# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 293.15*${_u_temperature} variable temp_converted equal 293.15*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 293.15 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 293.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "293.15 - 1.0" variable T_up equal "293.15 + 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 -197.6436 -197.6436 -349.17616 -349.17616 293.15 293.15 144444.44 144444.44 1120.5318 1120.5318 1000 75.573377 75.573377 -76.498674 -76.498674 294.1937 294.1937 538867.35 538867.35 135.64017 135.64017 Loop time of 26.3908 on 1 procs for 1000 steps with 4000 atoms Performance: 3.274 ns/day, 7.331 hours/ns, 37.892 timesteps/s, 151.568 katom-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 | 24.572 | 24.572 | 24.572 | 0.0 | 93.11 Neigh | 1.6231 | 1.6231 | 1.6231 | 0.0 | 6.15 Comm | 0.047175 | 0.047175 | 0.047175 | 0.0 | 0.18 Output | 0.00014227 | 0.00014227 | 0.00014227 | 0.0 | 0.00 Modify | 0.13149 | 0.13149 | 0.13149 | 0.0 | 0.50 Other | | 0.01648 | | | 0.06 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7575 ave 7575 max 7575 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: 643680 ave 643680 max 643680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 643680 Ave neighs/atom = 160.92 Neighbor list builds = 52 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 = ${P}" flag: Temp = 292.942208588424, Press = 137.00138177941 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 8.754 | 8.754 | 8.754 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 75.573377 75.573377 -76.498674 -76.498674 294.1937 294.1937 538867.35 538867.35 135.64017 135.64017 2000 133.03995 133.03995 -18.536774 -18.536774 293.23544 293.23544 2433536.9 2433536.9 56.378218 56.378218 Loop time of 7.35798 on 1 procs for 1000 steps with 4000 atoms Performance: 11.742 ns/day, 2.044 hours/ns, 135.907 timesteps/s, 543.627 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.2244 | 6.2244 | 6.2244 | 0.0 | 84.59 Neigh | 0.97103 | 0.97103 | 0.97103 | 0.0 | 13.20 Comm | 0.027955 | 0.027955 | 0.027955 | 0.0 | 0.38 Output | 5.9772e-05 | 5.9772e-05 | 5.9772e-05 | 0.0 | 0.00 Modify | 0.12233 | 0.12233 | 0.12233 | 0.0 | 1.66 Other | | 0.01217 | | | 0.17 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3892 ave 3892 max 3892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 146282 ave 146282 max 146282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146282 Ave neighs/atom = 36.5705 Neighbor list builds = 90 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.780860842982, Press = 102.922269902364 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, bins = 16 16 16 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.841 | 6.841 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 133.03995 133.03995 -18.536774 -18.536774 293.23544 293.23544 2433536.9 2433536.9 56.378218 56.378218 3000 150.19316 150.19316 -4.4237543 -4.4237543 299.1169 299.1169 13112838 13112838 12.364751 12.364751 Loop time of 2.35379 on 1 procs for 1000 steps with 4000 atoms Performance: 36.707 ns/day, 0.654 hours/ns, 424.847 timesteps/s, 1.699 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4946 | 1.4946 | 1.4946 | 0.0 | 63.50 Neigh | 0.70829 | 0.70829 | 0.70829 | 0.0 | 30.09 Comm | 0.020717 | 0.020717 | 0.020717 | 0.0 | 0.88 Output | 3.6819e-05 | 3.6819e-05 | 3.6819e-05 | 0.0 | 0.00 Modify | 0.11843 | 0.11843 | 0.11843 | 0.0 | 5.03 Other | | 0.01174 | | | 0.50 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2002 ave 2002 max 2002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29500 ave 29500 max 29500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29500 Ave neighs/atom = 7.375 Neighbor list builds = 159 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.930882479156, Press = 67.7758261993109 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, bins = 28 28 28 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.547 | 6.547 | 6.547 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 150.19316 150.19316 -4.4237543 -4.4237543 299.1169 299.1169 13112838 13112838 12.364751 12.364751 4000 150.8256 150.8256 -0.99301048 -0.99301048 293.70339 293.70339 69009574 69009574 2.3260642 2.3260642 Loop time of 1.08855 on 1 procs for 1000 steps with 4000 atoms Performance: 79.372 ns/day, 0.302 hours/ns, 918.656 timesteps/s, 3.675 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49593 | 0.49593 | 0.49593 | 0.0 | 45.56 Neigh | 0.4448 | 0.4448 | 0.4448 | 0.0 | 40.86 Comm | 0.018138 | 0.018138 | 0.018138 | 0.0 | 1.67 Output | 3.0186e-05 | 3.0186e-05 | 3.0186e-05 | 0.0 | 0.00 Modify | 0.1172 | 0.1172 | 0.1172 | 0.0 | 10.77 Other | | 0.01244 | | | 1.14 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1086 ave 1086 max 1086 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 6594 ave 6594 max 6594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6594 Ave neighs/atom = 1.6485 Neighbor list builds = 260 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.994430602334, Press = 47.8023275779082 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, bins = 48 48 48 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.971 | 6.971 | 6.971 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 150.8256 150.8256 -0.99301048 -0.99301048 293.70339 293.70339 69009574 69009574 2.3260642 2.3260642 5000 149.8809 149.8809 -0.27453991 -0.27453991 290.48588 290.48588 3.4815698e+08 3.4815698e+08 0.45897581 0.45897581 Loop time of 0.951401 on 1 procs for 1000 steps with 4000 atoms Performance: 90.813 ns/day, 0.264 hours/ns, 1051.081 timesteps/s, 4.204 Matom-step/s 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26038 | 0.26038 | 0.26038 | 0.0 | 27.37 Neigh | 0.53837 | 0.53837 | 0.53837 | 0.0 | 56.59 Comm | 0.020453 | 0.020453 | 0.020453 | 0.0 | 2.15 Output | 0.00021818 | 0.00021818 | 0.00021818 | 0.0 | 0.02 Modify | 0.11703 | 0.11703 | 0.11703 | 0.0 | 12.30 Other | | 0.01495 | | | 1.57 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 622 ave 622 max 622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1532 ave 1532 max 1532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1532 Ave neighs/atom = 0.383 Neighbor list builds = 410 Dangerous builds = 0 if "${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 348156978.675969 A^3 has become larger than 144444444.190373 A^3. Aborting calculation. Total wall time: 0:00:38