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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute chunk/atom command &mdash; LAMMPS 9 Dec 2015 documentation</title>
<title>compute chunk/atom command &mdash; LAMMPS 11 Dec 2015 documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 9 Dec 2015 documentation" href="index.html"/>
<link rel="top" title="LAMMPS 11 Dec 2015 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -149,17 +149,17 @@ style = <em>bin/1d</em> or <em>bin/2d</em> or <em>bin/3d</em> or <em>bin/sphere<
dim = <em>x</em> or <em>y</em> or <em>z</em>
origin = <em>lower</em> or <em>center</em> or <em>upper</em> or coordinate value (distance units)
delta = thickness of spatial bins in dim (distance units)
<em>bin/sphere</em> args = xorig yorig zorig rmin rmax nrbin
<em>bin/sphere</em> args = xorig yorig zorig rmin rmax nsbin
xorig,yorig,zorig = center point of sphere
srmin,srmax = bin from sphere radius rmin to rmax
nsbin = # of bins between rmin and rmax
<em>bin/cylinder</em> args = dim origin delta c1 c2 rmin rmax nrbin
nsbin = # of spherical shell bins between rmin and rmax
<em>bin/cylinder</em> args = dim origin delta c1 c2 rmin rmax ncbin
dim = <em>x</em> or <em>y</em> or <em>z</em> = axis of cylinder axis
origin = <em>lower</em> or <em>center</em> or <em>upper</em> or coordinate value (distance units)
delta = thickness of spatial bins in dim (distance units)
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
crmin,crmax = bin from cylinder radius rmin to rmax (distance units)
ncbin = # of bins between rmin and rmax
ncbin = # of concentric circle bins between rmin and rmax
<em>type</em> args = none
<em>molecule</em> args = none
<em>compute/fix/variable</em> = c_ID, c_ID[I], f_ID, f_ID[I], v_name with no args
@ -288,9 +288,9 @@ box and an <em>origin</em> of 1.0 means to start layers at the upper &#8220;b&#8
cross &#8220;c&#8221; face of the box. A <em>delta</em> value of 0.1 in <em>reduced</em> units
means there will be 10 layers from 0.0 to 1.0, regardless of the
current size or shape of the simulation box.</p>
<p>The <em>bin/sphere</em> style defines a set of spherical shells around the
origin (<em>xorig</em>,*yorig*,*zorig*), using <em>nsbin</em> shells with radii
equally spaced between <em>srmin</em> and <em>srmax</em>, for effectively a 1d
<p>The <em>bin/sphere</em> style defines a set of spherical shell bins around
the origin (<em>xorig</em>,*yorig*,*zorig*), using <em>nsbin</em> bins with radii
equally spaced between <em>srmin</em> and <em>srmax</em>. This is effectively a 1d
vector of bins. For example, if <em>srmin</em> = 1.0 and <em>srmax</em> = 10.0 and
<em>nsbin</em> = 9, then the first bin spans 1.0 &lt; r &lt; 2.0, and the last bin
spans 9.0 &lt; r 10.0. The geometry of the bins is the same whether the
@ -298,29 +298,30 @@ simulation box is orthogonal or triclinic; i.e. the spherical shells
are not tilted or scaled differently in different dimensions to
transform them into ellipsoidal shells.</p>
<p>The <em>bin/cylinder</em> style defines bins for a cylinder oriented along
the axis <em>dim</em> with the axis position in the other two radial
the axis <em>dim</em> with the axis coordinates in the other two radial
dimensions at (<em>c1</em>,*c2*). For dim = x, c1/c2 = y/z; for dim = y,
c1/c2 = x/z; for dim = z, c1/c2 = x/y. These can be thought of as a
2d array of bins, each of which is a pie-shaped wedge (radial
dimensions) of finite height (along the cylinder axis). The bin size
c1/c2 = x/z; for dim = z, c1/c2 = x/y. This is effectively a 2d array
of bins. The first dimension is along the cylinder axis, the second
dimension is radially outward from the cylinder axis. The bin size
and positions along the cylinder axis are specified by the <em>origin</em>
and <em>delta</em> values, the same as for the <em>bin/1d</em>, <em>bin/2d</em>, and
<em>bin/3d</em> styles. There are <em>ncbin</em> concentric circles in the radial
direction from the cylinder axis with radii equally spaced between
<em>crmin</em> and <em>crmax</em>. For example, if <em>crmin</em> = 1.0 and <em>crmax</em> = 10.0
and <em>ncbin</em> = 9, then the first bin spans 1.0 &lt; r &lt; 2.0, and the last
bin spans 9.0 &lt; r 10.0. The geometry of the bins in the radial
dimensions is the same whether the simulation box is orthogonal or
triclinic; i.e. the circles are not tilted or scaled differently in
the two different dimensions to transform them into ellipses.</p>
<em>bin/3d</em> styles. There are <em>ncbin</em> concentric circle bins in the
radial direction from the cylinder axis with radii equally spaced
between <em>crmin</em> and <em>crmax</em>. For example, if <em>crmin</em> = 1.0 and
<em>crmax</em> = 10.0 and <em>ncbin</em> = 9, then the first bin spans 1.0 &lt; r &lt;
2.0, and the last bin spans 9.0 &lt; r 10.0. The geometry of the bins in
the radial dimensions is the same whether the simulation box is
orthogonal or triclinic; i.e. the concetric circles are not tilted or
scaled differently in the two different dimensions to transform them
into ellipses.</p>
<p>The created bins (and hence the chunk IDs) are numbered consecutively
from 1 to the number of bins = <em>Nchunk</em>. For 2d and 3d bins, the
from 1 to the number of bins = <em>Nchunk</em>. For <em>bin2d</em> and <em>bin3d</em>, the
numbering varies most rapidly in the first dimension (which could be
x, y, or z), next rapidly in the 2nd dimension, and most slowly in the
3rd dimension. For spherical 1d bins, the innermost shell is chunk 1
and the outermost shell is chunk Nchunk = <em>nsbin</em>. For cylindrical
2d bins, the numbering varies most rapidly in the dimension along the
cylinder axis and most slowly in the radial direction.</p>
3rd dimension. For <em>bin/sphere</em>, the bin with smallest radii is chunk
1 and the bni with largest radii is chunk Nchunk = <em>ncbin</em>. For
<em>bin/cylinder</em>, the numbering varies most rapidly in the dimension
along the cylinder axis and most slowly in the radial direction.</p>
<p>Each time this compute is invoked, each atom is mapped to a bin based
on its current position. Note that between reneighboring timesteps,
atoms can move outside the current simulation box. If the box is
@ -718,7 +719,7 @@ the restarted simulation begins.</p>
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