JSON interface update

[dgasmith]

This PR does the following:

• Moves JSON specification to zero-index (will impact torsion drive)
• Pins QCEngine version via GitHub, so we can look at the latest release and the latest version
• Adds a new constraint specification that looks like:

    constraint_dict = {
        'freeze': [{
            "type": ("xyz", [0, 1, 2])
        }],
        'set': [{
            "type": ("angle", [1, 0, 4]),
            "value": 110.0
        }],
        'scan': [{
            "type": ("distance", [1, 0]),
            "start": 1.0,
            "stop": 1.2,
            "steps": 3
        }, {
            "type": ('dihedral', [0, 4, 5, 6]),
            "start": 110.0,
            "stop": 150.0,
            "steps": 3
        }]
    }

[codecov-io]

Codecov Report

Merging #44 into master will increase coverage by 3.33%.
The diff coverage is 90.32%.

[dgasmith]

@leeping Ready to go if you are happy with it.

[leeping]

Thank you very much for adding this. :) I've reviewed and I'll merge it now.

[dgasmith]

As a note the final dict looks like:

    constraint_dict = {
        'freeze': [{
            "type": "xyz", 
            "indices": [0, 1, 2]
        }],
        'set': [{
            "type": "angle", 
            "indices": [1, 0, 4],
            "value": 110.0
        }],
        'scan': [{
            "type": "distance",
            "indicies": [1, 0],
            "start": 1.0,
            "stop": 1.2,
            "steps": 3
        }, {
            "type": 'dihedral',
            "indices": [0, 4, 5, 6],
            "start": 110.0,
            "stop": 150.0,
            "steps": 3
        }]
    }