forked from lijiext/lammps
251 lines
7.9 KiB
HTML
251 lines
7.9 KiB
HTML
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
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<HTML>
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<HEAD>
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<META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
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</HEAD>
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<BODY>
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<H2>
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LAMMPS Data Format</H2>
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<P>
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<A HREF="README.html">Return</A> to top-level of LAMMPS documentation</P>
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<P>
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This file describes the format of the data file read into LAMMPS with
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the "read data" command. The data file contains basic
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information about the size of the problem to be run, the initial atomic
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coordinates, molecular topology, and (optionally) force-field
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coefficients. It will be easiest to understand this file if you read it
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while looking at a sample data file from the examples.</P>
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<P>
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This page has 2 sections:</P>
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<UL>
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<LI>
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<A HREF="#_cch3_930958962">Rules for formatting the Data File</A>
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<LI>
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<A HREF="#_cch3_930958969">Sample file with Annotations</A>
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</UL>
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<HR>
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<H3>
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<A NAME="_cch3_930958962">Rules for formatting the Data File: </A></H3>
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<P>
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Blank lines are important. After the header section, new entries are
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separated by blank lines. </P>
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<P>
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Indentation and space between words/numbers on one line is not
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important except that keywords (e.g. Masses, Bond Coeffs) must be
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left-justified and capitalized as shown. </P>
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<P>
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The header section (thru box bounds) must appear first in the file, the
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remaining entries (Masses, various Coeffs, Atoms, Bonds, etc) can come
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in any order. </P>
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<P>
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These entries must be in the file: header section, Masses, Atoms. </P>
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<P>
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These entries must be in the file if there are a non-zero number of
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them: Bonds, Angles, Dihedrals, Impropers. Force field coefficients
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can be specified in the input script, so do not have to appear in the
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data file. The one exception to this is class 2 force field
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coefficients which can only be specified in the data file.
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<P>
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The Nonbond Coeffs entry contains one line for each atom type. These
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are the coefficients for an interaction between 2 atoms of the same
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type. The cross-type coeffs are computed by the appropriate class I or
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class II mixing rules, or can be specified explicitly using the
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"nonbond coeff" command in the input command script. See the <A
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HREF="force_fields.html">force_fields</A> page for more information. </P>
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<P>
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In the Atoms entry, the atoms can be in any order so long as there are
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N entries. The 1st number on the line is the atom-tag (number from 1 to
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N) which is used to identify the atom throughout the simulation. The
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molecule-tag is a second identifier which is attached to the atom; it
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can be 0, or a counter for the molecule the atom is part of, or any
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other number you wish. The q value is the charge of the atom in
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electron units (e.g. +1 for a proton). The xyz values are the initial
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position of the atom. For 2-d simulations specify z as 0.0.</P>
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<P>
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The final 3 nx,ny,nz values on a line of the Atoms entry are optional.
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LAMMPS only reads them if the "true flag" command is
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specified in the input command script. Otherwise they are initialized
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to 0 by LAMMPS. Their meaning, for each dimension, is that
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"n" box-lengths are added to xyz to get the atom's
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"true" un-remapped position. This can be useful in pre- or
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post-processing to enable the unwrapping of long-chained molecules
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which wind thru the periodic box one or more times. The value of
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"n" can be positive, negative, or zero. For 2-d simulations
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specify nz as 0. </P>
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<P>
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Atom velocities are initialized to 0.0 if there is no Velocities entry.
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In the Velocities entry, the atoms can be in any order so long as there
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are N entries. The 1st number on the line is the atom-tag (number from
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1 to N) which is used to identify the atom which the given velocity
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will be assigned to.</P>
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<P>
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Entries for Velocities, Bonds, Angles, Dihedrals, Impropers must appear
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in the file after an Atoms entry.</P>
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<P>
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For simulations with periodic boundary conditions, xyz coords are
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remapped into the periodic box (from as far away as needed), so the
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initial coordinates need not be inside the box. The nx,ny,nz values
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(as read in or as set to zero by LAMMPS) are appropriately adjusted by
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this remapping. </P>
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<P>
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The number of coefficients specified on each line of coefficient
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entries (Nonbond Coeffs, Bond Coeffs, etc) depends on the
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"style" of interaction. This must be specified in the input
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command script before the "read data" command is issued, unless the
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default is used. See the <A
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HREF="input_commands.html">input_commands</A> page for a description
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of the various style options. The <A HREF="input_commands.html">input_commands</A>
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and <A HREF="force_fields.html">force_fields</A> pages explain the
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meaning and valid values for each of the coefficients. </P>
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<HR>
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<H3>
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<A NAME="_cch3_930958969">Sample file with Annotations</A></H3>
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<P>
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Here is a sample file with annotations in parenthesis and lengthy
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sections replaced by dots (...). Note that the blank lines are
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important in this example.</P>
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<PRE>
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LAMMPS Description (1st line of file)
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100 atoms (this must be the 3rd line, 1st 2 lines are ignored)
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95 bonds (# of bonds to be simulated)
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50 angles (include these lines even if number = 0)
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30 dihedrals
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20 impropers
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5 atom types (# of nonbond atom types)
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10 bond types (# of bond types = sets of bond coefficients)
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18 angle types
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20 dihedral types (do not include a bond,angle,dihedral,improper type
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2 improper types line if number of bonds,angles,etc is 0)
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-0.5 0.5 xlo xhi (for periodic systems this is box size,
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-0.5 0.5 ylo yhi for non-periodic it is min/max extent of atoms)
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-0.5 0.5 zlo zhi (do not include this line for 2-d simulations)
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Masses
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1 mass
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...
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N mass (N = # of atom types)
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Nonbond Coeffs
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1 coeff1 coeff2 ...
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...
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N coeff1 coeff2 ... (N = # of atom types)
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Bond Coeffs
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1 coeff1 coeff2 ...
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...
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N coeff1 coeff2 ... (N = # of bond types)
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Angle Coeffs
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1 coeff1 coeff2 ...
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...
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N coeff1 coeff2 ... (N = # of angle types)
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Dihedral Coeffs
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1 coeff1 coeff2 ...
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...
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N coeff1 coeff2 ... (N = # of dihedral types)
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Improper Coeffs
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1 coeff1 coeff2 ...
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...
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N coeff1 coeff2 ... (N = # of improper types)
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BondBond Coeffs
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1 coeff1 coeff2 ...
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...
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N coeff1 coeff2 ... (N = # of angle types)
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BondAngle Coeffs
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1 coeff1 coeff2 ...
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...
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N coeff1 coeff2 ... (N = # of angle types)
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MiddleBondTorsion Coeffs
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1 coeff1 coeff2 ...
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...
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N coeff1 coeff2 ... (N = # of dihedral types)
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EndBondTorsion Coeffs
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1 coeff1 coeff2 ...
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...
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N coeff1 coeff2 ... (N = # of dihedral types)
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AngleTorsion Coeffs
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1 coeff1 coeff2 ...
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...
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N coeff1 coeff2 ... (N = # of dihedral types)
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AngleAngleTorsion Coeffs
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1 coeff1 coeff2 ...
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...
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N coeff1 coeff2 ... (N = # of dihedral types)
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BondBond13 Coeffs
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1 coeff1 coeff2 ...
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...
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N coeff1 coeff2 ... (N = # of dihedral types)
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AngleAngle Coeffs
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1 coeff1 coeff2 ...
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...
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N coeff1 coeff2 ... (N = # of improper types)
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Atoms
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1 molecule-tag atom-type q x y z nx ny nz (nx,ny,nz are optional -
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... see "true flag" input command)
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...
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N molecule-tag atom-type q x y z nx ny nz (N = # of atoms)
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Velocities
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1 vx vy vz
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...
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...
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N vx vy vz (N = # of atoms)
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Bonds
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1 bond-type atom-1 atom-2
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...
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N bond-type atom-1 atom-2 (N = # of bonds)
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Angles
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1 angle-type atom-1 atom-2 atom-3 (atom-2 is the center atom in angle)
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...
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N angle-type atom-1 atom-2 atom-3 (N = # of angles)
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Dihedrals
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1 dihedral-type atom-1 atom-2 atom-3 atom-4 (atoms 2-3 form central bond)
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...
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N dihedral-type atom-1 atom-2 atom-3 atom-4 (N = # of dihedrals)
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Impropers
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1 improper-type atom-1 atom-2 atom-3 atom-4 (atom-2 is central atom)
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...
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N improper-type atom-1 atom-2 atom-3 atom-4 (N = # of impropers)
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</PRE>
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