# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.9200811892747867*${_u_distance} variable latticeconst_converted equal 3.9200811892747867*1 lattice fcc ${latticeconst_converted} lattice fcc 3.92008118927479 Lattice spacing in x,y,z = 3.9200812 3.9200812 3.9200812 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (39.200812 39.200812 39.200812) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (39.200812 39.200812 39.200812) create_atoms CPU = 0.001 seconds variable mass_converted equal 195.078*${_u_mass} variable mass_converted equal 195.078*1 kim interactions Pt #=== BEGIN kim interactions ================================== pair_style kim EAM_Dynamo_ZhouJohnsonWadley_2004NISTretabulation_Pt__MO_601539325066_000 pair_coeff * * Pt #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 195.078 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 60240.0308381353 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 60240.0308381353/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 60240.0308381353/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 60240.0308381353/(1*1*${_u_distance}) variable V0_metal equal 60240.0308381353/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 60240.0308381353*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 60240.0308381353 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 273.15*${_u_temperature} variable temp_converted equal 273.15*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 273.15 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 273.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "273.15 - 1.0" variable T_up equal "273.15 + 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_601539325066_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 = 8.1981926 ghost atom cutoff = 8.1981926 binsize = 4.0990963, 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) = 5.481 | 5.481 | 5.481 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -22938.793 -22938.793 -23079.988 -23079.988 273.15 273.15 60240.031 60240.031 2503.7312 2503.7312 1000 -22791.068 -22791.068 -22931.07 -22931.07 270.84434 270.84434 60905.434 60905.434 -2023.0409 -2023.0409 Loop time of 11.0112 on 1 procs for 1000 steps with 4000 atoms Performance: 7.847 ns/day, 3.059 hours/ns, 90.817 timesteps/s, 363.266 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 | 10.828 | 10.828 | 10.828 | 0.0 | 98.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.031952 | 0.031952 | 0.031952 | 0.0 | 0.29 Output | 9.1191e-05 | 9.1191e-05 | 9.1191e-05 | 0.0 | 0.00 Modify | 0.13704 | 0.13704 | 0.13704 | 0.0 | 1.24 Other | | 0.01388 | | | 0.13 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 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: 560000 ave 560000 max 560000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 560000 Ave neighs/atom = 140 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 = ${P}" flag: Temp = 272.990959730289, Press = 5.69713138413878 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1981926 ghost atom cutoff = 8.1981926 binsize = 4.0990963, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.481 | 5.481 | 5.481 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -22791.068 -22791.068 -22931.07 -22931.07 270.84434 270.84434 60905.434 60905.434 -2023.0409 -2023.0409 2000 -22773.59 -22773.59 -22916.222 -22916.222 275.93021 275.93021 60909.127 60909.127 448.53937 448.53937 Loop time of 12.0365 on 1 procs for 1000 steps with 4000 atoms Performance: 7.178 ns/day, 3.343 hours/ns, 83.081 timesteps/s, 332.323 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.847 | 11.847 | 11.847 | 0.0 | 98.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.03292 | 0.03292 | 0.03292 | 0.0 | 0.27 Output | 8.3376e-05 | 8.3376e-05 | 8.3376e-05 | 0.0 | 0.00 Modify | 0.1417 | 0.1417 | 0.1417 | 0.0 | 1.18 Other | | 0.0143 | | | 0.12 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 575536 ave 575536 max 575536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 575536 Ave neighs/atom = 143.884 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 273.180944865163, Press = 5.64533922226344 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1981926 ghost atom cutoff = 8.1981926 binsize = 4.0990963, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.481 | 5.481 | 5.481 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -22773.59 -22773.59 -22916.222 -22916.222 275.93021 275.93021 60909.127 60909.127 448.53937 448.53937 3000 -22776.619 -22776.619 -22915.657 -22915.657 268.97892 268.97892 60927.813 60927.813 -860.60411 -860.60411 Loop time of 12.2296 on 1 procs for 1000 steps with 4000 atoms Performance: 7.065 ns/day, 3.397 hours/ns, 81.769 timesteps/s, 327.076 katom-step/s 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.039 | 12.039 | 12.039 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.033084 | 0.033084 | 0.033084 | 0.0 | 0.27 Output | 9.8504e-05 | 9.8504e-05 | 9.8504e-05 | 0.0 | 0.00 Modify | 0.14266 | 0.14266 | 0.14266 | 0.0 | 1.17 Other | | 0.01441 | | | 0.12 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 577614 ave 577614 max 577614 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 577614 Ave neighs/atom = 144.4035 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T273.15.out" else "print 'not_converged' file output/vol_T273.15.out" print '${V}' file output/vol_T273.15.out 60862.8208623779 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0