# 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 2.863657310605049*\${_u_distance} variable latticeconst_converted equal 2.863657310605049*1 lattice bcc \${latticeconst_converted} lattice bcc 2.86365731060505 Lattice spacing in x,y,z = 2.8636573 2.8636573 2.8636573 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (28.636573 28.636573 28.636573) 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 (28.636573 28.636573 28.636573) create_atoms CPU = 0.000 seconds variable mass_converted equal 55.845*\${_u_mass} variable mass_converted equal 55.845*1 kim interactions Fe #=== BEGIN kim interactions ================================== pair_style kim MEAM_LAMMPS_ChoiKimSeol_2017_CoFe__MO_179158257180_002 pair_coeff * * Fe #=== END kim interactions ==================================== mass 1 \${mass_converted} mass 1 55.845 # initial volume variable v equal vol # assign formula variable V0 equal \${v} # evaluate initial value variable V0 equal 23483.5168277961 variable V0_metal equal \${V0}/(\${_u_distance}*\${_u_distance}*\${_u_distance}) variable V0_metal equal 23483.5168277961/(\${_u_distance}*\${_u_distance}*\${_u_distance}) variable V0_metal equal 23483.5168277961/(1*\${_u_distance}*\${_u_distance}) variable V0_metal equal 23483.5168277961/(1*1*\${_u_distance}) variable V0_metal equal 23483.5168277961/(1*1*1) variable V0_metal_times1000 equal \${V0_metal}*1000 variable V0_metal_times1000 equal 23483.5168277961*1000 print "Initial system volume: \${V0_metal} Angstroms^3" Initial system volume: 23483.5168277961 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 273.15*\${_u_temperature} variable temp_converted equal 273.15*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 273.15 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 273.15 \${temp_converted} \${Tdamp_converted} iso \${press_converted} \${press_converted} \${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 \${Tdamp_converted} iso \${press_converted} \${press_converted} \${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso \${press_converted} \${press_converted} \${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 \${press_converted} \${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 \${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 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 "273.15 - 1.0" variable T_up equal "273.15 + 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_179158257180_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 ghost atom cutoff = 6 binsize = 3, bins = 10 10 10 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) = 3.755 | 3.755 | 3.755 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -8509.4205 -8509.4205 -8580 -8580 273.15 273.15 23483.517 23483.517 3210.2349 3210.2349 1000 -8434.3934 -8434.3934 -8504.3593 -8504.3593 270.7751 270.7751 23665.327 23665.327 2923.7393 2923.7393 Loop time of 22.2005 on 1 procs for 1000 steps with 2000 atoms Performance: 3.892 ns/day, 6.167 hours/ns, 45.044 timesteps/s, 90.088 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.118 | 22.118 | 22.118 | 0.0 | 99.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.015174 | 0.015174 | 0.015174 | 0.0 | 0.07 Output | 9.0751e-05 | 9.0751e-05 | 9.0751e-05 | 0.0 | 0.00 Modify | 0.06139 | 0.06139 | 0.06139 | 0.0 | 0.28 Other | | 0.005754 | | | 0.03 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119 ave 4119 max 4119 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: 128000 ave 128000 max 128000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128000 Ave neighs/atom = 64 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 = 273.107886731048, Press = 139.933377054794 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 ghost atom cutoff = 6 binsize = 3, bins = 10 10 10 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) = 3.755 | 3.755 | 3.755 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -8434.3934 -8434.3934 -8504.3593 -8504.3593 270.7751 270.7751 23665.327 23665.327 2923.7393 2923.7393 2000 -8440.4806 -8440.4806 -8509.5821 -8509.5821 267.43008 267.43008 23689.2 23689.2 194.10936 194.10936 Loop time of 24.2083 on 1 procs for 1000 steps with 2000 atoms Performance: 3.569 ns/day, 6.725 hours/ns, 41.308 timesteps/s, 82.616 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 | 24.126 | 24.126 | 24.126 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014851 | 0.014851 | 0.014851 | 0.0 | 0.06 Output | 5.9683e-05 | 5.9683e-05 | 5.9683e-05 | 0.0 | 0.00 Modify | 0.062015 | 0.062015 | 0.062015 | 0.0 | 0.26 Other | | 0.005406 | | | 0.02 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119 ave 4119 max 4119 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: 128016 ave 128016 max 128016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128016 Ave neighs/atom = 64.008 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 = 272.633860558762, Press = 7.53173171316881 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 ghost atom cutoff = 6 binsize = 3, bins = 10 10 10 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) = 3.755 | 3.755 | 3.755 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -8440.4806 -8440.4806 -8509.5821 -8509.5821 267.43008 267.43008 23689.2 23689.2 194.10936 194.10936 3000 -8440.5029 -8440.5029 -8508.8529 -8508.8529 264.52148 264.52148 23694.22 23694.22 148.24077 148.24077 Loop time of 24.5242 on 1 procs for 1000 steps with 2000 atoms Performance: 3.523 ns/day, 6.812 hours/ns, 40.776 timesteps/s, 81.552 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 | 24.442 | 24.442 | 24.442 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014888 | 0.014888 | 0.014888 | 0.0 | 0.06 Output | 6.2958e-05 | 6.2958e-05 | 6.2958e-05 | 0.0 | 0.00 Modify | 0.06213 | 0.06213 | 0.06213 | 0.0 | 0.25 Other | | 0.00551 | | | 0.02 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4119 ave 4119 max 4119 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: 128048 ave 128048 max 128048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128048 Ave neighs/atom = 64.024 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_T273.15.out" else "print 'not_converged' file output/vol_T273.15.out" print '\${V}' file output/vol_T273.15.out 23702.0174933764 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0