Loading doc/src/fix_qeq.txt +7 −2 Original line number Diff line number Diff line Loading @@ -90,9 +90,14 @@ file specified by {qfile}. The file has the following format ... Ntype chi eta gamma zeta qcore :pre There is one line per atom type with the following parameters. There have to be parameters given for every atom type. Wildcard entries are possible using the same syntax as elsewhere in LAMMPS (i.e., n*m, n*, *m, *). Later entries will overwrite previous ones. Empty lines or any text following the pound sign (#) are ignored. Each line starts with the atom type followed by five parameters. Only a subset of the parameters is used by each QEq style as described below, thus the others can be set to 0.0 if desired. below, thus the others can be set to 0.0 if desired, but all five entries per line are required. {chi} = electronegativity in energy units {eta} = self-Coulomb potential in energy units Loading doc/src/fix_wall_ees.txt +17 −16 Original line number Diff line number Diff line Loading @@ -50,17 +50,17 @@ fix ees_cube all wall/region/ees myCube 1.0 1.0 2.5 :pre Fix {wall/ees} bounds the simulation domain on one or more of its faces with a flat wall that interacts with the ellipsoidal atoms in the group by generating a force on the atom in a direction perpendicular to the wall and a torque parallel with the wall. The energy of the wall and a torque parallel with the wall. The energy of wall-particle interactions E is given by: :c,image(Eqs/fix_wall_ees.jpg) Introduced by Babadi and Ejtehadi in "(Babadi)"_#BabadiEjtehadi. Here, {r} is the distance from the particle to the wall at position {coord}, and Rc is the {cutoff} distance at which the particle and wall no longer interact. Also, sigma_n is the distance between center of ellipsoid and the nearest point of its surface to the wall The energy of the wall (see the image below). and Rc is the {cutoff} distance at which the particle and wall no longer interact. Also, sigma_n is the distance between center of ellipsoid and the nearest point of its surface to the wall. The energy of the wall is: :c,image(JPG/fix_wall_ees_image.jpg) Loading @@ -68,20 +68,21 @@ Details of using this command and specifications are the same as fix/wall command. You can also find an example in USER/ees/ under examples/ directory. The prefactor {epsilon} can be thought of as an effective Hamaker constant with energy units for the strength of the ellipsoid-wall interaction. More specifically, the {epsilon} pre-factor = 8 * pi^2 * rho_wall * rho_ellipsoid * epsilon * sigma_a * sigma_b * sigma_c, where epsilon is the LJ parameters for the constituent LJ particles and sigma_a, sigma_b, and sigma_c are radii of ellipsoidal particles. Rho_wall and rho_ellipsoid are the number The prefactor {epsilon} can be thought of as an effective Hamaker constant with energy units for the strength of the ellipsoid-wall interaction. More specifically, the {epsilon} pre-factor = 8 * pi^2 * rho_wall * rho_ellipsoid * epsilon * sigma_a * sigma_b * sigma_c, where epsilon is the LJ parameters for the constituent LJ particles and sigma_a, sigma_b, and sigma_c are radii of ellipsoidal particles. Rho_wall and rho_ellipsoid are the number density of the constituent particles, in the wall and ellipsoid respectively, in units of 1/volume. NOTE: You must insure that r is always bigger than sigma_n for all particles in the group, or LAMMPS will generate an error. This all particles in the group, or LAMMPS will generate an error. This means you cannot start your simulation with particles touching the wall position {coord} (r = sigma_n) or with particles penetrating the wall (0 =< r < sigma_n) or with particles on the wrong side of the position {coord} (r = sigma_n) or with particles penetrating the wall (0 =< r < sigma_n) or with particles on the wrong side of the wall (r < 0). Loading doc/src/lammps.book +1 −0 Original line number Diff line number Diff line Loading @@ -21,6 +21,7 @@ Section_python.html Section_errors.html Section_history.html tutorial_bash_on_windows.html tutorial_drude.html tutorial_github.html tutorial_pylammps.html Loading lib/gpu/Install.py +2 −2 Original line number Diff line number Diff line Loading @@ -9,8 +9,8 @@ import sys,os,subprocess # help message help = """ Syntax from src dir: make lib-gpu args="-m machine -h hdir -a arch -p precision -e esuffix -m -o osuffix" Syntax from lib dir: python Install.py -m machine -h hdir -a arch -p precision -e esuffix -m -o osuffix Syntax from src dir: make lib-gpu args="-m machine -h hdir -a arch -p precision -e esuffix -b -o osuffix" Syntax from lib dir: python Install.py -m machine -h hdir -a arch -p precision -e esuffix -b -o osuffix specify one or more options, order does not matter Loading src/.gitignore +1 −0 Original line number Diff line number Diff line Loading @@ -57,6 +57,7 @@ /intel_buffers.cpp /intel_buffers.h /intel_intrinsics.h /intel_intrinsics_airebo.h /intel_preprocess.h /intel_simd.h Loading Loading
doc/src/fix_qeq.txt +7 −2 Original line number Diff line number Diff line Loading @@ -90,9 +90,14 @@ file specified by {qfile}. The file has the following format ... Ntype chi eta gamma zeta qcore :pre There is one line per atom type with the following parameters. There have to be parameters given for every atom type. Wildcard entries are possible using the same syntax as elsewhere in LAMMPS (i.e., n*m, n*, *m, *). Later entries will overwrite previous ones. Empty lines or any text following the pound sign (#) are ignored. Each line starts with the atom type followed by five parameters. Only a subset of the parameters is used by each QEq style as described below, thus the others can be set to 0.0 if desired. below, thus the others can be set to 0.0 if desired, but all five entries per line are required. {chi} = electronegativity in energy units {eta} = self-Coulomb potential in energy units Loading
doc/src/fix_wall_ees.txt +17 −16 Original line number Diff line number Diff line Loading @@ -50,17 +50,17 @@ fix ees_cube all wall/region/ees myCube 1.0 1.0 2.5 :pre Fix {wall/ees} bounds the simulation domain on one or more of its faces with a flat wall that interacts with the ellipsoidal atoms in the group by generating a force on the atom in a direction perpendicular to the wall and a torque parallel with the wall. The energy of the wall and a torque parallel with the wall. The energy of wall-particle interactions E is given by: :c,image(Eqs/fix_wall_ees.jpg) Introduced by Babadi and Ejtehadi in "(Babadi)"_#BabadiEjtehadi. Here, {r} is the distance from the particle to the wall at position {coord}, and Rc is the {cutoff} distance at which the particle and wall no longer interact. Also, sigma_n is the distance between center of ellipsoid and the nearest point of its surface to the wall The energy of the wall (see the image below). and Rc is the {cutoff} distance at which the particle and wall no longer interact. Also, sigma_n is the distance between center of ellipsoid and the nearest point of its surface to the wall. The energy of the wall is: :c,image(JPG/fix_wall_ees_image.jpg) Loading @@ -68,20 +68,21 @@ Details of using this command and specifications are the same as fix/wall command. You can also find an example in USER/ees/ under examples/ directory. The prefactor {epsilon} can be thought of as an effective Hamaker constant with energy units for the strength of the ellipsoid-wall interaction. More specifically, the {epsilon} pre-factor = 8 * pi^2 * rho_wall * rho_ellipsoid * epsilon * sigma_a * sigma_b * sigma_c, where epsilon is the LJ parameters for the constituent LJ particles and sigma_a, sigma_b, and sigma_c are radii of ellipsoidal particles. Rho_wall and rho_ellipsoid are the number The prefactor {epsilon} can be thought of as an effective Hamaker constant with energy units for the strength of the ellipsoid-wall interaction. More specifically, the {epsilon} pre-factor = 8 * pi^2 * rho_wall * rho_ellipsoid * epsilon * sigma_a * sigma_b * sigma_c, where epsilon is the LJ parameters for the constituent LJ particles and sigma_a, sigma_b, and sigma_c are radii of ellipsoidal particles. Rho_wall and rho_ellipsoid are the number density of the constituent particles, in the wall and ellipsoid respectively, in units of 1/volume. NOTE: You must insure that r is always bigger than sigma_n for all particles in the group, or LAMMPS will generate an error. This all particles in the group, or LAMMPS will generate an error. This means you cannot start your simulation with particles touching the wall position {coord} (r = sigma_n) or with particles penetrating the wall (0 =< r < sigma_n) or with particles on the wrong side of the position {coord} (r = sigma_n) or with particles penetrating the wall (0 =< r < sigma_n) or with particles on the wrong side of the wall (r < 0). Loading
doc/src/lammps.book +1 −0 Original line number Diff line number Diff line Loading @@ -21,6 +21,7 @@ Section_python.html Section_errors.html Section_history.html tutorial_bash_on_windows.html tutorial_drude.html tutorial_github.html tutorial_pylammps.html Loading
lib/gpu/Install.py +2 −2 Original line number Diff line number Diff line Loading @@ -9,8 +9,8 @@ import sys,os,subprocess # help message help = """ Syntax from src dir: make lib-gpu args="-m machine -h hdir -a arch -p precision -e esuffix -m -o osuffix" Syntax from lib dir: python Install.py -m machine -h hdir -a arch -p precision -e esuffix -m -o osuffix Syntax from src dir: make lib-gpu args="-m machine -h hdir -a arch -p precision -e esuffix -b -o osuffix" Syntax from lib dir: python Install.py -m machine -h hdir -a arch -p precision -e esuffix -b -o osuffix specify one or more options, order does not matter Loading
src/.gitignore +1 −0 Original line number Diff line number Diff line Loading @@ -57,6 +57,7 @@ /intel_buffers.cpp /intel_buffers.h /intel_intrinsics.h /intel_intrinsics_airebo.h /intel_preprocess.h /intel_simd.h Loading
