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Merge pull request #2304 from akohlmey/collected-small-changes

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Collected small changes for the next patch release
This commit is contained in:
Axel Kohlmeyer
2020-08-24 11:43:42 -04:00
committed by GitHub
parent 7e1a3bd4d5 47a44732e7
commit 93e4ed9770
37 changed files with 3058 additions and 150 deletions
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8
doc/src/fix_restrain.rst
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@ -13,7 +13,7 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* restrain = style name of this fix command
* one or more keyword/arg pairs may be appended
* keyword = *bond* or *angle* or *dihedral*
* keyword = *bond* or *lbound* or *angle* or *dihedral*
.. parsed-literal::
@ -23,7 +23,7 @@ Syntax
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)
*lbound* 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)
@ -46,7 +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 lbound 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
@ -150,7 +150,7 @@ is included in :math:`K`.
----------
The *lbond* keyword applies a lower bound bond restraint to the specified atoms
The *lbound* 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