# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 6.083469396829612*${_u_distance} variable latticeconst_converted equal 6.083469396829612*1 lattice fcc ${latticeconst_converted} lattice fcc 6.08346939682961 Lattice spacing in x,y,z = 6.0834694 6.0834694 6.0834694 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (60.834694 60.834694 60.834694) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (60.834694 60.834694 60.834694) create_atoms CPU = 0.001 seconds variable mass_converted equal 87.62*${_u_mass} variable mass_converted equal 87.62*1 kim interactions Sr #=== BEGIN kim interactions ================================== pair_style kim Morse_Shifted_GirifalcoWeizer_1959MedCutoff_Sr__MO_964297938209_004 pair_coeff * * Sr #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 87.62 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 225140.684924316 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 225140.684924316/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 225140.684924316/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 225140.684924316/(1*1*${_u_distance}) variable V0_metal equal 225140.684924316/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 225140.684924316*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 225140.684924316 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 253.15*${_u_temperature} variable temp_converted equal 253.15*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 253.15 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 253.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "253.15 - 1.0" variable T_up equal "253.15 + 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_964297938209_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 = 17.4319 ghost atom cutoff = 17.4319 binsize = 8.71595, 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 -6707.5723 -6707.5723 -6838.4284 -6838.4284 253.15 253.15 225140.68 225140.68 620.81125 620.81125 1000 -6571.6383 -6571.6383 -6704.1717 -6704.1717 256.39469 256.39469 229110.43 229110.43 -74.04111 -74.04111 Loop time of 30.511 on 1 procs for 1000 steps with 4000 atoms Performance: 2.832 ns/day, 8.475 hours/ns, 32.775 timesteps/s, 131.100 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 | 30.07 | 30.07 | 30.07 | 0.0 | 98.55 Neigh | 0.2357 | 0.2357 | 0.2357 | 0.0 | 0.77 Comm | 0.04503 | 0.04503 | 0.04503 | 0.0 | 0.15 Output | 0.00014932 | 0.00014932 | 0.00014932 | 0.0 | 0.00 Modify | 0.1416 | 0.1416 | 0.1416 | 0.0 | 0.46 Other | | 0.01889 | | | 0.06 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10895 ave 10895 max 10895 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: 1.51516e+06 ave 1.51516e+06 max 1.51516e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1515158 Ave neighs/atom = 378.7895 Neighbor list builds = 7 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 = ${P}" flag: Temp = 254.444938216701, Press = -7.70473765518135 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.4319 ghost atom cutoff = 17.4319 binsize = 8.71595, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 9.438 | 9.438 | 9.438 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -6571.6383 -6571.6383 -6704.1717 -6704.1717 256.39469 256.39469 229110.43 229110.43 -74.04111 -74.04111 2000 -6565.3535 -6565.3535 -6698.4733 -6698.4733 257.52926 257.52926 229083.7 229083.7 17.33076 17.33076 Loop time of 31.7474 on 1 procs for 1000 steps with 4000 atoms Performance: 2.721 ns/day, 8.819 hours/ns, 31.499 timesteps/s, 125.995 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 31.339 | 31.339 | 31.339 | 0.0 | 98.71 Neigh | 0.20162 | 0.20162 | 0.20162 | 0.0 | 0.64 Comm | 0.044883 | 0.044883 | 0.044883 | 0.0 | 0.14 Output | 7.8347e-05 | 7.8347e-05 | 7.8347e-05 | 0.0 | 0.00 Modify | 0.14408 | 0.14408 | 0.14408 | 0.0 | 0.45 Other | | 0.01735 | | | 0.05 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10895 ave 10895 max 10895 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.51669e+06 ave 1.51669e+06 max 1.51669e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1516688 Ave neighs/atom = 379.172 Neighbor list builds = 6 Dangerous builds = 0 if "${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_T253.15.out" else "print 'not_converged' file output/vol_T253.15.out" print '${V}' file output/vol_T253.15.out 229009.480642129 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0