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Cartesian coordinate input

Cartesian coordinate input

The default in NWChem is to specify the geometry information entirely in Cartesian coordinates, and examples of this format have appeared above (e.g, Water Molecule Input). Each center (usually an atom) is identified on a line of the following form:

   <string tag> <real x y z> [vx vy vz] \
       [charge <real charge>] [mass <real mass>] \
       [(nuc || nucl || nucleus) <string nucmodel>]

The string <tag> is the name of the atom or center, and its case (upper or lower) is important. The tag is limited to 16 characters and is interpreted as follows:

  • If the entry for <tag> begins with either the symbol or name of an element (regardless of case), then the center is treated as an atom of that type. The default charge is the atomic number (adjusted for the presence of ECPs by the ECP NELEC directive). Additional characters can be added to the string, to distinguish between atoms of the same element (For example, the tags oxygen, O, o34, olonepair, and Oxygen-ether, will all be interpreted as oxygen atoms.).
  • If the entry for <tag> begins with the characters bq or x (regardless of case), then the center is treated as a dummy center with a default zero charge (Note: a tag beginning with the characters xe will be interpreted as a xenon atom rather than as a dummy center.). Dummy centers may optionally have basis functions or non-zero charge.

It is important to be aware of the following points regarding the definitions and usage of the values specified for the variable <tag> to describe the centers in a system:

  • If the tag begins with characters that cannot be matched against an atom, and those characters are not BQ or X, then a fatal error is generated.
  • The tag of a center is used in the BASIS and ECP directives to associate functions with centers.
  • All centers with the same tag will have the same basis functions.
  • When using automatic symmetry detection, only centers with the same tag will be candidates for testing for symmetry equivalence.
  • The user-specified charges (of all centers, atomic and dummy) and any net total charge of the system are used to determine the number of electrons in the system.

The Cartesian coordinates of the atom in the molecule are specified as real numbers supplied for the variables x, y, and z following the characters entered for the tag. The values supplied for the coordinates must be in the units specified by the value of the variable on the first line of the GEOMETRY directive input.

After the Cartesian coordinate input, optional velocities may be entered as real numbers for the variables vx, vy, and vz. The velocities should be given in atomic units and are used in QMD and PSPW calculations.

The Cartesian coordinate input line also contains the optional keywords charge, mass and nucleus, which allow the user to specify the charge of the atom (or center) and its mass (in atomic mass units), and the nuclear model. The default charge for an atom is its atomic number, adjusted for the presence of ECPs. In order to specify a different value for the charge on a particular atom, the user must enter the keyword charge, followed by the desired value for the variable <charge>.

The default mass for an atom is taken to be the mass of its most abundant naturally occurring isotope or of the isotope with the longest half-life. To model some other isotope of the element, its mass must be defined explicitly by specifying the keyword mass, followed by the value (in atomic mass units) for the variable <mass>.

The default nuclear model is a point nucleus. The keyword nucleus (or nucl or nuc) followed by the model name <nucmodel> overrides this default. Allowed values of <nucmodel> are point or pt and finite or fi. The finite option is a nuclear model with a Gaussian shape. The RMS radius of the Gaussian is determined by the atomic mass number via the formula rRMS = 0.836*A1/3+0.57 fm. The mass number A is derived from the variable <mass>.

The geometry of the system can be specified entirely in Cartesian coordinates by supplying a <tag> line of the type described above for each atom or center. The user has the option, however, of supplying the geometry of some or all of the atoms or centers using a Z-matrix description. In such a case, the user supplies the input tag line described above for any centers to be described by Cartesian coordinates, and then specifies the remainder of the system using the optional ZMATRIX directive described below in Z-matrix input.