Vibrational Spectra Computation
A computed vibrational spectrum is not one eigenvalue calculation. It is a chain connecting a potential-energy surface, nuclear masses, a finite representation, vibrational eigenstates, a transition-property surface, and the observable reported by an experiment. A frequency calculation can be numerically converged while the potential is inaccurate. Accurate energies do not imply accurate intensities. A list of vibrational term values is not yet an infrared or Raman spectrum.
This notebook makes those distinctions concrete with two deliberately small benchmarks:
- a mass-weighted, stretch-only Hessian for linear CO, calibrated to declared harmonic target frequencies;
- a one-dimensional Morse model for HCl, parameterized from spectroscopic constants and solved by sinc discrete variable representation (DVR).
The first calculation exposes normal-mode projection, a translational zero mode, inversion parity, and the difference between infrared and Raman activity. The second separates harmonic error, anharmonic model error, discretization error, transition-property error, and comparison with compiled spectroscopic data.
The retained results are:
| Quantity | Computed value | What it establishes |
|---|---|---|
| CO symmetric stretch | calibrated Hessian target recovered | |
| CO antisymmetric stretch | calibrated Hessian target recovered | |
| HCl Morse dissociation parameter | value implied by and | |
| HCl DVR fundamental | numerical Morse term difference | |
| HCl higher-order term difference | value implied by selected compiled constants | |
| largest DVR error for | solver verified against exact Morse levels |
The tiny DVR error verifies the implementation for the Morse Hamiltonian. It does not show that the Morse model predicts HCl spectroscopy to eleven decimal places. The difference between the Morse and higher-order term values is already about ten orders of magnitude larger than the numerical error.
Run the investigation. The program and retained results below support the stated experiment. Follow Running an Experiment for environment and output-directory guidance. The recorded evidence applies to its stated parameters and environment.
Purpose and Canonical Scope
Section titled “Purpose and Canonical Scope”This page is the canonical home for the executable calculation that:
- constructs and diagonalizes a mass-weighted molecular Hessian;
- detects rigid translation and validates normal-mode normalization;
- assigns inversion parity and leading IR/Raman activity in a transparent CO stretch model;
- constructs a Morse potential from HCl spectroscopic constants;
- diagonalizes a one-dimensional vibrational Hamiltonian with sinc DVR;
- verifies numerical levels against the exact Morse spectrum;
- evaluates vibrational transition moments from a local dipole surface;
- compares band origins and relative intensities with compiled data; and
- reports a layered error and reproducibility record.
Neighboring pages retain broader canonical responsibilities:
- Normal Modes of Polyatomics owns the full Cartesian and internal-coordinate normal-mode theory, translation and rotation projection, molecular symmetry, degeneracy, Wilson’s method, and production frequency-analysis workflow.
- Vibrations of Diatomics owns the physical reduction to a radial nuclear coordinate and the rovibrational interpretation of diatomic states.
- Vibrational Spectroscopy owns band assignments, anharmonic spectral structure, hot bands, overtones, combination bands, and force-field inference.
- Infrared Spectroscopy owns electric-dipole absorption, instrument response, and IR data interpretation.
- Raman Spectroscopy owns polarizability tensors, Raman selection rules, polarization observables, and Raman instrumentation.
- Potential-Energy Surfaces owns the electronic-structure origin, topology, and dimensionality of molecular potentials.
- Numerical Mathematics owns the general theory of finite representations, eigensolvers, convergence studies, conditioning, and floating-point error.
The present page therefore uses a small Hessian and a one-dimensional DVR as auditable computational examples. It does not duplicate a general normal-mode course or treat a stick list as a complete laboratory spectrum.
Reproducibility Contract
Section titled “Reproducibility Contract”The executable artifact is a NumPy-only Python program:
- Download the program
- CO normal-mode data
- HCl potential data
- HCl level data
- HCl transition data
- HCl convergence data
- Machine-readable metadata and validation
Run the downloaded program from the folder where you saved it:
python vibrational-spectra.py --output-dir resultsThe default run uses:
| Item | Declared choice |
|---|---|
| language | Python 3 |
| numerical dependency | NumPy |
| random numbers | none |
| internal units | atomic units |
| HCl coordinate | |
| DVR interval | |
| DVR points | |
| DVR spacing | |
| retained level comparison | |
| retained transitions | |
| matrix eigensolver | real-symmetric numpy.linalg.eigh |
The program contains no hidden optimization, stochastic seed, fitted correction after diagonalization, or external quantum-chemistry call. Its metadata records the runtime versions, constants, model parameters, matrices, grid, validation thresholds, source identifiers, and limitations.
The two claims are intentionally different
Section titled “The two claims are intentionally different”The CO calculation is a calibrated algebra benchmark. Its two force constants are chosen to reproduce two declared stretch frequencies. Recovery of those frequencies validates matrix assembly and mode assignment, not the quality of an electronic-structure force field.
The HCl calculation is a representation and model-hierarchy benchmark. The two Morse parameters are inferred from and . Agreement with the two-term Morse formula verifies the DVR. Comparison with , , and measured band intensities then reveals physics omitted by that fitted model.
Calling either calculation an independent first-principles prediction would erase the most important fact about its provenance.
From a Potential to a Spectrum
Section titled “From a Potential to a Spectrum”A useful computational dependency graph is
Each arrow introduces distinct assumptions:
| Layer | Representative input | Representative failure |
|---|---|---|
| electronic model | Born–Oppenheimer surface | correlation, relativistic, or basis error |
| nuclear model | isotope masses, dimensionality | omitted rotation, coupling, nonadiabaticity |
| local approximation | Hessian at one minimum | anharmonicity, multiple minima, resonance |
| representation | basis or coordinate grid | truncation or boundary error |
| solver | symmetric diagonalization | residual or orthogonality failure |
| transition surface | or | wrong derivatives or limited expansion |
| observation model | populations and line profiles | wrong temperature, pressure, or instrument response |
This hierarchy matters because an energy residual tests only the solver layer. A measured intensity can be much more sensitive to the transition surface than the corresponding band origin is to the potential.
Harmonic Approximation
Section titled “Harmonic Approximation”Let collect Cartesian nuclear displacements from a stationary geometry . Expanding the potential gives
where
The linear term vanishes only if the geometry is stationary to the relevant accuracy. The Cartesian equation of motion is
with diagonal mass matrix . The generalized eigenproblem is
Mass weighting converts it to an ordinary symmetric problem:
If the mass-weighted eigenvectors satisfy , then the Cartesian vectors satisfy
The spectroscopic harmonic wavenumber is
In atomic units, , so the program converts an angular frequency to wavenumber by multiplying by per hartree.
What harmonic does and does not mean
Section titled “What harmonic does and does not mean”The harmonic approximation is local in configuration space. It assumes:
- one stable equilibrium;
- a quadratic potential over the wavefunction’s relevant support;
- constant masses and a chosen coordinate metric;
- separable normal coordinates after the quadratic transformation; and
- transition-property expansions that may be truncated independently.
It does not imply that chemical bonds are literal springs over arbitrary displacements. It does not provide dissociation. It cannot produce intrinsic anharmonic overtones from a linear dipole surface. It also cannot describe Fermi resonance, large-amplitude torsion, tunneling between minima, or a conical-intersection region.
CO₂ Stretch-Only Hessian
Section titled “CO₂ Stretch-Only Hessian”The first benchmark retains only collinear displacements
for O–C–O. Define the two bond extensions
The declared model potential is
Equivalently,
Every row sums to zero. Therefore uniform translation is an exact null vector before any diagonalization.
For , the two stretch frequencies have closed forms:
The program solves these relations backward for a pedagogical force field whose declared targets are
Using C and O isotopic masses gives
These are fitted model parameters, not reported experimental C–O force constants and not the output of an electronic-structure calculation.
Numerical modes
Section titled “Numerical modes”The diagonalization returns:
| Mode | () | Relative | Inversion | Leading activity |
|---|---|---|---|---|
| translation | ungerade | not a vibration | ||
| symmetric stretch | gerade | Raman allowed, IR forbidden | ||
| antisymmetric stretch | ungerade | IR allowed, Raman forbidden |
For the antisymmetric stretch, centre-of-mass stationarity requires
so choosing gives
The unequal Cartesian amplitudes are a mass effect. Plotting only arrows of equal length would obscure the normal coordinate actually diagonalized.
Validation of the Hessian calculation
Section titled “Validation of the Hessian calculation”The retained tests are:
| Check | Measured diagnostic | Threshold |
|---|---|---|
| translational invariance | ||
| symmetry of | ||
| eigenvector orthonormality | ||
| analytic frequency agreement | ||
| vibrational centre-of-mass residual | ||
| inversion-parity error |
The numerical eigensolver represents the translational eigenvalue by a tiny roundoff-scale number. The program sets eigenvalues below times the largest eigenvalue to zero. This is not used as the translation test: the exact Hessian row sums provide that independent check.
Two distinct benchmarks. Panel (a) shows the calibrated CO stretch patterns and their leading centrosymmetric IR/Raman activity. Panel (b) compares the HCl harmonic and Morse potentials with the first five DVR levels. Panel (c) compares relative intensity proxies from the Morse wavefunctions and local dipole polynomial with selected compiled band intensities. The CO targets and HCl spectroscopic constants are inputs, not independent predictions.
Frequency Is Not Spectral Activity
Section titled “Frequency Is Not Spectral Activity”A normal-mode eigenvalue says where a harmonic quantum would lie. Whether a transition is visible depends on an interaction operator.
For infrared absorption, expand the molecular dipole around equilibrium:
The vibrational transition moment is
Within the harmonic and linear-dipole approximation, a fundamental of mode requires a nonzero derivative
For nonresonant Raman scattering, the corresponding molecular quantity is the polarizability tensor:
A Raman-active mode requires an allowed component of . Measured Raman intensities also depend on incident frequency, polarization geometry, rotational averaging, populations, and instrument response.
Centrosymmetric mutual exclusion
Section titled “Centrosymmetric mutual exclusion”Under inversion:
- the electric dipole is ungerade;
- the polarizability is gerade;
- the CO symmetric stretch is gerade;
- the CO antisymmetric stretch is ungerade.
Thus the symmetric stretch is Raman allowed and IR forbidden at leading order, while the antisymmetric stretch is IR allowed and Raman forbidden. This is a symmetry statement about matrix elements. It is not inferred from which frequency is larger.
The qualifiers matter. Isotopic substitution, environmental symmetry breaking, higher-order operators, resonance enhancement, and mode mixing can modify simple activity rules.
Why the CO₂ picture is not an observed spectrum
Section titled “Why the CO₂ picture is not an observed spectrum”The stretch-only model omits the doubly degenerate bend. In real CO, the symmetric-stretch fundamental lies near the overtone of the bend and the two states share the required symmetry. Anharmonic coupling mixes them into the well-known Fermi dyad, with prominent Raman features near and rather than one untouched harmonic line.
Therefore it would be wrong to place the model’s symmetric target beside one experimental Raman peak and call the difference a frequency error. The observable states are mixed. The canonical spectroscopy pages develop that interpretation; here the example marks the boundary of a reduced Hessian calculation.
Anharmonic One-Dimensional Hamiltonian
Section titled “Anharmonic One-Dimensional Hamiltonian”For a diatomic coordinate on one electronic surface, define . The retained nuclear Hamiltonian is
in atomic units, with isotopologue-specific reduced mass
The benchmark uses the Morse potential
It has three useful properties:
- a quadratic minimum near ;
- asymmetric level spacings that decrease with ;
- a finite dissociation asymptote .
It remains one-dimensional and single-surface. It omits rotation, Born–Oppenheimer breakdown, nonadiabatic coupling, relativistic and radiative effects, and deviations of the true potential from the Morse shape.
Parameterizing the H³⁵Cl Morse Model
Section titled “Parameterizing the H³⁵Cl Morse Model”The exact Morse term values can be written
Matching the Morse expansion gives
In atomic units,
The selected HCl constants from the NIST Chemistry WebBook compilation are
With the declared H and Cl isotopic masses, the program obtains
A fitted dissociation parameter is not a measured bond energy
Section titled “A fitted dissociation parameter is not a measured bond energy”The relation
is exact for a Morse potential. Applying it to empirical low-order spectroscopic constants produces the dissociation parameter of the fitted Morse model. It need not equal the physical dissociation energy of the real molecule. Higher Dunham terms already demonstrate that the true potential is not exactly Morse.
Bound-state count
Section titled “Bound-state count”For the fitted Morse model, the number of bound levels is
The finite DVR matrix also returns 28 eigenvalues below the declared Morse asymptote. This count is a useful global check, although near-threshold states are much more sensitive to the right boundary than the low levels studied here.
Matrix Diagonalization with Sinc DVR
Section titled “Matrix Diagonalization with Sinc DVR”Choose a uniform grid
For the infinite-order sinc DVR of Colbert and Miller, the kinetic-energy matrix in atomic units is
The potential is diagonal:
The finite matrix problem is then
The program assembles the matrix explicitly and uses a real-symmetric dense eigensolver. With only 201 grid points, this is clearer than an iterative method and makes full orthogonality checks inexpensive.
Why the off-diagonal signs alternate
Section titled “Why the off-diagonal signs alternate”The second derivative of cardinal sinc functions is long ranged. Its off-diagonal matrix elements decay as and alternate in sign. Replacing this matrix by a three-point finite-difference stencil creates a different representation with different convergence behavior. Either can be valid, but mixing their formulas is not.
Finite interval and boundary placement
Section titled “Finite interval and boundary placement”The formal sinc basis describes an unbounded uniform grid, while the calculation truncates it to
The short-range Morse wall suppresses low-state amplitude at the left edge; the first several bound states decay well before the right edge. That physical localization explains why their finite-interval error is small. It does not justify assuming that high-lying or continuum states are equally converged.
Verification Against Exact Morse Levels
Section titled “Verification Against Exact Morse Levels”An analytic spectrum is unusually valuable because it separates representation and solver error from model error. For each grid, the program compares the first eight numerical term values directly with .
| largest error for () | fundamental error () | ||
|---|---|---|---|
| 81 | |||
| 101 | |||
| 121 | |||
| 151 | |||
| 201 |
The error decreases rapidly because the low Morse eigenfunctions are smooth and well localized. At the finest grids, floating-point and eigensolver differences dominate the printed last digits, so the final row should not be used to infer a clean asymptotic convergence order.
The independently retained 201-point eigenvector calculation has
Additional checks give:
| Diagnostic | Result |
|---|---|
| Hamiltonian symmetry error | |
| eigenvector orthonormality error | |
| DVR fundamental minus exact Morse | |
| eigenvalues below | |
| exact Morse bound-state count |
Do not use agreement with the fit as validation data
Section titled “Do not use agreement with the fit as validation data”The exact Morse values and the DVR share the same potential parameters. Their agreement is an implementation test. The selected and cannot then be reused as independent evidence that the model predicts HCl.
Independent pressure comes from quantities not enforced by the two-parameter fit: higher vibrational terms, overtone intensities, isotope transfer, near-dissociation behavior, or data outside the calibration set.
Harmonic, Morse, and Higher-Order Term Values
Section titled “Harmonic, Morse, and Higher-Order Term Values”The harmonic oscillator predicts evenly spaced levels:
The Morse term subtracts a quadratic contribution in . The selected higher-order comparison adds the compiled terms
Here is a truncated spectroscopic term expansion, not the DVR Hamiltonian and not an exact potential.
For transitions from :
| Band | Harmonic origin | Exact Morse and DVR | Selected higher-order terms | Higher-order minus Morse |
|---|---|---|---|---|
All values are in . Three trends are visible:
- the harmonic model increasingly overestimates overtone origins;
- the Morse correction captures the leading contraction of level spacings;
- omitted higher-order terms grow with excitation even when the low-level fundamental looks close.
The fifth-overtone discrepancy is a model-truncation warning, not a DVR failure.
Transition Moments from a Dipole Surface
Section titled “Transition Moments from a Dipole Surface”Energies alone do not determine IR strengths. The benchmark uses a local polynomial in , expressed in angstroms:
The selected derivatives are
They come from Kaiser’s HCl dipole-function analysis, with the derivatives and uncertainties clarified in the later published comment.
The program sets . This is a choice of irrelevant additive offset, not a claim that HCl has zero permanent dipole. For orthogonal states ,
because .
Operator matrix elements in the DVR
Section titled “Operator matrix elements in the DVR”For a local multiplicative operator, the DVR approximation is
No extra appears when the eigenvectors are coefficients in the orthonormal DVR basis. By contrast, a plotted coordinate-space probability density inferred from those coefficients scales as .
The benchmark reports the frequency-weighted proxy
and normalizes it to the band. This removes the overall unit factor but does not reproduce a finite-temperature rotational band integral in every laboratory convention.
Comparing Relative H³⁵Cl IR Intensities
Section titled “Comparing Relative H³⁵Cl IR Intensities”The selected NIST compilation lists absolute integrated band intensities of , , and for the , , and bands, respectively. It also records a different reported value of . The table below uses as its declared comparison value and retains the literature spread as an uncertainty warning.
| Band | (D) | Model relative proxy | Selected compiled relative intensity |
|---|---|---|---|
The local Morse-plus-dipole model gives the first overtone within about of the selected normalized value, but underestimates the second overtone by roughly a factor of . That is a physically useful failure. Higher overtones probe:
- the wavefunctions farther from equilibrium;
- higher derivatives and global behavior of ;
- non-Morse structure of the potential;
- rotational and temperature conventions in the integrated data; and
- uncertainties in older absolute-intensity measurements.
Tuning a fifth-order dipole coefficient until all three ratios agree would convert the comparison into a fit. It could be a legitimate inverse problem, but it would require parameter uncertainties, regularization, held-out data, and an explicit change of claim.
What an IR or Raman Comparison Requires
Section titled “What an IR or Raman Comparison Requires”Before comparing a computed stick to a measured feature, match the observable.
Species and state
Section titled “Species and state”Declare:
- isotopologue and isotopic abundance;
- electronic state;
- charge state;
- nuclear-spin species where relevant;
- sample phase and environment;
- temperature and pressure.
Natural-abundance HCl contains HCl and HCl. A calculation with one reduced mass should not be compared with an unresolved mixture without an isotope model.
Energy convention
Section titled “Energy convention”Distinguish:
The one-dimensional calculation returns pure vibrational term differences. A high-resolution HCl spectrum resolves rotational branches, hyperfine structure, and isotope shifts. Modern sub-Doppler measurements of the fundamental resolve individual HCl and HCl transitions at far higher precision than this reduced model attempts to describe.
Intensity convention
Section titled “Intensity convention”State whether the reported quantity is:
- a transition dipole;
- line strength;
- oscillator strength;
- integrated absorption coefficient;
- cross section;
- Raman activity;
- differential Raman cross section;
- peak height after convolution.
These quantities are related but not interchangeable. Population factors, degeneracies, rotational sums, polarization averages, and unit conventions can all intervene.
Line-shape and instrument model
Section titled “Line-shape and instrument model”A calculated stick list becomes a plotted spectrum only after assigning profiles such as
The profile may include Doppler, collisional, lifetime, inhomogeneous, and instrumental broadening. Choosing an arbitrary Gaussian width can be useful for visualization, but it is not an experimental prediction unless the width has physical provenance.
Raman needs a polarizability surface
Section titled “Raman needs a polarizability surface”The HCl part of this benchmark computes electric-dipole transition moments. It does not report Raman intensities because no HCl polarizability surface is declared. The CO panel reports only symmetry-allowed or symmetry-forbidden Raman activity. Assigning arbitrary Raman stick heights would add apparent information unsupported by the model.
Verification, Validation, Calibration, and Prediction
Section titled “Verification, Validation, Calibration, and Prediction”These terms answer different questions.
| Term | Question | Example here |
|---|---|---|
| verification | was the declared equation solved correctly? | DVR versus exact Morse levels |
| calibration | were parameters inferred from chosen data? | and from |
| validation | does the model describe data outside that fit? | higher term values and overtone ratios |
| prediction | does it forecast an unfit observable with declared uncertainty? | not claimed by this notebook |
The CO target recovery is also verification after calibration. It is not validation because both frequencies were used to determine the two force constants.
A layered error ledger
Section titled “A layered error ledger”For a transition origin, write schematically
The terms need not be statistically independent, so this is an accounting identity rather than permission to add unsigned errors in quadrature.
For the HCl fundamental:
| Layer | Evidence | Approximate scale |
|---|---|---|
| solver and DVR representation | exact Morse comparison | |
| Morse truncation relative to selected higher terms | ||
| rotation and hyperfine structure | omitted by construction | line dependent |
| constants and Born–Oppenheimer breakdown | compilation notes and precision data | target dependent |
| line shape and temperature | absent from stick model | experiment dependent |
Printing twelve decimal places for the DVR energy is useful for regression testing. It is not an uncertainty statement about a physical HCl band.
Sensitivity and Convergence Studies
Section titled “Sensitivity and Convergence Studies”A trustworthy vibrational calculation varies one approximation at a time.
Hessian calculations
Section titled “Hessian calculations”For a production molecular Hessian, vary:
- electronic-structure method;
- orbital or one-particle basis;
- geometry convergence threshold;
- numerical differentiation step, if applicable;
- integral and self-consistency thresholds;
- isotope masses;
- translation and rotation projection tolerances.
An apparently converged electronic energy does not guarantee a converged second derivative. Finite-difference Hessians amplify gradient noise, while analytic Hessians still inherit basis and method error.
Grid calculations
Section titled “Grid calculations”For a one-dimensional DVR, vary:
- ;
- ;
- point count ;
- grid spacing ;
- coordinate mapping, if used;
- number of retained states.
Convergence should be checked separately for:
- low energies;
- high bound states;
- wavefunction tails;
- transition moments;
- expectation values concentrated near a boundary.
Energy convergence alone can be misleading. A small wavefunction component in a region where is large may matter little for and substantially for an overtone moment.
Parameter sensitivity
Section titled “Parameter sensitivity”For the Morse spectrum,
First-order parameter propagation gives
For a transition from , subtract the corresponding lower-state expression. Sensitivity grows with excitation, one reason high overtones are valuable tests of a fitted potential.
Implementation Walkthrough
Section titled “Implementation Walkthrough”The program is organized around small, independently testable functions.
CO₂ branch
Section titled “CO₂ branch”- Convert isotope masses to electron masses.
- convert target wavenumbers to atomic-unit angular frequencies;
- solve analytically for and ;
- assemble from bond-gradient outer products;
- form ;
- diagonalize ;
- convert mass-weighted vectors to Cartesian displacements;
- classify translation, stretch character, and inversion parity;
- compare with analytic frequencies and conservation identities.
Building the Hessian from gradient vectors is preferable to manually typing nine unrelated entries:
This construction exposes symmetry and makes translational invariance easier to audit.
H³⁵Cl branch
Section titled “H³⁵Cl branch”- Construct , , and from declared constants.
- build the uniform coordinate grid.
- assemble the sinc-DVR kinetic matrix.
- evaluate the diagonal Morse potential.
- diagonalize .
- compare numerical and exact Morse levels.
- evaluate the local dipole polynomial on the grid.
- contract DVR vectors with the dipole values.
- form frequency-weighted relative intensity proxies.
- write level, transition, convergence, and metadata artifacts.
The two branches share a symmetric-eigenproblem pattern but retain separate physical validation. A common numerical primitive does not make the models equivalent.
Output Artifacts
Section titled “Output Artifacts”The program writes six deterministic data products:
| File | Contents |
|---|---|
vibrational-co2-normal-modes.csv | frequencies, relative Cartesian modes, parity, IR/Raman labels |
vibrational-h35cl-potential.csv | harmonic and Morse curves on a plot grid |
vibrational-h35cl-levels.csv | harmonic, exact Morse, DVR, and higher-order term values |
vibrational-h35cl-transitions.csv | origins, transition moments, model proxies, compiled intensities |
vibrational-h35cl-convergence.csv | point-count convergence against exact Morse levels |
vibrational-spectra-metadata.json | constants, matrices, grids, provenance, limitations, checks |
The figure source reads these CSV files directly. Thus the curves and points shown above are generated from the same records offered for download.
Minimum reproducibility record for extension
Section titled “Minimum reproducibility record for extension”An extended calculation should preserve:
- source-code version or immutable archive;
- package and interpreter versions;
- constants and isotope masses;
- potential and transition-surface provenance;
- coordinate definitions and units;
- basis, grid, and boundary choices;
- eigensolver and tolerances;
- convergence tables;
- raw eigenvalues and observables;
- validation references;
- plotting and convolution choices;
- known exclusions and claim boundary.
Reporting only a final spectrum image is not enough to reproduce or audit the calculation.
Extending the Benchmark
Section titled “Extending the Benchmark”The small models are useful starting points, not endpoints.
Replace the calibrated Hessian
Section titled “Replace the calibrated Hessian”Supply a Cartesian Hessian from an electronic-structure calculation, then:
- verify geometry stationarity;
- mass weight with the intended isotopologue;
- project translation and rotation;
- diagonalize the vibrational subspace;
- inspect imaginary frequencies;
- classify modes by symmetry and displacement;
- converge the electronic method and basis;
- compare with appropriate harmonic or anharmonic references.
For linear CO, a full calculation has vibrational degrees of freedom: one symmetric stretch, one antisymmetric stretch, and a doubly degenerate bend. The present three-coordinate axial model cannot recover the bends.
Replace Morse by a numerical potential
Section titled “Replace Morse by a numerical potential”Given tabulated :
- define a common zero of energy;
- interpolate with a method that does not introduce spurious oscillations;
- verify the minimum and long-range behavior;
- ensure the grid lies inside the trustworthy data domain;
- repeat domain and point-count convergence;
- compare interpolation choices;
- preserve the original potential points.
Extrapolating a high-order polynomial beyond the electronic-structure grid is especially dangerous near dissociation.
Add multiple modes
Section titled “Add multiple modes”A multidimensional vibrational Hamiltonian may be expressed in normal or internal coordinates:
The cost then grows with the product basis. Practical approaches include vibrational configuration interaction, contracted bases, sparse grids, multiconfiguration time-dependent Hartree, tensor methods, perturbation theory, and reduced-dimensional models. The choice must follow the coupling and target observable, not just the number of atoms.
Add rotation
Section titled “Add rotation”For a diatomic, the effective radial Hamiltonian at rotational quantum number contains
Diagonalizing each block produces rovibrational term values. Comparing individual IR lines then also requires rotational transition rules, populations, nuclear-spin weights, and possibly hyperfine structure.
Add time dependence
Section titled “Add time dependence”An IR pulse can be modeled through
followed by wavepacket propagation. Fourier analysis of a dipole autocorrelation or response function can generate a spectrum with coherent dynamics and finite-time resolution. That is a different computational claim from diagonalizing a stationary Hamiltonian.
Common Mistakes
Section titled “Common Mistakes”Treating a Hessian frequency as a measured peak
Section titled “Treating a Hessian frequency as a measured peak”A harmonic normal-mode frequency omits anharmonicity, resonances, rotation, environmental shifts, and instrument response. State which comparison is being made.
Forgetting mass weighting
Section titled “Forgetting mass weighting”Diagonalizing directly gives correct modes only in special equal-mass coordinates. The physical generalized problem is .
Removing small eigenvalues without identifying rigid motion
Section titled “Removing small eigenvalues without identifying rigid motion”A threshold alone cannot distinguish a true floppy vibration from a translation, rotation, or numerical artifact. Inspect mode vectors and symmetry.
Comparing different isotopologues
Section titled “Comparing different isotopologues”The electronic potential is nearly isotope independent at the Born–Oppenheimer level, but the nuclear kinetic energy is not. Use the matching masses.
Calling calibrated values predictions
Section titled “Calling calibrated values predictions”If two frequencies determine two force constants, exact recovery of those frequencies is algebraic closure. Validate against unused observables.
Confusing dissociation and distortion constants
Section titled “Confusing dissociation and distortion constants”Spectroscopy also uses for centrifugal-distortion constants in some contexts, while the Morse potential uses for dissociation from the minimum. Always include units and meaning.
Using the Morse dissociation parameter as a measured bond energy
Section titled “Using the Morse dissociation parameter as a measured bond energy”The relation assumes an exact Morse potential. Real molecular potentials contain higher terms and long-range structure.
Trusting one grid
Section titled “Trusting one grid”A stable printed eigenvalue at one does not demonstrate convergence. Vary spacing and boundaries independently.
Adding an extra quadrature weight in a DVR matrix element
Section titled “Adding an extra quadrature weight in a DVR matrix element”DVR eigenvector coefficients already refer to an orthonormal cardinal basis. Coordinate-space samples and basis coefficients have different normalizations.
Inferring intensity from frequency
Section titled “Inferring intensity from frequency”IR intensity needs a dipole surface; Raman intensity needs a polarizability surface. Neither follows from the Hessian eigenvalue alone.
Comparing peak height with integrated strength
Section titled “Comparing peak height with integrated strength”Peak height changes with broadening even when integrated area is fixed. Match the observable and line-shape convention.
Hiding experimental spread
Section titled “Hiding experimental spread”Compiled measurements can disagree. Selecting one value is acceptable only when the choice and alternatives remain visible.
Reporting solver precision as physical accuracy
Section titled “Reporting solver precision as physical accuracy”The DVR’s analytic error is many orders of magnitude below the model discrepancy. Physical significant figures must follow the full uncertainty budget.
Exercises
Section titled “Exercises”Exercise 1: mass-weighted equivalence
Section titled “Exercise 1: mass-weighted equivalence”Starting from
show that satisfies the symmetric eigenproblem with . Derive the corresponding normalization relation.
Solution
Substitute
into the generalized equation:
Multiplication on the left by gives
Thus
If the mass-weighted eigenvectors are Euclidean orthonormal,
then
This mass-metric normalization is why raw Cartesian arrow lengths should not be compared as though they formed a Euclidean-normalized vector.
Exercise 2: analytic CO₂ stretch modes
Section titled “Exercise 2: analytic CO₂ stretch modes”For the stretch-only Hessian, verify that
has
Construct the centre-of-mass-free antisymmetric vector and derive .
Solution
For the symmetric displacement,
and direct multiplication gives
Because the nonzero components belong to oxygen atoms,
implies
For the antisymmetric stretch, the oxygen atoms move in the same Cartesian direction while carbon moves oppositely:
Centre-of-mass stationarity requires
so . The outer-coupling coordinate vanishes for this pattern, so contributes nothing. Substitution into the generalized eigenproblem yields
Exercise 3: inversion and mutual exclusion
Section titled “Exercise 3: inversion and mutual exclusion”Under inversion, a collinear displacement transforms as
Find the inversion eigenvalues of the two CO stretch vectors. Explain the leading IR and Raman assignments.
Solution
For the symmetric stretch,
so it is gerade.
For the antisymmetric stretch,
so it is ungerade.
The electric dipole transforms as ungerade, while the polarizability tensor transforms as gerade. In a centrosymmetric molecule, a gerade vibrational fundamental can be Raman active but is electric-dipole forbidden; an ungerade fundamental can be IR active but is Raman forbidden at leading order. Therefore the symmetric stretch is Raman allowed and the antisymmetric stretch is IR allowed.
Exercise 4: Morse band origins
Section titled “Exercise 4: Morse band origins”Using
derive a closed expression for the band origin. Evaluate it for and using the retained HCl constants.
Solution
Subtracting gives
For ,
For ,
The harmonic values would be and , respectively.
Exercise 5: interpreting convergence
Section titled “Exercise 5: interpreting convergence”The maximum first-eight-level error drops from at to at and at . Why is fitting a power law to all five rows a poor error model? What additional calculation would test boundary error?
Solution
Sinc DVR can converge faster than any fixed algebraic power for smooth, well-resolved, localized eigenfunctions. The coarse grids are not necessarily in one asymptotic regime. At the finest grids, floating-point roundoff and differences between eigensolver paths dominate the last digits. A single fit
across coarse, rapidly converging, and roundoff-limited rows would therefore mix distinct regimes and assign a meaningless .
To test boundary error, hold the local spacing approximately fixed while varying and separately. One can also inspect the probability density near each edge. A state whose tail remains appreciable at is not boundary converged even if changing at fixed endpoints appears stable.
Exercise 6: constant dipole offsets
Section titled “Exercise 6: constant dipole offsets”Prove that adding a constant to the dipole surface leaves every off-diagonal transition moment unchanged for exactly orthogonal eigenstates. What diagnostic does a small numerical change provide?
Solution
For ,
Thus a constant offset affects diagonal permanent-dipole expectation values but not transition moments.
In finite precision, the observed change is
Repeating the contraction after adding a known therefore probes eigenvector orthogonality and consistent basis normalization. A large change would indicate a numerical or implementation problem.
Exercise 7: why overtones appear
Section titled “Exercise 7: why overtones appear”In a harmonic oscillator with a strictly linear dipole , explain why is forbidden. Name two mechanisms that make the transition nonzero in the benchmark.
Solution
For harmonic-oscillator ladder operators,
Therefore changes the vibrational quantum number only by . Orthogonality removes the constant term, so
Two mechanisms relax this result:
- the Morse eigenstates are anharmonic mixtures when represented in a harmonic basis, so the linear operator can connect components that produce a net overtone moment;
- nonlinear dipole terms such as , , and have matrix elements with larger changes in .
The computed overtone strength combines mechanical anharmonicity of the wavefunctions and electrical anharmonicity of the dipole surface.
Exercise 8: construct the error ledger
Section titled “Exercise 8: construct the error ledger”A student reports
and concludes that the HCl fundamental is known from the calculation to . Identify at least four missing uncertainty layers and give the strongest defensible statement supported by the notebook.
Solution
Missing layers include:
- error of the Morse functional form;
- uncertainty and provenance of and ;
- higher vibrational terms;
- rotation and vibration–rotation coupling;
- Born–Oppenheimer breakdown and isotope-dependent corrections;
- relativistic and radiative effects at precision targets;
- hyperfine structure;
- temperature, pressure, and line-shape conventions;
- distinction between a vibrational term difference and a measured line.
The strongest supported numerical statement is:
On the declared 201-point grid, the implementation solves the fitted one-dimensional HCl Morse Hamiltonian for its low levels to much better than , as verified against the exact Morse formula.
The comparison with selected higher-order terms shows a model discrepancy for the fundamental, already invalidating the claimed physical precision.
Exercise 9: isotope transfer as a validation test
Section titled “Exercise 9: isotope transfer as a validation test”Suppose the Born–Oppenheimer Morse potential parameters and are held fixed while Cl is replaced by Cl. Predict qualitatively how , , and the number of bound states change. Why is this a stronger test than refitting both isotopologues independently?
Solution
For fixed and ,
so
The Morse anharmonic constant satisfies
so
Replacing Cl by the heavier Cl increases the reduced mass. Both constants decrease, with decreasing more rapidly in relative scaling. The approximate bound-state count
therefore tends to increase.
Holding the potential fixed makes the isotope shift a transfer prediction of the nuclear kinetic model. Refitting and separately to each isotopologue can absorb disagreement and no longer tests transferability. At high precision, deviations from fixed-potential mass scaling reveal adiabatic and nonadiabatic Born–Oppenheimer-breakdown effects.
References
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