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)
3Dmol.js failed to load for some reason. Please check your browser console for error messages.
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()
3Dmol.js failed to load for some reason. Please check your browser console for error messages.
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)
From an h5 file
rsp_results = vlx.read_results("../output_files/alanine-ecd.h5", label="rsp")
rsp_drv.plot_ecd(rsp_results)
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)
3Dmol.js failed to load for some reason. Please check your browser console for error messages.
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)
3Dmol.js failed to load for some reason. Please check your browser console for error messages.
