# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.252865672111511*${_u_distance} variable latticeconst_converted equal 5.252865672111511*1 lattice fcc ${latticeconst_converted} lattice fcc 5.25286567211151 Lattice spacing in x,y,z = 5.2528657 5.2528657 5.2528657 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.528657 52.528657 52.528657) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.528657 52.528657 52.528657) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim Morse_QuinticSmoothed_Jelinek_1972_Ar__MO_908645784389_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 144940.209626461 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144940.209626461/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144940.209626461/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 144940.209626461/(1*1*${_u_distance}) variable V0_metal equal 144940.209626461/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 144940.209626461*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 144940.209626461 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 253.15*${_u_temperature} variable temp_converted equal 253.15*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 253.15 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 253.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "253.15 - 1.0" variable T_up equal "253.15 + 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_908645784389_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 -243.77408 -243.77408 -374.63018 -374.63018 253.15 253.15 144940.21 144940.21 964.32682 964.32682 1000 12.136341 12.136341 -116.79079 -116.79079 249.41828 249.41828 370869.41 370869.41 62.002198 62.002198 Loop time of 5.15962 on 1 procs for 1000 steps with 4000 atoms Performance: 16.745 ns/day, 1.433 hours/ns, 193.813 timesteps/s, 775.250 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 | 4.5482 | 4.5482 | 4.5482 | 0.0 | 88.15 Neigh | 0.44204 | 0.44204 | 0.44204 | 0.0 | 8.57 Comm | 0.02509 | 0.02509 | 0.02509 | 0.0 | 0.49 Output | 9.8765e-05 | 9.8765e-05 | 9.8765e-05 | 0.0 | 0.00 Modify | 0.13201 | 0.13201 | 0.13201 | 0.0 | 2.56 Other | | 0.01215 | | | 0.24 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4429 ave 4429 max 4429 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: 189910 ave 189910 max 189910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189910 Ave neighs/atom = 47.4775 Neighbor list builds = 36 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 = ${P}" flag: Temp = 252.887824409427, Press = 64.8364196461646 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 15 15 15 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.848 | 3.848 | 3.848 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 12.136341 12.136341 -116.79079 -116.79079 249.41828 249.41828 370869.41 370869.41 62.002198 62.002198 2000 88.905082 88.905082 -42.420205 -42.420205 254.05767 254.05767 1124873.2 1124873.2 67.973108 67.973108 Loop time of 2.55124 on 1 procs for 1000 steps with 4000 atoms Performance: 33.866 ns/day, 0.709 hours/ns, 391.966 timesteps/s, 1.568 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9963 | 1.9963 | 1.9963 | 0.0 | 78.25 Neigh | 0.3947 | 0.3947 | 0.3947 | 0.0 | 15.47 Comm | 0.019167 | 0.019167 | 0.019167 | 0.0 | 0.75 Output | 6.0323e-05 | 6.0323e-05 | 6.0323e-05 | 0.0 | 0.00 Modify | 0.13004 | 0.13004 | 0.13004 | 0.0 | 5.10 Other | | 0.01098 | | | 0.43 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2815 ave 2815 max 2815 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 64996 ave 64996 max 64996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64996 Ave neighs/atom = 16.249 Neighbor list builds = 58 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.862618132192, Press = 71.5678853449472 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 21 21 21 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.491 | 3.491 | 3.491 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 88.905082 88.905082 -42.420205 -42.420205 254.05767 254.05767 1124873.2 1124873.2 67.973108 67.973108 3000 119.93551 119.93551 -12.469658 -12.469658 256.14677 256.14677 5619753.3 5619753.3 21.939679 21.939679 Loop time of 1.08367 on 1 procs for 1000 steps with 4000 atoms Performance: 79.729 ns/day, 0.301 hours/ns, 922.793 timesteps/s, 3.691 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.61157 | 0.61157 | 0.61157 | 0.0 | 56.43 Neigh | 0.3285 | 0.3285 | 0.3285 | 0.0 | 30.31 Comm | 0.01475 | 0.01475 | 0.01475 | 0.0 | 1.36 Output | 3.7019e-05 | 3.7019e-05 | 3.7019e-05 | 0.0 | 0.00 Modify | 0.11795 | 0.11795 | 0.11795 | 0.0 | 10.88 Other | | 0.01086 | | | 1.00 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1450 ave 1450 max 1450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15624 ave 15624 max 15624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15624 Ave neighs/atom = 3.906 Neighbor list builds = 118 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.865204082645, Press = 58.5526958692013 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 36 36 36 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.676 | 3.676 | 3.676 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 119.93551 119.93551 -12.469658 -12.469658 256.14677 256.14677 5619753.3 5619753.3 21.939679 21.939679 4000 126.62132 126.62132 -3.8098143 -3.8098143 252.32788 252.32788 30062352 30062352 4.4598268 4.4598268 Loop time of 0.69402 on 1 procs for 1000 steps with 4000 atoms Performance: 124.492 ns/day, 0.193 hours/ns, 1440.881 timesteps/s, 5.764 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26622 | 0.26622 | 0.26622 | 0.0 | 38.36 Neigh | 0.28684 | 0.28684 | 0.28684 | 0.0 | 41.33 Comm | 0.012692 | 0.012692 | 0.012692 | 0.0 | 1.83 Output | 3.8392e-05 | 3.8392e-05 | 3.8392e-05 | 0.0 | 0.01 Modify | 0.11649 | 0.11649 | 0.11649 | 0.0 | 16.78 Other | | 0.01174 | | | 1.69 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 753 ave 753 max 753 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4198 ave 4198 max 4198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4198 Ave neighs/atom = 1.0495 Neighbor list builds = 204 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.846598666981, Press = 43.2013827768036 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 62 62 62 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.555 | 4.555 | 4.555 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 126.62132 126.62132 -3.8098143 -3.8098143 252.32788 252.32788 30062352 30062352 4.4598268 4.4598268 5000 129.12394 129.12394 -1.0884768 -1.0884768 251.90474 251.90474 1.5663996e+08 1.5663996e+08 0.87726137 0.87726137 Loop time of 0.807394 on 1 procs for 1000 steps with 4000 atoms Performance: 107.011 ns/day, 0.224 hours/ns, 1238.553 timesteps/s, 4.954 Matom-step/s 97.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17062 | 0.17062 | 0.17062 | 0.0 | 21.13 Neigh | 0.4937 | 0.4937 | 0.4937 | 0.0 | 61.15 Comm | 0.013406 | 0.013406 | 0.013406 | 0.0 | 1.66 Output | 3.8542e-05 | 3.8542e-05 | 3.8542e-05 | 0.0 | 0.00 Modify | 0.11655 | 0.11655 | 0.11655 | 0.0 | 14.44 Other | | 0.01308 | | | 1.62 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1144 ave 1144 max 1144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1144 Ave neighs/atom = 0.286 Neighbor list builds = 312 Dangerous builds = 0 if "${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 156639963.322226 A^3 has become larger than 144940209.626461 A^3. Aborting calculation. Total wall time: 0:00:10