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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13806 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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2015-07-30 16:49:30 +00:00
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2
doc/_static/css/theme.css vendored
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@ -3743,7 +3743,7 @@ hr {
display: block;
height: 1px;
border: 0;
border-top: 1px solid #e1e4e5;
border-top: 2px solid #e1e4e5;
margin: 24px 0;
padding: 0;
}

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doc/atom_modify.html
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@ -137,9 +137,9 @@
</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
<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)
</pre>

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doc/atom_style.html
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@ -136,13 +136,13 @@
</ul>
<pre class="literal-block">
args = none for any style except <em>body</em> and <em>hybrid</em>
<em>body</em> args = bstyle bstyle-args
<em>body</em> args = bstyle bstyle-args
bstyle = style of body particles
bstyle-args = additional arguments specific to the bstyle
see the <a class="reference internal" href="body.html"><em>body</em></a> doc page for details
<em>template</em> args = template-ID
<em>template</em> args = 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>hybrid</em> args = list of one or more sub-styles, each with their args
<em>hybrid</em> args = list of one or more sub-styles, each with their args
</pre>
<ul class="simple">
<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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doc/balance.html
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@ -141,19 +141,19 @@
<em>uniform</em> = evenly spaced cuts between processors in x dimension
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>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>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
<em>shift</em> args = dimstr Niter stopthresh
dimstr = sequence of letters containing &quot;x&quot; or &quot;y&quot; or &quot;z&quot;, 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
<em>rcb</em> args = none
<em>rcb</em> args = none
</pre>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>

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doc/bond_style.html
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@ -136,7 +136,7 @@
</ul>
<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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doc/boundary.html
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@ -136,9 +136,9 @@
</ul>
<pre class="literal-block">
<em>p</em> is periodic
<em>f</em> is non-periodic and fixed
<em>s</em> is non-periodic and shrink-wrapped
<em>m</em> is non-periodic and shrink-wrapped with a minimum value
<em>f</em> is non-periodic and fixed
<em>s</em> is non-periodic and shrink-wrapped
<em>m</em> is non-periodic and shrink-wrapped with a minimum value
</pre>
</div>
<div class="section" id="examples">

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doc/comm_modify.html
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@ -137,9 +137,9 @@
</ul>
<pre class="literal-block">
<em>mode</em> value = <em>single</em> or <em>multi</em> = communicate atoms within a single or multiple distances
<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
<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
</pre>
</div>
<div class="section" id="examples">

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doc/compute_angle_local.html
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@ -139,7 +139,7 @@
</ul>
<pre class="literal-block">
<em>theta</em> = tabulate angles
<em>eng</em> = tabulate angle energies
<em>eng</em> = tabulate angle energies
</pre>
</div>
<div class="section" id="examples">

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doc/compute_body_local.html
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@ -139,7 +139,7 @@
</ul>
<pre class="literal-block">
<em>type</em> = atom type of the body particle
<em>integer</em> = 1,2,3,etc = index of fields defined by body style
<em>integer</em> = 1,2,3,etc = index of fields defined by body style
</pre>
</div>
<div class="section" id="examples">

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doc/compute_bond_local.html
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@ -139,8 +139,8 @@
</ul>
<pre class="literal-block">
<em>dist</em> = bond distance
<em>eng</em> = bond energy
<em>force</em> = bond force
<em>eng</em> = bond energy
<em>force</em> = bond force
</pre>
</div>
<div class="section" id="examples">

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doc/compute_chunk_atom.html
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@ -165,29 +165,29 @@ style = <em>bin/1d</em> or <em>bin/2d</em> or <em>bin/3d</em> or <em>type</em> o
<pre class="literal-block">
<em>region</em> value = region-ID
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>
<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
<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 &lt;= 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>
<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>
<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>
<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
<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>
<em>units</em> value = <em>box</em> or <em>lattice</em> or <em>reduced</em>
</pre>
</div>
<div class="section" id="examples">

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doc/compute_fep.html
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@ -144,7 +144,7 @@
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
<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)
@ -157,7 +157,7 @@
<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>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>

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doc/compute_group_group.html
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@ -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">

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doc/compute_modify.html
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@ -139,9 +139,9 @@
<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>
<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>
<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>

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doc/compute_pair_local.html
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@ -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">

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doc/compute_property_atom.html
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@ -156,54 +156,54 @@
</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">

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@ -145,17 +145,17 @@
</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>

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doc/compute_reduce.html
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@ -140,7 +140,7 @@
</ul>
<pre class="literal-block">
<em>reduce</em> arg = none
<em>reduce/region</em> arg = region-ID
<em>reduce/region</em> arg = region-ID
region-ID = ID of region to use for choosing atoms
</pre>
<ul class="simple">
@ -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">

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doc/compute_saed.html
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@ -142,17 +142,17 @@
<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
<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
<em>dR_Ewald</em> value = Thickness of Ewald sphere slice intercepting
reciprocal space (inverse length units)
<em>c</em> values = c1 c2 c3
<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
<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
<em>echo</em> = flag to provide extra output for debugging purposes
</pre>
</div>
<div class="section" id="examples">

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doc/compute_slice.html
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@ -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>

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doc/compute_sna_atom.html
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@ -156,8 +156,8 @@ compute ID group-ID snav/atom ntypes rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 .
<em>1</em> = subset satisfying j1 == j2
<em>2</em> = subset satisfying j1 == j2 == j3
<em>3</em> = subset satisfying j2 &lt;= j1 &lt;= 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>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>

2
doc/compute_temp_asphere.html
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@ -140,7 +140,7 @@
<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>
<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>

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@ -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">
@ -151,11 +151,11 @@
<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
<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
<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
<em>cdof</em> value = dof_per_chunk
dof_per_chunk = define this many degrees-of-freedom per chunk
</pre>
</div>

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@ -139,12 +139,12 @@
</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
<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">

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doc/compute_temp_sphere.html
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@ -140,7 +140,7 @@
<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>
<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>

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doc/compute_ti.html
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@ -142,11 +142,11 @@ 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
<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
<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

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@ -139,17 +139,17 @@
</ul>
<pre class="literal-block">
<em>only_group</em> = no arg
<em>occupation</em> = no arg
<em>surface</em> arg = sgroup-ID
<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
<em>radius</em> arg = v_r
v_r = radius atom style variable for a poly-disperse Voronoi tessellation
<em>edge_histo</em> arg = maxedge
<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
<em>edge_threshold</em> arg = minlength
minlength = minimum length for an edge to be counted
<em>face_threshold</em> arg = minarea
<em>face_threshold</em> arg = minarea
minarea = minimum area for a face to be counted
</pre>
</div>

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@ -143,14 +143,14 @@
<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
<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
<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
<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
<em>echo</em> = flag to provide extra output for debugging purposes
</pre>
</div>
<div class="section" id="examples">

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@ -137,11 +137,11 @@
</ul>
<pre class="literal-block">
<em>box</em> args = none
<em>region</em> args = region-ID
<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
<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
<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
@ -154,18 +154,18 @@
<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
<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
<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
<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>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>

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@ -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">

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@ -136,12 +136,12 @@
</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
<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
<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)
@ -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">

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@ -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>

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@ -138,15 +138,15 @@
<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
<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
<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
<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)

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@ -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
@ -191,33 +191,33 @@
</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">

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@ -147,44 +147,44 @@
</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
<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
<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
<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
<em>center</em> values = flag Cx Cy Cz = center point of image
flag = &quot;s&quot; for static, &quot;d&quot; 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 &quot;up&quot; in image
<em>up</em> values = Ux Uy Uz = direction that is &quot;up&quot; 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
<em>zoom</em> value = zfactor = size that simulation box appears in image
zfactor = scale image size by factor &gt; 1 to enlarge, factor &lt; 1 to shrink
zfactor can be a variable (see below)
<em>persp</em> value = pfactor = amount of &quot;perspective&quot; in image
<em>persp</em> value = pfactor = amount of &quot;perspective&quot; in image
pfactor = amount of perspective (0 = none, &lt; 1 = some, &gt; 1 = highly skewed)
pfactor can be a variable (see below)
<em>box</em> values = yes/no diam = draw outline of simulation box
<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
<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
<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
<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
<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

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@ -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
<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
<em>every</em> arg = N
N = dump every this many timesteps
N can be a variable (see below)
<em>fileper</em> arg = Np
<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
<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
<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 &quot;none&quot;
<em>scale</em> arg = <em>yes</em> or <em>no</em>
<em>sfactor</em> arg = coordinate scaling factor (&gt; 0.0)
<em>tfactor</em> arg = time scaling factor (&gt; 0.0)
<em>sort</em> arg = <em>off</em> or <em>id</em> or N or -N
<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 &quot;none&quot;
<em>scale</em> arg = <em>yes</em> or <em>no</em>
<em>sfactor</em> arg = coordinate scaling factor (&gt; 0.0)
<em>tfactor</em> arg = time scaling factor (&gt; 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
<em>thresh</em> args = attribute operation value
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
operation = &quot;&lt;&quot; or &quot;&lt;=&quot; or &quot;&gt;&quot; or &quot;&gt;=&quot; or &quot;==&quot; or &quot;!=&quot;
value = numeric value to compare to
these 3 args can be replaced by the word &quot;none&quot; to turn off thresholding
<em>unwrap</em> arg = <em>yes</em> or <em>no</em>
<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>
@ -181,10 +181,10 @@
<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
<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
<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 = &quot;c&quot; or &quot;d&quot; or &quot;s&quot; plus &quot;a&quot; or &quot;f&quot;
@ -204,22 +204,22 @@
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
<em>backcolor</em> arg = color
color = name of color for background
<em>bcolor</em> args = type color
<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
<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
<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
<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
<em>bitrate</em> arg = rate
rate = target bitrate for movie in kbps
<em>framerate</em> arg = fps
<em>framerate</em> arg = fps
fps = frames per second for movie
</pre>
</div>

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@ -144,9 +144,9 @@
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
<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
<em>atom</em> args = aparam v_name
aparam = parameter to adapt over time
v_name = variable with name that calculates value of aparam
</pre>
@ -158,7 +158,7 @@
<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>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>

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@ -144,9 +144,9 @@
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
<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
<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
@ -159,11 +159,11 @@
<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>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>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>

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@ -149,9 +149,9 @@
<pre class="literal-block">
<em>every</em> value = Nevery
Nevery = add force every this many timesteps
<em>region</em> value = region-ID
<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
<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>

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@ -142,19 +142,19 @@
<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
<em>size</em> args = Lz
Lz = z size of lattice region appended in a single event(distance units)
<em>freq</em> args = freq
<em>freq</em> args = freq
freq = the number of timesteps between append events
<em>temp</em> args = target damp seed extent
<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>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>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>

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@ -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 &quot;related&quot; section for possible fields)
<em>field</em> = on-the-fly post-processing using mesh-based localization functions (see &quot;related&quot; 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 &quot;related&quot; section for possible fields)
<em>field</em> = on-the-fly post-processing using mesh-based localization functions (see &quot;related&quot; 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 &quot;temperature&quot;
# 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

8
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@ -143,14 +143,14 @@
</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>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>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
<em>region</em> value = region-ID
region-ID = ID of region to use as an exchange/move volume
</pre>
</div>

10
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@ -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>

32
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@ -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">
@ -160,24 +160,24 @@
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>
<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
<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
<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
<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
<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
<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
<em>title2</em> arg = string
string = text to print as 2nd line of output file
<em>title3</em> arg = string
<em>title3</em> arg = string
string = text to print as 3rd line of output file
</pre>
</div>

24
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@ -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">
@ -159,21 +159,21 @@
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>
<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
<em>start</em> args = Nstart
Nstart = start accumulating correlations on this timestep
<em>prefactor</em> args = value
<em>prefactor</em> args = value
value = prefactor to scale all the correlation data by
<em>file</em> arg = filename
<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
<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
<em>title2</em> arg = string
string = text to print as 2nd line of output file
<em>title3</em> arg = string
<em>title3</em> arg = string
string = text to print as 3rd line of output file
</pre>
</div>

26
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@ -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">
@ -161,24 +161,24 @@
<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
<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>
<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
<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>
<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
<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
<em>title2</em> arg = string
string = text to print as 2nd line of output file
<em>title3</em> arg = string
<em>title3</em> arg = string
string = text to print as 3rd line of output file, only for vector mode
</pre>
</div>

36
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@ -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">
@ -163,29 +163,29 @@ 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
<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>
<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>
<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>
<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
<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
<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
<em>title2</em> arg = string
string = text to print as 2nd line of output file
<em>title3</em> arg = string
<em>title3</em> arg = string
string = text to print as 3rd line of output file
</pre>
</div>

28
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@ -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">
@ -160,20 +160,20 @@
<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>
<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
<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
<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
<em>title2</em> arg = string
string = text to print as 2nd line of output file
<em>title3</em> arg = string
<em>title3</em> arg = string
string = text to print as 3rd line of output file
</pre>
</div>

24
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View File

@ -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">
@ -155,22 +155,22 @@
<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>
<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
<em>start</em> args = Nstart
Nstart = start averaging on this timestep
<em>off</em> arg = M = do not average this value
<em>off</em> arg = M = do not average this value
M = value # from 1 to Nvalues
<em>file</em> arg = filename
<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
<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
<em>title2</em> arg = string
string = text to print as 2nd line of output file
<em>title3</em> arg = string
<em>title3</em> arg = string
string = text to print as 3rd line of output file, only for vector mode
</pre>
</div>

2
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@ -142,7 +142,7 @@
dimstr = sequence of letters containing &quot;x&quot; or &quot;y&quot; or &quot;z&quot;, 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
rcb args = none
</pre></div>
</div>
<ul class="simple">

10
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View File

@ -145,17 +145,17 @@
<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
<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
<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
<em>atype</em> value = angletype
angletype = type of created angles
<em>dtype</em> value = dihedraltype
<em>dtype</em> value = dihedraltype
dihedraltype = type of created dihedrals
<em>itype</em> value = impropertype
<em>itype</em> value = impropertype
impropertype = type of created impropers
</pre>
</div>

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@ -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>
<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>tstat</em> arg = fix id of a thermostat or NULL (default: NULL)
</pre>
</div>
<div class="section" id="examples">

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@ -190,9 +190,9 @@ parameter = <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>xz</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>
<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>
<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>

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@ -144,37 +144,37 @@
<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>
<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
<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
<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 &quot;nearby&quot; (distance units)
<em>near</em> value = R
<em>near</em> value = R
R = only insert atom/molecule if further than R from existing particles (distance units)
<em>attempt</em> value = Q
<em>attempt</em> value = Q
Q = attempt a single insertion up to Q times
<em>rate</em> value = V
<em>rate</em> value = V
V = z velocity (y in 2d) at which insertion volume moves (velocity units)
<em>vx</em> values = vxlo vxhi
<em>vx</em> values = vxlo vxhi
vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units)
<em>vy</em> values = vylo vyhi
<em>vy</em> values = vylo vyhi
vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units)
<em>vz</em> values = vzlo vzhi
<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
<em>target</em> values = tx ty tz
tx,ty,tz = location of target point (distance units)
<em>mol</em> value = template-ID
<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
<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
<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
<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>
<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>

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@ -142,7 +142,7 @@
<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
<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>

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@ -140,7 +140,7 @@
<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
<em>pf/array</em> args = Napply
Napply = apply array forces every Napply steps
</pre>
</div>

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@ -148,11 +148,11 @@
<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
<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
<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>

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@ -141,10 +141,10 @@
<em>unwrap</em> arg = <em>on</em> or <em>off</em>
off = coordinates are wrapped back into the principal unit cell (default)
on = &quot;unwrapped&quot; coordinates using the image flags used
<em>fscale</em> arg = factor
<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>
<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>

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@ -143,20 +143,20 @@
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
<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
<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>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>
<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>

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@ -148,19 +148,19 @@
<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>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>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
<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>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>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>

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@ -146,27 +146,27 @@
<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
<em>setGamma</em> values = gamma
gamma = user set value for the force coupling constant.
<em>scaleGamma</em> values = type gammaFactor
<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
<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
<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.
<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">

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@ -156,10 +156,10 @@
<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
<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
<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>

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@ -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">

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@ -141,7 +141,7 @@ one or more keyword/value pairs may be appended</li>
<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
<em>angular</em> values = none
</pre>
<pre class="literal-block">
<em>rescale</em> values = none

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@ -139,14 +139,14 @@
<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
<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
<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
<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>

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@ -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">

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@ -260,8 +260,8 @@ Materials, 5, 124-127 (2006).</p>
Sigma=5 &lt;100&gt; 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
<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

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@ -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>
@ -155,7 +155,7 @@
<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
<em>nasr</em> value = n
n = number of iterations to enforce the acoustic sum rule
</pre>
</div>

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@ -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">

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@ -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>

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@ -143,7 +143,7 @@
<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
<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)
@ -153,25 +153,25 @@
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
<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
<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
<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
<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
<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
<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
<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>

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@ -141,9 +141,9 @@
</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
<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>

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@ -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>

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@ -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 &lt;i&gt;&amp;gamma;&lt;/i&gt;
<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 &lt;i&gt;&amp;gamma;&lt;/i&gt;
<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">

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</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 &lt;i&gt;&amp;gamma&lt;/i&gt;;
<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 &lt;i&gt;&amp;gamma&lt;/i&gt;;
<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">

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@ -145,8 +145,8 @@
<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
<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>

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<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>
<em>units</em> value = <em>box</em> or <em>lattice</em> or <em>fraction</em>
</pre>
</div>
<div class="section" id="examples">

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@ -142,11 +142,11 @@
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
<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
<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)

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</ul>
<pre class="literal-block">
<em>single</em> args = none
<em>molecule</em> args = none
<em>group</em> args = N groupID1 groupID2 ...
<em>molecule</em> args = none
<em>group</em> args = N groupID1 groupID2 ...
N = # of groups
groupID1, groupID2, ... = list of N group IDs
</pre>
@ -179,33 +179,33 @@
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
<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
<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
<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
<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
<em>pchain</em> values = Pchain
Pchain = length of the Nose/Hoover thermostat chain coupled with the barostat
<em>dilate</em> value = dilate-group-ID
<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
<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
<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
<em>infile</em> filename
filename = file with per-body values of mass, center-of-mass, moments of inertia
<em>mol</em> value = template-ID
<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>

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@ -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>

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<em>cvel</em> values = K vel
K = spring constant (force/distance units)
vel = velocity of pulling (distance/time units)
<em>cfor</em> values = force
<em>cfor</em> values = force
force = pulling force (force units)
</pre>
<ul class="simple">
@ -150,7 +150,7 @@
<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
<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)

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@ -141,7 +141,7 @@
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
<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

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@ -144,24 +144,24 @@
</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
<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 &lt;= tol &lt;= 1)
<em>shift</em> values = flag shiftseed
<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>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

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@ -148,28 +148,28 @@
</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">

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@ -143,7 +143,7 @@
<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
<em>rot</em> args = none
</pre>
</div>
<div class="section" id="examples">

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@ -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 &gt; 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 &gt; 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 &gt; 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 &gt; 0)
</pre></div>
</div>
</div>

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@ -139,10 +139,10 @@
<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>
</div>

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@ -143,7 +143,7 @@
</ul>
<pre class="literal-block">
<em>swap</em> value = Nswap = number of swaps to perform every N steps
<em>vtarget</em> value = V or INF = target velocity of swap partners (velocity units)
<em>vtarget</em> value = V or INF = target velocity of swap partners (velocity units)
</pre>
</div>
<div class="section" id="examples">

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@ -169,10 +169,10 @@ args = coord epsilon sigma cutoff
<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
<em>fld</em> value = <em>yes</em> or <em>no</em>
<em>fld</em> value = <em>yes</em> or <em>no</em>
<em>yes</em> = invoke the wall constraint to be compatible with implicit FLD
<em>no</em> = invoke the wall constraint in the normal way
<em>pbc</em> value = <em>yes</em> or <em>no</em>
<em>pbc</em> value = <em>yes</em> or <em>no</em>
<em>yes</em> = allow periodic boundary in a wall dimension
<em>no</em> = require non-perioidic boundaries in any wall dimension
</pre>

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@ -146,7 +146,7 @@
<pre class="literal-block">
<em>xplane</em> or <em>yplane</em> or <em>zplane</em> args = lo hi
lo,hi = position of lower and upper plane (distance units), either can be NULL)
<em>zcylinder</em> args = radius
<em>zcylinder</em> args = radius
radius = cylinder radius (distance units)
</pre>
<ul class="simple">
@ -158,7 +158,7 @@
dim = <em>x</em> or <em>y</em> or <em>z</em>
amplitude = size of oscillation (distance units)
period = time of oscillation (time units)
<em>shear</em> values = dim vshear
<em>shear</em> values = dim vshear
dim = <em>x</em> or <em>y</em> or <em>z</em>
vshear = magnitude of shear velocity (velocity units)
</pre>

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@ -141,15 +141,15 @@
<pre class="literal-block">
<em>pos</em> args = z
z = z coordinate at which the piston begins (distance units)
<em>vel</em> args = vz
<em>vel</em> args = vz
vz = final velocity of the piston (velocity units)
<em>ramp</em> = use a linear velocity ramp from 0 to vz
<em>temp</em> args = target damp seed extent
<em>ramp</em> = use a linear velocity ramp from 0 to vz
<em>temp</em> args = target damp seed extent
target = target velocity for region immediately ahead of the piston
damp = damping paramter (time units)
seed = random number seed for langevin kicks
extent = extent of thermostated region (distance units)
<em>units</em> value = <em>lattice</em> or <em>box</em>
<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>

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EDGE = current lo edge of simulation box
constant = number like 0.0 or -30.0 (distance units)
variable = <a class="reference internal" href="variable.html"><em>equal-style variable</em></a> like v_x or v_wiggle
<em>xhi</em>,*yhi*,*zhi* arg = EDGE or constant or variable
<em>xhi</em>,*yhi*,*zhi* arg = EDGE or constant or variable
EDGE = current hi edge of simulation box
constant = number like 50.0 or 100.3 (distance units)
variable = <a class="reference internal" href="variable.html"><em>equal-style variable</em></a> like v_x or v_wiggle

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@ -142,7 +142,7 @@
EDGE = current lo edge of simulation box
constant = number like 0.0 or -30.0 (distance units)
variable = <a class="reference internal" href="variable.html"><em>equal-style variable</em></a> like v_x or v_wiggle
<em>xhi</em>,*yhi*,*zhi* arg = EDGE or constant or variable
<em>xhi</em>,*yhi*,*zhi* arg = EDGE or constant or variable
EDGE = current hi edge of simulation box
constant = number like 50.0 or 100.3 (distance units)
variable = <a class="reference internal" href="variable.html"><em>equal-style variable</em></a> like v_x or v_wiggle

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@ -137,9 +137,9 @@
</ul>
<pre class="literal-block">
<em>delete</em> = no args
<em>clear</em> = no args
<em>region</em> args = region-ID
<em>type</em> or <em>id</em> or <em>molecule</em>
<em>clear</em> = no args
<em>region</em> args = region-ID
<em>type</em> or <em>id</em> or <em>molecule</em>
args = list of one or more atom types, atom IDs, or molecule IDs
any entry in list can be a sequence formatted as A:B or A:B:C where
A = starting index, B = ending index,
@ -150,19 +150,19 @@
args = logical value1 value2
logical = &quot;&lt;&gt;&quot;
value1,value2 = atom types or atom IDs or molecule IDs (depending on <em>style</em>)
<em>variable</em> args = variable-name
<em>include</em> args = molecule
<em>variable</em> args = variable-name
<em>include</em> args = molecule
molecule = add atoms to group with same molecule ID as atoms already in group
<em>subtract</em> args = two or more group IDs
<em>union</em> args = one or more group IDs
<em>intersect</em> args = two or more group IDs
<em>dynamic</em> args = parent-ID keyword value ...
<em>subtract</em> args = two or more group IDs
<em>union</em> args = one or more group IDs
<em>intersect</em> args = two or more group IDs
<em>dynamic</em> args = parent-ID keyword value ...
one or more keyword/value pairs may be appended
keyword = <em>region</em> or <em>var</em> or <em>every</em>
<em>region</em> value = region-ID
<em>var</em> value = name of variable
<em>every</em> value = N = update group every this many timesteps
<em>static</em> = no args
<em>static</em> = no args
</pre>
</div>
<div class="section" id="examples">

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@ -136,41 +136,41 @@
</ul>
<pre class="literal-block">
<em>none</em> value = none
<em>ewald</em> value = accuracy
<em>ewald</em> value = accuracy
accuracy = desired relative error in forces
<em>ewald/disp</em> value = accuracy
<em>ewald/disp</em> value = accuracy
accuracy = desired relative error in forces
<em>ewald/omp</em> value = accuracy
<em>ewald/omp</em> value = accuracy
accuracy = desired relative error in forces
<em>pppm</em> value = accuracy
<em>pppm</em> value = accuracy
accuracy = desired relative error in forces
<em>pppm/cg</em> value = accuracy (smallq)
<em>pppm/cg</em> value = accuracy (smallq)
accuracy = desired relative error in forces
smallq = cutoff for charges to be considered (optional) (charge units)
<em>pppm/disp</em> value = accuracy
<em>pppm/disp</em> value = accuracy
accuracy = desired relative error in forces
<em>pppm/tip4p</em> value = accuracy
<em>pppm/tip4p</em> value = accuracy
accuracy = desired relative error in forces
<em>pppm/disp/tip4p</em> value = accuracy
<em>pppm/disp/tip4p</em> value = accuracy
accuracy = desired relative error in forces
<em>pppm/gpu</em> value = accuracy
<em>pppm/gpu</em> value = accuracy
accuracy = desired relative error in forces
<em>pppm/omp</em> value = accuracy
<em>pppm/omp</em> value = accuracy
accuracy = desired relative error in forces
<em>pppm/cg/omp</em> value = accuracy
<em>pppm/cg/omp</em> value = accuracy
accuracy = desired relative error in forces
<em>pppm/tip4p/omp</em> value = accuracy
<em>pppm/tip4p/omp</em> value = accuracy
accuracy = desired relative error in forces
<em>pppm/stagger</em> value = accuracy
<em>pppm/stagger</em> value = accuracy
accuracy = desired relative error in forces
<em>msm</em> value = accuracy
<em>msm</em> value = accuracy
accuracy = desired relative error in forces
<em>msm/cg</em> value = accuracy (smallq)
<em>msm/cg</em> value = accuracy (smallq)
accuracy = desired relative error in forces
smallq = cutoff for charges to be considered (optional) (charge units)
<em>msm/omp</em> value = accuracy
<em>msm/omp</em> value = accuracy
accuracy = desired relative error in forces
<em>msm/cg/omp</em> value = accuracy (smallq)
<em>msm/cg/omp</em> value = accuracy (smallq)
accuracy = desired relative error in forces
smallq = cutoff for charges to be considered (optional) (charge units)
</pre>

10
doc/lattice.html
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@ -136,7 +136,7 @@
<li>scale = scale factor between lattice and simulation box</li>
</ul>
<div class="highlight-python"><div class="highlight"><pre>scale = reduced density rho* (for LJ units)
scale = lattice constant in distance units (for all other units)
scale = lattice constant in distance units (for all other units)
</pre></div>
</div>
<ul class="simple">
@ -146,14 +146,14 @@
<pre class="literal-block">
<em>origin</em> values = x y z
x,y,z = fractions of a unit cell (0 &lt;= x,y,z &lt; 1)
<em>orient</em> values = dim i j k
<em>orient</em> values = dim i j k
dim = <em>x</em> or <em>y</em> or <em>z</em>
i,j,k = integer lattice directions
<em>spacing</em> values = dx dy dz
<em>spacing</em> values = dx dy dz
dx,dy,dz = lattice spacings in the x,y,z box directions
<em>a1</em>,*a2*,*a3* values = x y z
<em>a1</em>,*a2*,*a3* values = x y z
x,y,z = primitive vector components that define unit cell
<em>basis</em> values = x y z
<em>basis</em> values = x y z
x,y,z = fractional coords of a basis atom (0 &lt;= x,y,z &lt; 1)
</pre>
</div>

4
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@ -143,9 +143,9 @@
<em>final</em> arg = filename
filename = file with initial coords for final replica
coords for intermediate replicas are linearly interpolated between first and last replica
<em>each</em> arg = filename
<em>each</em> arg = filename
filename = unique filename for each replica (except first) with its initial coords
<em>none</em> arg = no argument
<em>none</em> arg = no argument
all replicas assumed to already have their initial coords
</pre>
</div>

8
doc/package.html
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@ -152,7 +152,7 @@
auto = test whether tpa or bpa is faster
tpa = one thread per atom
bpa = one block per atom
<em>gpu</em> args = Ngpu keyword value ...
<em>gpu</em> args = Ngpu keyword value ...
Ngpu = # of GPUs per node
zero or more keyword/value pairs may be appended
keywords = <em>neigh</em> or <em>newton</em> or <em>binsize</em> or <em>split</em> or <em>gpuID</em> or <em>tpa</em> or <em>device</em>
@ -173,7 +173,7 @@
Nthreads = # of GPU threads used per atom
<em>device</em> value = device_type
device_type = <em>kepler</em> or <em>fermi</em> or <em>cypress</em> or <em>generic</em>
<em>intel</em> args = NPhi keyword value ...
<em>intel</em> args = NPhi keyword value ...
Nphi = # of coprocessors per node
zero or more keyword/value pairs may be appended
keywords = <em>omp</em> or <em>mode</em> or <em>balance</em> or <em>ghost</em> or <em>tpc</em> or <em>tptask</em> or <em>no_affinity</em>
@ -193,7 +193,7 @@
<em>tptask</em> value = Ntptask
Ntptask = max number of coprocessor threads per MPI task (default = 240)
<em>no_affinity</em> values = none
<em>kokkos</em> args = keyword value ...
<em>kokkos</em> args = keyword value ...
zero or more keyword/value pairs may be appended
keywords = <em>neigh</em> or <em>newton</em> or <em>binsize</em> or <em>comm</em> or <em>comm/exchange</em> or <em>comm/forward</em>
<em>neigh</em> value = <em>full</em> or <em>half/thread</em> or <em>half</em> or <em>n2</em> or <em>full/cluster</em>
@ -214,7 +214,7 @@
no = perform communication pack/unpack in non-KOKKOS mode
host = perform pack/unpack on host (e.g. with OpenMP threading)
device = perform pack/unpack on device (e.g. on GPU)
<em>omp</em> args = Nthreads keyword value ...
<em>omp</em> args = Nthreads keyword value ...
Nthread = # of OpenMP threads to associate with each MPI process
zero or more keyword/value pairs may be appended
keywords = <em>neigh</em>

16
doc/pair_awpmd.html
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@ -138,18 +138,18 @@
</ul>
<pre class="literal-block">
<em>hartree</em> value = none
<em>dproduct</em> value = none
<em>uhf</em> value = none
<em>free</em> value = none
<em>pbc</em> value = Plen
<em>dproduct</em> value = none
<em>uhf</em> value = none
<em>free</em> value = none
<em>pbc</em> value = Plen
Plen = periodic width of electron = -1 or positive value (distance units)
<em>fix</em> value = Flen
<em>fix</em> value = Flen
Flen = fixed width of electron = -1 or positive value (distance units)
<em>harm</em> value = width
<em>harm</em> value = width
width = harmonic width constraint
<em>ermscale</em> value = factor
<em>ermscale</em> value = factor
factor = scaling between electron mass and width variable mass
<em>flex_press</em> value = none
<em>flex_press</em> value = none
</pre>
</div>
<div class="section" id="examples">

6
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@ -174,13 +174,13 @@
<pre class="literal-block">
<em>born</em> args = cutoff
cutoff = global cutoff for non-Coulombic interactions (distance units)
<em>born/coul/long</em> or <em>born/coul/long/cs</em> args = cutoff (cutoff2)
<em>born/coul/long</em> or <em>born/coul/long/cs</em> args = cutoff (cutoff2)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>born/coul/msm</em> args = cutoff (cutoff2)
<em>born/coul/msm</em> args = cutoff (cutoff2)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<em>born/coul/wolf</em> args = alpha cutoff (cutoff2)
<em>born/coul/wolf</em> args = alpha cutoff (cutoff2)
alpha = damping parameter (inverse distance units)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)

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