The freqchk utility is used to retrieve frequency and thermochemistry data from a checkpoint file, with optional specification of an alternate temperature, pressure, scale factor, and/or isotope substitutions.
The full syntax of the freqchk command is:
$ freqchk checkpoint-file [options] [answers to prompts]
If the checkpoint file name does not include an extension, .fchk is assumed; both formatted and unformatted checkpoint files are accepted.
The following options are supported:
-o filename
Send output to the specified file. By default, output is displayed to the screen.
-nfd
Skip the diagonalization of the full (3Natoms)2 matrix (as with Freq=NoDiagFull).
-sel
Select normal modes for inclusion. The utility will prompt for required information as usual, and then pause to allow you to enter the desired modes (without prompting). You can specify mode numbers and/or atom lists as for Freq=ReadNormalModes. See the example below.
-read
Read normal modes from the checkpoint file rather than computing them.
-save
Save normal modes; only works with binary checkpoint files. When combined with -sel, only the selected modes will be in the checkpoint for a subsequent -read operation.
-np=N
Use N processors to compute the frequency analysis.
freqchk can prompt for all other information that it requires. The following annotated sessions illustrate its use in this mode (user input is set in boldface type):
$ freqchk
Checkpoint file? solvent.chk
Write Hyperchem files? n
Temperature (K)? [0=>298.15] 0 Zero must be entered; return doesn’t work
Pressure (Atm)? [0=>1 atm] 0
Scale factor for frequencies during thermochemistry? [0=>1/1.12] 0
Do you want the principal isotope masses? [Y]: Return accepts defaults
Isotopes for each atom are printed
Full mass-weighted force constant matrix:
Low frequencies --- -948.3077 .0008 .0020 .0026
…
Normal Gaussian frequency output follows …
1 2
?A ?A
Frequencies -- 1885.3939 3853.5773
Red. masses -- 1.0920 1.0366
Frc consts -- 2.2871 9.0697
IR Inten -- 17.3416 21.5997
Raman Activ -- 7.8442 67.0384
Depolar -- .7428 .2248
Atom AN X Y Z X Y Z Normal modes
1 8 .06 .00 .04 .04 .00 .02
2 1 -.70 .00 .03 .01 .00 -.71
…
-------------------
- Thermochemistry -
-------------------
Temperature 298.150 Kelvin. Pressure 1.00000 Atm.
Thermochemistry will use frequencies scaled by .8929.
…
Zero-point vibrational energy 53494.5 (Joules/Mol)
12.78550 (Kcal/Mol)
VIBRATIONAL TEMPERATURES: 2422.01 4950.36 5495.38 (KELVIN)
Zero-point and thermal corrections:
Zero-point correction= .020375 (Hartree/Particle)
Thermal corr to Energy= .023210
Thermal corr to Enthalpy= .024154
Thermal corr to Gibbs Free Energy= .045589
E=thermal energy; CV=constant volume molar heat capacity; S=entropy
E CV S
KCAL/MOL CAL/MOL-KELVIN CAL/MOL-KELVIN
TOTAL 14.564 6.001 45.114
ELECTRONIC .000 .000 .000
TRANSLATIONAL .889 2.981 34.609
ROTATIONAL .889 2.981 10.500
VIBRATIONAL 12.787 .039 .005
Partition functions
Q LOG10(Q) LN(Q)
TOTAL BOT .561443D-01 -1.250695 -2.880127
TOTAL V=0 .132155D+09 8.121085 18.699192
VIB (BOT) .424961D-09 -9.371650 -21.579023
VIB (V=0) .100030D+01 .000129 .000297
ELECTRONIC .100000D+01 .000000 .000000
TRANSLATIONAL .300436D+07 6.477751 14.915574
ROTATIONAL .439749D+02 1.643204 3.783618
$ freqchk solvent.chk Checkpoint filename can be placed on the command line
Write Hyperchem files? n
Temperature (K)? [0=>298.15] 300 Alternate temperature.
Pressure (Atm)? [0=>1 atm] 1.5 Alternate pressure.
Scale factor for freqs during thermochem? [0=>1/1.12] 1 No scaling.
Do you want to use the principal isotope masses? [Y]: n
For each atom, give the integer mass number.
In each case, the default is the principal isotope.
Atom number 1, atomic number 8: [16] Return accepts default.
Atom number 2, atomic number 1: [1] 2 Specify isotope masses as integers.
Frequency output follows ...
Frequency output follows, reflecting the values specified above. Note that if scaling is specified, only the thermochemistry data reflects it; the frequencies themselves are not scaled.
An additional prompt sometimes appears in a freqchk session:
Project out gradient direction? [N]
This prompt appears when the forces are significantly non-zero. A possible reason for the forces being non-zero is that the frequencies were done at a point along the IRC, so projecting out the gradient direction may be useful. If the forces are non-zero in other circumstances, the structure is not a stationary point and its geometry should be optimized in order to obtain a meaningful vibrational analysis. However, if you want to look at the frequencies, for example, to see if the starting point for an optimization has the correct curvature, then the direction of the gradient should not be projected out.
As an alternative to interactive mode, you can specify all freqchk input on the command line, as in this example, which performs the same operation as the final interactive session above:
$ freqchk solvent.chk N 300 1.5 1 N N
You will be prompted for the isotopes if the second-to-last parameter is N. The final parameter is the answer to the gradient direction prompt should it appear; if this parameter is omitted and the prompt is relevant, the utility will prompt you.
Selecting Modes. The following command and input selects modes 1-5 and any others involving nitrogen atoms, sending the output to the file ala_freq.out:
$ freqchk ala.chk -sel -o ala_freq.out N 0 0 0 N N 1-5 atoms=N3 Input ends with a blank line. $ more ala_freq.out Frequency data is ready for viewing. …
Last updated on: 9 Jun 2009