Skip to content

GitLab

Last edited by Andrew Wildman
Page history

Molecule

Table of contents

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

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.

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.

Example

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