# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.521392315626145*${_u_distance} variable latticeconst_converted equal 3.521392315626145*1 lattice fcc ${latticeconst_converted} lattice fcc 3.52139231562614 Lattice spacing in x,y,z = 3.5213923 3.5213923 3.5213923 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (35.213923 35.213923 35.213923) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (35.213923 35.213923 35.213923) create_atoms CPU = 0.001 seconds variable mass_converted equal 58.6934*${_u_mass} variable mass_converted equal 58.6934*1 kim interactions Ni #=== BEGIN kim interactions ================================== pair_style kim MEAM_LAMMPS_MurallesParkKim_NiTi__MO_182729415169_000 pair_coeff * * Ni #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 58.6934 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 43665.9825163134 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 43665.9825163134/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 43665.9825163134/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 43665.9825163134/(1*1*${_u_distance}) variable V0_metal equal 43665.9825163134/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 43665.9825163134*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 43665.9825163134 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 293.15*${_u_temperature} variable temp_converted equal 293.15*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 293.15 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 293.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "293.15 - 1.0" variable T_up equal "293.15 + 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_182729415169_000#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 = 7 ghost atom cutoff = 7 binsize = 3.5, 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 -19008.467 -19008.467 -19160 -19160 293.15 293.15 43665.983 43665.983 3706.6337 3706.6337 1000 -19191.513 -19191.513 -19345.027 -19345.027 296.98427 296.98427 44237.058 44237.058 3123.5882 3123.5882 Loop time of 170.545 on 1 procs for 1000 steps with 4000 atoms Performance: 0.507 ns/day, 47.374 hours/ns, 5.864 timesteps/s, 23.454 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 | 170.32 | 170.32 | 170.32 | 0.0 | 99.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.029933 | 0.029933 | 0.029933 | 0.0 | 0.02 Output | 9.3165e-05 | 9.3165e-05 | 9.3165e-05 | 0.0 | 0.00 Modify | 0.17366 | 0.17366 | 0.17366 | 0.0 | 0.10 Other | | 0.01998 | | | 0.01 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 = ${P}" flag: Temp = 292.122953835672, Press = 127.129846901426 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.378 | 5.378 | 5.378 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -19191.513 -19191.513 -19345.027 -19345.027 296.98427 296.98427 44237.058 44237.058 3123.5882 3123.5882 2000 -19217.222 -19217.222 -19366.963 -19366.963 289.68415 289.68415 44245.184 44245.184 1828.4775 1828.4775 Loop time of 163.449 on 1 procs for 1000 steps with 4000 atoms Performance: 0.529 ns/day, 45.402 hours/ns, 6.118 timesteps/s, 24.473 katom-step/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 163.21 | 163.21 | 163.21 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.032834 | 0.032834 | 0.032834 | 0.0 | 0.02 Output | 8.6993e-05 | 8.6993e-05 | 8.6993e-05 | 0.0 | 0.00 Modify | 0.18136 | 0.18136 | 0.18136 | 0.0 | 0.11 Other | | 0.02131 | | | 0.01 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6667 ave 6667 max 6667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 545944 ave 545944 max 545944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 545944 Ave neighs/atom = 136.486 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 293.318866590937, Press = 9.12813752577547 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.382 | 5.382 | 5.382 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -19217.222 -19217.222 -19366.963 -19366.963 289.68415 289.68415 44245.184 44245.184 1828.4775 1828.4775 3000 -19224.496 -19224.496 -19375.053 -19375.053 291.26288 291.26288 44231.732 44231.732 2074.3309 2074.3309 Loop time of 158.193 on 1 procs for 1000 steps with 4000 atoms Performance: 0.546 ns/day, 43.943 hours/ns, 6.321 timesteps/s, 25.286 katom-step/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 157.97 | 157.97 | 157.97 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.032548 | 0.032548 | 0.032548 | 0.0 | 0.02 Output | 8.6473e-05 | 8.6473e-05 | 8.6473e-05 | 0.0 | 0.00 Modify | 0.17232 | 0.17232 | 0.17232 | 0.0 | 0.11 Other | | 0.01746 | | | 0.01 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6752 ave 6752 max 6752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 549012 ave 549012 max 549012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 549012 Ave neighs/atom = 137.253 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 293.361126971364, Press = 5.68594180561851 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.382 | 5.382 | 5.382 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -19224.496 -19224.496 -19375.053 -19375.053 291.26288 291.26288 44231.732 44231.732 2074.3309 2074.3309 4000 -19221.716 -19221.716 -19373.467 -19373.467 293.57117 293.57117 44234.848 44234.848 2393.2857 2393.2857 Loop time of 156.113 on 1 procs for 1000 steps with 4000 atoms Performance: 0.553 ns/day, 43.365 hours/ns, 6.406 timesteps/s, 25.622 katom-step/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 155.89 | 155.89 | 155.89 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.032148 | 0.032148 | 0.032148 | 0.0 | 0.02 Output | 6.9129e-05 | 6.9129e-05 | 6.9129e-05 | 0.0 | 0.00 Modify | 0.1703 | 0.1703 | 0.1703 | 0.0 | 0.11 Other | | 0.01609 | | | 0.01 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6774 ave 6774 max 6774 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 549368 ave 549368 max 549368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 549368 Ave neighs/atom = 137.342 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T293.15.out" else "print 'not_converged' file output/vol_T293.15.out" print '${V}' file output/vol_T293.15.out 44290.6542462644 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0