# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.226186460256581*${_u_distance} variable latticeconst_converted equal 4.226186460256581*1 lattice fcc ${latticeconst_converted} lattice fcc 4.22618646025658 Lattice spacing in x,y,z = 4.2261865 4.2261865 4.2261865 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (42.261865 42.261865 42.261865) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (42.261865 42.261865 42.261865) create_atoms CPU = 0.001 seconds variable mass_converted equal 20.1797*${_u_mass} variable mass_converted equal 20.1797*1 kim interactions Ne #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958HighCutoff_Ne__MO_966254629593_004 pair_coeff * * Ne #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 20.1797 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 75482.4456404676 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 75482.4456404676/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 75482.4456404676/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 75482.4456404676/(1*1*${_u_distance}) variable V0_metal equal 75482.4456404676/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 75482.4456404676*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 75482.4456404676 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 313.15*${_u_temperature} variable temp_converted equal 313.15*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 313.15 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 313.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "313.15 - 1.0" variable T_up equal "313.15 + 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_966254629593_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 = 18 ghost atom cutoff = 18 binsize = 9, bins = 5 5 5 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) = 26.12 | 26.12 | 26.12 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 56.240762 56.240762 -105.63002 -105.63002 313.15 313.15 75482.446 75482.446 2290.559 2290.559 1000 153.2823 153.2823 -7.3429752 -7.3429752 310.74049 310.74049 635289.69 635289.69 286.71735 286.71735 Loop time of 43.5188 on 1 procs for 1000 steps with 4000 atoms Performance: 1.985 ns/day, 12.089 hours/ns, 22.979 timesteps/s, 91.914 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 39.696 | 39.696 | 39.696 | 0.0 | 91.22 Neigh | 3.5825 | 3.5825 | 3.5825 | 0.0 | 8.23 Comm | 0.065702 | 0.065702 | 0.065702 | 0.0 | 0.15 Output | 0.00011806 | 0.00011806 | 0.00011806 | 0.0 | 0.00 Modify | 0.14885 | 0.14885 | 0.14885 | 0.0 | 0.34 Other | | 0.02556 | | | 0.06 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7519 ave 7519 max 7519 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: 619218 ave 619218 max 619218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 619218 Ave neighs/atom = 154.8045 Neighbor list builds = 78 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 = ${P}" flag: Temp = 311.012180647425, Press = 316.964799029672 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 9.106 | 9.106 | 9.106 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 153.2823 153.2823 -7.3429752 -7.3429752 310.74049 310.74049 635289.69 635289.69 286.71735 286.71735 2000 159.62348 159.62348 -1.3759998 -1.3759998 311.46441 311.46441 3452127.8 3452127.8 50.333702 50.333702 Loop time of 7.42175 on 1 procs for 1000 steps with 4000 atoms Performance: 11.641 ns/day, 2.062 hours/ns, 134.739 timesteps/s, 538.956 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9994 | 5.9994 | 5.9994 | 0.0 | 80.83 Neigh | 1.2197 | 1.2197 | 1.2197 | 0.0 | 16.43 Comm | 0.03402 | 0.03402 | 0.03402 | 0.0 | 0.46 Output | 0.0001787 | 0.0001787 | 0.0001787 | 0.0 | 0.00 Modify | 0.14817 | 0.14817 | 0.14817 | 0.0 | 2.00 Other | | 0.02035 | | | 0.27 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3581 ave 3581 max 3581 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114966 ave 114966 max 114966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114966 Ave neighs/atom = 28.7415 Neighbor list builds = 111 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 311.268367860303, Press = 149.173906644195 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.196 | 7.196 | 7.196 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 159.62348 159.62348 -1.3759998 -1.3759998 311.46441 311.46441 3452127.8 3452127.8 50.333702 50.333702 3000 160.64509 160.64509 -0.36940449 -0.36940449 311.49345 311.49345 17439369 17439369 9.8515173 9.8515173 Loop time of 2.33608 on 1 procs for 1000 steps with 4000 atoms Performance: 36.985 ns/day, 0.649 hours/ns, 428.068 timesteps/s, 1.712 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.396 | 1.396 | 1.396 | 0.0 | 59.76 Neigh | 0.7673 | 0.7673 | 0.7673 | 0.0 | 32.85 Comm | 0.024318 | 0.024318 | 0.024318 | 0.0 | 1.04 Output | 4.4223e-05 | 4.4223e-05 | 4.4223e-05 | 0.0 | 0.00 Modify | 0.13316 | 0.13316 | 0.13316 | 0.0 | 5.70 Other | | 0.01522 | | | 0.65 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1839 ave 1839 max 1839 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 22798 ave 22798 max 22798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22798 Ave neighs/atom = 5.6995 Neighbor list builds = 171 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 311.353544094772, Press = 89.8376911982978 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 29 29 29 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.911 | 6.911 | 6.911 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 160.64509 160.64509 -0.36940449 -0.36940449 311.49345 311.49345 17439369 17439369 9.8515173 9.8515173 4000 161.0453 161.0453 -0.087385276 -0.087385276 311.7221 311.7221 84904611 84904611 2.025109 2.025109 Loop time of 1.18478 on 1 procs for 1000 steps with 4000 atoms Performance: 72.925 ns/day, 0.329 hours/ns, 844.035 timesteps/s, 3.376 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50725 | 0.50725 | 0.50725 | 0.0 | 42.81 Neigh | 0.50948 | 0.50948 | 0.50948 | 0.0 | 43.00 Comm | 0.022061 | 0.022061 | 0.022061 | 0.0 | 1.86 Output | 4.3121e-05 | 4.3121e-05 | 4.3121e-05 | 0.0 | 0.00 Modify | 0.13057 | 0.13057 | 0.13057 | 0.0 | 11.02 Other | | 0.01538 | | | 1.30 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1037 ave 1037 max 1037 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4716 ave 4716 max 4716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4716 Ave neighs/atom = 1.179 Neighbor list builds = 273 Dangerous builds = 0 if "${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 84904611.48633 A^3 has become larger than 75482445.6404676 A^3. Aborting calculation. Total wall time: 0:00:54