# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.188193768262863*${_u_distance} variable latticeconst_converted equal 3.188193768262863*1 lattice bcc ${latticeconst_converted} lattice bcc 3.18819376826286 Lattice spacing in x,y,z = 3.1881938 3.1881938 3.1881938 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (31.881938 31.881938 31.881938) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (31.881938 31.881938 31.881938) create_atoms CPU = 0.000 seconds variable mass_converted equal 183.84*${_u_mass} variable mass_converted equal 183.84*1 kim interactions W #=== BEGIN kim interactions ================================== variable kim_update equal 0 variable kim_periodic equal 1 pair_style meam/spline pair_coeff * * /tmp/kim-shared-library-parameter-file-directory-XXXXXXPLbgqJ/W_Lenosky_V2.meam.spline W #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 183.84 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 32406.6490316337 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 32406.6490316337/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 32406.6490316337/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 32406.6490316337/(1*1*${_u_distance}) variable V0_metal equal 32406.6490316337/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 32406.6490316337*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 32406.6490316337 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 273.15*${_u_temperature} variable temp_converted equal 273.15*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 273.15 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 273.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "273.15 - 1.0" variable T_up equal "273.15 + 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_163270462402_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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 9 9 9 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/spline, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/spline, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 5.147 | 5.147 | 5.147 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -17702.588 -17702.588 -17773.168 -17773.168 273.15 273.15 32406.649 32406.649 2326.2629 2326.2629 1000 -17630.787 -17630.787 -17702.922 -17702.922 279.17088 279.17088 32521.489 32521.489 -1333.7201 -1333.7201 Loop time of 82.3138 on 1 procs for 1000 steps with 2000 atoms Performance: 1.050 ns/day, 22.865 hours/ns, 12.149 timesteps/s, 24.297 katom-step/s 92.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 82.18 | 82.18 | 82.18 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.028552 | 0.028552 | 0.028552 | 0.0 | 0.03 Output | 8.1123e-05 | 8.1123e-05 | 8.1123e-05 | 0.0 | 0.00 Modify | 0.094262 | 0.094262 | 0.094262 | 0.0 | 0.11 Other | | 0.01075 | | | 0.01 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119 ave 4119 max 4119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112000 ave 112000 max 112000 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 224000 ave 224000 max 224000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224000 Ave neighs/atom = 112 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 = ${P}" flag: Temp = 271.77724568177, Press = 3.69983985633106 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.147 | 5.147 | 5.147 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -17630.787 -17630.787 -17702.922 -17702.922 279.17088 279.17088 32521.489 32521.489 -1333.7201 -1333.7201 2000 -17631.388 -17631.388 -17701.332 -17701.332 270.6882 270.6882 32503.517 32503.517 461.45062 461.45062 Loop time of 78.2196 on 1 procs for 1000 steps with 2000 atoms Performance: 1.105 ns/day, 21.728 hours/ns, 12.785 timesteps/s, 25.569 katom-step/s 96.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 78.107 | 78.107 | 78.107 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.017053 | 0.017053 | 0.017053 | 0.0 | 0.02 Output | 7.5722e-05 | 7.5722e-05 | 7.5722e-05 | 0.0 | 0.00 Modify | 0.086413 | 0.086413 | 0.086413 | 0.0 | 0.11 Other | | 0.009379 | | | 0.01 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119 ave 4119 max 4119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112000 ave 112000 max 112000 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 224000 ave 224000 max 224000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224000 Ave neighs/atom = 112 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 273.223982503455, Press = 5.17556633995343 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.147 | 5.147 | 5.147 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -17631.388 -17631.388 -17701.332 -17701.332 270.6882 270.6882 32503.517 32503.517 461.45062 461.45062 3000 -17631.383 -17631.383 -17701.421 -17701.421 271.05428 271.05428 32495.238 32495.238 1231.257 1231.257 Loop time of 75.7931 on 1 procs for 1000 steps with 2000 atoms Performance: 1.140 ns/day, 21.054 hours/ns, 13.194 timesteps/s, 26.388 katom-step/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 75.683 | 75.683 | 75.683 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.017655 | 0.017655 | 0.017655 | 0.0 | 0.02 Output | 6.8118e-05 | 6.8118e-05 | 6.8118e-05 | 0.0 | 0.00 Modify | 0.081291 | 0.081291 | 0.081291 | 0.0 | 0.11 Other | | 0.011 | | | 0.01 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119 ave 4119 max 4119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112000 ave 112000 max 112000 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 224000 ave 224000 max 224000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224000 Ave neighs/atom = 112 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T273.15.out" else "print 'not_converged' file output/vol_T273.15.out" print '${V}' file output/vol_T273.15.out 32508.7621738637 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0