''
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13806 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
2
doc/_static/css/theme.css
vendored
2
doc/_static/css/theme.css
vendored
@ -3743,7 +3743,7 @@ hr {
|
||||
display: block;
|
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height: 1px;
|
||||
border: 0;
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border-top: 1px solid #e1e4e5;
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border-top: 2px solid #e1e4e5;
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margin: 24px 0;
|
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padding: 0;
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||||
}
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|
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@ -137,11 +137,11 @@
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</ul>
|
||||
<pre class="literal-block">
|
||||
<em>id</em> value = <em>yes</em> or <em>no</em>
|
||||
<em>map</em> value = <em>array</em> or <em>hash</em>
|
||||
<em>first</em> value = group-ID = group whose atoms will appear first in internal atom lists
|
||||
<em>sort</em> values = Nfreq binsize
|
||||
Nfreq = sort atoms spatially every this many time steps
|
||||
binsize = bin size for spatial sorting (distance units)
|
||||
<em>map</em> value = <em>array</em> or <em>hash</em>
|
||||
<em>first</em> value = group-ID = group whose atoms will appear first in internal atom lists
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<em>sort</em> values = Nfreq binsize
|
||||
Nfreq = sort atoms spatially every this many time steps
|
||||
binsize = bin size for spatial sorting (distance units)
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||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
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||||
@ -136,13 +136,13 @@
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</ul>
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||||
<pre class="literal-block">
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args = none for any style except <em>body</em> and <em>hybrid</em>
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<em>body</em> args = bstyle bstyle-args
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bstyle = style of body particles
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||||
bstyle-args = additional arguments specific to the bstyle
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see the <a class="reference internal" href="body.html"><em>body</em></a> doc page for details
|
||||
<em>template</em> args = template-ID
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template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
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<em>hybrid</em> args = list of one or more sub-styles, each with their args
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<em>body</em> args = bstyle bstyle-args
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bstyle = style of body particles
|
||||
bstyle-args = additional arguments specific to the bstyle
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||||
see the <a class="reference internal" href="body.html"><em>body</em></a> doc page for details
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||||
<em>template</em> args = template-ID
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template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
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<em>hybrid</em> args = list of one or more sub-styles, each with their args
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||||
</pre>
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||||
<ul class="simple">
|
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<li>accelerated styles (with same args) = <em>angle/cuda</em> or <em>angle/kk</em> or <em>atomic/cuda</em> or <em>atomic/kk</em> or <em>bond/kk</em> or <em>charge/cuda</em> or <em>charge/kk</em> or <em>full/cuda</em> or <em>full/kk</em> or <em>molecular/kk</em></li>
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@ -138,22 +138,22 @@
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</ul>
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<pre class="literal-block">
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<em>x</em> args = <em>uniform</em> or Px-1 numbers between 0 and 1
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<em>uniform</em> = evenly spaced cuts between processors in x dimension
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numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension
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<em>x</em> can be specified together with <em>y</em> or <em>z</em>
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<em>y</em> args = <em>uniform</em> or Py-1 numbers between 0 and 1
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<em>uniform</em> = evenly spaced cuts between processors in y dimension
|
||||
numbers = Py-1 ascending values between 0 and 1, Py - # of processors in y dimension
|
||||
<em>y</em> can be specified together with <em>x</em> or <em>z</em>
|
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<em>z</em> args = <em>uniform</em> or Pz-1 numbers between 0 and 1
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||||
<em>uniform</em> = evenly spaced cuts between processors in z dimension
|
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numbers = Pz-1 ascending values between 0 and 1, Pz - # of processors in z dimension
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||||
<em>z</em> can be specified together with <em>x</em> or <em>y</em>
|
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<em>shift</em> args = dimstr Niter stopthresh
|
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dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
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Niter = # of times to iterate within each dimension of dimstr sequence
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stopthresh = stop balancing when this imbalance threshhold is reached
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<em>rcb</em> args = none
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<em>uniform</em> = evenly spaced cuts between processors in x dimension
|
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numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension
|
||||
<em>x</em> can be specified together with <em>y</em> or <em>z</em>
|
||||
<em>y</em> args = <em>uniform</em> or Py-1 numbers between 0 and 1
|
||||
<em>uniform</em> = evenly spaced cuts between processors in y dimension
|
||||
numbers = Py-1 ascending values between 0 and 1, Py - # of processors in y dimension
|
||||
<em>y</em> can be specified together with <em>x</em> or <em>z</em>
|
||||
<em>z</em> args = <em>uniform</em> or Pz-1 numbers between 0 and 1
|
||||
<em>uniform</em> = evenly spaced cuts between processors in z dimension
|
||||
numbers = Pz-1 ascending values between 0 and 1, Pz - # of processors in z dimension
|
||||
<em>z</em> can be specified together with <em>x</em> or <em>y</em>
|
||||
<em>shift</em> args = dimstr Niter stopthresh
|
||||
dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
|
||||
Niter = # of times to iterate within each dimension of dimstr sequence
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stopthresh = stop balancing when this imbalance threshhold is reached
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||||
<em>rcb</em> args = none
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||||
</pre>
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||||
<ul class="simple">
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||||
<li>zero or more keyword/value pairs may be appended</li>
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@ -161,7 +161,7 @@
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||||
</ul>
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||||
<pre class="literal-block">
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<em>out</em> value = filename
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filename = write each processor's sub-domain to a file
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filename = write each processor's sub-domain to a file
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||||
</pre>
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||||
</div>
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||||
<div class="section" id="examples">
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||||
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||||
@ -136,7 +136,7 @@
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||||
</ul>
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||||
<pre class="literal-block">
|
||||
args = none for any style except <em>hybrid</em>
|
||||
<em>hybrid</em> args = list of one or more styles
|
||||
<em>hybrid</em> args = list of one or more styles
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
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||||
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||||
@ -136,9 +136,9 @@
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</ul>
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||||
<pre class="literal-block">
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||||
<em>p</em> is periodic
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<em>f</em> is non-periodic and fixed
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<em>s</em> is non-periodic and shrink-wrapped
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<em>m</em> is non-periodic and shrink-wrapped with a minimum value
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||||
<em>f</em> is non-periodic and fixed
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<em>s</em> is non-periodic and shrink-wrapped
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<em>m</em> is non-periodic and shrink-wrapped with a minimum value
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||||
</pre>
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||||
</div>
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||||
<div class="section" id="examples">
|
||||
|
||||
@ -169,8 +169,8 @@ parameter = <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>xz</em>
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||||
</ul>
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||||
<pre class="literal-block">
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||||
<em>units</em> value = <em>lattice</em> or <em>box</em>
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||||
lattice = distances are defined in lattice units
|
||||
box = distances are defined in simulation box units
|
||||
lattice = distances are defined in lattice units
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||||
box = distances are defined in simulation box units
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -137,9 +137,9 @@
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||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>mode</em> value = <em>single</em> or <em>multi</em> = communicate atoms within a single or multiple distances
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||||
<em>cutoff</em> value = Rcut (distance units) = communicate atoms from this far away
|
||||
<em>group</em> value = group-ID = only communicate atoms in the group
|
||||
<em>vel</em> value = <em>yes</em> or <em>no</em> = do or do not communicate velocity info with ghost atoms
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||||
<em>cutoff</em> value = Rcut (distance units) = communicate atoms from this far away
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||||
<em>group</em> value = group-ID = only communicate atoms in the group
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||||
<em>vel</em> value = <em>yes</em> or <em>no</em> = do or do not communicate velocity info with ghost atoms
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -139,7 +139,7 @@
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||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>theta</em> = tabulate angles
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||||
<em>eng</em> = tabulate angle energies
|
||||
<em>eng</em> = tabulate angle energies
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -139,7 +139,7 @@
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||||
</ul>
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||||
<pre class="literal-block">
|
||||
<em>type</em> = atom type of the body particle
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||||
<em>integer</em> = 1,2,3,etc = index of fields defined by body style
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<em>integer</em> = 1,2,3,etc = index of fields defined by body style
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -139,8 +139,8 @@
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</ul>
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||||
<pre class="literal-block">
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<em>dist</em> = bond distance
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<em>eng</em> = bond energy
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<em>force</em> = bond force
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<em>eng</em> = bond energy
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||||
<em>force</em> = bond force
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||||
</pre>
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||||
</div>
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||||
<div class="section" id="examples">
|
||||
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||||
@ -164,30 +164,30 @@ style = <em>bin/1d</em> or <em>bin/2d</em> or <em>bin/3d</em> or <em>type</em> o
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||||
</ul>
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||||
<pre class="literal-block">
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||||
<em>region</em> value = region-ID
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||||
region-ID = ID of region atoms must be in to be part of a chunk
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||||
<em>nchunk</em> value = <em>once</em> or <em>every</em>
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||||
once = only compute the number of chunks once
|
||||
every = re-compute the number of chunks whenever invoked
|
||||
<em>limit</em> values = 0 or Nc max or Nc exact
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||||
0 = no limit on the number of chunks
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||||
Nc max = limit number of chunks to be <= Nc
|
||||
Nc exact = set number of chunks to exactly Nc
|
||||
<em>ids</em> value = <em>once</em> or <em>nfreq</em> or <em>every</em>
|
||||
once = assign chunk IDs to atoms only once, they persist thereafter
|
||||
nfreq = assign chunk IDs to atoms only once every Nfreq steps (if invoked by <a class="reference internal" href="fix_ave_chunk.html"><em>fix ave/chunk</em></a> which sets Nfreq)
|
||||
every = assign chunk IDs to atoms whenever invoked
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||||
<em>compress</em> value = <em>yes</em> or <em>no</em>
|
||||
yes = compress chunk IDs to eliminate IDs with no atoms
|
||||
no = do not compress chunk IDs even if some IDs have no atoms
|
||||
<em>discard</em> value = <em>yes</em> or <em>no</em> or <em>mixed</em>
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||||
yes = discard atoms with out-of-range chunk IDs by assigning a chunk ID = 0
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||||
no = keep atoms with out-of-range chunk IDs by assigning a valid chunk ID
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||||
mixed = keep or discard such atoms according to spatial binning rule
|
||||
<em>bound</em> values = x/y/z lo hi
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||||
x/y/z = <em>x</em> or <em>y</em> or <em>z</em> to bound sptial bins in this dimension
|
||||
lo = <em>lower</em> or coordinate value (distance units)
|
||||
hi = <em>upper</em> or coordinate value (distance units)
|
||||
<em>units</em> value = <em>box</em> or <em>lattice</em> or <em>reduced</em>
|
||||
region-ID = ID of region atoms must be in to be part of a chunk
|
||||
<em>nchunk</em> value = <em>once</em> or <em>every</em>
|
||||
once = only compute the number of chunks once
|
||||
every = re-compute the number of chunks whenever invoked
|
||||
<em>limit</em> values = 0 or Nc max or Nc exact
|
||||
0 = no limit on the number of chunks
|
||||
Nc max = limit number of chunks to be <= Nc
|
||||
Nc exact = set number of chunks to exactly Nc
|
||||
<em>ids</em> value = <em>once</em> or <em>nfreq</em> or <em>every</em>
|
||||
once = assign chunk IDs to atoms only once, they persist thereafter
|
||||
nfreq = assign chunk IDs to atoms only once every Nfreq steps (if invoked by <a class="reference internal" href="fix_ave_chunk.html"><em>fix ave/chunk</em></a> which sets Nfreq)
|
||||
every = assign chunk IDs to atoms whenever invoked
|
||||
<em>compress</em> value = <em>yes</em> or <em>no</em>
|
||||
yes = compress chunk IDs to eliminate IDs with no atoms
|
||||
no = do not compress chunk IDs even if some IDs have no atoms
|
||||
<em>discard</em> value = <em>yes</em> or <em>no</em> or <em>mixed</em>
|
||||
yes = discard atoms with out-of-range chunk IDs by assigning a chunk ID = 0
|
||||
no = keep atoms with out-of-range chunk IDs by assigning a valid chunk ID
|
||||
mixed = keep or discard such atoms according to spatial binning rule
|
||||
<em>bound</em> values = x/y/z lo hi
|
||||
x/y/z = <em>x</em> or <em>y</em> or <em>z</em> to bound sptial bins in this dimension
|
||||
lo = <em>lower</em> or coordinate value (distance units)
|
||||
hi = <em>upper</em> or coordinate value (distance units)
|
||||
<em>units</em> value = <em>box</em> or <em>lattice</em> or <em>reduced</em>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -140,14 +140,14 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>pair</em> args = pstyle pparam I J v_delta
|
||||
pstyle = pair style name, e.g. lj/cut
|
||||
pparam = parameter to perturb
|
||||
I,J = type pair(s) to set parameter for
|
||||
v_delta = variable with perturbation to apply (in the units of the parameter)
|
||||
<em>atom</em> args = aparam I v_delta
|
||||
aparam = parameter to perturb
|
||||
I = type to set parameter for
|
||||
v_delta = variable with perturbation to apply (in the units of the parameter)
|
||||
pstyle = pair style name, e.g. lj/cut
|
||||
pparam = parameter to perturb
|
||||
I,J = type pair(s) to set parameter for
|
||||
v_delta = variable with perturbation to apply (in the units of the parameter)
|
||||
<em>atom</em> args = aparam I v_delta
|
||||
aparam = parameter to perturb
|
||||
I = type to set parameter for
|
||||
v_delta = variable with perturbation to apply (in the units of the parameter)
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/value pairs may be appended</li>
|
||||
@ -155,11 +155,11 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>tail</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = ignore tail correction to pair energies (usually small in fep)
|
||||
<em>yes</em> = include tail correction to pair energies
|
||||
<em>volume</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = ignore volume changes (e.g. in <em>NVE</em> or <em>NVT</em> trajectories)
|
||||
<em>yes</em> = include volume changes (e.g. in <em>NpT</em> trajectories)
|
||||
<em>no</em> = ignore tail correction to pair energies (usually small in fep)
|
||||
<em>yes</em> = include tail correction to pair energies
|
||||
<em>volume</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = ignore volume changes (e.g. in <em>NVE</em> or <em>NVT</em> trajectories)
|
||||
<em>yes</em> = include volume changes (e.g. in <em>NpT</em> trajectories)
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -140,8 +140,8 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>pair</em> value = <em>yes</em> or <em>no</em>
|
||||
<em>kspace</em> value = <em>yes</em> or <em>no</em>
|
||||
<em>boundary</em> value = <em>yes</em> or <em>no</em>
|
||||
<em>kspace</em> value = <em>yes</em> or <em>no</em>
|
||||
<em>boundary</em> value = <em>yes</em> or <em>no</em>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -138,11 +138,11 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>extra</em> value = N
|
||||
N = # of extra degrees of freedom to subtract
|
||||
<em>dynamic</em> value = <em>yes</em> or <em>no</em>
|
||||
yes/no = do or do not recompute the number of atoms contributing to the temperature
|
||||
<em>thermo</em> value = <em>yes</em> or <em>no</em>
|
||||
yes/no = do or do not add contributions from fixes to the potential energy
|
||||
N = # of extra degrees of freedom to subtract
|
||||
<em>dynamic</em> value = <em>yes</em> or <em>no</em>
|
||||
yes/no = do or do not recompute the number of atoms contributing to the temperature
|
||||
<em>thermo</em> value = <em>yes</em> or <em>no</em>
|
||||
yes/no = do or do not add contributions from fixes to the potential energy
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -139,10 +139,10 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>dist</em> = pairwise distance
|
||||
<em>eng</em> = pairwise energy
|
||||
<em>force</em> = pairwise force
|
||||
<em>fx</em>,*fy*,*fz* = components of pairwise force
|
||||
<em>pN</em> = pair style specific quantities for allowed N values
|
||||
<em>eng</em> = pairwise energy
|
||||
<em>force</em> = pairwise force
|
||||
<em>fx</em>,*fy*,*fz* = components of pairwise force
|
||||
<em>pN</em> = pair style specific quantities for allowed N values
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -137,73 +137,73 @@
|
||||
<li>input = one or more atom attributes</li>
|
||||
</ul>
|
||||
<div class="highlight-python"><div class="highlight"><pre>possible attributes = id, mol, proc, type, mass,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz, mu,
|
||||
radius, diameter, omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz,
|
||||
shapex,shapey, shapez,
|
||||
quatw, quati, quatj, quatk, tqx, tqy, tqz,
|
||||
end1x, end1y, end1z, end2x, end2y, end2z,
|
||||
corner1x, corner1y, corner1z,
|
||||
corner2x, corner2y, corner2z,
|
||||
corner3x, corner3y, corner3z,
|
||||
nbonds,
|
||||
vfrac, s0,
|
||||
spin, eradius, ervel, erforce,
|
||||
rho, drho, e, de, cv,
|
||||
i_name, d_name
|
||||
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz, mu,
|
||||
radius, diameter, omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz,
|
||||
shapex,shapey, shapez,
|
||||
quatw, quati, quatj, quatk, tqx, tqy, tqz,
|
||||
end1x, end1y, end1z, end2x, end2y, end2z,
|
||||
corner1x, corner1y, corner1z,
|
||||
corner2x, corner2y, corner2z,
|
||||
corner3x, corner3y, corner3z,
|
||||
nbonds,
|
||||
vfrac, s0,
|
||||
spin, eradius, ervel, erforce,
|
||||
rho, drho, e, de, cv,
|
||||
i_name, d_name
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre>id = atom ID
|
||||
mol = molecule ID
|
||||
proc = ID of processor that owns atom
|
||||
type = atom type
|
||||
mass = atom mass
|
||||
x,y,z = unscaled atom coordinates
|
||||
xs,ys,zs = scaled atom coordinates
|
||||
xu,yu,zu = unwrapped atom coordinates
|
||||
ix,iy,iz = box image that the atom is in
|
||||
vx,vy,vz = atom velocities
|
||||
fx,fy,fz = forces on atoms
|
||||
q = atom charge
|
||||
mux,muy,muz = orientation of dipole moment of atom
|
||||
mu = magnitude of dipole moment of atom
|
||||
radius,diameter = radius,diameter of spherical particle
|
||||
omegax,omegay,omegaz = angular velocity of spherical particle
|
||||
angmomx,angmomy,angmomz = angular momentum of aspherical particle
|
||||
shapex,shapey,shapez = 3 diameters of aspherical particle
|
||||
quatw,quati,quatj,quatk = quaternion components for aspherical or body particles
|
||||
tqx,tqy,tqz = torque on finite-size particles
|
||||
end12x, end12y, end12z = end points of line segment
|
||||
corner123x, corner123y, corner123z = corner points of triangle
|
||||
nbonds = number of bonds assigned to an atom
|
||||
mol = molecule ID
|
||||
proc = ID of processor that owns atom
|
||||
type = atom type
|
||||
mass = atom mass
|
||||
x,y,z = unscaled atom coordinates
|
||||
xs,ys,zs = scaled atom coordinates
|
||||
xu,yu,zu = unwrapped atom coordinates
|
||||
ix,iy,iz = box image that the atom is in
|
||||
vx,vy,vz = atom velocities
|
||||
fx,fy,fz = forces on atoms
|
||||
q = atom charge
|
||||
mux,muy,muz = orientation of dipole moment of atom
|
||||
mu = magnitude of dipole moment of atom
|
||||
radius,diameter = radius,diameter of spherical particle
|
||||
omegax,omegay,omegaz = angular velocity of spherical particle
|
||||
angmomx,angmomy,angmomz = angular momentum of aspherical particle
|
||||
shapex,shapey,shapez = 3 diameters of aspherical particle
|
||||
quatw,quati,quatj,quatk = quaternion components for aspherical or body particles
|
||||
tqx,tqy,tqz = torque on finite-size particles
|
||||
end12x, end12y, end12z = end points of line segment
|
||||
corner123x, corner123y, corner123z = corner points of triangle
|
||||
nbonds = number of bonds assigned to an atom
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre>PERI package per-atom properties:
|
||||
vfrac = ???
|
||||
s0 = ???
|
||||
vfrac = ???
|
||||
s0 = ???
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre>USER-EFF and USER-AWPMD package per-atom properties:
|
||||
spin = electron spin
|
||||
eradius = electron radius
|
||||
ervel = electron radial velocity
|
||||
erforce = electron radial force
|
||||
spin = electron spin
|
||||
eradius = electron radius
|
||||
ervel = electron radial velocity
|
||||
erforce = electron radial force
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre>USER-SPH package per-atom properties:
|
||||
rho = ???
|
||||
drho = ???
|
||||
e = ???
|
||||
de = ???
|
||||
cv = ???
|
||||
rho = ???
|
||||
drho = ???
|
||||
e = ???
|
||||
de = ???
|
||||
cv = ???
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
<a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> per-atom properties:
|
||||
i_name = custom integer vector with name
|
||||
d_name = custom integer vector with name
|
||||
i_name = custom integer vector with name
|
||||
d_name = custom integer vector with name
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -138,9 +138,9 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
attributes = count, id, coord1, coord2, coord3
|
||||
count = # of atoms in chunk
|
||||
id = original chunk IDs before compression by <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a>
|
||||
coord123 = coordinates for spatial bins calculated by <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a>
|
||||
count = # of atoms in chunk
|
||||
id = original chunk IDs before compression by <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a>
|
||||
coord123 = coordinates for spatial bins calculated by <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -137,25 +137,25 @@
|
||||
<li>input = one or more attributes</li>
|
||||
</ul>
|
||||
<div class="highlight-python"><div class="highlight"><pre>possible attributes = natom1 natom2 ntype1 ntype2
|
||||
patom1 patom2 ptype1 ptype2
|
||||
batom1 batom2 btype
|
||||
aatom1 aatom2 aatom3 atype
|
||||
datom1 datom2 datom3 dtype
|
||||
iatom1 iatom2 iatom3 itype
|
||||
patom1 patom2 ptype1 ptype2
|
||||
batom1 batom2 btype
|
||||
aatom1 aatom2 aatom3 atype
|
||||
datom1 datom2 datom3 dtype
|
||||
iatom1 iatom2 iatom3 itype
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre>natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff)
|
||||
ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
|
||||
patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff)
|
||||
ptype1, ptype2 = type of 2 atoms in each pair (within force cutoff)
|
||||
batom1, batom2 = IDs of 2 atoms in each bond
|
||||
btype = bond type of each bond
|
||||
aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle
|
||||
atype = angle type of each angle
|
||||
datom1, datom2, datom3, datom4 = IDs of 4 atoms in each dihedral
|
||||
dtype = dihedral type of each dihedral
|
||||
iatom1, iatom2, iatom3, iatom4 = IDs of 4 atoms in each improper
|
||||
itype = improper type of each improper
|
||||
ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
|
||||
patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff)
|
||||
ptype1, ptype2 = type of 2 atoms in each pair (within force cutoff)
|
||||
batom1, batom2 = IDs of 2 atoms in each bond
|
||||
btype = bond type of each bond
|
||||
aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle
|
||||
atype = angle type of each angle
|
||||
datom1, datom2, datom3, datom4 = IDs of 4 atoms in each dihedral
|
||||
dtype = dihedral type of each dihedral
|
||||
iatom1, iatom2, iatom3, iatom4 = IDs of 4 atoms in each improper
|
||||
itype = improper type of each improper
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@ -140,8 +140,8 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>reduce</em> arg = none
|
||||
<em>reduce/region</em> arg = region-ID
|
||||
region-ID = ID of region to use for choosing atoms
|
||||
<em>reduce/region</em> arg = region-ID
|
||||
region-ID = ID of region to use for choosing atoms
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>mode = <em>sum</em> or <em>min</em> or <em>max</em> or <em>ave</em> or <em>sumsq</em> or <em>avesq</em></li>
|
||||
@ -149,11 +149,11 @@
|
||||
<li>input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
|
||||
</ul>
|
||||
<div class="highlight-python"><div class="highlight"><pre>x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
|
||||
c_ID = per-atom or local vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID
|
||||
f_ID = per-atom or local vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
c_ID = per-atom or local vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID
|
||||
f_ID = per-atom or local vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
@ -162,8 +162,8 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>replace</em> args = vec1 vec2
|
||||
vec1 = reduced value from this input vector will be replaced
|
||||
vec2 = replace it with vec1[N] where N is index of max/min value from vec2
|
||||
vec1 = reduced value from this input vector will be replaced
|
||||
vec2 = replace it with vec1[N] where N is index of max/min value from vec2
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -141,18 +141,18 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>Kmax</em> value = Maximum distance explored from reciprocal space origin
|
||||
(inverse length units)
|
||||
<em>Zone</em> values = z1 z2 z3
|
||||
z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all
|
||||
reciprocal space will be meshed up to <em>Kmax</em>
|
||||
<em>dR_Ewald</em> value = Thickness of Ewald sphere slice intercepting
|
||||
reciprocal space (inverse length units)
|
||||
<em>c</em> values = c1 c2 c3
|
||||
c1,c2,c3 = parameters to adjust the spacing of the reciprocal
|
||||
lattice nodes in the h, k, and l directions respectively
|
||||
<em>manual</em> = flag to use manual spacing of reciprocal lattice points
|
||||
based on the values of the <em>c</em> parameters
|
||||
<em>echo</em> = flag to provide extra output for debugging purposes
|
||||
(inverse length units)
|
||||
<em>Zone</em> values = z1 z2 z3
|
||||
z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all
|
||||
reciprocal space will be meshed up to <em>Kmax</em>
|
||||
<em>dR_Ewald</em> value = Thickness of Ewald sphere slice intercepting
|
||||
reciprocal space (inverse length units)
|
||||
<em>c</em> values = c1 c2 c3
|
||||
c1,c2,c3 = parameters to adjust the spacing of the reciprocal
|
||||
lattice nodes in the h, k, and l directions respectively
|
||||
<em>manual</em> = flag to use manual spacing of reciprocal lattice points
|
||||
based on the values of the <em>c</em> parameters
|
||||
<em>echo</em> = flag to provide extra output for debugging purposes
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -140,9 +140,9 @@
|
||||
<li>input = c_ID, c_ID[N], f_ID, f_ID[N]</li>
|
||||
</ul>
|
||||
<div class="highlight-python"><div class="highlight"><pre>c_ID = global vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of global array calculated by a compute with ID
|
||||
f_ID = global vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of global array calculated by a fix with ID
|
||||
c_ID[I] = Ith column of global array calculated by a compute with ID
|
||||
f_ID = global vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of global array calculated by a fix with ID
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@ -152,14 +152,14 @@ compute ID group-ID snav/atom ntypes rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 .
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>diagonal</em> value = <em>0</em> or <em>1</em> or <em>2</em> or <em>3</em>
|
||||
<em>0</em> = all j1, j2, j <= twojmax, j2 <= j1
|
||||
<em>1</em> = subset satisfying j1 == j2
|
||||
<em>2</em> = subset satisfying j1 == j2 == j3
|
||||
<em>3</em> = subset satisfying j2 <= j1 <= j
|
||||
<em>rmin0</em> value = parameter in distance to angle conversion (distance units)
|
||||
<em>switchflag</em> value = <em>0</em> or <em>1</em>
|
||||
<em>0</em> = do not use switching function
|
||||
<em>1</em> = use switching function
|
||||
<em>0</em> = all j1, j2, j <= twojmax, j2 <= j1
|
||||
<em>1</em> = subset satisfying j1 == j2
|
||||
<em>2</em> = subset satisfying j1 == j2 == j3
|
||||
<em>3</em> = subset satisfying j2 <= j1 <= j
|
||||
<em>rmin0</em> value = parameter in distance to angle conversion (distance units)
|
||||
<em>switchflag</em> value = <em>0</em> or <em>1</em>
|
||||
<em>0</em> = do not use switching function
|
||||
<em>1</em> = use switching function
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -139,10 +139,10 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>bias</em> value = bias-ID
|
||||
bias-ID = ID of a temperature compute that removes a velocity bias
|
||||
<em>dof</em> value = <em>all</em> or <em>rotate</em>
|
||||
all = compute temperature of translational and rotational degrees of freedom
|
||||
rotate = compute temperature of just rotational degrees of freedom
|
||||
bias-ID = ID of a temperature compute that removes a velocity bias
|
||||
<em>dof</em> value = <em>all</em> or <em>rotate</em>
|
||||
all = compute temperature of translational and rotational degrees of freedom
|
||||
rotate = compute temperature of just rotational degrees of freedom
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -139,8 +139,8 @@
|
||||
<li>value = <em>temp</em> or <em>kecom</em> or <em>internal</em></li>
|
||||
</ul>
|
||||
<div class="highlight-python"><div class="highlight"><pre>temp = temperature of each chunk
|
||||
kecom = kinetic energy of each chunk based on velocity of center of mass
|
||||
internal = internal kinetic energy of each chunk
|
||||
kecom = kinetic energy of each chunk based on velocity of center of mass
|
||||
internal = internal kinetic energy of each chunk
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
@ -149,14 +149,14 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>com</em> value = <em>yes</em> or <em>no</em>
|
||||
yes = subtract center-of-mass velocity from each chunk before calculating temperature
|
||||
no = do not subtract center-of-mass velocity
|
||||
<em>bias</em> value = bias-ID
|
||||
bias-ID = ID of a temperature compute that removes a velocity bias
|
||||
<em>adof</em> value = dof_per_atom
|
||||
dof_per_atom = define this many degrees-of-freedom per atom
|
||||
<em>cdof</em> value = dof_per_chunk
|
||||
dof_per_chunk = define this many degrees-of-freedom per chunk
|
||||
yes = subtract center-of-mass velocity from each chunk before calculating temperature
|
||||
no = do not subtract center-of-mass velocity
|
||||
<em>bias</em> value = bias-ID
|
||||
bias-ID = ID of a temperature compute that removes a velocity bias
|
||||
<em>adof</em> value = dof_per_atom
|
||||
dof_per_atom = define this many degrees-of-freedom per atom
|
||||
<em>cdof</em> value = dof_per_chunk
|
||||
dof_per_chunk = define this many degrees-of-freedom per chunk
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -139,13 +139,13 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>x</em> arg = Nx
|
||||
<em>y</em> arg = Ny
|
||||
<em>z</em> arg = Nz
|
||||
<em>xy</em> args = Nx Ny
|
||||
<em>yz</em> args = Ny Nz
|
||||
<em>xz</em> args = Nx Nz
|
||||
<em>xyz</em> args = Nx Ny Nz
|
||||
Nx,Ny,Nz = number of velocity bins in x,y,z dimensions
|
||||
<em>y</em> arg = Ny
|
||||
<em>z</em> arg = Nz
|
||||
<em>xy</em> args = Nx Ny
|
||||
<em>yz</em> args = Ny Nz
|
||||
<em>xz</em> args = Nx Nz
|
||||
<em>xyz</em> args = Nx Ny Nz
|
||||
Nx,Ny,Nz = number of velocity bins in x,y,z dimensions
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/value pairs may be appended</li>
|
||||
|
||||
@ -139,10 +139,10 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>bias</em> value = bias-ID
|
||||
bias-ID = ID of a temperature compute that removes a velocity bias
|
||||
<em>dof</em> value = <em>all</em> or <em>rotate</em>
|
||||
all = compute temperature of translational and rotational degrees of freedom
|
||||
rotate = compute temperature of just rotational degrees of freedom
|
||||
bias-ID = ID of a temperature compute that removes a velocity bias
|
||||
<em>dof</em> value = <em>all</em> or <em>rotate</em>
|
||||
all = compute temperature of translational and rotational degrees of freedom
|
||||
rotate = compute temperature of just rotational degrees of freedom
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -139,17 +139,17 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
pair style args = atype v_name1 v_name2
|
||||
atype = atom type (see asterisk form below)
|
||||
v_name1 = variable with name1 that is energy scale factor and function of lambda
|
||||
v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
|
||||
<em>tail</em> args = atype v_name1 v_name2
|
||||
atype = atom type (see asterisk form below)
|
||||
v_name1 = variable with name1 that is energy tail correction scale factor and function of lambda
|
||||
v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
|
||||
<em>kspace</em> args = atype v_name1 v_name2
|
||||
atype = atom type (see asterisk form below)
|
||||
v_name1 = variable with name1 that is K-Space scale factor and function of lambda
|
||||
v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
|
||||
atype = atom type (see asterisk form below)
|
||||
v_name1 = variable with name1 that is energy scale factor and function of lambda
|
||||
v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
|
||||
<em>tail</em> args = atype v_name1 v_name2
|
||||
atype = atom type (see asterisk form below)
|
||||
v_name1 = variable with name1 that is energy tail correction scale factor and function of lambda
|
||||
v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
|
||||
<em>kspace</em> args = atype v_name1 v_name2
|
||||
atype = atom type (see asterisk form below)
|
||||
v_name1 = variable with name1 that is K-Space scale factor and function of lambda
|
||||
v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -139,18 +139,18 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>only_group</em> = no arg
|
||||
<em>occupation</em> = no arg
|
||||
<em>surface</em> arg = sgroup-ID
|
||||
sgroup-ID = compute the dividing surface between group-ID and sgroup-ID
|
||||
this keyword adds a third column to the compute output
|
||||
<em>radius</em> arg = v_r
|
||||
v_r = radius atom style variable for a poly-disperse Voronoi tessellation
|
||||
<em>edge_histo</em> arg = maxedge
|
||||
maxedge = maximum number of Voronoi cell edges to be accounted in the histogram
|
||||
<em>edge_threshold</em> arg = minlength
|
||||
minlength = minimum length for an edge to be counted
|
||||
<em>face_threshold</em> arg = minarea
|
||||
minarea = minimum area for a face to be counted
|
||||
<em>occupation</em> = no arg
|
||||
<em>surface</em> arg = sgroup-ID
|
||||
sgroup-ID = compute the dividing surface between group-ID and sgroup-ID
|
||||
this keyword adds a third column to the compute output
|
||||
<em>radius</em> arg = v_r
|
||||
v_r = radius atom style variable for a poly-disperse Voronoi tessellation
|
||||
<em>edge_histo</em> arg = maxedge
|
||||
maxedge = maximum number of Voronoi cell edges to be accounted in the histogram
|
||||
<em>edge_threshold</em> arg = minlength
|
||||
minlength = minimum length for an edge to be counted
|
||||
<em>face_threshold</em> arg = minarea
|
||||
minarea = minimum area for a face to be counted
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -141,16 +141,16 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>2Theta</em> values = Min2Theta Max2Theta
|
||||
Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore
|
||||
(radians or degrees)
|
||||
<em>c</em> values = c1 c2 c3
|
||||
c1,c2,c3 = parameters to adjust the spacing of the reciprocal
|
||||
lattice nodes in the h, k, and l directions respectively
|
||||
<em>LP</em> value = switch to apply Lorentz-polarization factor
|
||||
0/1 = off/on
|
||||
<em>manual</em> = flag to use manual spacing of reciprocal lattice points
|
||||
based on the values of the <em>c</em> parameters
|
||||
<em>echo</em> = flag to provide extra output for debugging purposes
|
||||
Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore
|
||||
(radians or degrees)
|
||||
<em>c</em> values = c1 c2 c3
|
||||
c1,c2,c3 = parameters to adjust the spacing of the reciprocal
|
||||
lattice nodes in the h, k, and l directions respectively
|
||||
<em>LP</em> value = switch to apply Lorentz-polarization factor
|
||||
0/1 = off/on
|
||||
<em>manual</em> = flag to use manual spacing of reciprocal lattice points
|
||||
based on the values of the <em>c</em> parameters
|
||||
<em>echo</em> = flag to provide extra output for debugging purposes
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -137,14 +137,14 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>box</em> args = none
|
||||
<em>region</em> args = region-ID
|
||||
region-ID = particles will only be created if contained in the region
|
||||
<em>single</em> args = x y z
|
||||
x,y,z = coordinates of a single particle (distance units)
|
||||
<em>random</em> args = N seed region-ID
|
||||
N = number of particles to create
|
||||
seed = random # seed (positive integer)
|
||||
region-ID = create atoms within this region, use NULL for entire simulation box
|
||||
<em>region</em> args = region-ID
|
||||
region-ID = particles will only be created if contained in the region
|
||||
<em>single</em> args = x y z
|
||||
x,y,z = coordinates of a single particle (distance units)
|
||||
<em>random</em> args = N seed region-ID
|
||||
N = number of particles to create
|
||||
seed = random # seed (positive integer)
|
||||
region-ID = create atoms within this region, use NULL for entire simulation box
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/value pairs may be appended</li>
|
||||
@ -152,22 +152,22 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>mol</em> value = template-ID seed
|
||||
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
|
||||
seed = random # seed (positive integer)
|
||||
<em>basis</em> values = M itype
|
||||
M = which basis atom
|
||||
itype = atom type (1-N) to assign to this basis atom
|
||||
<em>remap</em> value = <em>yes</em> or <em>no</em>
|
||||
<em>var</em> value = name = variable name to evaluate for test of atom creation
|
||||
<em>set</em> values = dim vname
|
||||
dim = <em>x</em> or <em>y</em> or <em>z</em>
|
||||
name = name of variable to set with x,y,z atom position
|
||||
<em>rotate</em> values = Rx Ry Rz theta
|
||||
Rx,Ry,Rz = rotation vector for single molecule
|
||||
theta = rotation angle for single molecule (degrees)
|
||||
<em>units</em> value = <em>lattice</em> or <em>box</em>
|
||||
<em>lattice</em> = the geometry is defined in lattice units
|
||||
<em>box</em> = the geometry is defined in simulation box units
|
||||
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
|
||||
seed = random # seed (positive integer)
|
||||
<em>basis</em> values = M itype
|
||||
M = which basis atom
|
||||
itype = atom type (1-N) to assign to this basis atom
|
||||
<em>remap</em> value = <em>yes</em> or <em>no</em>
|
||||
<em>var</em> value = name = variable name to evaluate for test of atom creation
|
||||
<em>set</em> values = dim vname
|
||||
dim = <em>x</em> or <em>y</em> or <em>z</em>
|
||||
name = name of variable to set with x,y,z atom position
|
||||
<em>rotate</em> values = Rx Ry Rz theta
|
||||
Rx,Ry,Rz = rotation vector for single molecule
|
||||
theta = rotation angle for single molecule (degrees)
|
||||
<em>units</em> value = <em>lattice</em> or <em>box</em>
|
||||
<em>lattice</em> = the geometry is defined in lattice units
|
||||
<em>box</em> = the geometry is defined in simulation box units
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -139,14 +139,14 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>bond/types</em> value = # of bond types
|
||||
<em>angle/types</em> value = # of angle types
|
||||
<em>dihedral/types</em> value = # of dihedral types
|
||||
<em>improper/types</em> value = # of improper types
|
||||
<em>extra/bond/per/atom</em> value = # of bonds per atom
|
||||
<em>extra/angle/per/atom</em> value = # of angles per atom
|
||||
<em>extra/dihedral/per/atom</em> value = # of dihedrals per atom
|
||||
<em>extra/improper/per/atom</em> value = # of impropers per atom
|
||||
<em>extra/special/per/atom</em> value = # of special neighbors per atom
|
||||
<em>angle/types</em> value = # of angle types
|
||||
<em>dihedral/types</em> value = # of dihedral types
|
||||
<em>improper/types</em> value = # of improper types
|
||||
<em>extra/bond/per/atom</em> value = # of bonds per atom
|
||||
<em>extra/angle/per/atom</em> value = # of angles per atom
|
||||
<em>extra/dihedral/per/atom</em> value = # of dihedrals per atom
|
||||
<em>extra/improper/per/atom</em> value = # of impropers per atom
|
||||
<em>extra/special/per/atom</em> value = # of special neighbors per atom
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -136,15 +136,15 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>group</em> args = group-ID
|
||||
<em>region</em> args = region-ID
|
||||
<em>overlap</em> args = cutoff group1-ID group2-ID
|
||||
cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
|
||||
group1-ID = one atom in pair must be in this group
|
||||
group2-ID = other atom in pair must be in this group
|
||||
<em>porosity</em> args = region-ID fraction seed
|
||||
region-ID = region within which to perform deletions
|
||||
fraction = delete this fraction of atoms
|
||||
seed = random number seed (positive integer)
|
||||
<em>region</em> args = region-ID
|
||||
<em>overlap</em> args = cutoff group1-ID group2-ID
|
||||
cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
|
||||
group1-ID = one atom in pair must be in this group
|
||||
group2-ID = other atom in pair must be in this group
|
||||
<em>porosity</em> args = region-ID fraction seed
|
||||
region-ID = region within which to perform deletions
|
||||
fraction = delete this fraction of atoms
|
||||
seed = random number seed (positive integer)
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/value pairs may be appended</li>
|
||||
@ -152,8 +152,8 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>compress</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>bond</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>mol</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>bond</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>mol</em> value = <em>no</em> or <em>yes</em>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -143,12 +143,12 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>multi</em> arg = none
|
||||
<em>atom</em> arg = an atom type or range of types (see below)
|
||||
<em>bond</em> arg = a bond type or range of types (see below)
|
||||
<em>angle</em> arg = an angle type or range of types (see below)
|
||||
<em>dihedral</em> arg = a dihedral type or range of types (see below)
|
||||
<em>improper</em> arg = an improper type or range of types (see below)
|
||||
<em>stats</em> arg = none
|
||||
<em>atom</em> arg = an atom type or range of types (see below)
|
||||
<em>bond</em> arg = a bond type or range of types (see below)
|
||||
<em>angle</em> arg = an angle type or range of types (see below)
|
||||
<em>dihedral</em> arg = a dihedral type or range of types (see below)
|
||||
<em>improper</em> arg = an improper type or range of types (see below)
|
||||
<em>stats</em> arg = none
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keywords may be appended</li>
|
||||
|
||||
@ -137,26 +137,26 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>move</em> args = delx dely delz
|
||||
delx,dely,delz = distance to displace in each dimension (distance units)
|
||||
<em>ramp</em> args = ddim dlo dhi dim clo chi
|
||||
ddim = <em>x</em> or <em>y</em> or <em>z</em>
|
||||
dlo,dhi = displacement distance between dlo and dhi (distance units)
|
||||
dim = <em>x</em> or <em>y</em> or <em>z</em>
|
||||
clo,chi = lower and upper bound of domain to displace (distance units)
|
||||
<em>random</em> args = dx dy dz seed
|
||||
dx,dy,dz = random displacement magnitude in each dimension (distance units)
|
||||
seed = random # seed (positive integer)
|
||||
<em>rotate</em> args = Px Py Pz Rx Ry Rz theta
|
||||
Px,Py,Pz = origin point of axis of rotation (distance units)
|
||||
Rx,Ry,Rz = axis of rotation vector
|
||||
theta = angle of rotation (degrees)
|
||||
delx,dely,delz = distance to displace in each dimension (distance units)
|
||||
<em>ramp</em> args = ddim dlo dhi dim clo chi
|
||||
ddim = <em>x</em> or <em>y</em> or <em>z</em>
|
||||
dlo,dhi = displacement distance between dlo and dhi (distance units)
|
||||
dim = <em>x</em> or <em>y</em> or <em>z</em>
|
||||
clo,chi = lower and upper bound of domain to displace (distance units)
|
||||
<em>random</em> args = dx dy dz seed
|
||||
dx,dy,dz = random displacement magnitude in each dimension (distance units)
|
||||
seed = random # seed (positive integer)
|
||||
<em>rotate</em> args = Px Py Pz Rx Ry Rz theta
|
||||
Px,Py,Pz = origin point of axis of rotation (distance units)
|
||||
Rx,Ry,Rz = axis of rotation vector
|
||||
theta = angle of rotation (degrees)
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/value pairs may be appended</li>
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
keyword = <em>units</em>
|
||||
value = <em>box</em> or <em>lattice</em>
|
||||
value = <em>box</em> or <em>lattice</em>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -150,12 +150,12 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>atom</em> args = none
|
||||
<em>atom/mpiio</em> args = none
|
||||
<em>cfg</em> args = same as <em>custom</em> args, see below
|
||||
<em>cfg/mpiio</em> args = same as <em>custom</em> args, see below
|
||||
<em>dcd</em> args = none
|
||||
<em>xtc</em> args = none
|
||||
<em>xyz</em> args = none
|
||||
<em>atom/mpiio</em> args = none
|
||||
<em>cfg</em> args = same as <em>custom</em> args, see below
|
||||
<em>cfg/mpiio</em> args = same as <em>custom</em> args, see below
|
||||
<em>dcd</em> args = none
|
||||
<em>xtc</em> args = none
|
||||
<em>xyz</em> args = none
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
<em>xyz/mpiio</em> args = none
|
||||
@ -171,53 +171,53 @@
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
<em>local</em> args = list of local attributes
|
||||
possible attributes = index, c_ID, c_ID[N], f_ID, f_ID[N]
|
||||
index = enumeration of local values
|
||||
c_ID = local vector calculated by a compute with ID
|
||||
c_ID[N] = Nth column of local array calculated by a compute with ID
|
||||
f_ID = local vector calculated by a fix with ID
|
||||
f_ID[N] = Nth column of local array calculated by a fix with ID
|
||||
possible attributes = index, c_ID, c_ID[N], f_ID, f_ID[N]
|
||||
index = enumeration of local values
|
||||
c_ID = local vector calculated by a compute with ID
|
||||
c_ID[N] = Nth column of local array calculated by a compute with ID
|
||||
f_ID = local vector calculated by a fix with ID
|
||||
f_ID[N] = Nth column of local array calculated by a fix with ID
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
<em>custom</em> or <em>custom/mpiio</em> args = list of atom attributes
|
||||
possible attributes = id, mol, proc, procp1, type, element, mass,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu,
|
||||
xsu, ysu, zsu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz, mu,
|
||||
radius, diameter, omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz, tqx, tqy, tqz,
|
||||
c_ID, c_ID[N], f_ID, f_ID[N], v_name
|
||||
possible attributes = id, mol, proc, procp1, type, element, mass,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu,
|
||||
xsu, ysu, zsu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz, mu,
|
||||
radius, diameter, omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz, tqx, tqy, tqz,
|
||||
c_ID, c_ID[N], f_ID, f_ID[N], v_name
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
id = atom ID
|
||||
mol = molecule ID
|
||||
proc = ID of processor that owns atom
|
||||
procp1 = ID+1 of processor that owns atom
|
||||
type = atom type
|
||||
element = name of atom element, as defined by <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> command
|
||||
mass = atom mass
|
||||
x,y,z = unscaled atom coordinates
|
||||
xs,ys,zs = scaled atom coordinates
|
||||
xu,yu,zu = unwrapped atom coordinates
|
||||
xsu,ysu,zsu = scaled unwrapped atom coordinates
|
||||
ix,iy,iz = box image that the atom is in
|
||||
vx,vy,vz = atom velocities
|
||||
fx,fy,fz = forces on atoms
|
||||
q = atom charge
|
||||
mux,muy,muz = orientation of dipole moment of atom
|
||||
mu = magnitude of dipole moment of atom
|
||||
radius,diameter = radius,diameter of spherical particle
|
||||
omegax,omegay,omegaz = angular velocity of spherical particle
|
||||
angmomx,angmomy,angmomz = angular momentum of aspherical particle
|
||||
tqx,tqy,tqz = torque on finite-size particles
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID[N] = Nth column of per-atom array calculated by a compute with ID
|
||||
f_ID = per-atom vector calculated by a fix with ID
|
||||
f_ID[N] = Nth column of per-atom array calculated by a fix with ID
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
d_name = per-atom floating point vector with name, managed by fix property/atom
|
||||
i_name = per-atom integer vector with name, managed by fix property/atom
|
||||
mol = molecule ID
|
||||
proc = ID of processor that owns atom
|
||||
procp1 = ID+1 of processor that owns atom
|
||||
type = atom type
|
||||
element = name of atom element, as defined by <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> command
|
||||
mass = atom mass
|
||||
x,y,z = unscaled atom coordinates
|
||||
xs,ys,zs = scaled atom coordinates
|
||||
xu,yu,zu = unwrapped atom coordinates
|
||||
xsu,ysu,zsu = scaled unwrapped atom coordinates
|
||||
ix,iy,iz = box image that the atom is in
|
||||
vx,vy,vz = atom velocities
|
||||
fx,fy,fz = forces on atoms
|
||||
q = atom charge
|
||||
mux,muy,muz = orientation of dipole moment of atom
|
||||
mu = magnitude of dipole moment of atom
|
||||
radius,diameter = radius,diameter of spherical particle
|
||||
omegax,omegay,omegaz = angular velocity of spherical particle
|
||||
angmomx,angmomy,angmomz = angular momentum of aspherical particle
|
||||
tqx,tqy,tqz = torque on finite-size particles
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID[N] = Nth column of per-atom array calculated by a compute with ID
|
||||
f_ID = per-atom vector calculated by a fix with ID
|
||||
f_ID[N] = Nth column of per-atom array calculated by a fix with ID
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
d_name = per-atom floating point vector with name, managed by fix property/atom
|
||||
i_name = per-atom integer vector with name, managed by fix property/atom
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -147,47 +147,47 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>adiam</em> value = number = numeric value for atom diameter (distance units)
|
||||
<em>atom</em> = yes/no = do or do not draw atoms
|
||||
<em>bond</em> values = color width = color and width of bonds
|
||||
color = <em>atom</em> or <em>type</em> or <em>none</em>
|
||||
width = number or <em>atom</em> or <em>type</em> or <em>none</em>
|
||||
number = numeric value for bond width (distance units)
|
||||
<em>size</em> values = width height = size of images
|
||||
width = width of image in # of pixels
|
||||
height = height of image in # of pixels
|
||||
<em>view</em> values = theta phi = view of simulation box
|
||||
theta = view angle from +z axis (degrees)
|
||||
phi = azimuthal view angle (degrees)
|
||||
theta or phi can be a variable (see below)
|
||||
<em>center</em> values = flag Cx Cy Cz = center point of image
|
||||
flag = "s" for static, "d" for dynamic
|
||||
Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
|
||||
Cx,Cy,Cz can be variables (see below)
|
||||
<em>up</em> values = Ux Uy Uz = direction that is "up" in image
|
||||
Ux,Uy,Uz = components of up vector
|
||||
Ux,Uy,Uz can be variables (see below)
|
||||
<em>zoom</em> value = zfactor = size that simulation box appears in image
|
||||
zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
|
||||
zfactor can be a variable (see below)
|
||||
<em>persp</em> value = pfactor = amount of "perspective" in image
|
||||
pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
|
||||
pfactor can be a variable (see below)
|
||||
<em>box</em> values = yes/no diam = draw outline of simulation box
|
||||
yes/no = do or do not draw simulation box lines
|
||||
diam = diameter of box lines as fraction of shortest box length
|
||||
<em>axes</em> values = yes/no length diam = draw xyz axes
|
||||
yes/no = do or do not draw xyz axes lines next to simulation box
|
||||
length = length of axes lines as fraction of respective box lengths
|
||||
diam = diameter of axes lines as fraction of shortest box length
|
||||
<em>subbox</em> values = yes/no diam = draw outline of processor sub-domains
|
||||
yes/no = do or do not draw sub-domain lines
|
||||
diam = diameter of sub-domain lines as fraction of shortest box length
|
||||
<em>shiny</em> value = sfactor = shinyness of spheres and cylinders
|
||||
sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
|
||||
<em>ssao</em> value = yes/no seed dfactor = SSAO depth shading
|
||||
yes/no = turn depth shading on/off
|
||||
seed = random # seed (positive integer)
|
||||
dfactor = strength of shading from 0.0 to 1.0
|
||||
<em>atom</em> = yes/no = do or do not draw atoms
|
||||
<em>bond</em> values = color width = color and width of bonds
|
||||
color = <em>atom</em> or <em>type</em> or <em>none</em>
|
||||
width = number or <em>atom</em> or <em>type</em> or <em>none</em>
|
||||
number = numeric value for bond width (distance units)
|
||||
<em>size</em> values = width height = size of images
|
||||
width = width of image in # of pixels
|
||||
height = height of image in # of pixels
|
||||
<em>view</em> values = theta phi = view of simulation box
|
||||
theta = view angle from +z axis (degrees)
|
||||
phi = azimuthal view angle (degrees)
|
||||
theta or phi can be a variable (see below)
|
||||
<em>center</em> values = flag Cx Cy Cz = center point of image
|
||||
flag = "s" for static, "d" for dynamic
|
||||
Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
|
||||
Cx,Cy,Cz can be variables (see below)
|
||||
<em>up</em> values = Ux Uy Uz = direction that is "up" in image
|
||||
Ux,Uy,Uz = components of up vector
|
||||
Ux,Uy,Uz can be variables (see below)
|
||||
<em>zoom</em> value = zfactor = size that simulation box appears in image
|
||||
zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
|
||||
zfactor can be a variable (see below)
|
||||
<em>persp</em> value = pfactor = amount of "perspective" in image
|
||||
pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
|
||||
pfactor can be a variable (see below)
|
||||
<em>box</em> values = yes/no diam = draw outline of simulation box
|
||||
yes/no = do or do not draw simulation box lines
|
||||
diam = diameter of box lines as fraction of shortest box length
|
||||
<em>axes</em> values = yes/no length diam = draw xyz axes
|
||||
yes/no = do or do not draw xyz axes lines next to simulation box
|
||||
length = length of axes lines as fraction of respective box lengths
|
||||
diam = diameter of axes lines as fraction of shortest box length
|
||||
<em>subbox</em> values = yes/no diam = draw outline of processor sub-domains
|
||||
yes/no = do or do not draw sub-domain lines
|
||||
diam = diameter of sub-domain lines as fraction of shortest box length
|
||||
<em>shiny</em> value = sfactor = shinyness of spheres and cylinders
|
||||
sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
|
||||
<em>ssao</em> value = yes/no seed dfactor = SSAO depth shading
|
||||
yes/no = turn depth shading on/off
|
||||
seed = random # seed (positive integer)
|
||||
dfactor = strength of shading from 0.0 to 1.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -139,39 +139,39 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>append</em> arg = <em>yes</em> or <em>no</em>
|
||||
<em>buffer</em> arg = <em>yes</em> or <em>no</em>
|
||||
<em>element</em> args = E1 E2 ... EN, where N = # of atom types
|
||||
E1,...,EN = element name, e.g. C or Fe or Ga
|
||||
<em>every</em> arg = N
|
||||
N = dump every this many timesteps
|
||||
N can be a variable (see below)
|
||||
<em>fileper</em> arg = Np
|
||||
Np = write one file for every this many processors
|
||||
<em>first</em> arg = <em>yes</em> or <em>no</em>
|
||||
<em>format</em> arg = C-style format string for one line of output
|
||||
<em>flush</em> arg = <em>yes</em> or <em>no</em>
|
||||
<em>image</em> arg = <em>yes</em> or <em>no</em>
|
||||
<em>label</em> arg = string
|
||||
string = character string (e.g. BONDS) to use in header of dump local file
|
||||
<em>nfile</em> arg = Nf
|
||||
Nf = write this many files, one from each of Nf processors
|
||||
<em>pad</em> arg = Nchar = # of characters to convert timestep to
|
||||
<em>precision</em> arg = power-of-10 value from 10 to 1000000
|
||||
<em>region</em> arg = region-ID or "none"
|
||||
<em>scale</em> arg = <em>yes</em> or <em>no</em>
|
||||
<em>sfactor</em> arg = coordinate scaling factor (> 0.0)
|
||||
<em>tfactor</em> arg = time scaling factor (> 0.0)
|
||||
<em>sort</em> arg = <em>off</em> or <em>id</em> or N or -N
|
||||
off = no sorting of per-atom lines within a snapshot
|
||||
id = sort per-atom lines by atom ID
|
||||
N = sort per-atom lines in ascending order by the Nth column
|
||||
-N = sort per-atom lines in descending order by the Nth column
|
||||
<em>thresh</em> args = attribute operation value
|
||||
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
|
||||
operation = "<" or "<=" or ">" or ">=" or "==" or "!="
|
||||
value = numeric value to compare to
|
||||
these 3 args can be replaced by the word "none" to turn off thresholding
|
||||
<em>unwrap</em> arg = <em>yes</em> or <em>no</em>
|
||||
<em>buffer</em> arg = <em>yes</em> or <em>no</em>
|
||||
<em>element</em> args = E1 E2 ... EN, where N = # of atom types
|
||||
E1,...,EN = element name, e.g. C or Fe or Ga
|
||||
<em>every</em> arg = N
|
||||
N = dump every this many timesteps
|
||||
N can be a variable (see below)
|
||||
<em>fileper</em> arg = Np
|
||||
Np = write one file for every this many processors
|
||||
<em>first</em> arg = <em>yes</em> or <em>no</em>
|
||||
<em>format</em> arg = C-style format string for one line of output
|
||||
<em>flush</em> arg = <em>yes</em> or <em>no</em>
|
||||
<em>image</em> arg = <em>yes</em> or <em>no</em>
|
||||
<em>label</em> arg = string
|
||||
string = character string (e.g. BONDS) to use in header of dump local file
|
||||
<em>nfile</em> arg = Nf
|
||||
Nf = write this many files, one from each of Nf processors
|
||||
<em>pad</em> arg = Nchar = # of characters to convert timestep to
|
||||
<em>precision</em> arg = power-of-10 value from 10 to 1000000
|
||||
<em>region</em> arg = region-ID or "none"
|
||||
<em>scale</em> arg = <em>yes</em> or <em>no</em>
|
||||
<em>sfactor</em> arg = coordinate scaling factor (> 0.0)
|
||||
<em>tfactor</em> arg = time scaling factor (> 0.0)
|
||||
<em>sort</em> arg = <em>off</em> or <em>id</em> or N or -N
|
||||
off = no sorting of per-atom lines within a snapshot
|
||||
id = sort per-atom lines by atom ID
|
||||
N = sort per-atom lines in ascending order by the Nth column
|
||||
-N = sort per-atom lines in descending order by the Nth column
|
||||
<em>thresh</em> args = attribute operation value
|
||||
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
|
||||
operation = "<" or "<=" or ">" or ">=" or "==" or "!="
|
||||
value = numeric value to compare to
|
||||
these 3 args can be replaced by the word "none" to turn off thresholding
|
||||
<em>unwrap</em> arg = <em>yes</em> or <em>no</em>
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>these keywords apply only to the <em>image</em> and <em>movie</em> <a class="reference internal" href="dump_image.html"><em>styles</em></a></li>
|
||||
@ -179,48 +179,48 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>acolor</em> args = type color
|
||||
type = atom type or range of types (see below)
|
||||
color = name of color or color1/color2/...
|
||||
<em>adiam</em> args = type diam
|
||||
type = atom type or range of types (see below)
|
||||
diam = diameter of atoms of that type (distance units)
|
||||
<em>amap</em> args = lo hi style delta N entry1 entry2 ... entryN
|
||||
lo = number or <em>min</em> = lower bound of range of color map
|
||||
hi = number or <em>max</em> = upper bound of range of color map
|
||||
style = 2 letters = "c" or "d" or "s" plus "a" or "f"
|
||||
"c" for continuous
|
||||
"d" for discrete
|
||||
"s" for sequential
|
||||
"a" for absolute
|
||||
"f" for fractional
|
||||
delta = binsize (only used for style "s", otherwise ignored)
|
||||
binsize = range is divided into bins of this width
|
||||
N = # of subsequent entries
|
||||
entry = value color (for continuous style)
|
||||
value = number or <em>min</em> or <em>max</em> = single value within range
|
||||
color = name of color used for that value
|
||||
entry = lo hi color (for discrete style)
|
||||
lo/hi = number or <em>min</em> or <em>max</em> = lower/upper bound of subset of range
|
||||
color = name of color used for that subset of values
|
||||
entry = color (for sequential style)
|
||||
color = name of color used for a bin of values
|
||||
<em>backcolor</em> arg = color
|
||||
color = name of color for background
|
||||
<em>bcolor</em> args = type color
|
||||
type = bond type or range of types (see below)
|
||||
color = name of color or color1/color2/...
|
||||
<em>bdiam</em> args = type diam
|
||||
type = bond type or range of types (see below)
|
||||
diam = diameter of bonds of that type (distance units)
|
||||
<em>boxcolor</em> arg = color
|
||||
color = name of color for simulation box lines and processor sub-domain lines
|
||||
<em>color</em> args = name R G B
|
||||
name = name of color
|
||||
R,G,B = red/green/blue numeric values from 0.0 to 1.0
|
||||
<em>bitrate</em> arg = rate
|
||||
rate = target bitrate for movie in kbps
|
||||
<em>framerate</em> arg = fps
|
||||
fps = frames per second for movie
|
||||
type = atom type or range of types (see below)
|
||||
color = name of color or color1/color2/...
|
||||
<em>adiam</em> args = type diam
|
||||
type = atom type or range of types (see below)
|
||||
diam = diameter of atoms of that type (distance units)
|
||||
<em>amap</em> args = lo hi style delta N entry1 entry2 ... entryN
|
||||
lo = number or <em>min</em> = lower bound of range of color map
|
||||
hi = number or <em>max</em> = upper bound of range of color map
|
||||
style = 2 letters = "c" or "d" or "s" plus "a" or "f"
|
||||
"c" for continuous
|
||||
"d" for discrete
|
||||
"s" for sequential
|
||||
"a" for absolute
|
||||
"f" for fractional
|
||||
delta = binsize (only used for style "s", otherwise ignored)
|
||||
binsize = range is divided into bins of this width
|
||||
N = # of subsequent entries
|
||||
entry = value color (for continuous style)
|
||||
value = number or <em>min</em> or <em>max</em> = single value within range
|
||||
color = name of color used for that value
|
||||
entry = lo hi color (for discrete style)
|
||||
lo/hi = number or <em>min</em> or <em>max</em> = lower/upper bound of subset of range
|
||||
color = name of color used for that subset of values
|
||||
entry = color (for sequential style)
|
||||
color = name of color used for a bin of values
|
||||
<em>backcolor</em> arg = color
|
||||
color = name of color for background
|
||||
<em>bcolor</em> args = type color
|
||||
type = bond type or range of types (see below)
|
||||
color = name of color or color1/color2/...
|
||||
<em>bdiam</em> args = type diam
|
||||
type = bond type or range of types (see below)
|
||||
diam = diameter of bonds of that type (distance units)
|
||||
<em>boxcolor</em> arg = color
|
||||
color = name of color for simulation box lines and processor sub-domain lines
|
||||
<em>color</em> args = name R G B
|
||||
name = name of color
|
||||
R,G,B = red/green/blue numeric values from 0.0 to 1.0
|
||||
<em>bitrate</em> arg = rate
|
||||
rate = target bitrate for movie in kbps
|
||||
<em>framerate</em> arg = fps
|
||||
fps = frames per second for movie
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -140,15 +140,15 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>pair</em> args = pstyle pparam I J v_name
|
||||
pstyle = pair style name, e.g. lj/cut
|
||||
pparam = parameter to adapt over time
|
||||
I,J = type pair(s) to set parameter for
|
||||
v_name = variable with name that calculates value of pparam
|
||||
<em>kspace</em> arg = v_name
|
||||
v_name = variable with name that calculates scale factor on K-space terms
|
||||
<em>atom</em> args = aparam v_name
|
||||
aparam = parameter to adapt over time
|
||||
v_name = variable with name that calculates value of aparam
|
||||
pstyle = pair style name, e.g. lj/cut
|
||||
pparam = parameter to adapt over time
|
||||
I,J = type pair(s) to set parameter for
|
||||
v_name = variable with name that calculates value of pparam
|
||||
<em>kspace</em> arg = v_name
|
||||
v_name = variable with name that calculates scale factor on K-space terms
|
||||
<em>atom</em> args = aparam v_name
|
||||
aparam = parameter to adapt over time
|
||||
v_name = variable with name that calculates value of aparam
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/value pairs may be appended</li>
|
||||
@ -156,11 +156,11 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>scale</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = the variable value is the new setting
|
||||
<em>yes</em> = the variable value multiplies the original setting
|
||||
<em>reset</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = values will remain altered at the end of a run
|
||||
<em>yes</em> = reset altered values to their original values at the end of a run
|
||||
<em>no</em> = the variable value is the new setting
|
||||
<em>yes</em> = the variable value multiplies the original setting
|
||||
<em>reset</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = values will remain altered at the end of a run
|
||||
<em>yes</em> = reset altered values to their original values at the end of a run
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -140,16 +140,16 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>pair</em> args = pstyle pparam I J v_name
|
||||
pstyle = pair style name, e.g. lj/cut
|
||||
pparam = parameter to adapt over time
|
||||
I,J = type pair(s) to set parameter for
|
||||
v_name = variable with name that calculates value of pparam
|
||||
<em>kspace</em> arg = v_name
|
||||
v_name = variable with name that calculates scale factor on K-space terms
|
||||
<em>atom</em> args = aparam v_name
|
||||
aparam = parameter to adapt over time
|
||||
I = type(s) to set parameter for
|
||||
v_name = variable with name that calculates value of aparam
|
||||
pstyle = pair style name, e.g. lj/cut
|
||||
pparam = parameter to adapt over time
|
||||
I,J = type pair(s) to set parameter for
|
||||
v_name = variable with name that calculates value of pparam
|
||||
<em>kspace</em> arg = v_name
|
||||
v_name = variable with name that calculates scale factor on K-space terms
|
||||
<em>atom</em> args = aparam v_name
|
||||
aparam = parameter to adapt over time
|
||||
I = type(s) to set parameter for
|
||||
v_name = variable with name that calculates value of aparam
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/value pairs may be appended</li>
|
||||
@ -157,15 +157,15 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>scale</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = the variable value is the new setting
|
||||
<em>yes</em> = the variable value multiplies the original setting
|
||||
<em>reset</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = values will remain altered at the end of a run
|
||||
<em>yes</em> = reset altered values to their original values at the end
|
||||
of a run
|
||||
<em>after</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = parameters are adapted at timestep N
|
||||
<em>yes</em> = parameters are adapted one timestep after N
|
||||
<em>no</em> = the variable value is the new setting
|
||||
<em>yes</em> = the variable value multiplies the original setting
|
||||
<em>reset</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = values will remain altered at the end of a run
|
||||
<em>yes</em> = reset altered values to their original values at the end
|
||||
of a run
|
||||
<em>after</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = parameters are adapted at timestep N
|
||||
<em>yes</em> = parameters are adapted one timestep after N
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -148,11 +148,11 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>every</em> value = Nevery
|
||||
Nevery = add force every this many timesteps
|
||||
<em>region</em> value = region-ID
|
||||
region-ID = ID of region atoms must be in to have added force
|
||||
<em>energy</em> value = v_name
|
||||
v_name = variable with name that calculates the potential energy of each atom in the added force field
|
||||
Nevery = add force every this many timesteps
|
||||
<em>region</em> value = region-ID
|
||||
region-ID = ID of region atoms must be in to have added force
|
||||
<em>energy</em> value = v_name
|
||||
v_name = variable with name that calculates the potential energy of each atom in the added force field
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -140,23 +140,23 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>basis</em> values = M itype
|
||||
M = which basis atom
|
||||
itype = atom type (1-N) to assign to this basis atom
|
||||
<em>size</em> args = Lz
|
||||
Lz = z size of lattice region appended in a single event(distance units)
|
||||
<em>freq</em> args = freq
|
||||
freq = the number of timesteps between append events
|
||||
<em>temp</em> args = target damp seed extent
|
||||
target = target temperature for the region between zhi-extent and zhi (temperature units)
|
||||
damp = damping parameter (time units)
|
||||
seed = random number seed for langevin kicks
|
||||
extent = extent of thermostated region (distance units)
|
||||
<em>random</em> args = xmax ymax zmax seed
|
||||
<em>xmax</em>, <em>ymax</em>, <em>zmax</em> = maximum displacement in particular direction (distance units)
|
||||
<em>seed</em> = random number seed for random displacement
|
||||
<em>units</em> value = <em>lattice</em> or <em>box</em>
|
||||
<em>lattice</em> = the wall position is defined in lattice units
|
||||
<em>box</em> = the wall position is defined in simulation box units
|
||||
M = which basis atom
|
||||
itype = atom type (1-N) to assign to this basis atom
|
||||
<em>size</em> args = Lz
|
||||
Lz = z size of lattice region appended in a single event(distance units)
|
||||
<em>freq</em> args = freq
|
||||
freq = the number of timesteps between append events
|
||||
<em>temp</em> args = target damp seed extent
|
||||
target = target temperature for the region between zhi-extent and zhi (temperature units)
|
||||
damp = damping parameter (time units)
|
||||
seed = random number seed for langevin kicks
|
||||
extent = extent of thermostated region (distance units)
|
||||
<em>random</em> args = xmax ymax zmax seed
|
||||
<em>xmax</em>, <em>ymax</em>, <em>zmax</em> = maximum displacement in particular direction (distance units)
|
||||
<em>seed</em> = random number seed for random displacement
|
||||
<em>units</em> value = <em>lattice</em> or <em>box</em>
|
||||
<em>lattice</em> = the wall position is defined in lattice units
|
||||
<em>box</em> = the wall position is defined in simulation box units
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -138,9 +138,9 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>thermal</em> = thermal coupling with fields: temperature
|
||||
<em>two_temperature</em> = electron-phonon coupling with field: temperature and electron_temperature
|
||||
<em>hardy</em> = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
|
||||
<em>field</em> = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields)
|
||||
<em>two_temperature</em> = electron-phonon coupling with field: temperature and electron_temperature
|
||||
<em>hardy</em> = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
|
||||
<em>field</em> = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields)
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file</li>
|
||||
@ -164,28 +164,28 @@ fix AtC internal atc field
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre># initial fix to designate coupling type and group to apply it to
|
||||
# tag group physics material_file
|
||||
fix AtC internal atc thermal Ar_thermal.mat
|
||||
# tag group physics material_file
|
||||
fix AtC internal atc thermal Ar_thermal.mat
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre># create a uniform 12 x 2 x 2 mesh that covers region contain the group
|
||||
# nx ny nz region periodicity
|
||||
fix_modify AtC mesh create 12 2 2 mdRegion f p p
|
||||
# nx ny nz region periodicity
|
||||
fix_modify AtC mesh create 12 2 2 mdRegion f p p
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre># specify the control method for the type of coupling
|
||||
# physics control_type
|
||||
fix_modify AtC thermal control flux
|
||||
# physics control_type
|
||||
fix_modify AtC thermal control flux
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre># specify the initial values for the empirical field "temperature"
|
||||
# field node_group value
|
||||
fix_modify AtC initial temperature all 30
|
||||
# field node_group value
|
||||
fix_modify AtC initial temperature all 30
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre># create an output stream for nodal fields
|
||||
# filename output_frequency
|
||||
fix_modify AtC output atc_fe_output 100
|
||||
# filename output_frequency
|
||||
fix_modify AtC output atc_fe_output 100
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre>run 1000
|
||||
@ -196,32 +196,32 @@ fix AtC internal atc field
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre># initial fix to designate post-processing and the group to apply it to
|
||||
# no material file is allowed nor required
|
||||
fix AtC internal atc hardy
|
||||
# no material file is allowed nor required
|
||||
fix AtC internal atc hardy
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre># for hardy fix, specific kernel function (function type and range) to # be used as a localization function
|
||||
fix AtC kernel quartic_sphere 10.0
|
||||
fix AtC kernel quartic_sphere 10.0
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre># create a uniform 1 x 1 x 1 mesh that covers region contain the group
|
||||
# with periodicity this effectively creats a system average
|
||||
fix_modify AtC mesh create 1 1 1 box p p p
|
||||
# with periodicity this effectively creats a system average
|
||||
fix_modify AtC mesh create 1 1 1 box p p p
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre># change from default lagrangian map to eulerian
|
||||
# refreshed every 100 steps
|
||||
fix_modify AtC atom_element_map eulerian 100
|
||||
# refreshed every 100 steps
|
||||
fix_modify AtC atom_element_map eulerian 100
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre># start with no field defined
|
||||
# add mass density, potential energy density, stress and temperature
|
||||
fix_modify AtC fields add density energy stress temperature
|
||||
# add mass density, potential energy density, stress and temperature
|
||||
fix_modify AtC fields add density energy stress temperature
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre># create an output stream for nodal fields
|
||||
# filename output_frequency
|
||||
fix_modify AtC output nvtFE 100 text
|
||||
# filename output_frequency
|
||||
fix_modify AtC output nvtFE 100 text
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre>run 1000
|
||||
|
||||
@ -143,15 +143,15 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>types</em> values = two or more atom types
|
||||
<em>delta_mu</em> values = number_of_types-1 relative chemical potentials (energy units)
|
||||
<em>ke</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = no conservation of kinetic energy after atom swaps
|
||||
<em>yes</em> = kinetic energy is conserved after atom swaps
|
||||
<em>semi-grand</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = particle type counts and fractions conserved
|
||||
<em>yes</em> = semi-grand canonical ensemble, particle fractions not conserved
|
||||
<em>region</em> value = region-ID
|
||||
region-ID = ID of region to use as an exchange/move volume
|
||||
<em>delta_mu</em> values = number_of_types-1 relative chemical potentials (energy units)
|
||||
<em>ke</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = no conservation of kinetic energy after atom swaps
|
||||
<em>yes</em> = kinetic energy is conserved after atom swaps
|
||||
<em>semi-grand</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = particle type counts and fractions conserved
|
||||
<em>yes</em> = semi-grand canonical ensemble, particle fractions not conserved
|
||||
<em>region</em> value = region-ID
|
||||
region-ID = ID of region to use as an exchange/move volume
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -141,11 +141,11 @@ one or more input values can be listed</li>
|
||||
<li>value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[i], f_ID, f_ID[i], v_name</li>
|
||||
</ul>
|
||||
<div class="highlight-python"><div class="highlight"><pre>x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
|
||||
f_ID = per-atom vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
|
||||
f_ID = per-atom vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@ -142,13 +142,13 @@
|
||||
<li>value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name</li>
|
||||
</ul>
|
||||
<div class="highlight-python"><div class="highlight"><pre>vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
|
||||
density/number, density/mass = number or mass density
|
||||
temp = temperature
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
|
||||
f_ID = per-atom vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
density/number, density/mass = number or mass density
|
||||
temp = temperature
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
|
||||
f_ID = per-atom vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
@ -157,28 +157,28 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>norm</em> arg = <em>all</em> or <em>sample</em> or <em>none</em> = how output on <em>Nfreq</em> steps is normalized
|
||||
all = output is sum of atoms across all <em>Nrepeat</em> samples, divided by atom count
|
||||
sample = output is sum of <em>Nrepeat</em> sample averages, divided by <em>Nrepeat</em>
|
||||
none = output is sum of <em>Nrepeat</em> sums, divided by <em>Nrepeat</em>
|
||||
<em>ave</em> args = <em>one</em> or <em>running</em> or <em>window M</em>
|
||||
one = output new average value every Nfreq steps
|
||||
running = output cumulative average of all previous Nfreq steps
|
||||
window M = output average of M most recent Nfreq steps
|
||||
<em>bias</em> arg = bias-ID
|
||||
bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation
|
||||
<em>adof</em> value = dof_per_atom
|
||||
dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation
|
||||
<em>cdof</em> value = dof_per_chunk
|
||||
dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation
|
||||
<em>file</em> arg = filename
|
||||
filename = file to write results to
|
||||
<em>overwrite</em> arg = none = overwrite output file with only latest output
|
||||
<em>title1</em> arg = string
|
||||
string = text to print as 1st line of output file
|
||||
<em>title2</em> arg = string
|
||||
string = text to print as 2nd line of output file
|
||||
<em>title3</em> arg = string
|
||||
string = text to print as 3rd line of output file
|
||||
all = output is sum of atoms across all <em>Nrepeat</em> samples, divided by atom count
|
||||
sample = output is sum of <em>Nrepeat</em> sample averages, divided by <em>Nrepeat</em>
|
||||
none = output is sum of <em>Nrepeat</em> sums, divided by <em>Nrepeat</em>
|
||||
<em>ave</em> args = <em>one</em> or <em>running</em> or <em>window M</em>
|
||||
one = output new average value every Nfreq steps
|
||||
running = output cumulative average of all previous Nfreq steps
|
||||
window M = output average of M most recent Nfreq steps
|
||||
<em>bias</em> arg = bias-ID
|
||||
bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation
|
||||
<em>adof</em> value = dof_per_atom
|
||||
dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation
|
||||
<em>cdof</em> value = dof_per_chunk
|
||||
dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation
|
||||
<em>file</em> arg = filename
|
||||
filename = file to write results to
|
||||
<em>overwrite</em> arg = none = overwrite output file with only latest output
|
||||
<em>title1</em> arg = string
|
||||
string = text to print as 1st line of output file
|
||||
<em>title2</em> arg = string
|
||||
string = text to print as 2nd line of output file
|
||||
<em>title3</em> arg = string
|
||||
string = text to print as 3rd line of output file
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -141,10 +141,10 @@
|
||||
<li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
|
||||
</ul>
|
||||
<div class="highlight-python"><div class="highlight"><pre>c_ID = global scalar calculated by a compute with ID
|
||||
c_ID[I] = Ith component of global vector calculated by a compute with ID
|
||||
f_ID = global scalar calculated by a fix with ID
|
||||
f_ID[I] = Ith component of global vector calculated by a fix with ID
|
||||
v_name = global value calculated by an equal-style variable with name
|
||||
c_ID[I] = Ith component of global vector calculated by a compute with ID
|
||||
f_ID = global scalar calculated by a fix with ID
|
||||
f_ID[I] = Ith component of global vector calculated by a fix with ID
|
||||
v_name = global value calculated by an equal-style variable with name
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
@ -153,28 +153,28 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>type</em> arg = <em>auto</em> or <em>upper</em> or <em>lower</em> or <em>auto/upper</em> or <em>auto/lower</em> or <em>full</em>
|
||||
auto = correlate each value with itself
|
||||
upper = correlate each value with each succeeding value
|
||||
lower = correlate each value with each preceding value
|
||||
auto/upper = auto + upper
|
||||
auto/lower = auto + lower
|
||||
full = correlate each value with every other value, including itself = auto + upper + lower
|
||||
<em>ave</em> args = <em>one</em> or <em>running</em>
|
||||
one = zero the correlation accumulation every Nfreq steps
|
||||
running = accumulate correlations continuously
|
||||
<em>start</em> args = Nstart
|
||||
Nstart = start accumulating correlations on this timestep
|
||||
<em>prefactor</em> args = value
|
||||
value = prefactor to scale all the correlation data by
|
||||
<em>file</em> arg = filename
|
||||
filename = name of file to output correlation data to
|
||||
<em>overwrite</em> arg = none = overwrite output file with only latest output
|
||||
<em>title1</em> arg = string
|
||||
string = text to print as 1st line of output file
|
||||
<em>title2</em> arg = string
|
||||
string = text to print as 2nd line of output file
|
||||
<em>title3</em> arg = string
|
||||
string = text to print as 3rd line of output file
|
||||
auto = correlate each value with itself
|
||||
upper = correlate each value with each succeeding value
|
||||
lower = correlate each value with each preceding value
|
||||
auto/upper = auto + upper
|
||||
auto/lower = auto + lower
|
||||
full = correlate each value with every other value, including itself = auto + upper + lower
|
||||
<em>ave</em> args = <em>one</em> or <em>running</em>
|
||||
one = zero the correlation accumulation every Nfreq steps
|
||||
running = accumulate correlations continuously
|
||||
<em>start</em> args = Nstart
|
||||
Nstart = start accumulating correlations on this timestep
|
||||
<em>prefactor</em> args = value
|
||||
value = prefactor to scale all the correlation data by
|
||||
<em>file</em> arg = filename
|
||||
filename = name of file to output correlation data to
|
||||
<em>overwrite</em> arg = none = overwrite output file with only latest output
|
||||
<em>title1</em> arg = string
|
||||
string = text to print as 1st line of output file
|
||||
<em>title2</em> arg = string
|
||||
string = text to print as 2nd line of output file
|
||||
<em>title3</em> arg = string
|
||||
string = text to print as 3rd line of output file
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -146,11 +146,11 @@
|
||||
<li>value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
|
||||
</ul>
|
||||
<div class="highlight-python"><div class="highlight"><pre>x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
|
||||
c_ID = scalar or vector calculated by a compute with ID
|
||||
c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID
|
||||
f_ID = scalar or vector calculated by a fix with ID
|
||||
f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID
|
||||
v_name = value(s) calculated by an equal-style or atom-style variable with name
|
||||
c_ID = scalar or vector calculated by a compute with ID
|
||||
c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID
|
||||
f_ID = scalar or vector calculated by a fix with ID
|
||||
f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID
|
||||
v_name = value(s) calculated by an equal-style or atom-style variable with name
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
@ -159,27 +159,27 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>mode</em> arg = <em>scalar</em> or <em>vector</em>
|
||||
scalar = all input values are scalars
|
||||
vector = all input values are vectors
|
||||
<em>file</em> arg = filename
|
||||
filename = name of file to output histogram(s) to
|
||||
<em>ave</em> args = <em>one</em> or <em>running</em> or <em>window</em>
|
||||
one = output a new average value every Nfreq steps
|
||||
running = output cumulative average of all previous Nfreq steps
|
||||
window M = output average of M most recent Nfreq steps
|
||||
<em>start</em> args = Nstart
|
||||
Nstart = start averaging on this timestep
|
||||
<em>beyond</em> arg = <em>ignore</em> or <em>end</em> or <em>extra</em>
|
||||
ignore = ignore values outside histogram lo/hi bounds
|
||||
end = count values outside histogram lo/hi bounds in end bins
|
||||
extra = create 2 extra bins for value outside histogram lo/hi bounds
|
||||
<em>overwrite</em> arg = none = overwrite output file with only latest output
|
||||
<em>title1</em> arg = string
|
||||
string = text to print as 1st line of output file
|
||||
<em>title2</em> arg = string
|
||||
string = text to print as 2nd line of output file
|
||||
<em>title3</em> arg = string
|
||||
string = text to print as 3rd line of output file, only for vector mode
|
||||
scalar = all input values are scalars
|
||||
vector = all input values are vectors
|
||||
<em>file</em> arg = filename
|
||||
filename = name of file to output histogram(s) to
|
||||
<em>ave</em> args = <em>one</em> or <em>running</em> or <em>window</em>
|
||||
one = output a new average value every Nfreq steps
|
||||
running = output cumulative average of all previous Nfreq steps
|
||||
window M = output average of M most recent Nfreq steps
|
||||
<em>start</em> args = Nstart
|
||||
Nstart = start averaging on this timestep
|
||||
<em>beyond</em> arg = <em>ignore</em> or <em>end</em> or <em>extra</em>
|
||||
ignore = ignore values outside histogram lo/hi bounds
|
||||
end = count values outside histogram lo/hi bounds in end bins
|
||||
extra = create 2 extra bins for value outside histogram lo/hi bounds
|
||||
<em>overwrite</em> arg = none = overwrite output file with only latest output
|
||||
<em>title1</em> arg = string
|
||||
string = text to print as 1st line of output file
|
||||
<em>title2</em> arg = string
|
||||
string = text to print as 2nd line of output file
|
||||
<em>title3</em> arg = string
|
||||
string = text to print as 3rd line of output file, only for vector mode
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -141,20 +141,20 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
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)
|
||||
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)
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>one or more input values can be listed</li>
|
||||
<li>value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name</li>
|
||||
</ul>
|
||||
<div class="highlight-python"><div class="highlight"><pre>vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
|
||||
density/number, density/mass = number or mass density
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
|
||||
f_ID = per-atom vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
density/number, density/mass = number or mass density
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
|
||||
f_ID = per-atom vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
@ -163,30 +163,30 @@ dim = <em>x</em> or <em>y</em> or <em>z</em>
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>region</em> arg = region-ID
|
||||
<em>bound</em> args = x/y/z lo hi
|
||||
x/y/z = <em>x</em> or <em>y</em> or <em>z</em> to bound bins in this dimension
|
||||
lo = <em>lower</em> or coordinate value (distance units)
|
||||
hi = <em>upper</em> or coordinate value (distance units)
|
||||
<em>discard</em> arg = <em>mixed</em> or <em>no</em> or <em>yes</em>
|
||||
mixed = discard atoms outside bins only if bin bounds are explicitly set
|
||||
no = always keep out-of-bounds atoms
|
||||
yes = always discard out-of-bounds atoms
|
||||
<em>norm</em> arg = <em>all</em> or <em>sample</em>
|
||||
region-ID = ID of region atoms must be in to contribute to spatial averaging
|
||||
<em>ave</em> args = <em>one</em> or <em>running</em> or <em>window M</em>
|
||||
one = output new average value every Nfreq steps
|
||||
running = output cumulative average of all previous Nfreq steps
|
||||
window M = output average of M most recent Nfreq steps
|
||||
<em>units</em> arg = <em>box</em> or <em>lattice</em> or <em>reduced</em>
|
||||
<em>file</em> arg = filename
|
||||
filename = file to write results to
|
||||
<em>overwrite</em> arg = none = overwrite output file with only latest output
|
||||
<em>title1</em> arg = string
|
||||
string = text to print as 1st line of output file
|
||||
<em>title2</em> arg = string
|
||||
string = text to print as 2nd line of output file
|
||||
<em>title3</em> arg = string
|
||||
string = text to print as 3rd line of output file
|
||||
<em>bound</em> args = x/y/z lo hi
|
||||
x/y/z = <em>x</em> or <em>y</em> or <em>z</em> to bound bins in this dimension
|
||||
lo = <em>lower</em> or coordinate value (distance units)
|
||||
hi = <em>upper</em> or coordinate value (distance units)
|
||||
<em>discard</em> arg = <em>mixed</em> or <em>no</em> or <em>yes</em>
|
||||
mixed = discard atoms outside bins only if bin bounds are explicitly set
|
||||
no = always keep out-of-bounds atoms
|
||||
yes = always discard out-of-bounds atoms
|
||||
<em>norm</em> arg = <em>all</em> or <em>sample</em>
|
||||
region-ID = ID of region atoms must be in to contribute to spatial averaging
|
||||
<em>ave</em> args = <em>one</em> or <em>running</em> or <em>window M</em>
|
||||
one = output new average value every Nfreq steps
|
||||
running = output cumulative average of all previous Nfreq steps
|
||||
window M = output average of M most recent Nfreq steps
|
||||
<em>units</em> arg = <em>box</em> or <em>lattice</em> or <em>reduced</em>
|
||||
<em>file</em> arg = filename
|
||||
filename = file to write results to
|
||||
<em>overwrite</em> arg = none = overwrite output file with only latest output
|
||||
<em>title1</em> arg = string
|
||||
string = text to print as 1st line of output file
|
||||
<em>title2</em> arg = string
|
||||
string = text to print as 2nd line of output file
|
||||
<em>title3</em> arg = string
|
||||
string = text to print as 3rd line of output file
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -145,12 +145,12 @@
|
||||
<li>value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name</li>
|
||||
</ul>
|
||||
<div class="highlight-python"><div class="highlight"><pre>vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
|
||||
density/number, density/mass = number or mass density
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
|
||||
f_ID = per-atom vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
density/number, density/mass = number or mass density
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
|
||||
f_ID = per-atom vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
@ -159,22 +159,22 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>region</em> arg = region-ID
|
||||
region-ID = ID of region atoms must be in to contribute to spatial averaging
|
||||
<em>norm</em> arg = <em>all</em> or <em>sample</em>
|
||||
<em>units</em> arg = <em>box</em> or <em>lattice</em> or <em>reduced</em>
|
||||
<em>ave</em> args = <em>one</em> or <em>running</em> or <em>window M</em>
|
||||
one = output new average value every Nfreq steps
|
||||
running = output cumulative average of all previous Nfreq steps
|
||||
window M = output average of M most recent Nfreq steps
|
||||
<em>file</em> arg = filename
|
||||
filename = file to write results to
|
||||
<em>overwrite</em> arg = none = overwrite output file with only latest output
|
||||
<em>title1</em> arg = string
|
||||
string = text to print as 1st line of output file
|
||||
<em>title2</em> arg = string
|
||||
string = text to print as 2nd line of output file
|
||||
<em>title3</em> arg = string
|
||||
string = text to print as 3rd line of output file
|
||||
region-ID = ID of region atoms must be in to contribute to spatial averaging
|
||||
<em>norm</em> arg = <em>all</em> or <em>sample</em>
|
||||
<em>units</em> arg = <em>box</em> or <em>lattice</em> or <em>reduced</em>
|
||||
<em>ave</em> args = <em>one</em> or <em>running</em> or <em>window M</em>
|
||||
one = output new average value every Nfreq steps
|
||||
running = output cumulative average of all previous Nfreq steps
|
||||
window M = output average of M most recent Nfreq steps
|
||||
<em>file</em> arg = filename
|
||||
filename = file to write results to
|
||||
<em>overwrite</em> arg = none = overwrite output file with only latest output
|
||||
<em>title1</em> arg = string
|
||||
string = text to print as 1st line of output file
|
||||
<em>title2</em> arg = string
|
||||
string = text to print as 2nd line of output file
|
||||
<em>title3</em> arg = string
|
||||
string = text to print as 3rd line of output file
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -141,10 +141,10 @@
|
||||
<li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
|
||||
</ul>
|
||||
<div class="highlight-python"><div class="highlight"><pre>c_ID = global scalar, vector, or array calculated by a compute with ID
|
||||
c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID
|
||||
f_ID = global scalar, vector, or array calculated by a fix with ID
|
||||
f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID
|
||||
v_name = global value calculated by an equal-style variable with name
|
||||
c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID
|
||||
f_ID = global scalar, vector, or array calculated by a fix with ID
|
||||
f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID
|
||||
v_name = global value calculated by an equal-style variable with name
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
@ -153,25 +153,25 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>mode</em> arg = <em>scalar</em> or <em>vector</em>
|
||||
scalar = all input values are global scalars
|
||||
vector = all input values are global vectors or global arrays
|
||||
<em>ave</em> args = <em>one</em> or <em>running</em> or <em>window M</em>
|
||||
one = output a new average value every Nfreq steps
|
||||
running = output cummulative average of all previous Nfreq steps
|
||||
window M = output average of M most recent Nfreq steps
|
||||
<em>start</em> args = Nstart
|
||||
Nstart = start averaging on this timestep
|
||||
<em>off</em> arg = M = do not average this value
|
||||
M = value # from 1 to Nvalues
|
||||
<em>file</em> arg = filename
|
||||
filename = name of file to output time averages to
|
||||
<em>overwrite</em> arg = none = overwrite output file with only latest output
|
||||
<em>title1</em> arg = string
|
||||
string = text to print as 1st line of output file
|
||||
<em>title2</em> arg = string
|
||||
string = text to print as 2nd line of output file
|
||||
<em>title3</em> arg = string
|
||||
string = text to print as 3rd line of output file, only for vector mode
|
||||
scalar = all input values are global scalars
|
||||
vector = all input values are global vectors or global arrays
|
||||
<em>ave</em> args = <em>one</em> or <em>running</em> or <em>window M</em>
|
||||
one = output a new average value every Nfreq steps
|
||||
running = output cummulative average of all previous Nfreq steps
|
||||
window M = output average of M most recent Nfreq steps
|
||||
<em>start</em> args = Nstart
|
||||
Nstart = start averaging on this timestep
|
||||
<em>off</em> arg = M = do not average this value
|
||||
M = value # from 1 to Nvalues
|
||||
<em>file</em> arg = filename
|
||||
filename = name of file to output time averages to
|
||||
<em>overwrite</em> arg = none = overwrite output file with only latest output
|
||||
<em>title1</em> arg = string
|
||||
string = text to print as 1st line of output file
|
||||
<em>title2</em> arg = string
|
||||
string = text to print as 2nd line of output file
|
||||
<em>title3</em> arg = string
|
||||
string = text to print as 3rd line of output file, only for vector mode
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -148,7 +148,7 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>region</em> value = region-ID
|
||||
region-ID = ID of region atoms must be in to have added force
|
||||
region-ID = ID of region atoms must be in to have added force
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -139,10 +139,10 @@
|
||||
<li>style = <em>shift</em> or <em>rcb</em></li>
|
||||
</ul>
|
||||
<div class="highlight-python"><div class="highlight"><pre>shift args = dimstr Niter stopthresh
|
||||
dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
|
||||
Niter = # of times to iterate within each dimension of dimstr sequence
|
||||
stopthresh = stop balancing when this imbalance threshhold is reached
|
||||
rcb args = none
|
||||
dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
|
||||
Niter = # of times to iterate within each dimension of dimstr sequence
|
||||
stopthresh = stop balancing when this imbalance threshhold is reached
|
||||
rcb args = none
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
@ -151,7 +151,7 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>out</em> value = filename
|
||||
filename = write each processor's sub-domain to a file, at each re-balancing
|
||||
filename = write each processor's sub-domain to a file, at each re-balancing
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -142,8 +142,8 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>prob</em> values = fraction seed
|
||||
fraction = break a bond with this probability if otherwise eligible
|
||||
seed = random number seed (positive integer)
|
||||
fraction = break a bond with this probability if otherwise eligible
|
||||
seed = random number seed (positive integer)
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -143,20 +143,20 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>iparam</em> values = maxbond, newtype
|
||||
maxbond = max # of bonds of bondtype the itype atom can have
|
||||
newtype = change the itype atom to this type when maxbonds exist
|
||||
<em>jparam</em> values = maxbond, newtype
|
||||
maxbond = max # of bonds of bondtype the jtype atom can have
|
||||
newtype = change the jtype atom to this type when maxbonds exist
|
||||
<em>prob</em> values = fraction seed
|
||||
fraction = create a bond with this probability if otherwise eligible
|
||||
seed = random number seed (positive integer)
|
||||
<em>atype</em> value = angletype
|
||||
angletype = type of created angles
|
||||
<em>dtype</em> value = dihedraltype
|
||||
dihedraltype = type of created dihedrals
|
||||
<em>itype</em> value = impropertype
|
||||
impropertype = type of created impropers
|
||||
maxbond = max # of bonds of bondtype the itype atom can have
|
||||
newtype = change the itype atom to this type when maxbonds exist
|
||||
<em>jparam</em> values = maxbond, newtype
|
||||
maxbond = max # of bonds of bondtype the jtype atom can have
|
||||
newtype = change the jtype atom to this type when maxbonds exist
|
||||
<em>prob</em> values = fraction seed
|
||||
fraction = create a bond with this probability if otherwise eligible
|
||||
seed = random number seed (positive integer)
|
||||
<em>atype</em> value = angletype
|
||||
angletype = type of created angles
|
||||
<em>dtype</em> value = dihedraltype
|
||||
dihedraltype = type of created dihedrals
|
||||
<em>itype</em> value = impropertype
|
||||
impropertype = type of created impropers
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -139,11 +139,11 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>input</em> arg = colvars.state file name or prefix or NULL (default: NULL)
|
||||
<em>output</em> arg = output filename prefix (default: out)
|
||||
<em>seed</em> arg = seed for random number generator (default: 1966)
|
||||
<em>unwrap</em> arg = <em>yes</em> or <em>no</em>
|
||||
use unwrapped coordinates in collective variables (default: yes)
|
||||
<em>tstat</em> arg = fix id of a thermostat or NULL (default: NULL)
|
||||
<em>output</em> arg = output filename prefix (default: out)
|
||||
<em>seed</em> arg = seed for random number generator (default: 1966)
|
||||
<em>unwrap</em> arg = <em>yes</em> or <em>no</em>
|
||||
use unwrapped coordinates in collective variables (default: yes)
|
||||
<em>tstat</em> arg = fix id of a thermostat or NULL (default: NULL)
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -187,14 +187,14 @@ parameter = <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>xz</em>
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>remap</em> value = <em>x</em> or <em>v</em> or <em>none</em>
|
||||
x = remap coords of atoms in group into deforming box
|
||||
v = remap velocities of all atoms when they cross periodic boundaries
|
||||
none = no remapping of x or v
|
||||
<em>flip</em> value = <em>yes</em> or <em>no</em>
|
||||
allow or disallow box flips when it becomes highly skewed
|
||||
<em>units</em> value = <em>lattice</em> or <em>box</em>
|
||||
lattice = distances are defined in lattice units
|
||||
box = distances are defined in simulation box units
|
||||
x = remap coords of atoms in group into deforming box
|
||||
v = remap velocities of all atoms when they cross periodic boundaries
|
||||
none = no remapping of x or v
|
||||
<em>flip</em> value = <em>yes</em> or <em>no</em>
|
||||
allow or disallow box flips when it becomes highly skewed
|
||||
<em>units</em> value = <em>lattice</em> or <em>box</em>
|
||||
lattice = distances are defined in lattice units
|
||||
box = distances are defined in simulation box units
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -143,40 +143,40 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>region</em> value = region-ID
|
||||
region-ID = ID of region to use as insertion volume
|
||||
<em>id</em> value = <em>max</em> or <em>next</em>
|
||||
max = atom ID for new atom(s) is max ID of all current atoms plus one
|
||||
next = atom ID for new atom(s) increments by one for every deposition
|
||||
<em>global</em> values = lo hi
|
||||
lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units)
|
||||
<em>local</em> values = lo hi delta
|
||||
lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units)
|
||||
delta = lateral distance within which a neighbor is considered "nearby" (distance units)
|
||||
<em>near</em> value = R
|
||||
R = only insert atom/molecule if further than R from existing particles (distance units)
|
||||
<em>attempt</em> value = Q
|
||||
Q = attempt a single insertion up to Q times
|
||||
<em>rate</em> value = V
|
||||
V = z velocity (y in 2d) at which insertion volume moves (velocity units)
|
||||
<em>vx</em> values = vxlo vxhi
|
||||
vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units)
|
||||
<em>vy</em> values = vylo vyhi
|
||||
vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units)
|
||||
<em>vz</em> values = vzlo vzhi
|
||||
vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units)
|
||||
<em>target</em> values = tx ty tz
|
||||
tx,ty,tz = location of target point (distance units)
|
||||
<em>mol</em> value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
|
||||
<em>molfrac</em> values = f1 f2 ... fN
|
||||
f1 to fN = relative probability of creating each of N molecules in template-ID
|
||||
<em>rigid</em> value = fix-ID
|
||||
fix-ID = ID of <a class="reference internal" href="fix_rigid.html"><em>fix rigid/small</em></a> command
|
||||
<em>shake</em> value = fix-ID
|
||||
fix-ID = ID of <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command
|
||||
<em>units</em> value = <em>lattice</em> or <em>box</em>
|
||||
lattice = the geometry is defined in lattice units
|
||||
box = the geometry is defined in simulation box units
|
||||
region-ID = ID of region to use as insertion volume
|
||||
<em>id</em> value = <em>max</em> or <em>next</em>
|
||||
max = atom ID for new atom(s) is max ID of all current atoms plus one
|
||||
next = atom ID for new atom(s) increments by one for every deposition
|
||||
<em>global</em> values = lo hi
|
||||
lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units)
|
||||
<em>local</em> values = lo hi delta
|
||||
lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units)
|
||||
delta = lateral distance within which a neighbor is considered "nearby" (distance units)
|
||||
<em>near</em> value = R
|
||||
R = only insert atom/molecule if further than R from existing particles (distance units)
|
||||
<em>attempt</em> value = Q
|
||||
Q = attempt a single insertion up to Q times
|
||||
<em>rate</em> value = V
|
||||
V = z velocity (y in 2d) at which insertion volume moves (velocity units)
|
||||
<em>vx</em> values = vxlo vxhi
|
||||
vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units)
|
||||
<em>vy</em> values = vylo vyhi
|
||||
vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units)
|
||||
<em>vz</em> values = vzlo vzhi
|
||||
vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units)
|
||||
<em>target</em> values = tx ty tz
|
||||
tx,ty,tz = location of target point (distance units)
|
||||
<em>mol</em> value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
|
||||
<em>molfrac</em> values = f1 f2 ... fN
|
||||
f1 to fN = relative probability of creating each of N molecules in template-ID
|
||||
<em>rigid</em> value = fix-ID
|
||||
fix-ID = ID of <a class="reference internal" href="fix_rigid.html"><em>fix rigid/small</em></a> command
|
||||
<em>shake</em> value = fix-ID
|
||||
fix-ID = ID of <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command
|
||||
<em>units</em> value = <em>lattice</em> or <em>box</em>
|
||||
lattice = the geometry is defined in lattice units
|
||||
box = the geometry is defined in simulation box units
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -143,8 +143,8 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>units</em> value = <em>lattice</em> or <em>box</em>
|
||||
lattice = Xmax is defined in lattice units
|
||||
box = Xmax is defined in simulation box units
|
||||
lattice = Xmax is defined in lattice units
|
||||
box = Xmax is defined in simulation box units
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -141,9 +141,9 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>region</em> value = region-ID
|
||||
region-ID = ID of region atoms must be in to have added force
|
||||
<em>energy</em> value = v_name
|
||||
v_name = variable with name that calculates the potential energy of each atom in the added E-field
|
||||
region-ID = ID of region atoms must be in to have added force
|
||||
<em>energy</em> value = v_name
|
||||
v_name = variable with name that calculates the potential energy of each atom in the added E-field
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -138,10 +138,10 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>pf/callback</em> args = Ncall Napply
|
||||
Ncall = make callback every Ncall steps
|
||||
Napply = apply callback forces every Napply steps
|
||||
<em>pf/array</em> args = Napply
|
||||
Napply = apply array forces every Napply steps
|
||||
Ncall = make callback every Ncall steps
|
||||
Napply = apply callback forces every Napply steps
|
||||
<em>pf/array</em> args = Napply
|
||||
Napply = apply array forces every Napply steps
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -146,15 +146,15 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>chute</em> args = angle
|
||||
angle = angle in +x away from -z or -y axis in 3d/2d (in degrees)
|
||||
angle can be a variable (see below)
|
||||
<em>spherical</em> args = phi theta
|
||||
phi = azimuthal angle from +x axis (in degrees)
|
||||
theta = angle from +z or +y axis in 3d/2d (in degrees)
|
||||
phi or theta can be a variable (see below)
|
||||
<em>vector</em> args = x y z
|
||||
x y z = vector direction to apply the acceleration
|
||||
x or y or z can be a variable (see below)
|
||||
angle = angle in +x away from -z or -y axis in 3d/2d (in degrees)
|
||||
angle can be a variable (see below)
|
||||
<em>spherical</em> args = phi theta
|
||||
phi = azimuthal angle from +x axis (in degrees)
|
||||
theta = angle from +z or +y axis in 3d/2d (in degrees)
|
||||
phi or theta can be a variable (see below)
|
||||
<em>vector</em> args = x y z
|
||||
x y z = vector direction to apply the acceleration
|
||||
x or y or z can be a variable (see below)
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -142,7 +142,7 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>region</em> value = region-ID
|
||||
region-ID = ID of region atoms must be in to have added force
|
||||
region-ID = ID of region atoms must be in to have added force
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -139,14 +139,14 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>unwrap</em> arg = <em>on</em> or <em>off</em>
|
||||
off = coordinates are wrapped back into the principal unit cell (default)
|
||||
on = "unwrapped" coordinates using the image flags used
|
||||
<em>fscale</em> arg = factor
|
||||
factor = floating point number to scale IMD forces (default: 1.0)
|
||||
<em>trate</em> arg = transmission rate of coordinate data sets (default: 1)
|
||||
<em>nowait</em> arg = <em>on</em> or <em>off</em>
|
||||
off = LAMMPS waits to be connected to an IMD client before continuing (default)
|
||||
on = LAMMPS listens for an IMD client, but continues with the run
|
||||
off = coordinates are wrapped back into the principal unit cell (default)
|
||||
on = "unwrapped" coordinates using the image flags used
|
||||
<em>fscale</em> arg = factor
|
||||
factor = floating point number to scale IMD forces (default: 1.0)
|
||||
<em>trate</em> arg = transmission rate of coordinate data sets (default: 1)
|
||||
<em>nowait</em> arg = <em>on</em> or <em>off</em>
|
||||
off = LAMMPS waits to be connected to an IMD client before continuing (default)
|
||||
on = LAMMPS listens for an IMD client, but continues with the run
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -140,25 +140,25 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>sphere</em> args = x y z R
|
||||
x,y,z = initial position of center of indenter (distance units)
|
||||
R = sphere radius of indenter (distance units)
|
||||
any of x,y,z,R can be a variable (see below)
|
||||
<em>cylinder</em> args = dim c1 c2 R
|
||||
dim = <em>x</em> or <em>y</em> or <em>z</em> = axis of cylinder
|
||||
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
|
||||
R = cylinder radius of indenter (distance units)
|
||||
any of c1,c2,R can be a variable (see below)
|
||||
<em>plane</em> args = dim pos side
|
||||
dim = <em>x</em> or <em>y</em> or <em>z</em> = plane perpendicular to this dimension
|
||||
pos = position of plane in dimension x, y, or z (distance units)
|
||||
pos can be a variable (see below)
|
||||
side = <em>lo</em> or <em>hi</em>
|
||||
<em>side</em> value = <em>in</em> or <em>out</em>
|
||||
<em>in</em> = the indenter acts on particles inside the sphere or cylinder
|
||||
<em>out</em> = the indenter acts on particles outside the sphere or cylinder
|
||||
<em>units</em> value = <em>lattice</em> or <em>box</em>
|
||||
lattice = the geometry is defined in lattice units
|
||||
box = the geometry is defined in simulation box units
|
||||
x,y,z = initial position of center of indenter (distance units)
|
||||
R = sphere radius of indenter (distance units)
|
||||
any of x,y,z,R can be a variable (see below)
|
||||
<em>cylinder</em> args = dim c1 c2 R
|
||||
dim = <em>x</em> or <em>y</em> or <em>z</em> = axis of cylinder
|
||||
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
|
||||
R = cylinder radius of indenter (distance units)
|
||||
any of c1,c2,R can be a variable (see below)
|
||||
<em>plane</em> args = dim pos side
|
||||
dim = <em>x</em> or <em>y</em> or <em>z</em> = plane perpendicular to this dimension
|
||||
pos = position of plane in dimension x, y, or z (distance units)
|
||||
pos can be a variable (see below)
|
||||
side = <em>lo</em> or <em>hi</em>
|
||||
<em>side</em> value = <em>in</em> or <em>out</em>
|
||||
<em>in</em> = the indenter acts on particles inside the sphere or cylinder
|
||||
<em>out</em> = the indenter acts on particles outside the sphere or cylinder
|
||||
<em>units</em> value = <em>lattice</em> or <em>box</em>
|
||||
lattice = the geometry is defined in lattice units
|
||||
box = the geometry is defined in simulation box units
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -146,23 +146,23 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>angmom</em> value = <em>no</em> or scale
|
||||
<em>no</em> = do not thermostat rotational degrees of freedom via the angular momentum
|
||||
factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric factor as discussed below
|
||||
<em>gjf</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = use standard formulation
|
||||
<em>yes</em> = use Gronbech-Jensen/Farago formulation
|
||||
<em>omega</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = do not thermostat rotational degrees of freedom via the angular velocity
|
||||
<em>yes</em> = do thermostat rotational degrees of freedom via the angular velocity
|
||||
<em>scale</em> values = type ratio
|
||||
type = atom type (1-N)
|
||||
ratio = factor by which to scale the damping coefficient
|
||||
<em>tally</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = do not tally the energy added/subtracted to atoms
|
||||
<em>yes</em> = do tally the energy added/subtracted to atoms
|
||||
<em>zero</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = do not set total random force to zero
|
||||
<em>yes</em> = set total random force to zero
|
||||
<em>no</em> = do not thermostat rotational degrees of freedom via the angular momentum
|
||||
factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric factor as discussed below
|
||||
<em>gjf</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = use standard formulation
|
||||
<em>yes</em> = use Gronbech-Jensen/Farago formulation
|
||||
<em>omega</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = do not thermostat rotational degrees of freedom via the angular velocity
|
||||
<em>yes</em> = do thermostat rotational degrees of freedom via the angular velocity
|
||||
<em>scale</em> values = type ratio
|
||||
type = atom type (1-N)
|
||||
ratio = factor by which to scale the damping coefficient
|
||||
<em>tally</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = do not tally the energy added/subtracted to atoms
|
||||
<em>yes</em> = do tally the energy added/subtracted to atoms
|
||||
<em>zero</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = do not set total random force to zero
|
||||
<em>yes</em> = set total random force to zero
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -145,8 +145,8 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>zero</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = do not set total random force on centers of mass to zero
|
||||
<em>yes</em> = set total random force on centers of mass to zero
|
||||
<em>no</em> = do not set total random force on centers of mass to zero
|
||||
<em>yes</em> = set total random force on centers of mass to zero
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -150,8 +150,8 @@ keyword = <em>scale</em> or <em>tally</em> or <em>zero</em>
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
<em>zero</em> value = <em>no</em> or <em>yes</em>
|
||||
<em>no</em> = do not set total random force to zero
|
||||
<em>yes</em> = set total random force to zero
|
||||
<em>no</em> = do not set total random force to zero
|
||||
<em>yes</em> = set total random force to zero
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -144,29 +144,29 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>setArea</em> values = type node_area
|
||||
type = atom type (1-N)
|
||||
node_area = portion of the surface area of the composite object associated with the particular atom type (used when the force coupling constant is set by default).
|
||||
<em>setGamma</em> values = gamma
|
||||
gamma = user set value for the force coupling constant.
|
||||
<em>scaleGamma</em> values = type gammaFactor
|
||||
type = atom type (1-N)
|
||||
gammaFactor = factor to scale the <em>setGamma</em> gamma value by, for the specified atom type.
|
||||
<em>dx</em> values = dx_LB = the lattice spacing.
|
||||
<em>dm</em> values = dm_LB = the lattice-Boltzmann mass unit.
|
||||
<em>a0</em> values = a_0_real = the square of the speed of sound in the fluid.
|
||||
<em>noise</em> values = Temperature seed
|
||||
Temperature = fluid temperature.
|
||||
seed = random number generator seed (positive integer)
|
||||
<em>calcforce</em> values = N forcegroup-ID
|
||||
N = output the force and torque every N timesteps
|
||||
forcegroup-ID = ID of the particle group to calculate the force and torque of
|
||||
<em>trilinear</em> values = none (used to switch from the default Peskin interpolation stencil to the trilinear stencil).
|
||||
<em>D3Q19</em> values = none (used to switch from the default D3Q15, 15 velocity lattice, to the D3Q19, 19 velocity lattice).
|
||||
<em>read_restart</em> values = restart file = name of the restart file to use to restart a fluid run.
|
||||
<em>write_restart</em> values = N = write a restart file every N MD timesteps.
|
||||
<em>zwall_velocity</em> values = velocity_bottom velocity_top = velocities along the y-direction of the bottom and top walls (located at z=zmin and z=zmax).
|
||||
<em>bodyforce</em> values = bodyforcex bodyforcey bodyforcez = the x,y and z components of a constant body force added to the fluid.
|
||||
<em>printfluid</em> values = N = print the fluid density and velocity at each grid point every N timesteps.
|
||||
type = atom type (1-N)
|
||||
node_area = portion of the surface area of the composite object associated with the particular atom type (used when the force coupling constant is set by default).
|
||||
<em>setGamma</em> values = gamma
|
||||
gamma = user set value for the force coupling constant.
|
||||
<em>scaleGamma</em> values = type gammaFactor
|
||||
type = atom type (1-N)
|
||||
gammaFactor = factor to scale the <em>setGamma</em> gamma value by, for the specified atom type.
|
||||
<em>dx</em> values = dx_LB = the lattice spacing.
|
||||
<em>dm</em> values = dm_LB = the lattice-Boltzmann mass unit.
|
||||
<em>a0</em> values = a_0_real = the square of the speed of sound in the fluid.
|
||||
<em>noise</em> values = Temperature seed
|
||||
Temperature = fluid temperature.
|
||||
seed = random number generator seed (positive integer)
|
||||
<em>calcforce</em> values = N forcegroup-ID
|
||||
N = output the force and torque every N timesteps
|
||||
forcegroup-ID = ID of the particle group to calculate the force and torque of
|
||||
<em>trilinear</em> values = none (used to switch from the default Peskin interpolation stencil to the trilinear stencil).
|
||||
<em>D3Q19</em> values = none (used to switch from the default D3Q15, 15 velocity lattice, to the D3Q19, 19 velocity lattice).
|
||||
<em>read_restart</em> values = restart file = name of the restart file to use to restart a fluid run.
|
||||
<em>write_restart</em> values = N = write a restart file every N MD timesteps.
|
||||
<em>zwall_velocity</em> values = velocity_bottom velocity_top = velocities along the y-direction of the bottom and top walls (located at z=zmin and z=zmax).
|
||||
<em>bodyforce</em> values = bodyforcex bodyforcey bodyforcez = the x,y and z components of a constant body force added to the fluid.
|
||||
<em>printfluid</em> values = N = print the fluid density and velocity at each grid point every N timesteps.
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -140,7 +140,7 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>linear</em> values = xflag yflag zflag
|
||||
xflag,yflag,zflag = 0/1 to exclude/include each dimension.
|
||||
xflag,yflag,zflag = 0/1 to exclude/include each dimension.
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -154,13 +154,13 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>force</em> values = M xflag yflag zflag
|
||||
M = which rigid body from 1-Nbody (see asterisk form below)
|
||||
xflag,yflag,zflag = off/on if component of center-of-mass force is active
|
||||
<em>torque</em> values = M xflag yflag zflag
|
||||
M = which rigid body from 1-Nbody (see asterisk form below)
|
||||
xflag,yflag,zflag = off/on if component of center-of-mass torque is active
|
||||
<em>innerNodes</em> values = innergroup-ID
|
||||
innergroup-ID = ID of the atom group which does not experience a hydrodynamic force from the lattice-Boltzmann fluid
|
||||
M = which rigid body from 1-Nbody (see asterisk form below)
|
||||
xflag,yflag,zflag = off/on if component of center-of-mass force is active
|
||||
<em>torque</em> values = M xflag yflag zflag
|
||||
M = which rigid body from 1-Nbody (see asterisk form below)
|
||||
xflag,yflag,zflag = off/on if component of center-of-mass torque is active
|
||||
<em>innerNodes</em> values = innergroup-ID
|
||||
innergroup-ID = ID of the atom group which does not experience a hydrodynamic force from the lattice-Boltzmann fluid
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -138,8 +138,8 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>temp</em> value = compute ID that calculates a temperature
|
||||
<em>press</em> value = compute ID that calculates a pressure
|
||||
<em>energy</em> value = <em>yes</em> or <em>no</em>
|
||||
<em>press</em> value = compute ID that calculates a pressure
|
||||
<em>energy</em> value = <em>yes</em> or <em>no</em>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -140,8 +140,8 @@ one or more keyword/value pairs may be appended</li>
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>linear</em> values = xflag yflag zflag
|
||||
xflag,yflag,zflag = 0/1 to exclude/include each dimension
|
||||
<em>angular</em> values = none
|
||||
xflag,yflag,zflag = 0/1 to exclude/include each dimension
|
||||
<em>angular</em> values = none
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
<em>rescale</em> values = none
|
||||
|
||||
@ -138,17 +138,17 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>linear</em> args = Vx Vy Vz
|
||||
Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
|
||||
<em>wiggle</em> args = Ax Ay Az period
|
||||
Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL
|
||||
period = period of oscillation (time units)
|
||||
<em>rotate</em> args = Px Py Pz Rx Ry Rz period
|
||||
Px,Py,Pz = origin point of axis of rotation (distance units)
|
||||
Rx,Ry,Rz = axis of rotation vector
|
||||
period = period of rotation (time units)
|
||||
<em>variable</em> args = v_dx v_dy v_dz v_vx v_vy v_vz
|
||||
v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL
|
||||
v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL
|
||||
Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
|
||||
<em>wiggle</em> args = Ax Ay Az period
|
||||
Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL
|
||||
period = period of oscillation (time units)
|
||||
<em>rotate</em> args = Px Py Pz Rx Ry Rz period
|
||||
Px,Py,Pz = origin point of axis of rotation (distance units)
|
||||
Rx,Ry,Rz = axis of rotation vector
|
||||
period = period of rotation (time units)
|
||||
<em>variable</em> args = v_dx v_dy v_dz v_vx v_vy v_vz
|
||||
v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL
|
||||
v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/value pairs may be appended</li>
|
||||
|
||||
@ -141,11 +141,11 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>q</em> value = cell mass-like parameter (mass^2/distance^4 units)
|
||||
<em>mu</em> value = artificial viscosity (mass/length/time units)
|
||||
<em>p0</em> value = initial pressure in the shock equations (pressure units)
|
||||
<em>v0</em> value = initial simulation cell volume in the shock equations (distance^3 units)
|
||||
<em>e0</em> value = initial total energy (energy units)
|
||||
<em>tscale</em> value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
|
||||
<em>mu</em> value = artificial viscosity (mass/length/time units)
|
||||
<em>p0</em> value = initial pressure in the shock equations (pressure units)
|
||||
<em>v0</em> value = initial simulation cell volume in the shock equations (distance^3 units)
|
||||
<em>e0</em> value = initial total energy (energy units)
|
||||
<em>tscale</em> value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -142,7 +142,7 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>update</em> value = <em>dipole</em>
|
||||
dipole = update orientation of dipole moment during integration
|
||||
dipole = update orientation of dipole moment during integration
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -260,21 +260,21 @@ Materials, 5, 124-127 (2006).</p>
|
||||
Sigma=5 <100> tilt boundary. This is for a lattice constant of 3.5706
|
||||
Angs.</p>
|
||||
<p>file0:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>0.798410432046075 1.785300000000000 1.596820864092150
|
||||
-0.798410432046075 1.785300000000000 -1.596820864092150
|
||||
2.395231296138225 0.000000000000000 0.798410432046075
|
||||
0.798410432046075 0.000000000000000 -2.395231296138225
|
||||
1.596820864092150 1.785300000000000 -0.798410432046075
|
||||
1.596820864092150 -1.785300000000000 -0.798410432046075
|
||||
<div class="highlight-python"><div class="highlight"><pre> 0.798410432046075 1.785300000000000 1.596820864092150
|
||||
-0.798410432046075 1.785300000000000 -1.596820864092150
|
||||
2.395231296138225 0.000000000000000 0.798410432046075
|
||||
0.798410432046075 0.000000000000000 -2.395231296138225
|
||||
1.596820864092150 1.785300000000000 -0.798410432046075
|
||||
1.596820864092150 -1.785300000000000 -0.798410432046075
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>file1:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>-0.798410432046075 1.785300000000000 1.596820864092150
|
||||
0.798410432046075 1.785300000000000 -1.596820864092150
|
||||
0.798410432046075 0.000000000000000 2.395231296138225
|
||||
2.395231296138225 0.000000000000000 -0.798410432046075
|
||||
1.596820864092150 1.785300000000000 0.798410432046075
|
||||
1.596820864092150 -1.785300000000000 0.798410432046075
|
||||
0.798410432046075 1.785300000000000 -1.596820864092150
|
||||
0.798410432046075 0.000000000000000 2.395231296138225
|
||||
2.395231296138225 0.000000000000000 -0.798410432046075
|
||||
1.596820864092150 1.785300000000000 0.798410432046075
|
||||
1.596820864092150 -1.785300000000000 0.798410432046075
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
@ -144,8 +144,8 @@
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
<em>GAMMA</em> flags to treate the whole simulation box as a unit cell, so that the mapping
|
||||
info can be generated internally. In this case, dynamical matrix at only the gamma-point
|
||||
will/can be evaluated.
|
||||
info can be generated internally. In this case, dynamical matrix at only the gamma-point
|
||||
will/can be evaluated.
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>prefix = prefix for output files</li>
|
||||
@ -154,9 +154,9 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>sysdim</em> value = d
|
||||
d = dimension of the system, usually the same as the MD model dimension
|
||||
<em>nasr</em> value = n
|
||||
n = number of iterations to enforce the acoustic sum rule
|
||||
d = dimension of the system, usually the same as the MD model dimension
|
||||
<em>nasr</em> value = n
|
||||
n = number of iterations to enforce the acoustic sum rule
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -139,10 +139,10 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>method</em> value = <em>pimd</em> or <em>nmpimd</em> or <em>cmd</em>
|
||||
<em>fmass</em> value = scaling factor on mass
|
||||
<em>sp</em> value = scaling factor on Planck constant
|
||||
<em>temp</em> value = temperature (temperarate units)
|
||||
<em>nhc</em> value = Nc = number of chains in Nose-Hoover thermostat
|
||||
<em>fmass</em> value = scaling factor on mass
|
||||
<em>sp</em> value = scaling factor on Planck constant
|
||||
<em>temp</em> value = temperature (temperarate units)
|
||||
<em>nhc</em> value = Nc = number of chains in Nose-Hoover thermostat
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -137,8 +137,8 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>group</em> values = list of group IDs
|
||||
<em>molecule</em> values = none
|
||||
<em>file</em> values = filename
|
||||
<em>molecule</em> values = none
|
||||
<em>file</em> values = filename
|
||||
</pre>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
|
||||
|
||||
@ -142,37 +142,37 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>region</em> value = region-ID
|
||||
region-ID = ID of region to use as insertion volume
|
||||
<em>diam</em> values = dstyle args
|
||||
dstyle = <em>one</em> or <em>range</em> or <em>poly</em>
|
||||
<em>one</em> args = D
|
||||
D = single diameter for inserted particles (distance units)
|
||||
<em>range</em> args = Dlo Dhi
|
||||
Dlo,Dhi = range of diameters for inserted particles (distance units)
|
||||
<em>poly</em> args = Npoly D1 P1 D2 P2 ...
|
||||
Npoly = # of (D,P) pairs
|
||||
D1,D2,... = diameter for subset of inserted particles (distance units)
|
||||
P1,P2,... = percentage of inserted particles with this diameter (0-1)
|
||||
<em>vol</em> values = fraction Nattempt
|
||||
fraction = desired volume fraction for filling insertion volume
|
||||
Nattempt = max # of insertion attempts per atom
|
||||
<em>rate</em> value = V
|
||||
V = z velocity (3d) or y velocity (2d) at which
|
||||
insertion volume moves (velocity units)
|
||||
<em>vel</em> values (3d) = vxlo vxhi vylo vyhi vz
|
||||
<em>vel</em> values (2d) = vxlo vxhi vy
|
||||
vxlo,vxhi = range of x velocities for inserted particles (velocity units)
|
||||
vylo,vyhi = range of y velocities for inserted particles (velocity units)
|
||||
vz = z velocity (3d) assigned to inserted particles (velocity units)
|
||||
vy = y velocity (2d) assigned to inserted particles (velocity units)
|
||||
<em>mol</em> value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
|
||||
<em>molfrac</em> values = f1 f2 ... fN
|
||||
f1 to fN = relative probability of creating each of N molecules in template-ID
|
||||
<em>rigid</em> value = fix-ID
|
||||
fix-ID = ID of <a class="reference internal" href="fix_rigid.html"><em>fix rigid/small</em></a> command
|
||||
<em>shake</em> value = fix-ID
|
||||
fix-ID = ID of <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command
|
||||
region-ID = ID of region to use as insertion volume
|
||||
<em>diam</em> values = dstyle args
|
||||
dstyle = <em>one</em> or <em>range</em> or <em>poly</em>
|
||||
<em>one</em> args = D
|
||||
D = single diameter for inserted particles (distance units)
|
||||
<em>range</em> args = Dlo Dhi
|
||||
Dlo,Dhi = range of diameters for inserted particles (distance units)
|
||||
<em>poly</em> args = Npoly D1 P1 D2 P2 ...
|
||||
Npoly = # of (D,P) pairs
|
||||
D1,D2,... = diameter for subset of inserted particles (distance units)
|
||||
P1,P2,... = percentage of inserted particles with this diameter (0-1)
|
||||
<em>vol</em> values = fraction Nattempt
|
||||
fraction = desired volume fraction for filling insertion volume
|
||||
Nattempt = max # of insertion attempts per atom
|
||||
<em>rate</em> value = V
|
||||
V = z velocity (3d) or y velocity (2d) at which
|
||||
insertion volume moves (velocity units)
|
||||
<em>vel</em> values (3d) = vxlo vxhi vylo vyhi vz
|
||||
<em>vel</em> values (2d) = vxlo vxhi vy
|
||||
vxlo,vxhi = range of x velocities for inserted particles (velocity units)
|
||||
vylo,vyhi = range of y velocities for inserted particles (velocity units)
|
||||
vz = z velocity (3d) assigned to inserted particles (velocity units)
|
||||
vy = y velocity (2d) assigned to inserted particles (velocity units)
|
||||
<em>mol</em> value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
|
||||
<em>molfrac</em> values = f1 f2 ... fN
|
||||
f1 to fN = relative probability of creating each of N molecules in template-ID
|
||||
<em>rigid</em> value = fix-ID
|
||||
fix-ID = ID of <a class="reference internal" href="fix_rigid.html"><em>fix rigid/small</em></a> command
|
||||
<em>shake</em> value = fix-ID
|
||||
fix-ID = ID of <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -141,10 +141,10 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>file</em> value = filename
|
||||
<em>append</em> value = filename
|
||||
<em>screen</em> value = <em>yes</em> or <em>no</em>
|
||||
<em>title</em> value = string
|
||||
string = text to print as 1st line of output file
|
||||
<em>append</em> value = filename
|
||||
<em>screen</em> value = <em>yes</em> or <em>no</em>
|
||||
<em>title</em> value = string
|
||||
string = text to print as 1st line of output file
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -138,9 +138,9 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>mol</em> = molecule IDs
|
||||
<em>q</em> = charge
|
||||
<em>i_name</em> = new integer vector referenced by name
|
||||
<em>d_name</em> = new floating-point vector referenced by name
|
||||
<em>q</em> = charge
|
||||
<em>i_name</em> = new integer vector referenced by name
|
||||
<em>d_name</em> = new floating-point vector referenced by name
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero of more keyword/value pairs may be appended</li>
|
||||
|
||||
@ -141,18 +141,18 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>q</em> value = cell mass-like parameter (mass^2/distance^4 units)
|
||||
<em>mu</em> value = artificial viscosity (mass/distance/time units)
|
||||
<em>p0</em> value = initial pressure in the shock equations (pressure units)
|
||||
<em>v0</em> value = initial simulation cell volume in the shock equations (distance^3 units)
|
||||
<em>e0</em> value = initial total energy (energy units)
|
||||
<em>tscale</em> value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
|
||||
<em>damp</em> value = damping parameter (time units) inverse of friction <i>&gamma;</i>
|
||||
<em>seed</em> value = random number seed (positive integer)
|
||||
<em>f_max</em> value = upper cutoff frequency of the vibration spectrum (1/time units)
|
||||
<em>N_f</em> value = number of frequency bins (positive integer)
|
||||
<em>eta</em> value = coupling constant between the shock system and the quantum thermal bath (positive unitless)
|
||||
<em>beta</em> value = the quantum temperature is updated every beta time steps (positive integer)
|
||||
<em>T_init</em> value = quantum temperature for the initial state (temperature units)
|
||||
<em>mu</em> value = artificial viscosity (mass/distance/time units)
|
||||
<em>p0</em> value = initial pressure in the shock equations (pressure units)
|
||||
<em>v0</em> value = initial simulation cell volume in the shock equations (distance^3 units)
|
||||
<em>e0</em> value = initial total energy (energy units)
|
||||
<em>tscale</em> value = reduction in initial temperature (unitless fraction between 0.0 and 1.0)
|
||||
<em>damp</em> value = damping parameter (time units) inverse of friction <i>&gamma;</i>
|
||||
<em>seed</em> value = random number seed (positive integer)
|
||||
<em>f_max</em> value = upper cutoff frequency of the vibration spectrum (1/time units)
|
||||
<em>N_f</em> value = number of frequency bins (positive integer)
|
||||
<em>eta</em> value = coupling constant between the shock system and the quantum thermal bath (positive unitless)
|
||||
<em>beta</em> value = the quantum temperature is updated every beta time steps (positive integer)
|
||||
<em>T_init</em> value = quantum temperature for the initial state (temperature units)
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -144,7 +144,7 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>file</em> value = filename
|
||||
filename = name of file to write QEQ equilibration info to
|
||||
filename = name of file to write QEQ equilibration info to
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -139,10 +139,10 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>temp</em> value = target quantum temperature (temperature units)
|
||||
<em>damp</em> value = damping parameter (time units) inverse of friction <i>&gamma</i>;
|
||||
<em>seed</em> value = random number seed (positive integer)
|
||||
<em>f_max</em> value = upper cutoff frequency of the vibration spectrum (1/time units)
|
||||
<em>N_f</em> value = number of frequency bins (positive integer)
|
||||
<em>damp</em> value = damping parameter (time units) inverse of friction <i>&gamma</i>;
|
||||
<em>seed</em> value = random number seed (positive integer)
|
||||
<em>f_max</em> value = upper cutoff frequency of the vibration spectrum (1/time units)
|
||||
<em>N_f</em> value = number of frequency bins (positive integer)
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -143,12 +143,12 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>cutoff</em> value = I J Cutoff
|
||||
I, J = atom types
|
||||
Cutoff = Bond-order cutoff value for this pair of atom types
|
||||
<em>element</em> value = Element1, Element2, ...
|
||||
<em>position</em> value = posfreq filepos
|
||||
posfreq = write position files every this many timestep
|
||||
filepos = name of position output file
|
||||
I, J = atom types
|
||||
Cutoff = Bond-order cutoff value for this pair of atom types
|
||||
<em>element</em> value = Element1, Element2, ...
|
||||
<em>position</em> value = posfreq filepos
|
||||
posfreq = write position files every this many timestep
|
||||
filepos = name of position output file
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -140,8 +140,8 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>shift</em> value = group-ID
|
||||
group-ID = group of atoms whose coords are shifted
|
||||
<em>units</em> value = <em>box</em> or <em>lattice</em> or <em>fraction</em>
|
||||
group-ID = group of atoms whose coords are shifted
|
||||
<em>units</em> value = <em>box</em> or <em>lattice</em> or <em>fraction</em>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -139,17 +139,17 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>bond</em> args = atom1 atom2 Kstart Kstop r0
|
||||
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)
|
||||
<em>angle</em> 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)
|
||||
theta0 = equilibrium angle theta (degrees)
|
||||
<em>dihedral</em> args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
|
||||
atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
|
||||
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
|
||||
phi0 = equilibrium dihedral angle phi (degrees)
|
||||
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)
|
||||
<em>angle</em> 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)
|
||||
theta0 = equilibrium angle theta (degrees)
|
||||
<em>dihedral</em> args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
|
||||
atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
|
||||
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
|
||||
phi0 = equilibrium dihedral angle phi (degrees)
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -165,10 +165,10 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>single</em> args = none
|
||||
<em>molecule</em> args = none
|
||||
<em>group</em> args = N groupID1 groupID2 ...
|
||||
N = # of groups
|
||||
groupID1, groupID2, ... = list of N group IDs
|
||||
<em>molecule</em> args = none
|
||||
<em>group</em> args = N groupID1 groupID2 ...
|
||||
N = # of groups
|
||||
groupID1, groupID2, ... = list of N group IDs
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/value pairs may be appended</li>
|
||||
@ -176,37 +176,37 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>langevin</em> values = Tstart Tstop Tperiod seed
|
||||
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
|
||||
Tdamp = temperature damping parameter (time units)
|
||||
seed = random number seed to use for white noise (positive integer)
|
||||
<em>temp</em> values = Tstart Tstop Tdamp
|
||||
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
|
||||
Tdamp = temperature damping parameter (time units)
|
||||
<em>iso</em> or <em>aniso</em> values = Pstart Pstop Pdamp
|
||||
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
|
||||
Pdamp = pressure damping parameter (time units)
|
||||
<em>x</em> or <em>y</em> or <em>z</em> values = Pstart Pstop Pdamp
|
||||
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
|
||||
Pdamp = stress damping parameter (time units)
|
||||
<em>couple</em> = <em>none</em> or <em>xyz</em> or <em>xy</em> or <em>yz</em> or <em>xz</em>
|
||||
<em>tparam</em> values = Tchain Titer Torder
|
||||
Tchain = length of Nose/Hoover thermostat chain
|
||||
Titer = number of thermostat iterations performed
|
||||
Torder = 3 or 5 = Yoshida-Suzuki integration parameters
|
||||
<em>pchain</em> values = Pchain
|
||||
Pchain = length of the Nose/Hoover thermostat chain coupled with the barostat
|
||||
<em>dilate</em> value = dilate-group-ID
|
||||
dilate-group-ID = only dilate atoms in this group due to barostat volume changes
|
||||
<em>force</em> values = M xflag yflag zflag
|
||||
M = which rigid body from 1-Nbody (see asterisk form below)
|
||||
xflag,yflag,zflag = off/on if component of center-of-mass force is active
|
||||
<em>torque</em> values = M xflag yflag zflag
|
||||
M = which rigid body from 1-Nbody (see asterisk form below)
|
||||
xflag,yflag,zflag = off/on if component of center-of-mass torque is active
|
||||
<em>infile</em> filename
|
||||
filename = file with per-body values of mass, center-of-mass, moments of inertia
|
||||
<em>mol</em> value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
|
||||
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
|
||||
Tdamp = temperature damping parameter (time units)
|
||||
seed = random number seed to use for white noise (positive integer)
|
||||
<em>temp</em> values = Tstart Tstop Tdamp
|
||||
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
|
||||
Tdamp = temperature damping parameter (time units)
|
||||
<em>iso</em> or <em>aniso</em> values = Pstart Pstop Pdamp
|
||||
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
|
||||
Pdamp = pressure damping parameter (time units)
|
||||
<em>x</em> or <em>y</em> or <em>z</em> values = Pstart Pstop Pdamp
|
||||
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
|
||||
Pdamp = stress damping parameter (time units)
|
||||
<em>couple</em> = <em>none</em> or <em>xyz</em> or <em>xy</em> or <em>yz</em> or <em>xz</em>
|
||||
<em>tparam</em> values = Tchain Titer Torder
|
||||
Tchain = length of Nose/Hoover thermostat chain
|
||||
Titer = number of thermostat iterations performed
|
||||
Torder = 3 or 5 = Yoshida-Suzuki integration parameters
|
||||
<em>pchain</em> values = Pchain
|
||||
Pchain = length of the Nose/Hoover thermostat chain coupled with the barostat
|
||||
<em>dilate</em> value = dilate-group-ID
|
||||
dilate-group-ID = only dilate atoms in this group due to barostat volume changes
|
||||
<em>force</em> values = M xflag yflag zflag
|
||||
M = which rigid body from 1-Nbody (see asterisk form below)
|
||||
xflag,yflag,zflag = off/on if component of center-of-mass force is active
|
||||
<em>torque</em> values = M xflag yflag zflag
|
||||
M = which rigid body from 1-Nbody (see asterisk form below)
|
||||
xflag,yflag,zflag = off/on if component of center-of-mass torque is active
|
||||
<em>infile</em> filename
|
||||
filename = file with per-body values of mass, center-of-mass, moments of inertia
|
||||
<em>mol</em> value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -144,7 +144,7 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>region</em> value = region-ID
|
||||
region-ID = ID of region atoms must be in to have added force
|
||||
region-ID = ID of region atoms must be in to have added force
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -148,9 +148,9 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>b</em> values = one or more bond types
|
||||
<em>a</em> values = one or more angle types
|
||||
<em>t</em> values = one or more atom types
|
||||
<em>m</em> value = one or more mass values
|
||||
<em>a</em> values = one or more angle types
|
||||
<em>t</em> values = one or more atom types
|
||||
<em>m</em> value = one or more mass values
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/value pairs may be appended</li>
|
||||
@ -158,7 +158,7 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>mol</em> value = template-ID
|
||||
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
|
||||
template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -138,22 +138,22 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>cvel</em> values = K vel
|
||||
K = spring constant (force/distance units)
|
||||
vel = velocity of pulling (distance/time units)
|
||||
<em>cfor</em> values = force
|
||||
force = pulling force (force units)
|
||||
K = spring constant (force/distance units)
|
||||
vel = velocity of pulling (distance/time units)
|
||||
<em>cfor</em> values = force
|
||||
force = pulling force (force units)
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>keyword = <em>tether</em> or <em>couple</em></li>
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>tether</em> values = x y z R0
|
||||
x,y,z = point to which spring is tethered
|
||||
R0 = distance of end of spring from tether point (distance units)
|
||||
<em>couple</em> values = group-ID2 x y z R0
|
||||
group-ID2 = 2nd group to couple to fix group with a spring
|
||||
x,y,z = direction of spring, automatically computed with 'auto'
|
||||
R0 = distance of end of spring (distance units)
|
||||
x,y,z = point to which spring is tethered
|
||||
R0 = distance of end of spring from tether point (distance units)
|
||||
<em>couple</em> values = group-ID2 x y z R0
|
||||
group-ID2 = 2nd group to couple to fix group with a spring
|
||||
x,y,z = direction of spring, automatically computed with 'auto'
|
||||
R0 = distance of end of spring (distance units)
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -138,14 +138,14 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>tether</em> values = K x y z R0
|
||||
K = spring constant (force/distance units)
|
||||
x,y,z = point to which spring is tethered
|
||||
R0 = equilibrium distance from tether point (distance units)
|
||||
<em>couple</em> values = group-ID2 K x y z R0
|
||||
group-ID2 = 2nd group to couple to fix group with a spring
|
||||
K = spring constant (force/distance units)
|
||||
x,y,z = direction of spring
|
||||
R0 = equilibrium distance of spring (distance units)
|
||||
K = spring constant (force/distance units)
|
||||
x,y,z = point to which spring is tethered
|
||||
R0 = equilibrium distance from tether point (distance units)
|
||||
<em>couple</em> values = group-ID2 K x y z R0
|
||||
group-ID2 = 2nd group to couple to fix group with a spring
|
||||
K = spring constant (force/distance units)
|
||||
x,y,z = direction of spring
|
||||
R0 = equilibrium distance of spring (distance units)
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -144,28 +144,28 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>lamda</em> value = mean free path of SRD particles (distance units)
|
||||
<em>collision</em> value = <em>noslip</em> or <em>slip</em> = collision model
|
||||
<em>overlap</em> value = <em>yes</em> or <em>no</em> = whether big particles may overlap
|
||||
<em>inside</em> value = <em>error</em> or <em>warn</em> or <em>ignore</em> = how SRD particles which end up inside a big particle are treated
|
||||
<em>exact</em> value = <em>yes</em> or <em>no</em>
|
||||
<em>radius</em> value = rfactor = scale collision radius by this factor
|
||||
<em>bounce</em> value = Nbounce = max # of collisions an SRD particle can undergo in one timestep
|
||||
<em>search</em> value = sgrid = grid spacing for collision partner searching (distance units)
|
||||
<em>cubic</em> values = style tolerance
|
||||
style = <em>error</em> or <em>warn</em>
|
||||
tolerance = fractional difference allowed (0 <= tol <= 1)
|
||||
<em>shift</em> values = flag shiftseed
|
||||
flag = <em>yes</em> or <em>no</em> or <em>possible</em> = SRD bin shifting for better statistics
|
||||
<em>yes</em> = perform bin shifting each time SRD velocities are rescaled
|
||||
<em>no</em> = no shifting
|
||||
<em>possible</em> = shift depending on mean free path and bin size
|
||||
shiftseed = random # seed (positive integer)
|
||||
<em>tstat</em> value = <em>yes</em> or <em>no</em> = thermostat SRD particles or not
|
||||
<em>rescale</em> value = <em>yes</em> or <em>no</em> or <em>rotate</em> or <em>collide</em> = rescaling of SRD velocities
|
||||
<em>yes</em> = rescale during velocity rotation and collisions
|
||||
<em>no</em> = no rescaling
|
||||
<em>rotate</em> = rescale during velocity rotation, but not collisions
|
||||
<em>collide</em> = rescale during collisions, but not velocity rotation
|
||||
<em>collision</em> value = <em>noslip</em> or <em>slip</em> = collision model
|
||||
<em>overlap</em> value = <em>yes</em> or <em>no</em> = whether big particles may overlap
|
||||
<em>inside</em> value = <em>error</em> or <em>warn</em> or <em>ignore</em> = how SRD particles which end up inside a big particle are treated
|
||||
<em>exact</em> value = <em>yes</em> or <em>no</em>
|
||||
<em>radius</em> value = rfactor = scale collision radius by this factor
|
||||
<em>bounce</em> value = Nbounce = max # of collisions an SRD particle can undergo in one timestep
|
||||
<em>search</em> value = sgrid = grid spacing for collision partner searching (distance units)
|
||||
<em>cubic</em> values = style tolerance
|
||||
style = <em>error</em> or <em>warn</em>
|
||||
tolerance = fractional difference allowed (0 <= tol <= 1)
|
||||
<em>shift</em> values = flag shiftseed
|
||||
flag = <em>yes</em> or <em>no</em> or <em>possible</em> = SRD bin shifting for better statistics
|
||||
<em>yes</em> = perform bin shifting each time SRD velocities are rescaled
|
||||
<em>no</em> = no shifting
|
||||
<em>possible</em> = shift depending on mean free path and bin size
|
||||
shiftseed = random # seed (positive integer)
|
||||
<em>tstat</em> value = <em>yes</em> or <em>no</em> = thermostat SRD particles or not
|
||||
<em>rescale</em> value = <em>yes</em> or <em>no</em> or <em>rotate</em> or <em>collide</em> = rescaling of SRD velocities
|
||||
<em>yes</em> = rescale during velocity rotation and collisions
|
||||
<em>no</em> = no rescaling
|
||||
<em>rotate</em> = rescale during velocity rotation, but not collisions
|
||||
<em>collide</em> = rescale during collisions, but not velocity rotation
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -138,38 +138,38 @@
|
||||
<li>input = one or more atom attributes</li>
|
||||
</ul>
|
||||
<div class="highlight-python"><div class="highlight"><pre>possible attributes = id, mol, type, mass,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz,
|
||||
radius, omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz, tqx, tqy, tqz,
|
||||
c_ID, c_ID[N], f_ID, f_ID[N], v_name,
|
||||
d_name, i_name
|
||||
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz,
|
||||
radius, omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz, tqx, tqy, tqz,
|
||||
c_ID, c_ID[N], f_ID, f_ID[N], v_name,
|
||||
d_name, i_name
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-python"><div class="highlight"><pre>id = atom ID
|
||||
mol = molecule ID
|
||||
type = atom type
|
||||
mass = atom mass
|
||||
x,y,z = unscaled atom coordinates
|
||||
xs,ys,zs = scaled atom coordinates
|
||||
xu,yu,zu = unwrapped atom coordinates
|
||||
ix,iy,iz = box image that the atom is in
|
||||
vx,vy,vz = atom velocities
|
||||
fx,fy,fz = forces on atoms
|
||||
q = atom charge
|
||||
mux,muy,muz = orientation of dipolar atom
|
||||
radius = radius of spherical particle
|
||||
omegax,omegay,omegaz = angular velocity of spherical particle
|
||||
angmomx,angmomy,angmomz = angular momentum of aspherical particle
|
||||
tqx,tqy,tqz = torque on finite-size particles
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
|
||||
f_ID = per-atom vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
d_name = per-atom floating point vector name, managed by fix property/atom
|
||||
i_name = per-atom integer vector name, managed by fix property/atom
|
||||
mol = molecule ID
|
||||
type = atom type
|
||||
mass = atom mass
|
||||
x,y,z = unscaled atom coordinates
|
||||
xs,ys,zs = scaled atom coordinates
|
||||
xu,yu,zu = unwrapped atom coordinates
|
||||
ix,iy,iz = box image that the atom is in
|
||||
vx,vy,vz = atom velocities
|
||||
fx,fy,fz = forces on atoms
|
||||
q = atom charge
|
||||
mux,muy,muz = orientation of dipolar atom
|
||||
radius = radius of spherical particle
|
||||
omegax,omegay,omegaz = angular velocity of spherical particle
|
||||
angmomx,angmomy,angmomz = angular momentum of aspherical particle
|
||||
tqx,tqy,tqz = torque on finite-size particles
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
|
||||
f_ID = per-atom vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
d_name = per-atom floating point vector name, managed by fix property/atom
|
||||
i_name = per-atom integer vector name, managed by fix property/atom
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
|
||||
@ -142,8 +142,8 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>com</em> args = xflag yflag zflag
|
||||
xflag,yflag,zflag = 0/1 to exclude/include each dimension
|
||||
<em>rot</em> args = none
|
||||
xflag,yflag,zflag = 0/1 to exclude/include each dimension
|
||||
<em>rot</em> args = none
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
|
||||
@ -140,7 +140,7 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>function</em> value = function-ID
|
||||
function-ID = ID of the switching function (1, 2 or 3)
|
||||
function-ID = ID of the switching function (1, 2 or 3)
|
||||
</pre>
|
||||
<p><strong>Example:</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>fix ref all ti/rs 50.0 2000 1000
|
||||
|
||||
@ -141,7 +141,7 @@
|
||||
</ul>
|
||||
<pre class="literal-block">
|
||||
<em>function</em> value = function-ID
|
||||
function-ID = ID of the switching function (1 or 2)
|
||||
function-ID = ID of the switching function (1 or 2)
|
||||
</pre>
|
||||
<p><strong>Example:</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>fix ref all ti/spring 50.0 2000 1000 function 2
|
||||
|
||||
@ -142,29 +142,29 @@ fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile
|
||||
<li>remaining arguments for fix ttm:</li>
|
||||
</ul>
|
||||
<div class="highlight-python"><div class="highlight"><pre>C_e = electronic specific heat (energy/(electron*temperature) units)
|
||||
rho_e = electronic density (electrons/volume units)
|
||||
kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units)
|
||||
gamma_p = friction coefficient due to electron-ion interactions (mass/time units)
|
||||
gamma_s = friction coefficient due to electronic stopping (mass/time units)
|
||||
v_0 = electronic stopping critical velocity (velocity units)
|
||||
Nx = number of thermal solve grid points in the x-direction (positive integer)
|
||||
Ny = number of thermal solve grid points in the y-direction (positive integer)
|
||||
Nz = number of thermal solve grid points in the z-direction (positive integer)
|
||||
T_infile = filename to read initial electronic temperature from
|
||||
N = dump TTM temperatures every this many timesteps, 0 = no dump
|
||||
T_outfile = filename to write TTM temperatures to (only needed if N > 0)
|
||||
rho_e = electronic density (electrons/volume units)
|
||||
kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units)
|
||||
gamma_p = friction coefficient due to electron-ion interactions (mass/time units)
|
||||
gamma_s = friction coefficient due to electronic stopping (mass/time units)
|
||||
v_0 = electronic stopping critical velocity (velocity units)
|
||||
Nx = number of thermal solve grid points in the x-direction (positive integer)
|
||||
Ny = number of thermal solve grid points in the y-direction (positive integer)
|
||||
Nz = number of thermal solve grid points in the z-direction (positive integer)
|
||||
T_infile = filename to read initial electronic temperature from
|
||||
N = dump TTM temperatures every this many timesteps, 0 = no dump
|
||||
T_outfile = filename to write TTM temperatures to (only needed if N > 0)
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li>remaining arguments for fix ttm/mod:</li>
|
||||
</ul>
|
||||
<div class="highlight-python"><div class="highlight"><pre>init_file = file with the parameters to TTM
|
||||
Nx = number of thermal solve grid points in the x-direction (positive integer)
|
||||
Ny = number of thermal solve grid points in the y-direction (positive integer)
|
||||
Nz = number of thermal solve grid points in the z-direction (positive integer)
|
||||
T_infile = filename to read initial electronic temperature from
|
||||
N = dump TTM temperatures every this many timesteps, 0 = no dump
|
||||
T_outfile = filename to write TTM temperatures to (only needed if N > 0)
|
||||
Nx = number of thermal solve grid points in the x-direction (positive integer)
|
||||
Ny = number of thermal solve grid points in the y-direction (positive integer)
|
||||
Nz = number of thermal solve grid points in the z-direction (positive integer)
|
||||
T_infile = filename to read initial electronic temperature from
|
||||
N = dump TTM temperatures every this many timesteps, 0 = no dump
|
||||
T_outfile = filename to write TTM temperatures to (only needed if N > 0)
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
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Reference in New Issue
Block a user