# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.262299403548241*${_u_distance} variable latticeconst_converted equal 5.262299403548241*1 lattice fcc ${latticeconst_converted} lattice fcc 5.26229940354824 Lattice spacing in x,y,z = 5.2622994 5.2622994 5.2622994 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.622994 52.622994 52.622994) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.622994 52.622994 52.622994) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim Morse_SigmoidalSmoothed_Jelinek_1972_Ar__MO_071460865933_002 WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1127) 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 145722.516377902 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 145722.516377902/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 145722.516377902/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 145722.516377902/(1*1*${_u_distance}) variable V0_metal equal 145722.516377902/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 145722.516377902*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 145722.516377902 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 293.15*${_u_temperature} variable temp_converted equal 293.15*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 293.15 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 293.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "293.15 - 1.0" variable T_up equal "293.15 + 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_071460865933_002#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 = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, 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 0 151.3058 151.3058 -0.2267577 -0.2267577 293.15 293.15 145722.52 145722.52 1110.7041 1110.7041 1000 151.82618 151.82618 1.2027023 1.2027023 291.39133 291.39133 1055597.3 1055597.3 155.5032 155.5032 Loop time of 5.05818 on 1 procs for 1000 steps with 4000 atoms Performance: 17.081 ns/day, 1.405 hours/ns, 197.699 timesteps/s, 790.798 katom-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 | 4.1645 | 4.1645 | 4.1645 | 0.0 | 82.33 Neigh | 0.72486 | 0.72486 | 0.72486 | 0.0 | 14.33 Comm | 0.026206 | 0.026206 | 0.026206 | 0.0 | 0.52 Output | 0.00010767 | 0.00010767 | 0.00010767 | 0.0 | 0.00 Modify | 0.1286 | 0.1286 | 0.1286 | 0.0 | 2.54 Other | | 0.01386 | | | 0.27 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2909 ave 2909 max 2909 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: 63500 ave 63500 max 63500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63500 Ave neighs/atom = 15.875 Neighbor list builds = 82 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 = ${P}" flag: Temp = 291.37414601622, Press = 169.829294742424 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 21 21 21 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.491 | 3.491 | 3.491 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 151.82618 151.82618 1.2027023 1.2027023 291.39133 291.39133 1055597.3 1055597.3 155.5032 155.5032 2000 150.81859 150.81859 0.13071033 0.13071033 291.51592 291.51592 5922970.7 5922970.7 27.244485 27.244485 Loop time of 1.38553 on 1 procs for 1000 steps with 4000 atoms Performance: 62.359 ns/day, 0.385 hours/ns, 721.745 timesteps/s, 2.887 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.82324 | 0.82324 | 0.82324 | 0.0 | 59.42 Neigh | 0.3996 | 0.3996 | 0.3996 | 0.0 | 28.84 Comm | 0.018522 | 0.018522 | 0.018522 | 0.0 | 1.34 Output | 6.9721e-05 | 6.9721e-05 | 6.9721e-05 | 0.0 | 0.01 Modify | 0.1316 | 0.1316 | 0.1316 | 0.0 | 9.50 Other | | 0.01249 | | | 0.90 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1438 ave 1438 max 1438 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11436 ave 11436 max 11436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11436 Ave neighs/atom = 2.859 Neighbor list builds = 128 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 291.452952494463, Press = 81.3505699705468 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 36 36 36 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.676 | 3.676 | 3.676 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 150.81859 150.81859 0.13071033 0.13071033 291.51592 291.51592 5922970.7 5922970.7 27.244485 27.244485 3000 150.75049 150.75049 0.036325734 0.036325734 291.56678 291.56678 30700583 30700583 5.2472196 5.2472196 Loop time of 0.818908 on 1 procs for 1000 steps with 4000 atoms Performance: 105.506 ns/day, 0.227 hours/ns, 1221.139 timesteps/s, 4.885 Matom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34209 | 0.34209 | 0.34209 | 0.0 | 41.77 Neigh | 0.31462 | 0.31462 | 0.31462 | 0.0 | 38.42 Comm | 0.016276 | 0.016276 | 0.016276 | 0.0 | 1.99 Output | 5.4973e-05 | 5.4973e-05 | 5.4973e-05 | 0.0 | 0.01 Modify | 0.13222 | 0.13222 | 0.13222 | 0.0 | 16.15 Other | | 0.01364 | | | 1.67 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 821 ave 821 max 821 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2250 ave 2250 max 2250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2250 Ave neighs/atom = 0.5625 Neighbor list builds = 203 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 291.49532634513, Press = 48.9159817049331 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 62 62 62 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.556 | 4.556 | 4.556 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 150.75049 150.75049 0.036325734 0.036325734 291.56678 291.56678 30700583 30700583 5.2472196 5.2472196 4000 150.74583 150.74583 0.013354471 0.013354471 291.60219 291.60219 1.5227196e+08 1.5227196e+08 1.0575623 1.0575623 Loop time of 0.929981 on 1 procs for 1000 steps with 4000 atoms Performance: 92.905 ns/day, 0.258 hours/ns, 1075.291 timesteps/s, 4.301 Matom-step/s 96.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23417 | 0.23417 | 0.23417 | 0.0 | 25.18 Neigh | 0.52596 | 0.52596 | 0.52596 | 0.0 | 56.56 Comm | 0.017715 | 0.017715 | 0.017715 | 0.0 | 1.90 Output | 5.4482e-05 | 5.4482e-05 | 5.4482e-05 | 0.0 | 0.01 Modify | 0.13566 | 0.13566 | 0.13566 | 0.0 | 14.59 Other | | 0.01643 | | | 1.77 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 481 ave 481 max 481 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 450 ave 450 max 450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 450 Ave neighs/atom = 0.1125 Neighbor list builds = 309 Dangerous builds = 0 if "${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 152271960.938641 A^3 has become larger than 145722516.377902 A^3. Aborting calculation. Total wall time: 0:00:08