# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 273.15*${_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/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 38.030312 38.030312 -103.16402 -103.16402 273.15 273.15 75669.836 75669.836 1993.029 1993.029 1000 132.30169 132.30169 -7.8686981 -7.8686981 271.16912 271.16912 616172.43 616172.43 253.25406 253.25406 Loop time of 15.6596 on 1 procs for 1000 steps with 4000 atoms Performance: 5.517 ns/day, 4.350 hours/ns, 63.859 timesteps/s, 255.434 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 | 13.86 | 13.86 | 13.86 | 0.0 | 88.51 Neigh | 1.608 | 1.608 | 1.608 | 0.0 | 10.27 Comm | 0.041749 | 0.041749 | 0.041749 | 0.0 | 0.27 Output | 6.4631e-05 | 6.4631e-05 | 6.4631e-05 | 0.0 | 0.00 Modify | 0.13331 | 0.13331 | 0.13331 | 0.0 | 0.85 Other | | 0.01621 | | | 0.10 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4885 ave 4885 max 4885 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: 236828 ave 236828 max 236828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236828 Ave neighs/atom = 59.207 Neighbor list builds = 76 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 = ${P}" flag: Temp = 271.309317304463, Press = 271.894162974531 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.9 ghost atom cutoff = 12.9 binsize = 6.45, bins = 14 14 14 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.214 | 7.214 | 7.214 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 132.30169 132.30169 -7.8686981 -7.8686981 271.16912 271.16912 616172.43 616172.43 253.25406 253.25406 2000 138.77227 138.77227 -1.6062587 -1.6062587 271.57179 271.57179 3358971.1 3358971.1 44.790931 44.790931 Loop time of 3.31689 on 1 procs for 1000 steps with 4000 atoms Performance: 26.048 ns/day, 0.921 hours/ns, 301.487 timesteps/s, 1.206 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.416 | 2.416 | 2.416 | 0.0 | 72.84 Neigh | 0.73119 | 0.73119 | 0.73119 | 0.0 | 22.04 Comm | 0.023817 | 0.023817 | 0.023817 | 0.0 | 0.72 Output | 4.816e-05 | 4.816e-05 | 4.816e-05 | 0.0 | 0.00 Modify | 0.13285 | 0.13285 | 0.13285 | 0.0 | 4.01 Other | | 0.01302 | | | 0.39 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2392 ave 2392 max 2392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43682 ave 43682 max 43682 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43682 Ave neighs/atom = 10.9205 Neighbor list builds = 109 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 271.5057629798, Press = 132.35719520871 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.9 ghost atom cutoff = 12.9 binsize = 6.45, bins = 24 24 24 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.499 | 6.499 | 6.499 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 138.77227 138.77227 -1.6062587 -1.6062587 271.57179 271.57179 3358971.1 3358971.1 44.790931 44.790931 3000 140.12055 140.12055 -0.30223712 -0.30223712 271.65741 271.65741 17072561 17072561 8.7879907 8.7879907 Loop time of 1.32151 on 1 procs for 1000 steps with 4000 atoms Performance: 65.380 ns/day, 0.367 hours/ns, 756.710 timesteps/s, 3.027 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.721 | 0.721 | 0.721 | 0.0 | 54.56 Neigh | 0.43807 | 0.43807 | 0.43807 | 0.0 | 33.15 Comm | 0.01856 | 0.01856 | 0.01856 | 0.0 | 1.40 Output | 3.1169e-05 | 3.1169e-05 | 3.1169e-05 | 0.0 | 0.00 Modify | 0.13076 | 0.13076 | 0.13076 | 0.0 | 9.89 Other | | 0.01309 | | | 0.99 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1312 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 8556 ave 8556 max 8556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 8556 Ave neighs/atom = 2.139 Neighbor list builds = 169 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 271.57534635797, Press = 79.8040706954545 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.9 ghost atom cutoff = 12.9 binsize = 6.45, bins = 40 40 40 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.745 | 6.745 | 6.745 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 140.12055 140.12055 -0.30223712 -0.30223712 271.65741 271.65741 17072561 17072561 8.7879907 8.7879907 4000 140.58385 140.58385 -0.066634716 -0.066634716 272.0979 272.0979 83372480 83372480 1.8013515 1.8013515 Loop time of 0.918411 on 1 procs for 1000 steps with 4000 atoms Performance: 94.076 ns/day, 0.255 hours/ns, 1088.837 timesteps/s, 4.355 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36086 | 0.36086 | 0.36086 | 0.0 | 39.29 Neigh | 0.39249 | 0.39249 | 0.39249 | 0.0 | 42.74 Comm | 0.018172 | 0.018172 | 0.018172 | 0.0 | 1.98 Output | 4.8842e-05 | 4.8842e-05 | 4.8842e-05 | 0.0 | 0.01 Modify | 0.13171 | 0.13171 | 0.13171 | 0.0 | 14.34 Other | | 0.01513 | | | 1.65 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 742 ave 742 max 742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1780 ave 1780 max 1780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1780 Ave neighs/atom = 0.445 Neighbor list builds = 269 Dangerous builds = 0 if "${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 83372480.4060697 A^3 has become larger than 75669835.9948081 A^3. Aborting calculation. Total wall time: 0:00:21