# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.299560785293579*${_u_distance} variable latticeconst_converted equal 4.299560785293579*1 lattice fcc ${latticeconst_converted} lattice fcc 4.29956078529358 Lattice spacing in x,y,z = 4.2995608 4.2995608 4.2995608 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (42.995608 42.995608 42.995608) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (42.995608 42.995608 42.995608) create_atoms CPU = 0.001 seconds variable mass_converted equal 20.1797*${_u_mass} variable mass_converted equal 20.1797*1 kim interactions Ne #=== BEGIN kim interactions ================================== pair_style kim Morse_Shifted_Glyde_1970_Ne__MO_169434419764_004 pair_coeff * * Ne #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 20.1797 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 79482.6392486835 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 79482.6392486835/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 79482.6392486835/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 79482.6392486835/(1*1*${_u_distance}) variable V0_metal equal 79482.6392486835/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 79482.6392486835*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 79482.6392486835 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_169434419764_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 = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, 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) = 7.005 | 7.005 | 7.005 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 39.908736 39.908736 -111.62382 -111.62382 293.15 293.15 79482.639 79482.639 2036.3518 2036.3518 1000 143.97719 143.97719 -6.5198354 -6.5198354 291.1467 291.1467 649932.07 649932.07 263.03217 263.03217 Loop time of 6.73744 on 1 procs for 1000 steps with 4000 atoms Performance: 12.824 ns/day, 1.872 hours/ns, 148.424 timesteps/s, 593.697 katom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5681 | 5.5681 | 5.5681 | 0.0 | 82.64 Neigh | 0.98209 | 0.98209 | 0.98209 | 0.0 | 14.58 Comm | 0.033122 | 0.033122 | 0.033122 | 0.0 | 0.49 Output | 0.0001237 | 0.0001237 | 0.0001237 | 0.0 | 0.00 Modify | 0.13691 | 0.13691 | 0.13691 | 0.0 | 2.03 Other | | 0.01705 | | | 0.25 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3501 ave 3501 max 3501 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: 108302 ave 108302 max 108302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108302 Ave neighs/atom = 27.0755 Neighbor list builds = 78 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 = ${P}" flag: Temp = 291.137285939416, Press = 282.44092309692 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 18 18 18 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.953 | 3.953 | 3.953 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 143.97719 143.97719 -6.5198354 -6.5198354 291.1467 291.1467 649932.07 649932.07 263.03217 263.03217 2000 149.46215 149.46215 -1.2498834 -1.2498834 291.56265 291.56265 3563239.5 3563239.5 45.766266 45.766266 Loop time of 1.77465 on 1 procs for 1000 steps with 4000 atoms Performance: 48.686 ns/day, 0.493 hours/ns, 563.493 timesteps/s, 2.254 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.092 | 1.092 | 1.092 | 0.0 | 61.54 Neigh | 0.51023 | 0.51023 | 0.51023 | 0.0 | 28.75 Comm | 0.020879 | 0.020879 | 0.020879 | 0.0 | 1.18 Output | 3.9374e-05 | 3.9374e-05 | 3.9374e-05 | 0.0 | 0.00 Modify | 0.13742 | 0.13742 | 0.13742 | 0.0 | 7.74 Other | | 0.01404 | | | 0.79 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1754 ave 1754 max 1754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 20198 ave 20198 max 20198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20198 Ave neighs/atom = 5.0495 Neighbor list builds = 112 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 291.377232873603, Press = 135.550033553964 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 31 31 31 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.69 | 3.69 | 3.69 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 149.46215 149.46215 -1.2498834 -1.2498834 291.56265 291.56265 3563239.5 3563239.5 45.766266 45.766266 3000 150.45164 150.45164 -0.29357467 -0.29357467 291.62684 291.62684 18110031 18110031 8.8865758 8.8865758 Loop time of 0.909473 on 1 procs for 1000 steps with 4000 atoms Performance: 95.000 ns/day, 0.253 hours/ns, 1099.537 timesteps/s, 4.398 Matom-step/s 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41084 | 0.41084 | 0.41084 | 0.0 | 45.17 Neigh | 0.33271 | 0.33271 | 0.33271 | 0.0 | 36.58 Comm | 0.016858 | 0.016858 | 0.016858 | 0.0 | 1.85 Output | 6.1616e-05 | 6.1616e-05 | 6.1616e-05 | 0.0 | 0.01 Modify | 0.13531 | 0.13531 | 0.13531 | 0.0 | 14.88 Other | | 0.01369 | | | 1.51 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 973 ave 973 max 973 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3982 ave 3982 max 3982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3982 Ave neighs/atom = 0.9955 Neighbor list builds = 173 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 291.458239316041, Press = 81.603524949937 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 52 52 52 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.212 | 4.212 | 4.212 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 150.45164 150.45164 -0.29357467 -0.29357467 291.62684 291.62684 18110031 18110031 8.8865758 8.8865758 4000 150.67623 150.67623 -0.048679943 -0.048679943 291.58756 291.58756 88466147 88466147 1.8186227 1.8186227 Loop time of 0.876616 on 1 procs for 1000 steps with 4000 atoms Performance: 98.561 ns/day, 0.244 hours/ns, 1140.750 timesteps/s, 4.563 Matom-step/s 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27408 | 0.27408 | 0.27408 | 0.0 | 31.27 Neigh | 0.43319 | 0.43319 | 0.43319 | 0.0 | 49.42 Comm | 0.017622 | 0.017622 | 0.017622 | 0.0 | 2.01 Output | 5.3681e-05 | 5.3681e-05 | 5.3681e-05 | 0.0 | 0.01 Modify | 0.13582 | 0.13582 | 0.13582 | 0.0 | 15.49 Other | | 0.01585 | | | 1.81 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 573 ave 573 max 573 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 776 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 776 Ave neighs/atom = 0.194 Neighbor list builds = 274 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" jump SELF unstable print "ERROR: System volume ${V_metal} A^3 has become larger than ${V0_metal_times1000} A^3. Aborting calculation." ERROR: System volume 88466146.510167 A^3 has become larger than 79482639.2486835 A^3. Aborting calculation. Total wall time: 0:00:10