Harmonic Vibrational Analysis and Visualization of Normal Modes — `frequency()` and `hessian()`¶

Psi4 Native Hessian Methods

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 the scenes, frequency() is a light wrapper over hessian() that computes the Hessian then adds a thermochemical analysis.

psi4.frequency(name[, molecule, return_wfn, func, mode, dertype, irrep])[source]

Function to compute harmonic vibrational frequencies.

Aliases

frequencies(), freq()

Returns

float – Total electronic energy in Hartrees.

Returns

(float, Wavefunction) – energy and wavefunction when return_wfn specified.

Parameters

name (str) –
'scf' || 'mp2' || 'ci5' || etc.

First argument, usually unlabeled. Indicates the computational method to be applied to the system.
molecule (molecule) –
h2o || etc.

The target molecule, if not the last molecule defined.
return_wfn (boolean) –
'on' || \(\Rightarrow\) 'off' \(\Leftarrow\)

Indicate to additionally return the Wavefunction calculation 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) –
\(\Rightarrow\) gradient \(\Leftarrow\) || energy || cbs

Indicates the type of calculation to be performed on the molecule. The default dertype accesses 'gradient' or 'energy', while 'cbs' performs a multistage finite difference calculation. If a nested series of python functions is intended (see Function Intercalls), use keyword freq_func instead of func.
dertype (dertype) –
\(\Rightarrow\) 'hessian' \(\Leftarrow\) || 'gradient' || 'energy'

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 str) –
\(\Rightarrow\) -1 \(\Leftarrow\) || 1 || 'b2' || 'App' || etc.

Indicates which symmetry block (Cotton ordering) of vibrational frequencies to be computed. 1, '1', or 'a1' represents \(a_1\), requesting only the totally symmetric modes. -1 indicates a full frequency calculation.

Note

Analytic hessians are only available for RHF and UHF. 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

>>> # [1] Frequency calculation for all modes through highest available derivatives
>>> frequency('ccsd')

>>> # [2] 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()

>>> # [3] 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())

>>> # [4] Opt+Freq, skipping the gradient recalc at the start of the Hessian
>>> e, wfn = optimize('hf', return_wfn=True)
>>> frequencies('hf', ref_gradient=wfn.gradient())

psi4.hessian(name[, molecule, return_wfn, func, dertype, irrep])[source]

Function complementary to frequency(). Computes force constants, deciding analytic, finite difference of gradients, or finite difference of energies.

Returns: Matrix – Total non-mass-weighted electronic Hessian in Hartrees/Bohr/Bohr.
Returns: (Matrix, Wavefunction) – Hessian and wavefunction when return_wfn specified.
Examples

>>> # [1] Frequency calculation without thermochemical analysis
>>> hessian('mp3')

>>> # [2] 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)

It’s handy to collect the wavefunction after a frequency calculation through e, wfn = psi4.frequency(..., return_wfn=True) as the frequencies can be accessed through psi4.core.Wavefunction.frequencies(), the Hessian through psi4.core.Wavefunction.hessian(), and much other computation info through psi4.core.Wavefunction.frequency_analysis (note no parentheses). Examples of using this data structure can be found fd-freq-gradient and psi4/tests/pytests/test_vibanalysis.py. Formatted printing of vibrational results is available through psi4.driver.qcdb.vib.print_vibs().

Results accessible through `psi4.core.Wavefunction.frequency_analysis`¶
key	description (lbl & comment)	units	data (real/imaginary modes)
omega	frequency	cm^-1	ndarray(ndof) complex (real/imag)
q	normal mode, normalized mass-weighted	a0 u^1/2	ndarray(ndof, ndof) float
w	normal mode, un-mass-weighted	a0	ndarray(ndof, ndof) float
x	normal mode, normalized un-mass-weighted	a0	ndarray(ndof, ndof) float
degeneracy	degree of degeneracy		ndarray(ndof) int
TRV	translation/rotation/vibration		ndarray(ndof) str ‘TR’ or ‘V’ or ‘-’ for partial
gamma	irreducible representation		ndarray(ndof) str irrep or None if unclassifiable
mu	reduced mass	u	ndarray(ndof) float (+/+)
k	force constant	mDyne/A	ndarray(ndof) float (+/-)
DQ0	RMS deviation v=0	a0 u^1/2	ndarray(ndof) float (+/0)
Qtp0	Turning point v=0	a0 u^1/2	ndarray(ndof) float (+/0)
Xtp0	Turning point v=0	a0	ndarray(ndof) float (+/0)
theta_vib	char temp	K	ndarray(ndof) float (+/0)

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 frequency(). This feature can be enabled by setting the option 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 mass weighted.

Molden Interface Keywords¶

NORMAL_MODES_WRITE ¶

Do write a file containing the normal modes in Molden format? If so, the filename will end 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.

Type: boolean

Default: false

WRITER_FILE_LABEL ¶

Base filename for text files written by PSI, such as the MOLDEN output file, the Hessian file, the internal coordinate file, etc. Use the add_str_i function to make this string case sensitive.

Type: string

Default: No Default

psi4.driver.qcdb.vib Module¶

Functions¶

`compare_vibinfos`(expected, computed, tol, label)	Returns True if two dictionaries of vibration Datum objects are equivalent within a tolerance.
`filter_nonvib`(vibinfo[, remove])	From a dictionary of vibration Datum, remove normal coordinates.
`filter_omega_to_real`(omega)	Returns ndarray (float) of omega (complex) where imaginary entries are converted to negative reals.
`harmonic_analysis`(hess, geom, mass, ...[, ...])	Extract frequencies, normal modes and other properties from electronic Hessian.
`hessian_symmetrize`(hess, mol)	Apply Abelian symmetry of mol to Hessian hess.
`print_molden_vibs`(vibinfo, atom_symbol, geom)	Format vibrational analysis for Molden.
`print_vibs`(vibinfo[, atom_lbl, normco, ...])	Pretty printer for vibrational analysis.
`thermo`(vibinfo, T, P, multiplicity, ...[, ...])	Perform thermochemical analysis from vibrational output.

Harmonic Vibrational Analysis and Visualization of Normal Modes — frequency() and hessian()¶