Import GAUSSIAN File
Previous  Top  Next

Dialog Box: Import GAUSSIAN File [File menu or button in Startup or Control Window]

This will import either a GAUSSIAN log (.log) file or a formatted checkfile (.fch or .fchk), obtaining the atomic coordinates and the Cartesian force matrix. VIBRATZ will convert the force matrix from Hartrees/Bohr^2 to md/A and write a file named infile.car if the GAUSSIAN file is infile.fch or infile.log and will be set up to use Cartesian forces in this file.

Recent versions of GAUSSIAN can write the required information to a log file - the sections which CRYSCON requires are headed "Input orientation:" and "Force constants in Cartesian coordinates:". For older GAUSSIAN version it may be necessary to use a formatted checkfile - the required sections are "Current cartesian coordinates" and "Cartesian Force Constants"

It is assumed that no symmetry is being used by GAUSSIAN, and that all atoms are present in the input list, even if some are equivalent by symmetry - you can convert to a calculation using symmetry after the conversion is made (see below).

The following procedure can be used to import a GAUSSIAN or other molecular-orbital output file and convert the forces to valence force constants.

1) If some other type of molecular-orbital output file is being imported (not among the VIBRATZ-supported types), you can probably import the atomic coordinates using the Free-Form import option (cut-and-paste the coordinate section into a separate .inp file). If the Cartesian force matrix is in lower-diagonal form, it will probably be usable without modification (cut-and-paste into a separate text file with the .car extension). If the units are not md/A, it may be necessary to use a scale factor in the Cartesian Forces dialog.

2) If you have some observed frequencies, you can refine the Cartesian scale factor which appears in the Cartesian Forces dialog (Forces menu). To do this, just select any of the least-squares options and hit the Calculate button in the Control Window. (while Use Cartesian forces is selected in the Cartesian Forces dialog).

3) You must set up a complete valence force field (Urey-Bradley forces are not currently supported for the conversion) in the other dialogs of the Forces menu. You may be able to import part or all of these force specifications using the Read Force File option in the Forces menu - the file must have been previously written by VIBRATZ for the same or a similar structure. The force constant values may be zero or dummies - they are not used in the conversion. However, it is best to insert nominal values, then do a calculation using these valence forces to make sure that there are no zero frequencies, i.e. that the forces are complete.

It is theoretically possible to use the bonds and angles in a z-matrix to describe the forces in any molecule, since they constitute a complete geometric description. The specifications can be entered with the Manual Bonds, Manual Angles and Manual Tau dialogs in the Forces menu. In general, however, the z-matrix is a poor description because it uses torsional forces in place of 3-atom angles or even bonds (in cyclic molecules or parts thereof), and the torsion angles are not always valence angles (the legs are not bonds), and because dummy atoms are sometimes used. That is, a z-matrix is usually not a good chemical description of a molecule.

4) Now select Convert Cartesian to Internal in the Forces menu. The results (new force constants) of a special calculation will be shown in the Output Window, and at your option the old or dummy valence force constants will be replaced with the new values derived from the Cartesian matrix.

5) Change the setting in the Cartesian Forces dialog, accessed either from the Control Window or from the Forces menu, to non-Cartesian forces. Now a Calculation (Control Window) will use the new valence forces.

6) If desired, you can change the Symmetry (Input menu), that is use some point- or space-group rather than no symmetry. This will usually involve deleting some symmetry-equivalent input atoms, and possibly a change of orientation, both of which can be done in the Input Atoms dialog (Input menu). If you have used some Manual Forces it may be necessary to change atom numbers in these specifications.

There is a tutorial for importing GAUSSIAN files in the folder GAUSSIAN. The explanation is in the file Gaussian_import.txt.