\(\renewcommand{\AA}{\text{Å}}\)
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 extra/special/per/atom or group or nocoeff or fix
add arg = append or IDoffset or IDoffset MOLoffset or merge append = add new atoms with atom IDs appended to current IDs IDoffset = add new atoms with atom IDs having IDoffset added MOLoffset = add new atoms with molecule IDs having MOLoffset added (only when molecule IDs are enabled) merge = add new atoms with their atom IDs (and molecule 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 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 the simulation box: see the create_box and read_restart and commands for alternative methods. It is also one of 3 ways to specify initial atom coordinates: see the create_atoms and read_restart and 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. However, it is important to understand that several system parameters, like the number of types of different kinds and per atom settings are locked in after the first read_data command, which means that no type ID (including its offset) may have a larger value when processing additional data files than what is set by the first data file and the corresponding read_data command options. See more details on this situation 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
If the first read_data command defined an orthogonal or restricted triclinic or general triclinic simulation box (see the sub-section below on header keywords), then subsequent data files must define the same kind of simulation box. For orthogonal boxes, the new box can be a different size; see the next Note. For a restricted triclinic box, the 3 new tilt factors (“xy xz yz” keyword) must have the same values as in the original data file. For a general triclinic box, the new avec, bvec, cvec, and “abc origin” keywords must have the same values in the original data file. files. Also the shift keyword cannot be used in subsequent read_data commands for a general triclinic box.
Note
For orthogonal boxes, the simulation box size 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 atom IDs and molecule 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 atom-ID = M in the data file becomes atom-ID = 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. This is also done for molecule IDs, if the atom style does support molecule IDs or they are enabled via fix property/atom.
If IDoffset is specified, then IDoffset is a numeric value is given, e.g. 1000, so that an atom-ID = M in the data file becomes atom-ID = 1000+M. For systems with enabled molecule IDs, another numerical argument MOLoffset is required representing the equivalent offset for molecule IDs.
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 ensure there are no multiply defined atom IDs, as LAMMPS only performs an incomplete check that this is the case by ensuring the resulting max atom-ID >= the number of atoms. For molecule IDs, there is no check done at all.
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).
Note
Offsets are ignored on lines using type labels, as the type labels will determine the actual types directly depending on the current labelmap settings.
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 ensure 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.
The file will be read line by line, but there is a limit of 254 characters per line and characters beyond that limit will be ignored.
A data file has a header and a body. The header appears first. The first line of the header and thus of the data file is always skipped; it typically contains a description of the file or a comment from the software that created the file.
Then lines are read one line at a time. Lines can have a trailing comment starting with ‘#’ that is ignored. There must be at least one blank between any valid content and the comment. If a line is blank (i.e. contains only white-space after comments are deleted), it is skipped. If the line contains a header keyword, the corresponding value(s) is/are read from the line. A line that is not blank and does not contain a header keyword 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. There must be a blank between the keyword and any comment. The next line is always 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 that is an exact match to 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 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 the fix can infer the length of its Section from standard header settings, such as the number of atoms. Also the section-string may be specified as NULL, and in that case the fix ID is used as section name.
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 cannot 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. Each keyword takes a single value unless noted in this list. 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 for the simulation box size settings; their defaults are explained below. A keyword line need only appear if its 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 (2 values)
ylo yhi = simulation box boundaries in y dimension (2 values)
zlo zhi = simulation box boundaries in z dimension (2 values)
xy xz yz = simulation box tilt factors for triclinic system (3 values)
avec = first edge vector of a general triclinic simulation box (3 values)
bvec = second edge vector of a general triclinic simulation box (3 values)
cvec = third edge vector of a general triclinic simulation box (3 values)
abc origin = origin of a general triclinic simulation box (3 values)
Header specification of the simulation box size and shape
The last 8 keywords in the list of header keywords are for simulation boxes of 3 kinds which LAMMPS supports:
orthogonal box = faces are perpendicular to the xyz coordinate axes
restricted triclinic box = a parallelepiped defined by 3 edge vectors oriented in a constrained manner
general triclinic box = a parallelepiped defined by 3 arbitrary edge vectors
For restricted and general triclinic boxes, see the Howto_triclinic doc page for a fuller description than is given here.
The units of the values for all 8 keywords in in distance units; see the units command for details.
For all 3 kinds of simulation boxes, the system may be periodic or non-periodic in any dimension; see the boundary command for details.
When the simulation box is created by the read_data command, it is also partitioned into a regular 3d grid of subdomains, one per processor, based on the number of processors being used and the settings of the processors command. For each kind of simulation box the subdomains have the same shape as the simulation box, i.e. smaller orthogonal bricks for orthogonal boxes, smaller parallelepipeds for triclinic boxes. The partitioning can later be changed by the balance or fix balance commands.
For an orthogonal box, only the xlo xhi, ylo yhi, zlo zhi keywords are used. They define the extent of the simulation box in each dimension so that the resulting edge vectors of an orthogonal box are:
A = (xhi-xlo,0,0)
B = (0,yhi-ylo,0)
C = (0,0,zhi-zlo)
The origin (lower left corner) of the orthogonal box is at (xlo,ylo,zlo). The default values for these 3 keywords are -0.5 and 0.5 for each lo/hi pair. For a 2d simulation, the zlo and zhi values must straddle zero. The default zlo/zhi values do this, so that keyword is not needed in 2d.
For a restricted triclinic box, the xy xz yz keyword is used in addition to the xlo xhi, ylo yhi, zlo zhi keywords. The three xy,xz,yz values can be 0.0 or positive or negative, and are called “tilt factors” because they are the amount of displacement applied to edges of faces of an orthogonal box to transform it into a restricted triclinic parallelepiped.
The Howto_triclinic doc page discusses the tilt factors in detail and explains that the resulting edge vectors of a restricted triclinic box are:
A = (xhi-xlo,0,0)
B = (xy,yhi-ylo,0)
C = (xz,yz,zhi-zlo)
This restricted form of edge vectors requires that A be in the direction of the x-axis, B be in the xy plane with its y-component in the +y direction, and C have its z-component in the +z direction. The origin (lower left corner) of the restricted triclinic box is at (xlo,ylo,zlo).
For a 2d simulation, the zlo and zhi values must straddle zero. The default zlo/zhi values do this, so that keyword is not needed in 2d. The xz and yz values must also be zero in 2d. The shape of the 2d restricted triclinic simulation box is effectively a parallelogram.
Note
When a restricted triclinic box is used, the simulation domain should normally be periodic in any dimensions that 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 which also describes the shifting by the tilt factor. 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.
Note
Normally, the specified tilt factors (xy,xz,yz) should not skew the simulation box by more than half the distance of the corresponding parallel box length for computational efficiency. For example, if \(x_\text{lo} = 2\) and \(x_\text{hi} = 12\), then the \(x\) box length is 10 and the \(xy\) tilt factor should be between \(-5\) and \(5\). LAMMPS will issue a warning if this is not the case. See the last sub-section of the Howto_triclinic doc page for more details.
Note
If a simulation box is initially orthogonal, but will tilt during a simulation, e.g. via the fix deform command, then the box should be defined as restricted triclinic with all 3 tilt factors = 0.0. Alternatively, the change box command can be used to convert an orthogonal box to a restricted triclinic box.
For a general triclinic box, the avec, bvec, cvec, and abc origin keywords are used. The xlo xhi, ylo yhi, zlo zhi, and xy xz yz keywords are NOT used. The first 3 keywords define the 3 edge vectors A, B, C of the general triclinic box. They can be arbitrary vectors so long as they are distinct, non-zero, and not co-planar. They must also define a right-handed system such that (A x B) points in the direction of C. Note that a left-handed system can be converted to a right-handed system by simply swapping the order of any pair of the A, B, C vectors. The origin of the box (origin of the 3 edge vectors) is set by the abc origin keyword.
The default values for these 4 keywords are as follows:
avec = (1,0,0)
bvec = (0,1,0)
cvec = (0,0,1)
abc origin = (0,0,0) for 3d, (0,0,-0.5) for 2d
For 2d simulations, cvec = (0,0,1) is required, and the 3rd value of abc origin must be -0.5. These are the default values, so the cvec keyword is not needed in 2d.
Note
LAMMPS allows specification of general triclinic simulation boxes as a convenience for users who may be converting data from solid-state crystallographic representations or from DFT codes for input to LAMMPS. However, as explained on the Howto_triclinic doc page, internally, LAMMPS only uses restricted triclinic simulation boxes. This means the box and per-atom information (e.g. coordinates, velocities) in the data file are converted (rotated) from general to restricted triclinic form when the file is read. Other sections of the data file must also list their per-atom data appropriately if vector quantities are specified. This requirement is explained below for the relevant sections. The Howto_triclinic doc page also discusses other LAMMPS commands which can input/output general triclinic representations of the simulation box and per-atom data.
The following explanations apply to all 3 kinds of simulation boxes: orthogonal, restricted triclinic, and general triclinic.
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. For triclinic boxes, periodicity in x,y,z refers to the faces of the parallelepiped defined by the A,**B**,**C** edge vectors of the simulation box. See the boundary command doc page for a fuller discussion.
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.
If the system is non-periodic (in a dimension), then an image flag for that direction has no meaning, since there cannot be periodic images without periodicity and the data file is therefore - technically speaking - invalid. This situation would happen when a data file was written with periodic boundaries and then read back for non-periodic boundaries. Accepting a non-zero image flag can lead to unexpected results for any operations and computations in LAMMPS that internally use unwrapped coordinates (for example computing the center of mass of a group of atoms). Thus all non-zero image flags for non-periodic dimensions will be be reset to zero on reading the data file and LAMMPS will print a warning message, if that happens. This is equivalent to wrapping atoms individually back into the principal unit cell in that direction. This operation is equivalent to the behavior of the change_box command when used to change periodicity.
If those atoms with non-zero image flags are involved in bonded interactions, this reset can lead to undesired changes, when the image flag values differ between the atoms, i.e. the bonded interaction straddles domain boundaries. For example a bond can become stretched across the unit cell if one of its atoms is wrapped to one side of the cell and the second atom to the other. In those cases the data file needs to be pre-processed externally to become valid again. This can be done by first unwrapping coordinates and then wrapping entire molecules instead of individual atoms back into the principal simulation cell and finally expanding the cell dimensions in the non-periodic direction as needed, so that the image flag would be zero.
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 atoms extend from 0 to 50, you should not specify the box bounds as -10000 and 10000 unless you also use the processors command. 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.
Meaning of other header keywords
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
Atom Type Labels, Bond Type Labels, Angle Type Labels, Dihedral Type Labels, Improper Type Labels = type label maps
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. There must be at least one blank between valid content and the comment. 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.
Angle Type Labels section:
one line per angle type
line syntax: ID label
ID = angle type (1-N) label = alphanumeric type label
Define alphanumeric type labels for each numeric angle type. These can be used in the Angles section in place of a numeric type, but only if the this section appears before the Angles section.
See the Howto type labels doc page for the allowed syntax of type labels and a general discussion of how type labels can be used.
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, or type label) atom1,atom2,atom3 = IDs of 1st,2nd,3rd atom in angle
example:
2 2 17 29 430
The three 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). However, the type can be a numeric value or an alphanumeric label. The latter is only allowed if the type label has been defined by the labelmap command or an Angle Type Labels section earlier in the data file. See the Howto type labels doc page for the allowed syntax of type labels and a general discussion of how type labels can be used.
AngleTorsion Coeffs section:
one line per dihedral type
line syntax: ID coeffs
ID = dihedral type (1-N) coeffs = list of coeffs (see dihedral_coeff)
Atom Type Labels section:
one line per atom type
line syntax: ID label
ID = numeric atom type (1-N) label = alphanumeric type label
Define alphanumeric type labels for each numeric atom type. These can be used in the Atoms section in place of a numeric type, but only if the Atom Type Labels section appears before the Atoms section.
See the Howto type labels doc page for the allowed syntax of type labels and a general discussion of how type labels can be used.
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.
Note
For orthogonal and restricted and general triclinic simulation boxes, the atom coordinates (x,y,z) listed in this section should be inside the corresponding simulation box. For restricted triclinic boxes that means the parallelepiped defined by the xlo xhi, ylo yhi, zlo zhi, and xy xz yz, keywords. For general triclinic boxes that means the parallelepiped defined by the 3 edge vectors and origin specified by the avec, bvec, cvec, and abc origin header keywords. See the discussion in the header section above about how atom coordinates outside the simulation box are (or are not) remapped to be inside the box.
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 |
bpm/sphere |
atom-ID molecule-ID atom-type diameter density x y z |
charge |
atom-ID atom-type q x y z |
dielectric |
atom-ID atom-type q x y z mux muy muz area ed em epsilon curvature |
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 |
electron |
atom-ID atom-type q espin 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 |
mdpd |
atom-ID atom-type rho x y z |
molecular |
atom-ID molecule-ID atom-type x y z |
peri |
atom-ID atom-type volume density x y z |
rheo |
atom-ID atom-type status rho x y z |
rheo/thermal |
atom-ID atom-type status rho energy x y z |
smd |
atom-ID atom-type molecule volume mass kradius cradius x0 y0 z0 x y z |
sph |
atom-ID atom-type rho esph cv x y z |
sphere |
atom-ID atom-type diameter density x y z |
spin |
atom-ID atom-type x y z spx spy spz sp |
tdpd |
atom-ID atom-type x y z cc1 cc2 … ccNspecies |
template |
atom-ID atom-type molecule-ID template-index template-atom x y z |
tri |
atom-ID molecule-ID atom-type triangleflag density x y z |
wavepacket |
atom-ID atom-type charge espin 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, or type label)
bodyflag = 1 for body particles, 0 for point particles
ccN = chemical concentration for tDPD particles for each species (mole/volume units)
cradius = contact radius for SMD particles (distance units)
cs_re,cs_im = real/imaginary parts of wave packet 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)
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)
esph = energy (need units) for SPH particles
espin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
etag = integer ID of electron that each wave packet belongs to
kradius = kernel radius for SMD particles (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) (see general triclinic note below)
q = charge on atom (charge units)
rho = density (need units) for SPH particles
sp = magnitude of magnetic spin of atom (Bohr magnetons)
spx,spy,spz = components of magnetic spin of atom (unit vector) (see general triclinic note below)
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)
x0,y0,z0 = original (strain-free) coordinates of atom (distance units) (see general triclinic note below)
The units for these quantities depend on the unit style; see the units command for details.
For 2d simulations, the atom coordinate z must be specified as 0.0. If the data file is created by another program, then z values for a 2d simulation can be within epsilon of 0.0, and LAMMPS will force them to zero.
Note
If the data file defines a general triclinic box, then the following per-atom values in the list above are per-atom vectors which imply an orientation: (mux,muy,muz) and (spx,spy,spz). This means they should be specified consistent with the general triclinic box and its orientation relative to the standard x,y,z coordinate axes. For example a dipole moment vector which will be in the +x direction once LAMMPS converts from a general to restricted triclinic box, should be specified in the data file in the direction of the A edge vector. Likewise the (x0,y0,z0) per-atom strain-free coordinates should be inside the general triclinic simulation box as explained in the note above. See the Howto triclinic doc page for more details.
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 atom-type can be a numeric value or an alphanumeric label. The latter is only allowed if the type label has been defined by the labelmap command or an Atom Type Labels section earlier in the data file. See the Howto type labels doc page for the allowed syntax of type labels and a general discussion of how type labels can be used.
The molecule ID is a second 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 a non-bonded 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 (as separate files). 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 specific values for each sub-style 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 only appears once in the atom line. E.g. the atom line for atom_style hybrid dipole full would list “q” only once, with the dipole sub-style fields; “q” does not appear with the full sub-style fields.
atom-ID atom-type x y z q mux muy myz molecule-ID
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 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 Howto 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.
Bond Type Labels section:
one line per bond type
line syntax: ID label
ID = bond type (1-N) label = alphanumeric type label
Define alphanumeric type labels for each numeric bond type. These can be used in the Bonds section in place of a numeric type, but only if the this section appears before the Angles section.
See the Howto type labels doc page for the allowed syntax of type labels and a general discussion of how type labels can be used.
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, or type label) atom1,atom2 = IDs of 1st,2nd atom 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). However, the type can be a numeric value or an alphanumeric label. The latter is only allowed if the type label has been defined by the labelmap command or a Bond Type Labels section earlier in the data file. See the Howto type labels doc page for the allowed syntax of type labels and a general discussion of how type labels can be used.
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.
Dihedral Type Labels section:
one line per dihedral type
line syntax: ID label
ID = dihedral type (1-N) label = alphanumeric type label
Define alphanumeric type labels for each numeric dihedral type. These can be used in the Dihedrals section in place of a numeric type, but only if the this section appears before the Dihedrals section.
See the Howto type labels doc page for the allowed syntax of type labels and a general discussion of how type labels can be used.
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, or type label) atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atom 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). However, the type can be a numeric value or an alphanumeric label. The latter is only allowed if the type label has been defined by the labelmap command or a Dihedral Type Labels section earlier in the data file. See the Howto type labels doc page for the allowed syntax of type labels and a general discussion of how type labels can be used.
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.
If the data file defines a general triclinic box, then the quaternion for each ellipsoid should be specified for its orientation relative to the standard x,y,z coordinate axes. When the system is converted to a restricted triclinic box, the ellipsoid quaternions will be altered to reflect the new orientation of the ellipsoid.
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.
Improper Type Labels section:
one line per improper type
line syntax: ID label
ID = improper type (1-N) label = alphanumeric type label
Define alphanumeric type labels for each numeric improper type. These can be used in the Impropers section in place of a numeric type, but only if the this section appears before the Impropers section.
See the Howto type labels doc page for the allowed syntax of type labels and a general discussion of how type labels can be used.
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, or type label) atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atom 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). However, the type can be a numeric value or an alphanumeric label. The latter is only allowed if the type label has been defined by the labelmap command or a Improper Type Labels section earlier in the data file. See the Howto type labels doc page for the allowed syntax of type labels and a general discussion of how type labels can be used.
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. They should be values close to the center point of the line segment specified in the Atoms section of the data file, even if individual end points are outside the simulation box.
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.
If the data file defines a general triclinic box, then the x1,y1 and x2,y2 values for each line segment should be specified for its orientation relative to the standard x,y,z coordinate axes. When the system is converted to a restricted triclinic box, the x1,y1,x2,y2 values will be altered to reflect the new orientation of the line segment.
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 or atom type label) 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.
Using type labels instead of atom type numbers is only allowed if the type label has been defined by the labelmap command or a Atom Type Labels section earlier in the data file. See the Howto type labels doc page for the allowed syntax of type labels and a general discussion of how type labels can be used.
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. They should be values close to the center point of the triangle specified in the Atoms section of the data file, even if individual corner points are outside the simulation box.
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.
If the data file defines a general triclinic box, then the x1,y1,z1 and x2,y2,z2 and x3,y3,z3 values for each triangle should be specified for its orientation relative to the standard x,y,z coordinate axes. When the system is converted to a restricted triclinic box, the x1,y1,z1,x2,y2,z2,x3,y3,z3 values will be altered to reflect the new orientation of the triangle.
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)
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).
If the data file defines a general triclinic box, then each of the 3 vectors (translational velocity, angular momentum, angular velocity) should be specified for the rotated coordinate axes of the general triclinic box. See the Howto triclinic doc page for more details.
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 (re)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 Build settings doc page for details.
Label maps are currently not supported when using the KOKKOS package.
Default
The default for all the extra keywords is 0.