# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 2.8667457550764093*${_u_distance} variable latticeconst_converted equal 2.8667457550764093*1 lattice bcc ${latticeconst_converted} lattice bcc 2.86674575507641 Lattice spacing in x,y,z = 2.8667458 2.8667458 2.8667458 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (28.667458 28.667458 28.667458) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (28.667458 28.667458 28.667458) create_atoms CPU = 0.000 seconds variable mass_converted equal 55.845*${_u_mass} variable mass_converted equal 55.845*1 kim interactions Fe #=== BEGIN kim interactions ================================== pair_style kim EAM_Dynamo_ZhouFosterSills_2018_FeNiCr__MO_036303866285_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 23559.5794763511 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 23559.5794763511/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 23559.5794763511/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 23559.5794763511/(1*1*${_u_distance}) variable V0_metal equal 23559.5794763511/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 23559.5794763511*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 23559.5794763511 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 313.15*${_u_temperature} variable temp_converted equal 313.15*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 313.15 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 313.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "313.15 - 1.0" variable T_up equal "313.15 + 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, 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 -8479.7199 -8479.7199 -8560.635 -8560.635 313.15 313.15 23559.579 23559.579 3668.4184 3668.4184 1000 -8400.1962 -8400.1962 -8478.5641 -8478.5641 303.29195 303.29195 23470.608 23470.608 441.63758 441.63758 Loop time of 4.65843 on 1 procs for 1000 steps with 2000 atoms Performance: 18.547 ns/day, 1.294 hours/ns, 214.665 timesteps/s, 429.329 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 | 4.5649 | 4.5649 | 4.5649 | 0.0 | 97.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.020596 | 0.020596 | 0.020596 | 0.0 | 0.44 Output | 0.00015253 | 0.00015253 | 0.00015253 | 0.0 | 0.00 Modify | 0.065881 | 0.065881 | 0.065881 | 0.0 | 1.41 Other | | 0.006876 | | | 0.15 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 = ${P}" flag: Temp = 314.934887881576, Press = -39.4899557480283 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.577 | 4.577 | 4.577 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -8400.1962 -8400.1962 -8478.5641 -8478.5641 303.29195 303.29195 23470.608 23470.608 441.63758 441.63758 2000 -8395.2002 -8395.2002 -8477.0158 -8477.0158 316.63472 316.63472 23505.417 23505.417 -1672.9157 -1672.9157 Loop time of 5.77526 on 1 procs for 1000 steps with 2000 atoms Performance: 14.960 ns/day, 1.604 hours/ns, 173.152 timesteps/s, 346.305 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6702 | 5.6702 | 5.6702 | 0.0 | 98.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.022538 | 0.022538 | 0.022538 | 0.0 | 0.39 Output | 5.9712e-05 | 5.9712e-05 | 5.9712e-05 | 0.0 | 0.00 Modify | 0.074708 | 0.074708 | 0.074708 | 0.0 | 1.29 Other | | 0.007751 | | | 0.13 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5471 ave 5471 max 5471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 335966 ave 335966 max 335966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 335966 Ave neighs/atom = 167.983 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 313.425168028597, Press = -10.2201508292136 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.577 | 4.577 | 4.577 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -8395.2002 -8395.2002 -8477.0158 -8477.0158 316.63472 316.63472 23505.417 23505.417 -1672.9157 -1672.9157 3000 -8392.7515 -8392.7515 -8476.5228 -8476.5228 324.20358 324.20358 23523.449 23523.449 -3849.6516 -3849.6516 Loop time of 4.65936 on 1 procs for 1000 steps with 2000 atoms Performance: 18.543 ns/day, 1.294 hours/ns, 214.622 timesteps/s, 429.243 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5751 | 4.5751 | 4.5751 | 0.0 | 98.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018085 | 0.018085 | 0.018085 | 0.0 | 0.39 Output | 6.3879e-05 | 6.3879e-05 | 6.3879e-05 | 0.0 | 0.00 Modify | 0.05998 | 0.05998 | 0.05998 | 0.0 | 1.29 Other | | 0.006132 | | | 0.13 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5471 ave 5471 max 5471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 335954 ave 335954 max 335954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 335954 Ave neighs/atom = 167.977 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 313.209226489691, Press = -5.65506116500782 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.577 | 4.577 | 4.577 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -8392.7515 -8392.7515 -8476.5228 -8476.5228 324.20358 324.20358 23523.449 23523.449 -3849.6516 -3849.6516 4000 -8399.3382 -8399.3382 -8479.8087 -8479.8087 311.4292 311.4292 23474.796 23474.796 726.56867 726.56867 Loop time of 4.68876 on 1 procs for 1000 steps with 2000 atoms Performance: 18.427 ns/day, 1.302 hours/ns, 213.276 timesteps/s, 426.552 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6051 | 4.6051 | 4.6051 | 0.0 | 98.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018117 | 0.018117 | 0.018117 | 0.0 | 0.39 Output | 5.5013e-05 | 5.5013e-05 | 5.5013e-05 | 0.0 | 0.00 Modify | 0.059443 | 0.059443 | 0.059443 | 0.0 | 1.27 Other | | 0.006035 | | | 0.13 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5471 ave 5471 max 5471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 335972 ave 335972 max 335972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 335972 Ave neighs/atom = 167.986 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T313.15.out" else "print 'not_converged' file output/vol_T313.15.out" print '${V}' file output/vol_T313.15.out 23481.1021514139 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0