3.3 Molecular Coordinate Input ($molecule)

3.3.2 Reading Molecular Coordinates from a Previous Job or File

(May 16, 2021)

Often users wish to perform several calculations in sequence, where 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 in Section 3.5.

Example 3.8  Reading a geometry from a prior calculation.

$molecule
   READ
$end

In this example, the job1 scratch files are saved in a directory $QCSCRATCH/job1 and are then made available to the job2 calculation. This is achieved with the following commands:

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.

The READ function can also be used 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 3.9  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