forked from lijiext/lammps
738 lines
27 KiB
Plaintext
738 lines
27 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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read_data command :h3
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[Syntax:]
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read_data file keyword args ... :pre
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file = name of data file to read in :ulb,l
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zero or more keyword/arg pairs may be appended :l
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keyword = {fix} :l
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{fix} args = fix-ID header-string section-string
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fix-ID = ID of fix to process header lines and sections of data file
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header-string = header lines containing this string will be passed to fix
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section-string = section names with this string will be passed to fix :pre
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:ule
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[Examples:]
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read_data data.lj
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read_data ../run7/data.polymer.gz
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read_data data.protein fix mycmap crossterm CMAP :pre
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[Description:]
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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 "read_restart"_read_restart.html and
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"create_atoms"_create_atoms.html commands for alternative methods.
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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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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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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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If the keyword {fix} is used, it specifies a fix that will be used to
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process portions of the data file. Any header line containing
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{header-string} and any section with a name containing
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{section-string} will be passed to the fix. See the "fix
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cmap"_fix_cmap.html command for an example of a fix that operates in
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this manner. The doc page for the fix defines the syntax of the
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header line(s) and section(s) that it reads from the data file.
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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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:line
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These are the recognized header keywords. Header lines can come in
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any order. The value(s) are read from the beginning of the line.
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Thus the keyword {atoms} should be in a line like "1000 atoms"; the
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keyword {ylo yhi} should be in a line like "-10.0 10.0 ylo yhi"; the
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keyword {xy xz yz} 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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{atoms} = # of atoms in system
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{bonds} = # of bonds in system
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{angles} = # of angles in system
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{dihedrals} = # of dihedrals in system
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{impropers} = # of impropers in system
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{atom types} = # of atom types in system
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{bond types} = # of bond types in system
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{angle types} = # of angle types in system
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{dihedral types} = # of dihedral types in system
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{improper types} = # of improper types in system
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{extra bond per atom} = leave space for this many new bonds per atom
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{ellipsoids} = # of ellipsoids in system
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{lines} = # of line segments in system
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{triangles} = # of triangles in system
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{xlo xhi} = simulation box boundaries in x dimension
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{ylo yhi} = simulation box boundaries in y dimension
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{zlo zhi} = simulation box boundaries in z dimension
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{xy xz yz} = simulation box tilt factors for triclinic system :ul
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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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"boundary"_boundary.html command.
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If the {xy xz yz} 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). {Xy,xz,yz} 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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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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See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages
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for a geometric description of triclinic boxes, as defined by LAMMPS,
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and how to transform these parameters to and from other commonly used
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triclinic representations.
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When a triclinic system is used, the simulation domain must be
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periodic in any dimensions with a non-zero tilt factor, as defined by
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the "boundary"_boundary.html 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 "fix deform"_fix_deform.html 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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For 2d simulations, the {zlo zhi} 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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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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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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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 "boundary"_boundary.html 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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(mostly empty) box will be sub-optimal for performance when using
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"fixed" boundary conditions (see the "boundary"_boundary.html
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command). When using "shrink-wrap" boundary conditions (see the
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"boundary"_boundary.html 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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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 "fix
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bond/create"_fix_bond_create.html command. This will pre-allocate
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space in LAMMPS data structures for storing the new bonds.
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The "ellipsoids" and "lines" and "triangles" settings are only used
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with "atom_style ellipsoid or line or tri"_atom_style.html and
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specifies how many of the atoms are finite-size ellipsoids or lines or
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triangles; the remainder are point particles. See the discussion of
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ellipsoidflag and the {Ellipsoids} section below. See the discussion
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of lineflag and the {Lines} section below. See the discussion of
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triangleflag and the {Triangles} section below.
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:line
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These are the section keywords for the body of the file.
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{Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles} = atom-property sections
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{Bonds, Angles, Dihedrals, Impropers} = molecular topology sections
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{Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, \
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Improper Coeffs} = force field sections
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{BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, \
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EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, \
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BondBond13 Coeffs, AngleAngle Coeffs} = class 2 force field sections :ul
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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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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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10 1 17 -1.0 10.0 5.0 6.0 # salt ion :pre
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:line
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{Angle Coeffs} section:
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one line per angle type :ulb,l
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line syntax: ID coeffs :l
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ID = angle type (1-N)
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coeffs = list of coeffs :pre
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example: :l
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6 70 108.5 0 0 :pre
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:ule
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The number and meaning of the coefficients are specific to the defined
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angle style. See the "angle_style"_angle_style.html and
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"angle_coeff"_angle_coeff.html commands for details. Coefficients can
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also be set via the "angle_coeff"_angle_coeff.html command in the
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input script.
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:line
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{AngleAngle Coeffs} section:
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one line per improper type :ulb,l
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line syntax: ID coeffs :l
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ID = improper type (1-N)
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coeffs = list of coeffs (see "improper_coeff"_improper_coeff.html) :pre
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:ule
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:line
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{AngleAngleTorsion Coeffs} section:
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one line per dihedral type :ulb,l
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line syntax: ID coeffs :l
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ID = dihedral type (1-N)
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coeffs = list of coeffs (see "dihedral_coeff"_dihedral_coeff.html) :pre
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:ule
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:line
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{Angles} section:
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one line per angle :ulb,l
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line syntax: ID type atom1 atom2 atom3 :l
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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 :pre
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example: :b
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2 2 17 29 430 :pre
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:ule
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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 {Angles} section must appear
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after the {Atoms} section. All values in this section must be
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integers (1, not 1.0).
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:line
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{AngleTorsion Coeffs} section:
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one line per dihedral type :ulb,l
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line syntax: ID coeffs :l
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ID = dihedral type (1-N)
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coeffs = list of coeffs (see "dihedral_coeff"_dihedral_coeff.html) :pre
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:ule
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:line
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{Atoms} section:
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one line per atom
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line syntax: depends on atom style :ul
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An {Atoms} 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 "atom style"_atom_style.html in LAMMPS. As
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discussed below, each line can optionally have 3 flags (nx,ny,nz)
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appended to it, which indicate which image of a periodic simulation
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box the atom is in. These may be important to include for some kinds
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of analysis.
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angle: atom-ID molecule-ID atom-type x y z
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atomic: atom-ID atom-type x y z
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bond: atom-ID molecule-ID atom-type x y z
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charge: atom-ID atom-type q x y z
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dipole: atom-ID atom-type q x y z mux muy muz
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electron: atom-ID atom-type q spin eradius x y z
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ellipsoid: atom-ID atom-type ellipsoidflag density x y z
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full: atom-ID molecule-ID atom-type q x y z
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line: atom-ID molecule-ID atom-type lineflag density x y z
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meso: atom-ID atom-type rho e cv x y z
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molecular: atom-ID molecule-ID atom-type x y z
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peri: atom-ID atom-type volume density x y z
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sphere: atom-ID atom-type diameter density x y z
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tri: atom-ID molecule-ID atom-type triangleflag density x y z
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wavepacket: atom-ID atom-type charge spin eradius etag cs_re cs_im x y z
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hybrid: atom-ID atom-type x y z sub-style1 sub-style2 ... :tb(s=:)
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The keywords have these meanings:
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atom-ID = integer ID of atom
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molecule-ID = integer ID of molecule the atom belongs to
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atom-type = type of atom (1-Ntype)
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q = charge on atom (charge units)
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diameter = diameter of spherical atom (distance units)
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ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
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lineflag = 1 for line segment particles, 0 for point particles
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triangleflag = 1 for triangular particles, 0 for point particles
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density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
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volume = volume of atom (distance^3 units)
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x,y,z = coordinates of atom
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mux,muy,muz = components of dipole moment of atom (dipole units)
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rho = density (need units) for SPH particles
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e = energy (need units) for SPH particles
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cv = heat capacity (need units) for SPH particles
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spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
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eradius = electron radius (or fixed-core radius)
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etag = integer ID of electron that each wavepacket belongs to
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cs_re,cs_im = real/imaginary parts of wavepacket coefficients :ul
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The units for these quantities depend on the unit style; see the
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"units"_units.html command for details.
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For 2d simulations specify z as 0.0, or a value within the {zlo zhi}
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setting in the data file header.
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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 "atom_modify"_atom_modify.html 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), and velocities are not assigned in the data file, and you
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don't care if unique atom IDs appear in dump files, then the atom-IDs
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can all be set to 0.
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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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The diameter specifies the size of a finite-size spherical particle.
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It can be set to 0.0, which means that atom is a point particle.
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The ellipsoidflag, lineflag, and triangleflag determine whether the
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particle is a finite-size ellipsoid or line or triangle of finite
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size, or a point particle. Additional attributes must be defined for
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each ellipsoid in the {Ellipsoids} section. Additional attributes
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must be defined for each line in the {Lines} section. Additional
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attributes must be defined for each triangle in the {Triangles}
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section.
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Some pair styles and fixes and computes that operate on finite-size
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particles allow for a mixture of finite-size and point particles. See
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the doc pages of individual commands for details.
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The density is used in conjunction with the particle volume for
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finite-size particles to set the mass of the particle as mass =
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density * volume. In this context, volume can be a 3d quantity (for
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spheres or ellipsoids), a 2d quantity (for triangles), or a 1d
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quantity (for line segments). If the volume is 0.0, meaning a point
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particle, then the density value is used as the mass.
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For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
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specific values for each sub-style must be listed. The order of the
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sub-styles is the same as they were listed in the
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"atom_style"_atom_style.html command. The sub-style specific values
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are those that are not the 5 standard ones (ID,type,x,y,z). For
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example, for the "charge" sub-style, a "q" value would appear. For
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the "full" sub-style, a "molecule-ID" and "q" would appear. These are
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listed in the same order they appear as listed above. Thus if
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atom_style hybrid charge sphere :pre
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were used in the input script, each atom line would have these fields:
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atom-ID atom-type x y z q diameter density :pre
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Atom lines (all lines or none of them) can optionally list 3 trailing
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integer values: nx,ny,nz. For periodic dimensions, they specify which
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image of the simulation box the atom is considered to be in. An image
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of 0 means it is inside the box as defined. A value of 2 means add 2
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box lengths to get the true value. A value of -1 means subtract 1 box
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length to get the true value. LAMMPS updates these flags as atoms
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cross periodic boundaries during the simulation. The flags can be
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output with atom snapshots via the "dump"_dump.html command.
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If nx,ny,nz values are not set in the data file, LAMMPS initializes
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them to 0. If image information is needed for later analysis and they
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are not all initially 0, it's important to set them correctly in the
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data file. Also, if you plan to use the "replicate"_replicate.html
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command to generate a larger system, these flags must be listed
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correctly for bonded atoms when the bond crosses a periodic boundary.
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I.e. the values of the image flags should be different by 1 (in the
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appropriate dimension) for the two atoms in such a bond.
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Atom velocities and other atom quantities not defined above are set to
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0.0 when the {Atoms} section is read. Velocities can be set later by
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a {Velocities} section in the data file or by a
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"velocity"_velocity.html or "set"_set.html command in the input
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script.
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:line
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{Bond Coeffs} section:
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one line per bond type :ulb,l
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line syntax: ID coeffs :l
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ID = bond type (1-N)
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coeffs = list of coeffs :pre
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example: :l
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4 250 1.49 :pre
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:ule
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The number and meaning of the coefficients are specific to the defined
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bond style. See the "bond_style"_bond_style.html and
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"bond_coeff"_bond_coeff.html commands for details. Coefficients can
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also be set via the "bond_coeff"_bond_coeff.html command in the input
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script.
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:line
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{BondAngle Coeffs} section:
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one line per angle type :ulb,l
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line syntax: ID coeffs :l
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ID = angle type (1-N)
|
|
coeffs = list of coeffs (see class 2 section of "angle_coeff"_angle_coeff.html) :pre
|
|
:ule
|
|
|
|
:line
|
|
|
|
{BondBond Coeffs} section:
|
|
|
|
one line per angle type :ulb,l
|
|
line syntax: ID coeffs :l
|
|
ID = angle type (1-N)
|
|
coeffs = list of coeffs (see class 2 section of "angle_coeff"_angle_coeff.html) :pre
|
|
:ule
|
|
|
|
:line
|
|
|
|
{BondBond13 Coeffs} section:
|
|
|
|
one line per dihedral type :ulb,l
|
|
line syntax: ID coeffs :l
|
|
ID = dihedral type (1-N)
|
|
coeffs = list of coeffs (see class 2 section of "dihedral_coeff"_dihedral_coeff.html) :pre
|
|
:ule
|
|
|
|
:line
|
|
|
|
{Bonds} section:
|
|
|
|
one line per bond :ulb,l
|
|
line syntax: ID type atom1 atom2 :l
|
|
ID = bond number (1-Nbonds)
|
|
type = bond type (1-Nbondtype)
|
|
atom1,atom2 = IDs of 1st,2nd atoms in bond :pre
|
|
example: :l
|
|
12 3 17 29 :pre
|
|
:ule
|
|
|
|
The {Bonds} section must appear after the {Atoms} section. All values
|
|
in this section must be integers (1, not 1.0).
|
|
|
|
:line
|
|
|
|
{Dihedral Coeffs} section:
|
|
|
|
one line per dihedral type :ulb,l
|
|
line syntax: ID coeffs :l
|
|
ID = dihedral type (1-N)
|
|
coeffs = list of coeffs :pre
|
|
example: :l
|
|
3 0.6 1 0 1 :pre
|
|
:ule
|
|
|
|
The number and meaning of the coefficients are specific to the defined
|
|
dihedral style. See the "dihedral_style"_dihedral_style.html and
|
|
"dihedral_coeff"_dihedral_coeff.html commands for details.
|
|
Coefficients can also be set via the
|
|
"dihedral_coeff"_dihedral_coeff.html command in the input script.
|
|
|
|
:line
|
|
|
|
{Dihedrals} section:
|
|
|
|
one line per dihedral :ulb,l
|
|
line syntax: ID type atom1 atom2 atom3 atom4 :l
|
|
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
|
|
example: :l
|
|
12 4 17 29 30 21 :pre
|
|
:ule
|
|
|
|
The 4 atoms are ordered linearly within the dihedral. The {Dihedrals}
|
|
section must appear after the {Atoms} section. All values in this
|
|
section must be integers (1, not 1.0).
|
|
|
|
:line
|
|
|
|
{Ellipsoids} section:
|
|
|
|
one line per ellipsoid :ulb,l
|
|
line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk :l
|
|
atom-ID = ID of atom which is an ellipsoid
|
|
shapex,shapey,shapez = 3 diameters of ellipsoid (distance units)
|
|
quatw,quati,quatj,quatk = quaternion components for orientation of atom
|
|
example: :l
|
|
12 1 2 1 1 0 0 0 :pre
|
|
:ule
|
|
|
|
The {Ellipsoids} section must appear if "atom_style
|
|
ellipsoid"_atom_style.html is used and any atoms are listed in the
|
|
{Atoms} section with an ellipsoidflag = 1. The number of ellipsoids
|
|
should be specified in the header section via the "ellipsoids"
|
|
keyword.
|
|
|
|
The 3 shape values specify the 3 diameters or aspect ratios of a
|
|
finite-size ellipsoidal particle, when it is oriented along the 3
|
|
coordinate axes. They must all be non-zero values.
|
|
|
|
The values {quatw}, {quati}, {quatj}, and {quatk} set the orientation
|
|
of the atom as a quaternion (4-vector). Note that the shape
|
|
attributes specify the aspect ratios of an ellipsoidal particle, which
|
|
is oriented by default with its x-axis along the simulation box's
|
|
x-axis, and similarly for y and z. If this body is rotated (via the
|
|
right-hand rule) by an angle theta around a unit vector (a,b,c), then
|
|
the quaternion that represents its new orientation is given by
|
|
(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These
|
|
4 components are quatw, quati, quatj, and quatk as specified above.
|
|
LAMMPS normalizes each atom's quaternion in case (a,b,c) is not
|
|
specified as a unit vector.
|
|
|
|
The {Ellipsoids} section must appear after the {Atoms} section.
|
|
|
|
:line
|
|
|
|
{EndBondTorsion Coeffs} section:
|
|
|
|
one line per dihedral type :ulb,l
|
|
line syntax: ID coeffs :l
|
|
ID = dihedral type (1-N)
|
|
coeffs = list of coeffs (see class 2 section of "dihedral_coeff"_dihedral_coeff.html) :pre
|
|
:ule
|
|
|
|
:line
|
|
|
|
{Improper Coeffs} section:
|
|
|
|
one line per improper type :ulb,l
|
|
line syntax: ID coeffs :l
|
|
ID = improper type (1-N)
|
|
coeffs = list of coeffs :pre
|
|
example: :l
|
|
2 20 0.0548311 :pre
|
|
:ule
|
|
|
|
The number and meaning of the coefficients are specific to the defined
|
|
improper style. See the "improper_style"_improper_style.html and
|
|
"improper_coeff"_improper_coeff.html commands for details.
|
|
Coefficients can also be set via the
|
|
"improper_coeff"_improper_coeff.html command in the input script.
|
|
|
|
:line
|
|
|
|
{Impropers} section:
|
|
|
|
one line per improper :ulb,l
|
|
line syntax: ID type atom1 atom2 atom3 atom4 :l
|
|
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
|
|
example: :l
|
|
12 3 17 29 13 100 :pre
|
|
:ule
|
|
|
|
The ordering of the 4 atoms determines the definition of the improper
|
|
angle used in the formula for each "improper
|
|
style"_improper_style.html. See the doc pages for individual styles
|
|
for details.
|
|
|
|
The {Impropers} section must appear after the {Atoms} section. All
|
|
values in this section must be integers (1, not 1.0).
|
|
|
|
:line
|
|
|
|
{Lines} section:
|
|
|
|
one line per line segment :ulb,l
|
|
line syntax: atom-ID x1 y1 x2 y2 :l
|
|
atom-ID = ID of atom which is a line segment
|
|
x1,y1 = 1st end point
|
|
x2,y2 = 2nd end point
|
|
example: :l
|
|
12 1.0 0.0 2.0 0.0 :pre
|
|
:ule
|
|
|
|
The {Lines} section must appear if "atom_style line"_atom_style.html
|
|
is used and any atoms are listed in the {Atoms} section with a
|
|
lineflag = 1. The number of lines should be specified in the header
|
|
section via the "lines" keyword.
|
|
|
|
The 2 end points are the end points of the line segment. The ordering
|
|
of the 2 points should be such that using a right-hand rule to cross
|
|
the line segment with a unit vector in the +z direction, gives an
|
|
"outward" normal vector perpendicular to the line segment.
|
|
I.e. normal = (c2-c1) x (0,0,1). This orientation may be important
|
|
for defining some interactions.
|
|
|
|
The {Lines} section must appear after the {Atoms} section.
|
|
|
|
:line
|
|
|
|
{Masses} section:
|
|
|
|
one line per atom type :ulb,l
|
|
line syntax: ID mass :l
|
|
ID = atom type (1-N)
|
|
mass = mass value :pre
|
|
example: :l
|
|
3 1.01 :pre
|
|
:ule
|
|
|
|
This defines the mass of each atom type. This can also be set via the
|
|
"mass"_mass.html command in the input script. This section cannot be
|
|
used for atom styles that define a mass for individual atoms -
|
|
e.g. "atom_style sphere"_atom_style.html.
|
|
|
|
:line
|
|
|
|
{MiddleBondTorsion Coeffs} section:
|
|
|
|
one line per dihedral type :ulb,l
|
|
line syntax: ID coeffs :l
|
|
ID = dihedral type (1-N)
|
|
coeffs = list of coeffs (see class 2 section of "dihedral_coeff"_dihedral_coeff.html) :pre
|
|
:ule
|
|
|
|
:line
|
|
|
|
{Pair Coeffs} section:
|
|
|
|
one line per atom type :ulb,l
|
|
line syntax: ID coeffs :l
|
|
ID = atom type (1-N)
|
|
coeffs = list of coeffs :pre
|
|
example: :l
|
|
3 0.022 2.35197 0.022 2.35197 :pre
|
|
:ule
|
|
|
|
The number and meaning of the coefficients are specific to the defined
|
|
pair style. See the "pair_style"_pair_style.html and
|
|
"pair_coeff"_pair_coeff.html commands for details. Coefficients can
|
|
also be set via the "pair_coeff"_pair_coeff.html command in the input
|
|
script.
|
|
|
|
:line
|
|
|
|
{Triangles} section:
|
|
|
|
one line per triangle :ulb,l
|
|
line syntax: atom-ID x1 y1 x2 y2 :l
|
|
atom-ID = ID of atom which is a line segment
|
|
x1,y1,z1 = 1st corner point
|
|
x2,y2,z2 = 2nd corner point
|
|
x3,y3,z3 = 3rd corner point
|
|
example: :l
|
|
12 0.0 0.0 0.0 2.0 0.0 1.0 0.0 2.0 1.0 :pre
|
|
:ule
|
|
|
|
The {Triangles} section must appear if "atom_style
|
|
tri"_atom_style.html is used and any atoms are listed in the {Atoms}
|
|
section with a triangleflag = 1. The number of lines should be
|
|
specified in the header section via the "triangles" keyword.
|
|
|
|
The 3 corner points are the corner points of the triangle. The
|
|
ordering of the 3 points should be such that using a right-hand rule
|
|
to go from point1 to point2 to point3 gives an "outward" normal vector
|
|
to the face of the triangle. I.e. normal = (c2-c1) x (c3-c1). This
|
|
orientation may be important for defining some interactions.
|
|
|
|
The {Triangles} section must appear after the {Atoms} section.
|
|
|
|
:line
|
|
|
|
{Velocities} section:
|
|
|
|
one line per atom
|
|
line syntax: depends on atom style :ul
|
|
|
|
all styles except those listed: atom-ID vx vy vz
|
|
dipole: atom-ID vx vy vz wx wy wz
|
|
electron: atom-ID vx vy vz ervel
|
|
ellipsoid: atom-ID vx vy vz lx ly lz
|
|
sphere: atom-ID vx vy vz wx wy wz :tb(s=:)
|
|
|
|
where the keywords have these meanings:
|
|
|
|
vx,vy,vz = translational velocity of atom
|
|
lx,ly,lz = angular momentum of aspherical atom
|
|
wx,wy,wz = angular velocity of spherical atom
|
|
ervel = electron radial velocity (0 for fixed-core):ul
|
|
|
|
The velocity lines can appear in any order. This section can only be
|
|
used after an {Atoms} section. This is because the {Atoms} section
|
|
must have assigned a unique atom ID to each atom so that velocities
|
|
can be assigned to them.
|
|
|
|
Vx, vy, vz, and ervel are in "units"_units.html 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).
|
|
|
|
Translational velocities can also be set by the
|
|
"velocity"_velocity.html command in the input script.
|
|
|
|
:line
|
|
|
|
[Restrictions:]
|
|
|
|
To read gzipped data files, you must compile LAMMPS with the
|
|
-DLAMMPS_GZIP option - see the "Making
|
|
LAMMPS"_Section_start.html#start_2 section of the documentation.
|
|
|
|
[Related commands:]
|
|
|
|
"read_dump"_read_dump.html, "read_restart"_read_restart.html,
|
|
"create_atoms"_create_atoms.html
|
|
|
|
[Default:] none
|