# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.5564776659011836*${_u_distance} variable latticeconst_converted equal 3.5564776659011836*1 lattice diamond ${latticeconst_converted} lattice diamond 3.55647766590118 Lattice spacing in x,y,z = 3.5564777 3.5564777 3.5564777 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (35.564777 35.564777 35.564777) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 8000 atoms using lattice units in orthogonal box = (0 0 0) to (35.564777 35.564777 35.564777) create_atoms CPU = 0.001 seconds variable mass_converted equal 12.0107*${_u_mass} variable mass_converted equal 12.0107*1 kim interactions C #=== BEGIN kim interactions ================================== pair_style kim MEAM_LAMMPS_LeeLee_2005_C__MO_996970420049_001 pair_coeff * * C #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 12.0107 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 44984.2265010191 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 44984.2265010191/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 44984.2265010191/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 44984.2265010191/(1*1*${_u_distance}) variable V0_metal equal 44984.2265010191/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 44984.2265010191*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 44984.2265010191 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_996970420049_001#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 = 4.75 ghost atom cutoff = 4.75 binsize = 2.375, bins = 15 15 15 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) = 8.652 | 8.652 | 8.652 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -58698.255 -58698.255 -58960 -58960 253.15 253.15 44984.227 44984.227 6214.9466 6214.9466 1000 -58434.665 -58434.665 -58686.392 -58686.392 243.46139 243.46139 45226.508 45226.508 1545.3417 1545.3417 Loop time of 32.7255 on 1 procs for 1000 steps with 8000 atoms Performance: 2.640 ns/day, 9.090 hours/ns, 30.557 timesteps/s, 244.458 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 | 32.373 | 32.373 | 32.373 | 0.0 | 98.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.039892 | 0.039892 | 0.039892 | 0.0 | 0.12 Output | 0.00013677 | 0.00013677 | 0.00013677 | 0.0 | 0.00 Modify | 0.27966 | 0.27966 | 0.27966 | 0.0 | 0.85 Other | | 0.03304 | | | 0.10 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8601 ave 8601 max 8601 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: 688000 ave 688000 max 688000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 688000 Ave neighs/atom = 86 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 = ${P}" flag: Temp = 253.521273694426, Press = 178.139101799177 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.75 ghost atom cutoff = 4.75 binsize = 2.375, bins = 16 16 16 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 8.909 | 8.909 | 8.909 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -58434.665 -58434.665 -58686.392 -58686.392 243.46139 243.46139 45226.508 45226.508 1545.3417 1545.3417 2000 -58434.918 -58434.918 -58692.414 -58692.414 249.04032 249.04032 45246.09 45246.09 -589.75303 -589.75303 Loop time of 35.3219 on 1 procs for 1000 steps with 8000 atoms Performance: 2.446 ns/day, 9.812 hours/ns, 28.311 timesteps/s, 226.488 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 34.971 | 34.971 | 34.971 | 0.0 | 99.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.03931 | 0.03931 | 0.03931 | 0.0 | 0.11 Output | 9.8736e-05 | 9.8736e-05 | 9.8736e-05 | 0.0 | 0.00 Modify | 0.28046 | 0.28046 | 0.28046 | 0.0 | 0.79 Other | | 0.03151 | | | 0.09 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8601 ave 8601 max 8601 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 687880 ave 687880 max 687880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 687880 Ave neighs/atom = 85.985 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 253.508452916746, Press = 11.4081277986973 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.75 ghost atom cutoff = 4.75 binsize = 2.375, bins = 16 16 16 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 8.909 | 8.909 | 8.909 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -58434.918 -58434.918 -58692.414 -58692.414 249.04032 249.04032 45246.09 45246.09 -589.75303 -589.75303 3000 -58432.977 -58432.977 -58694.707 -58694.707 253.13592 253.13592 45256.733 45256.733 -1669.2767 -1669.2767 Loop time of 34.8692 on 1 procs for 1000 steps with 8000 atoms Performance: 2.478 ns/day, 9.686 hours/ns, 28.679 timesteps/s, 229.429 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 34.525 | 34.525 | 34.525 | 0.0 | 99.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.038219 | 0.038219 | 0.038219 | 0.0 | 0.11 Output | 0.0001157 | 0.0001157 | 0.0001157 | 0.0 | 0.00 Modify | 0.2756 | 0.2756 | 0.2756 | 0.0 | 0.79 Other | | 0.03014 | | | 0.09 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8601 ave 8601 max 8601 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 687910 ave 687910 max 687910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 687910 Ave neighs/atom = 85.98875 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 253.408915574, Press = 6.0709210798323 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.75 ghost atom cutoff = 4.75 binsize = 2.375, bins = 16 16 16 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 8.909 | 8.909 | 8.909 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -58432.977 -58432.977 -58694.707 -58694.707 253.13592 253.13592 45256.733 45256.733 -1669.2767 -1669.2767 4000 -58435.59 -58435.59 -58700.458 -58700.458 256.17 256.17 45236.041 45236.041 -58.340812 -58.340812 Loop time of 34.292 on 1 procs for 1000 steps with 8000 atoms Performance: 2.520 ns/day, 9.526 hours/ns, 29.161 timesteps/s, 233.290 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 33.953 | 33.953 | 33.953 | 0.0 | 99.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.03757 | 0.03757 | 0.03757 | 0.0 | 0.11 Output | 5.7548e-05 | 5.7548e-05 | 5.7548e-05 | 0.0 | 0.00 Modify | 0.27217 | 0.27217 | 0.27217 | 0.0 | 0.79 Other | | 0.02971 | | | 0.09 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8601 ave 8601 max 8601 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 687914 ave 687914 max 687914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 687914 Ave neighs/atom = 85.98925 Neighbor list builds = 0 Dangerous builds = 0 if "${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 45239.7278111547 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0