# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.299560785293579*${_u_distance} variable latticeconst_converted equal 4.299560785293579*1 lattice fcc ${latticeconst_converted} lattice fcc 4.29956078529358 Lattice spacing in x,y,z = 4.2995608 4.2995608 4.2995608 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (42.995608 42.995608 42.995608) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (42.995608 42.995608 42.995608) create_atoms CPU = 0.001 seconds variable mass_converted equal 20.1797*${_u_mass} variable mass_converted equal 20.1797*1 kim interactions Ne #=== BEGIN kim interactions ================================== pair_style kim Morse_Shifted_Glyde_1970_Ne__MO_169434419764_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 79482.6392486835 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 79482.6392486835/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 79482.6392486835/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 79482.6392486835/(1*1*${_u_distance}) variable V0_metal equal 79482.6392486835/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 79482.6392486835*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 79482.6392486835 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_169434419764_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 = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, 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) = 7.005 | 7.005 | 7.005 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 29.57051 29.57051 -111.62382 -111.62382 273.15 273.15 79482.639 79482.639 1897.4229 1897.4229 1000 132.79146 132.79146 -7.4369796 -7.4369796 271.28143 271.28143 636532.97 636532.97 242.47721 242.47721 Loop time of 6.75885 on 1 procs for 1000 steps with 4000 atoms Performance: 12.783 ns/day, 1.877 hours/ns, 147.954 timesteps/s, 591.817 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 | 5.602 | 5.602 | 5.602 | 0.0 | 82.88 Neigh | 0.97372 | 0.97372 | 0.97372 | 0.0 | 14.41 Comm | 0.032231 | 0.032231 | 0.032231 | 0.0 | 0.48 Output | 0.00011928 | 0.00011928 | 0.00011928 | 0.0 | 0.00 Modify | 0.13497 | 0.13497 | 0.13497 | 0.0 | 2.00 Other | | 0.0158 | | | 0.23 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3514 ave 3514 max 3514 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: 111038 ave 111038 max 111038 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111038 Ave neighs/atom = 27.7595 Neighbor list builds = 77 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 = ${P}" flag: Temp = 271.388158367283, Press = 262.80377691662 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.947 | 3.947 | 3.947 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 132.79146 132.79146 -7.4369796 -7.4369796 271.28143 271.28143 636532.97 636532.97 242.47721 242.47721 2000 139.22452 139.22452 -1.176631 -1.176631 271.61554 271.61554 3486287 3486287 43.912245 43.912245 Loop time of 1.79887 on 1 procs for 1000 steps with 4000 atoms Performance: 48.030 ns/day, 0.500 hours/ns, 555.904 timesteps/s, 2.224 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1171 | 1.1171 | 1.1171 | 0.0 | 62.10 Neigh | 0.51047 | 0.51047 | 0.51047 | 0.0 | 28.38 Comm | 0.020519 | 0.020519 | 0.020519 | 0.0 | 1.14 Output | 5.359e-05 | 5.359e-05 | 5.359e-05 | 0.0 | 0.00 Modify | 0.13748 | 0.13748 | 0.13748 | 0.0 | 7.64 Other | | 0.0133 | | | 0.74 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1773 ave 1773 max 1773 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 20932 ave 20932 max 20932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20932 Ave neighs/atom = 5.233 Neighbor list builds = 110 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 271.505185435516, Press = 127.797729392508 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 30 30 30 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.676 | 3.676 | 3.676 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 139.22452 139.22452 -1.176631 -1.176631 271.61554 271.61554 3486287 3486287 43.912245 43.912245 3000 140.09983 140.09983 -0.33203424 -0.33203424 271.67496 271.67496 17781487 17781487 8.4261993 8.4261993 Loop time of 0.917518 on 1 procs for 1000 steps with 4000 atoms Performance: 94.167 ns/day, 0.255 hours/ns, 1089.897 timesteps/s, 4.360 Matom-step/s 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42159 | 0.42159 | 0.42159 | 0.0 | 45.95 Neigh | 0.33016 | 0.33016 | 0.33016 | 0.0 | 35.98 Comm | 0.016667 | 0.016667 | 0.016667 | 0.0 | 1.82 Output | 7.4059e-05 | 7.4059e-05 | 7.4059e-05 | 0.0 | 0.01 Modify | 0.13536 | 0.13536 | 0.13536 | 0.0 | 14.75 Other | | 0.01367 | | | 1.49 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 955 ave 955 max 955 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3986 ave 3986 max 3986 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3986 Ave neighs/atom = 0.9965 Neighbor list builds = 172 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 271.575726902626, Press = 77.0240534454822 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 52 52 52 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.212 | 4.212 | 4.212 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 140.09983 140.09983 -0.33203424 -0.33203424 271.67496 271.67496 17781487 17781487 8.4261993 8.4261993 4000 140.3434 140.3434 -0.04544195 -0.04544195 271.59173 271.59173 87016066 87016066 1.7250173 1.7250173 Loop time of 0.867683 on 1 procs for 1000 steps with 4000 atoms Performance: 99.576 ns/day, 0.241 hours/ns, 1152.494 timesteps/s, 4.610 Matom-step/s 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27655 | 0.27655 | 0.27655 | 0.0 | 31.87 Neigh | 0.42169 | 0.42169 | 0.42169 | 0.0 | 48.60 Comm | 0.018787 | 0.018787 | 0.018787 | 0.0 | 2.17 Output | 5.3861e-05 | 5.3861e-05 | 5.3861e-05 | 0.0 | 0.01 Modify | 0.13543 | 0.13543 | 0.13543 | 0.0 | 15.61 Other | | 0.01517 | | | 1.75 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 544 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 810 ave 810 max 810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 810 Ave neighs/atom = 0.2025 Neighbor list builds = 273 Dangerous builds = 0 if "${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 87016065.6150893 A^3 has become larger than 79482639.2486835 A^3. Aborting calculation. Total wall time: 0:00:10