9. Analysis of the ProteinDF Calculation Results

9.1. General analysis tools

• pdf-top

Displays atomic orbitals with a large contribution to the specified molecular orbital.

Usage: pdf-top [Option]

Executing the command above obtains the following outputs:

$ pdf-top 115
MO level: 115
No. 1     8  C (  42.525,   37.241,   32.674) p(    px) (  8.18%;   8.18%)
No. 2     8  C (  42.525,   37.241,   32.674) p(    pz) (  7.77%;  15.95%)
No. 3    20  C (  43.858,   35.420,   31.228) p(    px) (  7.38%;  23.34%)
No. 4    11  N (  41.507,   35.639,   33.859) p(    px) (  6.74%;  30.08%)
No. 5    14  C (  42.553,   33.543,   32.877) p(    px) (  6.69%;  36.77%)
No. 6    20  C (  43.858,   35.420,   31.228) p(    pz) (  5.54%;  42.31%)
No. 7    14  C (  42.553,   33.543,   32.877) p(    pz) (  5.20%;  47.51%)
No. 8    11  N (  41.507,   35.639,   33.859) p(    pz) (  4.71%;  52.23%)
No. 9     9  C (  41.623,   36.994,   33.649) p(    px) (  4.39%;  56.62%)
No.10     9  C (  41.623,   36.994,   33.649) p(    pz) (  3.39%;  60.00%)

• pdf-pop

Outputs formal charges.

Usage: pdf-pop <MO_ID>

• pdf-mo

Outputs molecular orbital field data.

Usage: pdf-mo <MO_ID>

• pdf-esp

Outputs electrostatic potential field data.

Usage: pdf-esp

• pdf-dens

Outputs electron density field data.

Usage: pdf-dens

• pdf-archive

Aggregates calculation results to create archives.

Usage: pdf-archive

• pdf-report

Creates calculation result reports.

Usage: pdf-archive

The user can obtain energy convergence curve (Fig. 4) and orbital energy convergence history (Fig. 5), as shown below

Fig. 4: Energy convergence curve

Fig. 5: Orbital energy convergence history

9.2. Advanced (debug) tools

• pdf-mat2txt

Outputs the specified matrix file (binary format) to standard output.

Usage: pdf-mat2txt

• pdf-vtr2txt

Outputs the specified vector file (binary format) to standard output.

Usage: pdf-vtr2txt

• pdf-mpac2yml

Converts MessagePack files to YAML files.

Usage: mpac2yml.py [options] FILE

Options:
-h, --help  show this help message and exit

• pdf-yml2mpac

Converts YAML files to MessagePack files.

Usage: yml2mpac.py [options] YAML_FILE MPAC_FILE

Options:
-h, --help  show this help message and exit

• pdf-diff

Compares two calculation results.

Usage: pdf-diff

• pdf-matinfo

Outputs matrix information.

Usage: pdf-matinfo

• pdf-genmat

Generates matrices.

Usage: pdf-genmat