 50.9415*${_u_mass} variable mass_converted equal 50.9415*1 kim interactions V #=== BEGIN kim interactions ================================== pair_style kim EAM_Dynamo_Olsson_2009_V__MO_944449444863_000 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 27817.0125570601 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 27817.0125570601/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 27817.0125570601/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 27817.0125570601/(1*1*${_u_distance}) variable V0_metal equal 27817.0125570601/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 27817.0125570601*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 27817.0125570601 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_944449444863_000#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 = 6.545 ghost atom cutoff = 6.545 binsize = 3.2725, bins = 10 10 10 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) = 3.755 | 3.755 | 3.755 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -10549.421 -10549.421 -10620 -10620 273.15 273.15 27817.013 27817.013 2710.127 2710.127 1000 -10482.352 -10482.352 -10551.895 -10551.895 269.14078 269.14078 28295.532 28295.532 -1298.8733 -1298.8733 Loop time of 1.89785 on 1 procs for 1000 steps with 2000 atoms Performance: 45.525 ns/day, 0.527 hours/ns, 526.912 timesteps/s, 1.054 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8121 | 1.8121 | 1.8121 | 0.0 | 95.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.015781 | 0.015781 | 0.015781 | 0.0 | 0.83 Output | 6.4531e-05 | 6.4531e-05 | 6.4531e-05 | 0.0 | 0.00 Modify | 0.063614 | 0.063614 | 0.063614 | 0.0 | 3.35 Other | | 0.006267 | | | 0.33 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119 ave 4119 max 4119 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: 128000 ave 128000 max 128000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128000 Ave neighs/atom = 64 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 = ${P}" flag: Temp = 273.225243357041, Press = -131.126369436353 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.545 ghost atom cutoff = 6.545 binsize = 3.2725, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.755 | 3.755 | 3.755 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -10482.352 -10482.352 -10551.895 -10551.895 269.14078 269.14078 28295.532 28295.532 -1298.8733 -1298.8733 2000 -10476.352 -10476.352 -10547.246 -10547.246 274.36737 274.36737 28290.818 28290.818 -215.20368 -215.20368 Loop time of 2.46798 on 1 procs for 1000 steps with 2000 atoms Performance: 35.008 ns/day, 0.686 hours/ns, 405.190 timesteps/s, 810.379 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3775 | 2.3775 | 2.3775 | 0.0 | 96.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.015692 | 0.015692 | 0.015692 | 0.0 | 0.64 Output | 6.7536e-05 | 6.7536e-05 | 6.7536e-05 | 0.0 | 0.00 Modify | 0.068593 | 0.068593 | 0.068593 | 0.0 | 2.78 Other | | 0.006168 | | | 0.25 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119 ave 4119 max 4119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 137470 ave 137470 max 137470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137470 Ave neighs/atom = 68.735 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 273.270339595323, Press = -6.08884595874022 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.545 ghost atom cutoff = 6.545 binsize = 3.2725, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.755 | 3.755 | 3.755 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -10476.352 -10476.352 -10547.246 -10547.246 274.36737 274.36737 28290.818 28290.818 -215.20368 -215.20368 3000 -10474.114 -10474.114 -10542.684 -10542.684 265.37256 265.37256 28268.691 28268.691 1964.0207 1964.0207 Loop time of 2.58978 on 1 procs for 1000 steps with 2000 atoms Performance: 33.362 ns/day, 0.719 hours/ns, 386.133 timesteps/s, 772.267 katom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4959 | 2.4959 | 2.4959 | 0.0 | 96.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.016314 | 0.016314 | 0.016314 | 0.0 | 0.63 Output | 5.0705e-05 | 5.0705e-05 | 5.0705e-05 | 0.0 | 0.00 Modify | 0.071338 | 0.071338 | 0.071338 | 0.0 | 2.75 Other | | 0.006211 | | | 0.24 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119 ave 4119 max 4119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 137934 ave 137934 max 137934 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137934 Ave neighs/atom = 68.967 Neighbor list builds = 0 Dangerous builds = 0 if "${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 28284.6238448421 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0