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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li>read_data command</li>
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<div class="section" id="read-data-command">
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<span id="index-0"></span><h1>read_data command<a class="headerlink" href="#read-data-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>read_data file keyword args ...
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</pre></div>
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</div>
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<ul class="simple">
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<li>file = name of data file to read in</li>
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<li>zero or more keyword/arg pairs may be appended</li>
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<li>keyword = <em>add</em> or <em>offset</em> or <em>shift</em> or <em>extra/atom/types</em> or <em>extra/bond/types</em> or <em>extra/angle/types</em> or <em>extra/dihedral/types</em> or <em>extra/improper/types</em> or <em>group</em> or <em>nocoeff</em> or <em>fix</em></li>
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</ul>
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<pre class="literal-block">
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<em>add</em> arg = <em>append</em> or <em>Nstart</em> or <em>merge</em>
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append = add new atoms with IDs appended to current IDs
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Nstart = add new atoms with IDs starting with Nstart
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merge = add new atoms with their IDs unchanged
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<em>offset</em> args = toff boff aoff doff ioff
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toff = offset to add to atom types
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boff = offset to add to bond types
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aoff = offset to add to angle types
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doff = offset to add to dihedral types
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ioff = offset to add to improper types
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<em>shift</em> args = Sx Sy Sz
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Sx,Sy,Sz = distance to shift atoms when adding to system (distance units)
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<em>extra/atom/types</em> arg = # of extra atom types
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<em>extra/bond/types</em> arg = # of extra bond types
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<em>extra/angle/types</em> arg = # of extra angle types
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<em>extra/dihedral/types</em> arg = # of extra dihedral types
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<em>extra/improper/types</em> arg = # of extra improper types
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<em>group</em> args = groupID
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groupID = add atoms in data file to this group
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<em>nocoeff</em> = ignore force field parameters
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<em>fix</em> args = fix-ID header-string section-string
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fix-ID = ID of fix to process header lines and sections of data file
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header-string = header lines containing this string will be passed to fix
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section-string = section names with this string will be passed to fix
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>read_data data.lj
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read_data ../run7/data.polymer.gz
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read_data data.protein fix mycmap crossterm CMAP
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read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0
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read_data data.water add merge 1 group solvent
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Read in a data file containing information LAMMPS needs to run a
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simulation. The file can be ASCII text or a gzipped text file
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(detected by a .gz suffix). This is one of 3 ways to specify initial
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atom coordinates; see the <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> and
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<a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a> commands for alternative methods.
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Also see the explanation of the <a class="reference internal" href="Section_start.html#start-7"><span>-restart command-line switch</span></a> which can convert a restart file to
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a data file.</p>
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<p>This command can be used multiple times to add new atoms and their
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properties to an existing system by using the <em>add</em>, <em>offset</em>, and
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<em>shift</em> keywords. See more details below, which includes the use case
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for the <em>extra</em> keywords.</p>
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<p>The <em>group</em> keyword adds all the atoms in the data file to the
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specified group-ID. The group will be created if it does not already
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exist. This is useful if you are reading multiple data files and wish
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to put sets of atoms into different groups so they can be operated on
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later. E.g. a group of added atoms can be moved to new positions via
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the <a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a> command. Note that atoms
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read from the data file are also always added to the “all” group. The
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<a class="reference internal" href="group.html"><em>group</em></a> command discusses atom groups, as used in LAMMPS.</p>
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<p>The <em>nocoeff</em> keyword tells read_data to ignore force field parameters.
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The various Coeff sections are still read and have to have the correct
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number of lines, but they are not applied. This also allows to read a
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data file without having any pair, bond, angle, dihedral or improper
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styles defined, or to read a data file for a different force field.</p>
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<p>The use of the <em>fix</em> keyword is discussed below.</p>
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<hr class="docutils" />
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<p><strong>Reading multiple data files</strong></p>
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<p>The read_data command can be used multiple times with the same or
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different data files to build up a complex system from components
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contained in individual data files. For example one data file could
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contain fluid in a confined domain; a second could contain wall atoms,
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and the second file could be read a third time to create a wall on the
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other side of the fluid. The third set of atoms could be rotated to
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an opposing direction using the <a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a>
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command, after the third read_data command is used.</p>
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<p>The <em>add</em>, <em>offset</em>, <em>shift</em>, <em>extra</em>, and <em>group</em> keywords are
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useful in this context.</p>
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<p>If a simulation box does not yet exist, the <em>add</em> keyword
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cannot be used; the read_data command is being used for the first
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time. If a simulation box does exist, due to using the
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<a class="reference internal" href="create_box.html"><em>create_box</em></a> command, or a previous read_data command,
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then the <em>add</em> keyword must be used.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">The simulation box size (xlo to xhi, ylo to yhi, zlo to zhi) in
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the new data file will be merged with the existing simulation box to
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create a large enough box in each dimension to contain both the
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existing and new atoms. Each box dimension never shrinks due to this
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merge operation, it only stays the same or grows. Care must be used if
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you are growing the existing simulation box in a periodic dimension.
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If there are existing atoms with bonds that straddle that periodic
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boundary, then the atoms may become far apart if the box size grows.
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This will separate the atoms in the bond, which can lead to “lost”
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bond atoms or bad dynamics.</p>
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</div>
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<p>The three choices for the <em>add</em> argument affect how the IDs of atoms
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in the data file are treated. If <em>append</em> is specified, atoms in the
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data file are added to the current system, with their atom IDs reset
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so that an atomID = M in the data file becomes atomID = N+M, where N
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is the largest atom ID in the current system. This rule is applied to
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all occurrences of atom IDs in the data file, e.g. in the Velocity or
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Bonds section. If <em>Nstart</em> is specified, then <em>Nstart</em> is a numeric
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value is given, e.g. 1000, so that an atomID = M in the data file
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becomes atomID = 1000+M. If <em>merge</em> is specified, the data file atoms
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are added to the current system without changing their IDs. They are
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assumed to merge (without duplication) with the currently defined
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atoms. It is up to you to insure there are no multiply defined atom
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IDs, as LAMMPS only performs an incomplete check that this is the case
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by insuring the resulting max atomID >= the number of atoms.</p>
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<p>The <em>offset</em> and <em>shift</em> keywords can only be used if the <em>add</em>
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keyword is also specified.</p>
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<p>The <em>offset</em> keyword adds the specified offset values to the atom
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types, bond types, angle types, dihedral types, and improper types as
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they are read from the data file. E.g. if <em>toff</em> = 2, and the file
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uses atom types 1,2,3, then the added atoms will have atom types
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3,4,5. These offsets apply to all occurrences of types in the data
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file, e.g. for the Atoms or Masses or Pair Coeffs or Bond Coeffs
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sections. This makes it easy to use atoms and molecules and their
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attributes from a data file in different simulations, where you want
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their types (atom, bond, angle, etc) to be different depending on what
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other types already exist. All five offset values must be specified,
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but individual values will be ignored if the data file does not use
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that attribute (e.g. no bonds).</p>
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<p>The <em>shift</em> keyword can be used to specify an (Sx, Sy, Sz)
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displacement applied to the coordinates of each atom. Sz must be 0.0
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for a 2d simulation. This is a mechanism for adding structured
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collections of atoms at different locations within the simulation box,
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to build up a complex geometry. It is up to you to insure atoms do
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not end up overlapping unphysically which would lead to bad dynamics.
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Note that the <a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a> command can be used
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to move a subset of atoms after they have been read from a data file.
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Likewise, the <a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a> command can be used to
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remove overlapping atoms. Note that the shift values (Sx, Sy, Sz) are
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also added to the simulation box information (xlo, xhi, ylo, yhi, zlo,
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zhi) in the data file to shift its boundaries. E.g. xlo_new = xlo +
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Sx, xhi_new = xhi + Sx.</p>
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<p>The <em>extra</em> keywords can only be used the first time the read_data
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command is used. They are useful if you intend to add new atom, bond,
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angle, etc types later with additional read_data commands. This is
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because the maximum number of allowed atom, bond, angle, etc types is
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set by LAMMPS when the system is first initialized. If you do not use
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the <em>extra</em> keywords, then the number of these types will be limited
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to what appears in the first data file you read. For example, if the
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first data file is a solid substrate of Si, it will likely specify a
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single atom type. If you read a second data file with a different
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material (water molecules) that sit on top of the substrate, you will
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want to use different atom types for those atoms. You can only do
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this if you set the <em>extra/atom/types</em> keyword to a sufficiently large
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value when reading the substrate data file. Note that use of the
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<em>extra</em> keywords also allows each data file to contain sections like
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Masses or Pair Coeffs or Bond Coeffs which are sized appropriately for
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the number of types in that data file. If the <em>offset</em> keyword is
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used appropriately when each data file is read, the values in those
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sections will be stored correctly in the larger data structures
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allocated by the use of the <em>extra</em> keywords. E.g. the substrate file
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can list mass and pair coefficients for type 1 silicon atoms. The
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water file can list mass and pair coeffcients for type 1 and type 2
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hydrogen and oxygen atoms. Use of the <em>extra</em> and <em>offset</em> keywords
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will store those mass and pair coefficient values appropriately in
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data structures that allow for 3 atom types (Si, H, O). Of course,
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you would still need to specify coefficients for H/Si and O/Si
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interactions in your input script to have a complete pairwise
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interaction model.</p>
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<p>An alternative to using the <em>extra</em> keywords with the read_data
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command, is to use the <a class="reference internal" href="create_box.html"><em>create_box</em></a> command to
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initialize the simulation box and all the various type limits you need
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via its <em>extra</em> keywords. Then use the read_data command one or more
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times to populate the system with atoms, bonds, angles, etc, using the
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<em>offset</em> keyword if desired to alter types used in the various data
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files you read.</p>
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<hr class="docutils" />
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<p><strong>Format of a data file</strong></p>
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<p>The structure of the data file is important, though many settings and
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sections are optional or can come in any order. See the examples
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directory for sample data files for different problems.</p>
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<p>A data file has a header and a body. The header appears first. The
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first line of the header is always skipped; it typically contains a
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description of the file. Then lines are read one at a time. Lines
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can have a trailing comment starting with ‘#’ that is ignored. If the
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line is blank (only whitespace after comment is deleted), it is
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skipped. If the line contains a header keyword, the corresponding
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value(s) is read from the line. If it doesn’t contain a header
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keyword, the line begins the body of the file.</p>
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<p>The body of the file contains zero or more sections. The first line
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of a section has only a keyword. This line can have a trailing
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comment starting with ‘#’ that is either ignored or can be used to
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check for a style match, as described below. The next line is
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skipped. The remaining lines of the section contain values. The
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number of lines depends on the section keyword as described below.
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Zero or more blank lines can be used between sections. Sections can
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appear in any order, with a few exceptions as noted below.</p>
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<p>The keyword <em>fix</em> can be used one or more times. Each usage specifies
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a fix that will be used to process a specific portion of the data
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file. Any header line containing <em>header-string</em> and any section with
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a name containing <em>section-string</em> will be passed to the specified
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fix. See the <a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> command for
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an example of a fix that operates in this manner. The doc page for
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the fix defines the syntax of the header line(s) and section(s) that
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it reads from the data file. Note that the <em>header-string</em> can be
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specified as NULL, in which case no header lines are passed to the
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fix. This means that it can infer the length of its Section from
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standard header settings, such as the number of atoms.</p>
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<p>The formatting of individual lines in the data file (indentation,
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spacing between words and numbers) is not important except that header
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and section keywords (e.g. atoms, xlo xhi, Masses, Bond Coeffs) must
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be capitalized as shown and can’t have extra white space between their
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words - e.g. two spaces or a tab between the 2 words in “xlo xhi” or
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the 2 words in “Bond Coeffs”, is not valid.</p>
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<hr class="docutils" />
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<p><strong>Format of the header of a data file</strong></p>
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<p>These are the recognized header keywords. Header lines can come in
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any order. The value(s) are read from the beginning of the line.
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Thus the keyword <em>atoms</em> should be in a line like “1000 atoms”; the
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keyword <em>ylo yhi</em> should be in a line like “-10.0 10.0 ylo yhi”; the
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keyword <em>xy xz yz</em> should be in a line like “0.0 5.0 6.0 xy xz yz”.
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All these settings have a default value of 0, except the lo/hi box
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size defaults are -0.5 and 0.5. A line need only appear if the value
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is different than the default.</p>
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<ul class="simple">
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<li><em>atoms</em> = # of atoms in system</li>
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<li><em>bonds</em> = # of bonds in system</li>
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<li><em>angles</em> = # of angles in system</li>
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<li><em>dihedrals</em> = # of dihedrals in system</li>
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<li><em>impropers</em> = # of impropers in system</li>
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<li><em>atom types</em> = # of atom types in system</li>
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<li><em>bond types</em> = # of bond types in system</li>
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<li><em>angle types</em> = # of angle types in system</li>
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<li><em>dihedral types</em> = # of dihedral types in system</li>
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<li><em>improper types</em> = # of improper types in system</li>
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|
<li><em>extra bond per atom</em> = leave space for this many new bonds per atom</li>
|
|
<li><em>extra angle per atom</em> = leave space for this many new angles per atom</li>
|
|
<li><em>extra dihedral per atom</em> = leave space for this many new dihedrals per atom</li>
|
|
<li><em>extra improper per atom</em> = leave space for this many new impropers per atom</li>
|
|
<li><em>extra special per atom</em> = leave space for this many new special bonds per atom</li>
|
|
<li><em>ellipsoids</em> = # of ellipsoids in system</li>
|
|
<li><em>lines</em> = # of line segments in system</li>
|
|
<li><em>triangles</em> = # of triangles in system</li>
|
|
<li><em>bodies</em> = # of bodies in system</li>
|
|
<li><em>xlo xhi</em> = simulation box boundaries in x dimension</li>
|
|
<li><em>ylo yhi</em> = simulation box boundaries in y dimension</li>
|
|
<li><em>zlo zhi</em> = simulation box boundaries in z dimension</li>
|
|
<li><em>xy xz yz</em> = simulation box tilt factors for triclinic system</li>
|
|
</ul>
|
|
<p>The initial simulation box size is determined by the lo/hi settings.
|
|
In any dimension, the system may be periodic or non-periodic; see the
|
|
<a class="reference internal" href="boundary.html"><em>boundary</em></a> command. When the simulation box is created
|
|
it is also partitioned into a regular 3d grid of rectangular bricks,
|
|
one per processor, based on the number of processors being used and
|
|
the settings of the <a class="reference internal" href="processors.html"><em>processors</em></a> command. The
|
|
partitioning can later be changed by the <a class="reference internal" href="balance.html"><em>balance</em></a> or
|
|
<a class="reference internal" href="fix_balance.html"><em>fix balance</em></a> commands.</p>
|
|
<p>If the <em>xy xz yz</em> line does not appear, LAMMPS will set up an
|
|
axis-aligned (orthogonal) simulation box. If the line does appear,
|
|
LAMMPS creates a non-orthogonal simulation domain shaped as a
|
|
parallelepiped with triclinic symmetry. The parallelepiped has its
|
|
“origin” at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
|
|
from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
|
|
(xz,yz,zhi-zlo). <em>Xy,xz,yz</em> can be 0.0 or positive or negative values
|
|
and are called “tilt factors” because they are the amount of
|
|
displacement applied to faces of an originally orthogonal box to
|
|
transform it into the parallelepiped.</p>
|
|
<p>By default, the tilt factors (xy,xz,yz) can not skew the box more than
|
|
half the distance of the corresponding parallel box length. For
|
|
example, if xlo = 2 and xhi = 12, then the x box length is 10 and the
|
|
xy tilt factor must be between -5 and 5. Similarly, both xz and yz
|
|
must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not
|
|
a limitation, since if the maximum tilt factor is 5 (as in this
|
|
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
|
|
... are all geometrically equivalent. If you wish to define a box
|
|
with tilt factors that exceed these limits, you can use the <a class="reference internal" href="box.html"><em>box tilt</em></a> command, with a setting of <em>large</em>; a setting of
|
|
<em>small</em> is the default.</p>
|
|
<p>See <a class="reference internal" href="Section_howto.html#howto-12"><span>Section_howto 12</span></a> of the doc pages
|
|
for a geometric description of triclinic boxes, as defined by LAMMPS,
|
|
and how to transform these parameters to and from other commonly used
|
|
triclinic representations.</p>
|
|
<p>When a triclinic system is used, the simulation domain should normally
|
|
be periodic in the dimension that the tilt is applied to, which is
|
|
given by the second dimension of the tilt factor (e.g. y for xy tilt).
|
|
This is so that pairs of atoms interacting across that boundary will
|
|
have one of them shifted by the tilt factor. Periodicity is set by
|
|
the <a class="reference internal" href="boundary.html"><em>boundary</em></a> command. For example, if the xy tilt
|
|
factor is non-zero, then the y dimension should be periodic.
|
|
Similarly, the z dimension should be periodic if xz or yz is non-zero.
|
|
LAMMPS does not require this periodicity, but you may lose atoms if
|
|
this is not the case.</p>
|
|
<p>Also note that if your simulation will tilt the box, e.g. via the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> command, the simulation box must be setup to
|
|
be triclinic, even if the tilt factors are initially 0.0. You can
|
|
also change an orthogonal box to a triclinic box or vice versa by
|
|
using the <a class="reference internal" href="change_box.html"><em>change box</em></a> command with its <em>ortho</em> and
|
|
<em>triclinic</em> options.</p>
|
|
<p>For 2d simulations, the <em>zlo zhi</em> values should be set to bound the z
|
|
coords for atoms that appear in the file; the default of -0.5 0.5 is
|
|
valid if all z coords are 0.0. For 2d triclinic simulations, the xz
|
|
and yz tilt factors must be 0.0.</p>
|
|
<p>If the system is periodic (in a dimension), then atom coordinates can
|
|
be outside the bounds (in that dimension); they will be remapped (in a
|
|
periodic sense) back inside the box. Note that if the <em>add</em> option is
|
|
being used to add atoms to a simulation box that already exists, this
|
|
periodic remapping will be performed using simulation box bounds that
|
|
are the union of the existing box and the box boundaries in the new
|
|
data file.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">If the system is non-periodic (in a dimension), then all atoms
|
|
in the data file must have coordinates (in that dimension) that are
|
|
“greater than or equal to” the lo value and “less than or equal to”
|
|
the hi value. If the non-periodic dimension is of style “fixed” (see
|
|
the <a class="reference internal" href="boundary.html"><em>boundary</em></a> command), then the atom coords must be
|
|
strictly “less than” the hi value, due to the way LAMMPS assign atoms
|
|
to processors. Note that you should not make the lo/hi values
|
|
radically smaller/larger than the extent of the atoms. For example,
|
|
if your atoms extend from 0 to 50, you should not specify the box
|
|
bounds as -10000 and 10000. This is because LAMMPS uses the specified
|
|
box size to layout the 3d grid of processors. A huge (mostly empty)
|
|
box will be sub-optimal for performance when using “fixed” boundary
|
|
conditions (see the <a class="reference internal" href="boundary.html"><em>boundary</em></a> command). When using
|
|
“shrink-wrap” boundary conditions (see the <a class="reference internal" href="boundary.html"><em>boundary</em></a>
|
|
command), a huge (mostly empty) box may cause a parallel simulation to
|
|
lose atoms when LAMMPS shrink-wraps the box around the atoms. The
|
|
read_data command will generate an error in this case.</p>
|
|
</div>
|
|
<p>The “extra bond per atom” setting (angle, dihedral, improper) is only
|
|
needed if new bonds (angles, dihedrals, impropers) will be added to
|
|
the system when a simulation runs, e.g. by using the <a class="reference internal" href="fix_bond_create.html"><em>fix bond/create</em></a> command. This will pre-allocate
|
|
space in LAMMPS data structures for storing the new bonds (angles,
|
|
dihedrals, impropers).</p>
|
|
<p>The “extra special per atom” setting is typically only needed if new
|
|
bonds/angles/etc will be added to the system, e.g. by using the <a class="reference internal" href="fix_bond_create.html"><em>fix bond/create</em></a> command. Or if entire new molecules
|
|
will be added to the system, e.g. by using the <a class="reference internal" href="fix_deposit.html"><em>fix deposit</em></a> or <a class="reference internal" href="fix_pour.html"><em>fix pour</em></a> commands, which
|
|
will have more special 1-2,1-3,1-4 neighbors than any other molecules
|
|
defined in the data file. Using this setting will pre-allocate space
|
|
in the LAMMPS data structures for storing these neighbors. See the
|
|
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> and <a class="reference internal" href="molecule.html"><em>molecule</em></a> doc
|
|
pages for more discussion of 1-2,1-3,1-4 neighbors.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">All of the “extra” settings are only used if they appear in the
|
|
first data file read; see the description of the <em>add</em> keyword above
|
|
for reading multiple data files. If they appear in later data files,
|
|
they are ignored.</p>
|
|
</div>
|
|
<p>The “ellipsoids” and “lines” and “triangles” and “bodies” settings are
|
|
only used with <a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid or line or tri or body</em></a> and specify how many of the atoms are
|
|
finite-size ellipsoids or lines or triangles or bodies; the remainder
|
|
are point particles. See the discussion of ellipsoidflag and the
|
|
<em>Ellipsoids</em> section below. See the discussion of lineflag and the
|
|
<em>Lines</em> section below. See the discussion of triangleflag and the
|
|
<em>Triangles</em> section below. See the discussion of bodyflag and the
|
|
<em>Bodies</em> section below.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">For <a class="reference internal" href="atom_style.html"><em>atom_style template</em></a>, the molecular
|
|
topology (bonds,angles,etc) is contained in the molecule templates
|
|
read-in by the <a class="reference internal" href="molecule.html"><em>molecule</em></a> command. This means you
|
|
cannot set the <em>bonds</em>, <em>angles</em>, etc header keywords in the data
|
|
file, nor can you define <em>Bonds</em>, <em>Angles</em>, etc sections as discussed
|
|
below. You can set the <em>bond types</em>, <em>angle types</em>, etc header
|
|
keywords, though it is not necessary. If specified, they must match
|
|
the maximum values defined in any of the template molecules.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p><strong>Format of the body of a data file</strong></p>
|
|
<p>These are the section keywords for the body of the file.</p>
|
|
<ul class="simple">
|
|
<li><em>Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies</em> = atom-property sections</li>
|
|
<li><em>Bonds, Angles, Dihedrals, Impropers</em> = molecular topology sections</li>
|
|
<li><em>Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs</em> = force field sections</li>
|
|
<li><em>BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs</em> = class 2 force field sections</li>
|
|
</ul>
|
|
<p>These keywords will check an appended comment for a match with the
|
|
currently defined style:</p>
|
|
<ul class="simple">
|
|
<li><em>Atoms, Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs</em></li>
|
|
</ul>
|
|
<p>For example, these lines:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>Atoms # sphere
|
|
Pair Coeffs # lj/cut
|
|
</pre></div>
|
|
</div>
|
|
<p>will check if the currently-defined <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> is
|
|
<em>sphere</em>, and the current <a class="reference external" href="pair_style">pair_style</a> is <em>lj/cut</em>. If
|
|
not, LAMMPS will issue a warning to indicate that the data file
|
|
section likely does not contain the correct number or type of
|
|
parameters expected for the currently-defined style.</p>
|
|
<p>Each section is listed below in alphabetic order. The format of each
|
|
section is described including the number of lines it must contain and
|
|
rules (if any) for where it can appear in the data file.</p>
|
|
<p>Any individual line in the various sections can have a trailing
|
|
comment starting with “#” for annotation purposes. E.g. in the
|
|
Atoms section:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>10 1 17 -1.0 10.0 5.0 6.0 # salt ion
|
|
</pre></div>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p><em>Angle Coeffs</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per angle type</li>
|
|
<li>line syntax: ID coeffs</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>ID = angle type (1-N)
|
|
coeffs = list of coeffs
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>example:</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>6 70 108.5 0 0
|
|
</pre></div>
|
|
</div>
|
|
<p>The number and meaning of the coefficients are specific to the defined
|
|
angle style. See the <a class="reference internal" href="angle_style.html"><em>angle_style</em></a> and
|
|
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> commands for details. Coefficients can
|
|
also be set via the <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command in the
|
|
input script.</p>
|
|
<hr class="docutils" />
|
|
<p><em>AngleAngle Coeffs</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per improper type</li>
|
|
<li>line syntax: ID coeffs</li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
ID = improper type (1-N)
|
|
coeffs = list of coeffs (see <a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a>)
|
|
</pre>
|
|
<hr class="docutils" />
|
|
<p><em>AngleAngleTorsion Coeffs</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per dihedral type</li>
|
|
<li>line syntax: ID coeffs</li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
ID = dihedral type (1-N)
|
|
coeffs = list of coeffs (see <a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a>)
|
|
</pre>
|
|
<hr class="docutils" />
|
|
<p><em>Angles</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per angle</li>
|
|
<li>line syntax: ID type atom1 atom2 atom3</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>ID = number of angle (1-Nangles)
|
|
type = angle type (1-Nangletype)
|
|
atom1,atom2,atom3 = IDs of 1st,2nd,3rd atoms in angle
|
|
</pre></div>
|
|
</div>
|
|
<p>example:
|
|
.. parsed-literal:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>2 2 17 29 430
|
|
</pre></div>
|
|
</div>
|
|
<p>The 3 atoms are ordered linearly within the angle. Thus the central
|
|
atom (around which the angle is computed) is the atom2 in the list.
|
|
E.g. H,O,H for a water molecule. The <em>Angles</em> section must appear
|
|
after the <em>Atoms</em> section. All values in this section must be
|
|
integers (1, not 1.0).</p>
|
|
<hr class="docutils" />
|
|
<p><em>AngleTorsion Coeffs</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per dihedral type</li>
|
|
<li>line syntax: ID coeffs</li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
ID = dihedral type (1-N)
|
|
coeffs = list of coeffs (see <a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a>)
|
|
</pre>
|
|
<hr class="docutils" />
|
|
<p><em>Atoms</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per atom</li>
|
|
<li>line syntax: depends on atom style</li>
|
|
</ul>
|
|
<p>An <em>Atoms</em> section must appear in the data file if natoms > 0 in the
|
|
header section. The atoms can be listed in any order. These are the
|
|
line formats for each <a class="reference internal" href="atom_style.html"><em>atom style</em></a> in LAMMPS. As
|
|
discussed below, each line can optionally have 3 flags (nx,ny,nz)
|
|
appended to it, which indicate which image of a periodic simulation
|
|
box the atom is in. These may be important to include for some kinds
|
|
of analysis.</p>
|
|
<table border="1" class="docutils">
|
|
<colgroup>
|
|
<col width="14%" />
|
|
<col width="86%" />
|
|
</colgroup>
|
|
<tbody valign="top">
|
|
<tr class="row-odd"><td>angle</td>
|
|
<td>atom-ID molecule-ID atom-type x y z</td>
|
|
</tr>
|
|
<tr class="row-even"><td>atomic</td>
|
|
<td>atom-ID atom-type x y z</td>
|
|
</tr>
|
|
<tr class="row-odd"><td>body</td>
|
|
<td>atom-ID atom-type bodyflag mass x y z</td>
|
|
</tr>
|
|
<tr class="row-even"><td>bond</td>
|
|
<td>atom-ID molecule-ID atom-type x y z</td>
|
|
</tr>
|
|
<tr class="row-odd"><td>charge</td>
|
|
<td>atom-ID atom-type q x y z</td>
|
|
</tr>
|
|
<tr class="row-even"><td>dipole</td>
|
|
<td>atom-ID atom-type q x y z mux muy muz</td>
|
|
</tr>
|
|
<tr class="row-odd"><td>dpd</td>
|
|
<td>atom-ID atom-type theta x y z</td>
|
|
</tr>
|
|
<tr class="row-even"><td>electron</td>
|
|
<td>atom-ID atom-type q spin eradius x y z</td>
|
|
</tr>
|
|
<tr class="row-odd"><td>ellipsoid</td>
|
|
<td>atom-ID atom-type ellipsoidflag density x y z</td>
|
|
</tr>
|
|
<tr class="row-even"><td>full</td>
|
|
<td>atom-ID molecule-ID atom-type q x y z</td>
|
|
</tr>
|
|
<tr class="row-odd"><td>line</td>
|
|
<td>atom-ID molecule-ID atom-type lineflag density x y z</td>
|
|
</tr>
|
|
<tr class="row-even"><td>meso</td>
|
|
<td>atom-ID atom-type rho e cv x y z</td>
|
|
</tr>
|
|
<tr class="row-odd"><td>molecular</td>
|
|
<td>atom-ID molecule-ID atom-type x y z</td>
|
|
</tr>
|
|
<tr class="row-even"><td>peri</td>
|
|
<td>atom-ID atom-type volume density x y z</td>
|
|
</tr>
|
|
<tr class="row-odd"><td>smd</td>
|
|
<td>atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z</td>
|
|
</tr>
|
|
<tr class="row-even"><td>sphere</td>
|
|
<td>atom-ID atom-type diameter density x y z</td>
|
|
</tr>
|
|
<tr class="row-odd"><td>template</td>
|
|
<td>atom-ID molecule-ID template-index template-atom atom-type x y z</td>
|
|
</tr>
|
|
<tr class="row-even"><td>tri</td>
|
|
<td>atom-ID molecule-ID atom-type triangleflag density x y z</td>
|
|
</tr>
|
|
<tr class="row-odd"><td>wavepacket</td>
|
|
<td>atom-ID atom-type charge spin eradius etag cs_re cs_im x y z</td>
|
|
</tr>
|
|
<tr class="row-even"><td>hybrid</td>
|
|
<td>atom-ID atom-type x y z sub-style1 sub-style2 ...</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<p>The per-atom values have these meanings and units, listed alphabetically:</p>
|
|
<ul class="simple">
|
|
<li>atom-ID = integer ID of atom</li>
|
|
<li>atom-type = type of atom (1-Ntype)</li>
|
|
<li>bodyflag = 1 for body particles, 0 for point particles</li>
|
|
<li>contact-radius = ??? (distance units)</li>
|
|
<li>cs_re,cs_im = real/imaginary parts of wavepacket coefficients</li>
|
|
<li>cv = heat capacity (need units) for SPH particles</li>
|
|
<li>density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)</li>
|
|
<li>diameter = diameter of spherical atom (distance units)</li>
|
|
<li>e = energy (need units) for SPH particles</li>
|
|
<li>ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles</li>
|
|
<li>eradius = electron radius (or fixed-core radius)</li>
|
|
<li>etag = integer ID of electron that each wavepacket belongs to</li>
|
|
<li>kernel-radius = ??? (distance units)</li>
|
|
<li>lineflag = 1 for line segment particles, 0 for point or spherical particles</li>
|
|
<li>mass = mass of particle (mass units)</li>
|
|
<li>molecule-ID = integer ID of molecule the atom belongs to</li>
|
|
<li>mux,muy,muz = components of dipole moment of atom (dipole units)</li>
|
|
<li>q = charge on atom (charge units)</li>
|
|
<li>rho = density (need units) for SPH particles</li>
|
|
<li>spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)</li>
|
|
<li>template-atom = which atom within a template molecule the atom is</li>
|
|
<li>template-index = which molecule within the molecule template the atom is part of</li>
|
|
<li>theta = internal temperature of a DPD particle</li>
|
|
<li>triangleflag = 1 for triangular particles, 0 for point or sperhical particles</li>
|
|
<li>volume = volume of Peridynamic particle (distance^3 units)</li>
|
|
<li>x,y,z = coordinates of atom (distance units)</li>
|
|
</ul>
|
|
<p>The units for these quantities depend on the unit style; see the
|
|
<a class="reference internal" href="units.html"><em>units</em></a> command for details.</p>
|
|
<p>For 2d simulations specify z as 0.0, or a value within the <em>zlo zhi</em>
|
|
setting in the data file header.</p>
|
|
<p>The atom-ID is used to identify the atom throughout the simulation and
|
|
in dump files. Normally, it is a unique value from 1 to Natoms for
|
|
each atom. Unique values larger than Natoms can be used, but they
|
|
will cause extra memory to be allocated on each processor, if an atom
|
|
map array is used, but not if an atom map hash is used; see the
|
|
<a class="reference internal" href="atom_modify.html"><em>atom_modify</em></a> command for details. If an atom map is
|
|
not used (e.g. an atomic system with no bonds), and you don’t care if
|
|
unique atom IDs appear in dump files, then the atom-IDs can all be set
|
|
to 0.</p>
|
|
<p>The molecule ID is a 2nd identifier attached to an atom. Normally, it
|
|
is a number from 1 to N, identifying which molecule the atom belongs
|
|
to. It can be 0 if it is an unbonded atom or if you don’t care to
|
|
keep track of molecule assignments.</p>
|
|
<p>The diameter specifies the size of a finite-size spherical particle.
|
|
It can be set to 0.0, which means that atom is a point particle.</p>
|
|
<p>The ellipsoidflag, lineflag, triangleflag, and bodyflag determine
|
|
whether the particle is a finite-size ellipsoid or line or triangle or
|
|
body of finite size, or whether the particle is a point particle.
|
|
Additional attributes must be defined for each ellipsoid, line,
|
|
triangle, or body in the corresponding <em>Ellipsoids</em>, <em>Lines</em>,
|
|
<em>Triangles</em>, or <em>Bodies</em> section.</p>
|
|
<p>The <em>template-index</em> and <em>template-atom</em> are only defined used by
|
|
<a class="reference internal" href="atom_style.html"><em>atom_style template</em></a>. In this case the
|
|
<a class="reference internal" href="molecule.html"><em>molecule</em></a> command is used to define a molecule template
|
|
which contains one or more molecules. If an atom belongs to one of
|
|
those molecules, its <em>template-index</em> and <em>template-atom</em> are both set
|
|
to positive integers; if not the values are both 0. The
|
|
<em>template-index</em> is which molecule (1 to Nmols) the atom belongs to.
|
|
The <em>template-atom</em> is which atom (1 to Natoms) within the molecule
|
|
the atom is.</p>
|
|
<p>Some pair styles and fixes and computes that operate on finite-size
|
|
particles allow for a mixture of finite-size and point particles. See
|
|
the doc pages of individual commands for details.</p>
|
|
<p>For finite-size particles, the density is used in conjunction with the
|
|
particle volume to set the mass of each particle as mass = density *
|
|
volume. In this context, volume can be a 3d quantity (for spheres or
|
|
ellipsoids), a 2d quantity (for triangles), or a 1d quantity (for line
|
|
segments). If the volume is 0.0, meaning a point particle, then the
|
|
density value is used as the mass. One exception is for the body atom
|
|
style, in which case the mass of each particle (body or point
|
|
particle) is specified explicitly. This is because the volume of the
|
|
body is unknown.</p>
|
|
<p>For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
|
|
specific values for each sub-style must be listed. The order of the
|
|
sub-styles is the same as they were listed in the
|
|
<a class="reference internal" href="atom_style.html"><em>atom_style</em></a> command. The sub-style specific values
|
|
are those that are not the 5 standard ones (ID,type,x,y,z). For
|
|
example, for the “charge” sub-style, a “q” value would appear. For
|
|
the “full” sub-style, a “molecule-ID” and “q” would appear. These are
|
|
listed in the same order they appear as listed above. Thus if</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>atom_style hybrid charge sphere
|
|
</pre></div>
|
|
</div>
|
|
<p>were used in the input script, each atom line would have these fields:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>atom-ID atom-type x y z q diameter density
|
|
</pre></div>
|
|
</div>
|
|
<p>Note that if a non-standard value is defined by multiple sub-styles,
|
|
it must appear mutliple times in the atom line. E.g. the atom line
|
|
for atom_style hybrid dipole full would list “q” twice:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>atom-ID atom-type x y z q mux muy myz molecule-ID q
|
|
</pre></div>
|
|
</div>
|
|
<p>Atom lines specify the (x,y,z) coordinates of atoms. These can be
|
|
inside or outside the simulation box. When the data file is read,
|
|
LAMMPS wraps coordinates outside the box back into the box for
|
|
dimensions that are periodic. As discussed above, if an atom is
|
|
outside the box in a non-periodic dimension, it will be lost.</p>
|
|
<p>LAMMPS always stores atom coordinates as values which are inside the
|
|
simulation box. It also stores 3 flags which indicate which image of
|
|
the simulation box (in each dimension) the atom would be in if its
|
|
coordinates were unwrapped across periodic boundaries. An image flag
|
|
of 0 means the atom is still inside the box when unwrapped. A value
|
|
of 2 means add 2 box lengths to get the unwrapped coordinate. A value
|
|
of -1 means subtract 1 box length to get the unwrapped coordinate.
|
|
LAMMPS updates these flags as atoms cross periodic boundaries during
|
|
the simulation. The <a class="reference internal" href="dump.html"><em>dump</em></a> command can output atom atom
|
|
coordinates in wrapped or unwrapped form, as well as the 3 image
|
|
flags.</p>
|
|
<p>In the data file, atom lines (all lines or none of them) can
|
|
optionally list 3 trailing integer values (nx,ny,nz), which are used
|
|
to initialize the atom’s image flags. If nx,ny,nz values are not
|
|
listed in the data file, LAMMPS initializes them to 0. Note that the
|
|
image flags are immediately updated if an atom’s coordinates need to
|
|
wrapped back into the simulation box.</p>
|
|
<p>It is only important to set image flags correctly in a data file if a
|
|
simulation model relies on unwrapped coordinates for some calculation;
|
|
otherwise they can be left unspecified. Examples of LAMMPS commands
|
|
that use unwrapped coordinates internally are as follows:</p>
|
|
<ul class="simple">
|
|
<li>Atoms in a rigid body (see <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a>, <a class="reference internal" href="fix_rigid.html"><em>fix rigid/small</em></a>) must have consistent image flags, so that
|
|
when the atoms are unwrapped, they are near each other, i.e. as a
|
|
single body.</li>
|
|
<li>If the <a class="reference internal" href="replicate.html"><em>replicate</em></a> command is used to generate a larger
|
|
system, image flags must be consistent for bonded atoms when the bond
|
|
crosses a periodic boundary. I.e. the values of the image flags
|
|
should be different by 1 (in the appropriate dimension) for the two
|
|
atoms in such a bond.</li>
|
|
<li>If you plan to <a class="reference internal" href="dump.html"><em>dump</em></a> image flags and perform post-analysis
|
|
that will unwrap atom coordinates, it may be important that a
|
|
continued run (restarted from a data file) begins with image flags
|
|
that are consistent with the previous run.</li>
|
|
</ul>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">If your system is an infinite periodic crystal with bonds then
|
|
it is impossible to have fully consistent image flags. This is because
|
|
some bonds will cross periodic boundaries and connect two atoms with the
|
|
same image flag.</p>
|
|
</div>
|
|
<p>Atom velocities and other atom quantities not defined above are set to
|
|
0.0 when the <em>Atoms</em> section is read. Velocities can be set later by
|
|
a <em>Velocities</em> section in the data file or by a
|
|
<a class="reference internal" href="velocity.html"><em>velocity</em></a> or <a class="reference internal" href="set.html"><em>set</em></a> command in the input
|
|
script.</p>
|
|
<hr class="docutils" />
|
|
<p><em>Bodies</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one or more lines per body</li>
|
|
<li>first line syntax: atom-ID Ninteger Ndouble</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>Ninteger = # of integer quantities for this particle
|
|
Ndouble = # of floating-point quantities for this particle
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>0 or more integer lines with total of Ninteger values</li>
|
|
<li>0 or more double lines with total of Ndouble values</li>
|
|
<li>example:</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>12 3 6
|
|
2 3 2
|
|
1.0 2.0 3.0 1.0 2.0 4.0
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>example:</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>12 0 14
|
|
1.0 2.0 3.0 1.0 2.0 4.0 1.0
|
|
2.0 3.0 1.0 2.0 4.0 4.0 2.0
|
|
</pre></div>
|
|
</div>
|
|
<p>The <em>Bodies</em> section must appear if <a class="reference internal" href="atom_style.html"><em>atom_style body</em></a>
|
|
is used and any atoms listed in the <em>Atoms</em> section have a bodyflag =
|
|
1. The number of bodies should be specified in the header section via
|
|
the “bodies” keyword.</p>
|
|
<p>Each body can have a variable number of integer and/or floating-point
|
|
values. The number and meaning of the values is defined by the body
|
|
style, as described in the <a class="reference internal" href="body.html"><em>body</em></a> doc page. The body style
|
|
is given as an argument to the <a class="reference internal" href="atom_style.html"><em>atom_style body</em></a>
|
|
command.</p>
|
|
<p>The Ninteger and Ndouble values determine how many integer and
|
|
floating-point values are specified for this particle. Ninteger and
|
|
Ndouble can be as large as needed and can be different for every body.
|
|
Integer values are then listed next on subsequent lines. Lines are
|
|
read one at a time until Ninteger values are read. Floating-point
|
|
values follow on subsequent lines, Again lines are read one at a time
|
|
until Ndouble values are read. Note that if there are no values of a
|
|
particular type, no lines appear for that type.</p>
|
|
<p>The <em>Bodies</em> section must appear after the <em>Atoms</em> section.</p>
|
|
<hr class="docutils" />
|
|
<p><em>Bond Coeffs</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per bond type</li>
|
|
<li>line syntax: ID coeffs</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>ID = bond type (1-N)
|
|
coeffs = list of coeffs
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>example:</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>4 250 1.49
|
|
</pre></div>
|
|
</div>
|
|
<p>The number and meaning of the coefficients are specific to the defined
|
|
bond style. See the <a class="reference internal" href="bond_style.html"><em>bond_style</em></a> and
|
|
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> commands for details. Coefficients can
|
|
also be set via the <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a> command in the input
|
|
script.</p>
|
|
<hr class="docutils" />
|
|
<p><em>BondAngle Coeffs</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per angle type</li>
|
|
<li>line syntax: ID coeffs</li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
ID = angle type (1-N)
|
|
coeffs = list of coeffs (see class 2 section of <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a>)
|
|
</pre>
|
|
<hr class="docutils" />
|
|
<p><em>BondBond Coeffs</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per angle type</li>
|
|
<li>line syntax: ID coeffs</li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
ID = angle type (1-N)
|
|
coeffs = list of coeffs (see class 2 section of <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a>)
|
|
</pre>
|
|
<hr class="docutils" />
|
|
<p><em>BondBond13 Coeffs</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per dihedral type</li>
|
|
<li>line syntax: ID coeffs</li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
ID = dihedral type (1-N)
|
|
coeffs = list of coeffs (see class 2 section of <a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a>)
|
|
</pre>
|
|
<hr class="docutils" />
|
|
<p><em>Bonds</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per bond</li>
|
|
<li>line syntax: ID type atom1 atom2</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>ID = bond number (1-Nbonds)
|
|
type = bond type (1-Nbondtype)
|
|
atom1,atom2 = IDs of 1st,2nd atoms in bond
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>example:</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>12 3 17 29
|
|
</pre></div>
|
|
</div>
|
|
<p>The <em>Bonds</em> section must appear after the <em>Atoms</em> section. All values
|
|
in this section must be integers (1, not 1.0).</p>
|
|
<hr class="docutils" />
|
|
<p><em>Dihedral Coeffs</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per dihedral type</li>
|
|
<li>line syntax: ID coeffs</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>ID = dihedral type (1-N)
|
|
coeffs = list of coeffs
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>example:</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>3 0.6 1 0 1
|
|
</pre></div>
|
|
</div>
|
|
<p>The number and meaning of the coefficients are specific to the defined
|
|
dihedral style. See the <a class="reference internal" href="dihedral_style.html"><em>dihedral_style</em></a> and
|
|
<a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a> commands for details.
|
|
Coefficients can also be set via the
|
|
<a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a> command in the input script.</p>
|
|
<hr class="docutils" />
|
|
<p><em>Dihedrals</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per dihedral</li>
|
|
<li>line syntax: ID type atom1 atom2 atom3 atom4</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>ID = number of dihedral (1-Ndihedrals)
|
|
type = dihedral type (1-Ndihedraltype)
|
|
atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in dihedral
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>example:</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>12 4 17 29 30 21
|
|
</pre></div>
|
|
</div>
|
|
<p>The 4 atoms are ordered linearly within the dihedral. The <em>Dihedrals</em>
|
|
section must appear after the <em>Atoms</em> section. All values in this
|
|
section must be integers (1, not 1.0).</p>
|
|
<hr class="docutils" />
|
|
<p><em>Ellipsoids</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per ellipsoid</li>
|
|
<li>line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>atom-ID = ID of atom which is an ellipsoid
|
|
shapex,shapey,shapez = 3 diameters of ellipsoid (distance units)
|
|
quatw,quati,quatj,quatk = quaternion components for orientation of atom
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>example:</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>12 1 2 1 1 0 0 0
|
|
</pre></div>
|
|
</div>
|
|
<p>The <em>Ellipsoids</em> section must appear if <a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> is used and any atoms are listed in the
|
|
<em>Atoms</em> section with an ellipsoidflag = 1. The number of ellipsoids
|
|
should be specified in the header section via the “ellipsoids”
|
|
keyword.</p>
|
|
<p>The 3 shape values specify the 3 diameters or aspect ratios of a
|
|
finite-size ellipsoidal particle, when it is oriented along the 3
|
|
coordinate axes. They must all be non-zero values.</p>
|
|
<p>The values <em>quatw</em>, <em>quati</em>, <em>quatj</em>, and <em>quatk</em> set the orientation
|
|
of the atom as a quaternion (4-vector). Note that the shape
|
|
attributes specify the aspect ratios of an ellipsoidal particle, which
|
|
is oriented by default with its x-axis along the simulation box’s
|
|
x-axis, and similarly for y and z. If this body is rotated (via the
|
|
right-hand rule) by an angle theta around a unit vector (a,b,c), then
|
|
the quaternion that represents its new orientation is given by
|
|
(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These
|
|
4 components are quatw, quati, quatj, and quatk as specified above.
|
|
LAMMPS normalizes each atom’s quaternion in case (a,b,c) is not
|
|
specified as a unit vector.</p>
|
|
<p>The <em>Ellipsoids</em> section must appear after the <em>Atoms</em> section.</p>
|
|
<hr class="docutils" />
|
|
<p><em>EndBondTorsion Coeffs</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per dihedral type</li>
|
|
<li>line syntax: ID coeffs</li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
ID = dihedral type (1-N)
|
|
coeffs = list of coeffs (see class 2 section of <a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a>)
|
|
</pre>
|
|
<hr class="docutils" />
|
|
<p><em>Improper Coeffs</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per improper type</li>
|
|
<li>line syntax: ID coeffs</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>ID = improper type (1-N)
|
|
coeffs = list of coeffs
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>example:</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>2 20 0.0548311
|
|
</pre></div>
|
|
</div>
|
|
<p>The number and meaning of the coefficients are specific to the defined
|
|
improper style. See the <a class="reference internal" href="improper_style.html"><em>improper_style</em></a> and
|
|
<a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a> commands for details.
|
|
Coefficients can also be set via the
|
|
<a class="reference internal" href="improper_coeff.html"><em>improper_coeff</em></a> command in the input script.</p>
|
|
<hr class="docutils" />
|
|
<p><em>Impropers</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per improper</li>
|
|
<li>line syntax: ID type atom1 atom2 atom3 atom4</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>ID = number of improper (1-Nimpropers)
|
|
type = improper type (1-Nimpropertype)
|
|
atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in improper
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>example:</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>12 3 17 29 13 100
|
|
</pre></div>
|
|
</div>
|
|
<p>The ordering of the 4 atoms determines the definition of the improper
|
|
angle used in the formula for each <a class="reference internal" href="improper_style.html"><em>improper style</em></a>. See the doc pages for individual styles
|
|
for details.</p>
|
|
<p>The <em>Impropers</em> section must appear after the <em>Atoms</em> section. All
|
|
values in this section must be integers (1, not 1.0).</p>
|
|
<hr class="docutils" />
|
|
<p><em>Lines</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per line segment</li>
|
|
<li>line syntax: atom-ID x1 y1 x2 y2</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>atom-ID = ID of atom which is a line segment
|
|
x1,y1 = 1st end point
|
|
x2,y2 = 2nd end point
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>example:</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>12 1.0 0.0 2.0 0.0
|
|
</pre></div>
|
|
</div>
|
|
<p>The <em>Lines</em> section must appear if <a class="reference internal" href="atom_style.html"><em>atom_style line</em></a>
|
|
is used and any atoms are listed in the <em>Atoms</em> section with a
|
|
lineflag = 1. The number of lines should be specified in the header
|
|
section via the “lines” keyword.</p>
|
|
<p>The 2 end points are the end points of the line segment. The ordering
|
|
of the 2 points should be such that using a right-hand rule to cross
|
|
the line segment with a unit vector in the +z direction, gives an
|
|
“outward” normal vector perpendicular to the line segment.
|
|
I.e. normal = (c2-c1) x (0,0,1). This orientation may be important
|
|
for defining some interactions.</p>
|
|
<p>The <em>Lines</em> section must appear after the <em>Atoms</em> section.</p>
|
|
<hr class="docutils" />
|
|
<p><em>Masses</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per atom type</li>
|
|
<li>line syntax: ID mass</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>ID = atom type (1-N)
|
|
mass = mass value
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>example:</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>3 1.01
|
|
</pre></div>
|
|
</div>
|
|
<p>This defines the mass of each atom type. This can also be set via the
|
|
<a class="reference internal" href="mass.html"><em>mass</em></a> command in the input script. This section cannot be
|
|
used for atom styles that define a mass for individual atoms -
|
|
e.g. <a class="reference internal" href="atom_style.html"><em>atom_style sphere</em></a>.</p>
|
|
<hr class="docutils" />
|
|
<p><em>MiddleBondTorsion Coeffs</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per dihedral type</li>
|
|
<li>line syntax: ID coeffs</li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
ID = dihedral type (1-N)
|
|
coeffs = list of coeffs (see class 2 section of <a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a>)
|
|
</pre>
|
|
<hr class="docutils" />
|
|
<p><em>Pair Coeffs</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per atom type</li>
|
|
<li>line syntax: ID coeffs</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>ID = atom type (1-N)
|
|
coeffs = list of coeffs
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>example:</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>3 0.022 2.35197 0.022 2.35197
|
|
</pre></div>
|
|
</div>
|
|
<p>The number and meaning of the coefficients are specific to the defined
|
|
pair style. See the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> and
|
|
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> commands for details. Since pair
|
|
coefficients for types I != J are not specified, these will be
|
|
generated automatically by the pair style’s mixing rule. See the
|
|
individual pair_style doc pages and the <a class="reference internal" href="pair_modify.html"><em>pair_modify mix</em></a> command for details. Pair coefficients can also
|
|
be set via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command in the input
|
|
script.</p>
|
|
<hr class="docutils" />
|
|
<p><em>PairIJ Coeffs</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per pair of atom types for all I,J with I <= J</li>
|
|
<li>line syntax: ID1 ID2 coeffs</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>ID1 = atom type I = 1-N
|
|
ID2 = atom type J = I-N, with I <= J
|
|
coeffs = list of coeffs
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>examples:</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>3 3 0.022 2.35197 0.022 2.35197
|
|
3 5 0.022 2.35197 0.022 2.35197
|
|
</pre></div>
|
|
</div>
|
|
<p>This section must have N*(N+1)/2 lines where N = # of atom types. The
|
|
number and meaning of the coefficients are specific to the defined
|
|
pair style. See the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> and
|
|
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> commands for details. Since pair
|
|
coefficients for types I != J are all specified, these values will
|
|
turn off the default mixing rule defined by the pair style. See the
|
|
individual pair_style doc pages and the <a class="reference internal" href="pair_modify.html"><em>pair_modify mix</em></a> command for details. Pair coefficients can also
|
|
be set via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command in the input
|
|
script.</p>
|
|
<hr class="docutils" />
|
|
<p><em>Triangles</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per triangle</li>
|
|
<li>line syntax: atom-ID x1 y1 x2 y2</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>atom-ID = ID of atom which is a line segment
|
|
x1,y1,z1 = 1st corner point
|
|
x2,y2,z2 = 2nd corner point
|
|
x3,y3,z3 = 3rd corner point
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>example:</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>12 0.0 0.0 0.0 2.0 0.0 1.0 0.0 2.0 1.0
|
|
</pre></div>
|
|
</div>
|
|
<p>The <em>Triangles</em> section must appear if <a class="reference internal" href="atom_style.html"><em>atom_style tri</em></a> is used and any atoms are listed in the <em>Atoms</em>
|
|
section with a triangleflag = 1. The number of lines should be
|
|
specified in the header section via the “triangles” keyword.</p>
|
|
<p>The 3 corner points are the corner points of the triangle. The
|
|
ordering of the 3 points should be such that using a right-hand rule
|
|
to go from point1 to point2 to point3 gives an “outward” normal vector
|
|
to the face of the triangle. I.e. normal = (c2-c1) x (c3-c1). This
|
|
orientation may be important for defining some interactions.</p>
|
|
<p>The <em>Triangles</em> section must appear after the <em>Atoms</em> section.</p>
|
|
<hr class="docutils" />
|
|
<p><em>Velocities</em> section:</p>
|
|
<ul class="simple">
|
|
<li>one line per atom</li>
|
|
<li>line syntax: depends on atom style</li>
|
|
</ul>
|
|
<table border="1" class="docutils">
|
|
<colgroup>
|
|
<col width="42%" />
|
|
<col width="58%" />
|
|
</colgroup>
|
|
<tbody valign="top">
|
|
<tr class="row-odd"><td>all styles except those listed</td>
|
|
<td>atom-ID vx vy vz</td>
|
|
</tr>
|
|
<tr class="row-even"><td>electron</td>
|
|
<td>atom-ID vx vy vz ervel</td>
|
|
</tr>
|
|
<tr class="row-odd"><td>ellipsoid</td>
|
|
<td>atom-ID vx vy vz lx ly lz</td>
|
|
</tr>
|
|
<tr class="row-even"><td>sphere</td>
|
|
<td>atom-ID vx vy vz wx wy wz</td>
|
|
</tr>
|
|
<tr class="row-odd"><td>hybrid</td>
|
|
<td>atom-ID vx vy vz sub-style1 sub-style2 ...</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<p>where the keywords have these meanings:</p>
|
|
<p>vx,vy,vz = translational velocity of atom
|
|
lx,ly,lz = angular momentum of aspherical atom
|
|
wx,wy,wz = angular velocity of spherical atom
|
|
ervel = electron radial velocity (0 for fixed-core):ul</p>
|
|
<p>The velocity lines can appear in any order. This section can only be
|
|
used after an <em>Atoms</em> section. This is because the <em>Atoms</em> section
|
|
must have assigned a unique atom ID to each atom so that velocities
|
|
can be assigned to them.</p>
|
|
<p>Vx, vy, vz, and ervel are in <a class="reference internal" href="units.html"><em>units</em></a> of velocity. Lx, ly,
|
|
lz are in units of angular momentum (distance-velocity-mass). Wx, Wy,
|
|
Wz are in units of angular velocity (radians/time).</p>
|
|
<p>For atom_style hybrid, following the 4 initial values (ID,vx,vy,vz),
|
|
specific values for each sub-style must be listed. The order of the
|
|
sub-styles is the same as they were listed in the
|
|
<a class="reference internal" href="atom_style.html"><em>atom_style</em></a> command. The sub-style specific values
|
|
are those that are not the 5 standard ones (ID,vx,vy,vz). For
|
|
example, for the “sphere” sub-style, “wx”, “wy”, “wz” values would
|
|
appear. These are listed in the same order they appear as listed
|
|
above. Thus if</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>atom_style hybrid electron sphere
|
|
</pre></div>
|
|
</div>
|
|
<p>were used in the input script, each velocity line would have these
|
|
fields:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>atom-ID vx vy vz ervel wx wy wz
|
|
</pre></div>
|
|
</div>
|
|
<p>Translational velocities can also be set by the
|
|
<a class="reference internal" href="velocity.html"><em>velocity</em></a> command in the input script.</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>To read gzipped data files, you must compile LAMMPS with the
|
|
-DLAMMPS_GZIP option - see the <a class="reference internal" href="Section_start.html#start-2"><span>Making LAMMPS</span></a> section of the documentation.</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="read_dump.html"><em>read_dump</em></a>, <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>,
|
|
<a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a>, <a class="reference internal" href="write_data.html"><em>write_data</em></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
|
|
<p>The default for all the <em>extra</em> keywords is 0.</p>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
</div>
|
|
<footer>
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|
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<hr/>
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|
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<div role="contentinfo">
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<p>
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</p>
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