Skip to content

GitLab

  • Menu
Projects Groups Snippets
    • Loading...
  • Help
    • Help
    • Support
    • Community forum
    • Submit feedback
    • Contribute to GitLab
  • Sign in
  • chronusq_public chronusq_public
  • Project information
    • Project information
    • Activity
    • Labels
    • Planning hierarchy
    • Members
  • Repository
    • Repository
    • Files
    • Commits
    • Branches
    • Tags
    • Contributors
    • Graph
    • Compare
  • Issues 1
    • Issues 1
    • List
    • Boards
    • Service Desk
    • Milestones
  • Merge requests 0
    • Merge requests 0
  • CI/CD
    • CI/CD
    • Pipelines
    • Jobs
    • Schedules
  • Deployments
    • Deployments
    • Environments
    • Releases
  • Monitor
    • Monitor
    • Incidents
  • Analytics
    • Analytics
    • Value stream
    • CI/CD
    • Repository
  • Wiki
    • Wiki
  • Snippets
    • Snippets
  • Activity
  • Graph
  • Create a new issue
  • Jobs
  • Commits
  • Issue Boards
Collapse sidebar
  • ChronusQ
  • chronusq_publicchronusq_public
  • Wiki
  • Input sections
  • Molecule

Last edited by Ben Link May 12, 2022
Page history

Molecule

Table of contents

  • Table of contents
  • Details
  • Keywords
    • The GEOM Keyword
    • The READGEOM Keyword
    • User-Specified Nuclear Charge
  • 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
Clone repository

Overview and Features

Getting ChronusQ

Running ChronusQ

Input sections

     Overview
     QM and PROTQM
     Molecule
     Basis and DFBasis
     Ints
     DFTInts
     SCF
     RT
     Response
     CC
     MCSCF
     Misc

FAQ

Examples

     HF energy
     Relativistic DFT Energy
     Linear Response TDDFT
     Frequency dependent TDHF
     Model Order Reduction of TDDFT
     Electron dynamics

Keyword Reference

Binary Reference