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
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</PRE>
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<UL><LI>file = name of data file to read in
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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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read_data ../run7/data.polymer.gz
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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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</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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of a section has only a keyword. The next line is skipped. The
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remaining lines of the section contain values. The number of lines
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depends on the section keyword as described below. Zero or more blank
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lines can be used between sections. Sections can appear in any order,
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with a few exceptions as noted below.
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</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 "Bond" and "Coeffs" is not
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valid.
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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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<LI><I>extra bond per atom</I> = leave space for this many new bonds per atom
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<LI><I>ellipsoids</I> = # of ellipsoids in system
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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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<LI><I>zlo zhi</I> = simulation box boundaries in z dimension
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<LI><I>xy xz yz</I> = simulation box tilt factors for triclinic system
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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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<A HREF = "boundary.html">boundary</A> command.
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</P>
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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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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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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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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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2011-08-26 01:01:01 +08:00
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<P>See <A HREF = "Section_howto.html#howto_12">this section</A> of the doc pages for a
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geometric description of triclinic boxes, as defined by LAMMPS, and
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2010-10-15 07:31:42 +08:00
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how to transform these parameters to and from other commonly used
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triclinic representations.
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</P>
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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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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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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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and yz tilt factors must be 0.0.
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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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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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</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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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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shrink-wraps the box around the atoms.
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</P>
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<P>The "extra bond per atom" setting should be used if new bonds will be
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added to the system when a simulation runs, e.g. by using the <A HREF = "fix_bond_create.html">fix
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bond/create</A> command. This will pre-allocate
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space in LAMMPS data structures for storing the new bonds.
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</P>
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2011-04-16 07:14:41 +08:00
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<P>The "ellipsoids<A HREF = "atom_style.html"> setting is only used with atom_style
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ellipsoid</A> and specifies how many of the atoms are
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finite-size ellipsoids; the remainder are point particles. See the
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discussion of ellipsoidflag and the <I>Ellipsoids</I> section below.
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</P>
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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>
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<UL><LI><I>Atoms, Velocities, Ellipsoids, Masses</I> = atom-property sections
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<LI><I>Bonds, Angles, Dihedrals, Impropers</I> = molecular topology sections
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<LI><I>Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs</I> = force field sections
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<LI><I>BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs</I> = class 2 force field sections
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</UL>
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<P>Each section is listed below in alphabetic order. The format of each
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section is described including the number of lines it must contain and
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rules (if any) for where it can appear in the data file.
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</P>
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<P>Any individual line in the various sections can have a trailing
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comment starting with "#" for annotation purposes. E.g. in the
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Atoms section:
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</P>
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<PRE>10 1 17 -1.0 10.0 5.0 6.0 # salt ion
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</PRE>
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<HR>
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<P><I>Angle Coeffs</I> section:
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</P>
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<UL><LI>one line per angle type
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<LI>line syntax: ID coeffs
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<PRE> ID = angle type (1-N)
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coeffs = list of coeffs
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</PRE>
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<LI>example:
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<PRE> 6 70 108.5 0 0
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</PRE>
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</UL>
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<P>The number and meaning of the coefficients are specific to the defined
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angle style. See the <A HREF = "angle_style.html">angle_style</A> and
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<A HREF = "angle_coeff.html">angle_coeff</A> commands for details. Coefficients can
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also be set via the <A HREF = "angle_coeff.html">angle_coeff</A> command in the
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input script.
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</P>
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<HR>
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<P><I>AngleAngle Coeffs</I> section:
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</P>
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<UL><LI>one line per improper type
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<LI>line syntax: ID coeffs
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<PRE> ID = improper type (1-N)
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coeffs = list of coeffs (see <A HREF = "improper_coeff.html">improper_coeff</A>)
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</PRE>
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</UL>
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<HR>
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<P><I>AngleAngleTorsion Coeffs</I> section:
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</P>
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<UL><LI>one line per dihedral type
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<LI>line syntax: ID coeffs
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<PRE> ID = dihedral type (1-N)
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coeffs = list of coeffs (see <A HREF = "dihedral_coeff.html">dihedral_coeff</A>)
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</PRE>
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</UL>
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<HR>
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<P><I>Angles</I> section:
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</P>
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<UL><LI>one line per angle
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<LI>line syntax: ID type atom1 atom2 atom3
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<PRE> ID = number of angle (1-Nangles)
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type = angle type (1-Nangletype)
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atom1,atom2,atom3 = IDs of 1st,2nd,3rd atoms in angle
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</PRE>
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example:
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<BR>
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<PRE> 2 2 17 29 430
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</PRE>
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</UL>
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<P>The 3 atoms are ordered linearly within the angle. Thus the central
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atom (around which the angle is computed) is the atom2 in the list.
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E.g. H,O,H for a water molecule. The <I>Angles</I> section must appear
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after the <I>Atoms</I> section. All values in this section must be
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integers (1, not 1.0).
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</P>
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<HR>
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<P><I>AngleTorsion Coeffs</I> section:
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</P>
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<UL><LI>one line per dihedral type
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|
|
|
<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>
|
|
|
|
|
<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>
|
2011-08-28 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>
|
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
|
2008-07-25 07:46:15 +08:00
|
|
|
<LI>density = density of atom (mass/distance^3 units)
|
|
|
|
|
<LI>volume = volume of atom (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
|
|
|
|
|
map array is used (see the <A HREF = "atom_modify.html">atom_modify</A> command).
|
|
|
|
|
If an atom map array is not used (e.g. an atomic system with no
|
2011-04-14 05:39:34 +08:00
|
|
|
bonds), and velocities are not assigned in the data file, 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>
|
2011-10-20 06:43:40 +08:00
|
|
|
<P>The ellipsoidflag determines whether the particle is a finite-size
|
2011-04-16 07:14:41 +08:00
|
|
|
ellipsoid of finite size, or a point particle. Additional attributes
|
|
|
|
|
must be defined for each ellipsoid in the <I>Ellipsoids</I> section.
|
2011-04-14 05:39:34 +08:00
|
|
|
</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>The density is used in conjunction with the particle volume for
|
|
|
|
|
finite-size particles to set the mass of the particle as mass =
|
|
|
|
|
density * volume. If the volume is 0.0, meaning a point particle,
|
|
|
|
|
then the density value is used as the mass.
|
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>
|
2007-12-12 07:28:43 +08:00
|
|
|
<P>Atom lines (all lines or none of them) can optionally list 3 trailing
|
2007-02-10 05:37:30 +08:00
|
|
|
integer values: nx,ny,nz. For periodic dimensions, they specify which
|
2008-08-20 23:23:00 +08:00
|
|
|
image of the simulation box the atom is considered to be in. An image
|
|
|
|
|
of 0 means it is inside the box as defined. A value of 2 means add 2
|
|
|
|
|
box lengths to get the true value. A value of -1 means subtract 1 box
|
|
|
|
|
length to get the true value. LAMMPS updates these flags as atoms
|
|
|
|
|
cross periodic boundaries during the simulation. The flags can be
|
|
|
|
|
output with atom snapshots via the <A HREF = "dump.html">dump</A> command.
|
2007-12-12 07:28:43 +08:00
|
|
|
</P>
|
|
|
|
|
<P>If nx,ny,nz values are not set in the data file, LAMMPS initializes
|
|
|
|
|
them to 0. If image information is needed for later analysis and they
|
|
|
|
|
are not all initially 0, it's important to set them correctly in the
|
|
|
|
|
data file. Also, if you plan to use the <A HREF = "replicate.html">replicate</A>
|
|
|
|
|
command to generate a larger system, these flags must be listed
|
|
|
|
|
correctly 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.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
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>
|
|
|
|
|
|
|
|
|
|
<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
|
|
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<P><I>Ellipsoids</I> section:
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</P>
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<UL><LI>one line per ellipsoid
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<LI>line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk
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|
2011-10-20 06:43:40 +08:00
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<LI> atom-ID = ID of atom which is an ellipsoid
|
2011-04-16 07:14:41 +08:00
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shapex,shapey,shapez = 3 diameters of ellipsoid (distance units)
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quatw,quati,quatj,quatk = quaternion components for orientation of atom
|
2011-10-20 06:43:40 +08:00
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example:
|
2011-04-16 07:14:41 +08:00
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2011-10-20 06:43:40 +08:00
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<PRE> 12 1 2 1 1 0 0 0
|
2011-04-16 07:14:41 +08:00
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</PRE>
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</UL>
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<P>The <I>Ellipsoids</I> section must appear if <A HREF = "atom_style.html">atom_style
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ellipsoid</A> is used and any atoms are listed in the
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<I>Atoms</I> section with an ellipsoidflag = 1. The number of ellipsoids
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should be specified in the header section via the "ellipsoids"
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keyword.
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</P>
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<P>The 3 shape values specify the 3 diameters or aspect ratios of a
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finite-size ellipsoidal particle, when it is oriented along the 3
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coordinate axes. They must all be non-zero values.
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</P>
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<P>The values <I>quatw</I>, <I>quati</I>, <I>quatj</I>, and <I>quatk</I> set the orientation
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of the atom as a quaternion (4-vector). Note that the shape
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attributes specify the aspect ratios of an ellipsoidal particle, which
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is oriented by default with its x-axis along the simulation box's
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x-axis, and similarly for y and z. If this body is rotated (via the
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right-hand rule) by an angle theta around a unit vector (a,b,c), then
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the quaternion that represents its new orientation is given by
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(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These
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4 components are quatw, quati, quatj, and quatk as specified above.
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LAMMPS normalizes each atom's quaternion in case (a,b,c) is not
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specified as a unit vector.
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</P>
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<P>The <I>Ellipsoids</I> section must appear after the <I>Atoms</I> section.
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</P>
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<HR>
|
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|
2006-09-22 00:22:34 +08:00
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<P><I>EndBondTorsion Coeffs</I> section:
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</P>
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<UL><LI>one line per dihedral type
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|
<LI>line syntax: ID coeffs
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<PRE> ID = dihedral type (1-N)
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coeffs = list of coeffs (see class 2 section of <A HREF = "dihedral_coeff.html">dihedral_coeff</A>)
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|
</PRE>
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</UL>
|
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|
<HR>
|
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<P><I>Improper Coeffs</I> section:
|
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|
|
</P>
|
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|
|
<UL><LI>one line per improper type
|
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|
|
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|
|
|
|
<LI>line syntax: ID coeffs
|
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|
<PRE> ID = improper type (1-N)
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|
|
coeffs = list of coeffs
|
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|
|
</PRE>
|
|
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|
|
<LI>example:
|
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|
<PRE> 2 20 0.0548311
|
|
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|
|
</PRE>
|
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|
|
|
|
|
|
|
</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.
|
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|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P><I>Impropers</I> section:
|
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|
|
|
</P>
|
|
|
|
|
<UL><LI>one line per improper
|
|
|
|
|
|
|
|
|
|
<LI>line syntax: ID type atom1 atom2 atom3 atom4
|
|
|
|
|
|
|
|
|
|
<PRE> ID = number of improper (1-Nimpropers)
|
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|
|
|
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>
|
|
|
|
|
|
|
|
|
|
<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
|
|
|
|
|
<A HREF = "pair_coeff.html">pair_coeff</A> commands for details. Coefficients can
|
|
|
|
|
also be set via the <A HREF = "pair_coeff.html">pair_coeff</A> command in the input
|
|
|
|
|
script.
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<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>
|
2007-06-20 20:56:17 +08:00
|
|
|
<TR><TD >dipole</TD><TD > atom-ID vx vy vz wx wy wz</TD></TR>
|
2010-08-21 04:47:28 +08:00
|
|
|
<TR><TD >electron</TD><TD > atom-ID vx vy vz evel</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>
|
2011-04-14 05:39:34 +08:00
|
|
|
<TR><TD >sphere</TD><TD > atom-ID vx vy vz wx wy wz
|
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
|
2011-02-23 06:29:54 +08:00
|
|
|
evel = electron radial velocity (0 for fixed-core):ul
|
|
|
|
|
</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>
|
2010-08-21 04:47:28 +08:00
|
|
|
<P>Vx, vy, vz, and evel are in <A HREF = "units.html">units</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).
|
2007-03-06 23:13:57 +08:00
|
|
|
</P>
|
|
|
|
|
<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>
|
|
|
|
|
<P><A HREF = "read_restart.html">read_restart</A>, <A HREF = "create_atoms.html">create_atoms</A>
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B> none
|
|
|
|
|
</P>
|
|
|
|
|
</HTML>
|
