# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.742339283227921*${_u_distance} variable latticeconst_converted equal 3.742339283227921*1 lattice bcc ${latticeconst_converted} lattice bcc 3.74233928322792 Lattice spacing in x,y,z = 3.7423393 3.7423393 3.7423393 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (37.423393 37.423393 37.423393) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (37.423393 37.423393 37.423393) create_atoms CPU = 0.000 seconds variable mass_converted equal 180.9479*${_u_mass} variable mass_converted equal 180.9479*1 kim interactions Ta #=== BEGIN kim interactions ================================== pair_style kim LJ_ElliottAkerson_2015_Universal__MO_959249795837_003 pair_coeff * * Ta #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 180.9479 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 52411.848285638 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 52411.848285638/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 52411.848285638/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 52411.848285638/(1*1*${_u_distance}) variable V0_metal equal 52411.848285638/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 52411.848285638*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 52411.848285638 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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) = 17.04 | 17.04 | 17.04 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -63658.325 -63658.325 -63734.072 -63734.072 293.15 293.15 52411.848 52411.848 1543.4216 1543.4216 1000 -64820.987 -64820.987 -64895.565 -64895.565 288.62379 288.62379 51995.631 51995.631 6475.4039 6475.4039 Loop time of 11.3659 on 1 procs for 1000 steps with 2000 atoms Performance: 7.602 ns/day, 3.157 hours/ns, 87.983 timesteps/s, 175.966 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 | 11.046 | 11.046 | 11.046 | 0.0 | 97.18 Neigh | 0.16754 | 0.16754 | 0.16754 | 0.0 | 1.47 Comm | 0.062075 | 0.062075 | 0.062075 | 0.0 | 0.55 Output | 0.00019039 | 0.00019039 | 0.00019039 | 0.0 | 0.00 Modify | 0.069919 | 0.069919 | 0.069919 | 0.0 | 0.62 Other | | 0.02031 | | | 0.18 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16521 ave 16521 max 16521 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: 2.7893e+06 ave 2.7893e+06 max 2.7893e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2789298 Ave neighs/atom = 1394.649 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 = ${P}" flag: Temp = 307.060838896317, Press = 516.941474370021 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 17.31 | 17.31 | 17.31 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -64820.987 -64820.987 -64895.565 -64895.565 288.62379 288.62379 51995.631 51995.631 6475.4039 6475.4039 2000 -64966.556 -64966.556 -65039.476 -65039.476 282.2067 282.2067 51928.382 51928.382 3806.0903 3806.0903 Loop time of 11.3309 on 1 procs for 1000 steps with 2000 atoms Performance: 7.625 ns/day, 3.147 hours/ns, 88.254 timesteps/s, 176.509 katom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.011 | 11.011 | 11.011 | 0.0 | 97.17 Neigh | 0.1683 | 0.1683 | 0.1683 | 0.0 | 1.49 Comm | 0.06142 | 0.06142 | 0.06142 | 0.0 | 0.54 Output | 5.5724e-05 | 5.5724e-05 | 5.5724e-05 | 0.0 | 0.00 Modify | 0.071121 | 0.071121 | 0.071121 | 0.0 | 0.63 Other | | 0.01937 | | | 0.17 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16541 ave 16541 max 16541 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.79311e+06 ave 2.79311e+06 max 2.79311e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2793112 Ave neighs/atom = 1396.556 Neighbor list builds = 3 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 296.994045593407, Press = 8.40750178833889 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 17.31 | 17.31 | 17.31 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -64966.556 -64966.556 -65039.476 -65039.476 282.2067 282.2067 51928.382 51928.382 3806.0903 3806.0903 3000 -64979.967 -64979.967 -65053.587 -65053.587 284.91945 284.91945 51936.879 51936.879 106.0126 106.0126 Loop time of 11.5367 on 1 procs for 1000 steps with 2000 atoms Performance: 7.489 ns/day, 3.205 hours/ns, 86.680 timesteps/s, 173.360 katom-step/s 96.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.386 | 11.386 | 11.386 | 0.0 | 98.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.061033 | 0.061033 | 0.061033 | 0.0 | 0.53 Output | 5.363e-05 | 5.363e-05 | 5.363e-05 | 0.0 | 0.00 Modify | 0.070855 | 0.070855 | 0.070855 | 0.0 | 0.61 Other | | 0.01881 | | | 0.16 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16561 ave 16561 max 16561 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.79362e+06 ave 2.79362e+06 max 2.79362e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2793618 Ave neighs/atom = 1396.809 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 295.427590746258, Press = 17.9485536867711 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 17.31 | 17.31 | 17.31 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -64979.967 -64979.967 -65053.587 -65053.587 284.91945 284.91945 51936.879 51936.879 106.0126 106.0126 4000 -64968.433 -64968.433 -65042.44 -65042.44 286.4149 286.4149 51947.102 51947.102 -2010.614 -2010.614 Loop time of 11.7839 on 1 procs for 1000 steps with 2000 atoms Performance: 7.332 ns/day, 3.273 hours/ns, 84.862 timesteps/s, 169.723 katom-step/s 97.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.628 | 11.628 | 11.628 | 0.0 | 98.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.062839 | 0.062839 | 0.062839 | 0.0 | 0.53 Output | 6.4641e-05 | 6.4641e-05 | 6.4641e-05 | 0.0 | 0.00 Modify | 0.073528 | 0.073528 | 0.073528 | 0.0 | 0.62 Other | | 0.01945 | | | 0.17 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16547 ave 16547 max 16547 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.79381e+06 ave 2.79381e+06 max 2.79381e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2793814 Ave neighs/atom = 1396.907 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 294.299250488106, Press = 3.86035930260362 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 17.31 | 17.31 | 17.31 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -64968.433 -64968.433 -65042.44 -65042.44 286.4149 286.4149 51947.102 51947.102 -2010.614 -2010.614 5000 -64960.457 -64960.457 -65039.073 -65039.073 304.25416 304.25416 51928.758 51928.758 4790.2833 4790.2833 Loop time of 11.1347 on 1 procs for 1000 steps with 2000 atoms Performance: 7.759 ns/day, 3.093 hours/ns, 89.809 timesteps/s, 179.618 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.985 | 10.985 | 10.985 | 0.0 | 98.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.059963 | 0.059963 | 0.059963 | 0.0 | 0.54 Output | 3.5767e-05 | 3.5767e-05 | 3.5767e-05 | 0.0 | 0.00 Modify | 0.070154 | 0.070154 | 0.070154 | 0.0 | 0.63 Other | | 0.01916 | | | 0.17 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16533 ave 16533 max 16533 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.79278e+06 ave 2.79278e+06 max 2.79278e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2792778 Ave neighs/atom = 1396.389 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 293.810958559144, Press = 9.38566017873771 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 17.31 | 17.31 | 17.31 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -64960.457 -64960.457 -65039.073 -65039.073 304.25416 304.25416 51928.758 51928.758 4790.2833 4790.2833 6000 -64960.911 -64960.911 -65040.281 -65040.281 307.16832 307.16832 51963.252 51963.252 -6889.323 -6889.323 Loop time of 11.1776 on 1 procs for 1000 steps with 2000 atoms Performance: 7.730 ns/day, 3.105 hours/ns, 89.465 timesteps/s, 178.929 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.026 | 11.026 | 11.026 | 0.0 | 98.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.06072 | 0.06072 | 0.06072 | 0.0 | 0.54 Output | 5.9682e-05 | 5.9682e-05 | 5.9682e-05 | 0.0 | 0.00 Modify | 0.070769 | 0.070769 | 0.070769 | 0.0 | 0.63 Other | | 0.02007 | | | 0.18 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16545 ave 16545 max 16545 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.79327e+06 ave 2.79327e+06 max 2.79327e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2793272 Ave neighs/atom = 1396.636 Neighbor list builds = 0 Dangerous builds = 0 if "${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 51947.2338021053 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0