# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 2.8169555217027673*${_u_distance} variable latticeconst_converted equal 2.8169555217027673*1 lattice bcc ${latticeconst_converted} lattice bcc 2.81695552170277 Lattice spacing in x,y,z = 2.8169555 2.8169555 2.8169555 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (28.169555 28.169555 28.169555) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (28.169555 28.169555 28.169555) create_atoms CPU = 0.000 seconds variable mass_converted equal 55.845*${_u_mass} variable mass_converted equal 55.845*1 kim interactions Fe #=== BEGIN kim interactions ================================== pair_style kim EAM_Dynamo_MendelevBorovikov_2020_FeNiCr__MO_922363340570_000 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 22353.2136586035 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 22353.2136586035/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 22353.2136586035/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 22353.2136586035/(1*1*${_u_distance}) variable V0_metal equal 22353.2136586035/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 22353.2136586035*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 22353.2136586035 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_922363340570_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 8 8 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) = 4.577 | 4.577 | 4.577 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -7887.8987 -7887.8987 -7953.3104 -7953.3104 253.15 253.15 22353.214 22353.214 3125.5869 3125.5869 1000 -7868.6066 -7868.6066 -7933.44 -7933.44 250.91202 250.91202 23185.439 23185.439 -1134.4279 -1134.4279 Loop time of 5.95059 on 1 procs for 1000 steps with 2000 atoms Performance: 14.520 ns/day, 1.653 hours/ns, 168.051 timesteps/s, 336.101 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 | 5.8485 | 5.8485 | 5.8485 | 0.0 | 98.28 Neigh | 0.010187 | 0.010187 | 0.010187 | 0.0 | 0.17 Comm | 0.020908 | 0.020908 | 0.020908 | 0.0 | 0.35 Output | 8.6933e-05 | 8.6933e-05 | 8.6933e-05 | 0.0 | 0.00 Modify | 0.064279 | 0.064279 | 0.064279 | 0.0 | 1.08 Other | | 0.006626 | | | 0.11 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5471 ave 5471 max 5471 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: 344148 ave 344148 max 344148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 344148 Ave neighs/atom = 172.074 Neighbor list builds = 1 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 = ${P}" flag: Temp = 252.452607920988, Press = -49.9134372727803 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.577 | 4.577 | 4.577 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -7868.6066 -7868.6066 -7933.44 -7933.44 250.91202 250.91202 23185.439 23185.439 -1134.4279 -1134.4279 2000 -7869.1419 -7869.1419 -7934.3866 -7934.3866 252.50372 252.50372 23176.448 23176.448 -2384.8536 -2384.8536 Loop time of 5.40741 on 1 procs for 1000 steps with 2000 atoms Performance: 15.978 ns/day, 1.502 hours/ns, 184.931 timesteps/s, 369.863 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3232 | 5.3232 | 5.3232 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018228 | 0.018228 | 0.018228 | 0.0 | 0.34 Output | 7.1133e-05 | 7.1133e-05 | 7.1133e-05 | 0.0 | 0.00 Modify | 0.059675 | 0.059675 | 0.059675 | 0.0 | 1.10 Other | | 0.006212 | | | 0.11 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5471 ave 5471 max 5471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 344204 ave 344204 max 344204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 344204 Ave neighs/atom = 172.102 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 253.696295169765, Press = -6.6735681220672 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.577 | 4.577 | 4.577 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -7869.1419 -7869.1419 -7934.3866 -7934.3866 252.50372 252.50372 23176.448 23176.448 -2384.8536 -2384.8536 3000 -7904.4465 -7904.4465 -7970.0875 -7970.0875 254.03756 254.03756 23112.743 23112.743 -132.17272 -132.17272 Loop time of 5.63069 on 1 procs for 1000 steps with 2000 atoms Performance: 15.344 ns/day, 1.564 hours/ns, 177.598 timesteps/s, 355.196 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5298 | 5.5298 | 5.5298 | 0.0 | 98.21 Neigh | 0.017261 | 0.017261 | 0.017261 | 0.0 | 0.31 Comm | 0.018249 | 0.018249 | 0.018249 | 0.0 | 0.32 Output | 6.6926e-05 | 6.6926e-05 | 6.6926e-05 | 0.0 | 0.00 Modify | 0.059464 | 0.059464 | 0.059464 | 0.0 | 1.06 Other | | 0.005815 | | | 0.10 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5531 ave 5531 max 5531 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 353482 ave 353482 max 353482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 353482 Ave neighs/atom = 176.741 Neighbor list builds = 2 Dangerous builds = 0 if "${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" 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 23141.986534531 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0