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).
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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.
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Dihedrals section:
one line per dihedral
? line syntax: ID type atom1 atom2 atom3 atom4 ? ID = number of dihedral (1-Ndihedrals) ? type = dihedral type (1-Ndihedraltype)
? atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in dihedral ? example:
? 12 4 17 29 30 21
The 4 atoms are ordered linearly within the dihedral. The Dihedrals section must appear after the Atoms section. All values in this section must be integers (1, not 1.0).
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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 \
?
The 3 shape values specify the 3 diameters or aspect ratios of a finite-size ellipsoidal particle, when it is oriented along the 3 coordinate axes. They must all be non-zero values.
The values quatw, quati, quatj, and quatk set the orientation of the atom as a quaternion (4-vector). Note that the shape attributes specify the aspect ratios of an ellipsoidal particle, which is oriented by default with its x-axis along the
simulation box's x-axis, and similarly for y and z. If this body is rotated (via the right-hand rule) by an angle theta around a unit vector (a,b,c), then the quaternion that represents its new orientation is given by (cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These 4 components are quatw, quati, quatj, and quatk as specified above. LAMMPS normalizes each atom's quaternion in case (a,b,c) is not specified as a unit vector. The Ellipsoids section must appear after the Atoms section.
EndBondTorsion Coeffs section:
? ? ? ?
one line per dihedral type line syntax: ID coeffs ID = dihedral type (1-N)
coeffs = list of coeffs (see class 2 section of dihedral_coeff)
Improper Coeffs section:
one line per improper type ? line syntax: ID coeffs ? ID = improper type (1-N) ? coeffs = list of coeffs ? example:
? 2 20 0.0548311
The number and meaning of the coefficients are specific to the defined improper style. See the improper_style and improper_coeff commands for details. Coefficients can also be set via the improper_coeff command in the input script.
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Impropers section:
one line per improper
? line syntax: ID type atom1 atom2 atom3 atom4 ? ID = number of improper (1-Nimpropers) ? type = improper type (1-Nimpropertype)
? atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atoms in improper ? example:
? 12 3 17 29 13 100
The ordering of the 4 atoms determines the definition of the improper angle used in the formula for each improper style. See the doc pages for individual styles for details.
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The Impropers section must appear after the Atoms section. All values in this section must be integers (1, not 1.0).
Lines section:
one line per line segment
? line syntax: atom-ID x1 y1 x2 y2
? atom-ID = ID of atom which is a line segment ? x1,y1 = 1st end point ? x2,y2 = 2nd end point ? example:
? 12 1.0 0.0 2.0 0.0
The Lines section must appear if atom_style line is used and any atoms are listed in the Atoms section with a lineflag = 1. The number of lines should be specified in the header section via the \
?
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 \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.
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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.
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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.
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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 \
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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 \(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 electron ellipsoid sphere hybrid atom-ID vx vy vz atom-ID vx vy vz ervel atom-ID vx vy vz lx ly lz atom-ID vx vy vz wx wy wz 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 \would appear. These are listed in the same order they appear as listed above. Thus if atom_style hybrid electron sphere
were used in the input script, each velocity line would have these fields: atom-ID vx vy vz ervel wx wy wz
Translational velocities can also be set by the velocity command in the input script.
Restrictions:
To read gzipped data files, you must compile LAMMPS with the -DLAMMPS_GZIP option - see the Making LAMMPS section of the documentation. Related commands:
read_dump, read_restart, create_atoms, write_data Default: none
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands
atom_style command Syntax:
atom_style style args
? style
= angle or atomic or body or bond or charge or dipole or electron or ellipsoid or full or line or meso or molecular or peri or sphere or tri or template or hybrid
args = none for any style except body and hybrid body args = bstyle bstyle-args bstyle = style of body particles
bstyle-args = additional arguments specific to the bstyle see the body doc page for details template args = template-ID
template-ID = ID of molecule template specified in a separate molecule command hybrid args = list of one or more sub-styles, each with their args Examples:
atom_style atomic atom_style bond atom_style full
atom_style body nparticle 2 10 atom_style hybrid charge bond
atom_style hybrid charge body nparticle 2 5 atom_style template myMols Description: