Wolfram Language Paclet Repository
Community-contributed installable additions to the Wolfram Language
WolframChemistry`QuantumChemistry`
ComputeVibrationalModes  |
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Examples
(1)
Basic Examples
(1)
Compute the vibrational modes of water:
In[1]:=
mc=
["HartreeFock","6-31+G"];mol=
[Molecule["water"],mc]["ResultMolecule"];res=
[mol,mc]
 | ModelChemistry |
 | OptimizeMoleculeGeometry |
 | ComputeVibrationalModes |
Out[1]=
ElectronicStructureResult
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Find the frequencies:
In[2]:=
res["VibrationalFrequencies"]//Normal
Out[2]=
,,
1705.24
wavenumbers
3987.16
wavenumbers
4144.47
wavenumbers
Find all available properties:
In[3]:=
res["Properties"]
Out[3]=
{AtomCoordinates,AtomCount,AtomicNumbers,AtomicOrbitalIndices,AtomicOrbitalNames,AtomicOrbitalOverlapMatrix,AtomMasses,BasisFunctionCount,CalculationType,CartesianDisplacementVectors,CoreElectronCount,GaussianBasis,Hessian,InputMolecule,MassWeightedDisplacementVectors,MetaInformation,Method,MolecularMultipoleMoments,MolecularOrbitalCoefficients,MolecularOrbitalCount,MolecularOrbitalEnergies,MolecularOrbitalIndicesOfHOMO,Molecule,Multiplicity,NetCharge,PartialCharges,RotationalConstants,SCFEnergies,VibrationalForceConstants,VibrationalFrequencies,VibrationalTemperatures}
To visualize the animations first we need the displacement vectors for the vibrational modes:
In[4]:=
displacements=res["CartesianDisplacementVectors"]
Out[4]=
QuantityArray
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In[5]:=
coords=mol["AtomCoordinates"]
Out[5]=
QuantityArray
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In[6]:=
frequencies=res["VibrationalFrequencies"]
Out[6]=
QuantityArray
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In[7]:=
vp={0.07,-0.58,3.4};vv={0,0,1};molPlot3D[ωt_,mode_]:=MoleculePlot3D[mol,AtomCoordinates(coords+.2Sin[ωt]displacements〚mode〛),SphericalRegionSphere[{0,0,0},2],ViewVerticalDynamic[vv],ViewPointDynamic[vp]]
In[8]:=
animation[mode_]:=ListAnimate[Table[molPlot3D[ωt,mode],{ωt,0,2π,.1}],AnimationRate200frequencies〚mode〛/Max[frequencies]]
In[9]:=
animation[2]
Out[9]=
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""