Issue 1029 reformat geometry

[valentinsulzer]

Description

Reformats and simplifies geometries. See discussion in #1029

The geometry no longer has keys "primary" and "secondary". The first keys can either be spatial variables or "tabs", e.g.

geometry = {
        "negative electrode": {var.x_n: {"min": 0, "max": l_n}},
        "separator": {var.x_s: {"min": l_n, "max": l_n + l_s}},
        "positive electrode": {var.x_p: {"min": l_n + l_s, "max": 1}},
                "negative particle": {var.r_n: {"min": 0, "max": 1}},
                "positive particle": {var.r_p: {"min": 0, "max": 1}},
            }

    if current_collector_dimension == 0:
        geometry["current collector"] = {var.z: {"position": 1}}
    elif current_collector_dimension == 1:
        geometry["current collector"] = {
            var.z: {"min": 0, "max": 1},
            "tabs": {
                "negative": {"z_centre": pybamm.geometric_parameters.centre_z_tab_n},
                "positive": {"z_centre": pybamm.geometric_parameters.centre_z_tab_p},
            },
        }

Meshes are no longer lists, and auxiliary domains are used instead to figure out the number of repeats. There is a chance this could raise some obscure errors if a variable's auxiliary domains aren't set right, but not yet sure how to catch those.

Also fixes a bug with timescale (when time_units are hours) in quickplot.

Fixes #1029

Type of change

Please add a line in the relevant section of CHANGELOG.md to document the change (include PR #) - note reverse order of PR #s. If necessary, also add to the list of breaking changes.

• New feature (non-breaking change which adds functionality)
• Optimization (back-end change that speeds up the code)
• Bug fix (non-breaking change which fixes an issue)

Key checklist:

• No style issues: $ flake8
• All tests pass: $ python run-tests.py --unit
• The documentation builds: $ cd docs and then $ make clean; make html

You can run all three at once, using $ python run-tests.py --quick.

Further checks:

• Code is commented, particularly in hard-to-understand areas
• Tests added that prove fix is effective or that feature works

[rtimms]

thanks @tinosulzer this is so much neater!!