Merge aa4fac8 into 84baecd

.travis.yml

@@ -5,6 +5,6 @@ install:
   - pip install -r requirements_dev.txt
   - pip install -e .
 script:
-  - pytest --cov=mlcalcdriver
+  - pytest --cov=mlcalcdriver -v
 after_success:
   - coveralls

mlcalcdriver/base/posinp.py

@@ -194,6 +194,78 @@ def _from_lines(cls, lines):
             atoms.append(Atom(atom_type, position))
         return cls(atoms, units, boundary_conditions, cell=cell)
 
+    @classmethod
+    def from_dict(cls, posinp):
+        r"""
+        Initialize the input positions from a dictionary.
+
+        Parameters
+        ----------
+        posinp : dict
+            Posinp as a dictionary coming from an InputParams or
+            Logfile instance.
+
+        Returns
+        -------
+        Posinp
+            Posinp initialized from an dictionary.
+
+
+        >>> pos_dict = {
+        ...     "units": "reduced",
+        ...     "cell": [8.07007483423, 'inf', 4.65925987792],
+        ...     "positions": [
+        ...         {'C': [0.08333333333, 0.5, 0.25]},
+        ...         {'C': [0.41666666666, 0.5, 0.25]},
+        ...         {'C': [0.58333333333, 0.5, 0.75]},
+        ...         {'C': [0.91666666666, 0.5, 0.75]},
+        ...     ]
+        ... }
+        >>> pos = Posinp.from_dict(pos_dict)
+        >>> pos.boundary_conditions
+        'surface'
+
+        The value of the "cell" key allows to derive the boundary
+        conditions. Replacing 'inf' by a number gives a posinp with
+        periodic boundary conditions:
+
+        >>> pos_dict["cell"] = [8.07007483423, 10.0, 4.65925987792]
+        >>> pos = Posinp.from_dict(pos_dict)
+        >>> pos.boundary_conditions
+        'periodic'
+
+        If there is no "cell" key, then the boundary conditions are set
+        to "free". Here, given that the units are reduced, this raises
+        a ValueError:
+
+        >>> del pos_dict["cell"]
+        >>> pos = Posinp.from_dict(pos_dict)
+        Traceback (most recent call last):
+        ...
+        ValueError: Cannot use reduced units with free boundary conditions
+        """
+        # Lower the keys of the posinp if needed
+        if "positions" not in posinp:
+            ref_posinp = deepcopy(posinp)
+            for key in ref_posinp:
+                posinp[key.lower()] = ref_posinp[key]
+                del posinp[key]
+        # Read data from the dictionary
+        atoms = []  # atomic positions
+        for atom in posinp["positions"]:
+            atoms.append(Atom.from_dict(atom))
+        units = posinp.get("units", "atomic")  # Units of the coordinates
+        cell = posinp.get("cell")  # Simulation cell size
+        # Infer the boundary conditions from the value of cell
+        if cell is None:
+            boundary_conditions = "free"
+        else:
+            if cell[1] in [".inf", "inf"]:
+                boundary_conditions = "surface"
+            else:
+                boundary_conditions = "periodic"
+        return cls(atoms, units, boundary_conditions, cell=cell)
+
     @property
     def atoms(self):
         r"""
@@ -551,6 +623,19 @@ def __init__(self, atom_type, position):
         self.position = position
         self.mass = ATOMS_MASS[self.type]
 
+    @classmethod
+    def from_dict(cls, atom_dict):
+        r"""
+        Parameters
+        ----------
+        atom_dict : dict
+            Information about an atom given by a dict whose only key is
+            the atom type and the value is the atomic position. This
+            format is mainly found in bigdft logfiles.
+        """
+        [(atom_type, position)] = atom_dict.items()
+        return cls(atom_type, position)
+
     @property
     def type(self):
         r"""

mlcalcdriver/interfaces/ase_interface.py

@@ -1,4 +1,6 @@
 import ase
+import numpy as np
+from mlcalcdriver.base import Posinp
 
 def posinp_to_ase_atoms(posinp):
     symbols, positions, masses = "", [], []
@@ -16,3 +18,24 @@ def posinp_to_ase_atoms(posinp):
         symbols=symbols, positions=positions, masses=masses, cell=posinp.cell, pbc=pbc
     )
     return atoms
+
+def ase_atoms_to_posinp(atoms):
+    pos_dict = {"units": "angstroem"}
+    positions = []
+    for at in atoms:
+        positions.append({at.symbol: at.position})
+    cell = atoms.get_cell()
+    print(cell)
+    if cell.orthorhombic:
+        if (cell==0.0).all():
+            new_cell = None
+        elif cell[1,1] in [0.0, np.inf]:
+            new_cell = [cell[0,0], str(np.inf), cell[2,2]]
+        else:
+            new_cell = [dim[i] for i, dim in enumerate(cell)]
+    else:
+        raise NotImplementedError("Non orthorhombic cells are not supported yet.")
+    print(new_cell)
+    pos_dict["positions"] = positions
+    pos_dict["cell"] = new_cell
+    return Posinp.from_dict(pos_dict)

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name="mlcalcdriver",
-    version="0.1.0",
+    version="0.2.0",
     author="Olivier Malenfant-Thuot",
     author_email="malenfantthuotolivier@gmail.com",
     description="A package to drive atomic calculations using machine learned models.",

tests/posinp_files/periodic.xyz

@@ -0,0 +1,6 @@
+4   angstroem
+periodic  8.07007483423  8.9  4.65925987792
+C    0.08333333333    0.5    0.25
+C    0.41666666666    0.5    0.25
+C    0.58333333333    0.5    0.75
+C    0.91666666666    0.5    0.75

tests/posinp_files/surface2.xyz

@@ -0,0 +1,6 @@
+4   angstroem
+surface  8.07007483423  .inf  4.65925987792
+C    0.08333333333    0.5    0.25
+C    0.41666666666    0.5    0.25
+C    0.58333333333    0.5    0.75
+C    0.91666666666    0.5    0.75

tests/test_interface.py

@@ -0,0 +1,26 @@
+import os
+import pytest
+from mlcalcdriver import Posinp
+from mlcalcdriver.interfaces import posinp_to_ase_atoms, ase_atoms_to_posinp
+
+pos_folder = "tests/posinp_files/"
+
+class TestConversion:
+
+    def test_mol(self):
+        pos1 = Posinp.from_file(os.path.join(pos_folder, "N2.xyz"))
+        atoms = posinp_to_ase_atoms(pos1)
+        pos2 = ase_atoms_to_posinp(atoms)
+        assert pos1 == pos2
+
+    def test_surface(self):
+        pos1 = Posinp.from_file(os.path.join(pos_folder, "surface2.xyz"))
+        atoms = posinp_to_ase_atoms(pos1)
+        pos2 = ase_atoms_to_posinp(atoms)
+        assert pos1 == pos2
+
+    def test_periodic(self):
+        pos1 = Posinp.from_file(os.path.join(pos_folder, "periodic.xyz"))
+        atoms = posinp_to_ase_atoms(pos1)
+        pos2 = ase_atoms_to_posinp(atoms)
+        assert pos1 == pos2