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add docs for create_atoms mesh

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Axel Kohlmeyer
2022-05-06 00:47:05 -04:00
parent ff21142042
commit 773e3a87d9
1 changed files with 37 additions and 16 deletions
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doc/src/create_atoms.rst
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@ -11,7 +11,7 @@ Syntax
create_atoms type style args keyword values ... create_atoms type style args keyword values ...
* type = atom type (1-Ntypes) of atoms to create (offset for molecule creation) * type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)
* style = *box* or *region* or *single* or *random* * style = *box* or *region* or *single* or *mesh* or *random*
.. parsed-literal:: .. parsed-literal::
@ -20,6 +20,8 @@ Syntax
region-ID = particles will only be created if contained in the region region-ID = particles will only be created if contained in the region
*single* args = x y z *single* args = x y z
x,y,z = coordinates of a single particle (distance units) x,y,z = coordinates of a single particle (distance units)
*mesh* args = STL-file
STL-file = file with triangle mesh in STL format
*random* args = N seed region-ID *random* args = N seed region-ID
N = number of particles to create N = number of particles to create
seed = random # seed (positive integer) seed = random # seed (positive integer)
@ -50,6 +52,8 @@ Syntax
*rotate* values = theta Rx Ry Rz *rotate* values = theta Rx Ry Rz
theta = rotation angle for single molecule (degrees) theta = rotation angle for single molecule (degrees)
Rx,Ry,Rz = rotation vector for single molecule Rx,Ry,Rz = rotation vector for single molecule
*radiusscale* value = factor
factor = scale factor for setting atom radius
*overlap* value = Doverlap *overlap* value = Doverlap
Doverlap = only insert if at least this distance from all existing atoms Doverlap = only insert if at least this distance from all existing atoms
*maxtry* value = Ntry *maxtry* value = Ntry
@ -69,21 +73,22 @@ Examples
create_atoms 3 single 0 0 5 create_atoms 3 single 0 0 5
create_atoms 1 box var v set x xpos set y ypos create_atoms 1 box var v set x xpos set y ypos
create_atoms 2 random 50 12345 NULL overlap 2.0 maxtry 50 create_atoms 2 random 50 12345 NULL overlap 2.0 maxtry 50
create_atoms 1 mesh funnel.stl units box radiusscale 1.5
Description Description
""""""""""" """""""""""
This command creates atoms (or molecules) within the simulation box, This command creates atoms (or molecules) within the simulation box,
either on a lattice, or a single atom (or molecule), or a random either on a lattice, or a single atom (or molecule), or from a triangle
collection of atoms (or molecules). It is an alternative to reading mesh, or a random collection of atoms (or molecules). It is an
in atom coordinates explicitly via a :doc:`read_data <read_data>` or alternative to reading in atom coordinates explicitly via a
:doc:`read_restart <read_restart>` command. A simulation box must :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
already exist, which is typically created via the :doc:`create_box command. A simulation box must already exist, which is typically
<create_box>` command. Before using this command, a lattice must also created via the :doc:`create_box <create_box>` command. Before using
be defined using the :doc:`lattice <lattice>` command, unless you this command, a lattice must also be defined using the :doc:`lattice
specify the *single* style with units = box or the *random* style. <lattice>` command, unless you specify the *single* or *mesh* style with
For the remainder of this doc page, a created atom or molecule is units = box or the *random* style. For the remainder of this doc page,
referred to as a "particle". a created atom or molecule is referred to as a "particle".
If created particles are individual atoms, they are assigned the If created particles are individual atoms, they are assigned the
specified atom *type*, though this can be altered via the *basis* specified atom *type*, though this can be altered via the *basis*
@ -119,6 +124,13 @@ the specified coordinates. This can be useful for debugging purposes
or to create a tiny system with a handful of particles at specified or to create a tiny system with a handful of particles at specified
positions. positions.
For the *mesh* style, a file with a triangle mesh in `STL format
<https://en.wikipedia.org/wiki/STL_(file_format)#ASCII_STL>`_ is read
and a particle is placed into the center of each triangle. If the atom
style in use allows to set a per-atom radius this radius is set to the
largest distance of any of the triangle vertices from its center. The
radius can be adjusted with the *radiussscale* option.
For the *random* style, *N* particles are added to the system at For the *random* style, *N* particles are added to the system at
randomly generated coordinates, which can be useful for generating an randomly generated coordinates, which can be useful for generating an
amorphous system. The particles are created one by one using the amorphous system. The particles are created one by one using the
@ -316,6 +328,12 @@ 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 rule: if your right-hand's thumb points along *R*, then your fingers
wrap around the axis in the direction of rotation. wrap around the axis in the direction of rotation.
The *radiusscale* keyword only applies to the *mesh* style and allows to
adjust the radius of created particles, provided this is supported by
the atom style. Its value is a scaling factor (default: 1.0) that is
applied to the radius inferred from the size of the individual triangles
in the triangle mesh that the particle corresponds to.
The *overlap* keyword only applies to the *random* style. It prevents The *overlap* keyword only applies to the *random* style. It prevents
newly created particles from being created closer than the specified newly created particles from being created closer than the specified
*Doverlap* distance from any other particle. When the particles being *Doverlap* distance from any other particle. When the particles being
@ -424,9 +442,11 @@ values specified in the file read by the :doc:`molecule <molecule>`
command. E.g. the file typically defines bonds (angles,etc) between command. E.g. the file typically defines bonds (angles,etc) between
atoms in the molecule, and can optionally define charges on each atom. atoms in the molecule, and can optionally define charges on each atom.
Note that the *sphere* atom style sets the default particle diameter Note that the *sphere* atom style sets the default particle diameter to
to 1.0 as well as the density. This means the mass for the particle 1.0 as well as the density. This means the mass for the particle is not
is not 1.0, but is PI/6 \* diameter\^3 = 0.5236. 1.0, but is PI/6 \* diameter\^3 = 0.5236. When using the *mesh* style,
the particle diameter is adjusted from the size of the individual
triangles in the triangle mesh.
Note that the *ellipsoid* atom style sets the default particle shape Note that the *ellipsoid* atom style sets the default particle shape
to (0.0 0.0 0.0) and the density to 1.0 which means it is a point to (0.0 0.0 0.0) and the density to 1.0 which means it is a point
@ -460,5 +480,6 @@ Default
The default for the *basis* keyword is that all created atoms are The default for the *basis* keyword is that all created atoms are
assigned the argument *type* as their atom type (when single atoms are assigned the argument *type* as their atom type (when single atoms are
being created). The other defaults are *remap* = no, *rotate* = being created). The other defaults are *remap* = no, *rotate* = random,
random, *overlap* not checked, *maxtry* = 10, and *units* = lattice. *radiussscale* = 1.0, *overlap* not checked, *maxtry* = 10, and *units*
= lattice.