Loading doc/src/compute_temp_profile.txt +2 −2 Original line number Diff line number Diff line Loading @@ -69,8 +69,8 @@ velocity for each atom. Note that if there is only one atom in the bin, its thermal velocity will thus be 0.0. After the spatially-averaged velocity field has been subtracted from each atom, the temperature is calculated by the formula KE = (dim/2 N - dim*Nx*Ny*Nz) k T, where KE = total kinetic energy of the group of each atom, the temperature is calculated by the formula KE = (dim*N - dim*Nx*Ny*Nz) k T/2, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature. The dim*Nx*Ny*Nz term are degrees of freedom Loading doc/src/fix_reax_bonds.txt +26 −0 Original line number Diff line number Diff line Loading @@ -8,6 +8,7 @@ fix reax/bonds command :h3 fix reax/c/bonds command :h3 fix reax/c/bonds/kk command :h3 [Syntax:] Loading Loading @@ -47,6 +48,31 @@ commands"_Section_howto.html#howto_15. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. :line Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in "Section_accelerate"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line [Restrictions:] The fix reax/bonds command requires that the "pair_style Loading doc/src/fix_reaxc_species.txt +26 −0 Original line number Diff line number Diff line Loading @@ -7,6 +7,7 @@ :line fix reax/c/species command :h3 fix reax/c/species/kk command :h3 [Syntax:] Loading Loading @@ -129,6 +130,31 @@ No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. :line Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in "Section_accelerate"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line [Restrictions:] The fix species currently only works with Loading doc/src/suffix.txt +7 −0 Original line number Diff line number Diff line Loading @@ -94,6 +94,13 @@ Of course this is also possible by not using any suffix commands, and explictly appending or not appending the suffix to the relevant commands in your input script. NOTE: The default "run_style"_run_style.html verlet is invoked prior to reading the input script and is therefore not affected by a suffix command in the input script. The KOKKOS package requires "run_style verlet/kk", so when using the KOKKOS package it is necessary to either use the command line "-sf kk" command or add an explicit "run_style verlet" command to the input script. [Restrictions:] none [Related commands:] Loading examples/threebody/BNC.tersoff 0 → 100644 +74 −0 Original line number Diff line number Diff line # DATE: 2013-03-21 CONTRIBUTOR: Cem Sevik CITATION: Kinaci, Haskins, Sevik and Cagin, Phys Rev B, 86, 115410 (2012) # Tersoff parameters for B, C, and BN-C hybrid based graphene like nano structures # multiple entries can be added to this file, LAMMPS reads the ones it needs # these entries are in LAMMPS "metal" units: # A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms # other quantities are unitless # Cem Sevik (csevik at anadolu.edu.tr) takes full blame for this # file. It specifies B-N, B-C, and N-C interaction parameters # generated and published by the reseacrh group of Prof. Tahir Cagin. # 1. Physical Review B 84, 085409 2011 # Characterization of thermal transport in low-dimensional boron nitride nanostructures, # # 2. Physical Review B 86, 075403 2012 # Influence of disorder on thermal transport properties of boron nitride nanostructures # # 3. Physical Review B 86, 075403 2012, Please see for further information about B-C and N-C parameters # Thermal conductivity of BN-C nanostructures # # The file also specifies C-C, interaction parameters # generated and published by the reseacrh group of Dr. D. A. Broido # Physical Review B 81, 205441 2010 # Optimized Tersoff and Brenner empirical potential parameters for # lattice dynamics and phonon thermal transport in carbon nanotubes and graphene # Users in referring the full parameters can cite the full parameter paper (3) as: # A. Kinaci, J. B. Haskins, C. Sevik, T. Cagin, Physical Review B 86, 115410 (2012) # Thermal conductivity of BN-C nanostructures # # format of a single entry (one or more lines): # element 1, element 2, element 3, # m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A N B B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 N B N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 N B C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 B N B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 B N N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 B N C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 N N B 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866 N N N 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866 N N C 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866 B B B 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156 B B N 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156 B B C 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156 C C C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6 C C B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6 C C N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6 C B B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 C B N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 C B C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 C N B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 C N N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 C N C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 B C C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 B C B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 B C N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 N C C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 N C B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 N C N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 Loading
doc/src/compute_temp_profile.txt +2 −2 Original line number Diff line number Diff line Loading @@ -69,8 +69,8 @@ velocity for each atom. Note that if there is only one atom in the bin, its thermal velocity will thus be 0.0. After the spatially-averaged velocity field has been subtracted from each atom, the temperature is calculated by the formula KE = (dim/2 N - dim*Nx*Ny*Nz) k T, where KE = total kinetic energy of the group of each atom, the temperature is calculated by the formula KE = (dim*N - dim*Nx*Ny*Nz) k T/2, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the simulation, N = number of atoms in the group, k = Boltzmann constant, and T = temperature. The dim*Nx*Ny*Nz term are degrees of freedom Loading
doc/src/fix_reax_bonds.txt +26 −0 Original line number Diff line number Diff line Loading @@ -8,6 +8,7 @@ fix reax/bonds command :h3 fix reax/c/bonds command :h3 fix reax/c/bonds/kk command :h3 [Syntax:] Loading Loading @@ -47,6 +48,31 @@ commands"_Section_howto.html#howto_15. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. :line Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in "Section_accelerate"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line [Restrictions:] The fix reax/bonds command requires that the "pair_style Loading
doc/src/fix_reaxc_species.txt +26 −0 Original line number Diff line number Diff line Loading @@ -7,6 +7,7 @@ :line fix reax/c/species command :h3 fix reax/c/species/kk command :h3 [Syntax:] Loading Loading @@ -129,6 +130,31 @@ No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. :line Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in "Section_accelerate"_Section_accelerate.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. See "Section_accelerate"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line [Restrictions:] The fix species currently only works with Loading
doc/src/suffix.txt +7 −0 Original line number Diff line number Diff line Loading @@ -94,6 +94,13 @@ Of course this is also possible by not using any suffix commands, and explictly appending or not appending the suffix to the relevant commands in your input script. NOTE: The default "run_style"_run_style.html verlet is invoked prior to reading the input script and is therefore not affected by a suffix command in the input script. The KOKKOS package requires "run_style verlet/kk", so when using the KOKKOS package it is necessary to either use the command line "-sf kk" command or add an explicit "run_style verlet" command to the input script. [Restrictions:] none [Related commands:] Loading
examples/threebody/BNC.tersoff 0 → 100644 +74 −0 Original line number Diff line number Diff line # DATE: 2013-03-21 CONTRIBUTOR: Cem Sevik CITATION: Kinaci, Haskins, Sevik and Cagin, Phys Rev B, 86, 115410 (2012) # Tersoff parameters for B, C, and BN-C hybrid based graphene like nano structures # multiple entries can be added to this file, LAMMPS reads the ones it needs # these entries are in LAMMPS "metal" units: # A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms # other quantities are unitless # Cem Sevik (csevik at anadolu.edu.tr) takes full blame for this # file. It specifies B-N, B-C, and N-C interaction parameters # generated and published by the reseacrh group of Prof. Tahir Cagin. # 1. Physical Review B 84, 085409 2011 # Characterization of thermal transport in low-dimensional boron nitride nanostructures, # # 2. Physical Review B 86, 075403 2012 # Influence of disorder on thermal transport properties of boron nitride nanostructures # # 3. Physical Review B 86, 075403 2012, Please see for further information about B-C and N-C parameters # Thermal conductivity of BN-C nanostructures # # The file also specifies C-C, interaction parameters # generated and published by the reseacrh group of Dr. D. A. Broido # Physical Review B 81, 205441 2010 # Optimized Tersoff and Brenner empirical potential parameters for # lattice dynamics and phonon thermal transport in carbon nanotubes and graphene # Users in referring the full parameters can cite the full parameter paper (3) as: # A. Kinaci, J. B. Haskins, C. Sevik, T. Cagin, Physical Review B 86, 115410 (2012) # Thermal conductivity of BN-C nanostructures # # format of a single entry (one or more lines): # element 1, element 2, element 3, # m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A N B B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 N B N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 N B C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 B N B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 B N N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 B N C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 N N B 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866 N N N 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866 N N C 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866 B B B 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156 B B N 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156 B B C 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156 C C C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6 C C B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6 C C N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6 C B B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 C B N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 C B C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 C N B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 C N N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 C N C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 B C C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 B C B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 B C N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 N C C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 N C B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 N C N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78
