Q-Chem 4.3 User’s Manual

3.3 Molecular Coordinate Input ($molecule)

The $molecule section communicates to the program the charge, spin multiplicity, and geometry of the molecule being considered. The molecular coordinates input begins with two integers: the net charge and the spin multiplicity of the molecule. The net charge must be between -50 and 50, inclusive (0 for neutral molecules, 1 for cations, -1 for anions, etc.). The multiplicity must be between 1 and 10, inclusive (1 for a singlet, 2 for a doublet, 3 for a triplet, etc.). Each subsequent line of the molecular coordinate input corresponds to a single atom in the molecule (or dummy atom), irrespective of whether using Z-matrix internal coordinates or Cartesian coordinates.

Note: The coordinate system used for declaring an initial molecular geometry by default does not affect that used in a geometry optimization procedure. See Appendix A which discusses the OPTIMIZE package in further detail.

Q-Chem begins all calculations by rotating and translating the user-defined molecular geometry into a Standard Nuclear Orientation whereby the center of nuclear charge is placed at the origin. This is a standard feature of most quantum chemistry programs. This action can be turned off by using SYM_IGNORE=TRUE.

Note:  SYM_IGNORE=TRUE will also turn off determining and using of the point group symmetry.

Note: Q-Chem ignores commas and equal signs, and requires all distances, positions and angles to be entered as Angstroms and degrees unless the INPUT_BOHR $rem variable is set to TRUE, in which case all lengths are assumed to be in bohr.

Example 3.3  A molecule in Z-matrix coordinates. Note that the $molecule input begins with the charge and multiplicity.

   0 1
   H1 O distance
   H2 O distance H1 theta

   distance = 1.0
   theta = 104.5

3.3.1 Reading Molecular Coordinates From a Previous Calculation

Often users wish to perform several calculations in quick succession, whereby the later calculations rely on results obtained from the previous ones. For example, a geometry optimization at a low level of theory, followed by a vibrational analysis and then, perhaps, single-point energy at a higher level. Rather than having the user manually transfer the coordinates from the output of the optimization to the input file of a vibrational analysis or single point energy calculation, Q-Chem can transfer them directly from job to job.

To achieve this requires that:

Example 3.4  Reading a geometry from a prior calculation.


localhost-1> qchem job1.in job1.out job1
localhost-2> qchem job2.in job2.out job1

In this example, the job1 scratch files are saved in a directory $QCSCRATCH/job1 and are then made available to the job2 calculation.

Note: The program must be instructed to read specific scratch files by the input of job2.

Users are also able to use the READ function for molecular coordinate input using Q-Chem’s batch job file, as described later in this chapter.

3.3.2 Reading Molecular Coordinates from Another File

Users are able to use the READ function to read molecular coordinates from a second input file. The format for the coordinates in the second file follows that for standard Q-Chem input, and must be delimited with the $molecule and $end keywords.

Example 3.5  Reading molecular coordinates from another file. filename may be given either as the full file path, or path relative to the working directory.

   READ filename