5. Input of Coordinates

Coordinates can be either specified directly in the input file or read from an external file, and they can be in either Cartesian (“xyz”) or internal coordinate format (“Z-matrix”).

5.1. Reading coordinates from the input file

The easiest way to specify coordinates in the input file is by including a block like the following, enclosed by star symbols:

* CType Charge Multiplicity
... 
coordinate specifications 
...
*

Here CType can be one of xyz, int (or internal), or gzmt, which correspond to Cartesian coordinates, internal coordinates, and internal coordinates in Gaussian Z-matrix format.

The input of Cartesian coordinates in the “xyz” option is straightforward. Each line consists of the label for a given atom type and three numbers that specify the coordinates of the atom. The units can be either Ångström or Bohr. The default is to specify the coordinates in Ångströms (this can be changed through the keyword line or via the variable Units in the %coords main block described below).

* xyz Charge Multiplicity
Atom1   x1  y1  z1
Atom2   x2  y2  z2
 ...
*

For example for CO\(^+\) in a \(S=1/2\) state (multiplicity = \(2\times1/2+1=2\))

* xyz 1 2
C  0.0  0.0  0.0
O  0.0  0.0  1.1105
*

Internal coordinates are specified in the form of the familiar “Z-matrix”. A Z-matrix basically contains information about molecular connectivity, bond lengths, bond angles and dihedral angles. The program then constructs Cartesian coordinates from this information. Both sets of coordinates are printed in the output such that conversion between formats is facilitated. The input in that case looks like:

* int Charge Multiplicity
Atom1  0  0  0    0.0   0.0   0.0
Atom2  1  0  0    R1    0.0   0.0
Atom3  1  2  0    R2    A1    0.0
Atom4  1  2  3    R3    A2    D1
. . .
AtomN  NA NB NC   RN    AN    DN
*

The rules for connectivity in the “internal” mode are as follows:

  • NA: The atom that the actual atom has a distance (RN) with.

  • NB: The actual atom has an angle (AN) with atoms NA and NB.

  • NC: The actual atom has a dihedral angle (DN) with atoms NA, NB and NC. This is the angle between the actual atom and atom NC when looking down the NA-NB axis.

  • Note that - contrary to other parts in ORCA - atoms are counted starting from 1.

Angles are always given in degrees! The rules are compatible with those used in the well known MOPAC and ADF programs.

Finally, gzmt specifies internal coordinates in the format used by the Gaussian program. This resembles the following:

* gzmt 0 1
    C
    O   1   4.454280
    Si  2   1.612138    1   56.446186
    O   3   1.652560    2   114.631525  1   -73.696925
    C   4   1.367361    3   123.895399  2   -110.635060
    ...
*

An alternative way to specify coordinates in the input file is through the use of the %coords block, which is organized as follows:

%coords
 CTyp   xyz     # the type of coordinates = xyz or internal
 Charge 0       # the total charge of the molecule
 Mult   2       # the multiplicity = 2S+1
 Units  Angs    # the unit of length = angs or bohrs

 # the subblock coords is for the actual coordinates
 # for CTyp=xyz
  coords
     Atom1   x1  y1  z1
     Atom2   x2  y2  z2
  end
 # for CTyp=internal
  coords
     Atom1  0  0  0    0.0   0.0   0.0
     Atom2  1  0  0    R1    0.0   0.0
     Atom3  1  2  0    R2    A1    0.0
     Atom4  1  2  3    R3    A2    D1
      . . .
     AtomN  NA NB NC   RN    AN    DN
  end
end

5.2. Reading coordinates from external files

It is also possible to read the coordinates from external files. The most common format is a .xyz file, which can in principle contain more than one structure (see section Multiple XYZ File Scans for this multiple XYZ feature):

* xyzfile Charge Multiplicity Filename

For example:

* xyzfile 1 2 mycoords.xyz

A lot of graphical tools like Gabedit, molden or Jmol can write Gaussian Z-Matrices (.gzmt). ORCA can also read them from an external file with the following

* gzmtfile 1 2 mycoords.gzmt

Note that if multiple jobs are specified in the same input file then new jobs can read the coordinates from previous jobs. If no filename is given as fourth argument then the name of the actual job is automatically used.

... specification for the first job

$new_job
! keywords
* xyzfile 1 2

In this way, optimization and single point jobs can be very conveniently combined in a single, simple input file. Examples are provided in the following sections.

5.3. Special definitions

  • Dummy atoms are defined in exactly the same way as any other atom, by using “DA”, “X”, or “Xx” as the atomic symbol.

  • Ghost atoms are specified by adding “:” right after the symbol of the element (see Counterpoise Correction).

  • Point charges are specified with the symbol “Q”, followed by the charge (see Inclusion of Point Charges).

  • Embedding potentials are specified by adding a “>” right after the symbol of the element (see Embedding Potentials).

  • Non-standard isotopes or nuclear charges are specified with the statements “M = …” and “Z = …”, respectively, after the atomic coordinate definition.

    Note

    1. The nuclear charge can adopt non-integer values

    2. When the nuclear charge is modified throughca “Z = …” statement, the total charge of the system should still be calculated based on the unmodified charge. For example, for a calculation of a single hydrogen atom whose Z is set to 1.5, a charge of 0 and a spin multiplicity of 2 should be entered into the charge and multiplicity sections of the input file, despite that the actual total charge is 0.5.

  • Fragments can be conveniently defined by declaring the fragment number a given atom belongs to in parentheses “(n)” following the element symbol (see Fragment Specification).

  • Frozen coordinates, which are not changed during optimizations in Cartesian coordinates, are defined with a “$” symbol after the X, Y, and/or Z coordinate value (cf. constraints on all 3 Cartesian components Constrained Optimizations).