diff --git a/doc/src/JPG/dynamical_matrix_dynmat.jpg b/doc/src/JPG/dynamical_matrix_dynmat.jpg deleted file mode 100644 index 6c6adae72c..0000000000 Binary files a/doc/src/JPG/dynamical_matrix_dynmat.jpg and /dev/null differ diff --git a/doc/src/JPG/dynamical_matrix_force_constant.jpg b/doc/src/JPG/dynamical_matrix_force_constant.jpg deleted file mode 100644 index e1a0e50d14..0000000000 Binary files a/doc/src/JPG/dynamical_matrix_force_constant.jpg and /dev/null differ diff --git a/doc/src/dynamical_matrix.rst b/doc/src/dynamical_matrix.rst index 0f5b2093fc..c99f0f6ecc 100644 --- a/doc/src/dynamical_matrix.rst +++ b/doc/src/dynamical_matrix.rst @@ -40,42 +40,46 @@ Description Calculate the dynamical matrix by finite difference of the selected group, -.. image:: JPG/dynamical_matrix_dynmat.jpg - :align: center +.. math:: -where D is the dynamical matrix and Phi is the force constant matrix defined by + D = \frac{\Phi_{ij}^{\alpha\beta}}{\sqrt{M_i M_j}} -.. image:: JPG/dynamical_matrix_force_constant.jpg - :align: center +where D is the dynamical matrix and :math:`\Phi` is the force constant +matrix defined by -The output for the dynamical matrix is printed three elements at a time. The -three elements are the three beta elements for a respective i/alpha/j combination. -Each line is printed in order of j increasing first, alpha second, and i last. +.. math:: -If the style eskm is selected, the dynamical matrix will be in units of inverse squared -femtoseconds. These units will then conveniently leave frequencies in THz, where -frequencies, represented as omega, can be calculated from + \Phi_{ij}^{\alpha\beta} = \frac{\partial^2 U}{\partial x_{i,\alpha} \partial x_{j,\beta}} -:c, image(Eqs/dynamical\_matrix\_phonons.jpg) + +The output for the dynamical matrix is printed three elements at a time. +The three elements are the three :math:`\beta` elements for a respective +i/:math:`\alpha`/j combination. Each line is printed in order of j +increasing first, :math:`\alpha` second, and i last. + +If the style eskm is selected, the dynamical matrix will be in units of +inverse squared femtoseconds. These units will then conveniently leave +frequencies in THz. Restrictions """""""""""" - The command collects an array of nine times the number of atoms in a group on every single MPI rank, so the memory requirements can be very significant for large systems. This command is part of the USER-PHONON package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. +See the :doc:`Build package ` doc page for more info. Related commands """""""""""""""" :doc:`fix phonon ` -:doc:`compute hma ` uses an analytic formulation of the hessian -provided by Pair's single\_hessian. +:doc:`compute hma ` uses an analytic formulation of the +Hessian provided by a pair_style's Pair::single\_hessian() funcion, +if implemented. Default """""""