# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 273.15*${_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_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 -141.83642 -141.83642 -283.03075 -283.03075 273.15 273.15 148217.33 148217.33 1017.5067 1017.5067 1000 90.113896 90.113896 -52.247794 -52.247794 275.40834 275.40834 608699.21 608699.21 137.30863 137.30863 Loop time of 5.70209 on 1 procs for 1000 steps with 4000 atoms Performance: 15.152 ns/day, 1.584 hours/ns, 175.374 timesteps/s, 701.497 katom-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 | 4.9469 | 4.9469 | 4.9469 | 0.0 | 86.76 Neigh | 0.58235 | 0.58235 | 0.58235 | 0.0 | 10.21 Comm | 0.026373 | 0.026373 | 0.026373 | 0.0 | 0.46 Output | 0.0001065 | 0.0001065 | 0.0001065 | 0.0 | 0.00 Modify | 0.12772 | 0.12772 | 0.12772 | 0.0 | 2.24 Other | | 0.01862 | | | 0.33 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3774 ave 3774 max 3774 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: 127766 ave 127766 max 127766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127766 Ave neighs/atom = 31.9415 Neighbor list builds = 56 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 = ${P}" flag: Temp = 273.417748139763, Press = 135.079902856572 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.853 | 3.853 | 3.853 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 90.113896 90.113896 -52.247794 -52.247794 275.40834 275.40834 608699.21 608699.21 137.30863 137.30863 2000 127.52202 127.52202 -12.76409 -12.76409 271.39299 271.39299 2944771.3 2944771.3 45.343265 45.343265 Loop time of 1.91384 on 1 procs for 1000 steps with 4000 atoms Performance: 45.145 ns/day, 0.532 hours/ns, 522.510 timesteps/s, 2.090 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3354 | 1.3354 | 1.3354 | 0.0 | 69.78 Neigh | 0.42745 | 0.42745 | 0.42745 | 0.0 | 22.33 Comm | 0.017348 | 0.017348 | 0.017348 | 0.0 | 0.91 Output | 5.897e-05 | 5.897e-05 | 5.897e-05 | 0.0 | 0.00 Modify | 0.12046 | 0.12046 | 0.12046 | 0.0 | 6.29 Other | | 0.0131 | | | 0.68 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2030 ave 2030 max 2030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 28184 ave 28184 max 28184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28184 Ave neighs/atom = 7.046 Neighbor list builds = 99 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 273.048452612674, Press = 93.7848414127549 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 28 28 28 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.555 | 3.555 | 3.555 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 127.52202 127.52202 -12.76409 -12.76409 271.39299 271.39299 2944771.3 2944771.3 45.343265 45.343265 3000 137.23704 137.23704 -3.5471658 -3.5471658 272.35659 272.35659 15775356 15775356 9.2740131 9.2740131 Loop time of 0.913039 on 1 procs for 1000 steps with 4000 atoms Performance: 94.629 ns/day, 0.254 hours/ns, 1095.243 timesteps/s, 4.381 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47377 | 0.47377 | 0.47377 | 0.0 | 51.89 Neigh | 0.2932 | 0.2932 | 0.2932 | 0.0 | 32.11 Comm | 0.014335 | 0.014335 | 0.014335 | 0.0 | 1.57 Output | 4.4083e-05 | 4.4083e-05 | 4.4083e-05 | 0.0 | 0.00 Modify | 0.11922 | 0.11922 | 0.11922 | 0.0 | 13.06 Other | | 0.01247 | | | 1.37 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1094 ave 1094 max 1094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 6432 ave 6432 max 6432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6432 Ave neighs/atom = 1.608 Neighbor list builds = 170 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 273.042931971913, Press = 60.0435725611063 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 48 48 48 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.978 | 3.978 | 3.978 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 137.23704 137.23704 -3.5471658 -3.5471658 272.35659 272.35659 15775356 15775356 9.2740131 9.2740131 4000 142.66802 142.66802 -0.84902872 -0.84902872 277.64347 277.64347 81855103 81855103 1.8603516 1.8603516 Loop time of 0.794084 on 1 procs for 1000 steps with 4000 atoms Performance: 108.805 ns/day, 0.221 hours/ns, 1259.312 timesteps/s, 5.037 Matom-step/s 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26578 | 0.26578 | 0.26578 | 0.0 | 33.47 Neigh | 0.37869 | 0.37869 | 0.37869 | 0.0 | 47.69 Comm | 0.015865 | 0.015865 | 0.015865 | 0.0 | 2.00 Output | 4.6968e-05 | 4.6968e-05 | 4.6968e-05 | 0.0 | 0.01 Modify | 0.12015 | 0.12015 | 0.12015 | 0.0 | 15.13 Other | | 0.01354 | | | 1.71 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 590 ave 590 max 590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1664 ave 1664 max 1664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1664 Ave neighs/atom = 0.416 Neighbor list builds = 275 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.990982219065, Press = 42.141173226088 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 83 83 83 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.006 | 6.006 | 6.006 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 142.66802 142.66802 -0.84902872 -0.84902872 277.64347 277.64347 81855103 81855103 1.8603516 1.8603516 5000 141.86333 141.86333 -0.20670988 -0.20670988 274.84413 274.84413 4.0982738e+08 4.0982738e+08 0.36928466 0.36928466 Loop time of 1.46715 on 1 procs for 1000 steps with 4000 atoms Performance: 58.890 ns/day, 0.408 hours/ns, 681.593 timesteps/s, 2.726 Matom-step/s 95.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19245 | 0.19245 | 0.19245 | 0.0 | 13.12 Neigh | 1.1152 | 1.1152 | 1.1152 | 0.0 | 76.01 Comm | 0.020787 | 0.020787 | 0.020787 | 0.0 | 1.42 Output | 5.6646e-05 | 5.6646e-05 | 5.6646e-05 | 0.0 | 0.00 Modify | 0.12127 | 0.12127 | 0.12127 | 0.0 | 8.27 Other | | 0.01735 | | | 1.18 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 322 ave 322 max 322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 372 ave 372 max 372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 372 Ave neighs/atom = 0.093 Neighbor list builds = 429 Dangerous builds = 0 if "${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 409827377.745394 A^3 has become larger than 148217331.689156 A^3. Aborting calculation. Total wall time: 0:00:10