# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.4687884375453*${_u_distance} variable latticeconst_converted equal 4.4687884375453*1 lattice bcc ${latticeconst_converted} lattice bcc 4.4687884375453 Lattice spacing in x,y,z = 4.4687884 4.4687884 4.4687884 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (44.687884 44.687884 44.687884) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (44.687884 44.687884 44.687884) create_atoms CPU = 0.000 seconds variable mass_converted equal 39.0983*${_u_mass} variable mass_converted equal 39.0983*1 kim interactions K #=== BEGIN kim interactions ================================== pair_style kim LJ_ElliottAkerson_2015_Universal__MO_959249795837_003 pair_coeff * * K #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 39.0983 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 89242.0183577871 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 89242.0183577871/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 89242.0183577871/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 89242.0183577871/(1*1*${_u_distance}) variable V0_metal equal 89242.0183577871/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 89242.0183577871*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 89242.0183577871 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_959249795837_003#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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 5 5 5 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) = 10.33 | 10.33 | 10.33 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -8703.6544 -8703.6544 -8784.5696 -8784.5696 313.15 313.15 89242.018 89242.018 968.43437 968.43437 1000 -8758.3561 -8758.3561 -8838.6039 -8838.6039 310.56701 310.56701 89287.308 89287.308 -578.19049 -578.19049 Loop time of 9.69395 on 1 procs for 1000 steps with 2000 atoms Performance: 8.913 ns/day, 2.693 hours/ns, 103.157 timesteps/s, 206.314 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 | 9.4409 | 9.4409 | 9.4409 | 0.0 | 97.39 Neigh | 0.13259 | 0.13259 | 0.13259 | 0.0 | 1.37 Comm | 0.04439 | 0.04439 | 0.04439 | 0.0 | 0.46 Output | 7.2977e-05 | 7.2977e-05 | 7.2977e-05 | 0.0 | 0.00 Modify | 0.06409 | 0.06409 | 0.06409 | 0.0 | 0.66 Other | | 0.01189 | | | 0.12 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12281 ave 12281 max 12281 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: 1.63512e+06 ave 1.63512e+06 max 1.63512e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1635122 Ave neighs/atom = 817.561 Neighbor list builds = 4 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 = ${P}" flag: Temp = 315.00457922169, Press = 15.5257605353068 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 9.946 | 9.946 | 9.946 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -8758.3561 -8758.3561 -8838.6039 -8838.6039 310.56701 310.56701 89287.308 89287.308 -578.19049 -578.19049 2000 -8809.845 -8809.845 -8890.7003 -8890.7003 312.91839 312.91839 88951.906 88951.906 417.54435 417.54435 Loop time of 9.69446 on 1 procs for 1000 steps with 2000 atoms Performance: 8.912 ns/day, 2.693 hours/ns, 103.152 timesteps/s, 206.303 katom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.4026 | 9.4026 | 9.4026 | 0.0 | 96.99 Neigh | 0.17075 | 0.17075 | 0.17075 | 0.0 | 1.76 Comm | 0.042797 | 0.042797 | 0.042797 | 0.0 | 0.44 Output | 6.1786e-05 | 6.1786e-05 | 6.1786e-05 | 0.0 | 0.00 Modify | 0.066767 | 0.066767 | 0.066767 | 0.0 | 0.69 Other | | 0.01151 | | | 0.12 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12157 ave 12157 max 12157 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.63799e+06 ave 1.63799e+06 max 1.63799e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1637994 Ave neighs/atom = 818.997 Neighbor list builds = 5 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 314.215561369394, Press = 3.87965530871536 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 9.945 | 9.945 | 9.945 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -8809.845 -8809.845 -8890.7003 -8890.7003 312.91839 312.91839 88951.906 88951.906 417.54435 417.54435 3000 -8811.8924 -8811.8924 -8891.7141 -8891.7141 308.91792 308.91792 88965.387 88965.387 133.32498 133.32498 Loop time of 9.42551 on 1 procs for 1000 steps with 2000 atoms Performance: 9.167 ns/day, 2.618 hours/ns, 106.095 timesteps/s, 212.190 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.3082 | 9.3082 | 9.3082 | 0.0 | 98.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.041511 | 0.041511 | 0.041511 | 0.0 | 0.44 Output | 3.6528e-05 | 3.6528e-05 | 3.6528e-05 | 0.0 | 0.00 Modify | 0.065345 | 0.065345 | 0.065345 | 0.0 | 0.69 Other | | 0.01046 | | | 0.11 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12165 ave 12165 max 12165 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.64084e+06 ave 1.64084e+06 max 1.64084e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1640842 Ave neighs/atom = 820.421 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T313.15.out" else "print 'not_converged' file output/vol_T313.15.out" print '${V}' file output/vol_T313.15.out 89026.8768459414 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0