# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.524220451712608*${_u_distance} variable latticeconst_converted equal 3.524220451712608*1 lattice fcc ${latticeconst_converted} lattice fcc 3.52422045171261 Lattice spacing in x,y,z = 3.5242205 3.5242205 3.5242205 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (35.242205 35.242205 35.242205) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (35.242205 35.242205 35.242205) create_atoms CPU = 0.000 seconds variable mass_converted equal 58.6934*${_u_mass} variable mass_converted equal 58.6934*1 kim interactions Ni #=== BEGIN kim interactions ================================== pair_style kim EAM_Dynamo_AcklandTichyVitek_1987v2_Ni__MO_769632475533_000 pair_coeff * * Ni #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 58.6934 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 43771.275426841 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 43771.275426841/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 43771.275426841/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 43771.275426841/(1*1*${_u_distance}) variable V0_metal equal 43771.275426841/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 43771.275426841*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 43771.275426841 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 313.15*${_u_temperature} variable temp_converted equal 313.15*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 313.15 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 313.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "313.15 - 1.0" variable T_up equal "313.15 + 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_769632475533_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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 12 12 12 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) = 4.61 | 4.61 | 4.61 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -17674.119 -17674.119 -17835.99 -17835.99 313.15 313.15 43771.275 43771.275 3949.9291 3949.9291 1000 -17509.619 -17509.619 -17672.832 -17672.832 315.74631 315.74631 44567.671 44567.671 451.51694 451.51694 Loop time of 5.78764 on 1 procs for 1000 steps with 4000 atoms Performance: 14.928 ns/day, 1.608 hours/ns, 172.782 timesteps/s, 691.128 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 | 5.616 | 5.616 | 5.616 | 0.0 | 97.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.024302 | 0.024302 | 0.024302 | 0.0 | 0.42 Output | 0.00010354 | 0.00010354 | 0.00010354 | 0.0 | 0.00 Modify | 0.13411 | 0.13411 | 0.13411 | 0.0 | 2.32 Other | | 0.01309 | | | 0.23 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 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: 344000 ave 344000 max 344000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 344000 Ave neighs/atom = 86 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 = ${P}" flag: Temp = 311.947165772647, Press = -34.3973981375572 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 12 12 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.61 | 4.61 | 4.61 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -17509.619 -17509.619 -17672.832 -17672.832 315.74631 315.74631 44567.671 44567.671 451.51694 451.51694 2000 -17512.936 -17512.936 -17672.783 -17672.783 309.23581 309.23581 44609.501 44609.501 -1761.3244 -1761.3244 Loop time of 6.17382 on 1 procs for 1000 steps with 4000 atoms Performance: 13.995 ns/day, 1.715 hours/ns, 161.974 timesteps/s, 647.897 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9964 | 5.9964 | 5.9964 | 0.0 | 97.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.024557 | 0.024557 | 0.024557 | 0.0 | 0.40 Output | 6.7246e-05 | 6.7246e-05 | 6.7246e-05 | 0.0 | 0.00 Modify | 0.13906 | 0.13906 | 0.13906 | 0.0 | 2.25 Other | | 0.01373 | | | 0.22 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 343522 ave 343522 max 343522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 343522 Ave neighs/atom = 85.8805 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.892372154311, Press = -5.94750998856022 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 12 12 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.61 | 4.61 | 4.61 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -17512.936 -17512.936 -17672.783 -17672.783 309.23581 309.23581 44609.501 44609.501 -1761.3244 -1761.3244 3000 -17509.959 -17509.959 -17671.296 -17671.296 312.11686 312.11686 44630.719 44630.719 -2215.7211 -2215.7211 Loop time of 5.94525 on 1 procs for 1000 steps with 4000 atoms Performance: 14.533 ns/day, 1.651 hours/ns, 168.202 timesteps/s, 672.807 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7715 | 5.7715 | 5.7715 | 0.0 | 97.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.023408 | 0.023408 | 0.023408 | 0.0 | 0.39 Output | 4.1758e-05 | 4.1758e-05 | 4.1758e-05 | 0.0 | 0.00 Modify | 0.1376 | 0.1376 | 0.1376 | 0.0 | 2.31 Other | | 0.01274 | | | 0.21 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 343546 ave 343546 max 343546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 343546 Ave neighs/atom = 85.8865 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T313.15.out" else "print 'not_converged' file output/vol_T313.15.out" print '${V}' file output/vol_T313.15.out 44574.430039484 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0