# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.143073618412018*${_u_distance} variable latticeconst_converted equal 3.143073618412018*1 lattice bcc ${latticeconst_converted} lattice bcc 3.14307361841202 Lattice spacing in x,y,z = 3.1430736 3.1430736 3.1430736 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (31.430736 31.430736 31.430736) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (31.430736 31.430736 31.430736) create_atoms CPU = 0.000 seconds variable mass_converted equal 183.84*${_u_mass} variable mass_converted equal 183.84*1 kim interactions W #=== BEGIN kim interactions ================================== pair_style kim EAM_Dynamo_SetyawanGaoKurtz_2018_ReW__MO_680820064987_000 pair_coeff * * W #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 183.84 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 31050.1469652883 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 31050.1469652883/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 31050.1469652883/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 31050.1469652883/(1*1*${_u_distance}) variable V0_metal equal 31050.1469652883/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 31050.1469652883*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 31050.1469652883 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_680820064987_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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 9 9 9 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) = 4.134 | 4.134 | 4.134 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -17735.868 -17735.868 -17801.28 -17801.28 253.15 253.15 31050.147 31050.147 2250.1203 2250.1203 1000 -17682.314 -17682.314 -17745.647 -17745.647 245.10401 245.10401 31271.469 31271.469 -1007.2841 -1007.2841 Loop time of 4.16483 on 1 procs for 1000 steps with 2000 atoms Performance: 20.745 ns/day, 1.157 hours/ns, 240.106 timesteps/s, 480.211 katom-step/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0769 | 4.0769 | 4.0769 | 0.0 | 97.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.016413 | 0.016413 | 0.016413 | 0.0 | 0.39 Output | 0.00010822 | 0.00010822 | 0.00010822 | 0.0 | 0.00 Modify | 0.065625 | 0.065625 | 0.065625 | 0.0 | 1.58 Other | | 0.005758 | | | 0.14 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119 ave 4119 max 4119 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: 224000 ave 224000 max 224000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224000 Ave neighs/atom = 112 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 = ${P}" flag: Temp = 251.583024047782, Press = 88.5278170014344 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.134 | 4.134 | 4.134 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -17682.314 -17682.314 -17745.647 -17745.647 245.10401 245.10401 31271.469 31271.469 -1007.2841 -1007.2841 2000 -17680.018 -17680.018 -17745.912 -17745.912 255.01744 255.01744 31277.129 31277.129 -1329.3401 -1329.3401 Loop time of 4.57903 on 1 procs for 1000 steps with 2000 atoms Performance: 18.869 ns/day, 1.272 hours/ns, 218.387 timesteps/s, 436.774 katom-step/s 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4937 | 4.4937 | 4.4937 | 0.0 | 98.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014893 | 0.014893 | 0.014893 | 0.0 | 0.33 Output | 5.2759e-05 | 5.2759e-05 | 5.2759e-05 | 0.0 | 0.00 Modify | 0.064837 | 0.064837 | 0.064837 | 0.0 | 1.42 Other | | 0.005588 | | | 0.12 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119 ave 4119 max 4119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 224002 ave 224002 max 224002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224002 Ave neighs/atom = 112.001 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 253.06197510757, Press = 9.32529568013443 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.134 | 4.134 | 4.134 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -17680.018 -17680.018 -17745.912 -17745.912 255.01744 255.01744 31277.129 31277.129 -1329.3401 -1329.3401 3000 -17682.91 -17682.91 -17748.179 -17748.179 252.59829 252.59829 31258.734 31258.734 329.04285 329.04285 Loop time of 4.23254 on 1 procs for 1000 steps with 2000 atoms Performance: 20.413 ns/day, 1.176 hours/ns, 236.265 timesteps/s, 472.530 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1528 | 4.1528 | 4.1528 | 0.0 | 98.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014301 | 0.014301 | 0.014301 | 0.0 | 0.34 Output | 5.8109e-05 | 5.8109e-05 | 5.8109e-05 | 0.0 | 0.00 Modify | 0.060098 | 0.060098 | 0.060098 | 0.0 | 1.42 Other | | 0.005319 | | | 0.13 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119 ave 4119 max 4119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 224004 ave 224004 max 224004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224004 Ave neighs/atom = 112.002 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 253.127493062299, Press = 6.715629102498 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.134 | 4.134 | 4.134 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -17682.91 -17682.91 -17748.179 -17748.179 252.59829 252.59829 31258.734 31258.734 329.04285 329.04285 4000 -17680.067 -17680.067 -17745.187 -17745.187 252.02267 252.02267 31273.795 31273.795 -364.02256 -364.02256 Loop time of 4.2241 on 1 procs for 1000 steps with 2000 atoms Performance: 20.454 ns/day, 1.173 hours/ns, 236.737 timesteps/s, 473.474 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1447 | 4.1447 | 4.1447 | 0.0 | 98.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.013847 | 0.013847 | 0.013847 | 0.0 | 0.33 Output | 3.9284e-05 | 3.9284e-05 | 3.9284e-05 | 0.0 | 0.00 Modify | 0.060039 | 0.060039 | 0.060039 | 0.0 | 1.42 Other | | 0.005424 | | | 0.13 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119 ave 4119 max 4119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 224002 ave 224002 max 224002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224002 Ave neighs/atom = 112.001 Neighbor list builds = 0 Dangerous builds = 0 if "${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 31270.2206606287 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0