# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 6.070152866840363*${_u_distance} variable latticeconst_converted equal 6.070152866840363*1 lattice fcc ${latticeconst_converted} lattice fcc 6.07015286684036 Lattice spacing in x,y,z = 6.0701529 6.0701529 6.0701529 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (60.701529 60.701529 60.701529) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (60.701529 60.701529 60.701529) create_atoms CPU = 0.001 seconds variable mass_converted equal 87.62*${_u_mass} variable mass_converted equal 87.62*1 kim interactions Sr #=== BEGIN kim interactions ================================== pair_style kim Morse_Shifted_GirifalcoWeizer_1959HighCutoff_Sr__MO_497591319122_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 223665.440515879 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 223665.440515879/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 223665.440515879/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 223665.440515879/(1*1*${_u_distance}) variable V0_metal equal 223665.440515879/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 223665.440515879*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 223665.440515879 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_497591319122_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 = 20.5961 ghost atom cutoff = 20.5961 binsize = 10.29805, bins = 6 6 6 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) = 16.55 | 16.55 | 16.55 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -6791.5606 -6791.5606 -6922.4167 -6922.4167 253.15 253.15 223665.44 223665.44 624.90615 624.90615 1000 -6655.322 -6655.322 -6788.1373 -6788.1373 256.94027 256.94027 227400.18 227400.18 167.85662 167.85662 Loop time of 55.2989 on 1 procs for 1000 steps with 4000 atoms Performance: 1.562 ns/day, 15.361 hours/ns, 18.084 timesteps/s, 72.334 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 | 54.601 | 54.601 | 54.601 | 0.0 | 98.74 Neigh | 0.46037 | 0.46037 | 0.46037 | 0.0 | 0.83 Comm | 0.059281 | 0.059281 | 0.059281 | 0.0 | 0.11 Output | 0.00015406 | 0.00015406 | 0.00015406 | 0.0 | 0.00 Modify | 0.15661 | 0.15661 | 0.15661 | 0.0 | 0.28 Other | | 0.02138 | | | 0.04 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13969 ave 13969 max 13969 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: 2.55573e+06 ave 2.55573e+06 max 2.55573e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2555726 Ave neighs/atom = 638.9315 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 = ${P}" flag: Temp = 254.227633500764, Press = -0.197324195714506 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5961 ghost atom cutoff = 20.5961 binsize = 10.29805, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 16.42 | 16.42 | 16.42 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -6655.322 -6655.322 -6788.1373 -6788.1373 256.94027 256.94027 227400.18 227400.18 167.85662 167.85662 2000 -6653.9986 -6653.9986 -6783.3609 -6783.3609 250.26017 250.26017 227585.7 227585.7 120.4663 120.4663 Loop time of 55.0963 on 1 procs for 1000 steps with 4000 atoms Performance: 1.568 ns/day, 15.305 hours/ns, 18.150 timesteps/s, 72.600 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 54.472 | 54.472 | 54.472 | 0.0 | 98.87 Neigh | 0.40425 | 0.40425 | 0.40425 | 0.0 | 0.73 Comm | 0.056492 | 0.056492 | 0.056492 | 0.0 | 0.10 Output | 8.1914e-05 | 8.1914e-05 | 8.1914e-05 | 0.0 | 0.00 Modify | 0.14558 | 0.14558 | 0.14558 | 0.0 | 0.26 Other | | 0.01787 | | | 0.03 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13970 ave 13970 max 13970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.55857e+06 ave 2.55857e+06 max 2.55857e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2558574 Ave neighs/atom = 639.6435 Neighbor list builds = 6 Dangerous builds = 0 if "${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 227774.338498098 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0