# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.163879469037056*${_u_distance} variable latticeconst_converted equal 3.163879469037056*1 lattice bcc ${latticeconst_converted} lattice bcc 3.16387946903706 Lattice spacing in x,y,z = 3.1638795 3.1638795 3.1638795 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (31.638795 31.638795 31.638795) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (31.638795 31.638795 31.638795) create_atoms CPU = 0.000 seconds variable mass_converted equal 183.84*${_u_mass} variable mass_converted equal 183.84*1 kim interactions W #=== BEGIN kim interactions ================================== pair_style kim MEAM_LAMMPS_ShimParkCho_2003_NiW__MO_500937681860_002 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 31670.855213091 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 31670.855213091/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 31670.855213091/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 31670.855213091/(1*1*${_u_distance}) variable V0_metal equal 31670.855213091/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 31670.855213091*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 31670.855213091 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_500937681860_002#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 10 10 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) = 3.755 | 3.755 | 3.755 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -17244.253 -17244.253 -17320 -17320 293.15 293.15 31670.855 31670.855 2554.5905 2554.5905 1000 -17162.168 -17162.168 -17235.473 -17235.473 283.7004 283.7004 31784.835 31784.835 518.32191 518.32191 Loop time of 23.5343 on 1 procs for 1000 steps with 2000 atoms Performance: 3.671 ns/day, 6.537 hours/ns, 42.491 timesteps/s, 84.982 katom-step/s 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.434 | 23.434 | 23.434 | 0.0 | 99.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01949 | 0.01949 | 0.01949 | 0.0 | 0.08 Output | 0.00016342 | 0.00016342 | 0.00016342 | 0.0 | 0.00 Modify | 0.069473 | 0.069473 | 0.069473 | 0.0 | 0.30 Other | | 0.01109 | | | 0.05 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: 128000 ave 128000 max 128000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128000 Ave neighs/atom = 64 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 = ${P}" flag: Temp = 292.786164037935, Press = -56.8100643499801 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.755 | 3.755 | 3.755 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -17162.168 -17162.168 -17235.473 -17235.473 283.7004 283.7004 31784.835 31784.835 518.32191 518.32191 2000 -17165.925 -17165.925 -17242.799 -17242.799 297.5087 297.5087 31815.67 31815.67 -2971.6169 -2971.6169 Loop time of 28.7418 on 1 procs for 1000 steps with 2000 atoms Performance: 3.006 ns/day, 7.984 hours/ns, 34.792 timesteps/s, 69.585 katom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.625 | 28.625 | 28.625 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.022582 | 0.022582 | 0.022582 | 0.0 | 0.08 Output | 5.7788e-05 | 5.7788e-05 | 5.7788e-05 | 0.0 | 0.00 Modify | 0.081365 | 0.081365 | 0.081365 | 0.0 | 0.28 Other | | 0.01271 | | | 0.04 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119 ave 4119 max 4119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 127900 ave 127900 max 127900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127900 Ave neighs/atom = 63.95 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 293.021775999566, Press = -12.6780626138315 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.755 | 3.755 | 3.755 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -17165.925 -17165.925 -17242.799 -17242.799 297.5087 297.5087 31815.67 31815.67 -2971.6169 -2971.6169 3000 -17167.272 -17167.272 -17242.052 -17242.052 289.40766 289.40766 31809.127 31809.127 -2341.4013 -2341.4013 Loop time of 28.5933 on 1 procs for 1000 steps with 2000 atoms Performance: 3.022 ns/day, 7.943 hours/ns, 34.973 timesteps/s, 69.947 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.489 | 28.489 | 28.489 | 0.0 | 99.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.019924 | 0.019924 | 0.019924 | 0.0 | 0.07 Output | 8.4659e-05 | 8.4659e-05 | 8.4659e-05 | 0.0 | 0.00 Modify | 0.074901 | 0.074901 | 0.074901 | 0.0 | 0.26 Other | | 0.009803 | | | 0.03 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4115 ave 4115 max 4115 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 127918 ave 127918 max 127918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127918 Ave neighs/atom = 63.959 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 293.115250331301, Press = -5.70948245920424 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.755 | 3.755 | 3.755 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -17167.272 -17167.272 -17242.052 -17242.052 289.40766 289.40766 31809.127 31809.127 -2341.4013 -2341.4013 4000 -17174.635 -17174.635 -17249.262 -17249.262 288.81244 288.81244 31769.166 31769.166 913.35937 913.35937 Loop time of 26.6005 on 1 procs for 1000 steps with 2000 atoms Performance: 3.248 ns/day, 7.389 hours/ns, 37.593 timesteps/s, 75.187 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 26.511 | 26.511 | 26.511 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01601 | 0.01601 | 0.01601 | 0.0 | 0.06 Output | 0.00013202 | 0.00013202 | 0.00013202 | 0.0 | 0.00 Modify | 0.065931 | 0.065931 | 0.065931 | 0.0 | 0.25 Other | | 0.007462 | | | 0.03 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4116 ave 4116 max 4116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 127906 ave 127906 max 127906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127906 Ave neighs/atom = 63.953 Neighbor list builds = 0 Dangerous builds = 0 if "${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 31784.8273535551 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0