diff --git a/doc/src/fix_polarize.rst b/doc/src/fix_polarize.rst new file mode 100644 index 0000000000..66bafb94f9 --- /dev/null +++ b/doc/src/fix_polarize.rst @@ -0,0 +1,86 @@ +.. index:: fix polarize/bem/icc +.. index:: fix polarize/bem/gmres +.. index:: fix polarize/functional + +fix polarize command +=================== + +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID polarize nevery tolerance ... + +* ID, group-ID are documented in :doc:`fix ` command +* polarize/bem/icc, polarize/bem/gmres, or polarize/functional = style name of this fix command +* Nevery = this fixed is invoked every this many timesteps +* tolerance = the tolerance for the iterative solver to stop + + +Examples +"""""""" + +.. code-block:: LAMMPS + + fix 1 all polarize/bem/icc 1 0.0001 + fix 2 all polarize/bem/gmres 5 0.0001 + fix 3 all polarize/bem/functional 1 0.0001 + +Description +""""""""""" + +The three fix polarize in the USER-DIELECTRIC package compute the induced charges +at the interface between two impermeable media with different dielectric +constants. + +There are some example scripts for using this package with LAMMPS in the +examples/USER/dielectric directory. + +---------- + +The charges of the atoms in the specified group will be computed by the solver. +fix polarize bem/icc computes the induced charges at the boundary elements +(i.e. interface vertices) using the successive overrelaxation as described +in (Tyagi). fix polarize bem/gmres computes the induced charges at +the interface vertices using the successive overrelaxation +as described in (Barros). + +Restart, fix_modify, output, run start/stop, minimize info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +The :doc:`fix_modify ` + +This fix computes a global scalar which can be accessed by various +:doc:`output commands `. The scalar is the Colvars +energy mentioned above. The scalar value calculated by this fix is +"extensive". + +Restrictions +"""""""""""" + +This fix is part of the USER-DIELECTRIC package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` doc page for more info. + +There can only be one colvars fix active at a time. Since the interface +communicates only the minimum amount of information and colvars module +itself can handle an arbitrary number of collective variables, this is +not a limitation of functionality. + +Related commands +"""""""""""""""" + +:doc:`fix smd `, :doc:`fix spring `, + +Default +""""""" + +None. + +---------- + +.. _NguyenTD: + +**(NguyenTD)** Nguyen, Li, Bagchi, Solis, Olvera de la Cruz, Mol. Phys., DOI:10.1016/j.cpc.2019.03.006 +