initial commit of the aiida-cp2k cli

Author: dev-zero

aiida_cp2k/cli/__init__.py

@@ -0,0 +1,21 @@
+# -*- coding: utf-8 -*-
+
+# pylint: disable=wrong-import-position,wildcard-import
+"""Base command line interface module to wire up subcommands and loading the profile."""
+
+import click
+import click_completion
+
+from aiida.cmdline.params import options, types
+
+# Activate the completion of parameter types provided by the click_completion package
+click_completion.init()
+
+
+@click.group('aiida-cp2k', context_settings={'help_option_names': ['-h', '--help']})
+@options.PROFILE(type=types.ProfileParamType(load_profile=True))
+def cmd_root(profile):  # pylint: disable=unused-argument
+    """CLI for the `aiida-cp2k` plugin."""
+
+
+from .data import cmd_structure

aiida_cp2k/cli/data/__init__.py

@@ -0,0 +1,15 @@
+# -*- coding: utf-8 -*-
+
+# pylint: disable=cyclic-import,unused-import,wrong-import-position
+"""Module with CLI commands for various data types."""
+
+from .. import cmd_root
+
+
+@cmd_root.group('data')
+def cmd_data():
+    """Commands to create and inspect data nodes."""
+
+
+# Import the sub commands to register them with the CLI
+from .structure import cmd_structure

aiida_cp2k/cli/data/structure.py

@@ -0,0 +1,134 @@
+# -*- coding: utf-8 -*-
+"""Command line utilities to create and inspect `StructureData` nodes from CP2K input files."""
+
+from fractions import Fraction
+
+import click
+import numpy as np
+
+from aiida.cmdline.params import options
+from aiida.cmdline.utils import decorators, echo
+
+from . import cmd_data
+
+
+@cmd_data.group('structure')
+def cmd_structure():
+    """Commands to create and inspect `StructureData` nodes from CP2K input."""
+
+
+@cmd_structure.command('import')
+@click.argument('filename', type=click.File('r'))
+@options.DRY_RUN()
+@decorators.with_dbenv()
+def cmd_import(filename, dry_run):
+    """Import a `StructureData` from a CP2K input file."""
+
+    # pylint: disable=import-outside-toplevel,invalid-name,too-many-locals,too-many-statements,too-many-branches
+
+    from cp2k_input_tools.parser import CP2KInputParser
+    from aiida.orm.nodes.data.structure import StructureData, Kind, Site, symop_fract_from_ortho
+
+    parser = CP2KInputParser()
+    tree = parser.parse(filename)
+
+    for force_eval in tree['+force_eval']:
+        try:
+            cell = force_eval['+subsys']['+cell']
+            kinds = force_eval['+subsys']['+kind']
+            coord = force_eval['+subsys']['+coord']
+            break  # for now grab the first &COORD found
+        except KeyError:
+            continue
+    else:
+        echo.echo_error('no STRUCTURE, CELL, or KIND found in the given input file')
+
+    structure = StructureData()
+
+    # CP2K can get its cell information in two ways:
+    # - A, B, C: cell vectors
+    # - ABC: scaling of cell vectors, ALPHA_BETA_GAMMA: angles between the cell vectors
+    # We'll parse either form
+    if 'a' in cell:
+        unit_cell = np.array([cell['a'], cell['b'], cell['c']])  # unit vectors given
+
+        norms = [np.linalg.norm(v) for v in unit_cell]
+        angles = []
+
+        for i in range(3):
+            j = i - 1
+            k = i - 2
+
+            ll = norms[j] * norms[k]
+            if ll > 1e-16:
+                angle = np.arccos(np.dot(unit_cell[j], unit_cell[k]) / ll)
+            else:
+                angle = np.pi / 2
+
+            angles.append(angle)
+
+        tmat = symop_fract_from_ortho(norms + angles)
+
+    elif 'abc' in cell:
+        # length of unit vectors given
+        if 'alpha_beta_gamma' in cell:
+            # if we also have the angles, construct the cell
+            alpha, beta, gamma = cell.pop('alpha_beta_gamma')
+
+            cos_alpha = np.cos(alpha)
+            cos_beta = np.cos(beta)
+            cos_gamma = np.cos(gamma)
+            sin_gamma = np.sin(gamma)
+
+            unit_cell = np.array([
+                [1., 0., 0.],
+                [cos_gamma, sin_gamma, 0.],
+                [
+                    cos_beta,
+                    (cos_alpha - cos_gamma * cos_beta) / sin_gamma,
+                    np.sqrt(1. - cos_beta**2 - ((cos_alpha - cos_gamma * cos_beta) / sin_gamma)**2),
+                ],
+            ])
+        else:
+            unit_cell = np.eye(3)
+            alpha = beta = gamma = np.pi / 2
+
+        a, b, c = cell['abc']  # unpack and scale
+        unit_cell[0, :] *= a
+        unit_cell[1, :] *= b
+        unit_cell[2, :] *= c
+
+        tmat = symop_fract_from_ortho([a, b, c, alpha, beta, gamma])
+    else:
+        echo.echo_error('incomplete &CELL section')
+
+    if not coord.get('scaled', False):
+        tmat = np.eye(3)
+
+    structure.set_attribute('cell', unit_cell)
+
+    for kind in kinds:
+        name = kind['_']
+        element = kind.get('element', name)  # TODO: support getting the element from e.g. 'Fe1'
+        structure.append_kind(Kind(name=name, symbols=element))
+
+    if coord.get('units', 'angstrom').lower() != 'angstrom':
+        echo.echo_error('unit conversion for coordinations is not (yet) supported')
+
+    for coordline in coord['*']:
+        # coordinates are a series of strings according to the CP2K schema
+        fields = coordline.split()
+
+        name = fields[0]
+        # positions can be fractions AND they may be scaled
+        position = tmat @ np.array([float(Fraction(f)) for f in fields[1:4]])
+
+        structure.append_site(Site(kind_name=name, position=position))
+
+    formula = structure.get_formula()
+
+    if dry_run:
+        echo.echo_success('parsed structure with formula {}'.format(formula))
+    else:
+        structure.store()
+        echo.echo_success('parsed and stored StructureData<{}> with formula {}'.format(structure.pk, formula))

setup.json

@@ -25,9 +25,17 @@
         ],
         "aiida.workflows": [
             "cp2k.base = aiida_cp2k.workchains:Cp2kBaseWorkChain"
+        ],
+        "console_scripts": [
+            "aiida-cp2k = aiida_cp2k.cli:cmd_root"
         ]
     },
     "extras_require": {
+        "cli": [
+            "click",
+            "click-completion",
+            "cp2k-input-tools"
+        ],
         "test": [
             "pgtest==1.2.0",
             "pytest>=4.4,<5.0.0",