Thefreqchkutility 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 thefreqchkcommand is:
$freqchkcheckpoint-file[options] [answers to prompts]
If the checkpoint file name does not include an extension,.fchkis assumed; both formatted and unformatted checkpoint files are accepted.
The following options are supported:
-ofilename
Send output to the specified file. By default, output is displayed to the screen.
-nfd
Skip the diagonalization of the full (3Natoms)2matrix (as withFreq=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 forFreq=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-readoperation.
-np=N
UseNprocessors to compute the frequency analysis.
freqchkcan 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):
$freqchkCheckpoint file?solvent.chkWrite Hyperchem files?nTemperature (K)? [0=>298.15]0Zero must be entered; return doesn’t workPressure (Atm)? [0=>1 atm]0Scale factor for frequencies during thermochemistry? [0=>1/1.12]0Do you want the principal isotope masses? [Y]:Return accepts defaultsIsotopes for each atom are printedFull 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 ZNormal modes1 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= .045589E=thermal energy; CV=constant volume molar heat capacity; S=entropyE 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 .005Partition functionsQ 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.chkCheckpoint filename can be placed on the command lineWrite Hyperchem files?nTemperature (K)? [0=>298.15]300Alternate temperature.Pressure (Atm)? [0=>1 atm]1.5Alternate pressure.Scale factor for freqs during thermochem? [0=>1/1.12]1No scaling.Do you want to use the principal isotope masses? [Y]:nFor 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] 2Specify 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 afreqchksession:
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 allfreqchkinput 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 isN. 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 fileala_freq.out:
$freqchk ala.chk -sel -o ala_freq.out N 0 0 0 N N1-5 atoms=NInput ends with a blank line.$more ala_freq.outFrequency data is ready for viewing.…
Last update: 23 April 2013