implementation of bond style harmonic/restrain /w docs

doc/src/Commands_bond.rst

@@ -42,6 +42,7 @@ OPT.
    * :doc:`gaussian <bond_gaussian>`
    * :doc:`gromos (o) <bond_gromos>`
    * :doc:`harmonic (iko) <bond_harmonic>`
+   * :doc:`harmonic/restrain <bond_harmonic_restrain>`
    * :doc:`harmonic/shift (o) <bond_harmonic_shift>`
    * :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
    * :doc:`lepton (o) <bond_lepton>`

doc/src/bond_harmonic_restrain.rst

@@ -0,0 +1,79 @@
+.. index:: bond_style harmonic/restrain
+
+bond_style harmonic/restrain command
+====================================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   bond_style harmonic/restrain
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   bond_style harmonic
+   bond_coeff 5 80.0
+
+Description
+"""""""""""
+
+The *harmonic/restrain* bond style uses the potential
+
+.. math::
+
+   E = K (r - r_{t=0})^2
+
+where :math:`r_{t=0}` is the distance between the bond atoms at the
+beginning of the first :doc:`run <run>` or :doc:`minimize <minimize>`
+command after the bond style has been defined (*t=0*).  Note that the
+usual 1/2 factor is included in :math:`K`.  This will effectively
+restrain bonds to their initial length, whatever that is.
+
+The following coefficient must be defined for each bond type via the
+:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read_data <read_data>`
+or :doc:`read_restart <read_restart>` commands
+
+* :math:`K` (energy/distance\^2)
+
+Restart info
+""""""""""""
+
+This bond style supports the :doc:`write_restart <write_restart>` and
+:doc:`read_restart <read_restart>` commands. The state of the initial
+bond lengths is stored with the restart files and read back.
+  
+Restrictions
+""""""""""""
+
+This bond style can only be used if LAMMPS was built with the
+EXTRA-MOLECULE package.  See the :doc:`Build package <Build_package>`
+page for more info.
+
+This bond style does not write its coefficients to a data file since the
+:math:`r_{t=0}` values are for individual bonds and not bond types.
+Since it uses :doc:`fix property/atom <fix_property_atom>` internally,
+you should use the "nofix" argument to the :doc:`write_data command
+<write_data>` to avoid writing a section to the data file can cannot be
+read back in by the bond style.
+
+This bond style cannot be used with :doc:`fix shake or fix rattle
+<fix_shake>`, with :doc:`fix filter/corotate <fix_filter_corotate>`, or
+any :doc:`tip4p pair style <pair_lj_cut_tip4p>` since there is no specific
+equilibrium distance for a given bond type.
+
+
+Related commands
+""""""""""""""""
+
+:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`,
+:doc:`bond_harmonic <bond_harmonic>`
+
+Default
+"""""""
+
+none

doc/src/bond_style.rst

@@ -10,7 +10,7 @@ Syntax
 
    bond_style style args
 
-* style = *none* or *zero* or *hybrid* or *bpm/rotational* or *bpm/spring* or *class2* or *fene* or *fene/expand* or *fene/nm* or *gaussian* or *gromos* or *harmonic* or *harmonic/shift* or *harmonic/shift/cut* or *lepton* or *morse* or *nonlinear* or *oxdna/fene* or *oxdena2/fene* or *oxrna2/fene* or *quartic* or *special* or *table*
+* style = *none* or *zero* or *hybrid* or *bpm/rotational* or *bpm/spring* or *class2* or *fene* or *fene/expand* or *fene/nm* or *gaussian* or *gromos* or *harmonic* or *harmonic/restrain* *harmonic/shift* or *harmonic/shift/cut* or *lepton* or *morse* or *nonlinear* or *oxdna/fene* or *oxdena2/fene* or *oxrna2/fene* or *quartic* or *special* or *table*
 
 * args = none for any style except *hybrid*
 
@@ -93,6 +93,7 @@ accelerated styles exist.
 * :doc:`gaussian <bond_gaussian>` - multicentered Gaussian-based bond potential
 * :doc:`gromos <bond_gromos>` - GROMOS force field bond
 * :doc:`harmonic <bond_harmonic>` - harmonic bond
+* :doc:`harmonic/restrain <bond_harmonic_restrain>` - harmonic bond to restrain to original bond distance
 * :doc:`harmonic/shift <bond_harmonic_shift>` - shifted harmonic bond
 * :doc:`harmonic/shift/cut <bond_harmonic_shift_cut>` - shifted harmonic bond with a cutoff
 * :doc:`lepton <bond_lepton>` - bond potential from evaluating a string