# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.266347639262676*${_u_distance} variable latticeconst_converted equal 5.266347639262676*1 lattice fcc ${latticeconst_converted} lattice fcc 5.26634763926268 Lattice spacing in x,y,z = 5.2663476 5.2663476 5.2663476 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.663476 52.663476 52.663476) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.663476 52.663476 52.663476) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958LowCutoff_Ar__MO_720819638419_004 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 146059.083903987 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 146059.083903987/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 146059.083903987/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 146059.083903987/(1*1*${_u_distance}) variable V0_metal equal 146059.083903987/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 146059.083903987*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 146059.083903987 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_720819638419_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 = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, 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) = 6.244 | 6.244 | 6.244 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -179.69595 -179.69595 -320.89028 -320.89028 273.15 273.15 146059.08 146059.08 1032.5419 1032.5419 1000 70.993379 70.993379 -70.671093 -70.671093 274.05953 274.05953 529678.4 529678.4 124.22724 124.22724 Loop time of 7.31173 on 1 procs for 1000 steps with 4000 atoms Performance: 11.817 ns/day, 2.031 hours/ns, 136.767 timesteps/s, 547.066 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 | 6.4932 | 6.4932 | 6.4932 | 0.0 | 88.80 Neigh | 0.64596 | 0.64596 | 0.64596 | 0.0 | 8.83 Comm | 0.029073 | 0.029073 | 0.029073 | 0.0 | 0.40 Output | 8.9728e-05 | 8.9728e-05 | 8.9728e-05 | 0.0 | 0.00 Modify | 0.1295 | 0.1295 | 0.1295 | 0.0 | 1.77 Other | | 0.01394 | | | 0.19 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4321 ave 4321 max 4321 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: 177644 ave 177644 max 177644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177644 Ave neighs/atom = 44.411 Neighbor list builds = 51 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 = ${P}" flag: Temp = 272.242460338989, Press = 123.256882187599 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 15 15 15 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.944 | 3.944 | 3.944 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 70.993379 70.993379 -70.671093 -70.671093 274.05953 274.05953 529678.4 529678.4 124.22724 124.22724 2000 122.4991 122.4991 -17.442243 -17.442243 270.72602 270.72602 2357847.6 2357847.6 54.371521 54.371521 Loop time of 2.93842 on 1 procs for 1000 steps with 4000 atoms Performance: 29.404 ns/day, 0.816 hours/ns, 340.319 timesteps/s, 1.361 Matom-step/s 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2152 | 2.2152 | 2.2152 | 0.0 | 75.39 Neigh | 0.55111 | 0.55111 | 0.55111 | 0.0 | 18.76 Comm | 0.021417 | 0.021417 | 0.021417 | 0.0 | 0.73 Output | 9.5939e-05 | 9.5939e-05 | 9.5939e-05 | 0.0 | 0.00 Modify | 0.13753 | 0.13753 | 0.13753 | 0.0 | 4.68 Other | | 0.01305 | | | 0.44 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2368 ave 2368 max 2368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42408 ave 42408 max 42408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42408 Ave neighs/atom = 10.602 Neighbor list builds = 88 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.891001127941, Press = 95.0307864262415 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 24 24 24 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.61 | 3.61 | 3.61 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 122.4991 122.4991 -17.442243 -17.442243 270.72602 270.72602 2357847.6 2357847.6 54.371521 54.371521 3000 137.33263 137.33263 -4.556625 -4.556625 274.49438 274.49438 12685965 12685965 11.617196 11.617196 Loop time of 1.07658 on 1 procs for 1000 steps with 4000 atoms Performance: 80.254 ns/day, 0.299 hours/ns, 928.872 timesteps/s, 3.715 Matom-step/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.60081 | 0.60081 | 0.60081 | 0.0 | 55.81 Neigh | 0.32979 | 0.32979 | 0.32979 | 0.0 | 30.63 Comm | 0.015345 | 0.015345 | 0.015345 | 0.0 | 1.43 Output | 4.5916e-05 | 4.5916e-05 | 4.5916e-05 | 0.0 | 0.00 Modify | 0.11877 | 0.11877 | 0.11877 | 0.0 | 11.03 Other | | 0.01182 | | | 1.10 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1252 ave 1252 max 1252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 9170 ave 9170 max 9170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9170 Ave neighs/atom = 2.2925 Neighbor list builds = 157 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.927880648897, Press = 63.0030011021325 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 42 42 42 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.904 | 3.904 | 3.904 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 137.33263 137.33263 -4.556625 -4.556625 274.49438 274.49438 12685965 12685965 11.617196 11.617196 4000 143.65853 143.65853 -1.1149789 -1.1149789 280.07417 280.07417 66724315 66724315 2.2925135 2.2925135 Loop time of 0.786162 on 1 procs for 1000 steps with 4000 atoms Performance: 109.901 ns/day, 0.218 hours/ns, 1272.003 timesteps/s, 5.088 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29787 | 0.29787 | 0.29787 | 0.0 | 37.89 Neigh | 0.3411 | 0.3411 | 0.3411 | 0.0 | 43.39 Comm | 0.014701 | 0.014701 | 0.014701 | 0.0 | 1.87 Output | 6.5593e-05 | 6.5593e-05 | 6.5593e-05 | 0.0 | 0.01 Modify | 0.11914 | 0.11914 | 0.11914 | 0.0 | 15.15 Other | | 0.01328 | | | 1.69 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 713 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2226 ave 2226 max 2226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2226 Ave neighs/atom = 0.5565 Neighbor list builds = 258 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.922247086254, Press = 44.4887014358905 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 73 73 73 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.314 | 5.314 | 5.314 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 143.65853 143.65853 -1.1149789 -1.1149789 280.07417 280.07417 66724315 66724315 2.2925135 2.2925135 5000 141.27914 141.27914 -0.2416546 -0.2416546 273.78157 273.78157 3.3785924e+08 3.3785924e+08 0.4461561 0.4461561 Loop time of 1.34978 on 1 procs for 1000 steps with 4000 atoms Performance: 64.010 ns/day, 0.375 hours/ns, 740.861 timesteps/s, 2.963 Matom-step/s 97.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24706 | 0.24706 | 0.24706 | 0.0 | 18.30 Neigh | 0.91864 | 0.91864 | 0.91864 | 0.0 | 68.06 Comm | 0.020314 | 0.020314 | 0.020314 | 0.0 | 1.51 Output | 4.8581e-05 | 4.8581e-05 | 4.8581e-05 | 0.0 | 0.00 Modify | 0.14546 | 0.14546 | 0.14546 | 0.0 | 10.78 Other | | 0.01825 | | | 1.35 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 388 ave 388 max 388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 504 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 504 Ave neighs/atom = 0.126 Neighbor list builds = 407 Dangerous builds = 0 if "${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 337859244.229147 A^3 has become larger than 146059083.903987 A^3. Aborting calculation. Total wall time: 0:00:13