# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 333.15*${_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_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 -110.82174 -110.82174 -283.03075 -283.03075 333.15 333.15 148217.33 148217.33 1241.0117 1241.0117 1000 134.16766 134.16766 -39.826944 -39.826944 336.60436 336.60436 765751.39 765751.39 180.22126 180.22126 Loop time of 6.23633 on 1 procs for 1000 steps with 4000 atoms Performance: 13.854 ns/day, 1.732 hours/ns, 160.351 timesteps/s, 641.403 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 | 5.2755 | 5.2755 | 5.2755 | 0.0 | 84.59 Neigh | 0.76841 | 0.76841 | 0.76841 | 0.0 | 12.32 Comm | 0.029604 | 0.029604 | 0.029604 | 0.0 | 0.47 Output | 0.00010194 | 0.00010194 | 0.00010194 | 0.0 | 0.00 Modify | 0.1485 | 0.1485 | 0.1485 | 0.0 | 2.38 Other | | 0.01426 | | | 0.23 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3416 ave 3416 max 3416 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: 102202 ave 102202 max 102202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102202 Ave neighs/atom = 25.5505 Neighbor list builds = 67 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 = ${P}" flag: Temp = 330.809699713338, Press = 183.828037093902 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 18 18 18 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.856 | 3.856 | 3.856 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 134.16766 134.16766 -39.826944 -39.826944 336.60436 336.60436 765751.39 765751.39 180.22126 180.22126 2000 163.9483 163.9483 -9.4134404 -9.4134404 335.38004 335.38004 3981998.5 3981998.5 43.703495 43.703495 Loop time of 1.85002 on 1 procs for 1000 steps with 4000 atoms Performance: 46.702 ns/day, 0.514 hours/ns, 540.535 timesteps/s, 2.162 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2285 | 1.2285 | 1.2285 | 0.0 | 66.40 Neigh | 0.46212 | 0.46212 | 0.46212 | 0.0 | 24.98 Comm | 0.018341 | 0.018341 | 0.018341 | 0.0 | 0.99 Output | 5.4903e-05 | 5.4903e-05 | 5.4903e-05 | 0.0 | 0.00 Modify | 0.12977 | 0.12977 | 0.12977 | 0.0 | 7.01 Other | | 0.01124 | | | 0.61 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1801 ave 1801 max 1801 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 21084 ave 21084 max 21084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21084 Ave neighs/atom = 5.271 Neighbor list builds = 112 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.327557093554, Press = 106.260737510098 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 31 31 31 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.594 | 3.594 | 3.594 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 163.9483 163.9483 -9.4134404 -9.4134404 335.38004 335.38004 3981998.5 3981998.5 43.703495 43.703495 3000 170.89148 170.89148 -2.2339594 -2.2339594 334.9229 334.9229 21087475 21087475 8.6063626 8.6063626 Loop time of 0.875565 on 1 procs for 1000 steps with 4000 atoms Performance: 98.679 ns/day, 0.243 hours/ns, 1142.120 timesteps/s, 4.568 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42329 | 0.42329 | 0.42329 | 0.0 | 48.34 Neigh | 0.30065 | 0.30065 | 0.30065 | 0.0 | 34.34 Comm | 0.014976 | 0.014976 | 0.014976 | 0.0 | 1.71 Output | 6.0333e-05 | 6.0333e-05 | 6.0333e-05 | 0.0 | 0.01 Modify | 0.12475 | 0.12475 | 0.12475 | 0.0 | 14.25 Other | | 0.01184 | | | 1.35 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 962 ave 962 max 962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4676 ave 4676 max 4676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4676 Ave neighs/atom = 1.169 Neighbor list builds = 183 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.612406060617, Press = 65.8726719357002 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 53 53 53 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.154 | 4.154 | 4.154 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 170.89148 170.89148 -2.2339594 -2.2339594 334.9229 334.9229 21087475 21087475 8.6063626 8.6063626 4000 171.71253 171.71253 -0.54088967 -0.54088967 333.23592 333.23592 1.0755138e+08 1.0755138e+08 1.7042213 1.7042213 Loop time of 0.983349 on 1 procs for 1000 steps with 4000 atoms Performance: 87.863 ns/day, 0.273 hours/ns, 1016.933 timesteps/s, 4.068 Matom-step/s 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29599 | 0.29599 | 0.29599 | 0.0 | 30.10 Neigh | 0.50593 | 0.50593 | 0.50593 | 0.0 | 51.45 Comm | 0.018784 | 0.018784 | 0.018784 | 0.0 | 1.91 Output | 5.9422e-05 | 5.9422e-05 | 5.9422e-05 | 0.0 | 0.01 Modify | 0.14598 | 0.14598 | 0.14598 | 0.0 | 14.85 Other | | 0.0166 | | | 1.69 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 509 ave 509 max 509 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1104 ave 1104 max 1104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1104 Ave neighs/atom = 0.276 Neighbor list builds = 293 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.45307270492, Press = 45.9831875001762 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 91 91 91 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.781 | 6.781 | 6.781 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 171.71253 171.71253 -0.54088967 -0.54088967 333.23592 333.23592 1.0755138e+08 1.0755138e+08 1.7042213 1.7042213 5000 171.74579 171.74579 -0.1355082 -0.1355082 332.51603 332.51603 5.3054963e+08 5.3054963e+08 0.34558754 0.34558754 Loop time of 1.85136 on 1 procs for 1000 steps with 4000 atoms Performance: 46.668 ns/day, 0.514 hours/ns, 540.143 timesteps/s, 2.161 Matom-step/s 97.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22256 | 0.22256 | 0.22256 | 0.0 | 12.02 Neigh | 1.4344 | 1.4344 | 1.4344 | 0.0 | 77.48 Comm | 0.027219 | 0.027219 | 0.027219 | 0.0 | 1.47 Output | 4.8111e-05 | 4.8111e-05 | 4.8111e-05 | 0.0 | 0.00 Modify | 0.14704 | 0.14704 | 0.14704 | 0.0 | 7.94 Other | | 0.02009 | | | 1.09 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 274 ave 274 max 274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 252 ave 252 max 252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252 Ave neighs/atom = 0.063 Neighbor list builds = 453 Dangerous builds = 0 if "${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 530549625.301084 A^3 has become larger than 148217331.689156 A^3. Aborting calculation. Total wall time: 0:00:12