Added a doc page for the fix polarize/*

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 <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 <fix_modify>` 
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  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
+<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 <fix_smd>`, :doc:`fix spring <fix_spring>`,
+
+Default
+"""""""
+
+None.
+
+----------
+
+.. _NguyenTD:
+
+**(NguyenTD)** Nguyen, Li, Bagchi, Solis, Olvera de la Cruz, Mol. Phys., DOI:10.1016/j.cpc.2019.03.006
+