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.

$molecule
   0 1
   O
   H1 O distance
   H2 O distance H1 theta

   distance = 1.0
   theta = 104.5
$end

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:

The READ variable is entered into the molecular coordinate input
Scratch files from a previous calculation have been saved. These may be obtained explicitly by using the save option across multiple job runs as described below and in Chapter 2, or implicitly when running multiple calculations in one input file, as described later in this Chapter.

Example 3.4 Reading a geometry from a prior calculation.

$molecule
   READ
$end

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.

$molecule
   READ filename
$end