From 9b32dcb314dd6113a8af7fb7b87b974be1ebd6e6 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Mon, 15 Feb 2016 22:46:05 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14634
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/_sources/dump.txt            |   7 +
 doc/_sources/dump_custom_vtk.txt | 358 +++++++++++++++++++++++
 doc/dump.html                    |   6 +
 doc/dump.txt                     |   3 +
 doc/dump_custom_vtk.html         | 483 +++++++++++++++++++++++++++++++
 doc/dump_custom_vtk.txt          | 337 +++++++++++++++++++++
 doc/genindex.html                |   4 +
 doc/searchindex.js               |   2 +-
 8 files changed, 1199 insertions(+), 1 deletion(-)
 create mode 100644 doc/_sources/dump_custom_vtk.txt
 create mode 100644 doc/dump_custom_vtk.html
 create mode 100644 doc/dump_custom_vtk.txt

diff --git a/doc/_sources/dump.txt b/doc/_sources/dump.txt
index 2c05cd317c..23ec523c2f 100644
--- a/doc/_sources/dump.txt
+++ b/doc/_sources/dump.txt
@@ -3,6 +3,9 @@
 dump command
 ============
 
+:doc:`dump custom/vtk <dump_custom_vtk>` command
+================================================
+
 :doc:`dump h5md <dump_h5md>` command
 ====================================
 
@@ -48,6 +51,10 @@ Syntax
 
      *xyz/mpiio* args = none
 
+.. parsed-literal::
+
+     *custom/vtk* args = similar to custom args below, discussed on :doc:`dump custom/vtk <dump_custom_vtk>` doc page
+
 .. parsed-literal::
 
      *h5md* args = discussed on :doc:`dump h5md <dump_h5md>` doc page
diff --git a/doc/_sources/dump_custom_vtk.txt b/doc/_sources/dump_custom_vtk.txt
new file mode 100644
index 0000000000..0ac3fafe6a
--- /dev/null
+++ b/doc/_sources/dump_custom_vtk.txt
@@ -0,0 +1,358 @@
+.. index:: dump custom/vtk
+
+dump custom/vtk command
+=======================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   dump ID group-ID style N file args
+
+* ID = user-assigned name for the dump
+* group-ID = ID of the group of atoms to be dumped
+* style = *custom/vtk*
+* N = dump every this many timesteps
+* file = name of file to write dump info to
+* args = list of arguments for a particular style
+.. parsed-literal::
+
+     *custom/vtk* args = list of atom attributes
+       possible attributes = id, mol, proc, procp1, type, element, mass,
+   			  x, y, z, xs, ys, zs, xu, yu, zu, 
+   			  xsu, ysu, zsu, ix, iy, iz,
+   			  vx, vy, vz, fx, fy, fz,
+                             q, mux, muy, muz, mu,
+                             radius, diameter, omegax, omegay, omegaz,
+   			  angmomx, angmomy, angmomz, tqx, tqy, tqz,
+   			  spin, eradius, ervel, erforce,
+   			  c_ID, c_ID[N], f_ID, f_ID[N], v_name
+
+.. parsed-literal::
+
+         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 :doc:`dump_modify <dump_modify_vtk>` 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
+
+
+
+Examples
+""""""""
+
+.. parsed-literal::
+
+   dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
+   dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD[1] c_myD[2] c_myD[3] v_ke
+   dump e_data all custom/vtk 100 dump*.vtu id type spin eradius fx fy fz eforce
+
+The style *custom/vtk* is similar to the :doc:`custom <dump>` style but
+uses the VTK library to write data to VTK simple legacy or XML format
+depending on the filename extension specified. This can be either
+**.vtk* for the legacy format or **.vtp* and **.vtu*, respectively,
+for the XML format; see the `VTK homepage <http://www.vtk.org/VTK/img/file-formats.pdf>`_ for a detailed
+description of these formats.  Since this naming convention conflicts
+with the way binary output is usually specified (see below),
+:doc:`dump_modify binary <dump_modify_vtk>` allows to set the binary
+flag for this dump style explicitly.
+
+Description
+"""""""""""
+
+Dump a snapshot of atom quantities to one or more files every N
+timesteps. The timesteps on which dump output is written can also be
+controlled by a variable; see the :doc:`dump_modify every <dump_modify_vtk>` command for details.
+
+Only information for atoms in the specified group is dumped.  The
+:doc:`dump_modify thresh and region <dump_modify_vtk>` commands can also
+alter what atoms are included; see details below.
+
+As described below, special characters ("*", "%") in the filename
+determine the kind of output.
+
+.. warning::
+
+   Because periodic boundary conditions are enforced only
+   on timesteps when neighbor lists are rebuilt, the coordinates of an
+   atom written to a dump file may be slightly outside the simulation
+   box.
+
+.. warning::
+
+   Unless the :doc:`dump_modify sort <dump_modify_vtk>`
+   option is invoked, the lines of atom information written to dump files
+   will be in an indeterminate order for each snapshot.  This is even
+   true when running on a single processor, if the :doc:`atom_modify sort <atom_modify>` option is on, which it is by default.  In this
+   case atoms are re-ordered periodically during a simulation, due to
+   spatial sorting.  It is also true when running in parallel, because
+   data for a single snapshot is collected from multiple processors, each
+   of which owns a subset of the atoms.
+
+For the *custom/vtk* style, sorting is off by default. See the
+:doc:`dump_modify <dump_modify_vtk>` doc page for details.
+
+
+----------
+
+
+The dimensions of the simulation box are written to a separate file
+for each snapshot (either in legacy VTK or XML format depending on
+the format of the main dump file) with the suffix *_boundingBox*
+appended to the given dump filename.
+
+For an orthogonal simulation box this information is saved as a
+rectilinear grid (legacy .vtk or .vtr XML format).
+
+Triclinic simulation boxes (non-orthogonal) are saved as
+hexahedrons in either legacy .vtk or .vtu XML format.
+
+Style *custom/vtk* allows you to specify a list of atom attributes
+to be written to the dump file for each atom.  Possible attributes
+are listed above.  In contrast to the *custom* style, the attributes
+are rearranged to ensure correct ordering of vector components
+(except for computes and fixes - these have to be given in the right
+order) and duplicate entries are removed.
+
+You cannot specify a quantity that is not defined for a particular
+simulation - such as *q* for atom style *bond*, since that atom style
+doesn't assign charges.  Dumps occur at the very end of a timestep,
+so atom attributes will include effects due to fixes that are applied
+during the timestep.  An explanation of the possible dump custom/vtk attributes
+is given below. Since position data is required to write VTK files "x y z"
+do not have to be specified explicitly.
+
+The VTK format uses a single snapshot of the system per file, thus
+a wildcard "*" must be included in the filename, as discussed below.
+Otherwise the dump files will get overwritten with the new snapshot
+each time.
+
+
+----------
+
+
+Dumps are performed on timesteps that are a multiple of N (including
+timestep 0) and on the last timestep of a minimization if the
+minimization converges.  Note that this means a dump will not be
+performed on the initial timestep after the dump command is invoked,
+if the current timestep is not a multiple of N.  This behavior can be
+changed via the :doc:`dump_modify first <dump_modify_vtk>` command, which
+can also be useful if the dump command is invoked after a minimization
+ended on an arbitrary timestep.  N can be changed between runs by
+using the :doc:`dump_modify every <dump_modify_vtk>` command.
+The :doc:`dump_modify every <dump_modify_vtk>` command
+also allows a variable to be used to determine the sequence of
+timesteps on which dump files are written.  In this mode a dump on the
+first timestep of a run will also not be written unless the
+:doc:`dump_modify first <dump_modify_vtk>` command is used.
+
+Dump filenames can contain two wildcard characters.  If a "*"
+character appears in the filename, then one file per snapshot is
+written and the "*" character is replaced with the timestep value.
+For example, tmp.dump*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk,
+tmp.dump20000.vtk, etc.  Note that the :doc:`dump_modify pad <dump_modify_vtk>`
+command can be used to insure all timestep numbers are the same length
+(e.g. 00010), which can make it easier to read a series of dump files
+in order with some post-processing tools.
+
+If a "%" character appears in the filename, then each of P processors
+writes a portion of the dump file, and the "%" character is replaced
+with the processor ID from 0 to P-1 preceded by an underscore character.
+For example, tmp.dump%.vtp becomes tmp.dump_0.vtp, tmp.dump_1.vtp, ...
+tmp.dump_P-1.vtp, etc.  This creates smaller files and can be a fast
+mode of output on parallel machines that support parallel I/O for output.
+
+By default, P = the number of processors meaning one file per
+processor, but P can be set to a smaller value via the *nfile* or
+*fileper* keywords of the :doc:`dump_modify <dump_modify_vtk>` command.
+These options can be the most efficient way of writing out dump files
+when running on large numbers of processors.
+
+For the legacy VTK format "%" is ignored and P = 1, i.e., only
+processor 0 does write files.
+
+Note that using the "*" and "%" characters together can produce a
+large number of small dump files!
+
+If *dump_modify binary* is used, the dump file (or files, if "*" or
+"%" is also used) is written in binary format.  A binary dump file
+will be about the same size as a text version, but will typically
+write out much faster.
+
+
+----------
+
+
+This section explains the atom attributes that can be specified as
+part of the *custom/vtk* style.
+
+The *id*, *mol*, *proc*, *procp1*, *type*, *element*, *mass*, *vx*,
+*vy*, *vz*, *fx*, *fy*, *fz*, *q* attributes are self-explanatory.
+
+*id* is the atom ID.  *mol* is the molecule ID, included in the data
+file for molecular systems.  *type* is the atom type.  *element* is
+typically the chemical name of an element, which you must assign to
+each type via the :doc:`dump_modify element <dump_modify_vtk>` command.
+More generally, it can be any string you wish to associate with an
+atom type.  *mass* is the atom mass.  *vx*, *vy*, *vz*, *fx*, *fy*,
+*fz*, and *q* are components of atom velocity and force and atomic
+charge.
+
+There are several options for outputting atom coordinates.  The *x*,
+*y*, *z* attributes are used to write atom coordinates "unscaled", in
+the appropriate distance :doc:`units <units>` (Angstroms, sigma, etc).
+Additionaly, you can use *xs*, *ys*, *zs* if you want to also save the
+coordinates "scaled" to the box size, so that each value is 0.0 to
+1.0.  If the simulation box is triclinic (tilted), then all atom
+coords will still be between 0.0 and 1.0.  Use *xu*, *yu*, *zu* if you
+want the coordinates "unwrapped" by the image flags for each atom.
+Unwrapped means that if the atom has passed through a periodic
+boundary one or more times, the value is printed for what the
+coordinate would be if it had not been wrapped back into the periodic
+box.  Note that using *xu*, *yu*, *zu* means that the coordinate
+values may be far outside the box bounds printed with the snapshot.
+Using *xsu*, *ysu*, *zsu* is similar to using *xu*, *yu*, *zu*, except
+that the unwrapped coordinates are scaled by the box size. Atoms that
+have passed through a periodic boundary will have the corresponding
+cooordinate increased or decreased by 1.0.
+
+The image flags can be printed directly using the *ix*, *iy*, *iz*
+attributes.  For periodic dimensions, they specify which image of the
+simulation box the atom is considered to be in.  An image of 0 means
+it is inside the box as defined.  A value of 2 means add 2 box lengths
+to get the true value.  A value of -1 means subtract 1 box length to
+get the true value.  LAMMPS updates these flags as atoms cross
+periodic boundaries during the simulation.
+
+The *mux*, *muy*, *muz* attributes are specific to dipolar systems
+defined with an atom style of *dipole*.  They give the orientation of
+the atom's point dipole moment.  The *mu* attribute gives the
+magnitude of the atom's dipole moment.
+
+The *radius* and *diameter* attributes are specific to spherical
+particles that have a finite size, such as those defined with an atom
+style of *sphere*.
+
+The *omegax*, *omegay*, and *omegaz* attributes are specific to
+finite-size spherical particles that have an angular velocity.  Only
+certain atom styles, such as *sphere* define this quantity.
+
+The *angmomx*, *angmomy*, and *angmomz* attributes are specific to
+finite-size aspherical particles that have an angular momentum.  Only
+the *ellipsoid* atom style defines this quantity.
+
+The *tqx*, *tqy*, *tqz* attributes are for finite-size particles that
+can sustain a rotational torque due to interactions with other
+particles.
+
+The *spin*, *eradius*, *ervel*, and *erforce* attributes are for
+particles that represent nuclei and electrons modeled with the
+electronic force field (EFF).  See :doc:`atom_style electron <atom_style>` and :doc:`pair_style eff <pair_eff>` for more
+details.
+
+The *c_ID* and *c_ID[N]* attributes allow per-atom vectors or arrays
+calculated by a :doc:`compute <compute>` to be output.  The ID in the
+attribute should be replaced by the actual ID of the compute that has
+been defined previously in the input script.  See the
+:doc:`compute <compute>` command for details.  There are computes for
+calculating the per-atom energy, stress, centro-symmetry parameter,
+and coordination number of individual atoms.
+
+Note that computes which calculate global or local quantities, as
+opposed to per-atom quantities, cannot be output in a dump custom/vtk
+command.  Instead, global quantities can be output by the
+:doc:`thermo_style custom <thermo_style>` command, and local quantities
+can be output by the dump local command.
+
+If *c_ID* is used as an attribute, then the per-atom vector calculated
+by the compute is printed.  If *c_ID[N]* is used, then N must be in
+the range from 1-M, which will print the Nth column of the M-length
+per-atom array calculated by the compute.
+
+The *f_ID* and *f_ID[N]* attributes allow vector or array per-atom
+quantities calculated by a :doc:`fix <fix>` to be output.  The ID in the
+attribute should be replaced by the actual ID of the fix that has been
+defined previously in the input script.  The :doc:`fix ave/atom <fix_ave_atom>` command is one that calculates per-atom
+quantities.  Since it can time-average per-atom quantities produced by
+any :doc:`compute <compute>`, :doc:`fix <fix>`, or atom-style
+:doc:`variable <variable>`, this allows those time-averaged results to
+be written to a dump file.
+
+If *f_ID* is used as a attribute, then the per-atom vector calculated
+by the fix is printed.  If *f_ID[N]* is used, then N must be in the
+range from 1-M, which will print the Nth column of the M-length
+per-atom array calculated by the fix.
+
+The *v_name* attribute allows per-atom vectors calculated by a
+:doc:`variable <variable>` to be output.  The name in the attribute
+should be replaced by the actual name of the variable that has been
+defined previously in the input script.  Only an atom-style variable
+can be referenced, since it is the only style that generates per-atom
+values.  Variables of style *atom* can reference individual atom
+attributes, per-atom atom attributes, thermodynamic keywords, or
+invoke other computes, fixes, or variables when they are evaluated, so
+this is a very general means of creating quantities to output to a
+dump file.
+
+See :doc:`Section_modify <Section_modify>` of the manual for information
+on how to add new compute and fix styles to LAMMPS to calculate
+per-atom quantities which could then be output into dump files.
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+The *custom/vtk* style does not support writing of gzipped dump files.
+
+The *custom/vtk* dump style is part of the USER-VTK package. It is
+only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
+
+To use this dump style, you also must link to the VTK library.  See
+the info in lib/vtk/README and insure the Makefile.lammps file in that
+directory is appropriate for your machine.
+
+The *custom/vtk* dump style neither supports buffering nor custom
+format strings.
+
+Related commands
+""""""""""""""""
+
+:doc:`dump <dump>`, :doc:`dump image <dump_image>`,
+:doc:`dump_modify <dump_modify>`, :doc:`undump <undump>`
+
+Default
+"""""""
+
+By default, files are written in ASCII format. If the file extension
+is not one of .vtk, .vtp or .vtu, the legacy VTK file format is used.
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Section_commands.html#comm
diff --git a/doc/dump.html b/doc/dump.html
index ea6496ef57..1bd81cf845 100644
--- a/doc/dump.html
+++ b/doc/dump.html
@@ -127,6 +127,9 @@
   <div class="section" id="dump-command">
 <span id="index-0"></span><h1>dump command<a class="headerlink" href="#dump-command" title="Permalink to this headline">¶</a></h1>
 </div>
+<div class="section" id="dump-custom-vtk-command">
+<h1><a class="reference internal" href="dump_custom_vtk.html"><em>dump custom/vtk</em></a> command<a class="headerlink" href="#dump-custom-vtk-command" title="Permalink to this headline">¶</a></h1>
+</div>
 <div class="section" id="dump-h5md-command">
 <h1><a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a> command<a class="headerlink" href="#dump-h5md-command" title="Permalink to this headline">¶</a></h1>
 </div>
@@ -169,6 +172,9 @@
 <em>xyz/mpiio</em> args = none
 </pre>
 <pre class="literal-block">
+<em>custom/vtk</em> args = similar to custom args below, discussed on <a class="reference internal" href="dump_custom_vtk.html"><em>dump custom/vtk</em></a> doc page
+</pre>
+<pre class="literal-block">
 <em>h5md</em> args = discussed on <a class="reference internal" href="dump_h5md.html"><em>dump h5md</em></a> doc page
 </pre>
 <pre class="literal-block">
diff --git a/doc/dump.txt b/doc/dump.txt
index 74f1aa003d..e0f2795a62 100644
--- a/doc/dump.txt
+++ b/doc/dump.txt
@@ -7,6 +7,7 @@
 :line
    
 dump command :h3
+"dump custom/vtk"_dump_custom_vtk.html command :h3
 "dump h5md"_dump_h5md.html command :h3
 "dump image"_dump_image.html command :h3
 "dump movie"_dump_image.html command :h3
@@ -34,6 +35,8 @@ args = list of arguments for a particular style :l
   {xyz/gz} args = none :pre
   {xyz/mpiio} args = none :pre
 
+  {custom/vtk} args = similar to custom args below, discussed on "dump custom/vtk"_dump_custom_vtk.html doc page :pre
+
   {h5md} args = discussed on "dump h5md"_dump_h5md.html doc page :pre
 
   {image} args = discussed on "dump image"_dump_image.html doc page :pre
diff --git a/doc/dump_custom_vtk.html b/doc/dump_custom_vtk.html
new file mode 100644
index 0000000000..28d405f12b
--- /dev/null
+++ b/doc/dump_custom_vtk.html
@@ -0,0 +1,483 @@
+
+
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+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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+            
+  <div class="section" id="dump-custom-vtk-command">
+<span id="index-0"></span><h1>dump custom/vtk command<a class="headerlink" href="#dump-custom-vtk-command" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="syntax">
+<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre>dump ID group-ID style N file args
+</pre></div>
+</div>
+<ul class="simple">
+<li>ID = user-assigned name for the dump</li>
+<li>group-ID = ID of the group of atoms to be dumped</li>
+<li>style = <em>custom/vtk</em></li>
+<li>N = dump every this many timesteps</li>
+<li>file = name of file to write dump info to</li>
+<li>args = list of arguments for a particular style</li>
+</ul>
+<pre class="literal-block">
+<em>custom/vtk</em> args = list of atom attributes
+  possible attributes = id, mol, proc, procp1, type, element, mass,
+                     x, y, z, xs, ys, zs, xu, yu, zu,
+                     xsu, ysu, zsu, ix, iy, iz,
+                     vx, vy, vz, fx, fy, fz,
+                        q, mux, muy, muz, mu,
+                        radius, diameter, omegax, omegay, omegaz,
+                     angmomx, angmomy, angmomz, tqx, tqy, tqz,
+                     spin, eradius, ervel, erforce,
+                     c_ID, c_ID[N], f_ID, f_ID[N], v_name
+</pre>
+<pre class="literal-block">
+id = atom ID
+mol = molecule ID
+proc = ID of processor that owns atom
+procp1 = ID+1 of processor that owns atom
+type = atom type
+element = name of atom element, as defined by <code class="xref doc docutils literal"><span class="pre">dump_modify</span></code> 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
+</pre>
+</div>
+<div class="section" id="examples">
+<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre>dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
+dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD[1] c_myD[2] c_myD[3] v_ke
+dump e_data all custom/vtk 100 dump*.vtu id type spin eradius fx fy fz eforce
+</pre></div>
+</div>
+<p>The style <em>custom/vtk</em> is similar to the <a class="reference internal" href="dump.html"><em>custom</em></a> style but
+uses the VTK library to write data to VTK simple legacy or XML format
+depending on the filename extension specified. This can be either
+<a href="#id1"><span class="problematic" id="id2">**</span></a>.vtk* for the legacy format or <a href="#id3"><span class="problematic" id="id4">**</span></a>.vtp* and <a href="#id5"><span class="problematic" id="id6">**</span></a>.vtu*, respectively,
+for the XML format; see the <a class="reference external" href="http://www.vtk.org/VTK/img/file-formats.pdf">VTK homepage</a> for a detailed
+description of these formats.  Since this naming convention conflicts
+with the way binary output is usually specified (see below),
+<code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">binary</span></code> allows to set the binary
+flag for this dump style explicitly.</p>
+</div>
+<div class="section" id="description">
+<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
+<p>Dump a snapshot of atom quantities to one or more files every N
+timesteps. The timesteps on which dump output is written can also be
+controlled by a variable; see the <code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">every</span></code> command for details.</p>
+<p>Only information for atoms in the specified group is dumped.  The
+<code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">thresh</span> <span class="pre">and</span> <span class="pre">region</span></code> commands can also
+alter what atoms are included; see details below.</p>
+<p>As described below, special characters (&#8220;*&#8221;, &#8220;%&#8221;) in the filename
+determine the kind of output.</p>
+<div class="admonition warning">
+<p class="first admonition-title">Warning</p>
+<p class="last">Because periodic boundary conditions are enforced only
+on timesteps when neighbor lists are rebuilt, the coordinates of an
+atom written to a dump file may be slightly outside the simulation
+box.</p>
+</div>
+<div class="admonition warning">
+<p class="first admonition-title">Warning</p>
+<p class="last">Unless the <code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">sort</span></code>
+option is invoked, the lines of atom information written to dump files
+will be in an indeterminate order for each snapshot.  This is even
+true when running on a single processor, if the <a class="reference internal" href="atom_modify.html"><em>atom_modify sort</em></a> option is on, which it is by default.  In this
+case atoms are re-ordered periodically during a simulation, due to
+spatial sorting.  It is also true when running in parallel, because
+data for a single snapshot is collected from multiple processors, each
+of which owns a subset of the atoms.</p>
+</div>
+<p>For the <em>custom/vtk</em> style, sorting is off by default. See the
+<code class="xref doc docutils literal"><span class="pre">dump_modify</span></code> doc page for details.</p>
+<hr class="docutils" />
+<p>The dimensions of the simulation box are written to a separate file
+for each snapshot (either in legacy VTK or XML format depending on
+the format of the main dump file) with the suffix <em>_boundingBox</em>
+appended to the given dump filename.</p>
+<p>For an orthogonal simulation box this information is saved as a
+rectilinear grid (legacy .vtk or .vtr XML format).</p>
+<p>Triclinic simulation boxes (non-orthogonal) are saved as
+hexahedrons in either legacy .vtk or .vtu XML format.</p>
+<p>Style <em>custom/vtk</em> allows you to specify a list of atom attributes
+to be written to the dump file for each atom.  Possible attributes
+are listed above.  In contrast to the <em>custom</em> style, the attributes
+are rearranged to ensure correct ordering of vector components
+(except for computes and fixes - these have to be given in the right
+order) and duplicate entries are removed.</p>
+<p>You cannot specify a quantity that is not defined for a particular
+simulation - such as <em>q</em> for atom style <em>bond</em>, since that atom style
+doesn&#8217;t assign charges.  Dumps occur at the very end of a timestep,
+so atom attributes will include effects due to fixes that are applied
+during the timestep.  An explanation of the possible dump custom/vtk attributes
+is given below. Since position data is required to write VTK files &#8220;x y z&#8221;
+do not have to be specified explicitly.</p>
+<p>The VTK format uses a single snapshot of the system per file, thus
+a wildcard &#8220;*&#8221; must be included in the filename, as discussed below.
+Otherwise the dump files will get overwritten with the new snapshot
+each time.</p>
+<hr class="docutils" />
+<p>Dumps are performed on timesteps that are a multiple of N (including
+timestep 0) and on the last timestep of a minimization if the
+minimization converges.  Note that this means a dump will not be
+performed on the initial timestep after the dump command is invoked,
+if the current timestep is not a multiple of N.  This behavior can be
+changed via the <code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">first</span></code> command, which
+can also be useful if the dump command is invoked after a minimization
+ended on an arbitrary timestep.  N can be changed between runs by
+using the <code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">every</span></code> command.
+The <code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">every</span></code> command
+also allows a variable to be used to determine the sequence of
+timesteps on which dump files are written.  In this mode a dump on the
+first timestep of a run will also not be written unless the
+<code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">first</span></code> command is used.</p>
+<p>Dump filenames can contain two wildcard characters.  If a &#8220;*&#8221;
+character appears in the filename, then one file per snapshot is
+written and the &#8220;*&#8221; character is replaced with the timestep value.
+For example, tmp.dump*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk,
+tmp.dump20000.vtk, etc.  Note that the <code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">pad</span></code>
+command can be used to insure all timestep numbers are the same length
+(e.g. 00010), which can make it easier to read a series of dump files
+in order with some post-processing tools.</p>
+<p>If a &#8220;%&#8221; character appears in the filename, then each of P processors
+writes a portion of the dump file, and the &#8220;%&#8221; character is replaced
+with the processor ID from 0 to P-1 preceded by an underscore character.
+For example, tmp.dump%.vtp becomes tmp.dump_0.vtp, tmp.dump_1.vtp, ...
+tmp.dump_P-1.vtp, etc.  This creates smaller files and can be a fast
+mode of output on parallel machines that support parallel I/O for output.</p>
+<p>By default, P = the number of processors meaning one file per
+processor, but P can be set to a smaller value via the <em>nfile</em> or
+<em>fileper</em> keywords of the <code class="xref doc docutils literal"><span class="pre">dump_modify</span></code> command.
+These options can be the most efficient way of writing out dump files
+when running on large numbers of processors.</p>
+<p>For the legacy VTK format &#8220;%&#8221; is ignored and P = 1, i.e., only
+processor 0 does write files.</p>
+<p>Note that using the &#8220;*&#8221; and &#8220;%&#8221; characters together can produce a
+large number of small dump files!</p>
+<p>If <em>dump_modify binary</em> is used, the dump file (or files, if &#8220;*&#8221; or
+&#8220;%&#8221; is also used) is written in binary format.  A binary dump file
+will be about the same size as a text version, but will typically
+write out much faster.</p>
+<hr class="docutils" />
+<p>This section explains the atom attributes that can be specified as
+part of the <em>custom/vtk</em> style.</p>
+<p>The <em>id</em>, <em>mol</em>, <em>proc</em>, <em>procp1</em>, <em>type</em>, <em>element</em>, <em>mass</em>, <em>vx</em>,
+<em>vy</em>, <em>vz</em>, <em>fx</em>, <em>fy</em>, <em>fz</em>, <em>q</em> attributes are self-explanatory.</p>
+<p><em>id</em> is the atom ID.  <em>mol</em> is the molecule ID, included in the data
+file for molecular systems.  <em>type</em> is the atom type.  <em>element</em> is
+typically the chemical name of an element, which you must assign to
+each type via the <code class="xref doc docutils literal"><span class="pre">dump_modify</span> <span class="pre">element</span></code> command.
+More generally, it can be any string you wish to associate with an
+atom type.  <em>mass</em> is the atom mass.  <em>vx</em>, <em>vy</em>, <em>vz</em>, <em>fx</em>, <em>fy</em>,
+<em>fz</em>, and <em>q</em> are components of atom velocity and force and atomic
+charge.</p>
+<p>There are several options for outputting atom coordinates.  The <em>x</em>,
+<em>y</em>, <em>z</em> attributes are used to write atom coordinates &#8220;unscaled&#8221;, in
+the appropriate distance <a class="reference internal" href="units.html"><em>units</em></a> (Angstroms, sigma, etc).
+Additionaly, you can use <em>xs</em>, <em>ys</em>, <em>zs</em> if you want to also save the
+coordinates &#8220;scaled&#8221; to the box size, so that each value is 0.0 to
+1.0.  If the simulation box is triclinic (tilted), then all atom
+coords will still be between 0.0 and 1.0.  Use <em>xu</em>, <em>yu</em>, <em>zu</em> if you
+want the coordinates &#8220;unwrapped&#8221; by the image flags for each atom.
+Unwrapped means that if the atom has passed through a periodic
+boundary one or more times, the value is printed for what the
+coordinate would be if it had not been wrapped back into the periodic
+box.  Note that using <em>xu</em>, <em>yu</em>, <em>zu</em> means that the coordinate
+values may be far outside the box bounds printed with the snapshot.
+Using <em>xsu</em>, <em>ysu</em>, <em>zsu</em> is similar to using <em>xu</em>, <em>yu</em>, <em>zu</em>, except
+that the unwrapped coordinates are scaled by the box size. Atoms that
+have passed through a periodic boundary will have the corresponding
+cooordinate increased or decreased by 1.0.</p>
+<p>The image flags can be printed directly using the <em>ix</em>, <em>iy</em>, <em>iz</em>
+attributes.  For periodic dimensions, they specify which image of the
+simulation box the atom is considered to be in.  An image of 0 means
+it is inside the box as defined.  A value of 2 means add 2 box lengths
+to get the true value.  A value of -1 means subtract 1 box length to
+get the true value.  LAMMPS updates these flags as atoms cross
+periodic boundaries during the simulation.</p>
+<p>The <em>mux</em>, <em>muy</em>, <em>muz</em> attributes are specific to dipolar systems
+defined with an atom style of <em>dipole</em>.  They give the orientation of
+the atom&#8217;s point dipole moment.  The <em>mu</em> attribute gives the
+magnitude of the atom&#8217;s dipole moment.</p>
+<p>The <em>radius</em> and <em>diameter</em> attributes are specific to spherical
+particles that have a finite size, such as those defined with an atom
+style of <em>sphere</em>.</p>
+<p>The <em>omegax</em>, <em>omegay</em>, and <em>omegaz</em> attributes are specific to
+finite-size spherical particles that have an angular velocity.  Only
+certain atom styles, such as <em>sphere</em> define this quantity.</p>
+<p>The <em>angmomx</em>, <em>angmomy</em>, and <em>angmomz</em> attributes are specific to
+finite-size aspherical particles that have an angular momentum.  Only
+the <em>ellipsoid</em> atom style defines this quantity.</p>
+<p>The <em>tqx</em>, <em>tqy</em>, <em>tqz</em> attributes are for finite-size particles that
+can sustain a rotational torque due to interactions with other
+particles.</p>
+<p>The <em>spin</em>, <em>eradius</em>, <em>ervel</em>, and <em>erforce</em> attributes are for
+particles that represent nuclei and electrons modeled with the
+electronic force field (EFF).  See <a class="reference internal" href="atom_style.html"><em>atom_style electron</em></a> and <a class="reference internal" href="pair_eff.html"><em>pair_style eff</em></a> for more
+details.</p>
+<p>The <em>c_ID</em> and <em>c_ID[N]</em> attributes allow per-atom vectors or arrays
+calculated by a <a class="reference internal" href="compute.html"><em>compute</em></a> to be output.  The ID in the
+attribute should be replaced by the actual ID of the compute that has
+been defined previously in the input script.  See the
+<a class="reference internal" href="compute.html"><em>compute</em></a> command for details.  There are computes for
+calculating the per-atom energy, stress, centro-symmetry parameter,
+and coordination number of individual atoms.</p>
+<p>Note that computes which calculate global or local quantities, as
+opposed to per-atom quantities, cannot be output in a dump custom/vtk
+command.  Instead, global quantities can be output by the
+<a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> command, and local quantities
+can be output by the dump local command.</p>
+<p>If <em>c_ID</em> is used as an attribute, then the per-atom vector calculated
+by the compute is printed.  If <em>c_ID[N]</em> is used, then N must be in
+the range from 1-M, which will print the Nth column of the M-length
+per-atom array calculated by the compute.</p>
+<p>The <em>f_ID</em> and <em>f_ID[N]</em> attributes allow vector or array per-atom
+quantities calculated by a <a class="reference internal" href="fix.html"><em>fix</em></a> to be output.  The ID in the
+attribute should be replaced by the actual ID of the fix that has been
+defined previously in the input script.  The <a class="reference internal" href="fix_ave_atom.html"><em>fix ave/atom</em></a> command is one that calculates per-atom
+quantities.  Since it can time-average per-atom quantities produced by
+any <a class="reference internal" href="compute.html"><em>compute</em></a>, <a class="reference internal" href="fix.html"><em>fix</em></a>, or atom-style
+<a class="reference internal" href="variable.html"><em>variable</em></a>, this allows those time-averaged results to
+be written to a dump file.</p>
+<p>If <em>f_ID</em> is used as a attribute, then the per-atom vector calculated
+by the fix is printed.  If <em>f_ID[N]</em> is used, then N must be in the
+range from 1-M, which will print the Nth column of the M-length
+per-atom array calculated by the fix.</p>
+<p>The <em>v_name</em> attribute allows per-atom vectors calculated by a
+<a class="reference internal" href="variable.html"><em>variable</em></a> to be output.  The name in the attribute
+should be replaced by the actual name of the variable that has been
+defined previously in the input script.  Only an atom-style variable
+can be referenced, since it is the only style that generates per-atom
+values.  Variables of style <em>atom</em> can reference individual atom
+attributes, per-atom atom attributes, thermodynamic keywords, or
+invoke other computes, fixes, or variables when they are evaluated, so
+this is a very general means of creating quantities to output to a
+dump file.</p>
+<p>See <a class="reference internal" href="Section_modify.html"><em>Section_modify</em></a> of the manual for information
+on how to add new compute and fix styles to LAMMPS to calculate
+per-atom quantities which could then be output into dump files.</p>
+</div>
+<hr class="docutils" />
+<div class="section" id="restrictions">
+<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
+<p>The <em>custom/vtk</em> style does not support writing of gzipped dump files.</p>
+<p>The <em>custom/vtk</em> dump style is part of the USER-VTK package. It is
+only enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
+<p>To use this dump style, you also must link to the VTK library.  See
+the info in lib/vtk/README and insure the Makefile.lammps file in that
+directory is appropriate for your machine.</p>
+<p>The <em>custom/vtk</em> dump style neither supports buffering nor custom
+format strings.</p>
+</div>
+<div class="section" id="related-commands">
+<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
+<p><a class="reference internal" href="dump.html"><em>dump</em></a>, <a class="reference internal" href="dump_image.html"><em>dump image</em></a>,
+<a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a>, <a class="reference internal" href="undump.html"><em>undump</em></a></p>
+</div>
+<div class="section" id="default">
+<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
+<p>By default, files are written in ASCII format. If the file extension
+is not one of .vtk, .vtp or .vtu, the legacy VTK file format is used.</p>
+</div>
+</div>
+
+
+           </div>
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+          <footer>
+  
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diff --git a/doc/dump_custom_vtk.txt b/doc/dump_custom_vtk.txt
new file mode 100644
index 0000000000..2b0ba8175f
--- /dev/null
+++ b/doc/dump_custom_vtk.txt
@@ -0,0 +1,337 @@
+ "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+   
+dump custom/vtk command :h3
+
+[Syntax:]
+
+dump ID group-ID style N file args :pre
+
+ID = user-assigned name for the dump :ulb,l
+group-ID = ID of the group of atoms to be dumped :l
+style = {custom/vtk} :l
+N = dump every this many timesteps :l
+file = name of file to write dump info to :l
+args = list of arguments for a particular style :l
+  {custom/vtk} args = list of atom attributes
+    possible attributes = id, mol, proc, procp1, type, element, mass,
+			  x, y, z, xs, ys, zs, xu, yu, zu, 
+			  xsu, ysu, zsu, ix, iy, iz,
+			  vx, vy, vz, fx, fy, fz,
+                          q, mux, muy, muz, mu,
+                          radius, diameter, omegax, omegay, omegaz,
+			  angmomx, angmomy, angmomz, tqx, tqy, tqz,
+			  spin, eradius, ervel, erforce,
+			  c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
+
+      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 "dump_modify"_dump_modify_vtk.html 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 :pre
+:ule
+
+[Examples:]
+
+dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
+dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD\[1\] c_myD\[2\] c_myD\[3\] v_ke
+dump e_data all custom/vtk 100 dump*.vtu id type spin eradius fx fy fz eforce :pre
+
+The style {custom/vtk} is similar to the "custom"_dump.html style but
+uses the VTK library to write data to VTK simple legacy or XML format
+depending on the filename extension specified. This can be either
+{*.vtk} for the legacy format or {*.vtp} and {*.vtu}, respectively,
+for the XML format; see the "VTK
+homepage"_http://www.vtk.org/VTK/img/file-formats.pdf for a detailed
+description of these formats.  Since this naming convention conflicts
+with the way binary output is usually specified (see below),
+"dump_modify binary"_dump_modify_vtk.html allows to set the binary
+flag for this dump style explicitly.
+
+[Description:]
+
+Dump a snapshot of atom quantities to one or more files every N
+timesteps. The timesteps on which dump output is written can also be
+controlled by a variable; see the "dump_modify
+every"_dump_modify_vtk.html command for details.
+
+Only information for atoms in the specified group is dumped.  The
+"dump_modify thresh and region"_dump_modify_vtk.html commands can also
+alter what atoms are included; see details below.
+
+As described below, special characters ("*", "%") in the filename
+determine the kind of output.
+
+IMPORTANT NOTE: Because periodic boundary conditions are enforced only
+on timesteps when neighbor lists are rebuilt, the coordinates of an
+atom written to a dump file may be slightly outside the simulation
+box.
+
+IMPORTANT NOTE: Unless the "dump_modify sort"_dump_modify_vtk.html
+option is invoked, the lines of atom information written to dump files
+will be in an indeterminate order for each snapshot.  This is even
+true when running on a single processor, if the "atom_modify
+sort"_atom_modify.html option is on, which it is by default.  In this
+case atoms are re-ordered periodically during a simulation, due to
+spatial sorting.  It is also true when running in parallel, because
+data for a single snapshot is collected from multiple processors, each
+of which owns a subset of the atoms.
+
+For the {custom/vtk} style, sorting is off by default. See the
+"dump_modify"_dump_modify_vtk.html doc page for details.
+
+:line
+
+The dimensions of the simulation box are written to a separate file
+for each snapshot (either in legacy VTK or XML format depending on
+the format of the main dump file) with the suffix {_boundingBox}
+appended to the given dump filename.
+
+For an orthogonal simulation box this information is saved as a
+rectilinear grid (legacy .vtk or .vtr XML format).
+
+Triclinic simulation boxes (non-orthogonal) are saved as
+hexahedrons in either legacy .vtk or .vtu XML format.
+
+Style {custom/vtk} allows you to specify a list of atom attributes
+to be written to the dump file for each atom.  Possible attributes
+are listed above.  In contrast to the {custom} style, the attributes
+are rearranged to ensure correct ordering of vector components
+(except for computes and fixes - these have to be given in the right
+order) and duplicate entries are removed.
+
+You cannot specify a quantity that is not defined for a particular
+simulation - such as {q} for atom style {bond}, since that atom style
+doesn't assign charges.  Dumps occur at the very end of a timestep,
+so atom attributes will include effects due to fixes that are applied
+during the timestep.  An explanation of the possible dump custom/vtk attributes
+is given below. Since position data is required to write VTK files "x y z"
+do not have to be specified explicitly.
+
+The VTK format uses a single snapshot of the system per file, thus
+a wildcard "*" must be included in the filename, as discussed below.
+Otherwise the dump files will get overwritten with the new snapshot
+each time.
+
+:line
+
+Dumps are performed on timesteps that are a multiple of N (including
+timestep 0) and on the last timestep of a minimization if the
+minimization converges.  Note that this means a dump will not be
+performed on the initial timestep after the dump command is invoked,
+if the current timestep is not a multiple of N.  This behavior can be
+changed via the "dump_modify first"_dump_modify_vtk.html command, which
+can also be useful if the dump command is invoked after a minimization
+ended on an arbitrary timestep.  N can be changed between runs by
+using the "dump_modify every"_dump_modify_vtk.html command.
+The "dump_modify every"_dump_modify_vtk.html command
+also allows a variable to be used to determine the sequence of
+timesteps on which dump files are written.  In this mode a dump on the
+first timestep of a run will also not be written unless the
+"dump_modify first"_dump_modify_vtk.html command is used.
+
+Dump filenames can contain two wildcard characters.  If a "*"
+character appears in the filename, then one file per snapshot is
+written and the "*" character is replaced with the timestep value.
+For example, tmp.dump*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk,
+tmp.dump20000.vtk, etc.  Note that the "dump_modify pad"_dump_modify_vtk.html
+command can be used to insure all timestep numbers are the same length
+(e.g. 00010), which can make it easier to read a series of dump files
+in order with some post-processing tools.
+
+If a "%" character appears in the filename, then each of P processors
+writes a portion of the dump file, and the "%" character is replaced
+with the processor ID from 0 to P-1 preceded by an underscore character.
+For example, tmp.dump%.vtp becomes tmp.dump_0.vtp, tmp.dump_1.vtp, ...
+tmp.dump_P-1.vtp, etc.  This creates smaller files and can be a fast
+mode of output on parallel machines that support parallel I/O for output.
+
+By default, P = the number of processors meaning one file per
+processor, but P can be set to a smaller value via the {nfile} or
+{fileper} keywords of the "dump_modify"_dump_modify_vtk.html command.
+These options can be the most efficient way of writing out dump files
+when running on large numbers of processors.
+
+For the legacy VTK format "%" is ignored and P = 1, i.e., only
+processor 0 does write files.
+
+Note that using the "*" and "%" characters together can produce a
+large number of small dump files!
+
+If {dump_modify binary} is used, the dump file (or files, if "*" or
+"%" is also used) is written in binary format.  A binary dump file
+will be about the same size as a text version, but will typically
+write out much faster.
+
+:line
+
+This section explains the atom attributes that can be specified as
+part of the {custom/vtk} style.
+
+The {id}, {mol}, {proc}, {procp1}, {type}, {element}, {mass}, {vx},
+{vy}, {vz}, {fx}, {fy}, {fz}, {q} attributes are self-explanatory.
+
+{id} is the atom ID.  {mol} is the molecule ID, included in the data
+file for molecular systems.  {type} is the atom type.  {element} is
+typically the chemical name of an element, which you must assign to
+each type via the "dump_modify element"_dump_modify_vtk.html command.
+More generally, it can be any string you wish to associate with an
+atom type.  {mass} is the atom mass.  {vx}, {vy}, {vz}, {fx}, {fy},
+{fz}, and {q} are components of atom velocity and force and atomic
+charge.
+
+There are several options for outputting atom coordinates.  The {x},
+{y}, {z} attributes are used to write atom coordinates "unscaled", in
+the appropriate distance "units"_units.html (Angstroms, sigma, etc).
+Additionaly, you can use {xs}, {ys}, {zs} if you want to also save the
+coordinates "scaled" to the box size, so that each value is 0.0 to
+1.0.  If the simulation box is triclinic (tilted), then all atom
+coords will still be between 0.0 and 1.0.  Use {xu}, {yu}, {zu} if you
+want the coordinates "unwrapped" by the image flags for each atom.
+Unwrapped means that if the atom has passed through a periodic
+boundary one or more times, the value is printed for what the
+coordinate would be if it had not been wrapped back into the periodic
+box.  Note that using {xu}, {yu}, {zu} means that the coordinate
+values may be far outside the box bounds printed with the snapshot.
+Using {xsu}, {ysu}, {zsu} is similar to using {xu}, {yu}, {zu}, except
+that the unwrapped coordinates are scaled by the box size. Atoms that
+have passed through a periodic boundary will have the corresponding
+cooordinate increased or decreased by 1.0.
+
+The image flags can be printed directly using the {ix}, {iy}, {iz}
+attributes.  For periodic dimensions, they specify which image of the
+simulation box the atom is considered to be in.  An image of 0 means
+it is inside the box as defined.  A value of 2 means add 2 box lengths
+to get the true value.  A value of -1 means subtract 1 box length to
+get the true value.  LAMMPS updates these flags as atoms cross
+periodic boundaries during the simulation.
+
+The {mux}, {muy}, {muz} attributes are specific to dipolar systems
+defined with an atom style of {dipole}.  They give the orientation of
+the atom's point dipole moment.  The {mu} attribute gives the
+magnitude of the atom's dipole moment.
+
+The {radius} and {diameter} attributes are specific to spherical
+particles that have a finite size, such as those defined with an atom
+style of {sphere}.
+
+The {omegax}, {omegay}, and {omegaz} attributes are specific to
+finite-size spherical particles that have an angular velocity.  Only
+certain atom styles, such as {sphere} define this quantity.
+
+The {angmomx}, {angmomy}, and {angmomz} attributes are specific to
+finite-size aspherical particles that have an angular momentum.  Only
+the {ellipsoid} atom style defines this quantity.
+
+The {tqx}, {tqy}, {tqz} attributes are for finite-size particles that
+can sustain a rotational torque due to interactions with other
+particles.
+
+The {spin}, {eradius}, {ervel}, and {erforce} attributes are for
+particles that represent nuclei and electrons modeled with the
+electronic force field (EFF).  See "atom_style
+electron"_atom_style.html and "pair_style eff"_pair_eff.html for more
+details.
+
+The {c_ID} and {c_ID\[N\]} attributes allow per-atom vectors or arrays
+calculated by a "compute"_compute.html to be output.  The ID in the
+attribute should be replaced by the actual ID of the compute that has
+been defined previously in the input script.  See the
+"compute"_compute.html command for details.  There are computes for
+calculating the per-atom energy, stress, centro-symmetry parameter,
+and coordination number of individual atoms.
+
+Note that computes which calculate global or local quantities, as
+opposed to per-atom quantities, cannot be output in a dump custom/vtk
+command.  Instead, global quantities can be output by the
+"thermo_style custom"_thermo_style.html command, and local quantities
+can be output by the dump local command.
+
+If {c_ID} is used as an attribute, then the per-atom vector calculated
+by the compute is printed.  If {c_ID\[N\]} is used, then N must be in
+the range from 1-M, which will print the Nth column of the M-length
+per-atom array calculated by the compute.
+
+The {f_ID} and {f_ID\[N\]} attributes allow vector or array per-atom
+quantities calculated by a "fix"_fix.html to be output.  The ID in the
+attribute should be replaced by the actual ID of the fix that has been
+defined previously in the input script.  The "fix
+ave/atom"_fix_ave_atom.html command is one that calculates per-atom
+quantities.  Since it can time-average per-atom quantities produced by
+any "compute"_compute.html, "fix"_fix.html, or atom-style
+"variable"_variable.html, this allows those time-averaged results to
+be written to a dump file.
+
+If {f_ID} is used as a attribute, then the per-atom vector calculated
+by the fix is printed.  If {f_ID\[N\]} is used, then N must be in the
+range from 1-M, which will print the Nth column of the M-length
+per-atom array calculated by the fix.
+
+The {v_name} attribute allows per-atom vectors calculated by a
+"variable"_variable.html to be output.  The name in the attribute
+should be replaced by the actual name of the variable that has been
+defined previously in the input script.  Only an atom-style variable
+can be referenced, since it is the only style that generates per-atom
+values.  Variables of style {atom} can reference individual atom
+attributes, per-atom atom attributes, thermodynamic keywords, or
+invoke other computes, fixes, or variables when they are evaluated, so
+this is a very general means of creating quantities to output to a
+dump file.
+
+See "Section_modify"_Section_modify.html of the manual for information
+on how to add new compute and fix styles to LAMMPS to calculate
+per-atom quantities which could then be output into dump files.
+
+:line
+
+[Restrictions:]
+
+The {custom/vtk} style does not support writing of gzipped dump files.
+
+The {custom/vtk} dump style is part of the USER-VTK package. It is
+only enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+To use this dump style, you also must link to the VTK library.  See
+the info in lib/vtk/README and insure the Makefile.lammps file in that
+directory is appropriate for your machine.
+
+The {custom/vtk} dump style neither supports buffering nor custom
+format strings.
+
+[Related commands:]
+
+"dump"_dump.html, "dump image"_dump_image.html,
+"dump_modify"_dump_modify.html, "undump"_undump.html
+
+[Default:]
+
+By default, files are written in ASCII format. If the file extension
+is not one of .vtk, .vtp or .vtu, the legacy VTK file format is used.
+
diff --git a/doc/genindex.html b/doc/genindex.html
index 6e00a60370..c74d4bfaa6 100644
--- a/doc/genindex.html
+++ b/doc/genindex.html
@@ -870,6 +870,10 @@
   </dt>
 
       
+  <dt><a href="dump_custom_vtk.html#index-0">dump custom/vtk</a>
+  </dt>
+
+      
   <dt><a href="dump_h5md.html#index-0">dump h5md</a>
   </dt>
 
diff --git a/doc/searchindex.js b/doc/searchindex.js
index fe6621cb06..d3b448f099 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
@@ -1 +1 @@
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476,482,484,490,496,501,505],ansi:[12,16],answer:[3,4,8,12,303,372,373],anthoni:329,antiquewhit:196,antisymmetr:[9,40,378],antisymmetri:401,antonelli:[328,329],antonio:435,anymor:329,anyon:7,anyparticl:88,anyth:[8,11,170,222,242,457,459,461,486],anywai:[173,375,496,503],anywher:[12,170,388,425,447,501],aoff:[369,475],aparam:[89,200,201],apart:[3,171,249,316,371,380,448,475,484],aperiod:285,api:[11,12,197,409,473],appar:3,appear:[2,3,6,11,12,13,39,40,41,72,77,89,94,110,112,119,120,144,153,170,171,173,193,195,196,208,212,213,216,220,223,226,235,240,289,300,301,330,342,344,345,360,368,369,370,389,399,425,430,446,458,464,471,472,473,475,476,477,480,482,496,501,505],append:[],appendix:[29,394,446],appl:[220,259,260,464],appli:[2,3,4,5,6,8,9,12,17,18,29,33,41,50,57,59,61,63,71,72,89,90,108,120,144,145,150,156,158,160,164,169,170,172,176,178,183,189,192,193,195,196,199,200,201,202,203,205,208,215,216,220,221,222,224,227,228,230,231,233,234,235,236,237,238,240,241,243,244,245,246,250,259,260,264,265,266,267,273,278,279,282,283,284,286,290,293,301,302,303,305,306,308,309,312,316,317,318,320,322,323,324,325,327,329,330,331,334,342,360,363,368,369,370,380,382,384,386,391,394,401,405,406,407,408,410,411,413,419,423,428,430,433,438,441,442,443,444,445,455,462,467,475,476,478,479,480,484,485,487,492,496,501,502,503,504],applic:[1,6,9,12,17,197,205,219,223,224,233,235,237,240,284,289,302,308,316,327,334,360,375,461,485,496],applyt:3,appopri:17,approach:[6,7,9,14,193,205,236,285,286,298,303,326,327,329,331,334,360,381,391,393,397,398,404,408,428,440,442,444,455,465],appropri:[1,2,3,6,8,11,12,13,15,17,33,38,42,50,56,61,73,90,93,120,121,148,149,150,178,183,189,190,192,193,196,208,209,212,213,214,219,220,222,233,234,237,246,254,256,257,259,261,262,263,264,265,266,267,278,279,280,282,286,289,290,293,298,303,307,319,322,323,324,327,334,336,337,339,340,341,352,361,370,377,381,385,389,390,391,400,405,408,410,417,421,428,437,438,439,457,458,459,460,461,464,465,475,476,477,479,480,488,489,492,501,502],approri:238,approxim:[6,9,122,126,169,235,237,246,286,304,306,326,360,366,367,368,383,393,401,404,422,423,428,430,437,440,446,467,489,496],april:11,aprpopri:470,apu:[422,423],aqua:[195,196],aquamarin:196,ar_therm:205,ar_ttm:205,ara:13,arbitrari:[6,40,58,120,193,195,197,221,222,238,259,286,294,457,473,486,501],arbitrarili:[11,59,120,144,192,220,259,391,501],arcco:3,arch:[1,12,14,15,17],architect:358,architectur:[16,375,428],archiv:[6,7,11,12,321,388,482],arcsin:3,area:[6,41,93,116,120,168,216,222,246,327,334,398,405,435,463,472,485],aren:[120,292,344],arflag:12,arg:[3,11,12,22,40,41,44,55,59,63,71,89,121,158,164,168,170,173,174,178,192,193,194,196,199,200,201,202,204,206,208,209,210,211,212,213,214,215,216,217,218,221,222,223,228,233,235,238,239,240,241,249,256,261,262,263,289,302,303,304,305,309,312,313,315,326,329,336,337,338,339,341,342,346,358,370,375,382,383,384,386,387,388,393,394,397,401,406,408,413,417,421,422,423,424,433,441,443,445,456,472,473,475,478,480,482,484,486,488,493,494,501,502,504,505],argon:235,argonn:12,argument:[2,3,6,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,44,45,46,47,48,49,51,53,54,56,59,63,73,89,93,110,113,116,120,144,145,147,152,157,158,159,164,168,170,171,172,174,176,177,178,179,180,181,182,184,185,187,188,190,193,196,199,200,201,202,204,207,208,209,210,211,212,213,214,215,216,220,221,222,229,231,233,234,235,237,238,242,243,249,256,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,288,289,291,295,300,303,304,305,306,319,322,324,331,333,335,337,339,342,344,345,346,347,348,350,351,352,354,356,358,359,361,362,363,365,370,374,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,393,394,395,397,399,400,402,403,404,405,406,407,408,409,410,411,413,414,415,416,417,418,419,420,421,422,424,425,426,427,430,431,432,433,435,436,438,439,440,441,446,447,448,456,457,458,459,460,461,462,464,466,467,468,469,470,471,472,473,474,475,476,478,480,483,484,485,486,490,492,493,501,502,504],aris:[12,467],arithmet:[3,6,106,360,386,389,416,430,462,463],arkansa:9,arl:[9,82,83,230,307],armi:[9,82,83,230,307],armv8:17,arnold:360,around:[1,3,4,6,12,42,57,58,59,66,70,71,72,73,77,120,144,148,165,168,170,172,192,195,196,203,204,220,222,223,241,256,259,292,294,298,303,312,316,319,336,337,340,359,369,446,475,478,485,486,496,501],aroung:3,arrai:[],arrang:144,arrheniu:489,art:[9,470,489],artefact:237,articl:[6,446],articul:[7,288],artifact:[90,168,496],artifici:[257,293,450,451,453],arun:13,arxiv:[144,194,447],ascend:[41,196,240,249,303,480],asci:7,ascii:[13,304,330,370,399,402,425,475],ash:[422,423],asid:[8,170,425],asin:501,ask:[3,11],askari:435,askoos:13,asoci:195,aspect:[6,7,59,222,235,404,440,463,475,485,489],aspect_ratio:304,asper:4,aspher:[],asq:[422,423],assembl:4,assign:[1,2,3,6,7,11,12,14,15,17,18,33,39,40,41,50,57,59,61,63,66,71,72,75,92,96,107,109,114,117,118,122,144,145,150,165,167,169,170,173,183,192,193,194,195,196,197,199,200,201,204,208,211,216,218,219,220,223,225,235,240,243,244,2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37,43,44,55,177,178,189,345,346,355,387,456],compat:[3,5,7,8,9,11,12,13,17,18,41,71,121,123,181,193,197,201,207,208,209,211,212,213,214,216,285,297,323,326,333,336,339,360,375,409,428,430,458,472,473,501],compens:[6,217,218,301,371,401],compet:330,competit:361,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,168,193,194,195,197,240,330,361,375,428,475,476,480,501],compl:17,complain:[11,12,17],complement:425,complementari:[7,391,413],complet:[3,6,9,11,12,15,41,59,71,196,212,216,221,249,286,289,292,319,330,332,343,344,359,370,375,402,443,445,463,470,475,480,483,487,489,492,496,501],complex:[6,8,11,12,13,25,40,42,62,94,110,144,146,158,170,171,246,315,340,358,370,401,428,458,473,475,478,501],compli:[326,330],complic:[6,7,9,12,13,206,235,473],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,90,91,92,93,94,96,97,100,107,108,109,110,111,112,113,114,116,117,121,131,134,135,136,137,140,141,142,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,165,166,167,192,193,195,196,202,203,207,208,209,210,211,212,213,214,215,219,220,222,223,228,233,238,242,243,246,249,251,255,256,258,259,260,264,265,266,267,278,279,280,282,283,285,286,287,290,301,303,305,306,308,312,313,316,319,322,323,324,326,333,334,339,340,341,360,363,367,368,369,370,375,395,401,405,422,423,443,445,446,447,475,476,485,493,501,502],componenet:6,composit:[6,206,246,399],compound:[390,401,402,464],compres:[71,118,208],compress:[],compris:[40,340,440,463],compton:[122,169],comptu:3,compuat:361,comput:[],computation:[3,6,217,218,331,381],computational:496,compute_arrai:8,compute_fep:[201,421],compute_group_group:235,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[122,304],compute_scalar:8,compute_temp:8,compute_ti:201,compute_vector:8,compute_xrd:169,concaten:[2,3,504],concav:340,concentr:[71,399],concept:[6,150,160,208,484],conceptu:[3,6,71,158,220,222,370,391,408,425,480],concern:[6,73,89,194,236],concetr:71,concis:[11,330],conclud:12,concret:8,concurr:[9,16,361,501],conden:[331,459,461],condens:[6,152,331,377,393,399,413,464],condit:[],conducit:6,conduct:[],cone:478,confer:428,confid:[3,489],config:[12,193,472],configfil:221,configur:[1,2,6,12,15,17,38,59,126,172,190,192,193,195,199,220,221,222,223,227,235,242,243,273,286,294,330,358,368,370,377,381,400,425,428,457,459,461,464,470,475,477,478,489],confin:[475,489],conflict:[3,12,40,430,473],conform:[3,6,13,59,219,220,258,302,308,330,354,370,401,487],confus:[3,464],conjuct:395,conjug:[7,8,243,367,401,438,439],conjunct:[6,7,71,88,89,118,153,158,164,170,174,196,200,201,243,246,250,273,289,290,294,295,296,298,303,307,319,327,334,339,360,361,370,382,384,388,391,395,401,407,413,430,433,441,462,475,478,482,496,505],connect:[3,6,89,155,173,219,240,288,303,306,316,370,392,405,455,461,472,473,479,496],conput:3,consecut:[3,11,12,39,71,170,196,200,201,223,240,241,391,413,417,470,476,478],consequ:[1,6,206,331,412,489],conserv:[],consid:[6,9,70,71,78,89,119,152,155,156,173,193,196,200,201,207,209,212,216,218,219,223,247,260,285,303,326,327,330,331,334,361,388,401,408,439,440,446,455,470,471,473,476,477,478,480,483,485,493,496,501],consider:[6,8,243,244,322,323,324,375,484],consist:[3,6,8,9,11,12,40,42,65,69,79,95,107,112,115,116,119,150,153,155,170,182,192,197,202,203,208,222,223,226,228,233,236,243,244,245,256,259,261,262,263,264,265,266,267,268,269,271,272,273,274,276,277,278,279,280,281,282,290,293,298,300,302,303,322,323,324,325,335,360,361,363,369,370,375,377,381,383,389,391,401,404,408,411,422,423,425,428,430,440,443,445,446,458,465,473,475,476,477,478,479,480,487,496,501],consistent_fe_initi:205,consit:303,constant:[],constitu:[3,6,249,303,336,340,389,440],constitut:[443,445],constrain:[3,6,8,147,148,149,150,151,153,156,157,158,159,160,162,163,199,208,223,235,236,241,249,253,288,289,301,303,306,317,327,334,368,369,401,480,487,496],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,94,110,122,144,169,220,259,285,302,340,371,375,394,428,430,455,457,458,478,479,494,501],constructor:[8,11],consult:439,consum:[1,298,434,501],consumpt:358,contact:[],contact_stiff:[442,444],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,89,93,120,122,144,150,158,168,169,170,172,176,178,189,190,193,195,196,197,199,200,201,205,207,208,209,211,212,213,214,216,221,223,228,231,237,241,242,243,246,257,273,284,285,288,289,291,293,296,300,303,304,309,319,326,330,331,340,341,344,359,361,369,370,373,374,376,377,378,381,390,391,394,399,400,401,408,409,425,428,432,436,437,438,439,447,457,458,459,460,461,462,464,470,471,472,473,475,476,477,478,480,482,484,487,489,490,492,493,496,501,503,505],content:[12,18,439,491,493],context:[3,6,8,12,17,120,121,196,217,218,223,288,300,335,367,467,475,482,491,500,501,502],contibut:70,contigu:472,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,106,107,166,196,199,200,201,206,208,209,210,211,212,213,214,216,219,220,221,222,223,235,236,237,239,240,241,243,244,245,251,256,257,259,261,262,263,264,265,266,267,278,279,280,281,282,287,289,292,293,303,304,308,318,319,321,328,329,331,337,340,344,359,374,375,381,395,398,415,418,438,439,440,443,445,460,470,473,475,477,478,483,489,490,492,493,501,503],continuum:[6,7,9,205,331,443,445],contour_integr:205,contract:[59,220,222,259,290,303],contradictori:3,contrain:306,contraint:273,contrari:[237,244],contrast:[1,6,42,55,64,152,155,222,342,443,445,467,504],contrib:331,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,86,89,90,91,92,93,96,105,107,109,111,112,113,114,116,118,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,201,206,207,208,209,211,212,213,214,220,235,243,246,249,250,254,260,280,281,288,289,297,300,303,304,306,333,360,368,370,378,395,398,399,401,408,422,423,428,430,438,439,446,487,493,496],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,89,93,126,144,179,193,195,199,205,206,216,220,221,222,239,240,243,244,259,261,262,263,264,265,266,267,290,295,303,310,311,322,323,324,331,335,358,360,372,401,404,428,438,439,442,444,457,461,470,472,484,490,491],control_typ:205,controlfil:439,convect:93,conveni:[6,12,29,193,197,214,304,363,447,501],convent:[3,8,9,29,181,188,189,196,302,316,343,399,401,501],converg:[3,6,41,90,193,195,197,202,216,219,220,228,233,264,293,295,298,302,306,366,367,368,370,390,391,413,446,470,482,489],convers:[3,8,144,195,196,206,209,290,360,391,392,393,401,413,417,421,433,473,489,500],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,93,170,177,193,195,196,214,257,289,342,345,347,351,354,363,370,376,399,428,459,461,468,473,475,476,477,482,492,496,500,501,503,505],convex:[42,340],convinc:[7,12],cook:9,cooki:7,cool:[7,160,239,301],cooordin:193,cooper:[5,7],coord123:118,coord1:[3,118,208,212,213],coord2:[3,118,208,212,213],coord3:[3,118,208,212,213],coord:[],coordb:446,coordbb:446,coordiat:368,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,89,91,92,96,106,107,109,117,118,120,138,144,153,159,165,167,168,170,174,192,193,194,195,196,197,199,202,207,208,211,212,213,216,217,218,219,220,221,222,223,226,228,229,233,235,238,239,240,241,242,243,244,256,258,259,261,262,263,265,266,267,280,283,284,285,288,289,290,300,301,303,305,306,308,313,316,317,318,319,321,329,330,331,338,339,341,342,363,368,369,370,375,376,377,380,400,446,470,475,476,477,478,480,483,485,489,496,501,502],coordn:[118,208],coorind:[],copi:[0,3,4,8,11,12,15,17,40,123,195,331,370,388,438,473],copper:468,coproccesor:16,coprocessor:[1,4,7,9,16,17,375,488],coproprocessor:17,copy_arrai:8,copyright:[7,8,288],coral:196,core:[],core_shel:152,coreshel:[6,9,384,391,393],cornel:[6,176,487],corner123i:117,corner123x:117,corner123z:117,corner1i:117,corner1x:117,corner1z:117,corner2i:117,corner2x:117,corner2z:117,corner3i:117,corner3x:117,corner3z:117,corner:[3,6,40,117,195,340,341,363,463,475],cornflowerblu:196,cornsilk:196,corp:9,corpor:16,corr:390,correct:[3,6,9,11,12,16,17,59,89,90,105,106,114,120,152,157,164,195,222,235,237,243,259,260,280,288,290,293,330,336,340,360,370,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,398,399,400,401,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,433,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,463,464,466,467,468,475,490,493,496],correction_max_iter:205,correctli:[3,8,9,11,17,71,81,105,106,107,147,148,149,151,153,155,156,157,158,159,162,163,166,193,196,202,223,228,233,244,253,259,260,296,303,306,316,318,337,340,370,371,375,393,423,428,472,473,475,485,500,502],correl:[],correpond:231,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,89,99,100,113,116,117,118,119,122,123,131,134,135,136,137,138,140,141,142,144,147,148,157,164,168,169,176,177,178,179,180,181,182,184,185,187,188,190,192,193,195,196,200,201,202,208,210,211,212,213,215,218,220,222,229,233,234,238,243,246,247,255,256,257,259,261,262,263,264,265,266,267,268,269,273,276,278,279,280,282,285,286,290,295,303,305,306,322,324,326,335,336,337,339,340,341,343,345,346,347,348,350,351,354,356,361,365,367,369,370,376,377,379,382,383,384,385,386,387,388,389,390,391,394,395,399,400,401,402,403,404,405,406,407,408,411,413,414,415,416,417,418,419,420,421,422,425,426,428,430,431,432,433,435,436,438,439,440,441,446,447,448,457,458,459,460,461,464,466,467,468,470,472,473,475,476,478,488,489,490,492,493,496,501],correspondingli:[422,423,484],corrupt:3,cosin:[],cosineshift:27,cosmo:[237,242],cossq:[],cost:[1,6,10,11,12,17,39,41,71,113,122,145,169,195,196,208,212,213,216,217,218,232,259,295,331,360,361,373,391,413,417,428,430,457,472,484],costheta0:[457,459,461,464],costheta:436,costli:[11,90,237,371],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,89,92,96,107,109,113,116,118,150,160,165,167,183,193,195,196,200,201,208,209,212,216,222,233,242,292,293,294,298,301,303,305,319,320,326,330,331,332,336,340,342,344,352,357,359,366,368,371,375,378,403,407,408,411,438,439,471,472,473,475,477,479,482,483,490,491,496,501,502],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,90,111,112,120,145,171,175,294,296,332,360,361,368,375,382,384,385,386,387,390,391,392,393,394,401,405,406,408,413,417,421,424,430,433,438,439,441,446,456,461,462,464,467,480,487,493,496,500],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,93,118,120,121,158,168,174,202,203,206,208,211,212,213,215,216,223,228,232,235,241,259,273,289,306,322,323,340,361,368,369,370,372,375,403,407,430,493,501],counter:[3,337,470,481,483,489],counteract:235,counterbal:239,counterbalanc:29,counterpart:[193,303,470],counterproduct:18,coupl:[],courant:309,cours:[3,8,130,132,164,193,200,201,236,302,316,330,336,338,339,341,342,361,422,448,472,475,488,496,501,503],courtesi:363,cov:446,coval:[6,29,401,425,446,496],covari:237,cover:[6,71,190,196,205,246,401,463],coverag:[71,212],cpc:242,cpp:[1,3,6,8,9,11,12,13,89,193,200,201,233,306],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,196,210,226,244,332,358,361,375,388,456,470,488,489,492,493,494,501],cpuremain:493,cr2:169,cr3:169,crack:[4,371],crada:[5,7],crai:[5,7,13,18,193],crash:[3,12,371,496],craympi:375,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:205,create_faceset:205,create_group:194,create_nodeset:205,createatom:[],creation:[],crimson:196,critchlei:288,criteria:[3,120,171,195,196,217,218,219,254,368,435,463,477,480,501],criterion:[12,41,125,170,173,206,216,219,235,273,295,309,337,342,368,370,390,401,405,446,480,489,490],criterioni:489,critic:[6,48,49,257,326,331,368],crmax:71,crmin:71,cross:[3,12,22,71,91,148,168,178,193,195,207,212,218,222,256,258,280,303,312,316,318,327,334,346,363,370,386,395,398,399,406,407,408,413,415,417,436,441,443,445,459,461,468,475,479,485,503],crossov:1,crossterm:475,crozier:[0,7,13],crucial:293,crystal:[4,6,13,73,110,284,285,329,363,371,479,493,496],crystallin:[6,106,285,363,460,496],crystallis:326,crystallogr:[122,169],crystallograph:[363,493],crystallographi:[122,169,363],cs1:169,cs_chunk:6,cs_im:[40,475],cs_re:[40,475],csanyi:[144,437,447],cscl:425,csequ:6,csh:[11,12,388],cshrc:[11,12],csic:[400,457,459,461,464],csinfo:6,csisi:[400,457,459,461,464],csld:[],cst:399,cstherm:6,cstyle:472,csvr:[],ctcm:[376,399],ctemp_cor:226,cterm:308,ctr:9,ctype:11,cu1:169,cu2:169,cu3au:425,cube:[6,41,168,173,216,226,340,363,496],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:381,cummul:[3,6,214,217,218,219,221,232,237,243,245,319,322,323,324,325,327,334,407,493],cumul:[6,206,208,211,212,213,227,235,243,257,259,264,273,303,304,370],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,89,105,106,112,120,121,134,145,150,158,160,166,168,171,174,192,193,194,195,196,197,200,201,205,208,212,213,214,216,217,218,219,220,221,222,223,227,228,233,235,237,240,241,243,249,256,259,260,265,266,267,273,278,279,280,282,288,289,294,295,297,300,301,302,303,306,307,308,309,310,311,312,313,315,317,318,319,322,323,324,330,331,334,335,336,337,338,339,341,342,344,358,359,360,361,364,365,367,368,369,370,375,381,388,390,394,399,401,402,405,408,409,412,422,423,425,426,427,430,436,438,439,442,443,444,445,448,459,461,462,465,470,471,472,473,475,476,477,478,479,481,482,483,485,487,489,490,492,493,501,502,503,504,505],curv:[6,170,235,285],curvatur:[404,440,468],custom:[],cut0:473,cut1:484,cut2:484,cut:[],cuthi:[284,296],cutinn:[383,422,423],cutlo:[284,296],cutmax:436,cutoff1:[387,394,413,417,421,424,433,441],cutoff2:[382,384,385,387,393,394,413,417,421,424,433,441],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,89,94,110,112,119,120,144,168,171,173,174,218,219,224,231,284,293,294,296,298,300,303,307,319,332,336,340,342,358,360,361,368,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,406,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,438,439,440,441,446,447,448,449,450,451,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,473,477,480,484,496,501],cutoff_glob:[],cutoff_inn:[],cutoffa:400,cutoffc:400,cuu3:399,cval:169,cvd:326,cvel:308,cvff:[],cwiggl:[3,256,336,339,341,501],cyan:[2,195,196],cycl:[3,235,257,259,260,264],cyclic:[3,190],cygwin:12,cylind:[3,4,71,195,208,241,289,337,340,478],cylindr:[6,241,316,337],cypress:375,cyrot:381,cyrstal:285,d3q15:246,d3q19:246,d_double_doubl:15,d_e:331,d_flag2:292,d_flag:292,d_name:[117,193,292,321,485],d_single_doubl:15,d_single_singl:15,d_sx:292,d_sy:292,d_sz:292,daan:329,dai:12,daili:12,daivi:280,damag:[],dammak:298,damp:[3,6,199,204,243,244,245,250,259,260,264,290,293,294,298,303,322,323,335,337,338,367,368,370,382,384,386,391,394,401,405,413,421,433,441,456,462,489,496],damp_com:244,damp_drud:244,dampen:[303,496],dampflag:[337,405],dan:17,danger:[3,12,235,342,395,493],dangl:173,daniel:9,darden:[361,394],darkblu:196,darkcyan:196,darken:195,darkgoldenrod:196,darkgrai:196,darkgreen:196,darkkhaki:196,darkmagenta:196,darkolivegreen:196,darkorang:196,darkorchid:196,darkr:196,darksalmon:196,darkseagreen:196,darkslateblu:196,darkslategrai:196,darkturquois:196,darkviolet:196,dasgupta:294,dash:[405,492],dat:[6,93,190,205,471],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,304],dataset:304,datatyp:3,date:[0,6,12,13,192,438,439,501],datom1:119,datom2:119,datom3:119,datom4:119,datum:[3,6,42,65,68,69,79,95,112,119,193,209],davenport:424,davi:336,david:[9,19,360,361,459,461],daw:[399,436],dbg:14,dcd:[3,6,7,193,194,195,196,197,286,476,480],ddim:192,deactiv:421,dealt:242,debug:[6,7,11,12,13,14,17,122,126,169,170,286,291,358,360,375,409,430,465,473,474,482,485,492,501],deby:[],decai:[94,391,468],decid:[3,6,12,16,71,256,292,303,332,490],decipher:363,declar:194,declin:319,decod:195,decompos:[89,447],decomposit:[3,5,7,18,62,205,286,307],decoupl:[6,496],decreas:[3,193,202,203,210,219,222,228,233,235,243,330,360],decrement:308,deepli:357,deeppink:196,deepskyblu:196,def:[12,13,473],defaul:61,defect:[6,70,168,428],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,176,177,178,179,180,181,182,184,185,187,188,189,190,191,192,193,194,195,196,199,200,201,202,203,204,205,206,207,208,209,211,212,213,214,215,216,217,218,219,220,222,223,226,227,228,230,233,234,235,238,241,242,243,244,245,246,254,256,258,259,260,261,262,263,264,265,266,267,269,270,271,274,276,277,278,279,280,281,282,284,285,286,288,289,290,292,294,296,301,303,304,305,306,309,313,317,319,321,322,323,324,325,327,328,329,331,333,334,336,337,338,339,340,341,342,344,345,346,347,348,349,350,351,354,355,356,358,360,361,363,365,367,368,369,370,371,372,373,374,375,377,378,379,380,382,383,384,385,386,387,388,389,391,392,394,395,396,397,398,400,401,403,404,405,406,407,408,409,411,413,414,415,416,417,418,419,420,421,422,423,424,428,429,430,431,432,433,435,436,438,439,440,441,442,443,444,445,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,472,473,475,476,478,479,480,481,484,485,486,487,489,490,492,493,496,497,498,499,500,501,502],definit:[2,3,6,8,12,13,78,80,120,144,196,208,209,210,211,212,213,214,222,230,241,264,304,321,333,336,339,341,343,355,358,369,378,381,389,396,397,401,411,436,443,445,447,463,473,475,477,484,486,500,501],defint:493,deform:[],deg2theta:169,deg:496,degener:[3,288],degrad:[8,18,285,361,484],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,94,95,97,99,100,102,104,105,110,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,169,170,176,177,180,181,188,190,192,195,208,219,226,235,237,238,243,244,249,259,260,264,265,266,267,278,279,280,282,286,288,302,303,306,322,323,324,329,345,347,351,354,356,368,394,399,407,485,493,496,502],degress:[150,208],del:489,delai:[3,6,12,371,398,493],deleg:408,delet:[2,3,7,8,12,54,57,60,63,168,173,174,199,208,209,211,212,213,214,217,219,232,235,259,304,322,323,342,344,359,369,371,374,430,455,475,476,477,478,486,487,492,497,499,501,502],delete_atom:[],delete_bond:[],delete_el:205,deli:192,delimit:[473,501],deloc:[260,401,446],delr:425,delt_lo:489,delta:[],delta_1:381,delta_3:381,delta_7:381,delta_conf:3,delta_ij:[425,436],delta_mu:[],delta_pi:381,delta_r:436,delta_sigma:381,delta_ua:[],delx:192,delz:192,dem:[],demand:298,demo:11,demon:283,demonstr:[293,425],den:289,dendrim:407,denniston:[9,246,248,249,250,285],denomin:[7,175],denot:[122,226,244,285,296,298,391,406,408,439,443,445],dens:[71,219,401],densiti:[3,6,7,9,18,40,41,59,103,120,130,144,156,168,170,200,201,205,208,212,213,216,222,233,246,249,252,253,285,289,290,294,331,336,363,365,369,376,381,399,425,426,427,436,440,446,450,452,453,454,475,484,485,493,500],density_continu:445,density_summ:445,depart:[0,7],departur:[257,293],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,94,95,106,112,113,116,117,118,119,123,144,147,153,157,158,164,170,171,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,195,196,199,200,201,202,203,206,208,210,211,212,214,215,216,218,220,222,228,229,234,237,238,239,241,243,244,246,248,249,256,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,284,295,298,300,303,305,306,307,313,319,322,323,324,326,328,330,331,333,335,336,339,340,341,342,344,345,346,347,348,350,351,354,356,361,363,368,369,371,372,373,375,376,377,379,380,381,382,383,384,385,386,387,388,389,390,391,392,394,395,399,400,401,402,40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,equidist:258,equil:[3,294,364,482,505],equilater:485,equilibr:[3,4,5,6,7,9,59,93,170,199,206,209,219,220,235,257,259,260,280,281,293,294,295,296,327,328,329,334,390,391,438,439,471,485],equilibria:334,equilibribum:[217,218],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,153,154,177,179,220,222,235,236,237,244,246,259,264,280,293,294,298,302,306,308,316,319,326,327,329,334,345,347,351,354,390,425,432,446,496],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:205,equival:[6,12,13,29,59,61,128,129,137,142,168,172,196,211,214,220,222,235,243,259,280,290,302,303,339,395,401,446,459,461,475,478,483,484,493,496],equlibrium:6,equliibr:[294,296],er3:169,eradiu:[40,117,401,475],eras:[305,328],erat:[222,423],erc:391,erfc:[391,413,430],erforc:117,erg:500,erhart:[206,399,459,461],ermscal:378,ernst:9,eror:3,eros:425,erose_form:425,erot:[],errata:[459,461],erratum:336,erron:3,error:[],erta:405,ervel:[117,475],escap:[223,496],especi:[8,16,158,170,199,206,216,235,293,298,301,302,375,472],espresso:[9,297],essenti:[8,11,12,27,90,132,151,152,153,156,157,158,159,160,162,179,209,264,285,335,361,377,391,413,461,480,493],essex:29,establish:[89,239],estim:[1,3,6,10,12,38,41,56,93,145,205,216,227,257,319,326,360,361,366,430,439,458,489,493],esu:500,esub:425,eta:[6,246,259,293,294,296,335,400,402,404,436,460,464,500],eta_dot:259,eta_ij:436,eta_ji:402,etag:[40,475],etail:493,etap:259,etap_dot:259,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,91,92,93,97,113,114,117,119,145,147,150,151,152,153,154,156,157,158,159,160,162,164,170,172,173,174,183,193,195,196,199,200,205,206,207,208,211,212,213,214,217,218,222,223,233,235,236,243,259,289,300,304,331,332,340,344,359,360,368,369,370,371,373,399,400,408,421,423,428,434,438,439,457,459,461,464,470,473,475,476,477,482,484,485,489,490,491,492,493,494,496,500,501,503,505],ethernet:18,etol:[368,370,470,489],etot0:293,etot:[6,97,99,100,114,145,156,196,226,244,257,293,492,493],eu2:169,eu3:169,euler:[368,370],eulerian:205,euqat:449,europhi:246,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,89,90,93,111,121,144,146,150,160,168,170,192,193,195,196,200,201,202,203,205,207,208,209,210,211,212,213,214,215,222,228,236,238,239,241,242,243,244,285,291,294,305,309,313,322,323,324,333,336,339,341,342,344,360,361,366,368,375,428,430,436,442,444,446,458,470,471,473,477,478,480,482,483,484,485,489,491,493,501,502],evalut:[344,473],evan:[158,280],evanseck:[6,20,176,386,487],evapor:[],evaul:[8,368],evdwl:[111,438,439,493],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,123,168,171,172,186,190,193,196,199,200,201,206,207,208,211,212,213,214,216,217,218,220,222,223,226,241,244,257,259,260,285,289,298,300,303,304,315,319,327,331,334,336,340,342,353,360,366,368,370,375,380,401,402,405,408,411,430,440,464,465,475,476,478,480,481,482,484,485,487,490,492,493,494,496,505],evenli:[3,41,145,190,216,246,411,465],event:[],eventu:[3,6,12,15,172,294,489],ever:[54,56,242,319],evera:[389,404,440,456],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,93,117,123,132,158,173,193,194,195,196,197,199,200,201,202,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,227,232,233,235,237,239,240,241,246,247,255,259,260,264,283,284,285,289,290,291,292,293,294,295,296,298,300,301,303,304,306,308,319,321,322,323,324,325,326,327,330,331,332,333,334,342,344,359,361,370,371,372,375,395,398,408,421,438,439,446,452,469,470,471,475,477,479,480,482,483,484,489,490,491,493,501,505],everyth:[8,111],everywher:[120,415],eviri:401,evolut:[237,246,286,470],evolv:[246,286,332],ewald:[2,3,5,6,7,8,12,90,114,122,145,332,360,361,368,382,384,385,391,394,401,413,417,433,441,456,458],ewald_disp:394,ewalddisp:3,exact:[22,41,44,71,126,164,173,178,216,219,236,237,243,244,245,289,298,299,319,331,346,360,388,477,482,489,501,503,505],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,93,120,148,154,161,170,190,200,201,211,216,222,227,231,236,243,244,245,260,272,273,281,285,293,319,324,325,338,375,388,395,399,405,408,422,430,458,477,478,485,489,501],exager:496,examin:[6,8,9,17,219,285],examp:[473,501],exampl:[],exce:[3,6,16,17,18,41,58,71,172,207,208,211,212,213,214,216,220,222,227,232,259,285,300,304,310,311,319,368,375,475,501],exceed:[3,41,59,216,222,259,319,483],excel:401,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,91,92,112,113,116,121,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,170,174,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,196,199,202,208,209,211,215,216,220,222,229,234,235,238,241,243,245,259,260,261,262,263,264,265,266,267,268,269,272,273,276,278,279,280,281,282,286,295,296,303,305,306,316,319,322,324,325,331,335,339,342,343,344,345,346,347,348,350,351,354,355,356,360,361,363,365,369,370,371,373,374,375,376,377,379,382,383,384,385,386,387,388,389,390,391,393,394,395,399,400,401,402,403,404,405,406,407,408,413,414,415,416,417,418,419,420,421,422,423,426,431,432,433,435,438,439,440,441,448,456,457,458,459,460,461,464,466,467,468,470,472,473,475,477,478,480,483,484,485,486,487,489,493,496,500,501,502,504],excess:[210,401],exchang:[2,3,6,8,9,61,62,199,205,206,235,243,295,303,327,331,334,360,375,401,490],exchange:360,excit:[9,401],exclud:[3,6,9,12,16,17,63,71,116,144,150,157,158,174,193,208,212,217,218,247,255,288,301,303,326,337,342,368,369,371,383,405,408,411,422,423,430,455,487],exclus:[1,3,9,12,16,89,375,390,428,430,484,494],excurs:[259,470],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,171,195,240,297,344,359,362,374,471,473,483,486,489,501],exempl:446,exemplari:236,exemplifi:401,exert:[6,241,244,298,338,339,340,361],exhaust:[205,374,501],exhibit:[94,259,367,401,484],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,126,170,171,189,194,195,196,199,204,215,218,220,223,235,288,289,291,342,343,345,347,348,349,351,355,364,369,375,396,397,408,438,455,465,471,473,475,476,477,486,487,488,501,502,503],exit:[2,3,11,12,41,57,193,216,231,359,374,473,474,483,492,501],exlanatori:3,exp:[],expand:[],expans:[12,144,193,486,501],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,105,151,162,168,190,216,228,235,237,256,284,290,292,293,298,303,342,361,371,388,425,428,430,470,473,475,477,480,484,489,501],expens:[6,10,71,196,284,288,303,331,342,360,361,371,375,473],experi:[6,13,15,17,215,223,240,249,258,290,302,303,366,370,395,430,484,489],experienc:[6,12,248,249],experiment:[235,360,375,489],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,88,95,150,158,190,193,195,196,199,208,209,214,216,218,220,222,259,284,292,303,316,342,344,359,360,363,369,370,374,380,399,411,446,448,463,473,476,477,480,482,485,496,501,505],explan:[3,6,59,117,144,193,208,258,284,408,469,472,473,475,484],explanatori:[3,8,121,193,207,208,211,212,213,303,369,472,501],explantori:[3,299],explic:429,explicit:[6,9,11,22,44,77,89,117,120,164,178,200,201,222,310,311,346,365,377,378,381,386,388,399,401,412,422,462,469,472,476,479],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,113,116,147,157,160,168,170,176,177,179,180,181,182,184,185,187,188,190,193,196,202,212,215,222,229,234,236,238,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,292,293,295,303,305,306,322,324,325,331,335,339,345,347,348,350,351,354,356,369,375,376,377,379,382,383,384,385,386,387,388,389,390,391,392,394,395,398,399,400,402,403,404,405,406,407,408,412,413,414,415,416,417,418,419,420,421,422,426,428,430,431,432,433,435,440,441,448,449,450,451,452,453,454,456,457,458,459,460,461,462,464,466,467,468,475,477,478,484,485,487,488,494,496],explictli:[16,488],exploit:[9,15,17,286],explor:[122,169],expon:[3,294,296,399,404,407,421,429,441],exponenti:[89,436,457,464,468,489,501],expos:11,exposit:[205,395,398],express:[6,144,156,170,200,201,220,256,284,294,331,337,344,381,399,401,415,425,446,447,456,501],expressiont:381,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,84,85,86,89,90,93,97,100,101,111,113,121,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,199,202,203,206,214,215,221,224,228,233,234,235,237,238,239,241,243,245,257,259,264,273,284,285,301,302,303,305,308,313,316,318,322,323,324,325,326,328,329,331,333,336,340,341,404,425,428,439,440,447,492,493],extent:[1,3,41,42,45,57,71,168,172,193,204,212,216,241,338,341,360,363,377,442,444,458,472,475,478],exterior:[3,6,168,340],extern:[],extra:[3,6,8,11,12,16,17,40,41,46,61,71,105,113,114,116,122,145,147,148,149,151,153,156,157,158,159,160,162,163,169,170,171,172,176,196,211,216,218,259,291,292,293,303,319,368,369,372,373,394,405,408,411,425,430,472,473,475,478,487,496,501],extract:[3,6,11,13,36,63,89,111,119,121,123,200,201,296,370,391,402,425,447,473,480,492],extract_atom:11,extract_comput:[11,473],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,195,210,220,222,259,329,401,460,496],extrema:421,extrins:205,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[166,333],f_a:[459,460,461],f_ave:121,f_c:460,f_f:461,f_fix_id:293,f_harm:329,f_i:[29,436],f_id:[6,71,121,123,193,199,207,208,209,210,211,212,213,214,254,321,333,493,501],f_ij:436,f_indent:214,f_int:328,f_j:29,f_jj:93,f_k:436,f_langevin:331,f_max:[293,298],f_msst:257,f_r:[244,459,460,461],f_sigma:381,f_solid:329,f_ss:6,f_temp:[],face:[3,6,57,59,71,158,168,172,204,212,213,336,338,339,340,341,363,404,425,440,475,478],face_threshold:168,facet:168,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,237,289,319,329,405,446,487],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,89,93,105,112,119,120,122,144,164,169,172,176,187,192,193,195,196,200,201,209,216,220,222,223,235,240,243,245,246,257,259,260,264,286,290,294,302,306,309,311,319,323,327,334,335,336,340,351,361,363,369,375,377,378,381,382,384,386,391,392,393,395,396,397,401,405,408,412,413,425,428,430,432,433,439,441,448,457,462,472,475,478,479,484,487,489,490,493,496,500,501],factori:[3,473],factoriz:360,fail:[3,11,12,59,174,220,223,360,368,370,393,439,473],failur:[125,443,474,501],fairli:[11,430,484,489],faken:73,falcon:240,fall:[3,6,196,211,289,473,501],fals:[88,342,344,446,501],fame:8,famili:[464,472],familiar:[0,11],fan:436,far:[3,6,12,17,57,59,61,88,193,196,197,216,217,218,220,223,259,284,302,303,319,336,347,351,366,370,371,463,473,475,480,493],farago:243,farrel:[459,461],farther:193,fashion:[6,8,41,71,170,196,199,200,201,206,212,216,218,223,235,237,241,256,257,259,261,262,263,264,265,266,267,275,278,279,280,281,282,292,293,295,303,308,312,318,321,329,331,335,336,337,339,341,370,408,422,478,487,501,504],fasolino:410,fast:[6,7,9,12,13,17,39,193,270,293,332,360,361,383,422,423,428,456,458,477,482,484,493,502,505],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,108,113,116,147,157,176,177,179,180,181,182,184,185,187,188,190,193,196,202,215,216,222,229,234,238,242,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,290,294,295,303,305,306,319,322,324,326,328,331,335,339,345,347,348,350,351,354,356,360,361,372,373,375,376,377,379,381,382,383,384,385,386,387,388,389,390,391,394,395,399,400,402,403,404,405,406,407,408,413,414,415,416,417,418,419,420,421,422,426,431,432,433,435,440,441,448,456,457,458,459,460,461,464,466,467,468,470,478,484,488,496],fastest:[1,6,14,17,158,212,331,332,375,472],fatal:[3,492],fault:[70,439],faulti:12,fava:404,favor:219,favorit:7,fbmc:326,fcc:[],fcm:[275,501],fdirect:226,fdotr:409,fdt:[],fdti:89,fe2:169,fe3:169,fe_md_boundari:205,featu:8,featur:[],fecr:399,feedback:[7,240],feel:[7,240,241,249,284,340,342,370,430],felling:427,felt:340,femtosecond:500,fene:[],fennel:[391,413],fep:[],ferguson:[6,176,487],fermi:[1,12,15,156,375,461],fermion:[9,401],fernando:424,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,63,197,207,208,209,211,212,213,214,244,259,289,292,294,306,333,360,368,369,370,377,446,472,475,480,484,486,494,501,503],fewer:[1,3,11,15,16,61,249,484],fewest:3,fextern:233,feynman:286,fff:473,ffield:[390,402,438,439,446],ffmpeg:[3,12,195],ffplai:195,fft:[1,3,7,11,12,14,15,90,113,114,145,285,360,361,484],fft_inc:[12,361],fft_lib:12,fft_path:12,fftbench:[360,494],fftw2:12,fftw3:12,fftw:12,fhg:[7,9],ficiti:455,fictiti:[6,202,203,228,233,237,286,302,391,413,417,455],field1:[476,480],field2:476,field:[],fifth:[316,432],figur:[1,3,8,12,293,472,473],fij:394,file0:284,file1:[11,13,284,330,344,369,480,482,486],file2:[11,13,330,344,369,480,482,486],file:[],file_from:194,filen:369,filenam:[3,12,13,38,41,56,190,193,195,196,197,205,208,209,210,211,212,213,214,216,221,231,284,288,291,294,295,296,299,300,303,304,330,331,357,358,359,369,370,376,377,381,391,399,400,402,410,425,426,427,432,436,437,438,439,446,447,457,458,459,460,461,464,471,472,473,476,477,482,486,493,501,503,504,505],filennam:482,filep:[3,193,196,477,482,505],filepo:300,fill:[7,9,170,195,289,331,363,371,381,428,439,478],filter:[196,205],final_integr:8,final_integrate_respa:8,finchham:[6,152,393],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,89,121,173,190,197,206,219,220,231,232,235,258,284,289,290,298,302,366,368,370,371,391,408,413,417,425,446,456,458,496,501],find_custom:8,fine:[16,17,174,202,228,329,371,375,501],finer:[144,170,501],finest:360,finger:[170,192,256,478],finish:[6,11,41,216,344,357,359,360,372,374,375,463,480,501,502],finit:[],finni:[7,399,456],finvers:226,fiorin:[9,221],fire:[],firebrick:196,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,90,93,106,107,108,110,116,120,121,131,134,137,138,142,145,155,158,164,166,168,169,171,172,173,177,190,193,194,195,196,197,199,200,208,209,211,212,213,214,216,219,222,231,235,236,241,246,256,257,258,259,284,286,291,292,293,295,300,303,306,308,316,317,319,320,321,328,329,330,331,333,337,342,344,345,352,363,368,369,370,371,374,375,376,377,380,381,382,384,386,388,390,391,399,401,402,405,406,408,409,410,411,412,413,417,422,423,425,427,428,430,432,436,438,439,446,447,455,457,458,459,460,461,464,468,470,471,472,473,475,476,477,480,482,484,487,488,489,492,493,496,501,502,503,505],fischer:[6,9,19,20,176,386,487],fit:[3,6,9,12,38,56,190,231,302,319,377,381,410,425,430,451,458,460,483,501],five:[73,156,293,369,381,426,475,489],fix:[],fix_adapt:[164,201,421],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,206,289],fix_eo:9,fix_evapor:206,fix_flux:205,fix_gcmc:[206,369],fix_gl:237,fix_gld:237,fix_grav:289,fix_id:[3,220,257,259,261,262,263,264,265,266,267,290,293],fix_modifi:[],fix_mov:[192,337],fix_nh:8,fix_npt:237,fix_nvt:[206,235],fix_poem:[3,6],fix_pour:[3,223],fix_qbmsst:9,fix_qeq:[3,390],fix_rattl:306,fix_reax_bond:438,fix_rigid:[249,380],fix_saed_vtk:304,fix_setforc:8,fix_shak:306,fix_shardlow:9,fix_srd:3,fix_styl:264,fix_temp_rescal:325,fixedpoint:[220,259],fixextern:233,fixid:205,fji:394,flag1:[225,373],flag2:[225,373],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,88,91,92,96,106,107,109,122,165,169,173,193,195,196,197,214,219,221,225,240,243,247,249,255,256,285,292,303,316,318,319,326,330,339,342,358,361,369,373,37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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying &amp; extending LAMMPS","4. Packages","8. Performance &amp; scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","&lt;no title&gt;","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","&lt;no title&gt;","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":217,"default":[37,39,40,55,57,58,59,61,62,71,89,90,94,105,106,108,110,111,122,126,127,144,150,158,159,163,169,170,173,175,189,191,192,193,195,196,197,198,200,201,202,204,205,206,208,212,213,214,217,218,220,221,222,223,227,232,235,236,241,243,244,245,246,247,249,254,257,259,260,264,280,281,285,286,289,290,291,292,293,295,298,300,301,303,304,319,321,326,327,328,329,332,334,336,338,342,355,358,360,361,363,364,366,367,369,371,372,373,375,378,381,383,401,422,423,428,430,438,439,455,456,470,471,472,475,476,478,480,482,483,484,487,489,491,492,493,494,495,500,502,503,504],"function":501,"long":[210,382,384,385,386,387,391,393,394,413,417,421,433,441],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[200,201],addforc:202,addit:[12,13],addtorqu:203,adiabat:6,adjust_dt:309,adp:376,airebo:377,alloi:399,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:204,arrai:6,aspher:[6,84,148,261,265,269,270,278],atc:[9,205],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,83,87,94,98,99,102,103,104,110,114,115,117,144,145,168,204,206,207,292,501],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:215,awpmd:[9,378],balanc:[41,216],barostat:6,basal:67,beck:379,berendsen:[290,322],between:6,binary2txt:13,bodi:[6,8,42,68,149,262,266,271,279,380],bond:[8,13,69,217,218,219,299],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:381,born:[382,393],boundari:[7,57],box:[6,58,220],brownian:383,buck:[384,385,393,424],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,176,386,421],chunk:[6,66,71,75,92,96,107,109,118,150,165,167,208],citat:7,class2:[21,43,177,345,387],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[336,389,467],colvar:[9,13,221],com:[74,75,151],comb3:390,comb:[295,390],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,497,498,499,500,501,502,503,504,505],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,501],compute_modifi:105,condit:7,conduct:[6,327],conserv:396,constant:6,constraint:7,contact:[76,124],contact_radiu:[],coord:77,core:6,correl:[209,210],cosin:[23,24,25,26,27,28,179],cossq:347,coul:[382,384,385,386,387,391,392,393,406,413,417,421,433,441],coupl:6,creat:218,create_atom:170,create_bond:171,create_box:172,createatom:13,creation:7,csld:323,csvr:323,cubic:415,cuda:[9,14,113,116,147,157,202,215,229,234,238,259,268,305,306,322,324,335,382,384,386,387,399,405,406,413,414,416,419,431,457,459],custom:8,cut:[49,378,384,387,391,394,401,403,413,414,421,429,433],cvff:348,damag:[78,125],data2xmovi:13,data:6,databas:13,deby:[391,413],dec:[],defgrad:131,deform:[153,154,222],delete_atom:173,delete_bond:174,delta:24,deposit:223,descript:[20,21,2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t:[3,6,320],advertis:8,advis:[371,438],afer:3,affect:[1,6,10,14,15,16,17,40,60,61,71,90,121,145,154,168,174,196,197,202,209,210,212,213,214,215,218,219,220,221,223,224,234,240,242,244,250,257,261,262,263,264,266,267,268,274,279,280,281,283,304,305,318,332,342,355,361,367,368,369,371,372,373,376,402,423,424,431,473,474,476,478,479,481,484,486],affin:[16,17,18,223,376,391],afil:238,aforement:18,afresh:[292,484,502],afshar:396,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,148,149,150,151,152,153,154,157,158,159,160,162,163,170,171,173,174,177,178,183,192,193,194,195,196,197,198,200,201,202,206,207,209,210,217,218,219,220,221,223,227,236,247,248,249,250,251,256,257,258,260,266,267,268,274,279,280,281,283,286,290,294,302,304,307,316,321,323,324,325,327,328,329,330,331,335,337,339,343,346,347,353,360,366,367,369,370,372,374,375,376,377,378,382,389,391,400,401,402,403,409,410,411,422,423,424,426,427,428,429,433,437,439,440,447,448,457,458,460,461,462,465,471,473,475,476,477,478,479,481,482,484,486,488,490,493,494,497,501,502,503,504,505,506],afterrun:484,afterward:3,afterword:41,ag1:169,ag2:169,again:[6,11,12,16,17,62,144,150,156,164,193,197,223,240,290,346,360,371,423,424,471,473,474,476,478,483,490,492,502,504],against:[11,12,13,64,224,371,439,440],aggreg:[6,12,65,68,69,79,95,112,119,240,256,302,304,318,471,503],aggress:[240,490],agilio:[9,13],agre:[3,8,190,369,378,411,440],agreement:[5,7],ahd:408,ahead:339,aidan:[0,5,7,9,13,364],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:196,akohlmei:[7,9,13,198,241],aktulga:[7,9,297,440],al2o3:447,al2o3_001:[122,305],al3:169,ala:[247,447],alain:9,alat:[285,426],alb:[437,460,462],albeit:303,albert:9,alchem:[89,164],alcohol:335,alcu:[377,382],alcu_eam:437,alderton:395,alejandr:[260,261],alessandro:13,algebra:429,algorithm:[0,1,6,7,8,9,41,61,197,206,217,220,223,247,249,250,274,287,295,304,307,308,327,328,332,335,340,367,368,369,373,376,398,402,424,429,444,446,471,473,490],alia:[12,16],alias:[1,362],aliceblu:197,align:[6,12,29,41,71,172,190,213,217,242,364,476,479,497],alkali:402,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,158,163,164,165,166,167,168,169,170,171,172,173,174,176,178,183,189,190,193,194,195,196,197,198,200,201,202,203,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,226,227,228,229,230,231,232,233,234,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,253,255,256,258,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,299,300,301,302,303,304,305,306,307,308,309,310,311,312,316,317,319,320,321,322,323,324,327,328,329,330,331,332,333,334,335,337,338,339,340,341,342,343,344,345,346,347,351,356,359,360,361,362,363,364,366,369,370,371,372,373,375,376,377,378,379,381,382,383,385,386,387,388,389,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,473,474,475,476,477,478,479,480,481,483,484,485,486,487,488,489,490,491,493,494,495,497,501,502,503,504,505,506],allen:[29,89,395,405],allentildeslei:89,allign:3,allindex:344,alloc:[3,5,6,8,9,11,12,60,234,334,370,372,376,435,440,476,484],allocat:3,alloi:[],allosw:71,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,94,110,112,146,148,149,150,163,168,169,170,172,178,189,190,193,194,196,197,198,200,201,203,205,206,207,209,210,211,212,213,214,215,217,219,220,221,222,223,224,228,229,234,236,237,238,239,241,244,247,250,251,255,257,260,261,285,289,290,291,292,293,294,298,304,305,307,309,311,312,316,320,327,328,329,330,332,333,334,335,336,337,343,345,347,356,361,362,364,369,370,371,372,375,376,379,382,383,384,385,386,387,392,400,402,406,407,408,409,414,418,423,424,429,431,437,440,441,444,446,447,456,466,468,471,474,476,478,479,480,481,482,483,486,488,489,490,493,494,502,503],almost:[2,3,12,60,242,294,332,362,373,376,456],alo:392,alon:[6,7,220,300,439,440,474],alond:13,along:[6,8,9,12,29,40,71,89,122,168,169,170,192,193,196,209,220,242,247,248,252,257,259,294,304,307,309,313,317,318,327,331,332,338,341,343,364,367,368,369,371,392,395,406,409,412,414,418,426,439,440,459,476,479,486,487,502],alonso:[427,428],alpha:[6,12,51,201,247,286,294,295,299,369,377,380,383,392,396,398,400,401,403,408,413,414,426,432,436,461,463,494,497],alpha_:[],alpha_c:422,alpha_i:448,alpha_ialpha_j:[],alpha_lj:422,alphabet:[2,3,22,37,44,55,63,178,189,200,347,356,370,389,457,476],alphanum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441,455,459,461],compact:[63,200,389,457],compani:[5,7],compar:[1,3,4,6,8,12,17,39,88,114,122,153,169,178,189,197,227,295,343,345,361,362,369,371,426,447,471,490,491,497,501],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,177,178,189,346,347,356,388,457],compat:[3,5,7,8,9,11,12,13,17,18,41,71,121,123,181,193,198,202,208,209,210,212,213,214,215,217,286,298,324,327,334,337,340,361,376,410,429,431,459,473,474,502],compens:[6,218,219,302,372,402],compet:331,competit:362,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,168,193,195,196,198,241,331,362,376,429,476,477,481,502],compl:17,complain:[11,12,17],complement:426,complementari:[7,392,414],complet:[3,6,9,11,12,15,41,59,71,197,213,217,222,250,287,290,293,320,331,333,344,345,360,371,376,403,444,446,464,471,476,481,484,488,490,493,497,502],complex:[6,8,11,12,13,25,40,42,62,94,110,144,146,158,170,171,247,316,341,359,371,402,429,459,474,476,479,502],compli:[327,331],complic:[6,7,9,12,13,207,236,474],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,90,91,92,93,94,96,97,100,107,108,109,110,111,112,113,114,116,117,121,131,134,135,136,137,140,141,142,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,165,166,167,192,193,194,196,197,203,204,208,209,210,211,212,213,214,215,216,220,221,223,224,229,234,239,243,244,247,250,252,256,257,259,260,261,265,266,267,268,279,280,281,283,284,286,287,288,291,302,304,306,307,309,313,314,317,320,323,324,325,327,334,335,340,341,342,361,364,368,369,370,371,376,396,402,406,423,424,444,446,447,448,476,477,486,494,502,503],componenet:6,composit:[6,207,247,400],compound:[391,402,403,465],compres:[71,118,209],compress:[],compris:[40,341,441,464],compton:[122,169],comptu:3,compuat:362,comput:[],computation:[3,6,218,219,332,382],computational:497,compute_arrai:8,compute_fep:[202,422],compute_group_group:236,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[122,305],compute_scalar:8,compute_temp:8,compute_ti:202,compute_vector:8,compute_xrd:169,concaten:[2,3,505],concav:341,concentr:[71,400],concept:[6,150,160,209,485],conceptu:[3,6,71,158,221,223,371,392,409,426,481],concern:[6,73,89,195,237],concetr:71,concis:[11,331],conclud:12,concret:8,concurr:[9,16,362,502],conden:[332,460,462],condens:[6,152,332,378,394,400,414,465],condit:[],conducit:6,conduct:[],cone:479,confer:429,confid:[3,490],config:[12,193,473],configfil:222,configur:[1,2,6,12,15,17,38,59,126,172,190,192,193,196,200,221,222,223,224,228,236,243,244,274,287,295,331,359,369,371,378,382,401,426,429,458,460,462,465,471,476,478,479,490],confin:[476,490],conflict:[3,12,40,194,431,474],conform:[3,6,13,59,220,221,259,303,309,331,355,371,402,488],confus:[3,465],conjuct:396,conjug:[7,8,244,368,402,439,440],conjunct:[6,7,71,88,89,118,153,158,164,170,174,197,201,202,244,247,251,274,290,291,295,296,297,299,304,308,320,328,335,340,361,362,371,383,385,389,392,396,402,408,414,431,434,442,463,476,479,483,497,506],connect:[3,6,89,155,173,220,241,289,304,307,317,371,393,406,456,462,473,474,480,497],conput:3,consecut:[3,11,12,39,71,170,197,201,202,224,241,242,392,414,418,471,477,479],consequ:[1,6,207,332,413,490],conserv:[],consid:[6,9,70,71,78,89,119,152,155,156,173,193,194,197,201,202,208,210,213,217,219,220,224,248,261,286,304,327,328,331,332,335,362,389,402,409,440,441,447,456,471,472,474,477,478,479,481,484,486,494,497,502],consider:[6,8,244,245,323,324,325,376,485],consist:[3,6,8,9,11,12,40,42,65,69,79,95,107,112,115,116,119,150,153,155,170,182,192,198,203,204,209,223,224,227,229,234,237,244,245,246,257,260,262,263,264,265,266,267,268,269,270,272,273,274,275,277,278,279,280,281,282,283,291,294,299,301,303,304,323,324,325,326,336,361,362,364,370,371,376,378,382,384,390,392,402,405,409,412,423,424,426,429,431,441,444,446,447,459,466,474,476,477,478,479,480,481,488,497,502],consistent_fe_initi:206,consit:304,constant:[],constitu:[3,6,250,304,337,341,390,441],constitut:[444,446],constrain:[3,6,8,147,148,149,150,151,153,156,157,158,159,160,162,163,200,209,224,236,237,242,250,254,289,290,302,304,307,318,328,335,369,370,402,481,488,497],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,94,110,122,144,169,221,260,286,303,341,372,376,395,429,431,456,458,459,479,480,495,502],constructor:[8,11],consult:440,consum:[1,299,435,502],consumpt:359,contact:[],contact_stiff:[443,445],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,89,93,120,122,144,150,158,168,169,170,172,176,178,189,190,193,194,196,197,198,200,201,202,206,208,209,210,212,213,214,215,217,222,224,229,232,238,242,243,244,247,258,274,285,286,289,290,292,294,297,301,304,305,310,320,327,331,332,341,342,345,360,362,370,371,374,375,377,378,379,382,391,392,395,400,401,402,409,410,426,429,433,437,438,439,440,448,458,459,460,461,462,463,465,471,472,473,474,476,477,478,479,481,483,485,488,490,491,493,494,497,502,504,506],content:[12,18,440,492,494],context:[3,6,8,12,17,120,121,197,218,219,224,289,301,336,368,468,476,483,492,501,502,503],contibut:70,contigu:473,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,106,107,166,197,200,201,202,207,209,210,211,212,213,214,215,217,220,221,222,223,224,236,237,238,240,241,242,244,245,246,252,257,258,260,262,263,264,265,266,267,268,279,280,281,282,283,288,290,293,294,304,305,309,319,320,322,329,330,332,338,341,345,360,375,376,382,396,399,416,419,439,440,441,444,446,461,471,474,476,478,479,484,490,491,493,494,502,504],continuum:[6,7,9,206,332,444,446],contour_integr:206,contract:[59,221,223,260,291,304],contradictori:3,contrain:307,contraint:274,contrari:[238,245],contrast:[1,6,42,55,64,152,155,194,223,343,444,446,468,505],contrib:332,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,86,89,90,91,92,93,96,105,107,109,111,112,113,114,116,118,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,202,207,208,209,210,212,213,214,215,221,236,244,247,250,251,255,261,281,282,289,290,298,301,304,305,307,334,361,369,371,379,396,399,400,402,409,423,424,429,431,439,440,447,488,494,497],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,89,93,126,144,179,193,194,196,200,206,207,217,221,222,223,240,241,244,245,260,262,263,264,265,266,267,268,291,296,304,311,312,323,324,325,332,336,359,361,373,402,405,429,439,440,443,445,458,462,471,473,485,491,492],control_typ:206,controlfil:440,convect:93,conveni:[6,12,29,193,198,215,305,364,448,502],convent:[3,8,9,29,181,188,189,194,197,303,317,344,400,402,502],converg:[3,6,41,90,193,194,196,198,203,217,220,221,229,234,265,294,296,299,303,307,367,368,369,371,391,392,414,447,471,483,490],convers:[3,8,144,196,197,207,210,291,361,392,393,394,402,414,418,422,434,474,490,501],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,93,170,177,193,196,197,215,258,290,343,346,348,352,355,364,371,377,400,429,460,462,469,474,476,477,478,483,493,497,501,502,504,506],convex:[42,341],convinc:[7,12],cook:9,cooki:7,cool:[7,160,240,302],cooordin:[193,194],cooper:[5,7],coord123:118,coord1:[3,118,209,213,214],coord2:[3,118,209,213,214],coord3:[3,118,209,213,214],coord:[],coordb:447,coordbb:447,coordiat:369,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,89,91,92,96,106,107,109,117,118,120,138,144,153,159,165,167,168,170,174,192,193,194,195,196,197,198,200,203,208,209,212,213,214,217,218,219,220,221,222,223,224,227,229,230,234,236,239,240,241,242,243,244,245,257,259,260,262,263,264,266,267,268,281,284,285,286,289,290,291,301,302,304,306,307,309,314,317,318,319,320,322,330,331,332,339,340,342,343,364,369,370,371,376,377,378,381,401,447,471,476,477,478,479,481,484,486,490,497,502,503],coordn:[118,209],coorind:[],copi:[0,3,4,8,11,12,15,17,40,123,196,332,371,389,439,474],copper:469,coproccesor:16,coprocessor:[1,4,7,9,16,17,376,489],coproprocessor:17,copy_arrai:8,copyright:[7,8,289],coral:197,core:[],core_shel:152,coreshel:[6,9,385,392,394],cornel:[6,176,488],corner123i:117,corner123x:117,corner123z:117,corner1i:117,corner1x:117,corner1z:117,corner2i:117,corner2x:117,corner2z:117,corner3i:117,corner3x:117,corner3z:117,corner:[3,6,40,117,196,341,342,364,464,476],cornflowerblu:197,cornsilk:197,corp:9,corpor:16,corr:391,correct:[3,6,9,11,12,16,17,59,89,90,105,106,114,120,152,157,164,194,196,223,236,238,244,260,261,281,289,291,294,331,337,341,361,371,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,464,465,467,468,469,476,491,494,497],correction_max_iter:206,correctli:[3,8,9,11,17,71,81,105,106,107,147,148,149,151,153,155,156,157,158,159,162,163,166,193,197,203,224,229,234,245,254,260,261,297,304,307,317,319,338,341,371,372,376,394,424,429,473,474,476,486,501,503],correl:[],correpond:232,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,89,99,100,113,116,117,118,119,122,123,131,134,135,136,137,138,140,141,142,144,147,148,157,164,168,169,176,177,178,179,180,181,182,184,185,187,188,190,192,193,194,196,197,201,202,203,209,211,212,213,214,216,219,221,223,230,234,235,239,244,247,248,256,257,258,260,262,263,264,265,266,267,268,269,270,274,277,279,280,281,283,286,287,291,296,304,306,307,323,325,327,336,337,338,340,341,342,344,346,347,348,349,351,352,355,357,362,366,368,370,371,377,378,380,383,384,385,386,387,388,389,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,412,414,415,416,417,418,419,420,421,422,423,426,427,429,431,432,433,434,436,437,439,440,441,442,447,448,449,458,459,460,461,462,465,467,468,469,471,473,474,476,477,479,489,490,491,493,494,497,502],correspondingli:[423,424,485],corrupt:3,cosin:[],cosineshift:27,cosmo:[238,243],cossq:[],cost:[1,6,10,11,12,17,39,41,71,113,122,145,169,196,197,209,213,214,217,218,219,233,260,296,332,361,362,374,392,414,418,429,431,458,473,485],costheta0:[458,460,462,465],costheta:437,costli:[11,90,238,372],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,89,92,96,107,109,113,116,118,150,160,165,167,183,193,194,196,197,201,202,209,210,213,217,223,234,243,293,294,295,299,302,304,306,320,321,327,331,332,333,337,341,343,345,353,358,360,367,369,372,376,379,404,408,409,412,439,440,472,473,474,476,478,480,483,484,491,492,497,502,503],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,90,111,112,120,145,171,175,295,297,333,361,362,369,376,383,385,386,387,388,391,392,393,394,395,402,406,407,409,414,418,422,425,431,434,439,440,442,447,457,462,463,465,468,481,488,494,497,501],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,93,118,120,121,158,168,174,203,204,207,209,212,213,214,216,217,224,229,233,236,242,260,274,290,307,323,324,341,362,369,370,371,373,376,404,408,431,494,502],counter:[3,338,471,482,484,490],counteract:236,counterbal:240,counterbalanc:29,counterpart:[193,304,471],counterproduct:18,coupl:[],courant:310,cours:[3,8,130,132,164,193,201,202,237,303,317,331,337,339,340,342,343,362,423,449,473,476,489,497,502,504],courtesi:364,cov:447,coval:[6,29,402,426,447,497],covari:238,cover:[6,71,190,197,206,247,402,464],coverag:[71,213],cpc:243,cpp:[1,3,6,8,9,11,12,13,89,193,201,202,234,307],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,197,211,227,245,333,359,362,376,389,457,471,489,490,493,494,495,502],cpuremain:494,cr2:169,cr3:169,crack:[4,372],crada:[5,7],crai:[5,7,13,18,193],crash:[3,12,372,497],craympi:376,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:206,create_faceset:206,create_group:195,create_nodeset:206,createatom:[],creation:[],crimson:197,critchlei:289,criteria:[3,120,171,196,197,218,219,220,255,369,436,464,478,481,502],criterion:[12,41,125,170,173,207,217,220,236,274,296,310,338,343,369,371,391,402,406,447,481,490,491],criterioni:490,critic:[6,48,49,258,327,332,369],crmax:71,crmin:71,cross:[3,12,22,71,91,148,168,178,193,194,196,208,213,219,223,257,259,281,304,313,317,319,328,335,347,364,371,387,396,399,400,407,408,409,414,416,418,437,442,444,446,460,462,469,476,480,486,504],crossov:1,crossterm:476,crozier:[0,7,13],crucial:294,crystal:[4,6,13,73,110,285,286,330,364,372,480,494,497],crystallin:[6,106,286,364,461,497],crystallis:327,crystallogr:[122,169],crystallograph:[364,494],crystallographi:[122,169,364],cs1:169,cs_chunk:6,cs_im:[40,476],cs_re:[40,476],csanyi:[144,438,448],cscl:426,csequ:6,csh:[11,12,389],cshrc:[11,12],csic:[401,458,460,462,465],csinfo:6,csisi:[401,458,460,462,465],csld:[],cst:400,cstherm:6,cstyle:473,csvr:[],ctcm:[377,400],ctemp_cor:227,cterm:309,ctr:9,ctype:11,cu1:169,cu2:169,cu3au:426,cube:[6,41,168,173,217,227,341,364,497],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:382,cummul:[3,6,215,218,219,220,222,233,238,244,246,320,323,324,325,326,328,335,408,494],cumul:[6,207,209,212,213,214,228,236,244,258,260,265,274,304,305,371],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,89,105,106,112,120,121,134,145,150,158,160,166,168,171,174,192,193,194,195,196,197,198,201,202,206,209,213,214,215,217,218,219,220,221,222,223,224,228,229,234,236,238,241,242,244,250,257,260,261,266,267,268,274,279,280,281,283,289,290,295,296,298,301,302,303,304,307,308,309,310,311,312,313,314,316,318,319,320,323,324,325,331,332,335,336,337,338,339,340,342,343,345,359,360,361,362,365,366,368,369,370,371,376,382,389,391,395,400,402,403,406,409,410,413,423,424,426,427,428,431,437,439,440,443,444,445,446,449,460,462,463,466,471,472,473,474,476,477,478,479,480,482,483,484,486,488,490,491,493,494,502,503,504,505,506],curv:[6,170,236,286],curvatur:[405,441,469],custom:[],cut0:474,cut1:485,cut2:485,cut:[],cuthi:[285,297],cutinn:[384,423,424],cutlo:[285,297],cutmax:437,cutoff1:[388,395,414,418,422,425,434,442],cutoff2:[383,385,386,388,394,395,414,418,422,425,434,442],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,89,94,110,112,119,120,144,168,171,173,174,219,220,225,232,285,294,295,297,299,301,304,308,320,333,337,341,343,359,361,362,369,372,373,374,376,377,378,379,380,381,382,383,384,385,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,447,448,449,450,451,452,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,474,478,481,485,497,502],cutoff_glob:[],cutoff_inn:[],cutoffa:401,cutoffc:401,cuu3:400,cval:169,cvd:327,cvel:309,cvff:[],cwiggl:[3,257,337,340,342,502],cyan:[2,196,197],cycl:[3,236,258,260,261,265],cyclic:[3,190],cygwin:12,cylind:[3,4,71,196,209,242,290,338,341,479],cylindr:[6,242,317,338],cypress:376,cyrot:382,cyrstal:286,d3q15:247,d3q19:247,d_double_doubl:15,d_e:332,d_flag2:293,d_flag:293,d_name:[117,193,293,322,486],d_single_doubl:15,d_single_singl:15,d_sx:293,d_sy:293,d_sz:293,daan:330,dai:12,daili:12,daivi:281,damag:[],dammak:299,damp:[3,6,200,205,244,245,246,251,260,261,265,291,294,295,299,304,323,324,336,338,339,368,369,371,383,385,387,392,395,402,406,414,422,434,442,457,463,490,497],damp_com:245,damp_drud:245,dampen:[304,497],dampflag:[338,406],dan:17,danger:[3,12,236,343,396,494],dangl:173,daniel:9,darden:[362,395],darkblu:197,darkcyan:197,darken:196,darkgoldenrod:197,darkgrai:197,darkgreen:197,darkkhaki:197,darkmagenta:197,darkolivegreen:197,darkorang:197,darkorchid:197,darkr:197,darksalmon:197,darkseagreen:197,darkslateblu:197,darkslategrai:197,darkturquois:197,darkviolet:197,dasgupta:295,dash:[406,493],dat:[6,93,190,206,472],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,305],dataset:305,datatyp:3,date:[0,6,12,13,192,439,440,502],datom1:119,datom2:119,datom3:119,datom4:119,datum:[3,6,42,65,68,69,79,95,112,119,193,210],davenport:425,davi:337,david:[9,19,361,362,460,462],daw:[400,437],dbg:14,dcd:[3,6,7,193,195,196,197,198,287,477,481],ddim:192,deactiv:422,dealt:243,debug:[6,7,11,12,13,14,17,122,126,169,170,287,292,359,361,376,410,431,466,474,475,483,486,493,502],deby:[],decai:[94,392,469],decid:[3,6,12,16,71,257,293,304,333,491],decipher:364,declar:195,declin:320,decod:196,decompos:[89,448],decomposit:[3,5,7,18,62,206,287,308],decoupl:[6,497],decreas:[3,193,194,203,204,211,220,223,229,234,236,244,331,361],decrement:309,deepli:358,deeppink:197,deepskyblu:197,def:[12,13,474],defaul:61,defect:[6,70,168,429],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,176,177,178,179,180,181,182,184,185,187,188,189,190,191,192,193,194,195,196,197,200,201,202,203,204,205,206,207,208,209,210,212,213,214,215,216,217,218,219,220,221,223,224,227,228,229,231,234,235,236,239,242,243,244,245,246,247,255,257,259,260,261,262,263,264,265,266,267,268,270,271,272,275,277,278,279,280,281,282,283,285,286,287,289,290,291,293,295,297,302,304,305,306,307,310,314,318,320,322,323,324,325,326,328,329,330,332,334,335,337,338,339,340,341,342,343,345,346,347,348,349,350,351,352,355,356,357,359,361,362,364,366,368,369,370,371,372,373,374,375,376,378,379,380,381,383,384,385,386,387,388,389,390,392,393,395,396,397,398,399,401,402,404,405,406,407,408,409,410,412,414,415,416,417,418,419,420,421,422,423,424,425,429,430,431,432,433,434,436,437,439,440,441,442,443,444,445,446,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,485,486,487,488,490,491,493,494,497,498,499,500,501,502,503],definit:[2,3,6,8,12,13,78,80,120,144,197,209,210,211,212,213,214,215,223,231,242,265,305,322,334,337,340,342,344,356,359,370,379,382,390,397,398,402,412,437,444,446,448,464,474,476,478,485,487,501,502],defint:494,deform:[],deg2theta:169,deg:497,degener:[3,289],degrad:[8,18,286,362,485],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,94,95,97,99,100,102,104,105,110,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,169,170,176,177,180,181,188,190,192,196,209,220,227,236,238,239,244,245,250,260,261,265,266,267,268,279,280,281,283,287,289,303,304,307,323,324,325,330,346,348,352,355,357,369,395,400,408,486,494,497,503],degress:[150,209],del:490,delai:[3,6,12,372,399,494],deleg:409,delet:[2,3,7,8,12,54,57,60,63,168,173,174,200,209,210,212,213,214,215,218,220,233,236,260,305,323,324,343,345,360,370,372,375,431,456,476,477,478,479,487,488,493,498,500,502,503],delete_atom:[],delete_bond:[],delete_el:206,deli:192,delimit:[474,502],deloc:[261,402,447],delr:426,delt_lo:490,delta:[],delta_1:382,delta_3:382,delta_7:382,delta_conf:3,delta_ij:[426,437],delta_mu:[],delta_pi:382,delta_r:437,delta_sigma:382,delta_ua:[],delx:192,delz:192,dem:[],demand:299,demo:11,demon:284,demonstr:[294,426],den:290,dendrim:408,denniston:[9,247,249,250,251,286],denomin:[7,175],denot:[122,227,245,286,297,299,392,407,409,440,444,446],dens:[71,220,402],densiti:[3,6,7,9,18,40,41,59,103,120,130,144,156,168,170,201,202,206,209,213,214,217,223,234,247,250,253,254,286,290,291,295,332,337,364,366,370,377,382,400,426,427,428,437,441,447,451,453,454,455,476,485,486,494,501],density_continu:446,density_summ:446,depart:[0,7],departur:[258,294],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,94,95,106,112,113,116,117,118,119,123,144,147,153,157,158,164,170,171,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,194,196,197,200,201,202,203,204,207,209,211,212,213,215,216,217,219,221,223,229,230,235,238,239,240,242,244,245,247,249,250,257,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,285,296,299,301,304,306,307,308,314,320,323,324,325,327,329,331,332,334,336,337,340,341,342,343,345,346,347,348,349,351,352,355,357,362,364,369,370,372,373,374,376,377,378,380,381,382,383,384,385,386,387,388,389,390,391,392,393,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,426,427,429,430,432,433,434,436,437,439,440,441,442,447,448,449,457,458,459,460,461,462,463,465,467,468,469,471,473,476,478,479,482,486,488,490,493,494,496,502,503],dependend:6,depflag:12,dephas:[471,490],depos:224,deposit:[],deprec:[3,295,439],depth:[51,148,196,332,405,441],dequidt:9,der:[89,111,390,391,422,439,440,468,497],deriv:[6,7,8,9,38,56,63,89,144,164,190,210,221,223,236,244,257,260,262,263,264,265,266,267,268,285,291,295,299,329,330,332,337,338,341,368,370,378,382,390,395,402,403,407,416,420,421,426,429,439,440,457,459,468,497],derjagin:468,derlet:285,descend:197,descent:[7,368],descib:[40,196,295],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,90,114,117,120,122,134,144,145,148,149,150,154,155,158,161,163,164,168,169,170,172,173,182,187,190,193,194,195,200,201,202,209,210,211,212,213,214,215,217,220,221,222,223,224,226,227,232,237,238,241,242,243,244,245,246,247,249,250,251,255,259,260,261,265,273,282,285,287,292,293,294,295,296,297,304,309,317,320,321,322,323,324,325,326,327,328,329,330,335,337,338,340,345,361,362,364,367,368,369,370,371,375,378,379,381,383,384,385,387,388,389,390,391,392,395,400,402,403,405,406,407,409,412,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,436,437,438,439,440,441,442,447,448,449,456,457,458,459,460,461,462,463,465,467,468,469,471,473,474,476,477,478,479,480,486,489,490,493,502,503,504],descript:[],descriptor:[144,193,410],deserno:362,design:[0,3,6,7,8,9,11,13,14,15,17,122,152,155,169,206,220,226,227,260,261,285,286,305,327,332,379,380,381,384,387,392,394,402,422,423,424,427,428,437,440,459],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,90,93,116,121,145,152,170,183,192,209,215,221,223,234,236,237,244,245,246,250,260,281,289,290,291,292,295,299,304,307,320,323,324,325,326,331,338,353,358,361,362,364,367,369,370,371,396,400,408,423,424,458,460,462,472,473,474,476,480,485,490,491,493,494,502,503,504],desk:7,desktop:[4,6,7,10,12,196],despit:497,destabil:382,destre:355,destroi:[11,39,218,219],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,92,93,96,105,107,109,111,113,115,116,118,121,123,144,145,147,148,149,150,153,163,164,165,167,170,171,174,175,178,189,192,193,194,196,197,200,201,202,206,209,210,211,212,213,215,217,219,220,221,222,223,224,234,236,237,238,239,241,242,244,246,247,251,257,258,259,260,261,262,263,264,265,266,267,268,272,274,279,280,281,282,283,286,289,290,291,293,294,296,297,298,304,307,308,320,323,324,325,326,327,328,330,331,332,333,334,335,336,343,345,347,356,361,362,365,369,370,372,373,376,377,378,379,381,382,384,386,387,388,389,390,391,392,395,396,402,403,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,425,426,430,431,436,439,440,441,447,448,449,457,464,467,468,474,476,477,478,479,481,482,485,486,488,491,494,495,502,503,506],detect:[2,3,12,42,61,63,88,94,235,290,331,371,391,408,413,471,473,476,487,490,502],determ:376,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,89,105,111,113,116,122,123,131,145,158,159,168,169,170,192,193,194,196,197,198,199,203,204,205,208,209,210,211,212,213,214,215,216,217,221,223,224,227,229,236,239,240,242,244,245,250,255,257,258,260,266,267,268,279,280,281,283,285,287,290,291,294,301,302,303,304,305,306,310,312,314,320,323,324,325,327,333,334,337,338,339,340,341,342,343,356,361,362,364,370,372,373,376,378,379,386,391,395,399,400,404,406,409,410,418,426,429,431,440,441,447,456,459,463,468,473,476,477,479,481,483,486,490,492,493,495,501,502,503],determinist:308,detil:112,devan:[9,442],devanathan:462,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,241,265,289,294,295,298,378,382,402,428,429,447,465,478],devemi:9,deviat:[258,265,285,404],deviator:9,devic:[1,3,12,15,17,241,376],device_typ:376,devin:[296,391],devis:428,dfactor:196,dff:497,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,362],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,298,429],dhi:[59,192,223,290],dhug:[258,294],dhugoniot:[258,294],dia:426,diagnost:[],diagon:[3,6,85,144,145,146,221,260,291,304,335,444,446],diagonalstyl:448,diagram:[41,122,169,189,217,287],diallo:408,diam:[196,197,290,370],diamet:[3,6,40,42,117,170,193,194,196,197,201,202,244,290,304,320,322,336,338,370,390,405,406,416,441,464,468,476,477,486],diamond:[364,402,426],diamter:[40,290],dick:6,dicsuss:257,dictat:[207,258],did:[3,12,369,396,399,400,406,431,460,462,484],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,166,334,361],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,89,94,97,99,100,124,144,147,148,149,150,151,153,156,157,158,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,301,303,304,306,309,314,316,323,324,325,328,329,330,332,334,335,337,340,342,343,345,360,364,369,371,372,373,375,376,391,396,398,404,405,408,412,423,429,430,437,439,440,441,443,444,445,447,448,449,459,464,465,469,472,473,474,476,478,479,483,484,487,490,492,494,502,503],equat:[3,6,7,8,9,93,110,116,122,169,178,189,200,221,227,228,231,232,238,244,245,247,250,258,259,260,261,265,281,285,287,294,295,299,307,308,320,328,332,335,337,338,340,342,355,361,362,390,395,396,398,402,403,406,411,423,424,426,431,441,444,446,451,452,454,455,469,497],equi:261,equidist:259,equil:[3,295,365,483,506],equilater:486,equilibr:[3,4,5,6,7,9,59,93,170,200,207,210,220,221,236,258,260,261,281,282,294,295,296,297,328,329,330,335,391,392,439,440,472,486],equilibria:335,equilibribum:[218,219],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,153,154,177,179,221,223,236,237,238,245,247,260,265,281,294,295,299,303,307,309,317,320,327,328,330,335,346,348,352,355,391,426,433,447,497],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:206,equival:[6,12,13,29,59,61,128,129,137,142,168,172,197,212,215,221,223,236,244,260,281,291,303,304,340,396,402,447,460,462,476,479,484,485,494,497],equlibrium:6,equliibr:[295,297],er3:169,eradiu:[40,117,194,402,476],eras:[306,329],erat:[223,424],erc:392,erfc:[392,414,431],erforc:[117,194],erg:501,erhart:[207,400,460,462],ermscal:379,ernst:9,eror:3,eros:426,erose_form:426,erot:[],errata:[460,462],erratum:337,erron:3,error:[],erta:406,ervel:[117,194,476],escap:[224,497],especi:[8,16,158,170,200,207,217,236,294,299,302,303,376,473],espresso:[9,298],essenti:[8,11,12,27,90,132,151,152,153,156,157,158,159,160,162,179,210,265,286,336,362,378,392,414,462,481,494],essex:29,establish:[89,240],estim:[1,3,6,10,12,38,41,56,93,145,206,217,228,258,320,327,361,362,367,431,440,459,490,494],esu:501,esub:426,eta:[6,247,260,294,295,297,336,401,403,405,437,461,465,501],eta_dot:260,eta_ij:437,eta_ji:403,etag:[40,476],etail:494,etap:260,etap_dot:260,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,91,92,93,97,113,114,117,119,145,147,150,151,152,153,154,156,157,158,159,160,162,164,170,172,173,174,183,193,194,196,197,200,201,206,207,208,209,212,213,214,215,218,219,223,224,234,236,237,244,260,290,301,305,332,333,341,345,360,361,369,370,371,372,374,400,401,409,422,424,429,435,439,440,458,460,462,465,471,474,476,477,478,483,485,486,490,491,492,493,494,495,497,501,502,504,506],ethernet:18,etol:[369,371,471,490],etot0:294,etot:[6,97,99,100,114,145,156,197,227,245,258,294,493,494],eu2:169,eu3:169,euler:[369,371],eulerian:206,euqat:450,europhi:247,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,89,90,93,111,121,144,146,150,160,168,170,192,193,194,196,197,201,202,203,204,206,208,209,210,211,212,213,214,215,216,223,229,237,239,240,242,243,244,245,286,292,295,306,310,314,323,324,325,334,337,340,342,343,345,361,362,367,369,376,429,431,437,443,445,447,459,471,472,474,478,479,481,483,484,485,486,490,492,494,502,503],evalut:[345,474],evan:[158,281],evanseck:[6,20,176,387,488],evapor:[],evaul:[8,369],evdwl:[111,439,440,494],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,123,168,171,172,186,190,193,194,197,200,201,202,207,208,209,212,213,214,215,217,218,219,221,223,224,227,242,245,258,260,261,286,290,299,301,304,305,316,320,328,332,335,337,341,343,354,361,367,369,371,376,381,402,403,406,409,412,431,441,465,466,476,477,479,481,482,483,485,486,488,491,493,494,495,497,506],evenli:[3,41,145,190,217,247,412,466],event:[],eventu:[3,6,12,15,172,295,490],ever:[54,56,243,320],evera:[390,405,441,457],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,93,117,123,132,158,173,193,194,195,196,197,198,200,201,202,203,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,223,224,228,233,234,236,238,240,241,242,247,248,256,260,261,265,284,285,286,290,291,292,293,294,295,296,297,299,301,302,304,305,307,309,320,322,323,324,325,326,327,328,331,332,333,334,335,343,345,360,362,371,372,373,376,396,399,409,422,439,440,447,453,470,471,472,476,478,480,481,483,484,485,490,491,492,494,502,506],everyth:[8,111],everywher:[120,416],eviri:402,evolut:[238,247,287,471],evolv:[247,287,333],ewald:[2,3,5,6,7,8,12,90,114,122,145,333,361,362,369,383,385,386,392,395,402,414,418,434,442,457,459],ewald_disp:395,ewalddisp:3,exact:[22,41,44,71,126,164,173,178,217,220,237,238,244,245,246,290,299,300,320,332,347,361,389,478,483,490,502,504,506],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,93,120,148,154,161,170,190,201,202,212,217,223,228,232,237,244,245,246,261,273,274,282,286,294,320,325,326,339,376,389,396,400,406,409,423,431,459,478,479,486,490,502],exager:497,examin:[6,8,9,17,220,286],examp:[474,502],exampl:[],exce:[3,6,16,17,18,41,58,71,172,208,209,212,213,214,215,217,221,223,228,233,260,286,301,305,311,312,320,369,376,476,502],exceed:[3,41,59,217,223,260,320,484],excel:402,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,91,92,112,113,116,121,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,170,174,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,194,197,200,203,209,210,212,216,217,221,223,230,235,236,239,242,244,246,260,261,262,263,264,265,266,267,268,269,270,273,274,277,279,280,281,282,283,287,296,297,304,306,307,317,320,323,325,326,332,336,340,343,344,345,346,347,348,349,351,352,355,356,357,361,362,364,366,370,371,372,374,375,376,377,378,380,383,384,385,386,387,388,389,390,391,392,394,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,427,432,433,434,436,439,440,441,442,449,457,458,459,460,461,462,465,467,468,469,471,473,474,476,478,479,481,484,485,486,487,488,490,494,497,501,502,503,505],excess:[211,402],exchang:[2,3,6,8,9,61,62,200,206,207,236,244,296,304,328,332,335,361,376,402,491],exchange:361,excit:[9,402],exclud:[3,6,9,12,16,17,63,71,116,144,150,157,158,174,193,209,213,218,219,248,256,289,302,304,327,338,343,369,370,372,384,406,409,412,423,424,431,456,488],exclus:[1,3,9,12,16,89,376,391,429,431,485,495],excurs:[260,471],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,171,196,241,298,345,360,363,375,472,474,484,487,490,502],exempl:447,exemplari:237,exemplifi:402,exert:[6,242,245,299,339,340,341,362],exhaust:[206,375,502],exhibit:[94,260,368,402,485],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,126,170,171,189,195,196,197,200,205,216,219,221,224,236,289,290,292,343,344,346,348,349,350,352,356,365,370,376,397,398,409,439,456,466,472,474,476,477,478,487,488,489,502,503,504],exit:[2,3,11,12,41,57,193,217,232,360,375,474,475,484,493,502],exlanatori:3,exp:[],expand:[],expans:[12,144,193,487,502],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,105,151,162,168,190,217,229,236,238,257,285,291,293,294,299,304,343,362,372,389,426,429,431,471,474,476,478,481,485,490,502],expens:[6,10,71,197,285,289,304,332,343,361,362,372,376,474],experi:[6,13,15,17,216,224,241,250,259,291,303,304,367,371,396,431,485,490],experienc:[6,12,249,250],experiment:[236,361,376,490],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,88,95,150,158,190,193,194,196,197,200,209,210,215,217,219,221,223,260,285,293,304,317,343,345,360,361,364,370,371,375,381,400,412,447,449,464,474,477,478,481,483,486,497,502,506],explan:[3,6,59,117,144,193,194,209,259,285,409,470,473,474,476,485],explanatori:[3,8,121,193,194,208,209,212,213,214,304,370,473,502],explantori:[3,300],explic:430,explicit:[6,9,11,22,44,77,89,117,120,164,178,201,202,223,311,312,347,366,378,379,382,387,389,400,402,413,423,463,470,473,477,480],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,113,116,147,157,160,168,170,176,177,179,180,181,182,184,185,187,188,190,193,194,197,203,213,216,223,230,235,237,239,244,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,293,294,296,304,306,307,323,325,326,332,336,340,346,348,349,351,352,355,357,370,376,377,378,380,383,384,385,386,387,388,389,390,391,392,393,395,396,399,400,401,403,404,405,406,407,408,409,413,414,415,416,417,418,419,420,421,422,423,427,429,431,432,433,434,436,441,442,449,450,451,452,453,454,455,457,458,459,460,461,462,463,465,467,468,469,476,478,479,485,486,488,489,495,497],explictli:[16,489],exploit:[9,15,17,287],explor:[122,169],expon:[3,295,297,400,405,408,422,430,442],exponenti:[89,437,458,465,469,490,502],expos:11,exposit:[206,396,399],express:[6,144,156,170,201,202,221,257,285,295,332,338,345,382,400,402,416,426,447,448,457,502],expressiont:382,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,84,85,86,89,90,93,97,100,101,111,113,121,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,194,200,203,204,207,215,216,222,225,229,234,235,236,238,239,240,242,244,246,258,260,265,274,285,286,302,303,304,306,309,314,317,319,323,324,325,326,327,329,330,332,334,337,341,342,405,426,429,440,441,448,493,494],extent:[1,3,41,42,45,57,71,168,172,193,205,213,217,242,339,342,361,364,378,443,445,459,473,476,479],exterior:[3,6,168,341],extern:[],extra:[3,6,8,11,12,16,17,40,41,46,61,71,105,113,114,116,122,145,147,148,149,151,153,156,157,158,159,160,162,163,169,170,171,172,176,197,212,217,219,260,292,293,294,304,320,369,370,373,374,395,406,409,412,426,431,473,474,476,479,488,497,502],extract:[3,6,11,13,36,63,89,111,119,121,123,201,202,297,371,392,403,426,448,474,481,493],extract_atom:11,extract_comput:[11,474],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,196,211,221,223,260,330,402,461,497],extrema:422,extrins:206,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[166,334],f_a:[460,461,462],f_ave:121,f_c:461,f_f:462,f_fix_id:294,f_harm:330,f_i:[29,437],f_id:[6,71,121,123,193,194,200,208,209,210,211,212,213,214,215,255,322,334,494,502],f_ij:437,f_indent:215,f_int:329,f_j:29,f_jj:93,f_k:437,f_langevin:332,f_max:[294,299],f_msst:258,f_r:[245,460,461,462],f_sigma:382,f_solid:330,f_ss:6,f_temp:[],face:[3,6,57,59,71,158,168,172,205,213,214,337,339,340,341,342,364,405,426,441,476,479],face_threshold:168,facet:168,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,238,290,320,330,406,447,488],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,89,93,105,112,119,120,122,144,164,169,172,176,187,192,193,196,197,201,202,210,217,221,223,224,236,241,244,246,247,258,260,261,265,287,291,295,303,307,310,312,320,324,328,335,336,337,341,352,362,364,370,376,378,379,382,383,385,387,392,393,394,396,397,398,402,406,409,413,414,426,429,431,433,434,440,442,449,458,463,473,476,479,480,485,488,490,491,494,497,501,502],factori:[3,474],factoriz:361,fail:[3,11,12,59,174,221,224,361,369,371,394,440,474],failur:[125,444,475,502],fairli:[11,431,485,490],faken:73,falcon:241,fall:[3,6,197,212,290,474,502],fals:[88,343,345,447,502],fame:8,famili:[465,473],familiar:[0,11],fan:437,far:[3,6,12,17,57,59,61,88,193,194,197,198,217,218,219,221,224,260,285,303,304,320,337,348,352,367,371,372,464,474,476,481,494],farago:244,farrel:[460,462],farther:193,fashion:[6,8,41,71,170,197,200,201,202,207,213,217,219,224,236,238,242,257,258,260,262,263,264,265,266,267,268,276,279,280,281,282,283,293,294,296,304,309,313,319,322,330,332,336,337,338,340,342,371,409,423,479,488,502,505],fasolino:411,fast:[6,7,9,12,13,17,39,193,194,271,294,333,361,362,384,423,424,429,457,459,478,483,485,494,503,506],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,108,113,116,147,157,176,177,179,180,181,182,184,185,187,188,190,193,194,197,203,216,217,223,230,235,239,243,244,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,291,295,296,304,306,307,320,323,325,327,329,332,336,340,346,348,349,351,352,355,357,361,362,373,374,376,377,378,380,382,383,384,385,386,387,388,389,390,391,392,395,396,400,401,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,427,432,433,434,436,441,442,449,457,458,459,460,461,462,465,467,468,469,471,479,485,489,497],fastest:[1,6,14,17,158,213,332,333,376,473],fatal:[3,493],fault:[70,440],faulti:12,fava:405,favor:220,favorit:7,fbmc:327,fcc:[],fcm:[276,502],fdirect:227,fdotr:410,fdt:[],fdti:89,fe2:169,fe3:169,fe_md_boundari:206,featu:8,featur:[],fecr:400,feedback:[7,241],feel:[7,241,242,250,285,341,343,371,431],felling:428,felt:341,femtosecond:501,fene:[],fennel:[392,414],fep:[],ferguson:[6,176,488],fermi:[1,12,15,156,376,462],fermion:[9,402],fernando:425,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,63,198,208,209,210,212,213,214,215,245,260,290,293,295,307,334,361,369,370,371,378,447,473,476,481,485,487,495,502,504],fewer:[1,3,11,15,16,61,250,485],fewest:3,fextern:234,feynman:287,fff:474,ffield:[391,403,439,440,447],ffmpeg:[3,12,196],ffplai:196,fft:[1,3,7,11,12,14,15,90,113,114,145,286,361,362,485],fft_inc:[12,362],fft_lib:12,fft_path:12,fftbench:[361,495],fftw2:12,fftw3:12,fftw:12,fhg:[7,9],ficiti:456,fictiti:[6,203,204,229,234,238,287,303,392,414,418,456],field1:[477,481],field2:477,field:[],fifth:[317,433],figur:[1,3,8,12,294,473,474],fij:395,file0:285,file1:[11,13,285,331,345,370,481,483,487],file2:[11,13,331,345,370,481,483,487],file:[],file_from:195,filen:370,filenam:[3,12,13,38,41,56,190,193,194,196,197,198,206,209,210,211,212,213,214,215,217,222,232,285,289,292,295,296,297,300,301,304,305,331,332,358,359,360,370,371,377,378,382,392,400,401,403,411,426,427,428,433,437,438,439,440,447,448,458,459,460,461,462,465,472,473,474,477,478,483,487,494,502,504,505,506],filennam:483,filep:[3,193,194,197,478,483,506],filepo:301,fill:[7,9,170,196,290,332,364,372,382,429,440,479],filter:[197,206],final_integr:8,final_integrate_respa:8,finchham:[6,152,394],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,89,121,173,190,198,207,220,221,232,233,236,259,285,290,291,299,303,367,369,371,372,392,409,414,418,426,447,457,459,497,502],find_custom:8,fine:[16,17,174,203,229,330,372,376,502],finer:[144,170,502],finest:361,finger:[170,192,257,479],finish:[6,11,41,217,345,358,360,361,373,375,376,464,481,502,503],finit:[],finni:[7,400,457],finvers:227,fiorin:[9,222],fire:[],firebrick:197,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,90,93,106,107,108,110,116,120,121,131,134,137,138,142,145,155,158,164,166,168,169,171,172,173,177,190,193,194,195,196,197,198,200,201,209,210,212,213,214,215,217,220,223,232,236,237,242,247,257,258,259,260,285,287,292,293,294,296,301,304,307,309,317,318,320,321,322,329,330,331,332,334,338,343,345,346,353,364,369,370,371,372,375,376,377,378,381,382,383,385,387,389,391,392,400,402,403,406,407,409,410,411,412,413,414,418,423,424,426,428,429,431,433,437,439,440,447,448,456,458,459,460,461,462,465,469,471,472,473,474,476,477,478,481,483,485,488,489,490,493,494,497,502,503,504,506],fischer:[6,9,19,20,176,387,488],fit:[3,6,9,12,38,56,190,232,303,320,378,382,411,426,431,452,459,461,484,502],five:[73,156,294,370,382,427,476,490],fix:[],fix_adapt:[164,202,422],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,207,290],fix_eo:9,fix_evapor:207,fix_flux:206,fix_gcmc:[207,370],fix_gl:238,fix_gld:238,fix_grav:290,fix_id:[3,221,258,260,262,263,264,265,266,267,268,291,294],fix_modifi:[],fix_mov:[192,338],fix_nh:8,fix_npt:238,fix_nvt:[207,236],fix_poem:[3,6],fix_pour:[3,224],fix_qbmsst:9,fix_qeq:[3,391],fix_rattl:307,fix_reax_bond:439,fix_rigid:[250,381],fix_saed_vtk:305,fix_setforc:8,fix_shak:307,fix_shardlow:9,fix_srd:3,fix_styl:265,fix_temp_rescal:326,fixedpoint:[221,260],fixextern:234,fixid:206,fji:395,flag1:[226,374],flag2:[226,374],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,88,91,92,96,106,107,109,122,165,169,173,193,194,196,197,198,215,220,222,226,241,244,248,250,256,257,286,293,304,317,319,320,327,331,340,343,359,362,370,374,375,376,378,408,413,426,429,456,471,473,474,476,477,478,480,481,482,486,502],flag_buck:386,flag_coul:[386,395,418],flag_lj:[395,418],flagfld:[384,423,424],flaghi:[3,384,423,424],flaglog:[384,423,424],flagn:226,flagvf:[384,423,424],flat:[6,332,337,338,342],flavor:[2,7,12],fld:[9,337,384,423,424],flen:379,flex_press:379,flexibl:[3,6,8,171,196,209,213,222,238,261,328,335,402,461,494],flip:[3,6,223,260,339,340],floor:502,flop:12,floralwhit:197,flow:[],fluctuat:[6,64,89,221,236,237,244,247,260,265,285,286,308,330,332,355,398],fluid:[],fluid_veloc:251,flush:[3,197,493],flux:[],flv:196,fly:[7,9,12,41,196,200,206,211,224,227,304,307,333,382,429,494,497],fmackai:9,fmag:225,fmass:287,fmax:[369,494],fmomentum:227,fmsec:[2,197,244,245,257,260,291,304,323,324,485,496,501,503],fname:360,fno:[12,16],fnorm:[369,494],fnpt:227,fnvt:227,foce:409,fock:379,focu:307,fogarti:[9,297,440],foil:[144,285,448],fold:[318,485],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,40,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,82,93,94,99,100,110,117,120,121,123,144,145,148,149,150,156,158,163,166,168,170,171,176,179,180,181,182,184,185,187,188,190,193,195,196,197,200,206,207,208,209,210,211,212,213,214,215,217,222,223,224,227,228,231,232,234,236,237,238,241,243,244,245,247,250,258,260,265,266,267,268,279,280,281,283,286,287,289,292,293,294,295,297,299,301,303,304,305,307,322,323,324,325,328,329,330,331,332,334,335,343,344,348,349,350,351,352,355,357,359,364,366,369,370,371,376,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,397,398,399,400,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,430,431,432,433,434,436,437,438,439,440,441,442,444,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,462,463,464,465,467,468,469,471,473,474,476,477,479,481,483,484,485,488,490,491,492,497,502,503,505],foo:[4,8,11,12,193,196,234,474,487,502],foot:6,footprint:[12,376],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:250,forcefield:[303,408],forcegroup:247,forcezero:367,ford:395,forestgreen:197,forev:71,forget:[245,497],forgiv:260,fork:[12,193],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,89,91,92,94,96,106,107,109,120,144,145,164,165,174,178,197,200,201,202,219,237,238,244,246,250,257,281,286,297,299,303,304,332,337,341,346,347,350,355,366,368,370,371,378,379,382,389,397,398,400,402,404,408,409,413,425,426,428,429,433,434,437,439,440,441,447,448,449,457,459,460,461,462,468,470,473,474,476,481,486,493,497,502],formal:[6,78,80,93,237,238,244,260,287,320,328,447],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,178,190,193,194,195,196,197,198,209,212,213,214,215,217,219,232,286,289,293,295,297,300,304,305,316,331,332,343,344,347,366,370,371,377,378,382,389,400,403,413,426,428,438,439,440,442,448,459,465,466,473,474,476,477,478,481,492,493,494,502,504],former:[6,12,16,39,41,197,217,332,336,382,384,482,488,502],formerli:[7,13],formul:[1,40,64,145,203,229,244,260,281,295,297,303,307,331,361,378,382,400,402,405,426,436],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,89,91,92,93,97,99,100,109,116,122,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,169,170,175,177,178,189,192,193,201,202,203,204,209,210,211,212,215,216,223,229,239,240,242,244,245,257,285,286,292,301,306,314,318,320,323,324,325,334,337,340,342,343,345,346,347,349,356,364,370,378,379,381,382,387,388,389,390,395,396,400,401,405,406,407,408,410,413,414,416,417,418,420,421,423,424,426,430,431,432,441,442,449,457,458,460,461,462,465,467,468,472,476,479,486,493,494,501,502,503],forth:[1,6,11,12,13,14,15,375,474,479,483],fortran:[3,6,9,11,12,13,234,400,409,426,439,440],fortun:8,forward:[3,8,89,360,371,376],foster:[382,436,437],foul:173,found:[3,6,9,12,73,164,193,220,222,236,241,247,286,327,333,345,360,372,389,392,395,471,477,478,493],four:[6,11,54,81,106,107,144,166,258,332,355,370,371,429,471],fourier:[],fourth:[6,108,303,317,327,387,433,447],fox:[6,122,176,455,488],fphi:[38,56,459],fpic:12,fplo:[38,56,459],fprime:459,fqdn:243,fqq:395,frac:[],fraction:[1,3,6,8,12,16,39,41,80,113,145,173,192,196,197,207,218,219,220,221,258,290,294,301,302,320,325,326,364,371,376,382,384,406,423,424,481,486],fragment:[42,241,301],fraig:42,frame:[85,144,197,206,258,294,339,405],framer:[196,197],framework:[5,238,377,448],franc:9,fraun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223,260,307,320,342,477],press:[],pressdown:216,pressur:[],pressure_with_eviri:402,presum:[73,159,200,201,202,223,371,409,479],prevent:[2,3,6,40,124,224,235,290,320,331,355,361,367,369,371,376,396,409,435,451,452,454,456,474,478,484,486,497,502],previou:[],previouli:224,previous:[3,11,59,61,71,88,105,121,123,159,170,172,174,192,193,194,195,197,205,207,208,209,210,212,213,214,215,223,224,236,242,255,257,290,302,304,306,307,332,334,337,338,339,340,342,343,363,406,457,471,474,478,479,489,491,493,494,498,499,500,502,503],prevoiu:338,price:[6,395],primari:[0,6,9,332],primarili:[5,7,9,17,146],primaritli:[],prime:[227,245,407,429,460,462,473],primit:[3,6,340,341,364],princip:[3,241,447],principl:[6,9,11,241,261,295,402,410,429,458,473],prinicp:[42,304,370],print:[],printabl:2,printflag:410,printfluid:247,prior:[168,191,308,363,505],priori:485,prioriz:376,prism:[3,6,158,172,479],priveleg:3,privileg:[11,12,241],prob:[218,219],probab:449,probabl:[3,8,12,40,71,160,173,174,176,207,217,218,219,220,224,236,245,260,290,337,343,369,431,471,490,497],probe:502,problem:[],problemat:236,proc:[1,3,8,11,12,15,117,193,194,360,473],proce:[41,54,174,217,228,371,429,483,491,494],procedur:[6,12,39,41,197,207,217,236,244,245,246,260,262,263,264,265,266,267,268,279,280,281,282,283,286,323,324,325,326,329,330,369,371,378,384,477,497],proceed:[12,429],procesor:[41,473],process:[],processor:[],processsor:[41,217,473],procp1:[193,194],procsessor:495,procssor:485,produc:[1,3,4,6,7,9,12,13,14,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,45,46,47,48,49,51,53,54,56,63,65,68,69,71,79,95,112,113,114,116,117,118,119,121,123,145,147,157,168,176,177,179,180,181,182,184,185,187,188,190,193,194,197,200,203,208,209,210,212,213,214,215,216,217,220,223,230,234,235,237,238,239,244,245,246,255,257,260,262,263,264,265,266,267,268,269,270,277,279,280,281,283,290,294,295,296,299,304,305,306,307,321,322,323,325,332,333,334,336,337,340,345,346,348,349,351,352,355,357,362,369,371,374,376,377,378,380,383,384,385,386,387,388,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,427,432,433,434,436,437,440,441,442,449,458,459,460,461,462,465,467,468,469,471,473,478,479,481,482,485,490,491,502,503],product:[6,16,17,18,144,168,223,281,295,333,376,379,402,440,473,502],proessor:376,prof:289,profi:159,profil:[],program:[3,4,6,7,9,11,12,13,17,146,193,196,197,198,200,222,234,241,247,298,400,474,475,487,502],programm:[13,17],progress:[1,41,217,241,258,294,368,369,371,494,497],prohibit:486,project:[6,7,13,14,368,457],promis:7,promot:382,prompt:[8,11,12,241,487],proni:[3,237,238],proofread:8,prop:[6,293],propag:[4,9,205,260,294,310,402,409],propens:6,proper:[220,285,426,474],properati:293,properli:[203,229,304,308,316,370,371,398,474,503],properti:[],propoerti:320,proport:[6,39,41,89,106,107,166,217,244,245,246,294,328,335,336,406],proportion:244,propos:[6,144,207,221,236,260,281,299,414,428,461,463],prospect:7,protect:320,protein:[7,10,170,302,304,318,476,484],protocol:241,proton:[462,469,501],prototyp:[10,42,436],prouduc:[215,334],prove:[82,83,231,247,308],proven:281,provid:[1,3,4,6,7,8,9,11,12,13,14,15,16,17,18,29,40,42,61,67,70,122,143,146,164,168,169,170,195,196,198,208,209,215,220,221,222,223,234,236,241,243,247,251,258,260,286,294,295,298,299,304,308,309,327,329,330,333,334,345,359,361,362,367,371,376,378,382,384,389,391,392,396,401,402,406,408,411,413,422,423,426,428,429,437,438,439,440,447,448,456,457,458,460,461,462,465,473,478,484,486,489,490,494,495,502],proxim:192,psa:340,pscreen:[3,12,485],pscrozi:[0,7,13],psec:[197,223,240,244,245,260,291,304,323,324,496,501],psend:473,pseudo:[402,471,476,481],pseudodynam:327,pseudopotenti:[9,429],psf:6,psi:[403,468],psi_ij:403,pstart:[3,260,261,265,291,304],pstop:[3,260,261,265,291,304],pstyle:[89,111,201,202],psu:[439,440],psuedo:481,pt2:169,pt4:169,ptarget:221,pthread:[12,17],ptr:[6,11,234,474],ptype1:119,ptype2:119,pu3:169,pu4:169,pu6:169,publicli:5,publish:[7,247,251,295,392,426,429,460,462],pull:[309,317],puls:332,pump:[423,424],punctuat:[2,471,490],purchas:196,purdu:[9,13],pure:[11,320,409,427,428,460,462,485],purg:[3,477],purpl:[2,197],purport:11,purpos:[3,6,7,12,42,61,71,122,132,138,153,154,169,170,172,174,190,193,213,215,220,221,244,285,287,290,292,303,320,361,376,386,412,418,429,431,464,476,479,483,486,488,489,502,506],push:[3,8,203,216,223,242,259,285,302,309,369,406,449],pushd:242,put:[3,6,8,11,12,13,39,59,158,170,193,224,228,339,340,343,364,439,474,476,480],putenv:[487,502],px1:485,px2:485,pxx:[221,260,291,304,361,362,493,494],pxy:[3,6,494],pxz:[3,6,494],py1:485,py2:485,pydir:11,pyi:[221,260,291,304,361,362,494],pymol:[7,11,13],pymol_aspher:[],pympi:11,pypar:11,python:[],pythonpath:11,pyz:[3,6,494],pz1:485,pz2:485,pzz:[221,258,260,291,294,304,361,362,494],q_1:447,q_2:447,q_3:447,q_c:[],q_d:497,q_i:[403,422],q_j:422,qbmsst:[],qcore:295,qdamp:295,qdist:[392,414,418,422],qeq1:295,qeq2:295,qeq:[],qeqal:447,qeqallparallel:447,qfile:[295,392],qin:240,qini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,12,14,15,16,236,372,396,494],rebuilt:[3,12,193,194,195,196,198,372,376],recalcul:[71,89,320],receiv:[3,216,241,243,285,473],recent:[],reciproc:[6,12,122,168,169,286,361,383,385,386,392,395,402,414,418,434,442,490],recog:12,recoginz:3,recogn:[3,12,16,73,172,218,219,260,370,400,426,439,474,476,483,484,497],recomend:6,recommend:[7,9,12,14,16,196,197,294,330,361,402,409,423,424,429,440,441,444,446,447,485,495],recompil:[1,3,9,12,198,307],recomput:[105,132,174,228,309,399,488],reconstruct:[3,222,447],record:[198,222,309],recov:[221,260],recreat:344,rectangl:[41,217,364],rectangular:[7,41,62,172,217,236,364,476,478,480],rectilinear:[122,169,194],rector:53,recurs:[41,217,382,464],recust:41,recv:473,red:[2,10,196,197,220,287],redefin:[3,478,484,502],redirect:12,redo:12,reduc:[],reduct:[18,19,121,122,169,258,294,361],redund:403,ree:452,reed:[258,294],rees:[7,9,13],ref:[329,330,368],refactor:6,refer:[],referenc:[3,6,12,63,68,71,118,193,194,200,210,215,236,293,334,362,392,408,433,441,474,494,502],reflect:[],reformat:7,refresh:206,reg:479,regard:[6,59,257,307,308,313,436,440],regardless:[15,71,170,173,192,212,213,223,244,260,262,263,264,266,267,268,291,304,314,320,376,473,479,486],regim:[6,328,335,393,485],region:[],region_spher:8,region_styl:341,regist:[8,120,146,316,439,440],regoin:6,regress:502,regspher:170,regstrip:343,regul:6,regular:[1,3,9,41,62,90,168,172,193,196,207,217,236,332,362,393,412,473,476,478,480],reigon:502,reinhardt:[329,330],reject:[170,220,439,491],rel:[1,6,14,27,36,41,59,71,94,106,126,134,144,148,152,153,155,170,179,197,200,207,213,217,223,224,227,236,242,245,256,257,281,285,290,299,301,302,309,317,320,322,327,328,332,339,343,361,362,369,402,405,406,423,424,426,441,468,477,485,490,494,497,503],relat:[],relatic:[],relationship:[6,232,295,345,361,447,468,497,502],relax:[],releas:[0,5,7,8,13,218],relect:[3,431],reles:42,relev:[2,6,12,41,78,80,115,132,170,174,197,201,202,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,223,224,225,228,230,233,235,236,237,240,241,247,248,249,251,252,253,254,256,257,259,269,270,271,272,273,274,275,276,277,278,284,288,289,290,292,293,296,298,300,301,302,305,306,307,309,314,318,320,321,322,327,328,331,332,333,334,335,336,337,338,339,340,342,343,361,369,379,380,384,390,392,393,395,396,399,402,404,405,406,407,408,413,415,416,417,419,420,421,423,424,431,432,436,441,449,456,459,467,468,469,473,489,503],reli:[3,12,296,402,440,469,476,486],reloc:12,remain:[7,12,33,37,41,50,55,59,71,89,107,150,151,152,153,157,158,159,160,162,173,183,189,190,193,201,202,207,209,210,213,214,221,223,244,245,252,260,261,266,267,268,279,280,281,283,288,289,312,320,323,324,325,331,332,343,345,353,356,370,382,402,409,422,429,431,457,471,476,477,481,486,488,490,494,497,502,503],remaina:382,remaind:[170,193,224,290,320,333,462,476],remap:[3,6,12,59,61,71,153,170,192,213,223,242,257,281,361,476,477,478],remedi:[6,497],rememb:2,remov:[2,3,6,8,9,13,54,71,72,77,94,110,118,120,144,148,149,150,151,152,153,157,158,159,160,162,163,170,173,174,194,200,209,213,218,233,244,245,250,256,258,260,266,267,268,279,280,281,283,289,295,304,305,307,320,323,324,325,327,343,361,371,395,424,429,476,479,487,488,502,503],remove_bia:8,remove_bias_al:8,remove_molecul:206,remove_sourc:206,remove_speci:206,ren:169,renam:[12,344,487],render:[12,13,193,196,197],rendon:[260,261],reneighbor:[3,8,12,39,57,71,213,217,236,320,333,343,396,493,494],renssela:289,renumb:71,reorder:[3,12,39,473],rep:491,repeat:[2,6,196,197,213,220,221,236,313,364,382,460,462,464,471,490],repeatedli:2,repel:242,repes:193,replac:[2,3,6,11,12,41,63,91,92,121,147,148,149,150,151,152,153,156,157,158,159,160,162,163,193,194,196,197,198,209,210,212,213,214,215,217,220,224,244,265,292,299,301,392,416,477,478,483,484,494,502,503,504,506],replic:[],replica:[],replica_fil:12,report:[],repositori:[7,12,410,438,439,440],reprens:332,repres:[1,3,6,8,9,12,15,40,41,42,59,67,71,92,117,120,182,190,193,194,196,209,210,211,212,213,214,215,221,227,237,239,244,247,260,287,289,291,299,304,305,309,317,332,334,341,362,371,377,382,405,412,422,423,424,426,427,428,434,437,439,440,463,464,471,473,476,486,488,491,497,502,504],represent:[3,6,8,9,57,59,138,172,193,237,238,287,332,382,402,405,429,441,476,479,497],reprocess:481,reproduc:[3,260,338,392,400,406],repul:426,repuls:[6,7,9,36,40,45,46,112,242,295,337,338,341,378,382,390,392,396,402,406,408,422,426,430,447,456,462,465,468,469,486],reqir:[295,297],request:[3,6,8,12,41,106,173,190,193,241,247,302,308,320,322,359,361,431,439,440,471,481,486,490,502,503,504],requir:[],rerun:[],rescal:[],research:[5,7,9,82,83,231,247,251,308,429,471,490],resembl:299,reserv:[12,241,497],reservoir:[93,236,240,244,332],reset:[],reset_atomic_reference_posit:206,reset_dt:8,reset_target:8,reset_tim:206,reset_timestep:[],resid:13,residu:241,residue1:372,resist:[6,241],resolut:[211,447,459],resolv:[221,287,320,424],resort:3,resourc:[7,377,400],respa:[3,16,228,241,260,374,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,395,396,399,400,401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5:[6,375,502],run6:[6,375,502],run7:[6,375,476,477,481,502],run8:[6,375,502],run:[],run_styl:[],runloop:360,runtim:[12,17,196,376],russia:9,rutherford:332,rutuparna:[460,462],ryan:9,ryckaert:[307,355],rycroft:168,rydberg:429,s00:436,s0st:6,s2050:1,s2629:400,s319:206,s_fact:310,s_i:[6,402],s_ij:6,sack:7,saddl:[259,371],saddlebrown:197,sadigh:[207,400,427,428],saed_vtk:122,safe:[12,196,227,245,376],safe_zon:3,safest:[3,320],safeti:310,safezon:440,safran:468,sagui:[362,395],sai:[1,3,12,13,197,439,440,474],said:369,sakai:461,sall:[9,447],salmon:197,salt:[393,404,426,476],salter:447,same:[1,2,3,4,6,8,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,38,39,40,41,43,44,45,46,47,48,49,50,51,53,54,56,57,59,62,63,65,69,71,72,77,79,81,84,86,87,89,90,91,92,93,94,95,97,100,106,107,108,110,112,113,114,116,117,119,120,121,144,145,146,147,148,149,150,151,152,153,156,157,158,159,160,162,163,164,166,168,170,171,172,173,174,176,177,178,179,180,181,182,183,184,185,187,188,190,191,192,193,194,195,196,197,200,201,202,203,206,207,209,212,213,214,215,216,217,218,219,220,221,223,224,228,229,230,235,236,237,238,239,240,241,242,243,244,245,246,247,250,257,260,262,263,264,265,266,267,268,269,270,277,279,280,281,282,283,285,286,287,289,290,291,294,295,296,297,299,300,301,302,303,304,306,307,309,314,317,319,320,321,322,323,324,325,326,327,328,329,330,331,332,334,335,336,338,339,340,341,343,344,345,346,347,348,349,351,352,355,357,361,362,364,365,366,370,371,372,373,374,375,376,377,378,380,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,399,400,401,402,403,404,405,406,407,408,409,410,413,414,415,416,417,418,419,420,421,422,423,424,426,427,430,431,432,433,434,436,437,441,442,447,449,456,457,458,459,460,461,462,465,467,468,469,471,473,474,476,477,478,479,481,484,485,486,487,488,489,490,494,497,501,502,503,505],sampl:[1,2,4,6,9,10,11,12,14,93,106,148,149,163,168,192,196,200,209,210,213,214,222,224,234,236,238,240,260,261,287,290,299,301,305,317,318,320,324,327,330,342,372,382,399,476,490],sample_frequ:206,san:436,sandia:[0,5,7,9,13,14,17,70,115,403,426,436],sandybrown:197,saniti:[303,372],satellit:[6,152],satifsi:502,satisfi:[3,12,73,122,144,169,221,247,265,307,340,369,372,406,490],satur:393,save:[6,8,12,19,40,59,190,194,196,211,220,237,238,244,245,246,290,299,332,344,362,372,374,382,478,481,488],sb3:169,sb5:169,sc3:169,scalabl:[],scalar:[],scale:[0,1,3,4,5,6,9,10,13,18,40,59,63,71,72,93,117,120,121,144,156,164,190,192,193,194,196,197,200,201,202,206,207,210,221,223,236,240,241,242,244,246,247,258,260,262,263,264,265,266,267,268,287,291,294,295,304,311,312,320,322,324,327,329,330,332,336,343,361,362,364,370,373,377,378,379,393,399,402,406,409,423,424,426,429,436,443,445,463,477,479,481,485,488,490,493,494,502,503],scale_factor:[443,445],scalegamma:247,scalexi:[3,221,260,265],scalexz:[221,260,265],scaleyz:[221,260,265],scan:[197,219,360,477],scatter:[11,122,169],scatter_atom:11,scatter_coord:11,scenario:[6,40,61,220,293,302,320,333,341,372,480,481,485,493],scf:497,schaik:422,schedul:471,schell:461,schemat:220,scheme:[6,9,18,237,238,260,287,299,307,332,361,463],schlitter1:331,schlitter2:331,schlitter:331,schmid:396,schneider:[244,246],schoen:361,schr:497,schroding:402,schroeder:[110,497],schulten:[245,309,362,497],schunk:320,schwen:9,sci:[73,340,391,428,437,447],scienc:[8,206,220,241,309,329,400,427,447,461],scientif:[144,400],scm:11,scratch:[12,41,217],screen:[],screenshot:11,scripe:11,script:[],scripta:67,scsl:12,sdk:[],sea:11,seagreen:197,seamlessli:293,search:[0,2,3,8,12,94,110,171,173,197,198,320,367,368,369,371,373,471,477,478,490,502],seashel:197,sec:[12,496,501],second:[1,3,6,9,10,11,12,16,54,57,59,61,71,90,93,106,108,110,116,137,138,142,145,146,158,164,168,169,171,172,173,192,193,197,200,201,209,210,212,213,214,215,220,236,237,242,257,259,287,301,303,304,307,309,317,318,320,329,330,332,343,361,364,368,369,371,372,376,381,382,383,385,386,391,392,400,402,403,406,407,409,412,413,416,426,431,433,447,458,461,462,463,465,469,471,472,473,474,476,478,483,485,489,490,494,497,501,502,503,504,506],second_mo:447,secondari:[3,182],sectinn:505,section:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,58,59,63,64,65,66,67,68,69,71,74,75,78,79,80,81,82,85,88,89,90,91,92,93,95,96,99,100,101,102,103,104,106,107,108,109,111,112,113,115,116,117,118,119,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,146,147,148,149,150,151,153,154,155,156,157,158,159,160,161,162,163,164,165,166,168,169,171,176,177,178,179,180,181,182,183,184,185,187,188,189,190,192,193,194,195,196,198,200,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,226,227,229,230,232,233,235,236,237,238,239,241,243,244,245,246,247,248,249,250,251,253,254,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,275,277,278,279,280,281,282,283,285,286,287,289,290,291,293,294,295,29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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying &amp; extending LAMMPS","4. Packages","8. Performance &amp; scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","&lt;no title&gt;","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","&lt;no title&gt;","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":218,"default":[37,39,40,55,57,58,59,61,62,71,89,90,94,105,106,108,110,111,122,126,127,144,150,158,159,163,169,170,173,175,189,191,192,193,194,196,197,198,199,201,202,203,205,206,207,209,213,214,215,218,219,221,222,223,224,228,233,236,237,242,244,245,246,247,248,250,255,258,260,261,265,281,282,286,287,290,291,292,293,294,296,299,301,302,304,305,320,322,327,328,329,330,333,335,337,339,343,356,359,361,362,364,365,367,368,370,372,373,374,376,379,382,384,402,423,424,429,431,439,440,456,457,471,472,473,476,477,479,481,483,484,485,488,490,492,493,494,495,496,501,503,504,505],"function":502,"long":[211,383,385,386,387,388,392,394,395,414,418,422,434,442],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[201,202],addforc:203,addit:[12,13],addtorqu:204,adiabat:6,adjust_dt:310,adp:377,airebo:378,alloi:400,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:205,arrai:6,aspher:[6,84,148,262,266,270,271,279],atc:[9,206],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,83,87,94,98,99,102,103,104,110,114,115,117,144,145,168,205,207,208,293,502],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:216,awpmd:[9,379],balanc:[41,217],barostat:6,basal:67,beck:380,berendsen:[291,323],between:6,binary2txt:13,bodi:[6,8,42,68,149,263,267,272,280,381],bond:[8,13,69,218,219,220,300],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:382,born:[383,394],boundari:[7,57],box:[6,58,221],brownian:384,buck:[385,386,394,425],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,176,387,422],chunk:[6,66,71,75,92,96,107,109,118,150,165,167,209],citat:7,class2:[21,43,177,346,388],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[337,390,468],colvar:[9,13,222],com:[74,75,151],comb3:391,comb:[296,391],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,502],compute_modifi:105,condit:7,conduct:[6,328],conserv:397,constant:6,constraint:7,contact:[76,124],contact_radiu:[],coord:77,core:6,correl:[210,211],cosin:[23,24,25,26,27,28,179],cossq:348,coul:[383,385,386,387,388,392,393,394,407,414,418,422,434,442],coupl:6,creat:219,create_atom:170,create_bond:171,create_box:172,createatom:13,creation:7,csld:324,csvr:324,cubic:416,cuda:[9,14,113,116,147,157,203,216,230,235,239,260,269,306,307,323,325,336,383,385,387,388,400,406,407,414,415,417,420,432,458,460],custom:[8,193,194],cut:[49,379,385,388,392,395,402,404,414,415,422,430,434],cvff:349,damag:[78,125],data2xmovi:13,data:6,databas:13,deby:[392,414],dec:[],defgrad:131,deform:[153,154,223],delete_atom:173,delete_bond:174,delta:24,deposit:224,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],diagnost:7,diel:393,dielectr:175,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:178,dihedral_styl:[2,176,177,179,180,181,182,183,184,185,186,187,188,189,190],dilat:80,dimens:191,dipol:[6,29,395],direct:227,discuss:6,disp:6,displac:[81,88],displace_atom:192,distanc:350,distribut:[7,12],document:0,dpd:[9,82,83,396,397,398],drag:225,dreid:[6,408],drude:[6,9,155,226,227,245],dsf:[392,414],dsmc:399,dump:[6,8,193,194,195,196,198],dump_modifi:197,dynam:295,eam:[13,400],echo:199,edip:401,eff:[9,13,99,100,154,156,161,246,261,273,282,326,402],efield:229,eim:403,elast:6,emac:13,energi:[127,398],enforce2d:230,ensembl:7,erot:[84,85,86,87],error:[3,126],evapor:233,event:88,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,316,317,318,319,320,321,322,323,324,325,326,327,328,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],exp:[27,179],expand:[46,417],extend:[8,11],extern:234,fcc:285,fdt:398,featur:[7,8,502],feb:0,fene:[45,46],fep:[9,13,89,202],field:[6,7],file:6,finit:6,fire:295,fix:[2,6,8,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309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