# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 2.878154456615448*${_u_distance} variable latticeconst_converted equal 2.878154456615448*1 lattice bcc ${latticeconst_converted} lattice bcc 2.87815445661545 Lattice spacing in x,y,z = 2.8781545 2.8781545 2.8781545 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (28.781545 28.781545 28.781545) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (28.781545 28.781545 28.781545) create_atoms CPU = 0.000 seconds variable mass_converted equal 51.9961*${_u_mass} variable mass_converted equal 51.9961*1 kim interactions Cr #=== BEGIN kim interactions ================================== pair_style kim EAM_Dynamo_MendelevBorovikov_2020_FeNiCr__MO_922363340570_000 pair_coeff * * Cr #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 51.9961 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 23841.9783966701 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 23841.9783966701/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 23841.9783966701/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 23841.9783966701/(1*1*${_u_distance}) variable V0_metal equal 23841.9783966701/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 23841.9783966701*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 23841.9783966701 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_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 -8018.9264 -8018.9264 -8094.6738 -8094.6738 293.15 293.15 23841.978 23841.978 3393.4984 3393.4984 1000 -7936.4998 -7936.4998 -8010.793 -8010.793 287.52238 287.52238 24449.246 24449.246 2981.3503 2981.3503 Loop time of 5.29511 on 1 procs for 1000 steps with 2000 atoms Performance: 16.317 ns/day, 1.471 hours/ns, 188.853 timesteps/s, 377.707 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 | 5.2019 | 5.2019 | 5.2019 | 0.0 | 98.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.020217 | 0.020217 | 0.020217 | 0.0 | 0.38 Output | 6.8609e-05 | 6.8609e-05 | 6.8609e-05 | 0.0 | 0.00 Modify | 0.066169 | 0.066169 | 0.066169 | 0.0 | 1.25 Other | | 0.006775 | | | 0.13 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: 336000 ave 336000 max 336000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 336000 Ave neighs/atom = 168 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 = ${P}" flag: Temp = 292.980949939962, Press = -16.3308019877284 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.577 | 4.577 | 4.577 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -7936.4998 -7936.4998 -8010.793 -8010.793 287.52238 287.52238 24449.246 24449.246 2981.3503 2981.3503 2000 -7939.1503 -7939.1503 -8014.566 -8014.566 291.86668 291.86668 24450.285 24450.285 840.12901 840.12901 Loop time of 6.00199 on 1 procs for 1000 steps with 2000 atoms Performance: 14.395 ns/day, 1.667 hours/ns, 166.611 timesteps/s, 333.223 katom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9066 | 5.9066 | 5.9066 | 0.0 | 98.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.020046 | 0.020046 | 0.020046 | 0.0 | 0.33 Output | 6.0264e-05 | 6.0264e-05 | 6.0264e-05 | 0.0 | 0.00 Modify | 0.068525 | 0.068525 | 0.068525 | 0.0 | 1.14 Other | | 0.006709 | | | 0.11 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5471 ave 5471 max 5471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 336376 ave 336376 max 336376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 336376 Ave neighs/atom = 168.188 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.986496302327, Press = -6.77356535847215 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.577 | 4.577 | 4.577 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -7939.1503 -7939.1503 -8014.566 -8014.566 291.86668 291.86668 24450.285 24450.285 840.12901 840.12901 3000 -7937.2008 -7937.2008 -8013.2121 -8013.2121 294.17172 294.17172 24474.08 24474.08 -1063.738 -1063.738 Loop time of 6.13854 on 1 procs for 1000 steps with 2000 atoms Performance: 14.075 ns/day, 1.705 hours/ns, 162.905 timesteps/s, 325.810 katom-step/s 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0436 | 6.0436 | 6.0436 | 0.0 | 98.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.020237 | 0.020237 | 0.020237 | 0.0 | 0.33 Output | 4.279e-05 | 4.279e-05 | 4.279e-05 | 0.0 | 0.00 Modify | 0.068053 | 0.068053 | 0.068053 | 0.0 | 1.11 Other | | 0.006656 | | | 0.11 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5471 ave 5471 max 5471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 336286 ave 336286 max 336286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 336286 Ave neighs/atom = 168.143 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.855133606256, Press = -5.61902776067044 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.577 | 4.577 | 4.577 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -7937.2008 -7937.2008 -8013.2121 -8013.2121 294.17172 294.17172 24474.08 24474.08 -1063.738 -1063.738 4000 -7934.0421 -7934.0421 -8012.4786 -8012.4786 303.55733 303.55733 24484.555 24484.555 -904.39017 -904.39017 Loop time of 6.62383 on 1 procs for 1000 steps with 2000 atoms Performance: 13.044 ns/day, 1.840 hours/ns, 150.970 timesteps/s, 301.940 katom-step/s 89.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.5316 | 6.5316 | 6.5316 | 0.0 | 98.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01976 | 0.01976 | 0.01976 | 0.0 | 0.30 Output | 3.7611e-05 | 3.7611e-05 | 3.7611e-05 | 0.0 | 0.00 Modify | 0.065976 | 0.065976 | 0.065976 | 0.0 | 1.00 Other | | 0.006407 | | | 0.10 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5471 ave 5471 max 5471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 336270 ave 336270 max 336270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 336270 Ave neighs/atom = 168.135 Neighbor list builds = 0 Dangerous builds = 0 if "${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 24470.894540853 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0