# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.24405661970377*${_u_distance} variable latticeconst_converted equal 4.24405661970377*1 lattice fcc ${latticeconst_converted} lattice fcc 4.24405661970377 Lattice spacing in x,y,z = 4.2440566 4.2440566 4.2440566 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (42.440566 42.440566 42.440566) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (42.440566 42.440566 42.440566) create_atoms CPU = 0.001 seconds variable mass_converted equal 20.1797*${_u_mass} variable mass_converted equal 20.1797*1 kim interactions Ne #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958LowCutoff_Ne__MO_466741694288_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 76444.0182483146 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 76444.0182483146/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 76444.0182483146/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 76444.0182483146/(1*1*${_u_distance}) variable V0_metal equal 76444.0182483146/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 76444.0182483146*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 76444.0182483146 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_466741694288_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 = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, bins = 9 9 9 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) = 6.242 | 6.242 | 6.242 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 45.53705 45.53705 -95.657278 -95.657278 273.15 273.15 76444.018 76444.018 1972.8444 1972.8444 1000 133.3759 133.3759 -6.849988 -6.849988 271.2765 271.2765 630125.89 630125.89 248.47155 248.47155 Loop time of 5.81141 on 1 procs for 1000 steps with 4000 atoms Performance: 14.867 ns/day, 1.614 hours/ns, 172.075 timesteps/s, 688.301 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 | 4.8213 | 4.8213 | 4.8213 | 0.0 | 82.96 Neigh | 0.81089 | 0.81089 | 0.81089 | 0.0 | 13.95 Comm | 0.029898 | 0.029898 | 0.029898 | 0.0 | 0.51 Output | 0.00010797 | 0.00010797 | 0.00010797 | 0.0 | 0.00 Modify | 0.13342 | 0.13342 | 0.13342 | 0.0 | 2.30 Other | | 0.01574 | | | 0.27 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3249 ave 3249 max 3249 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: 90264 ave 90264 max 90264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90264 Ave neighs/atom = 22.566 Neighbor list builds = 77 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 = ${P}" flag: Temp = 271.320865347448, Press = 268.51657275693 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, bins = 19 19 19 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.576 | 3.576 | 3.576 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 133.3759 133.3759 -6.849988 -6.849988 271.2765 271.2765 630125.89 630125.89 248.47155 248.47155 2000 139.10225 139.10225 -1.2283534 -1.2283534 271.47907 271.47907 3438286.7 3438286.7 44.149963 44.149963 Loop time of 1.65666 on 1 procs for 1000 steps with 4000 atoms Performance: 52.153 ns/day, 0.460 hours/ns, 603.625 timesteps/s, 2.415 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0659 | 1.0659 | 1.0659 | 0.0 | 64.34 Neigh | 0.42349 | 0.42349 | 0.42349 | 0.0 | 25.56 Comm | 0.019124 | 0.019124 | 0.019124 | 0.0 | 1.15 Output | 4.6648e-05 | 4.6648e-05 | 4.6648e-05 | 0.0 | 0.00 Modify | 0.1347 | 0.1347 | 0.1347 | 0.0 | 8.13 Other | | 0.01336 | | | 0.81 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1632 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16674 ave 16674 max 16674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16674 Ave neighs/atom = 4.1685 Neighbor list builds = 109 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 271.500942814492, Press = 130.022350531457 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, bins = 32 32 32 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.704 | 3.704 | 3.704 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 139.10225 139.10225 -1.2283534 -1.2283534 271.47907 271.47907 3438286.7 3438286.7 44.149963 44.149963 3000 140.24952 140.24952 -0.22357504 -0.22357504 271.75472 271.75472 17455822 17455822 8.6030678 8.6030678 Loop time of 0.902232 on 1 procs for 1000 steps with 4000 atoms Performance: 95.763 ns/day, 0.251 hours/ns, 1108.363 timesteps/s, 4.433 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44242 | 0.44242 | 0.44242 | 0.0 | 49.04 Neigh | 0.29637 | 0.29637 | 0.29637 | 0.0 | 32.85 Comm | 0.016228 | 0.016228 | 0.016228 | 0.0 | 1.80 Output | 4.4734e-05 | 4.4734e-05 | 4.4734e-05 | 0.0 | 0.00 Modify | 0.13345 | 0.13345 | 0.13345 | 0.0 | 14.79 Other | | 0.01372 | | | 1.52 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 899 ave 899 max 899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3270 ave 3270 max 3270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3270 Ave neighs/atom = 0.8175 Neighbor list builds = 171 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 271.57524305643, Press = 78.3552246855283 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, bins = 55 55 55 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.329 | 4.329 | 4.329 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 140.24952 140.24952 -0.22357504 -0.22357504 271.75472 271.75472 17455822 17455822 8.6030678 8.6030678 4000 140.36954 140.36954 -0.067076645 -0.067076645 271.68415 271.68415 85133465 85133465 1.7607944 1.7607944 Loop time of 0.890488 on 1 procs for 1000 steps with 4000 atoms Performance: 97.025 ns/day, 0.247 hours/ns, 1122.980 timesteps/s, 4.492 Matom-step/s 98.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30173 | 0.30173 | 0.30173 | 0.0 | 33.88 Neigh | 0.41965 | 0.41965 | 0.41965 | 0.0 | 47.13 Comm | 0.01685 | 0.01685 | 0.01685 | 0.0 | 1.89 Output | 6.9089e-05 | 6.9089e-05 | 6.9089e-05 | 0.0 | 0.01 Modify | 0.13627 | 0.13627 | 0.13627 | 0.0 | 15.30 Other | | 0.01591 | | | 1.79 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 518 ave 518 max 518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 648 Ave neighs/atom = 0.162 Neighbor list builds = 271 Dangerous builds = 0 if "${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 85133464.851027 A^3 has become larger than 76444018.2483146 A^3. Aborting calculation. Total wall time: 0:00:09