# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.24417295455933*${_u_distance} variable latticeconst_converted equal 5.24417295455933*1 lattice fcc ${latticeconst_converted} lattice fcc 5.24417295455933 Lattice spacing in x,y,z = 5.244173 5.244173 5.244173 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.44173 52.44173 52.44173) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.44173 52.44173 52.44173) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958HighCutoff_Ar__MO_242741380554_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 144221.835764993 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144221.835764993/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144221.835764993/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 144221.835764993/(1*1*${_u_distance}) variable V0_metal equal 144221.835764993/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 144221.835764993*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 144221.835764993 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_242741380554_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 = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, 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) = 24.97 | 24.97 | 24.97 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -182.18969 -182.18969 -354.39869 -354.39869 333.15 333.15 144221.84 144221.84 1275.3922 1275.3922 1000 108.73969 108.73969 -65.952812 -65.952812 337.95448 337.95448 622137.31 622137.31 175.06695 175.06695 Loop time of 55.5543 on 1 procs for 1000 steps with 4000 atoms Performance: 1.555 ns/day, 15.432 hours/ns, 18.000 timesteps/s, 72.002 katom-step/s 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 51.851 | 51.851 | 51.851 | 0.0 | 93.33 Neigh | 3.4584 | 3.4584 | 3.4584 | 0.0 | 6.23 Comm | 0.071038 | 0.071038 | 0.071038 | 0.0 | 0.13 Output | 0.00014842 | 0.00014842 | 0.00014842 | 0.0 | 0.00 Modify | 0.14922 | 0.14922 | 0.14922 | 0.0 | 0.27 Other | | 0.02405 | | | 0.04 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10042 ave 10042 max 10042 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: 1.12939e+06 ave 1.12939e+06 max 1.12939e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1129386 Ave neighs/atom = 282.3465 Neighbor list builds = 59 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 = ${P}" flag: Temp = 333.610203925946, Press = 177.175562569673 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 11.03 | 11.03 | 11.03 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 108.73969 108.73969 -65.952812 -65.952812 337.95448 337.95448 622137.31 622137.31 175.06695 175.06695 2000 157.15109 157.15109 -14.685048 -14.685048 332.42867 332.42867 3042772.9 3042772.9 54.052795 54.052795 Loop time of 15.0666 on 1 procs for 1000 steps with 4000 atoms Performance: 5.735 ns/day, 4.185 hours/ns, 66.372 timesteps/s, 265.488 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.025 | 13.025 | 13.025 | 0.0 | 86.45 Neigh | 1.8337 | 1.8337 | 1.8337 | 0.0 | 12.17 Comm | 0.043224 | 0.043224 | 0.043224 | 0.0 | 0.29 Output | 7.9339e-05 | 7.9339e-05 | 7.9339e-05 | 0.0 | 0.00 Modify | 0.14696 | 0.14696 | 0.14696 | 0.0 | 0.98 Other | | 0.01803 | | | 0.12 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4835 ave 4835 max 4835 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 237526 ave 237526 max 237526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237526 Ave neighs/atom = 59.3815 Neighbor list builds = 99 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.850248188893, Press = 115.853277080181 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 14 14 14 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.573 | 7.573 | 7.573 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 157.15109 157.15109 -14.685048 -14.685048 332.42867 332.42867 3042772.9 3042772.9 54.052795 54.052795 3000 166.10566 166.10566 -3.4823137 -3.4823137 328.07944 328.07944 16282327 16282327 10.889154 10.889154 Loop time of 4.23202 on 1 procs for 1000 steps with 4000 atoms Performance: 20.416 ns/day, 1.176 hours/ns, 236.294 timesteps/s, 945.175 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8054 | 2.8054 | 2.8054 | 0.0 | 66.29 Neigh | 1.2398 | 1.2398 | 1.2398 | 0.0 | 29.30 Comm | 0.030384 | 0.030384 | 0.030384 | 0.0 | 0.72 Output | 4.798e-05 | 4.798e-05 | 4.798e-05 | 0.0 | 0.00 Modify | 0.14106 | 0.14106 | 0.14106 | 0.0 | 3.33 Other | | 0.01533 | | | 0.36 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2403 ave 2403 max 2403 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 47078 ave 47078 max 47078 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47078 Ave neighs/atom = 11.7695 Neighbor list builds = 169 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 333.011222856454, Press = 73.6679502680964 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 24 24 24 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.858 | 6.858 | 6.858 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 166.10566 166.10566 -3.4823137 -3.4823137 328.07944 328.07944 16282327 16282327 10.889154 10.889154 4000 171.68489 171.68489 -0.81544175 -0.81544175 333.71358 333.71358 84372282 84372282 2.1698471 2.1698471 Loop time of 1.86287 on 1 procs for 1000 steps with 4000 atoms Performance: 46.380 ns/day, 0.517 hours/ns, 536.807 timesteps/s, 2.147 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.86534 | 0.86534 | 0.86534 | 0.0 | 46.45 Neigh | 0.81111 | 0.81111 | 0.81111 | 0.0 | 43.54 Comm | 0.027819 | 0.027819 | 0.027819 | 0.0 | 1.49 Output | 5.2048e-05 | 5.2048e-05 | 5.2048e-05 | 0.0 | 0.00 Modify | 0.14172 | 0.14172 | 0.14172 | 0.0 | 7.61 Other | | 0.01682 | | | 0.90 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1318 ave 1318 max 1318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 9936 ave 9936 max 9936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9936 Ave neighs/atom = 2.484 Neighbor list builds = 276 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.856765440945, Press = 51.6472874331615 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 41 41 41 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.128 | 7.128 | 7.128 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 171.68489 171.68489 -0.81544175 -0.81544175 333.71358 333.71358 84372282 84372282 2.1698471 2.1698471 5000 170.40063 170.40063 -0.14441927 -0.14441927 329.93097 329.93097 4.2207234e+08 4.2207234e+08 0.43138918 0.43138918 Loop time of 1.31813 on 1 procs for 1000 steps with 4000 atoms Performance: 65.547 ns/day, 0.366 hours/ns, 758.648 timesteps/s, 3.035 Matom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42138 | 0.42138 | 0.42138 | 0.0 | 31.97 Neigh | 0.70897 | 0.70897 | 0.70897 | 0.0 | 53.79 Comm | 0.02888 | 0.02888 | 0.02888 | 0.0 | 2.19 Output | 5.0975e-05 | 5.0975e-05 | 5.0975e-05 | 0.0 | 0.00 Modify | 0.13935 | 0.13935 | 0.13935 | 0.0 | 10.57 Other | | 0.01951 | | | 1.48 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 751 ave 751 max 751 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2244 ave 2244 max 2244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2244 Ave neighs/atom = 0.561 Neighbor list builds = 428 Dangerous builds = 0 if "${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 422072340.12525 A^3 has become larger than 144221835.764993 A^3. Aborting calculation. Total wall time: 0:01:18