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Merge pull request #1957 from david-castillo/restrain_lbound

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add moving bond restraints and a lower bound only bond restraint
This commit is contained in:
Axel Kohlmeyer
2020-04-15 14:45:07 -04:00
committed by GitHub
parent 6bac08322c c5f6b5c687
commit 4c870be433
4 changed files with 164 additions and 11 deletions
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36
doc/src/fix_restrain.rst
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@ -17,10 +17,18 @@ Syntax
.. parsed-literal::
*bond* args = atom1 atom2 Kstart Kstop r0
*bond* args = atom1 atom2 Kstart Kstop r0start (r0stop)
atom1,atom2 = IDs of 2 atoms in bond
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
r0 = equilibrium bond distance (distance units)
r0start = equilibrium bond distance at start of run (distance units)
r0stop = equilibrium bond distance at end of run (optional) (distance units). If not
specified it is assumed to be equal to r0start
*lbond* args = atom1 atom2 Kstart Kstop r0start (r0stop)
atom1,atom2 = IDs of 2 atoms in bond
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
r0start = equilibrium bond distance at start of run (distance units)
r0stop = equilibrium bond distance at end of run (optional) (distance units). If not
specified it is assumed to be equal to r0start
*angle* args = atom1 atom2 atom3 Kstart Kstop theta0
atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
@ -38,6 +46,7 @@ Examples
.. code-block:: LAMMPS
fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
fix holdem all restrain lbond 45 48 2000.0 2000.0 2.75
fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0
@ -141,6 +150,29 @@ is included in :math:`K`.
----------
The *lbond* keyword applies a lower bound bond restraint to the specified atoms
using the same functional form used by the :doc:`bond_style harmonic <bond_harmonic>` command if the distance between
the atoms is smaller than the equilibrium bond distance and 0 otherwise. The potential associated with
the restraint is
.. math::
E = K (r - r_0)^2 ,if\;r < r_0
.. math::
E = 0 \qquad\quad\quad ,if\;r \ge r_0
with the following coefficients:
* :math:`K` (energy/distance\^2)
* :math:`r_0` (distance)
:math:`K` and :math:`r_0` are specified with the fix. Note that the usual 1/2 factor
is included in :math:`K`.
----------
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