# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 2.836713165044785*${_u_distance} variable latticeconst_converted equal 2.836713165044785*1 lattice bcc ${latticeconst_converted} lattice bcc 2.83671316504478 Lattice spacing in x,y,z = 2.8367132 2.8367132 2.8367132 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (28.367132 28.367132 28.367132) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (28.367132 28.367132 28.367132) create_atoms CPU = 0.000 seconds variable mass_converted equal 55.845*${_u_mass} variable mass_converted equal 55.845*1 kim interactions Fe #=== BEGIN kim interactions ================================== variable kim_update equal 0 variable kim_periodic equal 1 pair_style reax/c /tmp/kim-shared-library-parameter-file-directory-XXXXXXjMpsNl/lmp_control safezone 2.0 mincap 100 WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:98) pair_coeff * * /tmp/kim-shared-library-parameter-file-directory-XXXXXXjMpsNl/ffield.reax.Fe_O_C_H Fe Reading potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXjMpsNl/ffield.reax.Fe_O_C_H with DATE: 2011-02-18 fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 reax/c #=== 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 22826.8651204268 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 22826.8651204268/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 22826.8651204268/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 22826.8651204268/(1*1*${_u_distance}) variable V0_metal equal 22826.8651204268/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 22826.8651204268*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 22826.8651204268 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1000 timestep ${timestep_converted} timestep 1 variable temp_converted equal 313.15*${_u_temperature} variable temp_converted equal 313.15*1 variable Tdamp_converted equal 0.01*${_u_time} variable Tdamp_converted equal 0.01*1000 variable press_converted equal 0.0*${_u_pressure} variable press_converted equal 0.0*0.986923266716013 variable Pdamp_converted equal 0.1*${_u_time} variable Pdamp_converted equal 0.1*1000 # 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 10 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 10 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 10 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 10 iso 0 0 100 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_u_energy} variable etotal_metal equal etotal/23.0605480120695 variable pe_metal equal pe/${_u_energy} variable pe_metal equal pe/23.0605480120695 variable T_metal equal temp/${_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/0.986923266716013 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/SM_222964216001_001#item-citation - pair reaxff command: doi:10.1016/j.parco.2011.08.005 @Article{Aktulga12, author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama}, title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques}, journal = {Parallel Computing}, year = 2012, volume = 38, number = {4--5}, pages = {245--259} } - fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005 @Article{Aktulga12, author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama}, title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques}, journal = {Parallel Computing}, year = 2012, volume = 38, pages = {245--259} } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 5 5 5 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: full/ghost/bin/3d bin: standard (2) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 362.2 | 362.2 | 362.2 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -205006.46 -8889.9216 -206872.41 -8970.8368 313.15 313.15 22826.865 22826.865 3736.6709 3786.1818 1000 -203003.37 -8803.0591 -204879.44 -8884.4135 314.85021 314.85021 22881.653 22881.653 -1815.626 -1839.6831 Loop time of 166.282 on 1 procs for 1000 steps with 2000 atoms Performance: 0.520 ns/day, 46.189 hours/ns, 6.014 timesteps/s, 12.028 katom-step/s 85.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 130.67 | 130.67 | 130.67 | 0.0 | 78.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.047754 | 0.047754 | 0.047754 | 0.0 | 0.03 Output | 0.00011071 | 0.00011071 | 0.00011071 | 0.0 | 0.00 Modify | 35.547 | 35.547 | 35.547 | 0.0 | 21.38 Other | | 0.01302 | | | 0.01 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10691 ave 10691 max 10691 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 854124 ave 854124 max 854124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 854124 Ave neighs/atom = 427.062 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 = ${P}" flag: Temp = 309.957048843004, Press = 72.5791154846479 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 363.4 | 363.4 | 363.4 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -203003.37 -8803.0591 -204879.44 -8884.4135 314.85021 314.85021 22881.653 22881.653 -1815.626 -1839.6831 2000 -203200.02 -8811.587 -205120.61 -8894.8716 322.31998 322.31998 22884.992 22884.992 -1706.0782 -1728.6838 Loop time of 166.821 on 1 procs for 1000 steps with 2000 atoms Performance: 0.518 ns/day, 46.339 hours/ns, 5.994 timesteps/s, 11.989 katom-step/s 87.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 131.81 | 131.81 | 131.81 | 0.0 | 79.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.04281 | 0.04281 | 0.04281 | 0.0 | 0.03 Output | 5.8981e-05 | 5.8981e-05 | 5.8981e-05 | 0.0 | 0.00 Modify | 34.952 | 34.952 | 34.952 | 0.0 | 20.95 Other | | 0.01281 | | | 0.01 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10691 ave 10691 max 10691 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 873486 ave 873486 max 873486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 873486 Ave neighs/atom = 436.743 Neighbor list builds = 0 Dangerous builds = 0 if "${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 22854.5163381838 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0