# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.302538052201271*${_u_distance} variable latticeconst_converted equal 3.302538052201271*1 lattice bcc ${latticeconst_converted} lattice bcc 3.30253805220127 Lattice spacing in x,y,z = 3.3025381 3.3025381 3.3025381 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (33.025381 33.025381 33.025381) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (33.025381 33.025381 33.025381) create_atoms CPU = 0.000 seconds variable mass_converted equal 180.9479*${_u_mass} variable mass_converted equal 180.9479*1 kim interactions Ta #=== BEGIN kim interactions ================================== pair_style kim EAM_Dynamo_ZhouJohnsonWadley_2004NISTretabulation_CuTa__MO_950828638160_000 pair_coeff * * Ta #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 180.9479 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 36019.9819546838 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 36019.9819546838/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 36019.9819546838/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 36019.9819546838/(1*1*${_u_distance}) variable V0_metal equal 36019.9819546838/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 36019.9819546838*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 36019.9819546838 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_950828638160_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 = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, 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) = 4.196 | 4.196 | 4.196 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -16104.256 -16104.256 -16180.003 -16180.003 293.15 293.15 36019.982 36019.982 2246.2034 2246.2034 1000 -16020.993 -16020.993 -16096.688 -16096.688 292.94773 292.94773 36119.404 36119.404 -29.178057 -29.178057 Loop time of 4.24235 on 1 procs for 1000 steps with 2000 atoms Performance: 20.366 ns/day, 1.178 hours/ns, 235.718 timesteps/s, 471.437 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 | 4.1534 | 4.1534 | 4.1534 | 0.0 | 97.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.019656 | 0.019656 | 0.019656 | 0.0 | 0.46 Output | 8.4539e-05 | 8.4539e-05 | 8.4539e-05 | 0.0 | 0.00 Modify | 0.062778 | 0.062778 | 0.062778 | 0.0 | 1.48 Other | | 0.006447 | | | 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: 272000 ave 272000 max 272000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272000 Ave neighs/atom = 136 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 = ${P}" flag: Temp = 292.19677538022, Press = -32.6755021977789 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.195 | 4.195 | 4.195 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -16020.993 -16020.993 -16096.688 -16096.688 292.94773 292.94773 36119.404 36119.404 -29.178057 -29.178057 2000 -16029.756 -16029.756 -16106.895 -16106.895 298.53465 298.53465 36153.113 36153.113 -922.13534 -922.13534 Loop time of 4.98716 on 1 procs for 1000 steps with 2000 atoms Performance: 17.325 ns/day, 1.385 hours/ns, 200.515 timesteps/s, 401.030 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8983 | 4.8983 | 4.8983 | 0.0 | 98.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.019123 | 0.019123 | 0.019123 | 0.0 | 0.38 Output | 3.196e-05 | 3.196e-05 | 3.196e-05 | 0.0 | 0.00 Modify | 0.063488 | 0.063488 | 0.063488 | 0.0 | 1.27 Other | | 0.006163 | | | 0.12 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5395 ave 5395 max 5395 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 274724 ave 274724 max 274724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 274724 Ave neighs/atom = 137.362 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 293.596839298634, Press = -6.10495518325618 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.196 | 4.196 | 4.196 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -16029.756 -16029.756 -16106.895 -16106.895 298.53465 298.53465 36153.113 36153.113 -922.13534 -922.13534 3000 -16031.668 -16031.668 -16108.748 -16108.748 298.30724 298.30724 36136.028 36136.028 17.484031 17.484031 Loop time of 5.06106 on 1 procs for 1000 steps with 2000 atoms Performance: 17.072 ns/day, 1.406 hours/ns, 197.587 timesteps/s, 395.174 katom-step/s 98.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9723 | 4.9723 | 4.9723 | 0.0 | 98.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.019478 | 0.019478 | 0.019478 | 0.0 | 0.38 Output | 4.6868e-05 | 4.6868e-05 | 4.6868e-05 | 0.0 | 0.00 Modify | 0.063142 | 0.063142 | 0.063142 | 0.0 | 1.25 Other | | 0.006091 | | | 0.12 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5427 ave 5427 max 5427 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 273302 ave 273302 max 273302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 273302 Ave neighs/atom = 136.651 Neighbor list builds = 0 Dangerous builds = 0 if "${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 36128.5308010463 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0