# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.1435002833604813*${_u_distance} variable latticeconst_converted equal 3.1435002833604813*1 lattice bcc ${latticeconst_converted} lattice bcc 3.14350028336048 Lattice spacing in x,y,z = 3.1435003 3.1435003 3.1435003 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (31.435003 31.435003 31.435003) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (31.435003 31.435003 31.435003) create_atoms CPU = 0.000 seconds variable mass_converted equal 95.94*${_u_mass} variable mass_converted equal 95.94*1 kim interactions Mo #=== BEGIN kim interactions ================================== pair_style kim Morse_Shifted_GirifalcoWeizer_1959MedCutoff_Mo__MO_534363225491_004 pair_coeff * * Mo #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 95.94 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 31062.7936380339 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 31062.7936380339/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 31062.7936380339/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 31062.7936380339/(1*1*${_u_distance}) variable V0_metal equal 31062.7936380339/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 31062.7936380339*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 31062.7936380339 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_534363225491_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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 7 7 7 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) = 5.424 | 5.424 | 5.424 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -13311.679 -13311.679 -13387.426 -13387.426 293.15 293.15 31062.794 31062.794 2604.5988 2604.5988 1000 -13236.083 -13236.083 -13309.603 -13309.603 284.53083 284.53083 31238.546 31238.546 -2524.2426 -2524.2426 Loop time of 7.0901 on 1 procs for 1000 steps with 2000 atoms Performance: 12.186 ns/day, 1.969 hours/ns, 141.042 timesteps/s, 282.083 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 | 6.9938 | 6.9938 | 6.9938 | 0.0 | 98.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.025147 | 0.025147 | 0.025147 | 0.0 | 0.35 Output | 4.3041e-05 | 4.3041e-05 | 4.3041e-05 | 0.0 | 0.00 Modify | 0.063719 | 0.063719 | 0.063719 | 0.0 | 0.90 Other | | 0.007401 | | | 0.10 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7009 ave 7009 max 7009 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: 564000 ave 564000 max 564000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 564000 Ave neighs/atom = 282 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 = ${P}" flag: Temp = 290.884514688393, Press = -67.3830569859385 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 7 7 7 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.426 | 5.426 | 5.426 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -13236.083 -13236.083 -13309.603 -13309.603 284.53083 284.53083 31238.546 31238.546 -2524.2426 -2524.2426 2000 -13237.435 -13237.435 -13313.393 -13313.393 293.96604 293.96604 31174.918 31174.918 3462.5324 3462.5324 Loop time of 7.04142 on 1 procs for 1000 steps with 2000 atoms Performance: 12.270 ns/day, 1.956 hours/ns, 142.017 timesteps/s, 284.034 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.9468 | 6.9468 | 6.9468 | 0.0 | 98.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.024194 | 0.024194 | 0.024194 | 0.0 | 0.34 Output | 4.272e-05 | 4.272e-05 | 4.272e-05 | 0.0 | 0.00 Modify | 0.063336 | 0.063336 | 0.063336 | 0.0 | 0.90 Other | | 0.007033 | | | 0.10 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7009 ave 7009 max 7009 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 545714 ave 545714 max 545714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 545714 Ave neighs/atom = 272.857 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.377870140846, Press = 7.59238351739025 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 7 7 7 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.426 | 5.426 | 5.426 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -13237.435 -13237.435 -13313.393 -13313.393 293.96604 293.96604 31174.918 31174.918 3462.5324 3462.5324 3000 -13257.953 -13257.953 -13330.852 -13330.852 282.12865 282.12865 31292.699 31292.699 -6227.8304 -6227.8304 Loop time of 6.62643 on 1 procs for 1000 steps with 2000 atoms Performance: 13.039 ns/day, 1.841 hours/ns, 150.911 timesteps/s, 301.822 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.525 | 6.525 | 6.525 | 0.0 | 98.47 Neigh | 0.012443 | 0.012443 | 0.012443 | 0.0 | 0.19 Comm | 0.022785 | 0.022785 | 0.022785 | 0.0 | 0.34 Output | 5.5975e-05 | 5.5975e-05 | 5.5975e-05 | 0.0 | 0.00 Modify | 0.059389 | 0.059389 | 0.059389 | 0.0 | 0.90 Other | | 0.006725 | | | 0.10 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6949 ave 6949 max 6949 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 547310 ave 547310 max 547310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 547310 Ave neighs/atom = 273.655 Neighbor list builds = 1 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 293.158803668902, Press = -6.43379819107115 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 7 7 7 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.426 | 5.426 | 5.426 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -13257.953 -13257.953 -13330.852 -13330.852 282.12865 282.12865 31292.699 31292.699 -6227.8304 -6227.8304 4000 -13265.814 -13265.814 -13340.376 -13340.376 288.56361 288.56361 31225.222 31225.222 2027.5613 2027.5613 Loop time of 7.63161 on 1 procs for 1000 steps with 2000 atoms Performance: 11.321 ns/day, 2.120 hours/ns, 131.034 timesteps/s, 262.068 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.5041 | 7.5041 | 7.5041 | 0.0 | 98.33 Neigh | 0.025271 | 0.025271 | 0.025271 | 0.0 | 0.33 Comm | 0.02591 | 0.02591 | 0.02591 | 0.0 | 0.34 Output | 3.0307e-05 | 3.0307e-05 | 3.0307e-05 | 0.0 | 0.00 Modify | 0.068787 | 0.068787 | 0.068787 | 0.0 | 0.90 Other | | 0.007553 | | | 0.10 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6798 ave 6798 max 6798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 551440 ave 551440 max 551440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 551440 Ave neighs/atom = 275.72 Neighbor list builds = 2 Dangerous builds = 0 if "${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 31222.9427202954 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0