# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.24405661970377*${_u_distance} variable latticeconst_converted equal 4.24405661970377*1 lattice fcc ${latticeconst_converted} lattice fcc 4.24405661970377 Lattice spacing in x,y,z = 4.2440566 4.2440566 4.2440566 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (42.440566 42.440566 42.440566) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (42.440566 42.440566 42.440566) create_atoms CPU = 0.001 seconds variable mass_converted equal 20.1797*${_u_mass} variable mass_converted equal 20.1797*1 kim interactions Ne #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958LowCutoff_Ne__MO_466741694288_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 76444.0182483146 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 76444.0182483146/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 76444.0182483146/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 76444.0182483146/(1*1*${_u_distance}) variable V0_metal equal 76444.0182483146/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 76444.0182483146*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 76444.0182483146 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_466741694288_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 = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, 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) = 6.242 | 6.242 | 6.242 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 35.198823 35.198823 -95.657278 -95.657278 253.15 253.15 76444.018 76444.018 1828.393 1828.393 1000 122.66114 122.66114 -7.3607013 -7.3607013 251.53606 251.53606 617680.57 617680.57 230.21849 230.21849 Loop time of 6.22268 on 1 procs for 1000 steps with 4000 atoms Performance: 13.885 ns/day, 1.729 hours/ns, 160.703 timesteps/s, 642.810 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 | 5.1899 | 5.1899 | 5.1899 | 0.0 | 83.40 Neigh | 0.85356 | 0.85356 | 0.85356 | 0.0 | 13.72 Comm | 0.030256 | 0.030256 | 0.030256 | 0.0 | 0.49 Output | 9.4548e-05 | 9.4548e-05 | 9.4548e-05 | 0.0 | 0.00 Modify | 0.13409 | 0.13409 | 0.13409 | 0.0 | 2.15 Other | | 0.0148 | | | 0.24 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3269 ave 3269 max 3269 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: 91804 ave 91804 max 91804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91804 Ave neighs/atom = 22.951 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 = ${P}" flag: Temp = 251.508308367106, Press = 249.801774235909 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, bins = 19 19 19 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.576 | 3.576 | 3.576 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 122.66114 122.66114 -7.3607013 -7.3607013 251.53606 251.53606 617680.57 617680.57 230.21849 230.21849 2000 128.78187 128.78187 -1.3673072 -1.3673072 251.7824 251.7824 3362266.5 3362266.5 41.628532 41.628532 Loop time of 1.75324 on 1 procs for 1000 steps with 4000 atoms Performance: 49.280 ns/day, 0.487 hours/ns, 570.371 timesteps/s, 2.281 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1355 | 1.1355 | 1.1355 | 0.0 | 64.77 Neigh | 0.45121 | 0.45121 | 0.45121 | 0.0 | 25.74 Comm | 0.018916 | 0.018916 | 0.018916 | 0.0 | 1.08 Output | 3.5066e-05 | 3.5066e-05 | 3.5066e-05 | 0.0 | 0.00 Modify | 0.13515 | 0.13515 | 0.13515 | 0.0 | 7.71 Other | | 0.0124 | | | 0.71 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1637 ave 1637 max 1637 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17208 ave 17208 max 17208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17208 Ave neighs/atom = 4.302 Neighbor list builds = 109 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 251.63343433435, Press = 121.849452456269 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, bins = 32 32 32 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.704 | 3.704 | 3.704 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 128.78187 128.78187 -1.3673072 -1.3673072 251.7824 251.7824 3362266.5 3362266.5 41.628532 41.628532 3000 129.88056 129.88056 -0.28313359 -0.28313359 251.8105 251.8105 17094640 17094640 8.1435451 8.1435451 Loop time of 0.961321 on 1 procs for 1000 steps with 4000 atoms Performance: 89.876 ns/day, 0.267 hours/ns, 1040.236 timesteps/s, 4.161 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48355 | 0.48355 | 0.48355 | 0.0 | 50.30 Neigh | 0.31293 | 0.31293 | 0.31293 | 0.0 | 32.55 Comm | 0.016442 | 0.016442 | 0.016442 | 0.0 | 1.71 Output | 4.6718e-05 | 4.6718e-05 | 4.6718e-05 | 0.0 | 0.00 Modify | 0.13512 | 0.13512 | 0.13512 | 0.0 | 14.06 Other | | 0.01324 | | | 1.38 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 903 ave 903 max 903 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3420 ave 3420 max 3420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3420 Ave neighs/atom = 0.855 Neighbor list builds = 172 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 251.696192875418, Press = 73.5040747611195 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, bins = 55 55 55 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.329 | 4.329 | 4.329 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 129.88056 129.88056 -0.28313359 -0.28313359 251.8105 251.8105 17094640 17094640 8.1435451 8.1435451 4000 130.15707 130.15707 -0.083637153 -0.083637153 251.95948 251.95948 83541951 83541951 1.6640069 1.6640069 Loop time of 0.929767 on 1 procs for 1000 steps with 4000 atoms Performance: 92.926 ns/day, 0.258 hours/ns, 1075.538 timesteps/s, 4.302 Matom-step/s 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32801 | 0.32801 | 0.32801 | 0.0 | 35.28 Neigh | 0.43377 | 0.43377 | 0.43377 | 0.0 | 46.65 Comm | 0.016298 | 0.016298 | 0.016298 | 0.0 | 1.75 Output | 5.1576e-05 | 5.1576e-05 | 5.1576e-05 | 0.0 | 0.01 Modify | 0.13622 | 0.13622 | 0.13622 | 0.0 | 14.65 Other | | 0.01542 | | | 1.66 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 533 ave 533 max 533 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 702 ave 702 max 702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 702 Ave neighs/atom = 0.1755 Neighbor list builds = 270 Dangerous builds = 0 if "${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 83541950.8592494 A^3 has become larger than 76444018.2483146 A^3. Aborting calculation. Total wall time: 0:00:09