Harmonic Vibrational Analysis and Visualization of Normal Modes —
For further discussion of vibrational and thermochemical analysis, see Sec. Vibrational and Thermochemical Analysis.
frequency() is the only command most users will ever
need to access directly to perform frequency calculations. Behind
frequency() is a light wrapper over
hessian() that computes the Hessian then adds a
frequency(name[, molecule, return_wfn, func, mode, dertype, irrep])¶
Function to compute harmonic vibrational frequencies.
float – Total electronic energy in Hartrees.
Wavefunction) – energy and wavefunction when return_wfn specified.
- name (string) –
First argument, usually unlabeled. Indicates the computational method to be applied to the system.
- molecule (molecule) –
The target molecule, if not the last molecule defined.
- return_wfn (boolean) –
Indicate to additionally return the
Wavefunctioncalculation result as the second element (after float energy) of a tuple. Arrays of frequencies and the Hessian can be accessed through the wavefunction.
- func (function) –
Indicates the type of calculation to be performed on the molecule. The default dertype accesses
'cbs'performs a multistage finite difference calculation. If a nested series of python functions is intended (see Function Intercalls), use keyword
- mode (string) –
For a finite difference of energies or gradients frequency, indicates whether the calculations required to complete the frequency are to be run in one file (
'continuous') or are to be farmed out in an embarrassingly parallel fashion (
'reap')/ For the latter, run an initial job with
'sow'and follow instructions in its output file. For maximum flexibility,
return_wfnis always on in
- dertype (dertype) –
Indicates whether analytic (if available- they’re not), finite difference of gradients (if available) or finite difference of energies is to be performed.
- irrep (int or string) –
Indicates which symmetry block (Cotton ordering) of vibrational frequencies to be computed.
'a1'represents \(a_1\), requesting only the totally symmetric modes.
-1indicates a full frequency calculation.
Analytic hessians are only available for RHF. For all other methods, Frequencies will proceed through finite differences according to availability of gradients or energies.
name calls method scf Hartree–Fock (HF) [manual] Examples:
>>> #  Frequency calculation for all modes through highest available derivatives >>> frequency('ccsd')
1 2 3 4 5
>>> #  Frequency calculation for b2 modes through finite difference of gradients >>> # printing lowest mode frequency to screen and Hessian to output >>> E, wfn = frequencies('scf', dertype=1, irrep=4, return_wfn=True) >>> print wfn.frequencies().get(0, 0) >>> wfn.hessian().print_out()
1 2 3 4 5
>>> #  Frequency calculation at default conditions and Hessian reuse at STP >>> E, wfn = freq('mp2', return_wfn=True) >>> set t 273.15 >>> set p 100000 >>> thermo(wfn, wfn.frequencies())
- name (string) –
hessian(name[, molecule, return_wfn, func, dertype, irrep])¶
Function complementary to
frequency(). Computes force constants, deciding analytic, finite difference of gradients, or finite difference of energies.
Matrix– Total non-mass-weighted electronic Hessian in Hartrees/Bohr/Bohr.
Wavefunction) – Hessian and wavefunction when return_wfn specified.
>>> #  Frequency calculation without thermochemical analysis >>> hessian('mp3')
1 2 3 4 5 6
>>> #  Frequency calc w/o thermo analysis getting the Hessian >>> # in file, core.Matrix, and np.array forms >>> set hessian_write on >>> H, wfn = hessian('ccsd', return_wfn=True) >>> wfn.hessian().print_out() >>> np.array(H)
Visualization of Normal Modes¶
PSI4 has the ability to export a Molden file that stores information about
the harmonic frequencies and normal modes computed via
This feature can be enabled by setting the option |globals__normal_modes_write| to true.
The filename of the Molden file ends in ”.molden_normal_modes, and the prefix is
determined by WRITER_FILE_LABEL (if set), or else by the name of the
output file plus the name of the current molecule.
The normal coordinates saved in the Molden file are normalized and are not