read_data command

Syntax

read_data file keyword args ...
  • file = name of data file to read in

  • zero or more keyword/arg pairs may be appended

  • keyword = add or offset or shift or extra/atom/types or extra/bond/types or extra/angle/types or extra/dihedral/types or extra/improper/types or extra/bond/per/atom or extra/angle/per/atom or extra/dihedral/per/atom or extra/improper/per/atom or group or nocoeff or fix

    add arg = append or Nstart or merge
      append = add new atoms with IDs appended to current IDs
      Nstart = add new atoms with IDs starting with Nstart
      merge = add new atoms with their IDs unchanged
    offset args = toff boff aoff doff ioff
      toff = offset to add to atom types
      boff = offset to add to bond types
      aoff = offset to add to angle types
      doff = offset to add to dihedral types
      ioff = offset to add to improper types
    shift args = Sx Sy Sz
      Sx,Sy,Sz = distance to shift atoms when adding to system (distance units)
    extra/atom/types arg = # of extra atom types
    extra/bond/types arg = # of extra bond types
    extra/angle/types arg = # of extra angle types
    extra/dihedral/types arg = # of extra dihedral types
    extra/improper/types arg = # of extra improper types
    extra/bond/per/atom arg = leave space for this many new bonds per atom
    extra/angle/per/atom arg = leave space for this many new angles per atom
    extra/dihedral/per/atom arg = leave space for this many new dihedrals per atom
    extra/improper/per/atom arg = leave space for this many new impropers per atom
    extra/special/per/atom arg = leave space for extra 1-2,1-3,1-4 interactions per atom
    group args = groupID
      groupID = add atoms in data file to this group
    nocoeff = ignore force field parameters
    fix args = fix-ID header-string section-string
      fix-ID = ID of fix to process header lines and sections of data file
      header-string = header lines containing this string will be passed to fix
      section-string = section names with this string will be passed to fix
    

Examples

read_data data.lj
read_data ../run7/data.polymer.gz
read_data data.protein fix mycmap crossterm CMAP
read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0
read_data data.water add merge 1 group solvent

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 coefficients 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 (deprecated, use extra/bond/per/atom keyword)
  • extra angle per atom = leave space for this many new angles per atom (deprecated, use extra/angle/per/atom keyword)
  • extra dihedral per atom = leave space for this many new dihedrals per atom (deprecated, use extra/dihedral/per/atom keyword)
  • extra improper per atom = leave space for this many new impropers per atom (deprecated, use extra/improper/per/atom keyword)
  • extra special per atom = leave space for this many new special bonds per atom (deprecated, use extra/special/per/atom keyword)
  • 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 6.12 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. Using this header flag is deprecated; please use the extra/bond/per/atom keyword (and correspondingly for angles, dihedrals and impropers) in the read_data command instead. Either 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 header flag is deprecated; please use the extra/special/per/atom keyword instead. 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 applied in the first data file read and when no simulation box has yet been created; as soon as the simulation box is created (and read_data implies that), these settings are locked and cannot be changed anymore. Please 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
    
  • example:

    6 70 108.5 0 0
    

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:

2 2 17 29 430

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
edpd atom-ID atom-type edpd_temp edpd_cv x y z
mdpd atom-ID atom-type x y z
tdpd atom-ID atom-type x y z cc1 cc2 ... ccNspecies
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
  • cc = chemical concentration for tDPD particles for each species (mole/volume units)
  • 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
  • edpd_temp = temperature for eDPD particles (temperature units)
  • edpd_cv = volumetric heat capacity for eDPD particles (energy/temperature/volume units)
  • 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 spherical 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.

Note that for 2d simulations of spheres, this command will treat them as spheres when converting density to mass. However, they can also be modeled as 2d discs (circles) if the set density/disc command is used to reset their mass after the read_data command is used. A disc keyword can also be used with time integration fixes, such as fix nve/sphere and fix nvt/sphere to time integrate their motion as 2d discs (not 3d spheres), by changing their moment of inertia.

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
    
  • example:

    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
    
  • example:

    4 250 1.49
    

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
    
  • example:

    12 3 17 29
    

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
    
  • example:

    3 0.6 1 0 1
    

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
    
  • example:

    12 4 17 29 30 21
    

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
    
  • example:

    12 1 2 1 1 0 0 0
    

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
    
  • example:

    2 20 0.0548311
    

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
    
  • example:

    12 3 17 29 13 100
    

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
    
  • example:

    12 1.0 0.0 2.0 0.0
    

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
    
  • example:

    3 1.01
    

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
    
  • example:

    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
    
  • examples:

    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 z1 x2 y2 z2 x3 y3 z3

    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:

    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.


Restrictions

To read gzipped data files, you must compile LAMMPS with the -DLAMMPS_GZIP option - see the Making LAMMPS section of the documentation.

Default

The default for all the extra keywords is 0.