read_data command — LIGGGHTS v3.X documentation

# 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 = fix

    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

## Description

Read in a data file containing information LIGGGHTS(R)-PUBLIC 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.

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. 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.

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
- atom types = # of atom types in system
- bond types = # of bond types in system
- extra bond per atom = leave space for this many new bonds per atom
- ellipsoids = # of ellipsoids in system
- lines = # of line segments 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.

If the xy xz yz line does not appear, LIGGGHTS(R)-PUBLIC will set up an axis-aligned (orthogonal) simulation box. If the line does appear, LIGGGHTS(R)-PUBLIC 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.

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.

See Section_howto 12 of the doc pages for a geometric description of triclinic boxes, as defined by LIGGGHTS(R)-PUBLIC, and how to transform these parameters to and from other commonly used triclinic representations.

When a triclinic system is used, the simulation domain must be periodic in any dimensions with a non-zero tilt factor, as defined by the boundary command. I.e. if the xy tilt factor is non-zero, then both the x and y dimensions must be periodic. Similarly, x and z must be periodic if xz is non-zero and y and z must be periodic if yz is non-zero. Also note that if your simulation will tilt the box, e.g. via the fix deform command, the simulation box must be defined as triclinic, even if the tilt factors are initially 0.0.

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.

Warning

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 LIGGGHTS(R)-PUBLIC 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 LIGGGHTS(R)-PUBLIC 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 the first time that LIGGGHTS(R)-PUBLIC shrink-wraps the box around the atoms.

The “extra bond per atom” setting should be used if new bonds 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 LIGGGHTS(R)-PUBLIC data structures for storing the new bonds.

These are the section keywords for the body of the file.

- Atoms, Velocities, Masses, Ellipsoids, Lines = atom-property sections
- Bonds = molecular topology sections
- Pair Coeffs, PairIJ Coeffs, Bond Coeffs = force field sections
- BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs = class 2 force field sections

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

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 LIGGGHTS(R)-PUBLIC. 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.

bond | atom-ID molecule-ID atom-type x y z
ellipsoid | atom-ID atom-type ellipsoidflag density x y z
sphere | atom-ID atom-type diameter density x y z
line | atom-ID molecule-ID atom-type lineflag density x y z
molecular | atom-ID molecule-ID atom-type x y z
hybrid | atom-ID atom-type x y z sub-style1 sub-style2 ...

The keywords have these meanings:

- atom-ID = integer ID of atom
- molecule-ID = integer ID of molecule the atom belongs to
- atom-type = type of atom (1-Ntype)
- q = charge on atom (charge units)
- diameter = diameter of spherical atom (distance units)
- ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
- lineflag = 1 for line segment particles, 0 for point particles
- triangleflag = 1 for triangular particles, 0 for point particles
- density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
- mass = mass of particle (mass units)
- volume = volume of particle (distance^3 units)
- x,y,z = coordinates of atom

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 (see the atom_modify command). If an atom map array is not used (e.g. an atomic system with no bonds), and velocities are not assigned in the data file, 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 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 section.

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 (all lines or none of them) can optionally list 3 trailing integer values: nx,ny,nz. For periodic dimensions, they specify which image of the simulation box the atom is considered to be in. An image of 0 means it is inside the box as defined. A value of 2 means add 2 box lengths to get the true value. A value of -1 means subtract 1 box length to get the true value. LIGGGHTS(R)-PUBLIC updates these flags as atoms cross periodic boundaries during the simulation. The flags can be output with atom snapshots via the dump command.

If nx,ny,nz values are not set in the data file, LIGGGHTS(R)-PUBLIC initializes them to 0. If image information is needed for later analysis and they are not all initially 0, it’s important to set them correctly in the data file. Also, if you plan to use the replicate command to generate a larger system, these flags must be listed correctly 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.

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.

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.

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).

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. LIGGGHTS(R)-PUBLIC 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)

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 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

- 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 LIGGGHTS(R)-PUBLIC with the -DLAMMPS_GZIP option - see the Making LIGGGHTS(R)-PUBLIC section of the documentation.

## Related commands

read_dump, read_restart, create_atoms, write_data

Default: none