Harmonic Vibrational Analysis and Visualization of Normal Modes — frequency()
and hessian()
¶
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 keywordfreq_func
instead offunc
.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.
\(\Rightarrow\)
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 nonmassweighted 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 fdfreqgradient and
psi4/tests/pytests/test_vibanalysis.py. Formatted printing of vibrational
results is available through psi4.driver.qcdb.vib.print_vibs()
.
key 
description (lbl & comment) 
units 
data (real/imaginary modes) 

omega 
frequency 
cm^1 
ndarray(ndof) complex (real/imag) 
q 
normal mode, normalized massweighted 
a0 u^1/2 
ndarray(ndof, ndof) float 
w 
normal mode, unmassweighted 
a0 
ndarray(ndof, ndof) float 
x 
normal mode, normalized unmassweighted 
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¶

Returns True if two dictionaries of vibration Datum objects are equivalent within a tolerance. 

From a dictionary of vibration Datum, remove normal coordinates. 

Returns ndarray (float) of omega (complex) where imaginary entries are converted to negative reals. 

Extract frequencies, normal modes and other properties from electronic Hessian. 

Apply Abelian symmetry of mol to Hessian hess. 

Format vibrational analysis for Molden. 

Pretty printer for vibrational analysis. 

Perform thermochemical analysis from vibrational output. 