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 Fransson et al. (2022).

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)

                                                                                                                          
                                            Self Consistent Field Driver Setup                                            
                                           ====================================                                           
                                                                                                                          
                   Wave Function Model             : Spin-Restricted Kohn-Sham                                            
                   Initial Guess Model             : Restart from Checkpoint                                              
                   Convergence Accelerator         : Direct Inversion of Iterative Subspace                               
                   Max. Number of Iterations       : 50                                                                   
                   Max. Number of Error Vectors    : 10                                                                   
                   Convergence Threshold           : 1.0e-06                                                              
                   ERI Screening Threshold         : 1.0e-12                                                              
                   Linear Dependence Threshold     : 1.0e-06                                                              
                   Exchange-Correlation Functional : B3LYP                                                                
                   Molecular Grid Level            : 4                                                                    
                                                                                                                          
* Info * Using the B3LYP functional.                                                                                      
                                                                                                                          
         P. J. Stephens, F. J. Devlin, C. F. Chabalowski, and M. J. Frisch.,  J. Phys. Chem. 98, 11623 (1994)
                                                                                                                          
* Info * Using the Libxc library (v7.0.0).                                                                                
                                                                                                                          
         S. Lehtola, C. Steigemann, M. J.T. Oliveira, and M. A.L. Marques.,  SoftwareX 7, 1–5 (2018)
                                                                                                                          
* Info * Using the following algorithm for XC numerical integration.                                                      
                                                                                                                          
         J. Kussmann, H. Laqua and C. Ochsenfeld, J. Chem. Theory Comput. 2021, 17, 1512-1521
                                                                                                                          
* Info * Restarting from checkpoint file: vlx_results_hdf5_scf.h5                                                         
                                                                                                                          
                                                                                                                          
               Iter. |    Kohn-Sham Energy | Energy Change | Gradient Norm | Max. Gradient | Density Change               
               --------------------------------------------------------------------------------------------               
                  1       -76.358270371073    0.0000000000      0.00000009      0.00000001      0.00000000                
                                                                                                                          
* Info * Checkpoint written to file: vlx_results_hdf5_scf.h5                                                              
                                                                                                                          
* Info * SCF results written to file: vlx_results_hdf5.h5                                                                 
                                                                                                                          
               *** SCF converged in 1 iterations. Time: 0.50 sec.                                                         
                                                                                                                          
               Spin-Restricted Kohn-Sham:                                                                                 
               --------------------------                                                                                 
               Total Energy                       :      -76.3582703711 a.u.                                              
               Electronic Energy                  :      -85.4865540991 a.u.                                              
               Nuclear Repulsion Energy           :        9.1282837280 a.u.                                              
               ------------------------------------                                                                       
               Gradient Norm                      :        0.0000000850 a.u.                                              
                                                                                                                          
                                                                                                                          
               Ground State Information                                                                                   
               ------------------------                                                                                   
               Charge of Molecule            :  0.0                                                                       
               Multiplicity (2S+1)           :  1                                                                         
               Magnetic Quantum Number (M_S) :  0.0

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

References¶

Fransson, T., Delcey, M., Brumboiu, I. E., Hodecker, M., Li, X., Rinkevicius, Z., Dreuw, A., Rhee, Y. M., & Norman, P. (2022). Computational Chemistry from Laptop to HPC: A notebook exploration of quantum chemistry. KTH Royal Institute of Technology. 10.30746/978-91-988114-0-7