# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.8000004738569264*${_u_distance} variable latticeconst_converted equal 3.8000004738569264*1 lattice fcc ${latticeconst_converted} lattice fcc 3.80000047385693 Lattice spacing in x,y,z = 3.8000005 3.8000005 3.8000005 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (38.000005 38.000005 38.000005) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (38.000005 38.000005 38.000005) create_atoms CPU = 0.001 seconds variable mass_converted equal 102.9055*${_u_mass} variable mass_converted equal 102.9055*1 kim interactions Rh #=== BEGIN kim interactions ================================== variable kim_update equal 0 variable kim_periodic equal 1 pair_style adp pair_coeff * * /tmp/kim-shared-library-parameter-file-directory-XXXXXXel39lp/NiRh.adp.txt Rh #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 102.9055 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 54872.0205274848 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 54872.0205274848/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 54872.0205274848/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 54872.0205274848/(1*1*${_u_distance}) variable V0_metal equal 54872.0205274848/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 54872.0205274848*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 54872.0205274848 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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/SM_306597220004_000#item-citation CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.8454711 ghost atom cutoff = 8.8454711 binsize = 4.4227355, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.79 | 7.79 | 7.79 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -22827.791 -22827.791 -23000 -23000 333.15 333.15 54872.021 54872.021 3352.2443 3352.2443 1000 -22660.611 -22660.611 -22834.352 -22834.352 336.11382 336.11382 55242.926 55242.926 1072.4681 1072.4681 Loop time of 22.9325 on 1 procs for 1000 steps with 4000 atoms Performance: 3.768 ns/day, 6.370 hours/ns, 43.606 timesteps/s, 174.425 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 | 22.756 | 22.756 | 22.756 | 0.0 | 99.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.030974 | 0.030974 | 0.030974 | 0.0 | 0.14 Output | 0.00020518 | 0.00020518 | 0.00020518 | 0.0 | 0.00 Modify | 0.12948 | 0.12948 | 0.12948 | 0.0 | 0.56 Other | | 0.0163 | | | 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: 400000 ave 400000 max 400000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 400000 Ave neighs/atom = 100 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 = ${P}" flag: Temp = 335.534773072976, Press = 77.1250573971882 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 7.79 | 7.79 | 7.79 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -22660.611 -22660.611 -22834.352 -22834.352 336.11382 336.11382 55242.926 55242.926 1072.4681 1072.4681 2000 -22653.579 -22653.579 -22827.196 -22827.196 335.87487 335.87487 55280.748 55280.748 -319.47757 -319.47757 Loop time of 22.4908 on 1 procs for 1000 steps with 4000 atoms Performance: 3.842 ns/day, 6.247 hours/ns, 44.463 timesteps/s, 177.851 katom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.314 | 22.314 | 22.314 | 0.0 | 99.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.02851 | 0.02851 | 0.02851 | 0.0 | 0.13 Output | 7.1093e-05 | 7.1093e-05 | 7.1093e-05 | 0.0 | 0.00 Modify | 0.13318 | 0.13318 | 0.13318 | 0.0 | 0.59 Other | | 0.01468 | | | 0.07 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 406628 ave 406628 max 406628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 406628 Ave neighs/atom = 101.657 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 333.471403349546, Press = 5.00203151193522 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 7.79 | 7.79 | 7.79 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -22653.579 -22653.579 -22827.196 -22827.196 335.87487 335.87487 55280.748 55280.748 -319.47757 -319.47757 3000 -22644.743 -22644.743 -22813.858 -22813.858 327.16521 327.16521 55315.06 55315.06 -733.61314 -733.61314 Loop time of 22.2199 on 1 procs for 1000 steps with 4000 atoms Performance: 3.888 ns/day, 6.172 hours/ns, 45.005 timesteps/s, 180.019 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.055 | 22.055 | 22.055 | 0.0 | 99.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.027751 | 0.027751 | 0.027751 | 0.0 | 0.12 Output | 7.9098e-05 | 7.9098e-05 | 7.9098e-05 | 0.0 | 0.00 Modify | 0.1249 | 0.1249 | 0.1249 | 0.0 | 0.56 Other | | 0.01187 | | | 0.05 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 406880 ave 406880 max 406880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 406880 Ave neighs/atom = 101.72 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T333.15.out" else "print 'not_converged' file output/vol_T333.15.out" print '${V}' file output/vol_T333.15.out 55284.4901068645 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0