forked from lijiext/lammps
606 lines
20 KiB
Plaintext
606 lines
20 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 :pre
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file = name of data file to read in :ul
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[Examples:]
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read_data data.lj
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read_data ../run7/data.polymer.gz :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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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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{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 domain :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, then 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. See the "region
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prism"_region.html command for a description of how the extent of the
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parallelepiped is defined. The parallelepiped has its "origin" at
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(xlo,ylo,zlo) and 3 edge vectors starting from the origin given by a =
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(xhi-xlo,0,0); b = (xy,yhi-ylo,0); c = (xz,yz,zhi-zlo). Note that if
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your simulation will tilt the box, e.g. via the "fix
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deform"_fix_deform.html command, the simulation box must be triclinic,
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even if the tilt factors are initially 0.0.
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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 parallel box length. For example, if xlo = 2 and xhi
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= 12, then the x box length is 10 and the xy tilt factor must be
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between -5 and 5. Similarly, both xz and yz must be between
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-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
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since if the maximum tilt factor is 5 (as in this example), then
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configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
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equivalent.
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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.
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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 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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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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:line
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These are the section keywords for the body of the file.
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{Atoms, Velocities, Masses, Shapes, Dipoles} = atom-property sections
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{Bonds, Angles, Dihedrals, Impropers} = molecular topolgy 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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dpd: atom-ID atom-type x y z
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ellipsoid: atom-ID atom-type x y z quatw quati quatj quatk
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full: atom-ID molecule-ID atom-type q x y z
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granular: atom-ID atom-type diameter density x y z
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molecular: atom-ID molecule-ID atom-type 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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type-ID = type of atom (1-Ntype)
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q = charge on atom
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diameter = diameter of atom
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density = density of atom
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x,y,z = coordinates of atom
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mux,muy,muz = direction of dipole moment of atom
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quatw,quati,quatj,quatk = quaternion components for orientation of atom :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), 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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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 values {quatw}, {quati}, {quatj}, and {quatk} set the orientation
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of the atom as a quaternion (4-vector). Note that the
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"shape"_shape.html command or "Shapes" section of the data file
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specifies the aspect ratios of an ellipsoidal particle, which is
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oriented by default with its x-axis along the simulation box's x-axis,
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and similarly for y and z. If this body is rotated (via the
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right-hand rule) by an angle theta around a unit vector (a,b,c), then
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the quaternion that represents its new orientation is given by
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(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These
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4 components are quatw, quati, quatj, and quatk as specfied above.
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LAMMPS normalizes each atom's quaternion in case (a,b,c) was not a
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unit vector.
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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.
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Thus if
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atom_style hybrid charge granular :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 box the atom is considered to be in. An image of 0 means
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it is inside the box as defined. A value of 2 means add 2 box lengths
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to get the true value. A value of -1 means subtract 1 box length to
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get the true value. LAMMPS updates these flags as atoms cross
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periodic boundaries during the simulation. The flags can be output
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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)
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coeffs = list of coeffs (see class 2 section of "angle_coeff"_angle_coeff.html) :pre
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:ule
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:line
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{BondBond 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 (see class 2 section of "angle_coeff"_angle_coeff.html) :pre
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:ule
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:line
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{BondBond13 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 class 2 section of "dihedral_coeff"_dihedral_coeff.html) :pre
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:ule
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:line
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{Bonds} section:
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one line per bond :ulb,l
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line syntax: ID type atom1 atom2 :l
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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 :pre
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example: :l
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12 3 17 29 :pre
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:ule
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The {Bonds} section must appear after the {Atoms} section. All values
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in this section must be integers (1, not 1.0).
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:line
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{Dihedral 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 :pre
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example: :l
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3 0.6 1 0 1 :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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dihedral style. See the "dihedral_style"_dihedral_style.html and
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"dihedral_coeff"_dihedral_coeff.html commands for details.
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Coefficients can also be set via the
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"dihedral_coeff"_dihedral_coeff.html command in the input script.
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:line
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{Dihedrals} section:
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one line per dihedral :ulb,l
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line syntax: ID type atom1 atom2 atom3 atom4 :l
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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 :pre
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example: :l
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12 4 17 29 30 21 :pre
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:ule
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The 4 atoms are ordered linearly within the dihedral. The {Dihedrals}
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section must appear after the {Atoms} section. All values in this
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section must be integers (1, not 1.0).
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:line
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{Dipoles} section:
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one line per atom type :ulb,l
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line syntax: ID dipole-moment :
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ID = atom type (1-N)
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dipole-moment = value of dipole moment :pre
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example: :l
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2 0.5 :pre
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:ule
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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 "dipole"_dipole.html
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command in the input script.
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:line
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{EndBondTorsion 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 class 2 section of "dihedral_coeff"_dihedral_coeff.html) :pre
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:ule
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:line
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{Improper Coeffs} section:
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|
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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 :pre
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|
example: :l
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|
2 20 0.0548311 :pre
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|
:ule
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|
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|
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.
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|
|
|
:line
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|
{Impropers} section:
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|
one line per improper :ulb,l
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|
line syntax: ID type atom1 atom2 atom3 atom4 :l
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|
ID = number of improper (1-Nimpropers)
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|
type = improper type (1-Nimpropertype)
|
|
atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in improper :pre
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|
example: :l
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|
12 3 17 29 13 100 :pre
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|
: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).
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|
|
|
: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 should not
|
|
be used for atom styles that define a mass for individual atoms -
|
|
e.g. atom style granular.
|
|
|
|
: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
|
|
|
|
{Shapes} section:
|
|
|
|
one line per atom type :ulb,l
|
|
line syntax: ID x y z :l
|
|
ID = atom type (1-N)
|
|
x = x diameter
|
|
y = y diameter
|
|
z = z diameter :pre
|
|
example: :l
|
|
3 2.0 1.0 1.0 :pre
|
|
:ule
|
|
|
|
This defines the shape of each atom type. This can also be set via
|
|
the "shape"_mass.html command in the input script. This section
|
|
should only be used for atom styles that define a shape, e.g. atom
|
|
style dipole or ellipsoid.
|
|
|
|
: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
|
|
ellipsoid: atom-ID vx vy vz lx ly lz
|
|
granular: 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 granular atom :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 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 -DGZIP
|
|
option - see the "Making LAMMPS"_Section_start.html#2_2 section of the
|
|
documentation.
|
|
|
|
[Related commands:]
|
|
|
|
"read_restart"_read_restart.html, "create_atoms"_create_atoms.html
|
|
|
|
[Default:] none
|