forked from lijiext/lammps
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HTML
580 lines
17 KiB
HTML
<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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any order. The value(s) is read from the beginning of the line. Thus
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the keyword <I>atoms</I> should be in a line like "1000 atoms" and the
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keyword <I>ylo yhi</I> should be in a line like "-10.0 10.0 ylo yhi". All
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these settings have a default value of 0, except the lo/hi box size
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defaults are -0.5 and 0.5. A line need only appear if the value is
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different than the default.
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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>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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</UL>
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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.
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</P>
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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 system is non-periodic (in a dimension), then all atoms in the
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data file should have coordinates (in that dimension) between the lo
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and hi values. Furthermore, if running in parallel, the lo/hi values
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should be just a bit smaller/larger than the min/max extent of 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. Since LAMMPS uses the specified
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box size to layout the 3d grid of processors, this will be sub-optimal
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and may cause a parallel simulation to lose atoms when LAMMPS
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shrink-wraps the box to the atoms.
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</P>
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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; they will be remapped (in a periodic sense)
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back inside the box.
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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, Masses, Dipoles</I> = atom-property sections
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<LI><I>Bonds, Angles, Dihedrals, Impropers</I> = molecular topolgy 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 now listed 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
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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>Atoms</I> section:
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</P>
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<UL><LI>one line per atom
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<LI>line syntax: depends on atom style
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</UL>
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<P>An <I>Atoms</I> section must appear in the data file if natoms > 0 in the
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header section. The atoms can be listed in any order. These are the
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line formats for each <A HREF = "atom_style.html">atom style</A> in LAMMPS:
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</P>
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<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
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<TR><TD >angle</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
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<TR><TD >atomic</TD><TD > atom-ID atom-type x y z</TD></TR>
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<TR><TD >bond</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
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<TR><TD >charge</TD><TD > atom-ID atom-type q x y z</TD></TR>
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<TR><TD >dpd</TD><TD > atom-ID atom-type x y z</TD></TR>
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<TR><TD >full</TD><TD > atom-ID molecule-ID atom-type q x y z</TD></TR>
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<TR><TD >granular</TD><TD > atom-ID atom-type diameter density x y z</TD></TR>
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<TR><TD >molecular</TD><TD > atom-ID molecule-ID atom-type x y z
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</TD></TR></TABLE></DIV>
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<P>where the keywords have these meanings:
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</P>
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<UL><LI>atom-ID = integer ID of atom
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<LI>molecule-ID = integer ID of molecule the atom belongs to
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<LI>type-ID = type of atom (1-Ntype)
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<LI>q = charge on atom
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<LI>diameter = diameter of atom
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<LI>density = density of atom
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<LI>x,y,z = coordinates of atom
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</UL>
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<P>The units for these quantities depend on the unit style; see the
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<A HREF = "units.html">units</A> command for details.
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</P>
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<P>For 2d simulations specify z as 0.0, or a value is within the <I>zlo
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zhi</I> setting in the data file header.
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</P>
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<P>The atom-ID is used to identify the atom throughout the simulation and
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in dump files. Normally, it is a unique value from 1 to Natoms for
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each atom. Unique values larger than Natoms can be used, but they
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will cause extra memory to be allocated on each processor, if an atom
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map array is used (see the <A HREF = "atom_modify.html">atom_modify</A> command).
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If an atom map array is not used (e.g. an atomic system with no
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bonds), velocities are not assigned in the data file, and you don't
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care if unique atom IDs appear in dump files, then the atom-IDs can all
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be set to 0.
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</P>
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<P>The molecule ID is a 2nd identifier attached to an atom. Normally, it
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is a number from 1 to N, identifying which molecule the atom belongs
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to. It can be 0 if it is an unbonded atom or if you don't care to
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keep track of molecule assignments.
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</P>
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<P>Atom lines (all lines or none of them) can optionally list 3 final
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integer values: nx,ny,nz. For periodic dimensions, they specify which
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image of the box the atom is considered to be in. An image of 0 means
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the box as defined. A value of 2 means add 2 box lengths to get the
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true value. A value of -1 means subtract 1 box length to get the true
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value. LAMMPS updates these flags as atoms cross periodic boundaries
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during the simulation. The flags can be output with atom snapshots
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via the <A HREF = "dump.html">dump</A> command. If nx,ny,nz values are not set in
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the data file, LAMMPS initializes them to 0.
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</P>
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<P>Atom velocities are set to 0.0 when the <I>Atoms</I> section is read. They
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may later be set by a <I>Velocities</I> section in the data file or by a
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<A HREF = "velocity.html">velocity</A> command in the input script.
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</P>
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<HR>
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<P><I>Bond Coeffs</I> section:
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</P>
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<UL><LI>one line per bond type
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<LI>line syntax: ID coeffs
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<PRE> ID = bond 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> 4 250 1.49
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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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bond style. See the <A HREF = "bond_style.html">bond_style</A> and
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<A HREF = "bond_coeff.html">bond_coeff</A> commands for details. Coefficients can
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also be set via the <A HREF = "bond_coeff.html">bond_coeff</A> command in the input
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script.
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</P>
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<HR>
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<P><I>BondAngle 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 (see class 2 section of <A HREF = "angle_coeff.html">angle_coeff</A>)
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</PRE>
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</UL>
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<HR>
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<P><I>BondBond 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 (see class 2 section of <A HREF = "angle_coeff.html">angle_coeff</A>)
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</PRE>
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</UL>
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<HR>
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<P><I>BondBond13 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>Bonds</I> section:
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</P>
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<UL><LI>one line per bond
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<LI>line syntax: ID type atom1 atom2
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<PRE> ID = bond number (1-Nbonds)
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type = bond type (1-Nbondtype)
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atom1,atom2 = IDs of 1st,2nd atoms in bond
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</PRE>
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<LI>example:
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<PRE> 12 3 17 29
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</PRE>
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</UL>
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<P>The <I>Bonds</I> section must appear after the <I>Atoms</I> section. All values
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in this section must be integers (1, not 1.0).
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</P>
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<HR>
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<P><I>Dihedral 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
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</PRE>
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<LI>example:
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<PRE> 3 0.6 1 0 1
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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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dihedral style. See the <A HREF = "dihedral_style.html">dihedral_style</A> and
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<A HREF = "dihedral_coeff.html">dihedral_coeff</A> commands for details.
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Coefficients can also be set via the
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<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command in the input script.
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</P>
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<HR>
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<P><I>Dihedrals</I> section:
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</P>
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<UL><LI>one line per dihedral
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<LI>line syntax: ID type atom1 atom2 atom3 atom4
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<PRE> ID = number of dihedral (1-Ndihedrals)
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type = dihedral type (1-Ndihedraltype)
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atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in dihedral
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</PRE>
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<LI>example:
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<PRE> 12 4 17 29 30 21
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</PRE>
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</UL>
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<P>The 4 atoms are ordered linearly within the dihedral. The <I>Dihedrals</I>
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section must appear after the <I>Atoms</I> section. All values in this
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section must be integers (1, not 1.0).
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</P>
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<HR>
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<P><I>Dipoles</I> section:
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</P>
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<UL><LI>one line per atom type
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line syntax: ID dipole-moment
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<PRE> ID = atom type (1-N)
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dipole-moment = value of dipole moment
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</PRE>
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<LI>example:
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<PRE> 2 0.5
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</PRE>
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</UL>
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<P>This defines the dipole moment of each atom type (which can be 0.0 for
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some types). This can also be set via the <A HREF = "dipole.html">dipole</A>
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command in the input script.
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</P>
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<HR>
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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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<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>
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<P>The number and meaning of the coefficients are specific to the defined
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improper style. See the <A HREF = "improper_style.html">improper_style</A> and
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<A HREF = "improper_coeff.html">improper_coeff</A> commands for details.
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Coefficients can also be set via the
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|
<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>
|
|
<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
|
|
<A HREF = "mass.html">mass</A> command in the input script. This section should not
|
|
be used for atom styles that define a mass for individual atoms -
|
|
e.g. atom style granular.
|
|
</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>
|
|
<UL>one line per atom
|
|
|
|
<LI>line syntax: atom-ID vx vy vz
|
|
|
|
<PRE> atom-ID = integer ID of atom to assign velocity to
|
|
vx,vy,vz = components of velocity of the atom
|
|
</PRE>
|
|
<LI>example:
|
|
|
|
<PRE> 45 -3.4 0.05 1.25
|
|
</PRE>
|
|
|
|
</UL>
|
|
<P>The velocity lines can appear in any order. This section can only be
|
|
used after an <I>Atoms</I> section. The <I>Atoms</I> section must have assigned
|
|
a unique atom ID to each atom so that velocities can be assigned in
|
|
this way. Velocities can also be set by the <A HREF = "velocity.html">velocity</A>
|
|
command in the input script.
|
|
</P>
|
|
<HR>
|
|
|
|
<P><B>Restrictions:</B>
|
|
</P>
|
|
<P>To read gzipped data files, you must compile LAMMPS with the -DGZIP
|
|
option - see the <A HREF = "Section_start.html#2_2">Making LAMMPS</A> section of the
|
|
documentation.
|
|
</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>
|