# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 2.865952417254448*${_u_distance} variable latticeconst_converted equal 2.865952417254448*1 lattice bcc ${latticeconst_converted} lattice bcc 2.86595241725445 Lattice spacing in x,y,z = 2.8659524 2.8659524 2.8659524 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (28.659524 28.659524 28.659524) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (28.659524 28.659524 28.659524) create_atoms CPU = 0.000 seconds variable mass_converted equal 55.845*${_u_mass} variable mass_converted equal 55.845*1 kim interactions Fe #=== BEGIN kim interactions ================================== pair_style kim EAM_Dynamo_ZhouJohnsonWadley_2004_CuAgAuNiPdPtAlPbFeMoTaWMgCoTiZr__MO_870117231765_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 23540.0253877319 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 23540.0253877319/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 23540.0253877319/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 23540.0253877319/(1*1*${_u_distance}) variable V0_metal equal 23540.0253877319/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 23540.0253877319*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 23540.0253877319 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_870117231765_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 = 9.8256185 ghost atom cutoff = 9.8256185 binsize = 4.9128093, bins = 6 6 6 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) = 5.804 | 5.804 | 5.804 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -8499.0809 -8499.0809 -8579.9961 -8579.9961 313.15 313.15 23540.025 23540.025 3671.492 3671.492 1000 -8410.2775 -8410.2775 -8491.6821 -8491.6821 315.04414 315.04414 23823.348 23823.348 -2092.0973 -2092.0973 Loop time of 10.6847 on 1 procs for 1000 steps with 2000 atoms Performance: 8.086 ns/day, 2.968 hours/ns, 93.592 timesteps/s, 187.183 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 | 10.587 | 10.587 | 10.587 | 0.0 | 99.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.025279 | 0.025279 | 0.025279 | 0.0 | 0.24 Output | 0.00010823 | 0.00010823 | 0.00010823 | 0.0 | 0.00 Modify | 0.064673 | 0.064673 | 0.064673 | 0.0 | 0.61 Other | | 0.007935 | | | 0.07 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7009 ave 7009 max 7009 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: 660000 ave 660000 max 660000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 660000 Ave neighs/atom = 330 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 = ${P}" flag: Temp = 311.661681261671, Press = 61.8226022621761 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.8256185 ghost atom cutoff = 9.8256185 binsize = 4.9128093, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.806 | 5.806 | 5.806 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -8410.2775 -8410.2775 -8491.6821 -8491.6821 315.04414 315.04414 23823.348 23823.348 -2092.0973 -2092.0973 2000 -8422.7758 -8422.7758 -8502.1488 -8502.1488 307.18166 307.18166 23755.875 23755.875 213.74508 213.74508 Loop time of 14.2023 on 1 procs for 1000 steps with 2000 atoms Performance: 6.084 ns/day, 3.945 hours/ns, 70.411 timesteps/s, 140.822 katom-step/s 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.1 | 14.1 | 14.1 | 0.0 | 99.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.026598 | 0.026598 | 0.026598 | 0.0 | 0.19 Output | 0.0001521 | 0.0001521 | 0.0001521 | 0.0 | 0.00 Modify | 0.067366 | 0.067366 | 0.067366 | 0.0 | 0.47 Other | | 0.007916 | | | 0.06 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7009 ave 7009 max 7009 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 661156 ave 661156 max 661156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 661156 Ave neighs/atom = 330.578 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 313.134076387519, Press = 7.00233182235677 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.8256185 ghost atom cutoff = 9.8256185 binsize = 4.9128093, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.806 | 5.806 | 5.806 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -8422.7758 -8422.7758 -8502.1488 -8502.1488 307.18166 307.18166 23755.875 23755.875 213.74508 213.74508 3000 -8411.9142 -8411.9142 -8493.0334 -8493.0334 313.93955 313.93955 23770.888 23770.888 708.56968 708.56968 Loop time of 14.0878 on 1 procs for 1000 steps with 2000 atoms Performance: 6.133 ns/day, 3.913 hours/ns, 70.983 timesteps/s, 141.967 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.988 | 13.988 | 13.988 | 0.0 | 99.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.025845 | 0.025845 | 0.025845 | 0.0 | 0.18 Output | 6.3168e-05 | 6.3168e-05 | 6.3168e-05 | 0.0 | 0.00 Modify | 0.066399 | 0.066399 | 0.066399 | 0.0 | 0.47 Other | | 0.007648 | | | 0.05 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7009 ave 7009 max 7009 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 661018 ave 661018 max 661018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 661018 Ave neighs/atom = 330.509 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 313.005373045455, Press = 5.46031497672789 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.8256185 ghost atom cutoff = 9.8256185 binsize = 4.9128093, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.806 | 5.806 | 5.806 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -8411.9142 -8411.9142 -8493.0334 -8493.0334 313.93955 313.93955 23770.888 23770.888 708.56968 708.56968 4000 -8419.3117 -8419.3117 -8498.3318 -8498.3318 305.81579 305.81579 23805.742 23805.742 -2462.3943 -2462.3943 Loop time of 14.0752 on 1 procs for 1000 steps with 2000 atoms Performance: 6.138 ns/day, 3.910 hours/ns, 71.047 timesteps/s, 142.094 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.977 | 13.977 | 13.977 | 0.0 | 99.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.025165 | 0.025165 | 0.025165 | 0.0 | 0.18 Output | 4.0566e-05 | 4.0566e-05 | 4.0566e-05 | 0.0 | 0.00 Modify | 0.065599 | 0.065599 | 0.065599 | 0.0 | 0.47 Other | | 0.007556 | | | 0.05 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7009 ave 7009 max 7009 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 661158 ave 661158 max 661158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 661158 Ave neighs/atom = 330.579 Neighbor list builds = 0 Dangerous builds = 0 if "${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 23775.6425709374 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0