diff --git a/doc/src/dihedral_fourier.txt b/doc/src/dihedral_fourier.txt index 5cda91fe4..0a7a28c6e 100644 --- a/doc/src/dihedral_fourier.txt +++ b/doc/src/dihedral_fourier.txt @@ -1,77 +1,77 @@ "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line dihedral_style fourier command :h3 dihedral_style fourier/omp command :h3 [Syntax:] dihedral_style fourier :pre [Examples:] dihedral_style fourier dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0 :pre [Description:] The {fourier} dihedral style uses the potential: :c,image(Eqs/dihedral_fourier.jpg) The following coefficients must be defined for each dihedral type via the "dihedral_coeff"_dihedral_coeff.html command as in the example above, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html commands: m (integer >=1) K1 (energy) n1 (integer >= 0) d1 (degrees) -.... +\[...\] Km (energy) nm (integer >= 0) dm (degrees) :ul :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 +hardware, as discussed in "Section 5"_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 +See "Section 5"_Section_accelerate.html of the manual for more instructions on how to use the accelerated styles effectively. :line [Restrictions:] This angle style can only be used if LAMMPS was built with the USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] "dihedral_coeff"_dihedral_coeff.html [Default:] none diff --git a/doc/src/dihedral_spherical.txt b/doc/src/dihedral_spherical.txt index 3386c774f..86d22977f 100644 --- a/doc/src/dihedral_spherical.txt +++ b/doc/src/dihedral_spherical.txt @@ -1,87 +1,87 @@ "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line dihedral_style spherical command :h3 [Syntax:] dihedral_style spherical :pre [Examples:] dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0 dihedral_coeff 1 3 286.1 1 114 1 1 90 0 1 90.0 0 & 17.3 0 0.0 0 1 158 1 0 0.0 0 & 15.1 0 0.0 0 0 0.0 0 1 167.3 1 :pre [Description:] The {spherical} dihedral style uses the potential: :c,image(JPG/dihedral_spherical_angles.jpg) :c,image(Eqs/dihedral_spherical.jpg) For this dihedral style, the energy can be any function that combines the 4-body dihedral-angle (phi) and the two 3-body bond-angles (theta1, theta2). For this reason, there is usually no need to define 3-body "angle" forces separately for the atoms participating in these interactions. It is probably more efficient to incorporate 3-body angle forces into the dihedral interaction even if it requires adding additional terms to the expansion (as was done in the second example). A careful choice of parameters can prevent singularities that occur with traditional force-fields whenever theta1 or theta2 approach 0 or 180 degrees. The last example above corresponds to an interaction with a single energy minima located at phi=114, theta1=158, theta2=167.3 degrees, and it remains numerically stable at all angles (phi, theta1, theta2). In this example, the coefficients 17.3, and 15.1 can be physically interpreted as the harmonic spring constants for theta1 and theta2 around their minima. The coefficient 286.1 is the harmonic spring constant for phi after division by sin(158)*sin(167.3) (the minima positions for theta1 and theta2). The following coefficients must be defined for each dihedral type via the "dihedral_coeff"_dihedral_coeff.html command as in the example above, or in the Dihedral Coeffs section of a data file file read by the "read_data"_read_data.html command: n (integer >= 1) C1 (energy) K1 (typically an integer) a1 (degrees) u1 (typically 0.0 or 1.0) L1 (typically an integer) b1 (degrees, typically 0.0 or 90.0) v1 (typically 0.0 or 1.0) M1 (typically an integer) c1 (degrees, typically 0.0 or 90.0) w1 (typically 0.0 or 1.0) -.... +\[...\] Cn (energy) Kn (typically an integer) an (degrees) un (typically 0.0 or 1.0) Ln (typically an integer) bn (degrees, typically 0.0 or 90.0) vn (typically 0.0 or 1.0) Mn (typically an integer) cn (degrees, typically 0.0 or 90.0) wn (typically 0.0 or 1.0) :ul :line [Restrictions:] This dihedral style can only be used if LAMMPS was built with the USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] "dihedral_coeff"_dihedral_coeff.html [Default:] none