ipyvasp 0.9.5__py2.py3-none-any.whl → 0.9.7__py2.py3-none-any.whl

ipyvasp/_version.py

@@ -1 +1 @@
-__version__ = "0.9.5"
+__version__ = "0.9.7"

ipyvasp/bsdos.py

@@ -35,7 +35,8 @@ from ._enplots import (
 def _format_input(projections, sys_info):
     """
     Format input spins, atoms, orbs and labels according to selected `projections`.
-    For example: {'Ga-s':(0,[1]),'Ga-p':(0,[1,2,3]),'Ga-d':(0,[4,5,6,7,8])} #for Ga in GaAs, to pick Ga-1, use [0] instead of 0 at first place
+    For example: {'Ga-s':(0,[0]),'Ga-px+py':(0,[2,3]),'Ga-all':(0,'all')} #for Ga in GaAs, to pick Ga-1, use [0] instead of 0 at first place
+    or {'Ga-s':('Ga','s'),'Ga-px+py':(0,'px+py'),'all-d':('all','d')}
     In case of 3 items in tuple, the first item is spin index, the second is atoms, the third is orbs.
     """
     if not isinstance(projections, dict):
@@ -53,6 +54,11 @@ def _format_input(projections, sys_info):
     )  # will be error if two ranges there to compare for max
     norbs = len(sys_info.orbs)
 
+    orbs_map = {} # total if components given
+    if 'px' in sys_info.orbs: orbs_map['p'] = range(1,4)
+    if 'dxy' in sys_info.orbs: orbs_map['d'] = range(4,9)
+    if 'f0' in sys_info.orbs: orbs_map['f'] = range(9,16)
+
     # Set default values for different situations
     spins, atoms, orbs, labels = [], [], [], []
 
@@ -78,6 +84,24 @@ def _format_input(projections, sys_info):
                 )
 
             spins.append(S)  # Only add spins if given
+        
+        if isinstance(A,str):
+            if A.lower() == 'all':
+                A = range(max_ind + 1)
+            else:
+                if not A in sys_info.types.keys():
+                    raise KeyError(f"type {A!r} not found. Available are {list(sys_info.types.keys())}, 'all', or indexing with integeres/list of intergers.")
+                A = sys_info.types[A]
+        
+        if isinstance(B,str):
+            if B.lower() == 'all':
+                B = range(norbs)
+            else:
+                B = {b:[sys_info.orbs.index(b)] if b in sys_info.orbs else orbs_map.get(b,[]) for b in (a.strip() for a in B.split('+'))}
+                for key, value in B.items():
+                    if not value:
+                        raise KeyError(f"orbital {key!r} not found. Available are {sys_info.orbs}, 'all' or indexing with integers/list of intergers")
+                B = list(sorted(set([i for b in B.values() for i in b]))) # flatten
 
         if not isinstance(A, (int, np.integer, list, tuple, range)):
             raise TypeError(f"{A!r} is not an integer or list/tuple/range of integers.")
@@ -129,7 +153,7 @@ def _format_input(projections, sys_info):
 
     if spins and len(atoms) != len(spins):
         raise ValueError(
-            "You should provide spin for each projection or none at all. If not provided, spin is picked from corresponding eigenvalues (up/down) for all projections."
+            "You should provide spin for each projection or none at all. If not provided, spin is picked from corresponding eigenvalues (up/down) for all projections using 'spin' parameter explicity."
         )
 
     uatoms = np.unique(
@@ -139,7 +163,7 @@ def _format_input(projections, sys_info):
     uorbs = tuple(uorbs) if len(uorbs) < norbs else -1  # -1 means all orbitals
     uatoms = tuple(uatoms) if len(uatoms) == (max_ind + 1) else -1  # -1 means all atoms
     uspins = tuple(spins)
-
+    
     return (spins, uspins), (atoms, uatoms), (orbs, uorbs), labels
 
 
@@ -154,8 +178,8 @@ bands : list/tuple
     List of indices of bands. If given, this ovverides elim."""
 _proj_doc = """projections : dict
     Mapping from str -> [atoms, orbs]. Use dict to select specific projections, 
-    e.g. {'Ga-s': (0,[0]), 'Ga1-p': ([0],[1,2,3])} in case of GaAs. If values of the dict 
-    are callable, they must accept two arguments evals/tdos, occs/idos of from data and 
+    e.g. {'Ga-s':(0,[0]),'Ga-px+py':(0,[2,3]),'Ga-all':(0,'all')} or {'Ga-s':('Ga','s'),'Ga-px+py':(0,'px+py'),'all-d':('all','d')}. 
+    If values of the dict are callable, they must accept two arguments evals/tdos, occs/idos of from data and 
     should return array of shape[1:] (all but spin dimension)."""
 
 

ipyvasp/core/serializer.py

@@ -329,6 +329,23 @@ class PoscarData(Dict2Data):
         "Returns the symbols of the atoms in the poscar data without numbers"
         return np.array([lab.split()[0] for lab in self.labels])
     
+    @property
+    def G(self):
+        """Return metric tensor to be used with fractional coordinates.
+        
+        >>> D2 = points @ self.G @ points.T # assuming points is Nx3 numpy array, D2 is NxN matrix whose elements are dot product of coordinates in 3D space.
+        >>> assert (self.metric(points) == np.sqrt(np.diag(D2))).all()
+
+        Note: You can use `self.metric(points)` instead of doing a long operation like `np.sqrt(np.diag(points @ self.G @ points.T))`.
+        """
+        return self.basis @ self.basis.T  # becuase our vectors are row, transpose comes later
+    
+    def metric(self, points):
+        """Shortcut for `np.linalg.norm(self.to_cartesian(points),axis=<1 or 0>)`. `points` are assumed as fractional coordinates in `self.basis`.
+        You can compute metric from any point other than origin by just subtracting that point, e.g. `points - 0.5` will get metric from center of cell (1/2,1/2,1/2).
+        """
+        return np.linalg.norm(self.to_cartesian(points),axis=1 if np.ndim(points) == 2 else 0)
+    
     def get_sites(self, type_or_indices, as_coords=False):
         "Shortcut method for `POSCAR.data.positions[POSCAR.data.types['name']]` or with regular indexing."
         points = self.coords if as_coords else self.positions

{ipyvasp-0.9.5.dist-info → ipyvasp-0.9.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.9.5
+Version: 0.9.7
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor

{ipyvasp-0.9.5.dist-info → ipyvasp-0.9.7.dist-info}/RECORD

@@ -2,8 +2,8 @@ ipyvasp/__init__.py,sha256=rlorju9arMtHw1QRYPljday-PyZWJdSCxg4lw3g6t0Q,1409
 ipyvasp/__main__.py,sha256=eJV1TZSiT8mC_VqAeksNnBI2I8mKMiPkEIlwikbtOjI,216
 ipyvasp/_enplots.py,sha256=D38paN8zqZgluNAwmCwcocd7-_h_T0HTGolI1eBkDes,37484
 ipyvasp/_lattice.py,sha256=GxG0C4lwVGvBYIy3jwR1kahWR7L6kJlqjIiQGgESjcM,104135
-ipyvasp/_version.py,sha256=UvB3IZAWAs7vV6H9dpZvZPryrSNIyF5_bowVS4_YGFA,23
-ipyvasp/bsdos.py,sha256=1rG68S-dLEYveIWGK7r8CRa7Qqlqno0l1ncfo2ocihk,30424
+ipyvasp/_version.py,sha256=83qFJMFAgvdHV5e8Nh9ByUaQinNxBUPlTKjxfpge3xM,23
+ipyvasp/bsdos.py,sha256=JvYvHLqMp3eVaJ0amD-9kxp7FehQIFq3WFUxsO5dj0Q,31794
 ipyvasp/cli.py,sha256=aWFEVhNmnW8eSOp5uh95JaDwLQ9K9nlCQcbnOSuhWgw,6844
 ipyvasp/evals_dataframe.py,sha256=-sqxK7LPV6sYDO_XXmZ80FznOaXTkVdbqJKKvTUtMak,20637
 ipyvasp/lattice.py,sha256=t4s1qh6IJsoeXcCa9M9IhjAQp2s78lqiGhOfEkCW19s,30638
@@ -15,11 +15,11 @@ ipyvasp/widgets.py,sha256=hwCviQn5NmxFz15DTS2nKKJ0kdBq8taGude46KNDOtU,46605
 ipyvasp/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ipyvasp/core/parser.py,sha256=C3CaZsJbPME_ttYlYy4DXeOdL7dnkXs-cHRwFZL6bio,38058
 ipyvasp/core/plot_toolkit.py,sha256=3RoPsND5gPssBSfS5H4TjoZ2Qz7B97vpxeKadc2cRRs,36046
-ipyvasp/core/serializer.py,sha256=XpqnfVGsUXiN2CuVRPyqsSVouxRBO-UH6AnsHnPYvZY,36729
+ipyvasp/core/serializer.py,sha256=gghH1VK-LytzyRDast0Ko-ueBklWyp9mp6dkvPxI95g,37791
 ipyvasp/core/spatial_toolkit.py,sha256=8DBYTiBFWJ7OBKuvOPw7UoEVCyNjJhSW0OcudjYZvAw,14748
-ipyvasp-0.9.5.dist-info/LICENSE,sha256=F3SO5RiAZOMfmMGf1KOuk2g_c4ObvuBJhd9iBLDgXoQ,1263
-ipyvasp-0.9.5.dist-info/METADATA,sha256=Vfq6b9vA2i5LjHBcUTb8KkXkkCK3jldhXPNUm27MvsQ,2420
-ipyvasp-0.9.5.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
-ipyvasp-0.9.5.dist-info/entry_points.txt,sha256=C7m0Sjmr14wFjflCkWXLzr5N6-cQj8uJC9n82mUtzt8,44
-ipyvasp-0.9.5.dist-info/top_level.txt,sha256=ftziWlMWu_1VpDP1sRTFrkfBnWxAi393HYDVu4wRhUk,8
-ipyvasp-0.9.5.dist-info/RECORD,,
+ipyvasp-0.9.7.dist-info/LICENSE,sha256=F3SO5RiAZOMfmMGf1KOuk2g_c4ObvuBJhd9iBLDgXoQ,1263
+ipyvasp-0.9.7.dist-info/METADATA,sha256=5qUCLJfVl_yy9LGkgFmKaEKHU6HMrkRvZ2leqAERUJE,2420
+ipyvasp-0.9.7.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
+ipyvasp-0.9.7.dist-info/entry_points.txt,sha256=C7m0Sjmr14wFjflCkWXLzr5N6-cQj8uJC9n82mUtzt8,44
+ipyvasp-0.9.7.dist-info/top_level.txt,sha256=ftziWlMWu_1VpDP1sRTFrkfBnWxAi393HYDVu4wRhUk,8
+ipyvasp-0.9.7.dist-info/RECORD,,