# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 313.15*${_u_temperature} variable temp_converted equal 313.15*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 313.15 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 313.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "313.15 - 1.0" variable T_up equal "313.15 + 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 49.584334 49.584334 -112.28645 -112.28645 313.15 313.15 74353.279 74353.279 2325.3447 2325.3447 1000 153.38755 153.38755 -7.4770648 -7.4770648 311.20351 311.20351 627310.52 627310.52 288.00457 288.00457 Loop time of 9.2753 on 1 procs for 1000 steps with 4000 atoms Performance: 9.315 ns/day, 2.576 hours/ns, 107.813 timesteps/s, 431.253 katom-step/s 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.0791 | 8.0791 | 8.0791 | 0.0 | 87.10 Neigh | 0.99792 | 0.99792 | 0.99792 | 0.0 | 10.76 Comm | 0.034642 | 0.034642 | 0.034642 | 0.0 | 0.37 Output | 0.00012473 | 0.00012473 | 0.00012473 | 0.0 | 0.00 Modify | 0.14248 | 0.14248 | 0.14248 | 0.0 | 1.54 Other | | 0.02104 | | | 0.23 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3541 ave 3541 max 3541 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: 111700 ave 111700 max 111700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111700 Ave neighs/atom = 27.925 Neighbor list builds = 78 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 = ${P}" flag: Temp = 311.127840620898, Press = 320.580362176922 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.948 | 3.948 | 3.948 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 153.38755 153.38755 -7.4770648 -7.4770648 311.20351 311.20351 627310.52 627310.52 288.00457 288.00457 2000 159.65863 159.65863 -1.3055865 -1.3055865 311.3962 311.3962 3408920.6 3408920.6 51.090218 51.090218 Loop time of 2.26743 on 1 procs for 1000 steps with 4000 atoms Performance: 38.105 ns/day, 0.630 hours/ns, 441.029 timesteps/s, 1.764 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5856 | 1.5856 | 1.5856 | 0.0 | 69.93 Neigh | 0.5101 | 0.5101 | 0.5101 | 0.0 | 22.50 Comm | 0.020535 | 0.020535 | 0.020535 | 0.0 | 0.91 Output | 5.2128e-05 | 5.2128e-05 | 5.2128e-05 | 0.0 | 0.00 Modify | 0.1374 | 0.1374 | 0.1374 | 0.0 | 6.06 Other | | 0.01376 | | | 0.61 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1802 ave 1802 max 1802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 20932 ave 20932 max 20932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20932 Ave neighs/atom = 5.233 Neighbor list builds = 109 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 311.267766245646, Press = 151.174618118348 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 30 30 30 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.676 | 3.676 | 3.676 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 159.65863 159.65863 -1.3055865 -1.3055865 311.3962 311.3962 3408920.6 3408920.6 51.090218 51.090218 3000 160.80072 160.80072 -0.32392843 -0.32392843 311.70656 311.70656 17229875 17229875 9.9694808 9.9694808 Loop time of 1.02685 on 1 procs for 1000 steps with 4000 atoms Performance: 84.141 ns/day, 0.285 hours/ns, 973.854 timesteps/s, 3.895 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53548 | 0.53548 | 0.53548 | 0.0 | 52.15 Neigh | 0.32648 | 0.32648 | 0.32648 | 0.0 | 31.79 Comm | 0.016841 | 0.016841 | 0.016841 | 0.0 | 1.64 Output | 4.3502e-05 | 4.3502e-05 | 4.3502e-05 | 0.0 | 0.00 Modify | 0.13478 | 0.13478 | 0.13478 | 0.0 | 13.13 Other | | 0.01323 | | | 1.29 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1024 ave 1024 max 1024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4138 ave 4138 max 4138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4138 Ave neighs/atom = 1.0345 Neighbor list builds = 171 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 311.355000413858, Press = 91.0438164110839 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 51 51 51 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.176 | 4.176 | 4.176 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 160.80072 160.80072 -0.32392843 -0.32392843 311.70656 311.70656 17229875 17229875 9.9694808 9.9694808 4000 160.86751 160.86751 -0.063635336 -0.063635336 311.33221 311.33221 83897196 83897196 2.0487105 2.0487105 Loop time of 0.881736 on 1 procs for 1000 steps with 4000 atoms Performance: 97.989 ns/day, 0.245 hours/ns, 1134.126 timesteps/s, 4.537 Matom-step/s 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30916 | 0.30916 | 0.30916 | 0.0 | 35.06 Neigh | 0.40616 | 0.40616 | 0.40616 | 0.0 | 46.06 Comm | 0.018638 | 0.018638 | 0.018638 | 0.0 | 2.11 Output | 4.6518e-05 | 4.6518e-05 | 4.6518e-05 | 0.0 | 0.01 Modify | 0.13279 | 0.13279 | 0.13279 | 0.0 | 15.06 Other | | 0.01494 | | | 1.69 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 615 ave 615 max 615 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 848 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 848 Ave neighs/atom = 0.212 Neighbor list builds = 271 Dangerous builds = 0 if "${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 83897196.2678834 A^3 has become larger than 74353279.4273218 A^3. Aborting calculation. Total wall time: 0:00:13