# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 2.8599998205900192*${_u_distance} variable latticeconst_converted equal 2.8599998205900192*1 lattice bcc ${latticeconst_converted} lattice bcc 2.85999982059002 Lattice spacing in x,y,z = 2.8599998 2.8599998 2.8599998 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (28.599998 28.599998 28.599998) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (28.599998 28.599998 28.599998) create_atoms CPU = 0.000 seconds variable mass_converted equal 55.845*${_u_mass} variable mass_converted equal 55.845*1 kim interactions Fe #=== BEGIN kim interactions ================================== pair_style kim MJ_MorrisAgaLevashov_2008_Fe__MO_857282754307_003 WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1127) pair_coeff * * Fe #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 55.845 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 23393.6515974947 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 23393.6515974947/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 23393.6515974947/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 23393.6515974947/(1*1*${_u_distance}) variable V0_metal equal 23393.6515974947/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 23393.6515974947*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 23393.6515974947 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_857282754307_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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 11 11 11 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) = 3.701 | 3.701 | 3.701 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -3008.9663 -3008.9663 -3074.378 -3074.378 253.15 253.15 23393.652 23393.652 2986.5968 2986.5968 1000 -2950.1109 -2950.1109 -3013.1957 -3013.1957 244.14465 244.14465 23518.322 23518.322 543.98835 543.98835 Loop time of 1.12234 on 1 procs for 1000 steps with 2000 atoms Performance: 76.982 ns/day, 0.312 hours/ns, 890.999 timesteps/s, 1.782 Matom-step/s 93.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0446 | 1.0446 | 1.0446 | 0.0 | 93.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011042 | 0.011042 | 0.011042 | 0.0 | 0.98 Output | 0.00011056 | 0.00011056 | 0.00011056 | 0.0 | 0.01 Modify | 0.061418 | 0.061418 | 0.061418 | 0.0 | 5.47 Other | | 0.005126 | | | 0.46 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2941 ave 2941 max 2941 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: 116000 ave 116000 max 116000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116000 Ave neighs/atom = 58 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 = ${P}" flag: Temp = 251.838639287711, Press = -39.3015375101449 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.701 | 3.701 | 3.701 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -2950.1109 -2950.1109 -3013.1957 -3013.1957 244.14465 244.14465 23518.322 23518.322 543.98835 543.98835 2000 -2950.2453 -2950.2453 -3015.4357 -3015.4357 252.2937 252.2937 23548.241 23548.241 -1308.372 -1308.372 Loop time of 1.19919 on 1 procs for 1000 steps with 2000 atoms Performance: 72.048 ns/day, 0.333 hours/ns, 833.893 timesteps/s, 1.668 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1163 | 1.1163 | 1.1163 | 0.0 | 93.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011316 | 0.011316 | 0.011316 | 0.0 | 0.94 Output | 3.216e-05 | 3.216e-05 | 3.216e-05 | 0.0 | 0.00 Modify | 0.066166 | 0.066166 | 0.066166 | 0.0 | 5.52 Other | | 0.0054 | | | 0.45 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2941 ave 2941 max 2941 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 116004 ave 116004 max 116004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116004 Ave neighs/atom = 58.002 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.830075543696, Press = -8.10042988869368 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.701 | 3.701 | 3.701 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -2950.2453 -2950.2453 -3015.4357 -3015.4357 252.2937 252.2937 23548.241 23548.241 -1308.372 -1308.372 3000 -2943.744 -2943.744 -3008.398 -3008.398 250.21779 250.21779 23574.116 23574.116 -1930.6083 -1930.6083 Loop time of 1.19663 on 1 procs for 1000 steps with 2000 atoms Performance: 72.203 ns/day, 0.332 hours/ns, 835.682 timesteps/s, 1.671 Matom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1166 | 1.1166 | 1.1166 | 0.0 | 93.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011169 | 0.011169 | 0.011169 | 0.0 | 0.93 Output | 3.2291e-05 | 3.2291e-05 | 3.2291e-05 | 0.0 | 0.00 Modify | 0.06368 | 0.06368 | 0.06368 | 0.0 | 5.32 Other | | 0.005195 | | | 0.43 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2941 ave 2941 max 2941 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 116006 ave 116006 max 116006 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116006 Ave neighs/atom = 58.003 Neighbor list builds = 0 Dangerous builds = 0 if "${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 23535.9414715106 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0