# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.165199972689152*${_u_distance} variable latticeconst_converted equal 3.165199972689152*1 lattice bcc ${latticeconst_converted} lattice bcc 3.16519997268915 Lattice spacing in x,y,z = 3.1652 3.1652 3.1652 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (31.652 31.652 31.652) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (31.652 31.652 31.652) create_atoms CPU = 0.000 seconds variable mass_converted equal 183.84*${_u_mass} variable mass_converted equal 183.84*1 kim interactions W #=== BEGIN kim interactions ================================== pair_style kim EAM_MagneticCubic_DerletNguyenDudarev_2007_W__MO_195478838873_002 WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1127) pair_coeff * * W #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 183.84 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 31710.5270189675 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 31710.5270189675/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 31710.5270189675/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 31710.5270189675/(1*1*${_u_distance}) variable V0_metal equal 31710.5270189675/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 31710.5270189675*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 31710.5270189675 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 253.15*${_u_temperature} variable temp_converted equal 253.15*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 253.15 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 253.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "253.15 - 1.0" variable T_up equal "253.15 + 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_195478838873_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 = 6.2689 ghost atom cutoff = 6.2689 binsize = 3.13445, 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) = 3.701 | 3.701 | 3.701 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -17734.588 -17734.588 -17800 -17800 253.15 253.15 31710.527 31710.527 2203.2714 2203.2714 1000 -17671.793 -17671.793 -17736.996 -17736.996 252.343 252.343 31712.308 31712.308 1008.0223 1008.0223 Loop time of 2.65844 on 1 procs for 1000 steps with 2000 atoms Performance: 32.500 ns/day, 0.738 hours/ns, 376.160 timesteps/s, 752.320 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 | 2.5712 | 2.5712 | 2.5712 | 0.0 | 96.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012279 | 0.012279 | 0.012279 | 0.0 | 0.46 Output | 7.6604e-05 | 7.6604e-05 | 7.6604e-05 | 0.0 | 0.00 Modify | 0.069331 | 0.069331 | 0.069331 | 0.0 | 2.61 Other | | 0.005559 | | | 0.21 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2941 ave 2941 max 2941 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: 116000 ave 116000 max 116000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116000 Ave neighs/atom = 58 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 = ${P}" flag: Temp = 249.974485671489, Press = 96.646341020594 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2689 ghost atom cutoff = 6.2689 binsize = 3.13445, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.701 | 3.701 | 3.701 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -17671.793 -17671.793 -17736.996 -17736.996 252.343 252.343 31712.308 31712.308 1008.0223 1008.0223 2000 -17674.674 -17674.674 -17739.139 -17739.139 249.48677 249.48677 31701.595 31701.595 2626.3702 2626.3702 Loop time of 2.87527 on 1 procs for 1000 steps with 2000 atoms Performance: 30.049 ns/day, 0.799 hours/ns, 347.793 timesteps/s, 695.586 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8009 | 2.8009 | 2.8009 | 0.0 | 97.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010309 | 0.010309 | 0.010309 | 0.0 | 0.36 Output | 3.9284e-05 | 3.9284e-05 | 3.9284e-05 | 0.0 | 0.00 Modify | 0.059288 | 0.059288 | 0.059288 | 0.0 | 2.06 Other | | 0.004759 | | | 0.17 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2981 ave 2981 max 2981 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117406 ave 117406 max 117406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117406 Ave neighs/atom = 58.703 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 253.326652697291, Press = 13.5428441452858 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.2689 ghost atom cutoff = 6.2689 binsize = 3.13445, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.701 | 3.701 | 3.701 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -17674.674 -17674.674 -17739.139 -17739.139 249.48677 249.48677 31701.595 31701.595 2626.3702 2626.3702 3000 -17666.899 -17666.899 -17733.268 -17733.268 256.85545 256.85545 31718.758 31718.758 -36.721895 -36.721895 Loop time of 2.86515 on 1 procs for 1000 steps with 2000 atoms Performance: 30.156 ns/day, 0.796 hours/ns, 349.022 timesteps/s, 698.044 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7908 | 2.7908 | 2.7908 | 0.0 | 97.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010332 | 0.010332 | 0.010332 | 0.0 | 0.36 Output | 3.2782e-05 | 3.2782e-05 | 3.2782e-05 | 0.0 | 0.00 Modify | 0.059263 | 0.059263 | 0.059263 | 0.0 | 2.07 Other | | 0.004725 | | | 0.16 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3013 ave 3013 max 3013 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117210 ave 117210 max 117210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117210 Ave neighs/atom = 58.605 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T253.15.out" else "print 'not_converged' file output/vol_T253.15.out" print '${V}' file output/vol_T253.15.out 31722.0362944083 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0