# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 2.976109810173512*${_u_distance} variable latticeconst_converted equal 2.976109810173512*1 lattice bcc ${latticeconst_converted} lattice bcc 2.97610981017351 Lattice spacing in x,y,z = 2.9761098 2.9761098 2.9761098 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (29.761098 29.761098 29.761098) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (29.761098 29.761098 29.761098) create_atoms CPU = 0.000 seconds variable mass_converted equal 50.9415*${_u_mass} variable mass_converted equal 50.9415*1 kim interactions V #=== BEGIN kim interactions ================================== variable kim_update equal 0 variable kim_periodic equal 1 pair_style reax/c /tmp/kim-shared-library-parameter-file-directory-XXXXXXOfW8NM/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-XXXXXXOfW8NM/ffield.reax.V_O_C_H V Reading potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXOfW8NM/ffield.reax.V_O_C_H with DATE: 2011-02-18 WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:296) fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 reax/c #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 50.9415 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 26360.0879100994 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 26360.0879100994/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 26360.0879100994/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 26360.0879100994/(1*1*${_u_distance}) variable V0_metal equal 26360.0879100994/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 26360.0879100994*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 26360.0879100994 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1000 timestep ${timestep_converted} timestep 1 variable temp_converted equal 273.15*${_u_temperature} variable temp_converted equal 273.15*1 variable Tdamp_converted equal 0.01*${_u_time} variable Tdamp_converted equal 0.01*1000 variable press_converted equal 0.0*${_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 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 10 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 10 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 10 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 10 iso 0 0 100 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "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/SM_429148913211_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) = 357.4 | 357.4 | 357.4 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -257466.9 -11164.821 -259094.5 -11235.401 273.15 273.15 26360.088 26360.088 2822.5821 2859.9814 1000 -255881.43 -11096.069 -257506.84 -11166.553 272.78255 272.78255 26396.498 26396.498 2880.5139 2918.6807 Loop time of 156.529 on 1 procs for 1000 steps with 2000 atoms Performance: 0.552 ns/day, 43.480 hours/ns, 6.389 timesteps/s, 12.777 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 | 122.75 | 122.75 | 122.75 | 0.0 | 78.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.044242 | 0.044242 | 0.044242 | 0.0 | 0.03 Output | 0.00011785 | 0.00011785 | 0.00011785 | 0.0 | 0.00 Modify | 33.72 | 33.72 | 33.72 | 0.0 | 21.54 Other | | 0.01502 | | | 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: 745107 ave 745107 max 745107 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 745107 Ave neighs/atom = 372.5535 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 = ${P}" flag: Temp = 274.458689219094, Press = -43.0770680287067 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 357.5 | 357.5 | 357.5 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -255881.43 -11096.069 -257506.84 -11166.553 272.78255 272.78255 26396.498 26396.498 2880.5139 2918.6807 2000 -255872.97 -11095.702 -257455.47 -11164.326 265.58127 265.58127 26388.369 26388.369 3732.3003 3781.7533 Loop time of 160.1 on 1 procs for 1000 steps with 2000 atoms Performance: 0.540 ns/day, 44.472 hours/ns, 6.246 timesteps/s, 12.492 katom-step/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 127.15 | 127.15 | 127.15 | 0.0 | 79.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.045111 | 0.045111 | 0.045111 | 0.0 | 0.03 Output | 7.7315e-05 | 7.7315e-05 | 7.7315e-05 | 0.0 | 0.00 Modify | 32.894 | 32.894 | 32.894 | 0.0 | 20.55 Other | | 0.01596 | | | 0.01 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10635 ave 10635 max 10635 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 746623 ave 746623 max 746623 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 746623 Ave neighs/atom = 373.3115 Neighbor list builds = 0 Dangerous builds = 0 if "${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 26424.2141547758 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0