2006-09-22 00:22:34 +08:00
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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</CENTER>
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<HR>
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<H3>read_data command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>read_data file keyword args ...
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</PRE>
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<UL><LI>file = name of data file to read in
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2012-05-19 07:37:24 +08:00
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<LI>zero or more keyword/arg pairs may be appended
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<LI>keyword = <I>fix</I>
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<PRE> <I>fix</I> 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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2006-09-22 00:22:34 +08:00
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>read_data data.lj
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2012-05-19 07:37:24 +08:00
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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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2006-09-22 00:22:34 +08:00
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</PRE>
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<P><B>Description:</B>
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</P>
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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 HREF = "read_restart.html">read_restart</A> and
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<A HREF = "create_atoms.html">create_atoms</A> commands for alternative methods.
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2014-06-15 05:45:07 +08:00
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Also see the explanation of the <A HREF = "Section_start.html#start_7">-restart command-line
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switch</A> which can convert a restart file to
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a data file.
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2006-09-22 00:22:34 +08:00
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</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.
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</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.
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</P>
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<P>The body of the file contains zero or more sections. The first line
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2014-03-11 00:53:22 +08:00
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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.
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2006-09-22 00:22:34 +08:00
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</P>
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2013-07-26 01:02:34 +08:00
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<P>The keyword <I>fix</I> 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 <I>header-string</I> and any section with
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a name containing <I>section-string</I> will be passed to the specified
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fix. See the <A HREF = "fix_property_atom.html">fix property/atom</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 <I>header-string</I> 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.
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2012-05-19 07:37:24 +08:00
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</P>
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2006-09-22 00:22:34 +08:00
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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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2013-02-19 01:23:22 +08:00
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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.
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2006-09-22 00:22:34 +08:00
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</P>
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<HR>
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<P>These are the recognized header keywords. Header lines can come in
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2007-03-06 23:13:57 +08:00
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any order. The value(s) are read from the beginning of the line.
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Thus the keyword <I>atoms</I> should be in a line like "1000 atoms"; the
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keyword <I>ylo yhi</I> should be in a line like "-10.0 10.0 ylo yhi"; the
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keyword <I>xy xz yz</I> 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.
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2006-09-22 00:22:34 +08:00
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</P>
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<UL><LI><I>atoms</I> = # of atoms in system
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<LI><I>bonds</I> = # of bonds in system
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<LI><I>angles</I> = # of angles in system
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<LI><I>dihedrals</I> = # of dihedrals in system
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<LI><I>impropers</I> = # of impropers in system
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<LI><I>atom types</I> = # of atom types in system
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<LI><I>bond types</I> = # of bond types in system
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<LI><I>angle types</I> = # of angle types in system
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<LI><I>dihedral types</I> = # of dihedral types in system
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<LI><I>improper types</I> = # of improper types in system
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2009-01-06 06:26:31 +08:00
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<LI><I>extra bond per atom</I> = leave space for this many new bonds per atom
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2013-12-17 23:12:58 +08:00
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<LI><I>extra angle per atom</I> = leave space for this many new angles per atom
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<LI><I>extra dihedral per atom</I> = leave space for this many new dihedrals per atom
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<LI><I>extra improper per atom</I> = leave space for this many new impropers per atom
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2014-01-09 04:38:18 +08:00
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<LI><I>extra special per atom</I> = leave space for this many new special bonds per atom
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2011-04-16 07:14:41 +08:00
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<LI><I>ellipsoids</I> = # of ellipsoids in system
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2011-10-20 23:01:56 +08:00
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<LI><I>lines</I> = # of line segments in system
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<LI><I>triangles</I> = # of triangles in system
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<LI><I>bodies</I> = # of bodies in system
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2006-09-22 00:22:34 +08:00
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<LI><I>xlo xhi</I> = simulation box boundaries in x dimension
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<LI><I>ylo yhi</I> = simulation box boundaries in y dimension
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2007-03-06 23:13:57 +08:00
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<LI><I>zlo zhi</I> = simulation box boundaries in z dimension
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2010-10-15 07:23:43 +08:00
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<LI><I>xy xz yz</I> = simulation box tilt factors for triclinic system
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2006-09-22 00:22:34 +08:00
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</UL>
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<P>The initial simulation box size is determined by the lo/hi settings.
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In any dimension, the system may be periodic or non-periodic; see the
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2014-05-13 22:04:47 +08:00
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<A HREF = "boundary.html">boundary</A> command. When the simulation box is created
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it is also partitioned into a regular 3d grid of rectangular bricks,
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one per processor, based on the number of processors being used and
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the settings of the <A HREF = "processors.html">processors</A> command. The
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partitioning can later be changed by the <A HREF = "balance.html">balance</A> or
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<A HREF = "fix_balance.html">fix balance</A> commands.
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2006-09-22 00:22:34 +08:00
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</P>
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2009-01-06 06:26:31 +08:00
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<P>If the <I>xy xz yz</I> line does not appear, LAMMPS will set up an
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2007-03-06 23:13:57 +08:00
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axis-aligned (orthogonal) simulation box. If the line does appear,
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LAMMPS creates a non-orthogonal simulation domain shaped as a
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2010-10-15 07:23:43 +08:00
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parallelepiped with triclinic symmetry. The parallelepiped has its
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"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
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from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
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(xz,yz,zhi-zlo). <I>Xy,xz,yz</I> can be 0.0 or positive or negative values
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and are called "tilt factors" because they are the amount of
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displacement applied to faces of an originally orthogonal box to
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transform it into the parallelepiped.
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2007-06-20 20:56:17 +08:00
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</P>
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<P>The tilt factors (xy,xz,yz) can not skew the box more than half the
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2010-10-15 07:23:43 +08:00
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distance of the corresponding parallel box length. For example, if
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xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt
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factor must be between -5 and 5. Similarly, both xz and yz must be
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between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a
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limitation, since if the maximum tilt factor is 5 (as in this
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example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
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... are all geometrically equivalent.
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</P>
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2011-12-14 04:43:36 +08:00
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<P>See <A HREF = "Section_howto.html#howto_12">Section_howto 12</A> of the doc pages
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for a geometric description of triclinic boxes, as defined by LAMMPS,
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and how to transform these parameters to and from other commonly used
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2010-10-15 07:31:42 +08:00
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triclinic representations.
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2010-10-15 07:23:43 +08:00
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</P>
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2007-03-06 23:13:57 +08:00
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<P>When a triclinic system is used, the simulation domain must be
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2007-04-02 22:26:01 +08:00
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periodic in any dimensions with a non-zero tilt factor, as defined by
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the <A HREF = "boundary.html">boundary</A> command. I.e. if the xy tilt factor is
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2007-03-06 23:13:57 +08:00
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non-zero, then both the x and y dimensions must be periodic.
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Similarly, x and z must be periodic if xz is non-zero and y and z must
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2010-10-15 07:23:43 +08:00
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be periodic if yz is non-zero. Also note that if your simulation will
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tilt the box, e.g. via the <A HREF = "fix_deform.html">fix deform</A> command, the
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simulation box must be defined as triclinic, even if the tilt factors
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are initially 0.0.
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2007-03-06 23:13:57 +08:00
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</P>
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<P>For 2d simulations, the <I>zlo zhi</I> values should be set to bound the z
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coords for atoms that appear in the file; the default of -0.5 0.5 is
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valid if all z coords are 0.0. For 2d triclinic simulations, the xz
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2007-04-02 22:26:01 +08:00
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and yz tilt factors must be 0.0.
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2007-03-06 23:13:57 +08:00
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</P>
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2006-09-22 00:22:34 +08:00
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<P>If the system is periodic (in a dimension), then atom coordinates can
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2009-04-04 00:19:32 +08:00
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be outside the bounds (in that dimension); they will be remapped (in a
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periodic sense) back inside the box.
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2006-09-22 00:22:34 +08:00
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</P>
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2008-05-20 23:38:43 +08:00
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<P>IMPORTANT NOTE: If the system is non-periodic (in a dimension), then
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all atoms in the data file must have coordinates (in that dimension)
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2008-05-21 05:19:34 +08:00
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that are "greater than or equal to" the lo value and "less than or
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equal to" the hi value. If the non-periodic dimension is of style
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"fixed" (see the <A HREF = "boundary.html">boundary</A> command), then the atom
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coords must be strictly "less than" the hi value, due to the way
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LAMMPS assign atoms to processors. Note that you should not make the
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lo/hi values radically smaller/larger than the extent of the atoms.
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For example, if your atoms extend from 0 to 50, you should not specify
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the box bounds as -10000 and 10000. This is because LAMMPS uses the
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2008-05-20 23:38:43 +08:00
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specified box size to layout the 3d grid of processors. A huge
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2010-10-06 00:12:36 +08:00
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(mostly empty) box will be sub-optimal for performance when using
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"fixed" boundary conditions (see the <A HREF = "boundary.html">boundary</A>
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command). When using "shrink-wrap" boundary conditions (see the
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<A HREF = "boundary.html">boundary</A> command), a huge (mostly empty) box may cause
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a parallel simulation to lose atoms the first time that LAMMPS
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2009-04-04 00:19:32 +08:00
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shrink-wraps the box around the atoms.
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2008-05-20 23:38:43 +08:00
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</P>
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2014-01-09 04:38:18 +08:00
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<P>The "extra bond per atom" setting (angle, dihedral, improper) is only
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needed if new bonds (angles, dihedrals, impropers) will be added to
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2013-12-17 23:12:58 +08:00
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the system when a simulation runs, e.g. by using the <A HREF = "fix_bond_create.html">fix
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2009-01-06 06:26:31 +08:00
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bond/create</A> command. This will pre-allocate
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2013-12-17 23:12:58 +08:00
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space in LAMMPS data structures for storing the new bonds (angles,
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dihedrals, impropers).
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2009-01-06 06:26:31 +08:00
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</P>
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2014-01-09 04:38:18 +08:00
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<P>The "extra special per atom" setting is only needed if new molecules
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will be added to the system, e.g. by using the <A HREF = "fix_deposit.html">fix
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deposit</A> or <A HREF = "fix_pour.html">fix pour</A> commands, which
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will have more special 1-2,1-3,1-4 neighbors than any other molecules
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defined in the data file. This will pre-allocate space in the LAMMPS
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data structures for storing these neighbors. See the
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<A HREF = "special_bonds.html">special_bonds</A> and <A HREF = "molecule.html">molecule</A> doc
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pages for more discussion of 1-2,1-3,1-4 neighbors.
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</P>
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2013-02-01 00:39:48 +08:00
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<P>The "ellipsoids" and "lines" and "triangles" and "bodies" settings are
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only used with <A HREF = "atom_style.html">atom_style ellipsoid or line or tri or
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body</A> and specify how many of the atoms are
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finite-size ellipsoids or lines or triangles or bodies; the remainder
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are point particles. See the discussion of ellipsoidflag and the
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<I>Ellipsoids</I> section below. See the discussion of lineflag and the
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<I>Lines</I> section below. See the discussion of triangleflag and the
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<I>Triangles</I> section below. See the discussion of bodyflag and the
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<I>Bodies</I> section below.
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2011-04-16 07:14:41 +08:00
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</P>
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2014-01-26 07:36:16 +08:00
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<P>IMPORTANT NOTE: For <A HREF = "atom_style.html">atom_style template</A>, the
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molecular topology (bonds,angles,etc) is contained in the molecule
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templates read-in by the <A HREF = "molecule.html">molecule</A> command. This means
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you cannot set the <I>bonds</I>, <I>angles</I>, etc header keywords in the data
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file, nor can you define <I>Bonds</I>, <I>Angles</I>, etc sections as discussed
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below. You can set the <I>bond types</I>, <I>angle types</I>, etc header
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keywords, though it is not necessary. If specified, they must match
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the maximum values defined in any of the template molecules.
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</P>
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2006-09-22 00:22:34 +08:00
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<HR>
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<P>These are the section keywords for the body of the file.
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</P>
|
2013-02-01 00:39:48 +08:00
|
|
|
<UL><LI><I>Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies</I> = atom-property sections
|
2008-03-01 09:13:20 +08:00
|
|
|
<LI><I>Bonds, Angles, Dihedrals, Impropers</I> = molecular topology sections
|
2013-04-24 04:53:50 +08:00
|
|
|
<LI><I>Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs</I> = force field sections
|
2006-09-22 00:22:34 +08:00
|
|
|
<LI><I>BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs</I> = class 2 force field sections
|
|
|
|
|
</UL>
|
2014-03-11 00:53:22 +08:00
|
|
|
<P>These keywords will check an appended comment for a match with the
|
|
|
|
|
currently defined style:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI><I>Atoms, Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs</I>
|
|
|
|
|
</UL>
|
|
|
|
|
<P>For example, these lines:
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>Atoms # sphere
|
|
|
|
|
Pair Coeffs # lj/cut
|
|
|
|
|
</PRE>
|
|
|
|
|
<P>will check if the currently-defined <A HREF = "atom_style.html">atom_style</A> is
|
|
|
|
|
<I>sphere</I>, and the current <A HREF = "pair_style">pair_style</A> is <I>lj/cut</I>. 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>
|
2007-06-20 20:56:17 +08:00
|
|
|
<P>Each section is listed below in alphabetic order. The format of each
|
2006-09-22 00:22:34 +08:00
|
|
|
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>
|
|
|
|
|
<PRE>10 1 17 -1.0 10.0 5.0 6.0 # salt ion
|
|
|
|
|
</PRE>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>Angle Coeffs</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per angle type
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID coeffs
|
|
|
|
|
|
|
|
|
|
<PRE> ID = angle type (1-N)
|
|
|
|
|
coeffs = list of coeffs
|
|
|
|
|
</PRE>
|
|
|
|
|
<LI>example:
|
|
|
|
|
|
|
|
|
|
<PRE> 6 70 108.5 0 0
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P>The number and meaning of the coefficients are specific to the defined
|
|
|
|
|
angle style. See the <A HREF = "angle_style.html">angle_style</A> and
|
|
|
|
|
<A HREF = "angle_coeff.html">angle_coeff</A> commands for details. Coefficients can
|
|
|
|
|
also be set via the <A HREF = "angle_coeff.html">angle_coeff</A> command in the
|
|
|
|
|
input script.
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>AngleAngle Coeffs</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per improper type
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID coeffs
|
|
|
|
|
|
|
|
|
|
<PRE> ID = improper type (1-N)
|
|
|
|
|
coeffs = list of coeffs (see <A HREF = "improper_coeff.html">improper_coeff</A>)
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>AngleAngleTorsion Coeffs</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per dihedral type
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID coeffs
|
|
|
|
|
|
|
|
|
|
<PRE> ID = dihedral type (1-N)
|
|
|
|
|
coeffs = list of coeffs (see <A HREF = "dihedral_coeff.html">dihedral_coeff</A>)
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>Angles</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per angle
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID type atom1 atom2 atom3
|
|
|
|
|
|
|
|
|
|
<PRE> ID = number of angle (1-Nangles)
|
|
|
|
|
type = angle type (1-Nangletype)
|
|
|
|
|
atom1,atom2,atom3 = IDs of 1st,2nd,3rd atoms in angle
|
|
|
|
|
</PRE>
|
|
|
|
|
example:
|
|
|
|
|
<BR>
|
|
|
|
|
<PRE> 2 2 17 29 430
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<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 <I>Angles</I> section must appear
|
|
|
|
|
after the <I>Atoms</I> section. All values in this section must be
|
|
|
|
|
integers (1, not 1.0).
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>AngleTorsion Coeffs</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per dihedral type
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID coeffs
|
|
|
|
|
|
|
|
|
|
<PRE> ID = dihedral type (1-N)
|
|
|
|
|
coeffs = list of coeffs (see <A HREF = "dihedral_coeff.html">dihedral_coeff</A>)
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>Atoms</I> section:
|
|
|
|
|
</P>
|
2007-02-10 05:37:30 +08:00
|
|
|
<UL><LI>one line per atom
|
2006-09-22 00:22:34 +08:00
|
|
|
<LI>line syntax: depends on atom style
|
|
|
|
|
</UL>
|
2007-02-10 05:37:30 +08:00
|
|
|
<P>An <I>Atoms</I> 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
|
2007-12-12 07:28:43 +08:00
|
|
|
line formats for each <A HREF = "atom_style.html">atom style</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.
|
2007-02-10 05:37:30 +08:00
|
|
|
</P>
|
2010-05-02 08:59:55 +08:00
|
|
|
<DIV ALIGN=center><TABLE BORDER=1 >
|
2007-02-10 05:37:30 +08:00
|
|
|
<TR><TD >angle</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
|
|
|
|
|
<TR><TD >atomic</TD><TD > atom-ID atom-type x y z</TD></TR>
|
2013-02-01 00:39:48 +08:00
|
|
|
<TR><TD >body</TD><TD > atom-ID atom-type bodyflag mass x y z</TD></TR>
|
2007-02-10 05:37:30 +08:00
|
|
|
<TR><TD >bond</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
|
|
|
|
|
<TR><TD >charge</TD><TD > atom-ID atom-type q x y z</TD></TR>
|
2007-06-20 20:56:17 +08:00
|
|
|
<TR><TD >dipole</TD><TD > atom-ID atom-type q x y z mux muy muz</TD></TR>
|
2010-08-25 23:39:16 +08:00
|
|
|
<TR><TD >electron</TD><TD > atom-ID atom-type q spin eradius x y z</TD></TR>
|
2011-04-16 07:14:41 +08:00
|
|
|
<TR><TD >ellipsoid</TD><TD > atom-ID atom-type ellipsoidflag density x y z</TD></TR>
|
2007-02-10 05:37:30 +08:00
|
|
|
<TR><TD >full</TD><TD > atom-ID molecule-ID atom-type q x y z</TD></TR>
|
2011-10-20 23:01:56 +08:00
|
|
|
<TR><TD >line</TD><TD > atom-ID molecule-ID atom-type lineflag density x y z</TD></TR>
|
2011-08-28 04:35:24 +08:00
|
|
|
<TR><TD >meso</TD><TD > atom-ID atom-type rho e cv x y z</TD></TR>
|
2007-06-20 20:56:17 +08:00
|
|
|
<TR><TD >molecular</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
|
2008-07-25 22:42:02 +08:00
|
|
|
<TR><TD >peri</TD><TD > atom-ID atom-type volume density x y z</TD></TR>
|
2011-04-14 05:39:34 +08:00
|
|
|
<TR><TD >sphere</TD><TD > atom-ID atom-type diameter density x y z</TD></TR>
|
2014-01-26 07:06:52 +08:00
|
|
|
<TR><TD >template</TD><TD > atom-ID molecule-ID template-index template-atom atom-type x y z</TD></TR>
|
2011-10-20 23:01:56 +08:00
|
|
|
<TR><TD >tri</TD><TD > atom-ID molecule-ID atom-type triangleflag density x y z</TD></TR>
|
2011-06-14 07:22:11 +08:00
|
|
|
<TR><TD >wavepacket</TD><TD > atom-ID atom-type charge spin eradius etag cs_re cs_im x y z</TD></TR>
|
2007-06-20 20:56:17 +08:00
|
|
|
<TR><TD >hybrid</TD><TD > atom-ID atom-type x y z sub-style1 sub-style2 ...
|
2007-02-10 05:37:30 +08:00
|
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
|
|
2007-12-12 07:28:43 +08:00
|
|
|
<P>The keywords have these meanings:
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<UL><LI>atom-ID = integer ID of atom
|
|
|
|
|
<LI>molecule-ID = integer ID of molecule the atom belongs to
|
2011-04-14 05:39:34 +08:00
|
|
|
<LI>atom-type = type of atom (1-Ntype)
|
2008-07-25 07:46:15 +08:00
|
|
|
<LI>q = charge on atom (charge units)
|
2011-04-14 05:39:34 +08:00
|
|
|
<LI>diameter = diameter of spherical atom (distance units)
|
2011-04-16 07:14:41 +08:00
|
|
|
<LI>ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
|
2011-10-20 23:01:56 +08:00
|
|
|
<LI>lineflag = 1 for line segment particles, 0 for point particles
|
|
|
|
|
<LI>triangleflag = 1 for triangular particles, 0 for point particles
|
2013-02-01 00:39:48 +08:00
|
|
|
<LI>bodyflag = 1 for body particles, 0 for point particles
|
2014-01-26 07:06:52 +08:00
|
|
|
<LI>template-index = which molecule within the molecule template the atom is part of
|
|
|
|
|
<LI>template-atom = which atom within a template molecule the atom is
|
2011-10-20 23:01:56 +08:00
|
|
|
<LI>density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
|
2013-02-01 00:39:48 +08:00
|
|
|
<LI>mass = mass of particle (mass units)
|
|
|
|
|
<LI>volume = volume of particle (distance^3 units)
|
2007-04-20 07:25:27 +08:00
|
|
|
<LI>x,y,z = coordinates of atom
|
2011-04-14 05:39:34 +08:00
|
|
|
<LI>mux,muy,muz = components of dipole moment of atom (dipole units)
|
2011-08-28 04:35:24 +08:00
|
|
|
<LI>rho = density (need units) for SPH particles
|
|
|
|
|
<LI>e = energy (need units) for SPH particles
|
|
|
|
|
<LI>cv = heat capacity (need units) for SPH particles
|
2011-02-23 06:29:54 +08:00
|
|
|
<LI>spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
|
2011-06-14 07:22:11 +08:00
|
|
|
<LI>eradius = electron radius (or fixed-core radius)
|
|
|
|
|
<LI>etag = integer ID of electron that each wavepacket belongs to
|
|
|
|
|
<LI>cs_re,cs_im = real/imaginary parts of wavepacket coefficients
|
2006-09-22 00:22:34 +08:00
|
|
|
</UL>
|
|
|
|
|
<P>The units for these quantities depend on the unit style; see the
|
|
|
|
|
<A HREF = "units.html">units</A> command for details.
|
|
|
|
|
</P>
|
2007-06-20 20:56:17 +08:00
|
|
|
<P>For 2d simulations specify z as 0.0, or a value within the <I>zlo zhi</I>
|
|
|
|
|
setting in the data file header.
|
2006-09-22 00:22:34 +08:00
|
|
|
</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
|
2014-01-26 07:06:52 +08:00
|
|
|
map array is used, but not if an atom map hash is used; see the
|
|
|
|
|
<A HREF = "atom_modify.html">atom_modify</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.
|
2006-09-22 00:22:34 +08:00
|
|
|
</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
|
2007-02-10 05:37:30 +08:00
|
|
|
to. It can be 0 if it is an unbonded atom or if you don't care to
|
|
|
|
|
keep track of molecule assignments.
|
|
|
|
|
</P>
|
2011-04-14 05:39:34 +08:00
|
|
|
<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.
|
2009-06-27 02:22:33 +08:00
|
|
|
</P>
|
2013-02-01 00:39:48 +08:00
|
|
|
<P>The ellipsoidflag, lineflag, triangleflag, and bodyflag determine
|
|
|
|
|
whether the particle is a finite-size ellipsoid or line or triangle or
|
2013-02-01 01:46:29 +08:00
|
|
|
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 <I>Ellipsoids</I>, <I>Lines</I>,
|
|
|
|
|
<I>Triangles</I>, or <I>Bodies</I> section.
|
2011-04-14 05:39:34 +08:00
|
|
|
</P>
|
2014-01-26 07:06:52 +08:00
|
|
|
<P>The <I>template-index</I> and <I>template-atom</I> are only defined used by
|
|
|
|
|
<A HREF = "atom_style.html">atom_style template</A>. In this case the
|
|
|
|
|
<A HREF = "molecule.html">molecule</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 <I>template-index</I> and <I>template-atom</I> are both set
|
|
|
|
|
to positive integers; if not the values are both 0. The
|
|
|
|
|
<I>template-index</I> is which molecule (1 to Nmols) the atom belongs to.
|
|
|
|
|
The <I>template-atom</I> is which atom (1 to Natoms) within the molecule
|
|
|
|
|
the atom is.
|
|
|
|
|
</P>
|
2011-04-14 05:39:34 +08:00
|
|
|
<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>
|
2013-02-01 00:39:48 +08:00
|
|
|
<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
|
2013-02-01 01:46:29 +08:00
|
|
|
density value is used as the mass. One exception is for the body atom
|
2013-02-01 00:39:48 +08:00
|
|
|
style, in which case the mass of each particle (body or point
|
|
|
|
|
particle) is specified explicitly. This is because the volume of the
|
2013-02-01 01:46:29 +08:00
|
|
|
body is unknown.
|
2009-06-27 02:22:33 +08:00
|
|
|
</P>
|
2007-06-20 20:56:17 +08:00
|
|
|
<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 HREF = "atom_style.html">atom_style</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
|
2011-04-16 07:14:41 +08:00
|
|
|
listed in the same order they appear as listed above. Thus if
|
2007-06-20 20:56:17 +08:00
|
|
|
</P>
|
2011-04-14 05:39:34 +08:00
|
|
|
<PRE>atom_style hybrid charge sphere
|
2007-06-20 20:56:17 +08:00
|
|
|
</PRE>
|
|
|
|
|
<P>were used in the input script, each atom line would have these fields:
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>atom-ID atom-type x y z q diameter density
|
|
|
|
|
</PRE>
|
2012-06-07 23:02:09 +08:00
|
|
|
<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>
|
|
|
|
|
<PRE>atom-ID atom-type x y z q mux muy myz molecule-ID q
|
|
|
|
|
</PRE>
|
2014-01-10 00:32:42 +08:00
|
|
|
<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 HREF = "dump.html">dump</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><LI>Atoms in a rigid body (see <A HREF = "fix_rigid.html">fix rigid</A>, <A HREF = "fix_rigid.html">fix
|
|
|
|
|
rigid/small</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>If the <A HREF = "replicate.html">replicate</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>If you plan to <A HREF = "dump.html">dump</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.
|
|
|
|
|
</UL>
|
2007-06-20 20:56:17 +08:00
|
|
|
<P>Atom velocities and other atom quantities not defined above are set to
|
2007-12-12 07:28:43 +08:00
|
|
|
0.0 when the <I>Atoms</I> section is read. Velocities can be set later by
|
|
|
|
|
a <I>Velocities</I> section in the data file or by a
|
|
|
|
|
<A HREF = "velocity.html">velocity</A> or <A HREF = "set.html">set</A> command in the input
|
|
|
|
|
script.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
2013-02-01 00:39:48 +08:00
|
|
|
<P><I>Bodies</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one or more lines per body
|
|
|
|
|
|
|
|
|
|
<LI>first line syntax: atom-ID ninteger ndouble
|
|
|
|
|
|
|
|
|
|
<PRE> ninteger = # of integer quantities for this particle
|
|
|
|
|
ndouble = # of floating-point quantities for this particle
|
|
|
|
|
</PRE>
|
|
|
|
|
<LI>0 or more integer lines: one line for every 10 integer quantities
|
|
|
|
|
|
|
|
|
|
<LI>0 or more double lines: one line for every 10 double quantities
|
|
|
|
|
|
|
|
|
|
<LI>example:
|
|
|
|
|
|
|
|
|
|
<PRE> 12 3 6
|
|
|
|
|
2 3 2
|
|
|
|
|
1.0 2.0 3.0 1.0 2.0 4.0
|
|
|
|
|
</PRE>
|
|
|
|
|
<LI>example:
|
|
|
|
|
|
|
|
|
|
<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>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P>The <I>Bodies</I> section must appear if <A HREF = "atom_style.html">atom_style body</A>
|
2013-02-01 01:46:29 +08:00
|
|
|
is used and any atoms listed in the <I>Atoms</I> section have a bodyflag =
|
|
|
|
|
1. The number of bodies should be specified in the header section via
|
|
|
|
|
the "bodies" keyword.
|
2013-02-01 00:39:48 +08:00
|
|
|
</P>
|
|
|
|
|
<P>Each body can have a variable number of integer and/or floating-point
|
2013-02-01 01:46:29 +08:00
|
|
|
values. The number and meaning of the values is defined by the body
|
|
|
|
|
style, as described in the <A HREF = "body.html">body</A> doc page. The body style
|
|
|
|
|
is given as an argument to the <A HREF = "atom_style.html">atom_style body</A>
|
|
|
|
|
command.
|
2013-02-01 00:39:48 +08:00
|
|
|
</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 on subsequent lines, 10 values per
|
|
|
|
|
line. Floating-point values follow on subsequent lines, again 10 per
|
|
|
|
|
line. If the number of lines is not evenly divisible by 10, the last
|
|
|
|
|
line in that group contains the remaining values, e.g. 4 values out of
|
|
|
|
|
14 in the last example above, for floating-point values. If there are
|
|
|
|
|
no values of a particular type, no lines appear for that type,
|
|
|
|
|
e.g. there are no integer lines in the last example above.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The <I>Bodies</I> section must appear after the <I>Atoms</I> section.
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
2006-09-22 00:22:34 +08:00
|
|
|
<P><I>Bond Coeffs</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per bond type
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID coeffs
|
|
|
|
|
|
|
|
|
|
<PRE> ID = bond type (1-N)
|
|
|
|
|
coeffs = list of coeffs
|
|
|
|
|
</PRE>
|
|
|
|
|
<LI>example:
|
|
|
|
|
|
|
|
|
|
<PRE> 4 250 1.49
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P>The number and meaning of the coefficients are specific to the defined
|
|
|
|
|
bond style. See the <A HREF = "bond_style.html">bond_style</A> and
|
|
|
|
|
<A HREF = "bond_coeff.html">bond_coeff</A> commands for details. Coefficients can
|
|
|
|
|
also be set via the <A HREF = "bond_coeff.html">bond_coeff</A> command in the input
|
|
|
|
|
script.
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>BondAngle Coeffs</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per angle type
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID coeffs
|
|
|
|
|
|
|
|
|
|
<PRE> ID = angle type (1-N)
|
|
|
|
|
coeffs = list of coeffs (see class 2 section of <A HREF = "angle_coeff.html">angle_coeff</A>)
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>BondBond Coeffs</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per angle type
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID coeffs
|
|
|
|
|
|
|
|
|
|
<PRE> ID = angle type (1-N)
|
|
|
|
|
coeffs = list of coeffs (see class 2 section of <A HREF = "angle_coeff.html">angle_coeff</A>)
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>BondBond13 Coeffs</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per dihedral type
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID coeffs
|
|
|
|
|
|
|
|
|
|
<PRE> ID = dihedral type (1-N)
|
|
|
|
|
coeffs = list of coeffs (see class 2 section of <A HREF = "dihedral_coeff.html">dihedral_coeff</A>)
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>Bonds</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per bond
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID type atom1 atom2
|
|
|
|
|
|
|
|
|
|
<PRE> ID = bond number (1-Nbonds)
|
|
|
|
|
type = bond type (1-Nbondtype)
|
|
|
|
|
atom1,atom2 = IDs of 1st,2nd atoms in bond
|
|
|
|
|
</PRE>
|
|
|
|
|
<LI>example:
|
|
|
|
|
|
|
|
|
|
<PRE> 12 3 17 29
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P>The <I>Bonds</I> section must appear after the <I>Atoms</I> section. All values
|
|
|
|
|
in this section must be integers (1, not 1.0).
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>Dihedral Coeffs</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per dihedral type
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID coeffs
|
|
|
|
|
|
|
|
|
|
<PRE> ID = dihedral type (1-N)
|
|
|
|
|
coeffs = list of coeffs
|
|
|
|
|
</PRE>
|
|
|
|
|
<LI>example:
|
|
|
|
|
|
|
|
|
|
<PRE> 3 0.6 1 0 1
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P>The number and meaning of the coefficients are specific to the defined
|
|
|
|
|
dihedral style. See the <A HREF = "dihedral_style.html">dihedral_style</A> and
|
|
|
|
|
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> commands for details.
|
|
|
|
|
Coefficients can also be set via the
|
|
|
|
|
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script.
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>Dihedrals</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per dihedral
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID type atom1 atom2 atom3 atom4
|
|
|
|
|
|
|
|
|
|
<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>
|
|
|
|
|
<LI>example:
|
|
|
|
|
|
|
|
|
|
<PRE> 12 4 17 29 30 21
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P>The 4 atoms are ordered linearly within the dihedral. The <I>Dihedrals</I>
|
|
|
|
|
section must appear after the <I>Atoms</I> section. All values in this
|
|
|
|
|
section must be integers (1, not 1.0).
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
2011-04-16 07:14:41 +08:00
|
|
|
<P><I>Ellipsoids</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per ellipsoid
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk
|
|
|
|
|
|
2013-01-26 08:32:41 +08:00
|
|
|
<PRE> atom-ID = ID of atom which is an ellipsoid
|
2011-04-16 07:14:41 +08:00
|
|
|
shapex,shapey,shapez = 3 diameters of ellipsoid (distance units)
|
2013-01-26 08:32:41 +08:00
|
|
|
quatw,quati,quatj,quatk = quaternion components for orientation of atom
|
|
|
|
|
</PRE>
|
|
|
|
|
<LI>example:
|
2011-04-16 07:14:41 +08:00
|
|
|
|
2011-10-20 06:43:40 +08:00
|
|
|
<PRE> 12 1 2 1 1 0 0 0
|
2011-04-16 07:14:41 +08:00
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P>The <I>Ellipsoids</I> section must appear if <A HREF = "atom_style.html">atom_style
|
|
|
|
|
ellipsoid</A> is used and any atoms are listed in the
|
|
|
|
|
<I>Atoms</I> 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 <I>quatw</I>, <I>quati</I>, <I>quatj</I>, and <I>quatk</I> 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 <I>Ellipsoids</I> section must appear after the <I>Atoms</I> section.
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
2006-09-22 00:22:34 +08:00
|
|
|
<P><I>EndBondTorsion Coeffs</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per dihedral type
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID coeffs
|
|
|
|
|
|
|
|
|
|
<PRE> ID = dihedral type (1-N)
|
|
|
|
|
coeffs = list of coeffs (see class 2 section of <A HREF = "dihedral_coeff.html">dihedral_coeff</A>)
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>Improper Coeffs</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per improper type
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID coeffs
|
|
|
|
|
|
|
|
|
|
<PRE> ID = improper type (1-N)
|
|
|
|
|
coeffs = list of coeffs
|
|
|
|
|
</PRE>
|
|
|
|
|
<LI>example:
|
|
|
|
|
|
|
|
|
|
<PRE> 2 20 0.0548311
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P>The number and meaning of the coefficients are specific to the defined
|
|
|
|
|
improper style. See the <A HREF = "improper_style.html">improper_style</A> and
|
|
|
|
|
<A HREF = "improper_coeff.html">improper_coeff</A> commands for details.
|
|
|
|
|
Coefficients can also be set via the
|
|
|
|
|
<A HREF = "improper_coeff.html">improper_coeff</A> command in the input script.
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>Impropers</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per improper
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID type atom1 atom2 atom3 atom4
|
|
|
|
|
|
|
|
|
|
<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>
|
|
|
|
|
<LI>example:
|
|
|
|
|
|
|
|
|
|
<PRE> 12 3 17 29 13 100
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
2007-06-28 04:56:05 +08:00
|
|
|
<P>The ordering of the 4 atoms determines the definition of the improper
|
|
|
|
|
angle used in the formula for each <A HREF = "improper_style.html">improper
|
|
|
|
|
style</A>. See the doc pages for individual styles
|
|
|
|
|
for details.
|
|
|
|
|
</P>
|
2006-09-22 00:22:34 +08:00
|
|
|
<P>The <I>Impropers</I> section must appear after the <I>Atoms</I> section. All
|
|
|
|
|
values in this section must be integers (1, not 1.0).
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
2011-10-20 23:01:56 +08:00
|
|
|
<P><I>Lines</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per line segment
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: atom-ID x1 y1 x2 y2
|
|
|
|
|
|
2013-01-26 08:32:41 +08:00
|
|
|
<PRE> atom-ID = ID of atom which is a line segment
|
2011-10-20 23:01:56 +08:00
|
|
|
x1,y1 = 1st end point
|
2013-01-26 08:32:41 +08:00
|
|
|
x2,y2 = 2nd end point
|
|
|
|
|
</PRE>
|
|
|
|
|
<LI>example:
|
2011-10-20 23:01:56 +08:00
|
|
|
|
|
|
|
|
<PRE> 12 1.0 0.0 2.0 0.0
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P>The <I>Lines</I> section must appear if <A HREF = "atom_style.html">atom_style line</A>
|
|
|
|
|
is used and any atoms are listed in the <I>Atoms</I> 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 <I>Lines</I> section must appear after the <I>Atoms</I> section.
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
2006-09-22 00:22:34 +08:00
|
|
|
<P><I>Masses</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per atom type
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID mass
|
|
|
|
|
|
|
|
|
|
<PRE> ID = atom type (1-N)
|
|
|
|
|
mass = mass value
|
|
|
|
|
</PRE>
|
|
|
|
|
<LI>example:
|
|
|
|
|
|
|
|
|
|
<PRE> 3 1.01
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P>This defines the mass of each atom type. This can also be set via the
|
2011-04-14 05:39:34 +08:00
|
|
|
<A HREF = "mass.html">mass</A> command in the input script. This section cannot be
|
|
|
|
|
used for atom styles that define a mass for individual atoms -
|
|
|
|
|
e.g. <A HREF = "atom_style.html">atom_style sphere</A>.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>MiddleBondTorsion Coeffs</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per dihedral type
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID coeffs
|
|
|
|
|
|
|
|
|
|
<PRE> ID = dihedral type (1-N)
|
|
|
|
|
coeffs = list of coeffs (see class 2 section of <A HREF = "dihedral_coeff.html">dihedral_coeff</A>)
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>Pair Coeffs</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per atom type
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID coeffs
|
|
|
|
|
|
|
|
|
|
<PRE> ID = atom type (1-N)
|
|
|
|
|
coeffs = list of coeffs
|
|
|
|
|
</PRE>
|
|
|
|
|
<LI>example:
|
|
|
|
|
|
|
|
|
|
<PRE> 3 0.022 2.35197 0.022 2.35197
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P>The number and meaning of the coefficients are specific to the defined
|
|
|
|
|
pair style. See the <A HREF = "pair_style.html">pair_style</A> and
|
2013-04-24 04:53:50 +08:00
|
|
|
<A HREF = "pair_coeff.html">pair_coeff</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 HREF = "pair_modify.html">pair_modify
|
|
|
|
|
mix</A> command for details. Pair coefficients can also
|
|
|
|
|
be set via the <A HREF = "pair_coeff.html">pair_coeff</A> command in the input
|
|
|
|
|
script.
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>PairIJ Coeffs</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per pair of atom types for all I,J with I <= J
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID1 ID2 coeffs
|
|
|
|
|
|
|
|
|
|
<PRE> ID1 = atom type I = 1-N
|
|
|
|
|
ID2 = atom type J = I-N, with I <= J
|
|
|
|
|
coeffs = list of coeffs
|
|
|
|
|
</PRE>
|
|
|
|
|
<LI>examples:
|
|
|
|
|
|
|
|
|
|
<PRE> 3 3 0.022 2.35197 0.022 2.35197
|
|
|
|
|
3 5 0.022 2.35197 0.022 2.35197
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<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 HREF = "pair_style.html">pair_style</A> and
|
|
|
|
|
<A HREF = "pair_coeff.html">pair_coeff</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 HREF = "pair_modify.html">pair_modify
|
|
|
|
|
mix</A> command for details. Pair coefficients can also
|
|
|
|
|
be set via the <A HREF = "pair_coeff.html">pair_coeff</A> command in the input
|
2006-09-22 00:22:34 +08:00
|
|
|
script.
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
2011-10-20 23:01:56 +08:00
|
|
|
<P><I>Triangles</I> section:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per triangle
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: atom-ID x1 y1 x2 y2
|
|
|
|
|
|
2013-01-26 08:32:41 +08:00
|
|
|
<PRE> atom-ID = ID of atom which is a line segment
|
2011-10-20 23:01:56 +08:00
|
|
|
x1,y1,z1 = 1st corner point
|
|
|
|
|
x2,y2,z2 = 2nd corner point
|
2013-01-26 08:32:41 +08:00
|
|
|
x3,y3,z3 = 3rd corner point
|
|
|
|
|
</PRE>
|
|
|
|
|
<LI>example:
|
2011-10-20 23:01:56 +08:00
|
|
|
|
|
|
|
|
<PRE> 12 0.0 0.0 0.0 2.0 0.0 1.0 0.0 2.0 1.0
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P>The <I>Triangles</I> section must appear if <A HREF = "atom_style.html">atom_style
|
|
|
|
|
tri</A> is used and any atoms are listed in the <I>Atoms</I>
|
|
|
|
|
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 <I>Triangles</I> section must appear after the <I>Atoms</I> section.
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
2006-09-22 00:22:34 +08:00
|
|
|
<P><I>Velocities</I> section:
|
|
|
|
|
</P>
|
2007-03-06 23:13:57 +08:00
|
|
|
<UL><LI>one line per atom
|
|
|
|
|
<LI>line syntax: depends on atom style
|
2006-09-22 00:22:34 +08:00
|
|
|
</UL>
|
2010-05-02 08:59:55 +08:00
|
|
|
<DIV ALIGN=center><TABLE BORDER=1 >
|
2007-04-20 07:25:27 +08:00
|
|
|
<TR><TD >all styles except those listed</TD><TD > atom-ID vx vy vz</TD></TR>
|
2012-02-07 23:13:31 +08:00
|
|
|
<TR><TD >electron</TD><TD > atom-ID vx vy vz ervel</TD></TR>
|
2007-04-20 07:25:27 +08:00
|
|
|
<TR><TD >ellipsoid</TD><TD > atom-ID vx vy vz lx ly lz</TD></TR>
|
2012-06-07 23:02:09 +08:00
|
|
|
<TR><TD >sphere</TD><TD > atom-ID vx vy vz wx wy wz</TD></TR>
|
|
|
|
|
<TR><TD >hybrid</TD><TD > atom-ID vx vy vz sub-style1 sub-style2 ...
|
2007-03-06 23:13:57 +08:00
|
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
|
|
2007-04-20 07:25:27 +08:00
|
|
|
<P>where the keywords have these meanings:
|
|
|
|
|
</P>
|
2011-02-23 06:29:54 +08:00
|
|
|
<P>vx,vy,vz = translational velocity of atom
|
|
|
|
|
lx,ly,lz = angular momentum of aspherical atom
|
2011-04-14 05:39:34 +08:00
|
|
|
wx,wy,wz = angular velocity of spherical atom
|
2012-02-07 23:13:31 +08:00
|
|
|
ervel = electron radial velocity (0 for fixed-core):ul
|
2011-02-23 06:29:54 +08:00
|
|
|
</P>
|
2006-09-22 00:22:34 +08:00
|
|
|
<P>The velocity lines can appear in any order. This section can only be
|
2007-04-20 07:25:27 +08:00
|
|
|
used after an <I>Atoms</I> section. This is because the <I>Atoms</I> section
|
|
|
|
|
must have assigned a unique atom ID to each atom so that velocities
|
|
|
|
|
can be assigned to them.
|
|
|
|
|
</P>
|
2012-02-07 23:13:31 +08:00
|
|
|
<P>Vx, vy, vz, and ervel are in <A HREF = "units.html">units</A> of velocity. Lx, ly,
|
2010-08-21 04:47:28 +08:00
|
|
|
lz are in units of angular momentum (distance-velocity-mass). Wx, Wy,
|
|
|
|
|
Wz are in units of angular velocity (radians/time).
|
2007-03-06 23:13:57 +08:00
|
|
|
</P>
|
2012-06-07 23:02:09 +08:00
|
|
|
<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 HREF = "atom_style.html">atom_style</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>
|
|
|
|
|
<PRE>atom_style hybrid electron sphere
|
|
|
|
|
</PRE>
|
|
|
|
|
<P>were used in the input script, each velocity line would have these
|
|
|
|
|
fields:
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>atom-ID vx vy vz ervel wx wy wz
|
|
|
|
|
</PRE>
|
2007-03-06 23:13:57 +08:00
|
|
|
<P>Translational velocities can also be set by the
|
|
|
|
|
<A HREF = "velocity.html">velocity</A> command in the input script.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><B>Restrictions:</B>
|
|
|
|
|
</P>
|
2008-01-18 07:46:30 +08:00
|
|
|
<P>To read gzipped data files, you must compile LAMMPS with the
|
2011-08-26 00:46:23 +08:00
|
|
|
-DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#start_2">Making
|
|
|
|
|
LAMMPS</A> section of the documentation.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
2012-06-02 00:41:20 +08:00
|
|
|
<P><A HREF = "read_dump.html">read_dump</A>, <A HREF = "read_restart.html">read_restart</A>,
|
2013-04-04 01:06:31 +08:00
|
|
|
<A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "write_data.html">write_data</A>
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B> none
|
|
|
|
|
</P>
|
|
|
|
|
</HTML>
|
