# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 333.15*${_u_temperature} variable temp_converted equal 333.15*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 333.15 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 333.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "333.15 - 1.0" variable T_up equal "333.15 + 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 76.551729 76.551729 -95.657278 -95.657278 333.15 333.15 76444.018 76444.018 2406.1985 2406.1985 1000 165.62278 165.62278 -5.8134362 -5.8134362 331.65499 331.65499 660337.02 660337.02 297.12479 297.12479 Loop time of 5.72918 on 1 procs for 1000 steps with 4000 atoms Performance: 15.081 ns/day, 1.591 hours/ns, 174.545 timesteps/s, 698.181 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 | 4.7213 | 4.7213 | 4.7213 | 0.0 | 82.41 Neigh | 0.83513 | 0.83513 | 0.83513 | 0.0 | 14.58 Comm | 0.028292 | 0.028292 | 0.028292 | 0.0 | 0.49 Output | 8.0471e-05 | 8.0471e-05 | 8.0471e-05 | 0.0 | 0.00 Modify | 0.13081 | 0.13081 | 0.13081 | 0.0 | 2.28 Other | | 0.01356 | | | 0.24 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3181 ave 3181 max 3181 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: 86210 ave 86210 max 86210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86210 Ave neighs/atom = 21.5525 Neighbor list builds = 80 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 = ${P}" flag: Temp = 330.957648556561, Press = 330.811029464573 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, bins = 19 19 19 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.576 | 3.576 | 3.576 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 165.62278 165.62278 -5.8134362 -5.8134362 331.65499 331.65499 660337.02 660337.02 297.12479 297.12479 2000 170.16778 170.16778 -1.118323 -1.118323 331.36458 331.36458 3600186.9 3600186.9 51.490106 51.490106 Loop time of 1.62489 on 1 procs for 1000 steps with 4000 atoms Performance: 53.173 ns/day, 0.451 hours/ns, 615.424 timesteps/s, 2.462 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0363 | 1.0363 | 1.0363 | 0.0 | 63.78 Neigh | 0.42614 | 0.42614 | 0.42614 | 0.0 | 26.23 Comm | 0.018077 | 0.018077 | 0.018077 | 0.0 | 1.11 Output | 3.1529e-05 | 3.1529e-05 | 3.1529e-05 | 0.0 | 0.00 Modify | 0.13206 | 0.13206 | 0.13206 | 0.0 | 8.13 Other | | 0.01231 | | | 0.76 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1584 ave 1584 max 1584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15536 ave 15536 max 15536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15536 Ave neighs/atom = 3.884 Neighbor list builds = 113 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 331.147400717394, Press = 154.252367395141 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, bins = 33 33 33 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.72 | 3.72 | 3.72 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 170.16778 170.16778 -1.118323 -1.118323 331.36458 331.36458 3600186.9 3600186.9 51.490106 51.490106 3000 171.06261 171.06261 -0.22098634 -0.22098634 331.35973 331.35973 18145567 18145567 10.102906 10.102906 Loop time of 0.885995 on 1 procs for 1000 steps with 4000 atoms Performance: 97.517 ns/day, 0.246 hours/ns, 1128.674 timesteps/s, 4.515 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44143 | 0.44143 | 0.44143 | 0.0 | 49.82 Neigh | 0.28489 | 0.28489 | 0.28489 | 0.0 | 32.15 Comm | 0.01517 | 0.01517 | 0.01517 | 0.0 | 1.71 Output | 4.3251e-05 | 4.3251e-05 | 4.3251e-05 | 0.0 | 0.00 Modify | 0.13147 | 0.13147 | 0.13147 | 0.0 | 14.84 Other | | 0.01299 | | | 1.47 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 910 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3150 ave 3150 max 3150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3150 Ave neighs/atom = 0.7875 Neighbor list builds = 172 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 331.238181169017, Press = 92.7671047987861 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, bins = 56 56 56 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.371 | 4.371 | 4.371 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 171.06261 171.06261 -0.22098634 -0.22098634 331.35973 331.35973 18145567 18145567 10.102906 10.102906 4000 171.27479 171.27479 -0.061714448 -0.061714448 331.46209 331.46209 88008498 88008498 2.0787286 2.0787286 Loop time of 0.912298 on 1 procs for 1000 steps with 4000 atoms Performance: 94.706 ns/day, 0.253 hours/ns, 1096.133 timesteps/s, 4.385 Matom-step/s 98.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31876 | 0.31876 | 0.31876 | 0.0 | 34.94 Neigh | 0.4258 | 0.4258 | 0.4258 | 0.0 | 46.67 Comm | 0.017939 | 0.017939 | 0.017939 | 0.0 | 1.97 Output | 5.5434e-05 | 5.5434e-05 | 5.5434e-05 | 0.0 | 0.01 Modify | 0.13449 | 0.13449 | 0.13449 | 0.0 | 14.74 Other | | 0.01525 | | | 1.67 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 521 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 660 ave 660 max 660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 660 Ave neighs/atom = 0.165 Neighbor list builds = 277 Dangerous builds = 0 if "${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 88008498.1944759 A^3 has become larger than 76444018.2483146 A^3. Aborting calculation. Total wall time: 0:00:09