# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.292160376906395*${_u_distance} variable latticeconst_converted equal 5.292160376906395*1 lattice fcc ${latticeconst_converted} lattice fcc 5.29216037690639 Lattice spacing in x,y,z = 5.2921604 5.2921604 5.2921604 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.921604 52.921604 52.921604) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.921604 52.921604 52.921604) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Smoothed_Bernardes_1958_Ar__MO_764178710049_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 148217.331689156 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 148217.331689156/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 148217.331689156/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 148217.331689156/(1*1*${_u_distance}) variable V0_metal equal 148217.331689156/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 148217.331689156*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 148217.331689156 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_764178710049_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 = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 11 11 11 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) = 5.37 | 5.37 | 5.37 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -131.49819 -131.49819 -283.03075 -283.03075 293.15 293.15 148217.33 148217.33 1092.0083 1092.0083 1000 105.36 105.36 -47.099755 -47.099755 294.94373 294.94373 665007.13 665007.13 153.17878 153.17878 Loop time of 5.91692 on 1 procs for 1000 steps with 4000 atoms Performance: 14.602 ns/day, 1.644 hours/ns, 169.007 timesteps/s, 676.027 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 | 5.1027 | 5.1027 | 5.1027 | 0.0 | 86.24 Neigh | 0.64404 | 0.64404 | 0.64404 | 0.0 | 10.88 Comm | 0.026003 | 0.026003 | 0.026003 | 0.0 | 0.44 Output | 9.7373e-05 | 9.7373e-05 | 9.7373e-05 | 0.0 | 0.00 Modify | 0.13144 | 0.13144 | 0.13144 | 0.0 | 2.22 Other | | 0.01261 | | | 0.21 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3654 ave 3654 max 3654 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: 117772 ave 117772 max 117772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117772 Ave neighs/atom = 29.443 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 = ${P}" flag: Temp = 293.946853253578, Press = 154.835054986745 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.852 | 3.852 | 3.852 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 105.36 105.36 -47.099755 -47.099755 294.94373 294.94373 665007.13 665007.13 153.17878 153.17878 2000 138.93941 138.93941 -11.011467 -11.011467 290.09014 290.09014 3338014.8 3338014.8 44.265965 44.265965 Loop time of 2.29447 on 1 procs for 1000 steps with 4000 atoms Performance: 37.656 ns/day, 0.637 hours/ns, 435.830 timesteps/s, 1.743 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5524 | 1.5524 | 1.5524 | 0.0 | 67.66 Neigh | 0.55311 | 0.55311 | 0.55311 | 0.0 | 24.11 Comm | 0.022063 | 0.022063 | 0.022063 | 0.0 | 0.96 Output | 6.4591e-05 | 6.4591e-05 | 6.4591e-05 | 0.0 | 0.00 Modify | 0.15337 | 0.15337 | 0.15337 | 0.0 | 6.68 Other | | 0.01347 | | | 0.59 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1926 ave 1926 max 1926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25104 ave 25104 max 25104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25104 Ave neighs/atom = 6.276 Neighbor list builds = 105 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 293.089863100316, Press = 98.7602494872182 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 29 29 29 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.567 | 3.567 | 3.567 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 138.93941 138.93941 -11.011467 -11.011467 290.09014 290.09014 3338014.8 3338014.8 44.265965 44.265965 3000 147.5254 147.5254 -3.0141354 -3.0141354 291.22894 291.22894 17757963 17757963 8.7867968 8.7867968 Loop time of 0.868546 on 1 procs for 1000 steps with 4000 atoms Performance: 99.477 ns/day, 0.241 hours/ns, 1151.350 timesteps/s, 4.605 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44068 | 0.44068 | 0.44068 | 0.0 | 50.74 Neigh | 0.28452 | 0.28452 | 0.28452 | 0.0 | 32.76 Comm | 0.014093 | 0.014093 | 0.014093 | 0.0 | 1.62 Output | 7.7756e-05 | 7.7756e-05 | 7.7756e-05 | 0.0 | 0.01 Modify | 0.11808 | 0.11808 | 0.11808 | 0.0 | 13.59 Other | | 0.01109 | | | 1.28 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1032 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 5764 ave 5764 max 5764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5764 Ave neighs/atom = 1.441 Neighbor list builds = 174 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.730540317096, Press = 62.2114648982484 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 50 50 50 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.045 | 4.045 | 4.045 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 147.5254 147.5254 -3.0141354 -3.0141354 291.22894 291.22894 17757963 17757963 8.7867968 8.7867968 4000 149.96335 149.96335 -0.75229268 -0.75229268 291.56963 291.56963 91396184 91396184 1.7479279 1.7479279 Loop time of 0.769558 on 1 procs for 1000 steps with 4000 atoms Performance: 112.272 ns/day, 0.214 hours/ns, 1299.447 timesteps/s, 5.198 Matom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24589 | 0.24589 | 0.24589 | 0.0 | 31.95 Neigh | 0.37896 | 0.37896 | 0.37896 | 0.0 | 49.24 Comm | 0.01388 | 0.01388 | 0.01388 | 0.0 | 1.80 Output | 4.251e-05 | 4.251e-05 | 4.251e-05 | 0.0 | 0.01 Modify | 0.1178 | 0.1178 | 0.1178 | 0.0 | 15.31 Other | | 0.01299 | | | 1.69 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 554 ave 554 max 554 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1410 ave 1410 max 1410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1410 Ave neighs/atom = 0.3525 Neighbor list builds = 284 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.349891526743, Press = 43.5493484782844 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 86 86 86 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.281 | 6.281 | 6.281 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 149.96335 149.96335 -0.75229268 -0.75229268 291.56963 291.56963 91396184 91396184 1.7479279 1.7479279 5000 150.54757 150.54757 -0.18428158 -0.18428158 291.60099 291.60099 4.5358822e+08 4.5358822e+08 0.35423069 0.35423069 Loop time of 1.5535 on 1 procs for 1000 steps with 4000 atoms Performance: 55.616 ns/day, 0.432 hours/ns, 643.709 timesteps/s, 2.575 Matom-step/s 97.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19844 | 0.19844 | 0.19844 | 0.0 | 12.77 Neigh | 1.1862 | 1.1862 | 1.1862 | 0.0 | 76.36 Comm | 0.018564 | 0.018564 | 0.018564 | 0.0 | 1.19 Output | 5.0646e-05 | 5.0646e-05 | 5.0646e-05 | 0.0 | 0.00 Modify | 0.13189 | 0.13189 | 0.13189 | 0.0 | 8.49 Other | | 0.01837 | | | 1.18 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 316 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 336 ave 336 max 336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 336 Ave neighs/atom = 0.084 Neighbor list builds = 439 Dangerous builds = 0 if "${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 453588223.418683 A^3 has become larger than 148217331.689156 A^3. Aborting calculation. Total wall time: 0:00:11