Merge pull request #147 from OMalenfantThuot/improvements

new class method for posinp, from_ase

mlcalcdriver/base/posinp.py

@@ -9,6 +9,7 @@
 import numpy as np
 from ase.cell import Cell
 from mlcalcdriver.globals import ATOMS_MASS, B_TO_ANG, ANG_TO_B
+from mlcalcdriver.interfaces import ase_atoms_to_pos_dict
 
 
 __all__ = ["Posinp", "Atom"]
@@ -280,6 +281,17 @@ def from_dict(cls, posinp):
                 boundary_conditions = "periodic"
         return cls(atoms, units, boundary_conditions, cell=cell, angles=angles)
 
+    @classmethod
+    def from_ase(cls, atoms):
+        r"""
+        Parameters
+        ----------
+        atoms : ase.Atoms
+            ase.Atoms instance from which the information is
+            taken to create the Posinp.
+        """
+        return cls.from_dict(ase_atoms_to_pos_dict(atoms))
+
     @property
     def atoms(self):
         r"""

mlcalcdriver/globals.py

@@ -3,9 +3,6 @@
 classes and workflows of the package.
 """
 
-# Mass of the different types of atoms in atomic mass units
-# TODO: Add more types of atoms
-# (found in $SRC_DIR/bigdft/src/orbitals/eleconf-inc.f90)
 ATOMS_MASS = {
     "H": 1.00794,
     "He": 4.002602,
@@ -30,6 +27,79 @@
     "Sc": 44.955910,
     "Ti": 47.88,
     "V": 50.9415,
+    "Cr": 51.996,
+    "Mn": 54.938,
+    "Fe": 55.933,
+    "Co": 58.933,
+    "Ni": 58.693,
+    "Cu": 63.546,
+    "Zn": 65.39,
+    "Ga": 69.732,
+    "Ge": 72.61,
+    "As": 74.922,
+    "Se": 78.09,
+    "Br": 79.904,
+    "Kr": 84.80,
+    "Rb": 84.468,
+    "Sr": 87.62,
+    "Y": 88.906,
+    "Zr": 91.224,
+    "Nb": 92.906,
+    "Mo": 95.94,
+    "Tc": 98.907,
+    "Ru": 101.07,
+    "Rh": 102.906,
+    "Pd": 106.42,
+    "Ag": 107.868,
+    "Cd": 112.411,
+    "In": 114.818,
+    "Sn": 118.71,
+    "Sb": 121.760,
+    "Te": 127.6,
+    "I": 126.904,
+    "Xe": 131.29,
+    "Cs": 132.905,
+    "Ba": 137.327,
+    "La": 138.906,
+    "Ce": 140.115,
+    "Pr": 140.908,
+    "Nd": 144.24,
+    "Pm": 144.913,
+    "Sm": 150.36,
+    "Eu": 151.966,
+    "Gd": 157.25,
+    "Tb": 158.925,
+    "Dy": 162.50,
+    "Ho": 164.930,
+    "Er": 167.26,
+    "Tm": 168.934,
+    "Yb": 173.04,
+    "Lu": 174.967,
+    "Hf": 178.49,
+    "Ta": 180.948,
+    "W": 183.85,
+    "Re": 186.207,
+    "Os": 190.23,
+    "Ir": 192.22,
+    "Pt": 195.08,
+    "Au": 196.967,
+    "Hg": 200.59,
+    "Tl": 204.383,
+    "Pb": 207.2,
+    "Bi": 208.980,
+    "Po": 208.982,
+    "At": 209.987,
+    "Rn": 222.018,
+    "Fr": 223.020,
+    "Ra": 226.025,
+    "Ac": 227.028,
+    "Th": 232.038,
+    "Pa": 231.036,
+    "U": 238.029,
+    "Np": 237.048,
+    "Pu": 244.064,
+    "Am": 243.061,
+    "Cm": 247.070
 }
 r"""
 `Dictionnary` containing elemental masses, in atomic mass units.

mlcalcdriver/interfaces/ase_interface.py

@@ -1,6 +1,5 @@
 import ase
 import numpy as np
-from mlcalcdriver.base import Posinp
 
 
 def posinp_to_ase_atoms(posinp):
@@ -20,7 +19,7 @@ def posinp_to_ase_atoms(posinp):
     return atoms
 
 
-def ase_atoms_to_posinp(atoms):
+def ase_atoms_to_pos_dict(atoms):
     r"""
     Converts an :class:`ase.Atoms` instance to a
     :class:`Posinp` instance.
@@ -32,4 +31,4 @@ def ase_atoms_to_posinp(atoms):
     cell = atoms.get_cell()
     pos_dict["positions"] = positions
     pos_dict["cell"] = cell
-    return Posinp.from_dict(pos_dict)
+    return pos_dict

tests/test_interface.py

@@ -1,7 +1,7 @@
 import os
 import pytest
 from mlcalcdriver import Posinp
-from mlcalcdriver.interfaces import posinp_to_ase_atoms, ase_atoms_to_posinp
+from mlcalcdriver.interfaces import posinp_to_ase_atoms
 
 pos_folder = "tests/posinp_files/"
 
@@ -11,17 +11,17 @@ 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)
+        pos2 = Posinp.from_ase(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)
+        pos2 = Posinp.from_ase(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)
+        pos2 = Posinp.from_ase(atoms)
         assert pos1 == pos2