# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.246869719028479*${_u_distance} variable latticeconst_converted equal 5.246869719028479*1 lattice fcc ${latticeconst_converted} lattice fcc 5.24686971902848 Lattice spacing in x,y,z = 5.2468697 5.2468697 5.2468697 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.468697 52.468697 52.468697) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.468697 52.468697 52.468697) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Truncated_Nguyen_2005_Ar__MO_398194508715_001 pair_coeff * * Ar #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 39.948 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 144444.444190373 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144444.444190373/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144444.444190373/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 144444.444190373/(1*1*${_u_distance}) variable V0_metal equal 144444.444190373/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 144444.444190373*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 144444.444190373 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_398194508715_001#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 = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, 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) = 15.41 | 15.41 | 15.41 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -176.96715 -176.96715 -349.17616 -349.17616 333.15 333.15 144444.44 144444.44 1273.4272 1273.4272 1000 110.59896 110.59896 -63.09867 -63.09867 336.02984 336.02984 639188.42 639188.42 174.79489 174.79489 Loop time of 23.8379 on 1 procs for 1000 steps with 4000 atoms Performance: 3.624 ns/day, 6.622 hours/ns, 41.950 timesteps/s, 167.800 katom-step/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.942 | 21.942 | 21.942 | 0.0 | 92.05 Neigh | 1.7068 | 1.7068 | 1.7068 | 0.0 | 7.16 Comm | 0.045191 | 0.045191 | 0.045191 | 0.0 | 0.19 Output | 0.00018429 | 0.00018429 | 0.00018429 | 0.0 | 0.00 Modify | 0.12701 | 0.12701 | 0.12701 | 0.0 | 0.53 Other | | 0.01649 | | | 0.07 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7007 ave 7007 max 7007 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: 540570 ave 540570 max 540570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 540570 Ave neighs/atom = 135.1425 Neighbor list builds = 60 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 = ${P}" flag: Temp = 333.164729359598, Press = 179.466861175324 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 8.368 | 8.368 | 8.368 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 110.59896 110.59896 -63.09867 -63.09867 336.02984 336.02984 639188.42 639188.42 174.79489 174.79489 2000 157.90691 157.90691 -13.753955 -13.753955 332.08959 332.08959 3165245.5 3165245.5 52.973477 52.973477 Loop time of 6.33571 on 1 procs for 1000 steps with 4000 atoms Performance: 13.637 ns/day, 1.760 hours/ns, 157.835 timesteps/s, 631.342 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.172 | 5.172 | 5.172 | 0.0 | 81.63 Neigh | 0.99305 | 0.99305 | 0.99305 | 0.0 | 15.67 Comm | 0.028221 | 0.028221 | 0.028221 | 0.0 | 0.45 Output | 6.6225e-05 | 6.6225e-05 | 6.6225e-05 | 0.0 | 0.00 Modify | 0.12903 | 0.12903 | 0.12903 | 0.0 | 2.04 Other | | 0.01338 | | | 0.21 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3511 ave 3511 max 3511 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113650 ave 113650 max 113650 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113650 Ave neighs/atom = 28.4125 Neighbor list builds = 102 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.940403545297, Press = 115.176041830583 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.843 | 6.843 | 6.843 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 157.90691 157.90691 -13.753955 -13.753955 332.08959 332.08959 3165245.5 3165245.5 52.973477 52.973477 3000 166.63956 166.63956 -3.4558483 -3.4558483 329.0611 329.0611 16979389 16979389 10.447652 10.447652 Loop time of 2.02566 on 1 procs for 1000 steps with 4000 atoms Performance: 42.653 ns/day, 0.563 hours/ns, 493.667 timesteps/s, 1.975 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2148 | 1.2148 | 1.2148 | 0.0 | 59.97 Neigh | 0.65915 | 0.65915 | 0.65915 | 0.0 | 32.54 Comm | 0.020065 | 0.020065 | 0.020065 | 0.0 | 0.99 Output | 4.5355e-05 | 4.5355e-05 | 4.5355e-05 | 0.0 | 0.00 Modify | 0.11997 | 0.11997 | 0.11997 | 0.0 | 5.92 Other | | 0.01162 | | | 0.57 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1831 ave 1831 max 1831 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 22712 ave 22712 max 22712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22712 Ave neighs/atom = 5.678 Neighbor list builds = 172 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 333.047939760264, Press = 72.9137675588037 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, bins = 30 30 30 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.572 | 6.572 | 6.572 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 166.63956 166.63956 -3.4558483 -3.4558483 329.0611 329.0611 16979389 16979389 10.447652 10.447652 4000 168.7509 168.7509 -0.80478534 -0.80478534 328.01698 328.01698 87857498 87857498 2.0440283 2.0440283 Loop time of 1.00914 on 1 procs for 1000 steps with 4000 atoms Performance: 85.617 ns/day, 0.280 hours/ns, 990.939 timesteps/s, 3.964 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43165 | 0.43165 | 0.43165 | 0.0 | 42.77 Neigh | 0.42949 | 0.42949 | 0.42949 | 0.0 | 42.56 Comm | 0.018122 | 0.018122 | 0.018122 | 0.0 | 1.80 Output | 3.8973e-05 | 3.8973e-05 | 3.8973e-05 | 0.0 | 0.00 Modify | 0.11721 | 0.11721 | 0.11721 | 0.0 | 11.61 Other | | 0.01264 | | | 1.25 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4880 ave 4880 max 4880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4880 Ave neighs/atom = 1.22 Neighbor list builds = 277 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 333.018157960178, Press = 51.0699741321597 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, bins = 52 52 52 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.108 | 7.108 | 7.108 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 168.7509 168.7509 -0.80478534 -0.80478534 328.01698 328.01698 87857498 87857498 2.0440283 2.0440283 5000 171.70657 171.70657 -0.20342136 -0.20342136 332.57154 332.57154 4.3823004e+08 4.3823004e+08 0.41820749 0.41820749 Loop time of 1.14056 on 1 procs for 1000 steps with 4000 atoms Performance: 75.752 ns/day, 0.317 hours/ns, 876.764 timesteps/s, 3.507 Matom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28584 | 0.28584 | 0.28584 | 0.0 | 25.06 Neigh | 0.67403 | 0.67403 | 0.67403 | 0.0 | 59.10 Comm | 0.022851 | 0.022851 | 0.022851 | 0.0 | 2.00 Output | 5.4612e-05 | 5.4612e-05 | 5.4612e-05 | 0.0 | 0.00 Modify | 0.13962 | 0.13962 | 0.13962 | 0.0 | 12.24 Other | | 0.01816 | | | 1.59 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 587 ave 587 max 587 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1254 ave 1254 max 1254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1254 Ave neighs/atom = 0.3135 Neighbor list builds = 431 Dangerous builds = 0 if "${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 438230041.442295 A^3 has become larger than 144444444.190373 A^3. Aborting calculation. Total wall time: 0:00:34