# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 2.863645777106285*${_u_distance} variable latticeconst_converted equal 2.863645777106285*1 lattice bcc ${latticeconst_converted} lattice bcc 2.86364577710629 Lattice spacing in x,y,z = 2.8636458 2.8636458 2.8636458 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (28.636458 28.636458 28.636458) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (28.636458 28.636458 28.636458) create_atoms CPU = 0.000 seconds variable mass_converted equal 55.845*${_u_mass} variable mass_converted equal 55.845*1 kim interactions Fe #=== BEGIN kim interactions ================================== pair_style kim MEAM_LAMMPS_KimLee_2006_PtFe__MO_343168101490_002 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 23483.2330864207 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 23483.2330864207/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 23483.2330864207/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 23483.2330864207/(1*1*${_u_distance}) variable V0_metal equal 23483.2330864207/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 23483.2330864207*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 23483.2330864207 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_343168101490_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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, 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) = 3.753 | 3.753 | 3.753 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -8509.8399 -8509.8399 -8580.4194 -8580.4194 273.15 273.15 23483.233 23483.233 3210.2838 3210.2838 1000 -8434.4641 -8434.4641 -8504.4537 -8504.4537 270.86693 270.86693 23670.427 23670.427 2889.0357 2889.0357 Loop time of 52.8833 on 1 procs for 1000 steps with 2000 atoms Performance: 1.634 ns/day, 14.690 hours/ns, 18.910 timesteps/s, 37.819 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 | 52.791 | 52.791 | 52.791 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.017162 | 0.017162 | 0.017162 | 0.0 | 0.03 Output | 7.3658e-05 | 7.3658e-05 | 7.3658e-05 | 0.0 | 0.00 Modify | 0.067477 | 0.067477 | 0.067477 | 0.0 | 0.13 Other | | 0.00772 | | | 0.01 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: 176000 ave 176000 max 176000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176000 Ave neighs/atom = 88 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 = ${P}" flag: Temp = 273.09109342284, Press = 138.912869557984 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.753 | 3.753 | 3.753 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -8434.4641 -8434.4641 -8504.4537 -8504.4537 270.86693 270.86693 23670.427 23670.427 2889.0357 2889.0357 2000 -8439.8228 -8439.8228 -8510.0874 -8510.0874 271.93145 271.93145 23678.453 23678.453 1295.023 1295.023 Loop time of 55.9182 on 1 procs for 1000 steps with 2000 atoms Performance: 1.545 ns/day, 15.533 hours/ns, 17.883 timesteps/s, 35.767 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 55.838 | 55.838 | 55.838 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014115 | 0.014115 | 0.014115 | 0.0 | 0.03 Output | 6.0704e-05 | 6.0704e-05 | 6.0704e-05 | 0.0 | 0.00 Modify | 0.061129 | 0.061129 | 0.061129 | 0.0 | 0.11 Other | | 0.005256 | | | 0.01 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119 ave 4119 max 4119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 192454 ave 192454 max 192454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192454 Ave neighs/atom = 96.227 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 273.044787795641, Press = 8.53908409545038 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.753 | 3.753 | 3.753 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -8439.8228 -8439.8228 -8510.0874 -8510.0874 271.93145 271.93145 23678.453 23678.453 1295.023 1295.023 3000 -8440.2355 -8440.2355 -8508.8963 -8508.8963 265.72432 265.72432 23694.111 23694.111 481.39459 481.39459 Loop time of 55.6667 on 1 procs for 1000 steps with 2000 atoms Performance: 1.552 ns/day, 15.463 hours/ns, 17.964 timesteps/s, 35.928 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 55.587 | 55.587 | 55.587 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014024 | 0.014024 | 0.014024 | 0.0 | 0.03 Output | 5.4973e-05 | 5.4973e-05 | 5.4973e-05 | 0.0 | 0.00 Modify | 0.060344 | 0.060344 | 0.060344 | 0.0 | 0.11 Other | | 0.005005 | | | 0.01 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119 ave 4119 max 4119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 192608 ave 192608 max 192608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 192608 Ave neighs/atom = 96.304 Neighbor list builds = 0 Dangerous builds = 0 if "${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 23706.0973566915 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0