# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.150153368711472*${_u_distance} variable latticeconst_converted equal 3.150153368711472*1 lattice bcc ${latticeconst_converted} lattice bcc 3.15015336871147 Lattice spacing in x,y,z = 3.1501534 3.1501534 3.1501534 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (31.501534 31.501534 31.501534) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (31.501534 31.501534 31.501534) create_atoms CPU = 0.000 seconds variable mass_converted equal 95.94*${_u_mass} variable mass_converted equal 95.94*1 kim interactions Mo #=== BEGIN kim interactions ================================== pair_style kim EAM_Dynamo_ZhouJohnsonWadley_2004_Mo__MO_271256517527_005 pair_coeff * * Mo #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 95.94 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 31260.4406254048 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 31260.4406254048/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 31260.4406254048/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 31260.4406254048/(1*1*${_u_distance}) variable V0_metal equal 31260.4406254048/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 31260.4406254048*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 31260.4406254048 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 333.15*${_u_temperature} variable temp_converted equal 333.15*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 333.15 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 333.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "333.15 - 1.0" variable T_up equal "333.15 + 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_271256517527_005#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 = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, 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 -13533.925 -13533.925 -13620.008 -13620.008 333.15 333.15 31260.441 31260.441 2941.2786 2941.2786 1000 -13452.828 -13452.828 -13537.431 -13537.431 327.42472 327.42472 31408.167 31408.167 -1389.8333 -1389.8333 Loop time of 3.78387 on 1 procs for 1000 steps with 2000 atoms Performance: 22.834 ns/day, 1.051 hours/ns, 264.280 timesteps/s, 528.560 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 | 3.6897 | 3.6897 | 3.6897 | 0.0 | 97.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.021034 | 0.021034 | 0.021034 | 0.0 | 0.56 Output | 6.6054e-05 | 6.6054e-05 | 6.6054e-05 | 0.0 | 0.00 Modify | 0.066481 | 0.066481 | 0.066481 | 0.0 | 1.76 Other | | 0.006633 | | | 0.18 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5471 ave 5471 max 5471 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: 272000 ave 272000 max 272000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272000 Ave neighs/atom = 136 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 = ${P}" flag: Temp = 332.170902784188, Press = -56.4547066266959 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.196 | 4.196 | 4.196 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -13452.828 -13452.828 -13537.431 -13537.431 327.42472 327.42472 31408.167 31408.167 -1389.8333 -1389.8333 2000 -13444.134 -13444.134 -13529.366 -13529.366 329.85956 329.85956 31405.44 31405.44 -707.56097 -707.56097 Loop time of 4.22493 on 1 procs for 1000 steps with 2000 atoms Performance: 20.450 ns/day, 1.174 hours/ns, 236.690 timesteps/s, 473.380 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1385 | 4.1385 | 4.1385 | 0.0 | 97.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018843 | 0.018843 | 0.018843 | 0.0 | 0.45 Output | 8.0371e-05 | 8.0371e-05 | 8.0371e-05 | 0.0 | 0.00 Modify | 0.061368 | 0.061368 | 0.061368 | 0.0 | 1.45 Other | | 0.006145 | | | 0.15 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5471 ave 5471 max 5471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 277930 ave 277930 max 277930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 277930 Ave neighs/atom = 138.965 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.782108525142, Press = -5.14900873660657 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1002173 ghost atom cutoff = 8.1002173 binsize = 4.0501087, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.196 | 4.196 | 4.196 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -13444.134 -13444.134 -13529.366 -13529.366 329.85956 329.85956 31405.44 31405.44 -707.56097 -707.56097 3000 -13441.266 -13441.266 -13528.319 -13528.319 336.90427 336.90427 31371.93 31371.93 2196.9318 2196.9318 Loop time of 4.28818 on 1 procs for 1000 steps with 2000 atoms Performance: 20.148 ns/day, 1.191 hours/ns, 233.199 timesteps/s, 466.399 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2029 | 4.2029 | 4.2029 | 0.0 | 98.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018711 | 0.018711 | 0.018711 | 0.0 | 0.44 Output | 4.9623e-05 | 4.9623e-05 | 4.9623e-05 | 0.0 | 0.00 Modify | 0.060718 | 0.060718 | 0.060718 | 0.0 | 1.42 Other | | 0.005816 | | | 0.14 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5471 ave 5471 max 5471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 278814 ave 278814 max 278814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 278814 Ave neighs/atom = 139.407 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T333.15.out" else "print 'not_converged' file output/vol_T333.15.out" print '${V}' file output/vol_T333.15.out 31393.7235208477 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0