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# ASE Databases: An Introduction

Note

Go to the end to download the full example code.

# ASE Databases: An Introduction

ASE has its own database format that can be used for storing and retrieving atoms (and associated data) in a compact and convenient way. In the following, we will create databases and interact with them through python scripts and the command line.

## Setting up a database

To construct a database we first need some atomic structures so let’s quickly create some. As you have seen the ASE command line tool provides many convenient commands and in particular we can use the `build` command to create some atomic structures. Remember, if you are unsure how to use a particular command you can always append `-h` to the particular command (ie. `ase build -h`) to see the help for that particular command.

We choose to build aluminium, copper and gold in the diamond crystal structure for which ASE already knows the lattice constants:

    $ ase build -x fcc Al
    $ ase build -x fcc Cu
    $ ase build -x fcc Au

This creates three files: `Al.json`, `Cu.json` and `Au.json`. If you want to, you can inspect them with ASE’s `gui` command, however we want to construct a database containing these structures. To do this we can use `convert`:

    $ ase convert Al.json Cu.json Au.json database.db

This has created an ASE database name `database.db`.

Additionally, one can use the `ase build` command to build Si, Ge and C and convert them into a ASE database named `database.db` using the following:

    from pathlib import Path

    from ase.build import bulk
    from ase.calculators.emt import EMT
    from ase.db import connect
    from ase.filters import FrechetCellFilter
    from ase.optimize import BFGS

    dbfile = Path('database.db')
    dbfile.unlink(missing_ok=True)

    structures = ['Al', 'Cu', 'Au']
    db = connect(dbfile)

    for structure in structures:
        db.write(bulk(structure))

    import matplotlib.gridspec as gridspec
    import matplotlib.pyplot as plt

    from ase.visualize.plot import plot_atoms

    fig = plt.figure()
    gs = gridspec.GridSpec(2, 2, figure=fig, hspace=0.3, wspace=0.2)

    ax1 = fig.add_subplot(gs[0, 0])
    ax2 = fig.add_subplot(gs[0, 1])
    ax3 = fig.add_subplot(gs[1, 0])

    # Hide unused bottom-right cell
    ax_unused = fig.add_subplot(gs[1, 1])
    ax_unused.axis('off')

    # --- Center bottom axis manually ---
    pos1 = ax1.get_position()
    pos3 = ax3.get_position()
    new_x0 = 0.5 - pos3.width / 2
    ax3.set_position([new_x0, pos3.y0, pos3.width, pos3.height])

    for name, ax in zip(structures, [ax1, ax2, ax3]):
        plot_atoms(bulk(name) * 3, ax, rotation='0x,30y,0z', show_unit_cell=0)
        ax.set_title(name)
        ax.set_axis_off()

## Inspecting a database on the command line

We can inspect the database using the `db` command:

    $ ase db database.db

which will display three entries, one for each structure. From this point it is advised to bring up the help for the `db` command every time you need it.

From the help we can see that it is possible to make selections (queries in database lingo) in the database by:

    $ ase db database.db Al

which will show all structures containing silicon. To see the details of a particular row we can do:

    $ ase db database.db Al -l

From which we can get an overview of the stored data. We can also view all structures in a database using:

    $ ase gui database.db

or if we want to view a single one we can do:

    $ ase gui database.db@Al

where everything after the @ is interpreted as a query.

## Opening a database using a Python script

To open a database using Python, we can use the `ase.database.connect`

  method which returns a database object from which we can make selections:

    db = connect(dbfile)
    for row in db.select():
        atoms = row.toatoms()
        print(atoms)

    Atoms(symbols='Al', pbc=True, cell=[[0.0, 2.025, 2.025], [2.025, 0.0, 2.025], [2.025, 2.025, 0.0]])
    Atoms(symbols='Cu', pbc=True, cell=[[0.0, 1.805, 1.805], [1.805, 0.0, 1.805], [1.805, 1.805, 0.0]])
    Atoms(symbols='Au', pbc=True, cell=[[0.0, 2.04, 2.04], [2.04, 0.0, 2.04], [2.04, 2.04, 0.0]])

We can make selections in the database using `db.select(some_selection)` which returns all rows matching `some_selection`. In this case `some_selection` was omitted which means that we select all rows in the database. For each row the associated `ase.Atoms` objects is retrieved by using the `row.toatoms()` method.

Hint

In order to see the documentation for a particular python function import it and use the `help` function. For example

    from ase.db import connect
    db = connect('database.db')
    help(db.select)

will show the documentation for the select method of the database object. Another useful function is `dir` which shows all attributes of a python object. For example

    from ase.db import connect
    db = connect('database.db')
    row = db.select(id=1)[0]
    dir(row)

will show all attributes of the row object.

Using a python script, print the formula for each row in your database.

## Write new entries to a database using Python

Next, we loop through all materials, relax them (see exercise “Structure Optimization”) and save the relaxed structure as a new entry in the database with an added column relaxed equal to `True` that we can use later for selecting only these materials. A new entry in the database can be written using the `write()` method of a database object.

Hint

To relax crystals we have to specify that the cell parameters should be relaxed as well. This is done by wrapping `ase.filters.FrechetCellFilter` around the atoms object like

    filter = FrechetCellFilter(atoms)

and feeding `filter` into the optimization routine see `help(FrechetCellFilter)` for more explanation.

    for row in db.select():
        atoms = row.toatoms()
        calc = EMT()
        atoms.calc = calc
        atoms.get_stress()
        filter = FrechetCellFilter(atoms)
        opt = BFGS(filter)
        opt.run(fmax=0.05)
        db.write(atoms=atoms, relaxed=True)

          Step     Time          Energy          fmax
    BFGS:    0 09:17:15       -0.001502        0.161794
    BFGS:    1 09:17:15       -0.002532        0.135189
    BFGS:    2 09:17:15       -0.004882        0.002382
          Step     Time          Energy          fmax
    BFGS:    0 09:17:15       -0.005682        0.160183
    BFGS:    1 09:17:15       -0.006560        0.095504
    BFGS:    2 09:17:15       -0.007036        0.001838
          Step     Time          Energy          fmax
    BFGS:    0 09:17:15        0.002606        0.308859
    BFGS:    1 09:17:15        0.000034        0.077987
    BFGS:    2 09:17:15       -0.000135        0.002381

Here, we are using EMT, which is a force-field calculator. This is not accurate enough for production level computations. For production level computations, self consistent calculations, such as using GPAW, have to be used.

## Adding data to existing database

Now we want to calculate some data and include the data in the database which can be done using the `update` method of the database object. Then use the `atoms.get_potential_energy()` method to calculate the energy of the materials and store it under the `energy` keyword.

    for row in db.select(relaxed=True):
        atoms = row.toatoms()
        calc = EMT()
        atoms.calc = calc
        e = atoms.get_potential_energy()
        db.update(row.id, data={'energy': e})

Now, we can inspect the database again using the `ase db` command. To see the new column `bandgap` you can display all columns using the `-c++` option:

    $ ase db database -c++

## Browsing data

The database can also be visualized in a browser by using:

    $ ase database database.db -w
    $ firefox http://0.0.0.0:5000/

This opens a local webserver which can be opened in firefox like above. The layout can be customized further than our simple example however this would probably be too much for now. To see a more advanced example of such a web interfaced database in action you can check out the 2D database https://cmrdb.fysik.dtu.dk/c2db.

## Advanced tutorial

An additional tutorial using the ASE databases for adsorbates on metals can be found at ASE Databases: Surface adsorption study.

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