Jupyter notebooks

Jupyter notebooks#

Here, we explain how to visualize VeloxChem results in the Jupyter Notebook. The calculation can either be performed and visualized in the Jupyter Notebook or the results can be imported from a VeloxChem h5 file and then visualized.

Molecular structure#

In Jupyter notebook, a Veloxchem molecule object can be visualize using the show function. This is powevered by Py3DMol. The atom_indices and atom_labels options can be used.

Directly from a Jupyter Notebook cell

import veloxchem as vlx
molecule = vlx.Molecule.read_smiles('C1=CC=C(C=C1)C(=O)O')
molecule.show(atom_indices=True, atom_labels=True)

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From an h5 file

biph_dict = vlx.read_results("../output_files/biphenyl-scf.h5", label="scf")
biph = vlx.Molecule.from_dict(biph_dict)
biph.show()

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Structure optimization#

Directly from a Jupyter Notebook cell

molecule = vlx.Molecule.read_smiles('CCO')
basis = vlx.MolecularBasis.read(molecule, 'def2-svp')

scf_drv = vlx.ScfRestrictedDriver()
scf_drv.ostream.mute()
scf_drv.xcfun = 'b3lyp'
scf_drv.dispersion = 'd4'
results = scf_drv.compute(molecule, basis)

opt_drv = vlx.OptimizationDriver(scf_drv)
opt_results = opt_drv.compute(molecule, basis, results)
opt_drv.show_convergence(opt_results)

From an h5 file

opt_results = vlx.read_results("../output_files/bithio-S0-opt.h5", label="opt")
opt_drv.show_convergence(opt_results)

Spectrum plotting#

Directly from a Jupyter Notebook cell

molecule = vlx.Molecule.read_smiles('CCO')
basis = vlx.MolecularBasis.read(molecule, 'def2-svp')

scf_drv = vlx.ScfRestrictedDriver()
scf_drv.ostream.mute()
scf_drv.xcfun = 'b3lyp'
results = scf_drv.compute(molecule, basis)

rsp_drv = vlx.lreigensolver.LinearResponseEigenSolver()
rsp_drv.ostream.mute()
rsp_drv.nstates = 10
rsp_drv.nto = True
rsp_results = rsp_drv.compute(molecule, basis, results)
rsp_drv.plot(rsp_results)
../_images/39ff95adee6d5d2c21cbce5ceadf2d514eb6a0ba8d57d284c3edc4081e565565.png

From an h5 file

rsp_results = vlx.read_results("../output_files/alanine-ecd.h5", label="rsp")
rsp_drv.plot_ecd(rsp_results)
../_images/241b09cb88f2f78b4d505b7eacf90a66d6cf8e2bee027bcfe05e337f24bf0bf7.png

Normal modes#

Directly from a Jupyter Notebook cell

molecule = vlx.Molecule.read_smiles('CCO')
basis = vlx.MolecularBasis.read(molecule, 'def2-svp')

scf_drv = vlx.ScfRestrictedDriver()
scf_drv.ostream.mute()
scf_drv.xcfun = 'b3lyp'
results = scf_drv.compute(molecule, basis)

vib_drv = vlx.VibrationalAnalysis(scf_drv)
vib_drv.ostream.mute()
vib_results = vib_drv.compute(molecule, basis)
vib_drv.plot(vib_results)
vib_drv.animate(vib_results, mode=14)
../_images/6b117ca57c17b0c44350b11a11a3561528498491082d7d7708a6a57d8a7ee65b.png

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From an h5 file

vib_results = vlx.read_results("../output_files/acro-raman.h5", label="vib")
vib_drv.plot_raman(vib_results)
vib_drv.animate(vib_results, mode=14)

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../_images/4a8393f34e63db3b64fed57f002db2576282beb731586b3eeba15fc25214ae6f.png
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