Table of contents
- Table of contents
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.
||Signed Integer||Overall molecular charge (in electrons)||Yes||N/A|
||Unsigned Integer||Approximate spin multiplicity||No||0|
||Multiline String||Geometry specification from input file (in Angstroms)||Yes if
||String||Location of geometry specification (
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
"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
Location to retrieve geometry. Either
INPUTFILE (default) or
ChronusQ currently supports reading geometry specification from a Gaussian formatted checkpoint file. If this is desired, set
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)
GEOMkeyword must also be specified.
FCHK: Geometry specification in fhck file from the Gaussian software package
GEOMkeyword will be ignored.
- Atoms are assumed to be the default isotope.
User-Specified Nuclear Charge
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
[Molecule] charge = 0 mult = 3 geom: O 0. 0. 0.608586 O 0. 0. -0.608586