# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.248509056866169*${_u_distance} variable latticeconst_converted equal 5.248509056866169*1 lattice fcc ${latticeconst_converted} lattice fcc 5.24850905686617 Lattice spacing in x,y,z = 5.2485091 5.2485091 5.2485091 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.485091 52.485091 52.485091) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.485091 52.485091 52.485091) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_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 144579.877647162 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144579.877647162/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144579.877647162/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 144579.877647162/(1*1*${_u_distance}) variable V0_metal equal 144579.877647162/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 144579.877647162*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 144579.877647162 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 253.15*${_u_temperature} variable temp_converted equal 253.15*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 253.15 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 253.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "253.15 - 1.0" variable T_up equal "253.15 + 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_126566794224_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 = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, 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) = 10.2 | 10.2 | 10.2 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -215.16593 -215.16593 -346.02203 -346.02203 253.15 253.15 144579.88 144579.88 966.73067 966.73067 1000 35.088414 35.088414 -96.807483 -96.807483 255.16156 255.16156 431430.75 431430.75 85.248347 85.248347 Loop time of 19.7844 on 1 procs for 1000 steps with 4000 atoms Performance: 4.367 ns/day, 5.496 hours/ns, 50.545 timesteps/s, 202.180 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 | 18.539 | 18.539 | 18.539 | 0.0 | 93.71 Neigh | 1.0614 | 1.0614 | 1.0614 | 0.0 | 5.36 Comm | 0.040594 | 0.040594 | 0.040594 | 0.0 | 0.21 Output | 7.4279e-05 | 7.4279e-05 | 7.4279e-05 | 0.0 | 0.00 Modify | 0.12598 | 0.12598 | 0.12598 | 0.0 | 0.64 Other | | 0.01693 | | | 0.09 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7267 ave 7267 max 7267 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: 580612 ave 580612 max 580612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 580612 Ave neighs/atom = 145.153 Neighbor list builds = 42 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 = ${P}" flag: Temp = 253.488645796131, Press = 84.9917882849162 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.6 | 5.6 | 5.6 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 35.088414 35.088414 -96.807483 -96.807483 255.16156 255.16156 431430.75 431430.75 85.248347 85.248347 2000 105.08331 105.08331 -27.736105 -27.736105 256.94817 256.94817 1570130.9 1570130.9 64.754493 64.754493 Loop time of 7.22877 on 1 procs for 1000 steps with 4000 atoms Performance: 11.952 ns/day, 2.008 hours/ns, 138.336 timesteps/s, 553.345 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.3178 | 6.3178 | 6.3178 | 0.0 | 87.40 Neigh | 0.75036 | 0.75036 | 0.75036 | 0.0 | 10.38 Comm | 0.026633 | 0.026633 | 0.026633 | 0.0 | 0.37 Output | 8.497e-05 | 8.497e-05 | 8.497e-05 | 0.0 | 0.00 Modify | 0.12166 | 0.12166 | 0.12166 | 0.0 | 1.68 Other | | 0.01223 | | | 0.17 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4145 ave 4145 max 4145 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 162722 ave 162722 max 162722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162722 Ave neighs/atom = 40.6805 Neighbor list builds = 70 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.997141669239, Press = 81.7697338971712 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 15 15 15 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.068 | 4.068 | 4.068 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 105.08331 105.08331 -27.736105 -27.736105 256.94817 256.94817 1570130.9 1570130.9 64.754493 64.754493 3000 122.66362 122.66362 -7.7623235 -7.7623235 252.31784 252.31784 8245693.4 8245693.4 15.746125 15.746125 Loop time of 2.49477 on 1 procs for 1000 steps with 4000 atoms Performance: 34.632 ns/day, 0.693 hours/ns, 400.839 timesteps/s, 1.603 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6886 | 1.6886 | 1.6886 | 0.0 | 67.69 Neigh | 0.65496 | 0.65496 | 0.65496 | 0.0 | 26.25 Comm | 0.019786 | 0.019786 | 0.019786 | 0.0 | 0.79 Output | 3.6799e-05 | 3.6799e-05 | 3.6799e-05 | 0.0 | 0.00 Modify | 0.12025 | 0.12025 | 0.12025 | 0.0 | 4.82 Other | | 0.01111 | | | 0.45 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2109 ave 2109 max 2109 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34212 ave 34212 max 34212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34212 Ave neighs/atom = 8.553 Neighbor list builds = 136 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.948432689902, Press = 59.7040485906103 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 27 27 27 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.765 | 3.765 | 3.765 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 122.66362 122.66362 -7.7623235 -7.7623235 252.31784 252.31784 8245693.4 8245693.4 15.746125 15.746125 4000 128.17012 128.17012 -1.9568554 -1.9568554 251.73946 251.73946 43848242 43848242 3.1042294 3.1042294 Loop time of 1.10998 on 1 procs for 1000 steps with 4000 atoms Performance: 77.839 ns/day, 0.308 hours/ns, 900.915 timesteps/s, 3.604 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55112 | 0.55112 | 0.55112 | 0.0 | 49.65 Neigh | 0.41188 | 0.41188 | 0.41188 | 0.0 | 37.11 Comm | 0.016712 | 0.016712 | 0.016712 | 0.0 | 1.51 Output | 2.694e-05 | 2.694e-05 | 2.694e-05 | 0.0 | 0.00 Modify | 0.11838 | 0.11838 | 0.11838 | 0.0 | 10.66 Other | | 0.01187 | | | 1.07 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1110 ave 1110 max 1110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 7946 ave 7946 max 7946 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7946 Ave neighs/atom = 1.9865 Neighbor list builds = 223 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.564725575536, Press = 42.9435743767722 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 46 46 46 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.139 | 4.139 | 4.139 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 128.17012 128.17012 -1.9568554 -1.9568554 251.73946 251.73946 43848242 43848242 3.1042294 3.1042294 5000 129.65332 129.65332 -0.50041836 -0.50041836 251.79123 251.79123 2.2488434e+08 2.2488434e+08 0.61419697 0.61419697 Loop time of 0.904551 on 1 procs for 1000 steps with 4000 atoms Performance: 95.517 ns/day, 0.251 hours/ns, 1105.520 timesteps/s, 4.422 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28248 | 0.28248 | 0.28248 | 0.0 | 31.23 Neigh | 0.47299 | 0.47299 | 0.47299 | 0.0 | 52.29 Comm | 0.017414 | 0.017414 | 0.017414 | 0.0 | 1.93 Output | 4.4734e-05 | 4.4734e-05 | 4.4734e-05 | 0.0 | 0.00 Modify | 0.11751 | 0.11751 | 0.11751 | 0.0 | 12.99 Other | | 0.01412 | | | 1.56 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 608 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1930 ave 1930 max 1930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1930 Ave neighs/atom = 0.4825 Neighbor list builds = 363 Dangerous builds = 0 if "${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 224884335.324327 A^3 has become larger than 144579877.647162 A^3. Aborting calculation. Total wall time: 0:00:32