lammps/doc/read_data.txt

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)

:line

read_data command :h3

[Syntax:]

read_data file :pre

file = name of data file to read in :ul

[Examples:]

read_data data.lj
read_data ../run7/data.polymer.gz :pre

[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"_read_restart.html and
"create_atoms"_create_atoms.html 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 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 "Bond" and "Coeffs" is not
valid.

:line

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
{ellipsoids} = # of ellipsoids 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 :ul

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"_boundary.html command.

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.

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 "this section"_Section_howto.html#howto_12 of the doc pages for a
geometric description of triclinic boxes, as defined by LAMMPS, and
how to transform these parameters to and from other commonly used
triclinic representations.

When a triclinic system is used, the simulation domain must be
periodic in any dimensions with a non-zero tilt factor, as defined by
the "boundary"_boundary.html 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"_fix_deform.html 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.

IMPORTANT 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"_boundary.html 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"_boundary.html
command).  When using "shrink-wrap" boundary conditions (see the
"boundary"_boundary.html command), a huge (mostly empty) box may cause
a parallel simulation to lose atoms the first time that LAMMPS
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"_fix_bond_create.html command.  This will pre-allocate
space in LAMMPS data structures for storing the new bonds.

The "ellipsoids" setting is only used with atom_style
ellipsoid"_atom_style.html and specifies how many of the atoms are
finite-size ellipsoids; the remainder are point particles.  See the
discussion of ellipseflag and the {Ellipsoids} section below.

:line

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

{Atoms, Velocities, Ellipsoids, Masses} = atom-property sections 
{Bonds, Angles, Dihedrals, Impropers} = molecular topology sections 
{Pair 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 :ul

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 :pre

:line

{Angle Coeffs} section:

one line per angle type :ulb,l
line syntax: ID coeffs :l
  ID = angle type (1-N)
  coeffs = list of coeffs :pre
example: :l
  6 70 108.5 0 0 :pre
:ule

The number and meaning of the coefficients are specific to the defined
angle style.  See the "angle_style"_angle_style.html and
"angle_coeff"_angle_coeff.html commands for details.  Coefficients can
also be set via the "angle_coeff"_angle_coeff.html command in the
input script.

:line

{AngleAngle Coeffs} section:

one line per improper type :ulb,l
line syntax: ID coeffs :l
  ID = improper type (1-N)
  coeffs = list of coeffs (see "improper_coeff"_improper_coeff.html) :pre
:ule

:line

{AngleAngleTorsion Coeffs} section:

one line per dihedral type :ulb,l
line syntax: ID coeffs :l
  ID = dihedral type (1-N)
  coeffs = list of coeffs (see "dihedral_coeff"_dihedral_coeff.html) :pre
:ule

:line

{Angles} section:

one line per angle :ulb,l
line syntax: ID type atom1 atom2 atom3 :l
  ID = number of angle (1-Nangles)
  type = angle type (1-Nangletype)
  atom1,atom2,atom3 = IDs of 1st,2nd,3rd atoms in angle :pre
example: :b
  2 2 17 29 430 :pre
:ule

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).

:line

{AngleTorsion Coeffs} section:

one line per dihedral type :ulb,l
line syntax: ID coeffs :l
  ID = dihedral type (1-N)
  coeffs = list of coeffs (see "dihedral_coeff"_dihedral_coeff.html) :pre
:ule

:line

{Atoms} section:

one line per atom
line syntax: depends on atom style :ul

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"_atom_style.html 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
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
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
molecular: atom-ID molecule-ID atom-type x y z
peri: atom-ID atom-type volume density x y z
sphere: atom-ID atom-type diameter 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 ...  :tb(s=:)

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
density = density of atom (mass/distance^3 units)
volume = volume of atom (distance^3 units)
x,y,z = coordinates of atom
mux,muy,muz = components of dipole moment of atom (dipole units)
spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
eradius = electron radius (or fixed-core radius)
etag = integer ID of electron that each wavepacket belongs to
cs_re,cs_im = real/imaginary parts of wavepacket coefficients :ul

The units for these quantities depend on the unit style; see the
"units"_units.html 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"_atom_modify.html 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 ellipseflag determines whether the particle is a finite-size
ellipsoid of finite size, or a point particle.  Additional attributes
must be defined for each ellipsoid in the {Ellipsoids} 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.

The density is used in conjunction with the particle volume for
finite-size particles to set the mass of the particle as mass =
density * volume.  If the volume is 0.0, meaning a point particle,
then the density value is used as the mass.

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"_atom_style.html 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 :pre

were used in the input script, each atom line would have these fields:

atom-ID atom-type x y z q diameter density :pre

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.  LAMMPS updates these flags as atoms
cross periodic boundaries during the simulation.  The flags can be
output with atom snapshots via the "dump"_dump.html command.

If nx,ny,nz values are not set in the data file, LAMMPS 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"_replicate.html
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"_velocity.html or "set"_set.html command in the input
script.

:line

{Bond Coeffs} section:

one line per bond type :ulb,l
line syntax: ID coeffs :l
  ID = bond type (1-N)
  coeffs = list of coeffs :pre
example: :l
  4 250 1.49 :pre
:ule

The number and meaning of the coefficients are specific to the defined
bond style.  See the "bond_style"_bond_style.html and
"bond_coeff"_bond_coeff.html commands for details.  Coefficients can
also be set via the "bond_coeff"_bond_coeff.html command in the input
script.

:line

{BondAngle Coeffs} section:

one line per angle type :ulb,l
line syntax: ID coeffs :l
  ID = angle type (1-N)
  coeffs = list of coeffs (see class 2 section of "angle_coeff"_angle_coeff.html) :pre
:ule

:line

{BondBond Coeffs} section:

one line per angle type :ulb,l
line syntax: ID coeffs :l
  ID = angle type (1-N)
  coeffs = list of coeffs (see class 2 section of "angle_coeff"_angle_coeff.html) :pre
:ule

:line

{BondBond13 Coeffs} section:

one line per dihedral type :ulb,l
line syntax: ID coeffs :l
  ID = dihedral type (1-N)
  coeffs = list of coeffs (see class 2 section of "dihedral_coeff"_dihedral_coeff.html) :pre
:ule

:line

{Bonds} section:

one line per bond :ulb,l
line syntax: ID type atom1 atom2 :l
  ID = bond number (1-Nbonds)
  type = bond type (1-Nbondtype)
  atom1,atom2 = IDs of 1st,2nd atoms in bond :pre
example: :l
  12 3 17 29 :pre
:ule

The {Bonds} section must appear after the {Atoms} section.  All values
in this section must be integers (1, not 1.0).

:line

{Dihedral Coeffs} section:

one line per dihedral type :ulb,l
line syntax: ID coeffs :l
  ID = dihedral type (1-N)
  coeffs = list of coeffs :pre
example: :l
  3 0.6 1 0 1 :pre
:ule

The number and meaning of the coefficients are specific to the defined
dihedral style.  See the "dihedral_style"_dihedral_style.html and
"dihedral_coeff"_dihedral_coeff.html commands for details.
Coefficients can also be set via the
"dihedral_coeff"_dihedral_coeff.html command in the input script.

:line

{Dihedrals} section:

one line per dihedral :ulb,l
line syntax: ID type atom1 atom2 atom3 atom4 :l
  ID = number of dihedral (1-Ndihedrals)
  type = dihedral type (1-Ndihedraltype)
  atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in dihedral :pre
example: :l
  12 4 17 29 30 21 :pre
:ule

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).

:line

{Ellipsoids} section:

one line per ellipsoid :ulb,l
line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk :l
  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
type = bond type (1-Nbondtype)
  atom1,atom2 = IDs of 1st,2nd atoms in bond :pre
example: :l
  12 3 17 29 :pre
:ule

The {Ellipsoids} section must appear if "atom_style
ellipsoid"_atom_style.html 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.

:line

{EndBondTorsion Coeffs} section:

one line per dihedral type :ulb,l
line syntax: ID coeffs :l
  ID = dihedral type (1-N)
  coeffs = list of coeffs (see class 2 section of "dihedral_coeff"_dihedral_coeff.html) :pre
:ule

:line

{Improper Coeffs} section:

one line per improper type :ulb,l
line syntax: ID coeffs :l
  ID = improper type (1-N)
  coeffs = list of coeffs :pre
example: :l
  2 20 0.0548311 :pre
:ule

The number and meaning of the coefficients are specific to the defined
improper style.  See the "improper_style"_improper_style.html and
"improper_coeff"_improper_coeff.html commands for details.
Coefficients can also be set via the
"improper_coeff"_improper_coeff.html command in the input script.

:line

{Impropers} section:

one line per improper :ulb,l
line syntax: ID type atom1 atom2 atom3 atom4 :l
  ID = number of improper (1-Nimpropers)
  type = improper type (1-Nimpropertype)
  atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in improper :pre
example: :l
  12 3 17 29 13 100 :pre
:ule

The ordering of the 4 atoms determines the definition of the improper
angle used in the formula for each "improper
style"_improper_style.html.  See the doc pages for individual styles
for details.

The {Impropers} section must appear after the {Atoms} section.  All
values in this section must be integers (1, not 1.0).

:line

{Masses} section:

one line per atom type :ulb,l
line syntax: ID mass :l
  ID = atom type (1-N)
  mass = mass value :pre
example: :l
  3 1.01 :pre
:ule

This defines the mass of each atom type.  This can also be set via the
"mass"_mass.html command in the input script.  This section cannot be
used for atom styles that define a mass for individual atoms -
e.g. "atom_style sphere"_atom_style.html.

:line

{MiddleBondTorsion Coeffs} section:

one line per dihedral type :ulb,l
line syntax: ID coeffs :l
  ID = dihedral type (1-N)
  coeffs = list of coeffs (see class 2 section of "dihedral_coeff"_dihedral_coeff.html) :pre
:ule

:line

{Pair Coeffs} section:

one line per atom type :ulb,l
line syntax: ID coeffs :l
  ID = atom type (1-N)
  coeffs = list of coeffs :pre
example: :l
  3 0.022 2.35197 0.022 2.35197 :pre
:ule

The number and meaning of the coefficients are specific to the defined
pair style.  See the "pair_style"_pair_style.html and
"pair_coeff"_pair_coeff.html commands for details.  Coefficients can
also be set via the "pair_coeff"_pair_coeff.html command in the input
script.

:line

{Velocities} section:

one line per atom
line syntax: depends on atom style :ul

all styles except those listed: atom-ID vx vy vz
dipole: atom-ID vx vy vz wx wy wz
electron: atom-ID vx vy vz evel
ellipsoid: atom-ID vx vy vz lx ly lz
sphere: atom-ID vx vy vz wx wy wz :tb(s=:)

where the keywords have these meanings:

vx,vy,vz = translational velocity of atom
lx,ly,lz = angular momentum of aspherical atom
wx,wy,wz = angular velocity of spherical atom
evel = 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 evel are in "units"_units.html of velocity.  Lx, ly,
lz are in units of angular momentum (distance-velocity-mass).  Wx, Wy,
Wz are in units of angular velocity (radians/time).

Translational velocities can also be set by the
"velocity"_velocity.html command in the input script.

:line

[Restrictions:]

To read gzipped data files, you must compile LAMMPS with the
-DLAMMPS_GZIP option - see the "Making
LAMMPS"_Section_start.html#start_2 section of the documentation.

[Related commands:]

"read_restart"_read_restart.html, "create_atoms"_create_atoms.html

[Default:] none