-
Description
-
Read in a data file containing information LAMMPS needs to run a
-simulation. The file can be ASCII text or a gzipped text file
-(detected by a .gz suffix). This is one of 3 ways to specify initial
-atom coordinates; see the read_restart and
-create_atoms commands for alternative methods.
-Also see the explanation of the -restart command-line switch which can convert a restart file to
-a data file.
-
This command can be used multiple times to add new atoms and their
-properties to an existing system by using the add, offset, and
-shift keywords. See more details below, which includes the use case
-for the extra keywords.
-
The group keyword adds all the atoms in the data file to the
-specified group-ID. The group will be created if it does not already
-exist. This is useful if you are reading multiple data files and wish
-to put sets of atoms into different groups so they can be operated on
-later. E.g. a group of added atoms can be moved to new positions via
-the displace_atoms command. Note that atoms
-read from the data file are also always added to the “all” group. The
-group command discusses atom groups, as used in LAMMPS.
-
The nocoeff keyword tells read_data to ignore force field parameters.
-The various Coeff sections are still read and have to have the correct
-number of lines, but they are not applied. This also allows to read a
-data file without having any pair, bond, angle, dihedral or improper
-styles defined, or to read a data file for a different force field.
-
The use of the fix keyword is discussed below.
-
-
Reading multiple data files
-
The read_data command can be used multiple times with the same or
-different data files to build up a complex system from components
-contained in individual data files. For example one data file could
-contain fluid in a confined domain; a second could contain wall atoms,
-and the second file could be read a third time to create a wall on the
-other side of the fluid. The third set of atoms could be rotated to
-an opposing direction using the displace_atoms
-command, after the third read_data command is used.
-
The add, offset, shift, extra, and group keywords are
-useful in this context.
-
If a simulation box does not yet exist, the add keyword
-cannot be used; the read_data command is being used for the first
-time. If a simulation box does exist, due to using the
-create_box command, or a previous read_data command,
-then the add keyword must be used.
-
-
Note
-
The simulation box size (xlo to xhi, ylo to yhi, zlo to zhi) in
-the new data file will be merged with the existing simulation box to
-create a large enough box in each dimension to contain both the
-existing and new atoms. Each box dimension never shrinks due to this
-merge operation, it only stays the same or grows. Care must be used if
-you are growing the existing simulation box in a periodic dimension.
-If there are existing atoms with bonds that straddle that periodic
-boundary, then the atoms may become far apart if the box size grows.
-This will separate the atoms in the bond, which can lead to “lost”
-bond atoms or bad dynamics.
-
-
The three choices for the add argument affect how the IDs of atoms
-in the data file are treated. If append is specified, atoms in the
-data file are added to the current system, with their atom IDs reset
-so that an atomID = M in the data file becomes atomID = N+M, where N
-is the largest atom ID in the current system. This rule is applied to
-all occurrences of atom IDs in the data file, e.g. in the Velocity or
-Bonds section. If Nstart is specified, then Nstart is a numeric
-value is given, e.g. 1000, so that an atomID = M in the data file
-becomes atomID = 1000+M. If merge is specified, the data file atoms
-are added to the current system without changing their IDs. They are
-assumed to merge (without duplication) with the currently defined
-atoms. It is up to you to insure there are no multiply defined atom
-IDs, as LAMMPS only performs an incomplete check that this is the case
-by insuring the resulting max atomID >= the number of atoms.
-
The offset and shift keywords can only be used if the add
-keyword is also specified.
-
The offset keyword adds the specified offset values to the atom
-types, bond types, angle types, dihedral types, and improper types as
-they are read from the data file. E.g. if toff = 2, and the file
-uses atom types 1,2,3, then the added atoms will have atom types
-3,4,5. These offsets apply to all occurrences of types in the data
-file, e.g. for the Atoms or Masses or Pair Coeffs or Bond Coeffs
-sections. This makes it easy to use atoms and molecules and their
-attributes from a data file in different simulations, where you want
-their types (atom, bond, angle, etc) to be different depending on what
-other types already exist. All five offset values must be specified,
-but individual values will be ignored if the data file does not use
-that attribute (e.g. no bonds).
-
The shift keyword can be used to specify an (Sx, Sy, Sz)
-displacement applied to the coordinates of each atom. Sz must be 0.0
-for a 2d simulation. This is a mechanism for adding structured
-collections of atoms at different locations within the simulation box,
-to build up a complex geometry. It is up to you to insure atoms do
-not end up overlapping unphysically which would lead to bad dynamics.
-Note that the displace_atoms command can be used
-to move a subset of atoms after they have been read from a data file.
-Likewise, the delete_atoms command can be used to
-remove overlapping atoms. Note that the shift values (Sx, Sy, Sz) are
-also added to the simulation box information (xlo, xhi, ylo, yhi, zlo,
-zhi) in the data file to shift its boundaries. E.g. xlo_new = xlo +
-Sx, xhi_new = xhi + Sx.
-
The extra keywords can only be used the first time the read_data
-command is used. They are useful if you intend to add new atom, bond,
-angle, etc types later with additional read_data commands. This is
-because the maximum number of allowed atom, bond, angle, etc types is
-set by LAMMPS when the system is first initialized. If you do not use
-the extra keywords, then the number of these types will be limited
-to what appears in the first data file you read. For example, if the
-first data file is a solid substrate of Si, it will likely specify a
-single atom type. If you read a second data file with a different
-material (water molecules) that sit on top of the substrate, you will
-want to use different atom types for those atoms. You can only do
-this if you set the extra/atom/types keyword to a sufficiently large
-value when reading the substrate data file. Note that use of the
-extra keywords also allows each data file to contain sections like
-Masses or Pair Coeffs or Bond Coeffs which are sized appropriately for
-the number of types in that data file. If the offset keyword is
-used appropriately when each data file is read, the values in those
-sections will be stored correctly in the larger data structures
-allocated by the use of the extra keywords. E.g. the substrate file
-can list mass and pair coefficients for type 1 silicon atoms. The
-water file can list mass and pair coeffcients for type 1 and type 2
-hydrogen and oxygen atoms. Use of the extra and offset keywords
-will store those mass and pair coefficient values appropriately in
-data structures that allow for 3 atom types (Si, H, O). Of course,
-you would still need to specify coefficients for H/Si and O/Si
-interactions in your input script to have a complete pairwise
-interaction model.
-
An alternative to using the extra keywords with the read_data
-command, is to use the create_box command to
-initialize the simulation box and all the various type limits you need
-via its extra keywords. Then use the read_data command one or more
-times to populate the system with atoms, bonds, angles, etc, using the
-offset keyword if desired to alter types used in the various data
-files you read.
-
-
Format of a data file
-
The structure of the data file is important, though many settings and
-sections are optional or can come in any order. See the examples
-directory for sample data files for different problems.
-
A data file has a header and a body. The header appears first. The
-first line of the header is always skipped; it typically contains a
-description of the file. Then lines are read one at a time. Lines
-can have a trailing comment starting with ‘#’ that is ignored. If the
-line is blank (only whitespace after comment is deleted), it is
-skipped. If the line contains a header keyword, the corresponding
-value(s) is read from the line. If it doesn’t contain a header
-keyword, the line begins the body of the file.
-
The body of the file contains zero or more sections. The first line
-of a section has only a keyword. This line can have a trailing
-comment starting with ‘#’ that is either ignored or can be used to
-check for a style match, as described below. The next line is
-skipped. The remaining lines of the section contain values. The
-number of lines depends on the section keyword as described below.
-Zero or more blank lines can be used between sections. Sections can
-appear in any order, with a few exceptions as noted below.
-
The keyword fix can be used one or more times. Each usage specifies
-a fix that will be used to process a specific portion of the data
-file. Any header line containing header-string and any section with
-a name containing section-string will be passed to the specified
-fix. See the fix property/atom command for
-an example of a fix that operates in this manner. The doc page for
-the fix defines the syntax of the header line(s) and section(s) that
-it reads from the data file. Note that the header-string can be
-specified as NULL, in which case no header lines are passed to the
-fix. This means that it can infer the length of its Section from
-standard header settings, such as the number of atoms.
-
The formatting of individual lines in the data file (indentation,
-spacing between words and numbers) is not important except that header
-and section keywords (e.g. atoms, xlo xhi, Masses, Bond Coeffs) must
-be capitalized as shown and can’t have extra white space between their
-words - e.g. two spaces or a tab between the 2 words in “xlo xhi” or
-the 2 words in “Bond Coeffs”, is not valid.
-
-
Format of the header of a data file
-
These are the recognized header keywords. Header lines can come in
-any order. The value(s) are read from the beginning of the line.
-Thus the keyword atoms should be in a line like “1000 atoms”; the
-keyword ylo yhi should be in a line like “-10.0 10.0 ylo yhi”; the
-keyword xy xz yz should be in a line like “0.0 5.0 6.0 xy xz yz”.
-All these settings have a default value of 0, except the lo/hi box
-size defaults are -0.5 and 0.5. A line need only appear if the value
-is different than the default.
-
-- atoms = # of atoms in system
-- bonds = # of bonds in system
-- angles = # of angles in system
-- dihedrals = # of dihedrals in system
-- impropers = # of impropers in system
-- atom types = # of atom types in system
-- bond types = # of bond types in system
-- angle types = # of angle types in system
-- dihedral types = # of dihedral types in system
-- improper types = # of improper types in system
-- extra bond per atom = leave space for this many new bonds per atom
-- extra angle per atom = leave space for this many new angles per atom
-- extra dihedral per atom = leave space for this many new dihedrals per atom
-- extra improper per atom = leave space for this many new impropers per atom
-- extra special per atom = leave space for this many new special bonds per atom
-- ellipsoids = # of ellipsoids in system
-- lines = # of line segments in system
-- triangles = # of triangles in system
-- bodies = # of bodies in system
-- xlo xhi = simulation box boundaries in x dimension
-- ylo yhi = simulation box boundaries in y dimension
-- zlo zhi = simulation box boundaries in z dimension
-- xy xz yz = simulation box tilt factors for triclinic system
-
-
The initial simulation box size is determined by the lo/hi settings.
-In any dimension, the system may be periodic or non-periodic; see the
-boundary command. When the simulation box is created
-it is also partitioned into a regular 3d grid of rectangular bricks,
-one per processor, based on the number of processors being used and
-the settings of the processors command. The
-partitioning can later be changed by the balance or
-fix balance commands.
-
If the xy xz yz line does not appear, LAMMPS will set up an
-axis-aligned (orthogonal) simulation box. If the line does appear,
-LAMMPS creates a non-orthogonal simulation domain shaped as a
-parallelepiped with triclinic symmetry. The parallelepiped has its
-“origin” at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
-from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
-(xz,yz,zhi-zlo). Xy,xz,yz can be 0.0 or positive or negative values
-and are called “tilt factors” because they are the amount of
-displacement applied to faces of an originally orthogonal box to
-transform it into the parallelepiped.
-
By default, the tilt factors (xy,xz,yz) can not skew the box more than
-half the distance of the corresponding parallel box length. For
-example, if xlo = 2 and xhi = 12, then the x box length is 10 and the
-xy tilt factor must be between -5 and 5. Similarly, both xz and yz
-must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not
-a limitation, since if the maximum tilt factor is 5 (as in this
-example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
-... are all geometrically equivalent. If you wish to define a box
-with tilt factors that exceed these limits, you can use the box tilt command, with a setting of large; a setting of
-small is the default.
-
See Section_howto 12 of the doc pages
-for a geometric description of triclinic boxes, as defined by LAMMPS,
-and how to transform these parameters to and from other commonly used
-triclinic representations.
-
When a triclinic system is used, the simulation domain should normally
-be periodic in the dimension that the tilt is applied to, which is
-given by the second dimension of the tilt factor (e.g. y for xy tilt).
-This is so that pairs of atoms interacting across that boundary will
-have one of them shifted by the tilt factor. Periodicity is set by
-the boundary command. For example, if the xy tilt
-factor is non-zero, then the y dimension should be periodic.
-Similarly, the z dimension should be periodic if xz or yz is non-zero.
-LAMMPS does not require this periodicity, but you may lose atoms if
-this is not the case.
-
Also note that if your simulation will tilt the box, e.g. via the fix deform command, the simulation box must be setup to
-be triclinic, even if the tilt factors are initially 0.0. You can
-also change an orthogonal box to a triclinic box or vice versa by
-using the change box command with its ortho and
-triclinic options.
-
For 2d simulations, the zlo zhi values should be set to bound the z
-coords for atoms that appear in the file; the default of -0.5 0.5 is
-valid if all z coords are 0.0. For 2d triclinic simulations, the xz
-and yz tilt factors must be 0.0.
-
If the system is periodic (in a dimension), then atom coordinates can
-be outside the bounds (in that dimension); they will be remapped (in a
-periodic sense) back inside the box. Note that if the add option is
-being used to add atoms to a simulation box that already exists, this
-periodic remapping will be performed using simulation box bounds that
-are the union of the existing box and the box boundaries in the new
-data file.
-
-
Note
-
If the system is non-periodic (in a dimension), then all atoms
-in the data file must have coordinates (in that dimension) that are
-“greater than or equal to” the lo value and “less than or equal to”
-the hi value. If the non-periodic dimension is of style “fixed” (see
-the boundary command), then the atom coords must be
-strictly “less than” the hi value, due to the way LAMMPS assign atoms
-to processors. Note that you should not make the lo/hi values
-radically smaller/larger than the extent of the atoms. For example,
-if your atoms extend from 0 to 50, you should not specify the box
-bounds as -10000 and 10000. This is because LAMMPS uses the specified
-box size to layout the 3d grid of processors. A huge (mostly empty)
-box will be sub-optimal for performance when using “fixed” boundary
-conditions (see the boundary command). When using
-“shrink-wrap” boundary conditions (see the boundary
-command), a huge (mostly empty) box may cause a parallel simulation to
-lose atoms when LAMMPS shrink-wraps the box around the atoms. The
-read_data command will generate an error in this case.
-
-
The “extra bond per atom” setting (angle, dihedral, improper) is only
-needed if new bonds (angles, dihedrals, impropers) will be added to
-the system when a simulation runs, e.g. by using the fix bond/create command. This will pre-allocate
-space in LAMMPS data structures for storing the new bonds (angles,
-dihedrals, impropers).
-
The “extra special per atom” setting is typically only needed if new
-bonds/angles/etc will be added to the system, e.g. by using the fix bond/create command. Or if entire new molecules
-will be added to the system, e.g. by using the fix deposit or fix pour commands, which
-will have more special 1-2,1-3,1-4 neighbors than any other molecules
-defined in the data file. Using this setting will pre-allocate space
-in the LAMMPS data structures for storing these neighbors. See the
-special_bonds and molecule doc
-pages for more discussion of 1-2,1-3,1-4 neighbors.
-
-
Note
-
All of the “extra” settings are only used if they appear in the
-first data file read; see the description of the add keyword above
-for reading multiple data files. If they appear in later data files,
-they are ignored.
-
-
The “ellipsoids” and “lines” and “triangles” and “bodies” settings are
-only used with atom_style ellipsoid or line or tri or body and specify how many of the atoms are
-finite-size ellipsoids or lines or triangles or bodies; the remainder
-are point particles. See the discussion of ellipsoidflag and the
-Ellipsoids section below. See the discussion of lineflag and the
-Lines section below. See the discussion of triangleflag and the
-Triangles section below. See the discussion of bodyflag and the
-Bodies section below.
-
-
Note
-
For atom_style template, the molecular
-topology (bonds,angles,etc) is contained in the molecule templates
-read-in by the molecule command. This means you
-cannot set the bonds, angles, etc header keywords in the data
-file, nor can you define Bonds, Angles, etc sections as discussed
-below. You can set the bond types, angle types, etc header
-keywords, though it is not necessary. If specified, they must match
-the maximum values defined in any of the template molecules.
-
-
-
Format of the body of a data file
-
These are the section keywords for the body of the file.
-
-- Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies = atom-property sections
-- Bonds, Angles, Dihedrals, Impropers = molecular topology sections
-- Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs = force field sections
-- BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs = class 2 force field sections
-
-
These keywords will check an appended comment for a match with the
-currently defined style:
-
-- Atoms, Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs
-
-
For example, these lines:
-
Atoms # sphere
-Pair Coeffs # lj/cut
-
-
-
will check if the currently-defined atom_style is
-sphere, and the current pair_style is lj/cut. If
-not, LAMMPS will issue a warning to indicate that the data file
-section likely does not contain the correct number or type of
-parameters expected for the currently-defined style.
-
Each section is listed below in alphabetic order. The format of each
-section is described including the number of lines it must contain and
-rules (if any) for where it can appear in the data file.
-
Any individual line in the various sections can have a trailing
-comment starting with “#” for annotation purposes. E.g. in the
-Atoms section:
-
10 1 17 -1.0 10.0 5.0 6.0 # salt ion
-
-
-
-
Angle Coeffs section:
-
-- one line per angle type
-- line syntax: ID coeffs
-
-
ID = angle type (1-N)
-coeffs = list of coeffs
-
-
-
-
-
The number and meaning of the coefficients are specific to the defined
-angle style. See the angle_style and
-angle_coeff commands for details. Coefficients can
-also be set via the angle_coeff command in the
-input script.
-
-
AngleAngle Coeffs section:
-
-- one line per improper type
-- line syntax: ID coeffs
-
-
-ID = improper type (1-N)
-coeffs = list of coeffs (see improper_coeff)
-
-
-
AngleAngleTorsion Coeffs section:
-
-- one line per dihedral type
-- line syntax: ID coeffs
-
-
-ID = dihedral type (1-N)
-coeffs = list of coeffs (see dihedral_coeff)
-
-
-
Angles section:
-
-- one line per angle
-- line syntax: ID type atom1 atom2 atom3
-
-
ID = number of angle (1-Nangles)
-type = angle type (1-Nangletype)
-atom1,atom2,atom3 = IDs of 1st,2nd,3rd atoms in angle
-
-
-
example:
-.. parsed-literal:
-
-
The 3 atoms are ordered linearly within the angle. Thus the central
-atom (around which the angle is computed) is the atom2 in the list.
-E.g. H,O,H for a water molecule. The Angles section must appear
-after the Atoms section. All values in this section must be
-integers (1, not 1.0).
-
-
AngleTorsion Coeffs section:
-
-- one line per dihedral type
-- line syntax: ID coeffs
-
-
-ID = dihedral type (1-N)
-coeffs = list of coeffs (see dihedral_coeff)
-
-
-
Atoms section:
-
-- one line per atom
-- line syntax: depends on atom style
-
-
An Atoms section must appear in the data file if natoms > 0 in the
-header section. The atoms can be listed in any order. These are the
-line formats for each atom style in LAMMPS. As
-discussed below, each line can optionally have 3 flags (nx,ny,nz)
-appended to it, which indicate which image of a periodic simulation
-box the atom is in. These may be important to include for some kinds
-of analysis.
-
-
-
-
-
-
-| angle |
-atom-ID molecule-ID atom-type x y z |
-
-| atomic |
-atom-ID atom-type x y z |
-
-| body |
-atom-ID atom-type bodyflag mass x y z |
-
-| bond |
-atom-ID molecule-ID atom-type x y z |
-
-| charge |
-atom-ID atom-type q x y z |
-
-| dipole |
-atom-ID atom-type q x y z mux muy muz |
-
-| dpd |
-atom-ID atom-type theta x y z |
-
-| electron |
-atom-ID atom-type q spin eradius x y z |
-
-| ellipsoid |
-atom-ID atom-type ellipsoidflag density x y z |
-
-| full |
-atom-ID molecule-ID atom-type q x y z |
-
-| line |
-atom-ID molecule-ID atom-type lineflag density x y z |
-
-| meso |
-atom-ID atom-type rho e cv x y z |
-
-| molecular |
-atom-ID molecule-ID atom-type x y z |
-
-| peri |
-atom-ID atom-type volume density x y z |
-
-| smd |
-atom-ID atom-type molecule volume mass kernel-radius contact-radius x y z |
-
-| sphere |
-atom-ID atom-type diameter density x y z |
-
-| template |
-atom-ID molecule-ID template-index template-atom atom-type x y z |
-
-| tri |
-atom-ID molecule-ID atom-type triangleflag density x y z |
-
-| wavepacket |
-atom-ID atom-type charge spin eradius etag cs_re cs_im x y z |
-
-| hybrid |
-atom-ID atom-type x y z sub-style1 sub-style2 ... |
-
-
-
-
The per-atom values have these meanings and units, listed alphabetically:
-
-- atom-ID = integer ID of atom
-- atom-type = type of atom (1-Ntype)
-- bodyflag = 1 for body particles, 0 for point particles
-- contact-radius = ??? (distance units)
-- cs_re,cs_im = real/imaginary parts of wavepacket coefficients
-- cv = heat capacity (need units) for SPH particles
-- density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
-- diameter = diameter of spherical atom (distance units)
-- e = energy (need units) for SPH particles
-- ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
-- eradius = electron radius (or fixed-core radius)
-- etag = integer ID of electron that each wavepacket belongs to
-- kernel-radius = ??? (distance units)
-- lineflag = 1 for line segment particles, 0 for point or spherical particles
-- mass = mass of particle (mass units)
-- molecule-ID = integer ID of molecule the atom belongs to
-- mux,muy,muz = components of dipole moment of atom (dipole units)
-- q = charge on atom (charge units)
-- rho = density (need units) for SPH particles
-- spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
-- template-atom = which atom within a template molecule the atom is
-- template-index = which molecule within the molecule template the atom is part of
-- theta = internal temperature of a DPD particle
-- triangleflag = 1 for triangular particles, 0 for point or sperhical particles
-- volume = volume of Peridynamic particle (distance^3 units)
-- x,y,z = coordinates of atom (distance units)
-
-
The units for these quantities depend on the unit style; see the
-units command for details.
-
For 2d simulations specify z as 0.0, or a value within the zlo zhi
-setting in the data file header.
-
The atom-ID is used to identify the atom throughout the simulation and
-in dump files. Normally, it is a unique value from 1 to Natoms for
-each atom. Unique values larger than Natoms can be used, but they
-will cause extra memory to be allocated on each processor, if an atom
-map array is used, but not if an atom map hash is used; see the
-atom_modify command for details. If an atom map is
-not used (e.g. an atomic system with no bonds), and you don’t care if
-unique atom IDs appear in dump files, then the atom-IDs can all be set
-to 0.
-
The molecule ID is a 2nd identifier attached to an atom. Normally, it
-is a number from 1 to N, identifying which molecule the atom belongs
-to. It can be 0 if it is an unbonded atom or if you don’t care to
-keep track of molecule assignments.
-
The diameter specifies the size of a finite-size spherical particle.
-It can be set to 0.0, which means that atom is a point particle.
-
The ellipsoidflag, lineflag, triangleflag, and bodyflag determine
-whether the particle is a finite-size ellipsoid or line or triangle or
-body of finite size, or whether the particle is a point particle.
-Additional attributes must be defined for each ellipsoid, line,
-triangle, or body in the corresponding Ellipsoids, Lines,
-Triangles, or Bodies section.
-
The template-index and template-atom are only defined used by
-atom_style template. In this case the
-molecule command is used to define a molecule template
-which contains one or more molecules. If an atom belongs to one of
-those molecules, its template-index and template-atom are both set
-to positive integers; if not the values are both 0. The
-template-index is which molecule (1 to Nmols) the atom belongs to.
-The template-atom is which atom (1 to Natoms) within the molecule
-the atom is.
-
Some pair styles and fixes and computes that operate on finite-size
-particles allow for a mixture of finite-size and point particles. See
-the doc pages of individual commands for details.
-
For finite-size particles, the density is used in conjunction with the
-particle volume to set the mass of each particle as mass = density *
-volume. In this context, volume can be a 3d quantity (for spheres or
-ellipsoids), a 2d quantity (for triangles), or a 1d quantity (for line
-segments). If the volume is 0.0, meaning a point particle, then the
-density value is used as the mass. One exception is for the body atom
-style, in which case the mass of each particle (body or point
-particle) is specified explicitly. This is because the volume of the
-body is unknown.
-
For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
-specific values for each sub-style must be listed. The order of the
-sub-styles is the same as they were listed in the
-atom_style command. The sub-style specific values
-are those that are not the 5 standard ones (ID,type,x,y,z). For
-example, for the “charge” sub-style, a “q” value would appear. For
-the “full” sub-style, a “molecule-ID” and “q” would appear. These are
-listed in the same order they appear as listed above. Thus if
-
atom_style hybrid charge sphere
-
-
-
were used in the input script, each atom line would have these fields:
-
atom-ID atom-type x y z q diameter density
-
-
-
Note that if a non-standard value is defined by multiple sub-styles,
-it must appear mutliple times in the atom line. E.g. the atom line
-for atom_style hybrid dipole full would list “q” twice:
-
atom-ID atom-type x y z q mux muy myz molecule-ID q
-
-
-
Atom lines specify the (x,y,z) coordinates of atoms. These can be
-inside or outside the simulation box. When the data file is read,
-LAMMPS wraps coordinates outside the box back into the box for
-dimensions that are periodic. As discussed above, if an atom is
-outside the box in a non-periodic dimension, it will be lost.
-
LAMMPS always stores atom coordinates as values which are inside the
-simulation box. It also stores 3 flags which indicate which image of
-the simulation box (in each dimension) the atom would be in if its
-coordinates were unwrapped across periodic boundaries. An image flag
-of 0 means the atom is still inside the box when unwrapped. A value
-of 2 means add 2 box lengths to get the unwrapped coordinate. A value
-of -1 means subtract 1 box length to get the unwrapped coordinate.
-LAMMPS updates these flags as atoms cross periodic boundaries during
-the simulation. The dump command can output atom atom
-coordinates in wrapped or unwrapped form, as well as the 3 image
-flags.
-
In the data file, atom lines (all lines or none of them) can
-optionally list 3 trailing integer values (nx,ny,nz), which are used
-to initialize the atom’s image flags. If nx,ny,nz values are not
-listed in the data file, LAMMPS initializes them to 0. Note that the
-image flags are immediately updated if an atom’s coordinates need to
-wrapped back into the simulation box.
-
It is only important to set image flags correctly in a data file if a
-simulation model relies on unwrapped coordinates for some calculation;
-otherwise they can be left unspecified. Examples of LAMMPS commands
-that use unwrapped coordinates internally are as follows:
-
-- Atoms in a rigid body (see fix rigid, fix rigid/small) must have consistent image flags, so that
-when the atoms are unwrapped, they are near each other, i.e. as a
-single body.
-- If the replicate command is used to generate a larger
-system, image flags must be consistent for bonded atoms when the bond
-crosses a periodic boundary. I.e. the values of the image flags
-should be different by 1 (in the appropriate dimension) for the two
-atoms in such a bond.
-- If you plan to dump image flags and perform post-analysis
-that will unwrap atom coordinates, it may be important that a
-continued run (restarted from a data file) begins with image flags
-that are consistent with the previous run.
-
-
-
Note
-
If your system is an infinite periodic crystal with bonds then
-it is impossible to have fully consistent image flags. This is because
-some bonds will cross periodic boundaries and connect two atoms with the
-same image flag.
-
-
Atom velocities and other atom quantities not defined above are set to
-0.0 when the Atoms section is read. Velocities can be set later by
-a Velocities section in the data file or by a
-velocity or set command in the input
-script.
-
-
Bodies section:
-
-- one or more lines per body
-- first line syntax: atom-ID Ninteger Ndouble
-
-
Ninteger = # of integer quantities for this particle
-Ndouble = # of floating-point quantities for this particle
-
-
-
-- 0 or more integer lines with total of Ninteger values
-- 0 or more double lines with total of Ndouble values
-- example:
-
-
12 3 6
-2 3 2
-1.0 2.0 3.0 1.0 2.0 4.0
-
-
-
-
12 0 14
-1.0 2.0 3.0 1.0 2.0 4.0 1.0
-2.0 3.0 1.0 2.0 4.0 4.0 2.0
-
-
-
The Bodies section must appear if atom_style body
-is used and any atoms listed in the Atoms section have a bodyflag =
-1. The number of bodies should be specified in the header section via
-the “bodies” keyword.
-
Each body can have a variable number of integer and/or floating-point
-values. The number and meaning of the values is defined by the body
-style, as described in the body doc page. The body style
-is given as an argument to the atom_style body
-command.
-
The Ninteger and Ndouble values determine how many integer and
-floating-point values are specified for this particle. Ninteger and
-Ndouble can be as large as needed and can be different for every body.
-Integer values are then listed next on subsequent lines. Lines are
-read one at a time until Ninteger values are read. Floating-point
-values follow on subsequent lines, Again lines are read one at a time
-until Ndouble values are read. Note that if there are no values of a
-particular type, no lines appear for that type.
-
The Bodies section must appear after the Atoms section.
-
-
Bond Coeffs section:
-
-- one line per bond type
-- line syntax: ID coeffs
-
-
ID = bond type (1-N)
-coeffs = list of coeffs
-
-
-
-
-
The number and meaning of the coefficients are specific to the defined
-bond style. See the bond_style and
-bond_coeff commands for details. Coefficients can
-also be set via the bond_coeff command in the input
-script.
-
-
BondAngle Coeffs section:
-
-- one line per angle type
-- line syntax: ID coeffs
-
-
-ID = angle type (1-N)
-coeffs = list of coeffs (see class 2 section of angle_coeff)
-
-
-
BondBond Coeffs section:
-
-- one line per angle type
-- line syntax: ID coeffs
-
-
-ID = angle type (1-N)
-coeffs = list of coeffs (see class 2 section of angle_coeff)
-
-
-
BondBond13 Coeffs section:
-
-- one line per dihedral type
-- line syntax: ID coeffs
-
-
-ID = dihedral type (1-N)
-coeffs = list of coeffs (see class 2 section of dihedral_coeff)
-
-
-
Bonds section:
-
-- one line per bond
-- line syntax: ID type atom1 atom2
-
-
ID = bond number (1-Nbonds)
-type = bond type (1-Nbondtype)
-atom1,atom2 = IDs of 1st,2nd atoms in bond
-
-
-
-
-
The Bonds section must appear after the Atoms section. All values
-in this section must be integers (1, not 1.0).
-
-
Dihedral Coeffs section:
-
-- one line per dihedral type
-- line syntax: ID coeffs
-
-
ID = dihedral type (1-N)
-coeffs = list of coeffs
-
-
-
-
-
The number and meaning of the coefficients are specific to the defined
-dihedral style. See the dihedral_style and
-dihedral_coeff commands for details.
-Coefficients can also be set via the
-dihedral_coeff command in the input script.
-
-
Dihedrals section:
-
-- one line per dihedral
-- line syntax: ID type atom1 atom2 atom3 atom4
-
-
ID = number of dihedral (1-Ndihedrals)
-type = dihedral type (1-Ndihedraltype)
-atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in dihedral
-
-
-
-
-
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).
-
-
Ellipsoids section:
-
-- one line per ellipsoid
-- line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk
-
-
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
-
-
-
-
-
The Ellipsoids section must appear if atom_style ellipsoid 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.
-
-
EndBondTorsion Coeffs section:
-
-- one line per dihedral type
-- line syntax: ID coeffs
-
-
-ID = dihedral type (1-N)
-coeffs = list of coeffs (see class 2 section of dihedral_coeff)
-
-
-
Improper Coeffs section:
-
-- one line per improper type
-- line syntax: ID coeffs
-
-
ID = improper type (1-N)
-coeffs = list of coeffs
-
-
-
-
-
The number and meaning of the coefficients are specific to the defined
-improper style. See the improper_style and
-improper_coeff commands for details.
-Coefficients can also be set via the
-improper_coeff command in the input script.
-
-
Impropers section:
-
-- one line per improper
-- line syntax: ID type atom1 atom2 atom3 atom4
-
-
ID = number of improper (1-Nimpropers)
-type = improper type (1-Nimpropertype)
-atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in improper
-
-
-
-
-
The ordering of the 4 atoms determines the definition of the improper
-angle used in the formula for each improper style. 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).
-
-
Lines section:
-
-- one line per line segment
-- line syntax: atom-ID x1 y1 x2 y2
-
-
atom-ID = ID of atom which is a line segment
-x1,y1 = 1st end point
-x2,y2 = 2nd end point
-
-
-
-
-
The Lines section must appear if atom_style line
-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.
-
-
Masses section:
-
-- one line per atom type
-- line syntax: ID mass
-
-
ID = atom type (1-N)
-mass = mass value
-
-
-
-
-
This defines the mass of each atom type. This can also be set via the
-mass 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.
-
-
MiddleBondTorsion Coeffs section:
-
-- one line per dihedral type
-- line syntax: ID coeffs
-
-
-ID = dihedral type (1-N)
-coeffs = list of coeffs (see class 2 section of dihedral_coeff)
-
-
-
Pair Coeffs section:
-
-- one line per atom type
-- line syntax: ID coeffs
-
-
ID = atom type (1-N)
-coeffs = list of coeffs
-
-
-
-
3 0.022 2.35197 0.022 2.35197
-
-
-
The number and meaning of the coefficients are specific to the defined
-pair style. See the pair_style and
-pair_coeff commands for details. Since pair
-coefficients for types I != J are not specified, these will be
-generated automatically by the pair style’s mixing rule. See the
-individual pair_style doc pages and the pair_modify mix command for details. Pair coefficients can also
-be set via the pair_coeff command in the input
-script.
-
-
PairIJ Coeffs section:
-
-- one line per pair of atom types for all I,J with I <= J
-- line syntax: ID1 ID2 coeffs
-
-
ID1 = atom type I = 1-N
-ID2 = atom type J = I-N, with I <= J
-coeffs = list of coeffs
-
-
-
-
3 3 0.022 2.35197 0.022 2.35197
-3 5 0.022 2.35197 0.022 2.35197
-
-
-
This section must have N*(N+1)/2 lines where N = # of atom types. The
-number and meaning of the coefficients are specific to the defined
-pair style. See the pair_style and
-pair_coeff commands for details. Since pair
-coefficients for types I != J are all specified, these values will
-turn off the default mixing rule defined by the pair style. See the
-individual pair_style doc pages and the pair_modify mix command for details. Pair coefficients can also
-be set via the pair_coeff command in the input
-script.
-
-
Triangles section:
-
-- one line per triangle
-- line syntax: atom-ID x1 y1 x2 y2
-
-
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
-
-
-
-
12 0.0 0.0 0.0 2.0 0.0 1.0 0.0 2.0 1.0
-
-
-
The Triangles section must appear if atom_style tri 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.
-
-
Velocities section:
-
-- one line per atom
-- line syntax: depends on atom style
-
-
-
-
-
-
-
-| all styles except those listed |
-atom-ID vx vy vz |
-
-| 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 |
-
-| hybrid |
-atom-ID vx vy vz sub-style1 sub-style2 ... |
-
-
-
-
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 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).
-
For atom_style hybrid, following the 4 initial values (ID,vx,vy,vz),
-specific values for each sub-style must be listed. The order of the
-sub-styles is the same as they were listed in the
-atom_style command. The sub-style specific values
-are those that are not the 5 standard ones (ID,vx,vy,vz). For
-example, for the “sphere” sub-style, “wx”, “wy”, “wz” values would
-appear. These are listed in the same order they appear as listed
-above. Thus if
-
atom_style hybrid electron sphere
-
-
-
were used in the input script, each velocity line would have these
-fields:
-
atom-ID vx vy vz ervel wx wy wz
-
-
-
Translational velocities can also be set by the
-velocity command in the input script.
-
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