# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 313.15*${_u_temperature} variable temp_converted equal 313.15*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 313.15 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 313.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "313.15 - 1.0" variable T_up equal "313.15 + 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 66.213502 66.213502 -95.657278 -95.657278 313.15 313.15 76444.018 76444.018 2261.7471 2261.7471 1000 154.77064 154.77064 -5.9245392 -5.9245392 310.87572 310.87572 651713.69 651713.69 283.25089 283.25089 Loop time of 5.74572 on 1 procs for 1000 steps with 4000 atoms Performance: 15.037 ns/day, 1.596 hours/ns, 174.043 timesteps/s, 696.171 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 | 4.751 | 4.751 | 4.751 | 0.0 | 82.69 Neigh | 0.82138 | 0.82138 | 0.82138 | 0.0 | 14.30 Comm | 0.028489 | 0.028489 | 0.028489 | 0.0 | 0.50 Output | 0.00011471 | 0.00011471 | 0.00011471 | 0.0 | 0.00 Modify | 0.13112 | 0.13112 | 0.13112 | 0.0 | 2.28 Other | | 0.01365 | | | 0.24 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3191 ave 3191 max 3191 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: 86794 ave 86794 max 86794 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86794 Ave neighs/atom = 21.6985 Neighbor list builds = 79 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 = ${P}" flag: Temp = 311.065174513404, Press = 312.460187272891 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, bins = 19 19 19 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.576 | 3.576 | 3.576 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 154.77064 154.77064 -5.9245392 -5.9245392 310.87572 310.87572 651713.69 651713.69 283.25089 283.25089 2000 159.82684 159.82684 -1.1964208 -1.1964208 311.51042 311.51042 3551471.5 3551471.5 48.959956 48.959956 Loop time of 1.69616 on 1 procs for 1000 steps with 4000 atoms Performance: 50.939 ns/day, 0.471 hours/ns, 589.566 timesteps/s, 2.358 Matom-step/s 96.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0901 | 1.0901 | 1.0901 | 0.0 | 64.27 Neigh | 0.43856 | 0.43856 | 0.43856 | 0.0 | 25.86 Comm | 0.019316 | 0.019316 | 0.019316 | 0.0 | 1.14 Output | 4.8561e-05 | 4.8561e-05 | 4.8561e-05 | 0.0 | 0.00 Modify | 0.13421 | 0.13421 | 0.13421 | 0.0 | 7.91 Other | | 0.01395 | | | 0.82 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1597 ave 1597 max 1597 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15856 ave 15856 max 15856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15856 Ave neighs/atom = 3.964 Neighbor list builds = 112 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 311.273623440606, Press = 146.318036581269 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, bins = 33 33 33 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.72 | 3.72 | 3.72 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 159.82684 159.82684 -1.1964208 -1.1964208 311.51042 311.51042 3551471.5 3551471.5 48.959956 48.959956 3000 160.97017 160.97017 -0.074513742 -0.074513742 311.55187 311.55187 17930375 17930375 9.6842099 9.6842099 Loop time of 0.878755 on 1 procs for 1000 steps with 4000 atoms Performance: 98.321 ns/day, 0.244 hours/ns, 1137.973 timesteps/s, 4.552 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42988 | 0.42988 | 0.42988 | 0.0 | 48.92 Neigh | 0.28826 | 0.28826 | 0.28826 | 0.0 | 32.80 Comm | 0.016019 | 0.016019 | 0.016019 | 0.0 | 1.82 Output | 4.6036e-05 | 4.6036e-05 | 4.6036e-05 | 0.0 | 0.01 Modify | 0.13131 | 0.13131 | 0.13131 | 0.0 | 14.94 Other | | 0.01324 | | | 1.51 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3098 ave 3098 max 3098 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3098 Ave neighs/atom = 0.7745 Neighbor list builds = 172 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 311.353758321711, Press = 88.0319105870749 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, bins = 56 56 56 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.371 | 4.371 | 4.371 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 160.97017 160.97017 -0.074513742 -0.074513742 311.55187 311.55187 17930375 17930375 9.6842099 9.6842099 4000 161.09246 161.09246 -0.048957369 -0.048957369 311.739 311.739 87116892 87116892 1.9758908 1.9758908 Loop time of 0.895513 on 1 procs for 1000 steps with 4000 atoms Performance: 96.481 ns/day, 0.249 hours/ns, 1116.679 timesteps/s, 4.467 Matom-step/s 97.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30216 | 0.30216 | 0.30216 | 0.0 | 33.74 Neigh | 0.42756 | 0.42756 | 0.42756 | 0.0 | 47.74 Comm | 0.016299 | 0.016299 | 0.016299 | 0.0 | 1.82 Output | 8.6663e-05 | 8.6663e-05 | 8.6663e-05 | 0.0 | 0.01 Modify | 0.13397 | 0.13397 | 0.13397 | 0.0 | 14.96 Other | | 0.01544 | | | 1.72 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 666 ave 666 max 666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 666 Ave neighs/atom = 0.1665 Neighbor list builds = 274 Dangerous builds = 0 if "${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 87116892.0495669 A^3 has become larger than 76444018.2483146 A^3. Aborting calculation. Total wall time: 0:00:09