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Update docs: fix_restrain

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This commit is contained in:
Richard Berger
2019-11-14 21:15:55 -05:00
parent aed67fc96e
commit c182d3f545
2 changed files with 29 additions and 238 deletions
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58
doc/src/fix_restrain.rst
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@ -7,7 +7,7 @@ Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix ID group-ID restrain keyword args ...
@ -39,7 +39,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
@ -98,7 +98,7 @@ conventional force field terms. If the restraint is applied during a
dynamics run (as opposed to during an energy minimization), a large
restraint coefficient can significantly reduce the stable timestep
size, especially if the atoms are initially far from the preferred
conformation. You may need to experiment to determine what value of K
conformation. You may need to experiment to determine what value of :math:`K`
works best for a given application.
For the case of finding a minimum energy structure for a single
@ -107,7 +107,7 @@ parameters or constructing a potential energy surface), commands such
as the following may be useful:
.. parsed-literal::
.. code-block:: LAMMPS
# minimize molecule energy with restraints
velocity all create 600.0 8675309 mom yes rot yes dist gaussian
@ -134,16 +134,18 @@ The *bond* keyword applies a bond restraint to the specified atoms
using the same functional form used by the :doc:`bond\_style harmonic <bond_harmonic>` command. The potential associated with
the restraint is
.. image:: Eqs/bond_harmonic.jpg
:align: center
.. math::
E = K (r - r_0)^2
with the following coefficients:
* K (energy/distance\^2)
* r0 (distance)
* :math:`K` (energy/distance\^2)
* :math:`r_0` (distance)
K and r0 are specified with the fix. Note that the usual 1/2 factor
is included in K.
:math:`K` and :math:`r_0` are specified with the fix. Note that the usual 1/2 factor
is included in :math:`K`.
----------
@ -153,16 +155,17 @@ The *angle* keyword applies an angle restraint to the specified atoms
using the same functional form used by the :doc:`angle\_style harmonic <angle_harmonic>` command. The potential associated with
the restraint is
.. image:: Eqs/angle_harmonic.jpg
:align: center
.. math::
E = K (\theta - \theta_0)^2
with the following coefficients:
* K (energy/radian\^2)
* theta0 (degrees)
* :math:`K` (energy/radian\^2)
* :math:`\theta_0` (degrees)
K and theta0 are specified with the fix. Note that the usual 1/2
factor is included in K.
:math:`K` and :math:`\theta_0` are specified with the fix. Note that the usual 1/2
factor is included in :math:`K`.
----------
@ -173,20 +176,22 @@ atoms using a simplified form of the function used by the
:doc:`dihedral\_style charmm <dihedral_charmm>` command. The potential
associated with the restraint is
.. image:: Eqs/dihedral_charmm.jpg
:align: center
.. math::
E = K [ 1 + \cos (n \phi - d) ]
with the following coefficients:
* K (energy)
* n (multiplicity, >= 0)
* d (degrees) = phi0 + 180
* :math:`K` (energy)
* :math:`n` (multiplicity, >= 0)
* :math:`d` (degrees) = :math:`\phi_0 + 180`
K and phi0 are specified with the fix. Note that the value of the
dihedral multiplicity *n* is set by default to 1. You can use the
:math:`K` and :math:`\phi_0` are specified with the fix. Note that the value of the
dihedral multiplicity :math:`n` is set by default to 1. You can use the
optional *mult* keyword to set it to a different positive integer.
Also note that the energy will be a minimum when the
current dihedral angle phi is equal to phi0.
current dihedral angle :math:`\phi` is equal to :math:`\phi_0`.
----------
@ -233,8 +238,3 @@ Restrictions
**Related commands:** none
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html