Running on a laptop/desktop

Running on a laptop/desktop#

In a Jupyter notebook#

On a personal computer, we recommend importing the VeloxChem Python module and running calculations in Jupyter notebooks. This provides a very flexible framework for the creation of workflows, as amply illustrated in the eChem book [FDB+22].

../_images/jupyter_nb.png

Using an input file#

Calculations can also be run in the terminal window using input files in the form of Python scripts or text files.

Python script

Terminal command:

python myjob.py > myjob.out

The Python script input file named myjob.py above can e.g. take the form:

import veloxchem as vlx

xyz_string = """
3
water
O    0.0000000    0.0000000   -0.1653507
H    0.7493682    0.0000000    0.4424329
H   -0.7493682    0.0000000    0.4424329
"""

molecule = vlx.Molecule.read_xyz_string(xyz_string)
basis = vlx.MolecularBasis.read(molecule, "def2-svp")

scf_drv = vlx.ScfRestrictedDriver()

scf_drv.xcfun = "b3lyp"
scf_drv.filename = "vlx_results_hdf5"

scf_results = scf_drv.compute(molecule, basis)

The results of the calculation are stored in an HDF5 file with a user specified name. This file can be directly read and analyzed with VIAMD.

Text file

Terminal command:

vlx myjob.inp [myjob.out]

An input file in text format consists of multiple groups marked with @group name and @end. The default unit for Cartesian coordinates of atoms is Angstrom. An example of the input file named myjob.inp above reads:

@jobs
task: scf
@end

@method settings
xcfun: b3lyp
basis: def2-svp
@end

@molecule
charge: 0
multiplicity: 1
xyz:
O  0.00000  0.00000  0.00000
H  0.00000  0.00000  1.79524
H  1.69319  0.00000 -0.59904
@end
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