# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.637506820261479*${_u_distance} variable latticeconst_converted equal 3.637506820261479*1 lattice fcc ${latticeconst_converted} lattice fcc 3.63750682026148 Lattice spacing in x,y,z = 3.6375068 3.6375068 3.6375068 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (36.375068 36.375068 36.375068) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (36.375068 36.375068 36.375068) create_atoms CPU = 0.001 seconds variable mass_converted equal 106.42*${_u_mass} variable mass_converted equal 106.42*1 kim interactions Pd #=== BEGIN kim interactions ================================== pair_style kim EAM_Dynamo_ZhouBarteltSills_2021_PdHHe__MO_865505436319_000 pair_coeff * * Pd #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 106.42 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 48129.5109598337 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 48129.5109598337/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 48129.5109598337/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 48129.5109598337/(1*1*${_u_distance}) variable V0_metal equal 48129.5109598337/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 48129.5109598337*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 48129.5109598337 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 293.15*${_u_temperature} variable temp_converted equal 293.15*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 293.15 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 293.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "293.15 - 1.0" variable T_up equal "293.15 + 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_865505436319_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 = 9 ghost atom cutoff = 9 binsize = 4.5, 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) = 7.386 | 7.386 | 7.386 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 34736.06 34736.06 34584.528 34584.528 293.15 293.15 48129.511 48129.511 3362.8439 3362.8439 1000 34899.274 34899.274 34746.244 34746.244 296.04724 296.04724 48923.391 48923.391 -597.50031 -597.50031 Loop time of 16.7663 on 1 procs for 1000 steps with 4000 atoms Performance: 5.153 ns/day, 4.657 hours/ns, 59.644 timesteps/s, 238.574 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 | 16.602 | 16.602 | 16.602 | 0.0 | 99.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.029579 | 0.029579 | 0.029579 | 0.0 | 0.18 Output | 0.00011842 | 0.00011842 | 0.00011842 | 0.0 | 0.00 Modify | 0.12175 | 0.12175 | 0.12175 | 0.0 | 0.73 Other | | 0.0124 | | | 0.07 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: 992000 ave 992000 max 992000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 992000 Ave neighs/atom = 248 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 = ${P}" flag: Temp = 294.290484053796, Press = -24.086355612248 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.006 | 7.006 | 7.006 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 34899.274 34899.274 34746.244 34746.244 296.04724 296.04724 48923.391 48923.391 -597.50031 -597.50031 2000 34915.112 34915.112 34761.521 34761.521 297.13131 297.13131 48959.532 48959.532 132.57128 132.57128 Loop time of 19.6329 on 1 procs for 1000 steps with 4000 atoms Performance: 4.401 ns/day, 5.454 hours/ns, 50.935 timesteps/s, 203.739 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.454 | 19.454 | 19.454 | 0.0 | 99.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.03175 | 0.03175 | 0.03175 | 0.0 | 0.16 Output | 8.8686e-05 | 8.8686e-05 | 8.8686e-05 | 0.0 | 0.00 Modify | 0.13415 | 0.13415 | 0.13415 | 0.0 | 0.68 Other | | 0.0132 | | | 0.07 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8316 ave 8316 max 8316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 958002 ave 958002 max 958002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 958002 Ave neighs/atom = 239.5005 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T293.15.out" else "print 'not_converged' file output/vol_T293.15.out" print '${V}' file output/vol_T293.15.out 48901.2544601305 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0