# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 6.1438429802656245*${_u_distance} variable latticeconst_converted equal 6.1438429802656245*1 lattice fcc ${latticeconst_converted} lattice fcc 6.14384298026562 Lattice spacing in x,y,z = 6.143843 6.143843 6.143843 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (61.43843 61.43843 61.43843) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (61.43843 61.43843 61.43843) create_atoms CPU = 0.001 seconds variable mass_converted equal 131.293*${_u_mass} variable mass_converted equal 131.293*1 kim interactions Xe #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958MedCutoff_Xe__MO_849320763277_004 pair_coeff * * Xe #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 131.293 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 231910.452548941 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 231910.452548941/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 231910.452548941/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 231910.452548941/(1*1*${_u_distance}) variable V0_metal equal 231910.452548941/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 231910.452548941*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 231910.452548941 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 333.15*${_u_temperature} variable temp_converted equal 333.15*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 333.15 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 333.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "333.15 - 1.0" variable T_up equal "333.15 + 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_849320763277_004#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 = 17.9 ghost atom cutoff = 17.9 binsize = 8.95, bins = 7 7 7 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) = 9.434 | 9.434 | 9.434 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -493.68906 -493.68906 -665.89806 -665.89806 333.15 333.15 231910.45 231910.45 793.149 793.149 1000 -175.86312 -175.86312 -346.06581 -346.06581 329.26865 329.26865 392136.29 392136.29 -0.76114595 -0.76114595 Loop time of 24.1457 on 1 procs for 1000 steps with 4000 atoms Performance: 3.578 ns/day, 6.707 hours/ns, 41.415 timesteps/s, 165.661 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 | 23.262 | 23.262 | 23.262 | 0.0 | 96.34 Neigh | 0.67083 | 0.67083 | 0.67083 | 0.0 | 2.78 Comm | 0.045479 | 0.045479 | 0.045479 | 0.0 | 0.19 Output | 0.00015154 | 0.00015154 | 0.00015154 | 0.0 | 0.00 Modify | 0.14697 | 0.14697 | 0.14697 | 0.0 | 0.61 Other | | 0.01981 | | | 0.08 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9207 ave 9207 max 9207 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: 981014 ave 981014 max 981014 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 981014 Ave neighs/atom = 245.2535 Neighbor list builds = 22 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 = ${P}" flag: Temp = 332.081686040562, Press = 3.69532338257519 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.9 ghost atom cutoff = 17.9 binsize = 8.95, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.138 | 7.138 | 7.138 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -175.86312 -175.86312 -346.06581 -346.06581 329.26865 329.26865 392136.29 392136.29 -0.76114595 -0.76114595 2000 -106.32274 -106.32274 -279.86902 -279.86902 335.73705 335.73705 480604.57 480604.57 -30.284538 -30.284538 Loop time of 18.303 on 1 procs for 1000 steps with 4000 atoms Performance: 4.721 ns/day, 5.084 hours/ns, 54.636 timesteps/s, 218.544 katom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.775 | 17.775 | 17.775 | 0.0 | 97.11 Neigh | 0.31482 | 0.31482 | 0.31482 | 0.0 | 1.72 Comm | 0.038548 | 0.038548 | 0.038548 | 0.0 | 0.21 Output | 9.4016e-05 | 9.4016e-05 | 9.4016e-05 | 0.0 | 0.00 Modify | 0.15549 | 0.15549 | 0.15549 | 0.0 | 0.85 Other | | 0.0191 | | | 0.10 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8473 ave 8473 max 8473 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 802076 ave 802076 max 802076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 802076 Ave neighs/atom = 200.519 Neighbor list builds = 13 Dangerous builds = 0 if "${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_T333.15.out" else "print 'not_converged' file output/vol_T333.15.out" print '${V}' file output/vol_T333.15.out 432157.975123142 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0