Molecule

Table of contents
Details
Keywords
Example

Details

The MOLECULE input section specifies the molecular information: such as geometry, (approxmiate) spin multiplicity, and charge. The MOLECULE section is a required section for all ChronusQ jobs.

Keywords

Keyword	Type	Description	Required?	Default
`CHARGE`	Signed Integer	Overall molecular charge (in electrons)	Yes	N/A
`MULT`	Unsigned Integer	Approximate spin multiplicity	No	0
`GEOM`	Multiline String	Geometry specification from input file (in Angstroms)	Yes if `READGEOM` is `INPUTFILE`	N/A
`READGEOM`	String	Location of geometry specification (`INPUTFILE` or `FCHK`)	No	`INPUTFILE`

The `GEOM` Keyword

The GEOM keyword provides the specification for the position and identity of all atoms in the system. It is a multiline keyword, meaning it expects data to be provided as indented lines after the declaration. The data lines for the GEOM keyword are in the format:

  ATOMIC_SYMBOL  POSITION_X  POSITION_Y  POSITION_Z  QM_NUCLEI

Currently, only cartesian coordinates in Angstroms are available. As an example, take this specification of the geometry of ammonia:

geom:
  N   -0.00000    0.00000    0.00000
  H    1.01733   -0.06831   -0.01031
  H   -0.31160   -0.66357    0.70776
  H   -0.31160   -0.38951   -0.89427

Note that the geometry must be indented relative to the GEOM keyword.

"QM_NUCLEI" specifies whether or not a specified atom is meant to be treated quantum-mechanically with NEO methods. As of 0.6.0, only protons may be treated quantum-mechanically. This input only takes "Q" if wishing to use NEO. There is no input required for specifying conventional nuclear treatment. For example, below is the previous ammonia geometry with all three protons treated with NEO and the nitrogen conventionally:

geom:
  N   -0.00000    0.00000    0.00000
  H    1.01733   -0.06831   -0.01031 Q
  H   -0.31160   -0.66357    0.70776 Q
  H   -0.31160   -0.38951   -0.89427 Q

The `READGEOM` Keyword

Location to retrieve geometry. Either INPUTFILE (default) or FCHK.

ChronusQ currently supports reading geometry specification from a Gaussian formatted checkpoint file. If this is desired, set READGEOM to FCHK. You must also specify the formatted checkpoint file on the invocation of ChronusQ. (See Running ChronusQ)

INPUTFILE: Geometry specification in ChronusQ input file (see example below)
- The GEOM keyword must also be specified.
FCHK: Geometry specification in fhck file from the Gaussian software package
- The GEOM keyword will be ignored.
- Atoms are assumed to be the default isotope.

User-Specified Nuclear Charge

When READGEOM=INPUTFILE, the user has the option of specifying atomic nuclear charges in the GEOM entry. This can be done by adding parentheses after the atomic symbol containing the nuclear charge value. Below is the example given in the GEOM Keyword section, but now one H atom has Z=0.5.

geom:
  N        -0.00000    0.00000    0.00000
  H(0.5)    1.01733   -0.06831   -0.01031
  H        -0.31160   -0.66357    0.70776
  H        -0.31160   -0.38951   -0.89427

Example

[Molecule]
charge = 0
mult = 3
geom: 
  O               0.               0.        0.608586
  O               0.               0.       -0.608586