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Merge pull request #737 from akohlmey/collected-bugfixes

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Collected bugfixes and small updates for next patch
This commit is contained in:
Steve Plimpton
2017-12-07 08:23:06 -07:00
committed by GitHub
parent 73d509f339 4a3a6b4455
commit bae45e2493
9 changed files with 30 additions and 30 deletions
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22
doc/src/create_atoms.txt
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@ -36,9 +36,9 @@ keyword = {mol} or {basis} or {remap} or {var} or {set} or {units} :l
{set} values = dim name
dim = {x} or {y} or {z}
name = name of variable to set with x, y, or z atom position
{rotate} values = Rx Ry Rz theta
Rx,Ry,Rz = rotation vector for single molecule
{rotate} values = theta Rx Ry Rz
theta = rotation angle for single molecule (degrees)
Rx,Ry,Rz = rotation vector for single molecule
{units} value = {lattice} or {box}
{lattice} = the geometry is defined in lattice units
{box} = the geometry is defined in simulation box units :pre
@ -242,15 +242,15 @@ write_dump all atom sinusoid.lammpstrj :pre
:c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg)
The {rotate} keyword can be used with the {single} style, when adding
a single molecule to specify the orientation at which the molecule is
inserted. The axis of rotation is determined by the rotation vector
(Rx,Ry,Rz) that goes through the insertion point. The specified
{theta} determines the angle of rotation around that axis. Note that
the direction of rotation for the atoms around the rotation axis is
consistent with the right-hand rule: if your right-hand's thumb points
along {R}, then your fingers wrap around the axis in the direction of
rotation.
The {rotate} keyword can only be used with the {single} style and
when adding a single molecule. It allows to specify the orientation
at which the molecule is inserted. The axis of rotation is
determined by the rotation vector (Rx,Ry,Rz) that goes through the
insertion point. The specified {theta} determines the angle of
rotation around that axis. Note that the direction of rotation for
the atoms around the rotation axis is consistent with the right-hand
rule: if your right-hand's thumb points along {R}, then your fingers
wrap around the axis in the direction of rotation.
The {units} keyword determines the meaning of the distance units used
to specify the coordinates of the one particle created by the {single}

2
doc/src/create_bonds.txt
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@ -18,7 +18,7 @@ style = {many} or {single/bond} or {single/angle} or {single/dihedral} :ule,l
group2-ID = ID of second group, bonds will be between atoms in the 2 groups
btype = bond type of created bonds
rmin = minimum distance between pair of atoms to bond together
rmax = minimum distance between pair of atoms to bond together
rmax = maximum distance between pair of atoms to bond together
{single/bond} args = btype batom1 batom2
btype = bond type of new bond
batom1,batom2 = atom IDs for two atoms in bond