# Variables that can be adjusted by kim-lammps-preprocessor to switch unit sets for # Simulator Models variable _u_distance equal 1.0 variable _u_energy equal 1.0 variable _u_mass equal 1.0 variable _u_time equal 1.0 variable _u_pressure equal 1.0 variable _u_temperature equal 1.0 # This line may be swapped out by kim-lammps-preprocessor if running against a Simulator # Model whose atom_style is not 'atomic' atom_style atomic # 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.090069212019444*${_u_distance} variable latticeconst_converted equal 4.090069212019444*1 lattice fcc ${latticeconst_converted} lattice fcc 4.09006921201944 Lattice spacing in x,y,z = 4.09007 4.09007 4.09007 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (40.9007 40.9007 40.9007) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms create_atoms CPU = 0.000360012 secs variable mass_converted equal 107.8682*${_u_mass} variable mass_converted equal 107.8682*1 # specify which KIM Model to use pair_style kim EAM_Dynamo_WuTrinkle_2009_CuAg__MO_270337113239_005 pair_coeff * * Ag mass 1 ${mass_converted} mass 1 107.8682 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 68421.4024155245 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 68421.4024155245/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 68421.4024155245/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 68421.4024155245/(1*1*${_u_distance}) variable V0_metal equal 68421.4024155245/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 68421.4024155245*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 68421.4024155245 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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 0.1*${_u_time} variable Tdamp_converted equal 0.1*1 variable press_converted equal 0.0*${_u_pressure} variable press_converted equal 0.0*1 variable Pdamp_converted equal 1*${_u_time} variable Pdamp_converted equal 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 0.1 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.1 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.1 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.1 iso 0 0 1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 5000 fix avgmyPress all ave/time 5 20 100 v_P_metal ave running start 5000 fix avgmyVol all ave/time 5 20 100 v_V_metal ave running start 5000 # 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 - 0.2" variable T_up equal "273.15 + 0.2" variable P_low equal "0.0 - 0.2" variable P_up equal "0.0 + 0.2" # 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 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -11258.793 -11258.793 -11399.988 -11399.988 273.15 273.15 68421.402 68421.402 2204.156 2204.156 1000 -11113.491 -11113.491 -11256.829 -11256.829 277.29884 277.29884 69526.153 69526.153 924.52884 924.52884 Loop time of 23.5495 on 1 procs for 1000 steps with 4000 atoms Performance: 3.669 ns/day, 6.542 hours/ns, 42.464 timesteps/s 37.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.99 | 22.99 | 22.99 | 0.0 | 97.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.080438 | 0.080438 | 0.080438 | 0.0 | 0.34 Output | 4.6015e-05 | 4.6015e-05 | 4.6015e-05 | 0.0 | 0.00 Modify | 0.41834 | 0.41834 | 0.41834 | 0.0 | 1.78 Other | | 0.06062 | | | 0.26 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 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: 536000 ave 536000 max 536000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 536000 Ave neighs/atom = 134 Neighbor list builds = 0 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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -11113.491 -11113.491 -11256.829 -11256.829 277.29884 277.29884 69526.153 69526.153 924.52884 924.52884 2000 -11125.753 -11125.753 -11265.018 -11265.018 269.4182 269.4182 69533.611 69533.611 -226.09134 -226.09134 Loop time of 29.1583 on 1 procs for 1000 steps with 4000 atoms Performance: 2.963 ns/day, 8.100 hours/ns, 34.296 timesteps/s 36.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.562 | 28.562 | 28.562 | 0.0 | 97.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.098361 | 0.098361 | 0.098361 | 0.0 | 0.34 Output | 4.3869e-05 | 4.3869e-05 | 4.3869e-05 | 0.0 | 0.00 Modify | 0.41773 | 0.41773 | 0.41773 | 0.0 | 1.43 Other | | 0.0801 | | | 0.27 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5858 ave 5858 max 5858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 535466 ave 535466 max 535466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 535466 Ave neighs/atom = 133.867 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -11125.753 -11125.753 -11265.018 -11265.018 269.4182 269.4182 69533.611 69533.611 -226.09134 -226.09134 3000 -11118.529 -11118.529 -11262.01 -11262.01 277.57431 277.57431 69505.141 69505.141 743.91152 743.91152 Loop time of 29.3013 on 1 procs for 1000 steps with 4000 atoms Performance: 2.949 ns/day, 8.139 hours/ns, 34.128 timesteps/s 35.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.652 | 28.652 | 28.652 | 0.0 | 97.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.16122 | 0.16122 | 0.16122 | 0.0 | 0.55 Output | 3.5048e-05 | 3.5048e-05 | 3.5048e-05 | 0.0 | 0.00 Modify | 0.40764 | 0.40764 | 0.40764 | 0.0 | 1.39 Other | | 0.08034 | | | 0.27 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5859 ave 5859 max 5859 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 535658 ave 535658 max 535658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 535658 Ave neighs/atom = 133.915 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -11118.529 -11118.529 -11262.01 -11262.01 277.57431 277.57431 69505.141 69505.141 743.91152 743.91152 4000 -11122.564 -11122.564 -11263.261 -11263.261 272.18899 272.18899 69517.777 69517.777 261.18619 261.18619 Loop time of 27.7232 on 1 procs for 1000 steps with 4000 atoms Performance: 3.117 ns/day, 7.701 hours/ns, 36.071 timesteps/s 37.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.147 | 27.147 | 27.147 | 0.0 | 97.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.059113 | 0.059113 | 0.059113 | 0.0 | 0.21 Output | 4.5061e-05 | 4.5061e-05 | 4.5061e-05 | 0.0 | 0.00 Modify | 0.47668 | 0.47668 | 0.47668 | 0.0 | 1.72 Other | | 0.03997 | | | 0.14 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5855 ave 5855 max 5855 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 535586 ave 535586 max 535586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 535586 Ave neighs/atom = 133.897 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -11122.564 -11122.564 -11263.261 -11263.261 272.18899 272.18899 69517.777 69517.777 261.18619 261.18619 5000 -11124.248 -11124.248 -11265.594 -11265.594 273.44399 273.44399 69523.523 69523.523 -42.489262 -42.489262 Loop time of 28.3059 on 1 procs for 1000 steps with 4000 atoms Performance: 3.052 ns/day, 7.863 hours/ns, 35.328 timesteps/s 37.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.79 | 27.79 | 27.79 | 0.0 | 98.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.058306 | 0.058306 | 0.058306 | 0.0 | 0.21 Output | 2.5988e-05 | 2.5988e-05 | 2.5988e-05 | 0.0 | 0.00 Modify | 0.41795 | 0.41795 | 0.41795 | 0.0 | 1.48 Other | | 0.03978 | | | 0.14 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5858 ave 5858 max 5858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 535614 ave 535614 max 535614 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 535614 Ave neighs/atom = 133.904 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 269.018823505673, Press = 144.57290044917 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -11124.248 -11124.248 -11265.594 -11265.594 273.44399 273.44399 69523.523 69523.523 -42.489262 -42.489262 6000 -11119.834 -11119.834 -11263.313 -11263.313 277.57083 277.57083 69510.882 69510.882 431.00426 431.00426 Loop time of 29.3445 on 1 procs for 1000 steps with 4000 atoms Performance: 2.944 ns/day, 8.151 hours/ns, 34.078 timesteps/s 36.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.693 | 28.693 | 28.693 | 0.0 | 97.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.17917 | 0.17917 | 0.17917 | 0.0 | 0.61 Output | 2.5988e-05 | 2.5988e-05 | 2.5988e-05 | 0.0 | 0.00 Modify | 0.43256 | 0.43256 | 0.43256 | 0.0 | 1.47 Other | | 0.03996 | | | 0.14 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5857 ave 5857 max 5857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 535620 ave 535620 max 535620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 535620 Ave neighs/atom = 133.905 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.978137486492, Press = -0.919152579765657 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 6000 -11119.834 -11119.834 -11263.313 -11263.313 277.57083 277.57083 69510.882 69510.882 431.00426 431.00426 7000 -11122.634 -11122.634 -11264.836 -11264.836 275.09963 275.09963 69395.959 69395.959 2130.1165 2130.1165 Loop time of 27.9862 on 1 procs for 1000 steps with 4000 atoms Performance: 3.087 ns/day, 7.774 hours/ns, 35.732 timesteps/s 37.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.274 | 27.274 | 27.274 | 0.0 | 97.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13809 | 0.13809 | 0.13809 | 0.0 | 0.49 Output | 3.2902e-05 | 3.2902e-05 | 3.2902e-05 | 0.0 | 0.00 Modify | 0.5539 | 0.5539 | 0.5539 | 0.0 | 1.98 Other | | 0.01989 | | | 0.07 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5849 ave 5849 max 5849 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 535650 ave 535650 max 535650 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 535650 Ave neighs/atom = 133.912 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.962855989076, Press = 3.63985387965295 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 7000 -11122.634 -11122.634 -11264.836 -11264.836 275.09963 275.09963 69395.959 69395.959 2130.1165 2130.1165 8000 -11121.922 -11121.922 -11262.235 -11262.235 271.44358 271.44358 69551.616 69551.616 -53.889935 -53.889935 Loop time of 28.5468 on 1 procs for 1000 steps with 4000 atoms Performance: 3.027 ns/day, 7.930 hours/ns, 35.030 timesteps/s 36.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.887 | 27.887 | 27.887 | 0.0 | 97.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.15825 | 0.15825 | 0.15825 | 0.0 | 0.55 Output | 3.3855e-05 | 3.3855e-05 | 3.3855e-05 | 0.0 | 0.00 Modify | 0.48209 | 0.48209 | 0.48209 | 0.0 | 1.69 Other | | 0.0199 | | | 0.07 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5850 ave 5850 max 5850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 535952 ave 535952 max 535952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 535952 Ave neighs/atom = 133.988 Neighbor list builds = 0 Dangerous builds = 0 if "${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" jump SELF break # Write final averaged volume to file if temperature and volume have converged; otherwise wirte a # flag to indicate non-convergence. variable myStep equal step if "${myStep} < 2000000" then "print '${V}' file output/vol_T273.15.out" else "print 'not_converged' file output/vol_T273.15.out" print '${V}' file output/vol_T273.15.out 69540.6004112751 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0