# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.4687884375453*${_u_distance} variable latticeconst_converted equal 4.4687884375453*1 lattice bcc ${latticeconst_converted} lattice bcc 4.4687884375453 Lattice spacing in x,y,z = 4.4687884 4.4687884 4.4687884 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (44.687884 44.687884 44.687884) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (44.687884 44.687884 44.687884) create_atoms CPU = 0.000 seconds variable mass_converted equal 39.0983*${_u_mass} variable mass_converted equal 39.0983*1 kim interactions K #=== BEGIN kim interactions ================================== pair_style kim LJ_ElliottAkerson_2015_Universal__MO_959249795837_003 pair_coeff * * K #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 39.0983 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 89242.0183577871 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 89242.0183577871/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 89242.0183577871/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 89242.0183577871/(1*1*${_u_distance}) variable V0_metal equal 89242.0183577871/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 89242.0183577871*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 89242.0183577871 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_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 = 5 5 5 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) = 10.33 | 10.33 | 10.33 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -8719.1579 -8719.1579 -8784.5696 -8784.5696 253.15 253.15 89242.018 89242.018 782.87692 782.87692 1000 -8782.415 -8782.415 -8847.7182 -8847.7182 252.73027 252.73027 89203.226 89203.226 -537.7809 -537.7809 Loop time of 9.49961 on 1 procs for 1000 steps with 2000 atoms Performance: 9.095 ns/day, 2.639 hours/ns, 105.267 timesteps/s, 210.535 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 | 9.2808 | 9.2808 | 9.2808 | 0.0 | 97.70 Neigh | 0.099295 | 0.099295 | 0.099295 | 0.0 | 1.05 Comm | 0.044302 | 0.044302 | 0.044302 | 0.0 | 0.47 Output | 9.0099e-05 | 9.0099e-05 | 9.0099e-05 | 0.0 | 0.00 Modify | 0.062887 | 0.062887 | 0.062887 | 0.0 | 0.66 Other | | 0.01226 | | | 0.13 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12537 ave 12537 max 12537 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: 1.64229e+06 ave 1.64229e+06 max 1.64229e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1642288 Ave neighs/atom = 821.144 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 = ${P}" flag: Temp = 255.727413449126, Press = -9.45137002711339 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 9.946 | 9.946 | 9.946 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -8782.415 -8782.415 -8847.7182 -8847.7182 252.73027 252.73027 89203.226 89203.226 -537.7809 -537.7809 2000 -8853.555 -8853.555 -8918.3958 -8918.3958 250.94081 250.94081 88678.226 88678.226 1334.5139 1334.5139 Loop time of 9.20535 on 1 procs for 1000 steps with 2000 atoms Performance: 9.386 ns/day, 2.557 hours/ns, 108.632 timesteps/s, 217.265 katom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.9265 | 8.9265 | 8.9265 | 0.0 | 96.97 Neigh | 0.16297 | 0.16297 | 0.16297 | 0.0 | 1.77 Comm | 0.041044 | 0.041044 | 0.041044 | 0.0 | 0.45 Output | 7.7605e-05 | 7.7605e-05 | 7.7605e-05 | 0.0 | 0.00 Modify | 0.062888 | 0.062888 | 0.062888 | 0.0 | 0.68 Other | | 0.01191 | | | 0.13 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12251 ave 12251 max 12251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.64688e+06 ave 1.64688e+06 max 1.64688e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1646878 Ave neighs/atom = 823.439 Neighbor list builds = 5 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 254.69979210931, Press = 3.63096870561842 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 9.946 | 9.946 | 9.946 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -8853.555 -8853.555 -8918.3958 -8918.3958 250.94081 250.94081 88678.226 88678.226 1334.5139 1334.5139 3000 -8840.9841 -8840.9841 -8909.7117 -8909.7117 265.98282 265.98282 88881.582 88881.582 -448.31874 -448.31874 Loop time of 9.92399 on 1 procs for 1000 steps with 2000 atoms Performance: 8.706 ns/day, 2.757 hours/ns, 100.766 timesteps/s, 201.532 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.73 | 9.73 | 9.73 | 0.0 | 98.05 Neigh | 0.071247 | 0.071247 | 0.071247 | 0.0 | 0.72 Comm | 0.044061 | 0.044061 | 0.044061 | 0.0 | 0.44 Output | 3.7851e-05 | 3.7851e-05 | 3.7851e-05 | 0.0 | 0.00 Modify | 0.067603 | 0.067603 | 0.067603 | 0.0 | 0.68 Other | | 0.01106 | | | 0.11 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12219 ave 12219 max 12219 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.64436e+06 ave 1.64436e+06 max 1.64436e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1644360 Ave neighs/atom = 822.18 Neighbor list builds = 2 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 254.253462673394, Press = -0.288192353927346 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 9.945 | 9.945 | 9.945 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -8840.9841 -8840.9841 -8909.7117 -8909.7117 265.98282 265.98282 88881.582 88881.582 -448.31874 -448.31874 4000 -8840.0604 -8840.0604 -8906.5209 -8906.5209 257.20897 257.20897 88768.704 88768.704 1448.3851 1448.3851 Loop time of 10.1989 on 1 procs for 1000 steps with 2000 atoms Performance: 8.472 ns/day, 2.833 hours/ns, 98.050 timesteps/s, 196.100 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.073 | 10.073 | 10.073 | 0.0 | 98.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.045166 | 0.045166 | 0.045166 | 0.0 | 0.44 Output | 4.5416e-05 | 4.5416e-05 | 4.5416e-05 | 0.0 | 0.00 Modify | 0.069695 | 0.069695 | 0.069695 | 0.0 | 0.68 Other | | 0.01093 | | | 0.11 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12187 ave 12187 max 12187 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.64258e+06 ave 1.64258e+06 max 1.64258e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1642584 Ave neighs/atom = 821.292 Neighbor list builds = 0 Dangerous builds = 0 if "${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 88877.6359895271 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0