Merge pull request #6 from OMalenfantThuot/test_posinp

Test posinp

README.md

@@ -23,7 +23,7 @@ No documentation for the moment.
 
 ### From PyPi
 
-To install the latest version available on PyPi: []
+To install the latest version available on PyPi:
 
 `pip install mlcalcdriver`
 

mlcalcdriver/base/posinp.py

@@ -194,77 +194,77 @@ 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)
+#    @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):
@@ -428,10 +428,6 @@ def __eq__(self, other):
         except AttributeError:
             return False
 
-    def __ne__(self, other):
-        # This is only for the python2 version to work
-        return not self.__eq__(other)
-
     def __str__(self):
         r"""
         Convert the Posinp to a string in the xyz format.
@@ -627,18 +623,18 @@ 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)
+#    @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):

tests/posinp_files/additional_atom.xyz

@@ -0,0 +1,6 @@
+3   reduced
+surface  8.07007483423  1.0  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/free_reduced.xyz

@@ -0,0 +1,6 @@
+4   reduced
+free  8.07007483423  1.0  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/missing_atom.xyz

@@ -0,0 +1,5 @@
+4   atomic
+free
+C    0.6661284109   0.000000000   1.153768252
+C    3.330642055    0.000000000   1.153768252
+C    4.662898877    0.000000000   3.461304757