# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.229680836200714*${_u_distance} variable latticeconst_converted equal 4.229680836200714*1 lattice fcc ${latticeconst_converted} lattice fcc 4.22968083620071 Lattice spacing in x,y,z = 4.2296808 4.2296808 4.2296808 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (42.296808 42.296808 42.296808) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (42.296808 42.296808 42.296808) create_atoms CPU = 0.001 seconds variable mass_converted equal 20.1797*${_u_mass} variable mass_converted equal 20.1797*1 kim interactions Ne #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958MedCutoff_Ne__MO_160637895352_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 75669.8359948081 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 75669.8359948081/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 75669.8359948081/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 75669.8359948081/(1*1*${_u_distance}) variable V0_metal equal 75669.8359948081/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 75669.8359948081*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 75669.8359948081 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 253.15*${_u_temperature} variable temp_converted equal 253.15*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 253.15 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 253.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "253.15 - 1.0" variable T_up equal "253.15 + 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_160637895352_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 = 12.9 ghost atom cutoff = 12.9 binsize = 6.45, 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) = 13.12 | 13.12 | 13.12 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 27.692085 27.692085 -103.16402 -103.16402 253.15 253.15 75669.836 75669.836 1847.0997 1847.0997 1000 121.40385 121.40385 -8.674451 -8.674451 251.6453 251.6453 603115.99 603115.99 231.76501 231.76501 Loop time of 15.7911 on 1 procs for 1000 steps with 4000 atoms Performance: 5.471 ns/day, 4.386 hours/ns, 63.327 timesteps/s, 253.307 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 | 14.013 | 14.013 | 14.013 | 0.0 | 88.74 Neigh | 1.5859 | 1.5859 | 1.5859 | 0.0 | 10.04 Comm | 0.04214 | 0.04214 | 0.04214 | 0.0 | 0.27 Output | 0.00011543 | 0.00011543 | 0.00011543 | 0.0 | 0.00 Modify | 0.13363 | 0.13363 | 0.13363 | 0.0 | 0.85 Other | | 0.01662 | | | 0.11 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4927 ave 4927 max 4927 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: 240972 ave 240972 max 240972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240972 Ave neighs/atom = 60.243 Neighbor list builds = 75 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 = ${P}" flag: Temp = 251.553337056464, Press = 254.033722664794 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.9 ghost atom cutoff = 12.9 binsize = 6.45, bins = 14 14 14 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.214 | 7.214 | 7.214 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 121.40385 121.40385 -8.674451 -8.674451 251.6453 251.6453 603115.99 603115.99 231.76501 231.76501 2000 128.48113 128.48113 -1.6444987 -1.6444987 251.73686 251.73686 3280678.4 3280678.4 42.366702 42.366702 Loop time of 3.36743 on 1 procs for 1000 steps with 4000 atoms Performance: 25.658 ns/day, 0.935 hours/ns, 296.963 timesteps/s, 1.188 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4646 | 2.4646 | 2.4646 | 0.0 | 73.19 Neigh | 0.7342 | 0.7342 | 0.7342 | 0.0 | 21.80 Comm | 0.023701 | 0.023701 | 0.023701 | 0.0 | 0.70 Output | 4.5646e-05 | 4.5646e-05 | 4.5646e-05 | 0.0 | 0.00 Modify | 0.13196 | 0.13196 | 0.13196 | 0.0 | 3.92 Other | | 0.01288 | | | 0.38 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2452 ave 2452 max 2452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 44910 ave 44910 max 44910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44910 Ave neighs/atom = 11.2275 Neighbor list builds = 107 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 251.630719741768, Press = 124.236090017046 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.9 ghost atom cutoff = 12.9 binsize = 6.45, bins = 24 24 24 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.5 | 6.5 | 6.5 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 128.48113 128.48113 -1.6444987 -1.6444987 251.73686 251.73686 3280678.4 3280678.4 42.366702 42.366702 3000 129.80379 129.80379 -0.3596295 -0.3596295 251.80995 251.80995 16704851 16704851 8.3082663 8.3082663 Loop time of 1.34572 on 1 procs for 1000 steps with 4000 atoms Performance: 64.204 ns/day, 0.374 hours/ns, 743.097 timesteps/s, 2.972 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.73602 | 0.73602 | 0.73602 | 0.0 | 54.69 Neigh | 0.448 | 0.448 | 0.448 | 0.0 | 33.29 Comm | 0.018581 | 0.018581 | 0.018581 | 0.0 | 1.38 Output | 4.0466e-05 | 4.0466e-05 | 4.0466e-05 | 0.0 | 0.00 Modify | 0.13013 | 0.13013 | 0.13013 | 0.0 | 9.67 Other | | 0.01295 | | | 0.96 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1321 ave 1321 max 1321 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 8830 ave 8830 max 8830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 8830 Ave neighs/atom = 2.2075 Neighbor list builds = 169 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 251.694003419904, Press = 74.9853152944276 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.9 ghost atom cutoff = 12.9 binsize = 6.45, bins = 40 40 40 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.745 | 6.745 | 6.745 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 129.80379 129.80379 -0.3596295 -0.3596295 251.80995 251.80995 16704851 16704851 8.3082663 8.3082663 4000 130.11046 130.11046 -0.051773415 -0.051773415 251.80766 251.80766 81769360 81769360 1.7001896 1.7001896 Loop time of 0.938581 on 1 procs for 1000 steps with 4000 atoms Performance: 92.054 ns/day, 0.261 hours/ns, 1065.438 timesteps/s, 4.262 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37539 | 0.37539 | 0.37539 | 0.0 | 40.00 Neigh | 0.39994 | 0.39994 | 0.39994 | 0.0 | 42.61 Comm | 0.01832 | 0.01832 | 0.01832 | 0.0 | 1.95 Output | 4.4694e-05 | 4.4694e-05 | 4.4694e-05 | 0.0 | 0.00 Modify | 0.13023 | 0.13023 | 0.13023 | 0.0 | 13.88 Other | | 0.01466 | | | 1.56 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 745 ave 745 max 745 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1856 ave 1856 max 1856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1856 Ave neighs/atom = 0.464 Neighbor list builds = 266 Dangerous builds = 0 if "${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 81769359.5685697 A^3 has become larger than 75669835.9948081 A^3. Aborting calculation. Total wall time: 0:00:21