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An overview of the code#

Let’s dive into the code and see what is where. Almost all the files that you will work with are in the subdirectory pyscf_step, so change into that directory and look at the files:

(seamm-dev) psaxe@PaulsPersonal pyscf_step % ls -l
ls -l
total 96
-rw-r--r--  1 psaxe  staff    661 Aug 23 10:11 __init__.py
drwxr-xr-x  8 psaxe  staff    256 Aug 23 11:46 __pycache__
-rw-r--r--  1 psaxe  staff  18471 Aug 23 10:11 _version.py
drwxr-xr-x  3 psaxe  staff     96 Aug 23 10:11 data
-rw-r--r--  1 psaxe  staff   5298 Aug 23 11:39 pyscf.py
-rw-r--r--  1 psaxe  staff   3618 Aug 23 11:39 pyscf_parameters.py
-rw-r--r--  1 psaxe  staff   2887 Aug 23 10:11 pyscf_step.py
-rw-r--r--  1 psaxe  staff   6582 Aug 23 10:11 tk_pyscf.py

(seamm-dev) psaxe@PaulsPersonal pyscf_step % ls -l data
ls -l data
total 8
-rw-r--r--  1 psaxe  staff  1558 Aug 23 10:11 references.bib
pyscf_step.py

This file contains factories for creating the graphical and non-graphical classes for the PySCF step. You shouldn’t change anything in this file other than the description:

my_description = {
    "description": "An interface for PySCF",
    "group": "Simulations",
    "name": "PySCF",
}

The only part of this that is used at the moment is the group, which defines where in the left hand panel of SEAMM this plug-in appears. By default it is “Simulations”, which is why our brand new plug-in showed up in the simulation section. When you make plug-ins, you might want to change this to an appropriate area for your plug-in. You can either use one of the existing groupings, or create a new one by typing a new name.

pyscf_parameters.py

This file defines the parameters that the plug-in provides to control what it does. The skeleton created by the cookiecutter has one parameter as an example:

parameters = {
    "time": {
        "default": 100.0,
        "kind": "float",
        "default_units": "ps",
        "enumeration": tuple(),
        "format_string": ".1f",
        "description": "Simulation time:",
        "help_text": ("The time to simulate in the dynamics run."),
    },
}

That is why the dialog showed a parameters for Simulation time. We’ll edit this in a minute.

tk_pyscf.py

This contains the TkPySCF class, which defines the GUI for the plug-in. Generally any file in SEAMM starting with “tk_” is part of the GUI.

pyscf.py

This contains the PySCF class, which handles running PySCF when the flowchart is executed. We’ll also come back to this file.

data/references.bib

Contains the references that users should cite when using this plug-in. This will be covered in another tutorial; however, a reference to the plug-in has been automatically generated from the questions the cookiecutter asked, and will be printed when this step is irun.

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