# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 2.938573092222214*${_u_distance} variable latticeconst_converted equal 2.938573092222214*1 lattice bcc ${latticeconst_converted} lattice bcc 2.93857309222221 Lattice spacing in x,y,z = 2.9385731 2.9385731 2.9385731 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (29.385731 29.385731 29.385731) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (29.385731 29.385731 29.385731) create_atoms CPU = 0.000 seconds variable mass_converted equal 51.9961*${_u_mass} variable mass_converted equal 51.9961*1 kim interactions Cr #=== BEGIN kim interactions ================================== pair_style kim EAM_Dynamo_BonnyTerentyevPasianot_2011_FeNiCr__MO_677715648236_000 pair_coeff * * Cr #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 51.9961 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 25375.2010949908 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 25375.2010949908/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 25375.2010949908/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 25375.2010949908/(1*1*${_u_distance}) variable V0_metal equal 25375.2010949908/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 25375.2010949908*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 25375.2010949908 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 8 8 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) = 4.196 | 4.196 | 4.196 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -6964.5054 -6964.5054 -7045.4205 -7045.4205 313.15 313.15 25375.201 25375.201 3405.9462 3405.9462 1000 -7059.7362 -7059.7362 -7140.681 -7140.681 313.26458 313.26458 24146.105 24146.105 -1175.3485 -1175.3485 Loop time of 5.6718 on 1 procs for 1000 steps with 2000 atoms Performance: 15.233 ns/day, 1.576 hours/ns, 176.311 timesteps/s, 352.622 katom-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 | 5.5298 | 5.5298 | 5.5298 | 0.0 | 97.50 Neigh | 0.046411 | 0.046411 | 0.046411 | 0.0 | 0.82 Comm | 0.021089 | 0.021089 | 0.021089 | 0.0 | 0.37 Output | 8.7525e-05 | 8.7525e-05 | 8.7525e-05 | 0.0 | 0.00 Modify | 0.066752 | 0.066752 | 0.066752 | 0.0 | 1.18 Other | | 0.007623 | | | 0.13 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5208 ave 5208 max 5208 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: 306238 ave 306238 max 306238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306238 Ave neighs/atom = 153.119 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 = ${P}" flag: Temp = 314.161914458678, Press = -32.0234600204244 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.575 | 4.575 | 4.575 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -7059.7362 -7059.7362 -7140.681 -7140.681 313.26458 313.26458 24146.105 24146.105 -1175.3485 -1175.3485 2000 -7109.4045 -7109.4045 -7189.7712 -7189.7712 311.02746 311.02746 23577.706 23577.706 1264.9599 1264.9599 Loop time of 5.91705 on 1 procs for 1000 steps with 2000 atoms Performance: 14.602 ns/day, 1.644 hours/ns, 169.003 timesteps/s, 338.006 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7847 | 5.7847 | 5.7847 | 0.0 | 97.76 Neigh | 0.036131 | 0.036131 | 0.036131 | 0.0 | 0.61 Comm | 0.01985 | 0.01985 | 0.01985 | 0.0 | 0.34 Output | 5.9091e-05 | 5.9091e-05 | 5.9091e-05 | 0.0 | 0.00 Modify | 0.06917 | 0.06917 | 0.06917 | 0.0 | 1.17 Other | | 0.007183 | | | 0.12 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5133 ave 5133 max 5133 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 311826 ave 311826 max 311826 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 311826 Ave neighs/atom = 155.913 Neighbor list builds = 4 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 314.167464558309, Press = 7.82710509654942 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.575 | 4.575 | 4.575 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -7109.4045 -7109.4045 -7189.7712 -7189.7712 311.02746 311.02746 23577.706 23577.706 1264.9599 1264.9599 3000 -7115.5265 -7115.5265 -7196.0008 -7196.0008 311.44385 311.44385 23597.272 23597.272 436.87165 436.87165 Loop time of 5.86981 on 1 procs for 1000 steps with 2000 atoms Performance: 14.719 ns/day, 1.631 hours/ns, 170.363 timesteps/s, 340.727 katom-step/s 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7681 | 5.7681 | 5.7681 | 0.0 | 98.27 Neigh | 0.0088619 | 0.0088619 | 0.0088619 | 0.0 | 0.15 Comm | 0.018862 | 0.018862 | 0.018862 | 0.0 | 0.32 Output | 9.012e-05 | 9.012e-05 | 9.012e-05 | 0.0 | 0.00 Modify | 0.067328 | 0.067328 | 0.067328 | 0.0 | 1.15 Other | | 0.006561 | | | 0.11 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5182 ave 5182 max 5182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 311592 ave 311592 max 311592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 311592 Ave neighs/atom = 155.796 Neighbor list builds = 1 Dangerous builds = 0 if "${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 23716.0574684162 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0