# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.205006867647171*${_u_distance} variable latticeconst_converted equal 4.205006867647171*1 lattice fcc ${latticeconst_converted} lattice fcc 4.20500686764717 Lattice spacing in x,y,z = 4.2050069 4.2050069 4.2050069 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (42.050069 42.050069 42.050069) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (42.050069 42.050069 42.050069) create_atoms CPU = 0.001 seconds variable mass_converted equal 20.1797*${_u_mass} variable mass_converted equal 20.1797*1 kim interactions Ne #=== BEGIN kim interactions ================================== pair_style kim Exp6_KongChakrabarty_1973_ArNe__MO_946046425752_002 WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1122) WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1127) 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 74353.2794273218 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 74353.2794273218/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 74353.2794273218/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 74353.2794273218/(1*1*${_u_distance}) variable V0_metal equal 74353.2794273218/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 74353.2794273218*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 74353.2794273218 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_946046425752_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 = 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) = 7.005 | 7.005 | 7.005 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 18.569655 18.569655 -112.28645 -112.28645 253.15 253.15 74353.279 74353.279 1879.8051 1879.8051 1000 121.38441 121.38441 -8.5896227 -8.5896227 251.44358 251.44358 588811.04 588811.04 242.20134 242.20134 Loop time of 8.8566 on 1 procs for 1000 steps with 4000 atoms Performance: 9.755 ns/day, 2.460 hours/ns, 112.910 timesteps/s, 451.641 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 | 7.7634 | 7.7634 | 7.7634 | 0.0 | 87.66 Neigh | 0.91212 | 0.91212 | 0.91212 | 0.0 | 10.30 Comm | 0.031793 | 0.031793 | 0.031793 | 0.0 | 0.36 Output | 0.00011399 | 0.00011399 | 0.00011399 | 0.0 | 0.00 Modify | 0.13239 | 0.13239 | 0.13239 | 0.0 | 1.49 Other | | 0.01677 | | | 0.19 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3620 ave 3620 max 3620 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: 120610 ave 120610 max 120610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120610 Ave neighs/atom = 30.1525 Neighbor list builds = 74 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 = ${P}" flag: Temp = 251.454678281885, Press = 261.52907171697 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.948 | 3.948 | 3.948 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 121.38441 121.38441 -8.5896227 -8.5896227 251.44358 251.44358 588811.04 588811.04 242.20134 242.20134 2000 128.49956 128.49956 -1.645046 -1.645046 251.77356 251.77356 3205328.4 3205328.4 43.662115 43.662115 Loop time of 2.24111 on 1 procs for 1000 steps with 4000 atoms Performance: 38.552 ns/day, 0.623 hours/ns, 446.207 timesteps/s, 1.785 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5827 | 1.5827 | 1.5827 | 0.0 | 70.62 Neigh | 0.49136 | 0.49136 | 0.49136 | 0.0 | 21.92 Comm | 0.020954 | 0.020954 | 0.020954 | 0.0 | 0.94 Output | 7.9058e-05 | 7.9058e-05 | 7.9058e-05 | 0.0 | 0.00 Modify | 0.13266 | 0.13266 | 0.13266 | 0.0 | 5.92 Other | | 0.01339 | | | 0.60 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1857 ave 1857 max 1857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 22646 ave 22646 max 22646 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22646 Ave neighs/atom = 5.6615 Neighbor list builds = 106 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 251.626394638237, Press = 127.253725389932 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 30 30 30 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.676 | 3.676 | 3.676 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 128.49956 128.49956 -1.645046 -1.645046 251.77356 251.77356 3205328.4 3205328.4 43.662115 43.662115 3000 129.79109 129.79109 -0.36377559 -0.36377559 251.79341 251.79341 16318097 16318097 8.4800187 8.4800187 Loop time of 1.02867 on 1 procs for 1000 steps with 4000 atoms Performance: 83.992 ns/day, 0.286 hours/ns, 972.128 timesteps/s, 3.889 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53614 | 0.53614 | 0.53614 | 0.0 | 52.12 Neigh | 0.3296 | 0.3296 | 0.3296 | 0.0 | 32.04 Comm | 0.016884 | 0.016884 | 0.016884 | 0.0 | 1.64 Output | 4.3832e-05 | 4.3832e-05 | 4.3832e-05 | 0.0 | 0.00 Modify | 0.1325 | 0.1325 | 0.1325 | 0.0 | 12.88 Other | | 0.0135 | | | 1.31 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 989 ave 989 max 989 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4532 ave 4532 max 4532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4532 Ave neighs/atom = 1.133 Neighbor list builds = 170 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 251.691876423935, Press = 76.7933239514606 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 50 50 50 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.141 | 4.141 | 4.141 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 129.79109 129.79109 -0.36377559 -0.36377559 251.79341 251.79341 16318097 16318097 8.4800187 8.4800187 4000 130.10394 130.10394 -0.073764905 -0.073764905 251.8376 251.8376 79861204 79861204 1.7387174 1.7387174 Loop time of 0.845216 on 1 procs for 1000 steps with 4000 atoms Performance: 102.222 ns/day, 0.235 hours/ns, 1183.129 timesteps/s, 4.733 Matom-step/s 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29673 | 0.29673 | 0.29673 | 0.0 | 35.11 Neigh | 0.38472 | 0.38472 | 0.38472 | 0.0 | 45.52 Comm | 0.016182 | 0.016182 | 0.016182 | 0.0 | 1.91 Output | 4.7049e-05 | 4.7049e-05 | 4.7049e-05 | 0.0 | 0.01 Modify | 0.13239 | 0.13239 | 0.13239 | 0.0 | 15.66 Other | | 0.01516 | | | 1.79 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 586 ave 586 max 586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 914 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 914 Ave neighs/atom = 0.2285 Neighbor list builds = 266 Dangerous builds = 0 if "${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 79861204.0146772 A^3 has become larger than 74353279.4273218 A^3. Aborting calculation. Total wall time: 0:00:13