bandu 1.3.1__py3-none-any.whl → 1.3.3__py3-none-any.whl

bandu/abinit_reader.py

@@ -963,11 +963,7 @@ class AbinitNetCDF():
         self.nband:int = int(self.dataset.dimensions['bantot'].size / self.nkpt)
         self.typat:list = self.dataset.variables['atom_species'][:].tolist()
         self.zion:np.ndarray = self.dataset.variables['atomic_numbers'][:]
-        _all_ions = [int(self.zion[i-1]) for i in self.typat]
-        self.znucltypat:list = []
-        for i in _all_ions:
-            if i not in self.znucltypat:
-                self.znucltypat.append(i)
+        self.znucltypat:list = [int(nuc) for nuc in self.zion]
         self.bands = [self.nband]
 #---------------------------------------------------------------------------------------------------------------------#
 #------------------------------------------------------ METHODS ------------------------------------------------------#

bandu/bandu.py

@@ -8,7 +8,7 @@ from . import wfk_class as wc
 class BandU():
     def __init__(
         self, wfks:Generator, energy_level:float, width:float, grid:bool=True, fft:bool=True, norm:bool=True,
-        sym:bool=True, low_mem:bool=False, plot:bool=True
+        sym:bool=True, low_mem:bool=False, plot:bool=True, real_imag_sep:bool=True
     )->None:
         '''
         BandU object with methods for finding states and computing BandU functions from states.
@@ -56,7 +56,10 @@ class BandU():
         self._FindStates(energy_level, width, wfks)
         print(f'{self.found_states} states found within specified energy range')
         # construct principal orbital components
-        principal_vals = self._PrincipalComponents()
+        if real_imag_sep:
+            principal_vals = self._RealImagPrnplComps()
+        else:
+            principal_vals = self._PrincipalComponents()
         # plot eigenvalues from PCA
         if plot:
             self._PlotEigs(principal_vals)
@@ -64,7 +67,11 @@ class BandU():
         for i in range(self.found_states):
             self.bandu_fxns[i] = self.bandu_fxns[i].Normalize()
         # compute ratios
-        omega_vals, omega_check = self._CheckOmega()
+        if not real_imag_sep:
+            omega_vals, omega_check = self._CheckOmega()
+        else:
+            omega_vals = 0
+            omega_check = 0
         # write output file
         fermi = self.bandu_fxns[0].fermi_energy
         with open('eigenvalues.out', 'w') as f:
@@ -163,7 +170,7 @@ class BandU():
                     dupes.extend(shifted_dupe)
                     self.duped_states += self.found_states
         self.bandu_fxns.extend(dupes)
-        #-----------------------------------------------------------------------------------------------------------------#
+    #-----------------------------------------------------------------------------------------------------------------#
     # find principal components
     def _PrincipalComponents(
         self
@@ -191,6 +198,40 @@ class BandU():
             self.bandu_fxns[i].wfk_coeffs = mat[i,:]
         return principal_vals 
     #-----------------------------------------------------------------------------------------------------------------#
+    # find principal components with real and imaginary separated
+    def _RealImagPrnplComps(
+        self
+    )->np.ndarray:
+        x = self.bandu_fxns[0].ngfftx
+        y = self.bandu_fxns[0].ngffty
+        z = self.bandu_fxns[0].ngfftz
+        mat = np.zeros((2*self.found_states,x*y*z), dtype=complex)
+        for i in range(self.found_states):
+            ind = 2*i
+            real_coeffs = self.bandu_fxns[i].wfk_coeffs.real
+            imag_coeffs = self.bandu_fxns[i].wfk_coeffs.imag
+            mat[ind,:] = real_coeffs.reshape((1,x*y*z))
+            mat[ind+1,:] = imag_coeffs.reshape((1,x*y*z))
+        print('Computing overlap matrix')
+        overlap_mat = np.matmul(np.conj(mat),mat.T)
+        # diagonlize matrix
+        principal_vals, principal_vecs = np.linalg.eig(overlap_mat)
+        principal_vecs = principal_vecs.T
+        # organize eigenvectors and eigenvalues
+        sorted_inds = np.flip(principal_vals.argsort())
+        principal_vals = np.take(principal_vals, sorted_inds)
+        principal_vecs = np.take(principal_vecs, sorted_inds, axis=0)
+        mat = np.matmul(principal_vecs, mat)
+        for i in range(2*self.found_states):
+            if i < self.found_states:
+                self.bandu_fxns[i].wfk_coeffs = mat[i,:]
+            else:
+                new_coeffs = copy(self.bandu_fxns[0])
+                new_coeffs.wfk_coeffs = mat[i,:]
+                self.bandu_fxns.append(new_coeffs)
+        self.found_states *= 2
+        return principal_vals 
+    #-----------------------------------------------------------------------------------------------------------------#
     # find ratio of real and imaginary components
     def _CheckOmega(
         self

bandu/xsf_reader.py

@@ -13,8 +13,20 @@ atom_labels = {1:'H', 2:'He', 3:'Li', 4:'Be', 5:'B', 6:'C', 7:'N', 8:'O', 9:'F',
 class XSF():
     def __init__(
             self, 
-            xsf_file:str='WFK.xsf'
+            xsf_file:str='WFK.xsf',
+            datagrid:str='BEGIN_DATAGRID_3D_principal_orbital_component'
         )->None:
+        '''
+        Class for reading in XSF files
+
+        Parameters
+        ----------
+        xsf_file : str
+            Path to XSF file
+        datagrid : str
+            Name of datagrid to be read in\n
+            Default is "BEGIN_DATAGRID_3D_principal_orbital_component"
+        '''
     # if xsf file is supplied, read in parameters
         self.xsf_file = xsf_file
         with open(xsf_file, 'r') as xsf:
@@ -40,7 +52,7 @@ class XSF():
                     del coord[0]
                     self.coords[atom,:] = coord
             # once density block is reached, get ngfft spacing and end init
-            if line.strip() == 'BEGIN_DATAGRID_3D_principal_orbital_component':
+            if line.strip() == datagrid:
                 ngfft_spacing = self.xsf_lines[i+1].strip().split(' ')
                 ngfft_spacing = [int(val) for val in ngfft_spacing]
                 self.ngfftx = ngfft_spacing[0]
@@ -54,11 +66,6 @@ class XSF():
     )->np.ndarray:
         '''
         Method for reading in density grid from XSF file. Returns grid as N dimensional numpy array.
-
-        Parameters
-        ----------
-        undo_xsf : bool
-            If True (which is the default), then the XSF formatting is undone by removing end points.
         '''
         density_lines:list|np.ndarray=[]
         for i, line in enumerate(self.xsf_lines):

{bandu-1.3.1.dist-info → bandu-1.3.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bandu
-Version: 1.3.1
+Version: 1.3.3
 Summary: The BandU program constructs a rank ordered series of crystal orbitals using principal component analysis. These principal orbital components can then be projected on the Fermi surface and visualized
 Author-email: Patrick Cross <pcross@wisc.edu>
 Project-URL: Homepage, https://github.com/pcross0405/BandU

bandu-1.3.3.dist-info/RECORD

@@ -0,0 +1,14 @@
+bandu/abinit_reader.py,sha256=ivrHoozX_oN-bbhMW-vb4FzodcIVM-wcO8-MRzo39H4,47556
+bandu/bandu.py,sha256=p6qdt1LG1uPFPMGiZfypTOhxlT84xYU52juy8pSv-4s,14666
+bandu/brillouin_zone.py,sha256=-SarCuvUthk5h_sFHM6KDHLns1eCWGk_v5fHngWFu08,7997
+bandu/colors.py,sha256=OcIBwVh9ieu04n1cruRgyoYslKsdfJKf-u4oWMd3CwQ,2316
+bandu/isosurface_class.py,sha256=M6XAuy89uyX3v_JX3wYd5VqAWel9JiMQ7wRBhFhhn3A,10236
+bandu/plotter.py,sha256=jvxsvabzTxgWUZxX2XtO1VFoMdiu0C_qXdODJqpBfrA,27718
+bandu/translate.py,sha256=YGTkwne4bdrw649OjRKBio7IBsCNVoa__rjkFZK6uRI,2217
+bandu/wfk_class.py,sha256=j7bvEAb9eUU77mHGNLGdPpmpgVBb6bsKQqej9n0cANc,26203
+bandu/xsf_reader.py,sha256=tkJaBiUHsEKvpdJishi-MZyU1NYYMsgH_8UuuYsG07A,5030
+bandu-1.3.3.dist-info/licenses/LICENSE,sha256=jk_B-WYDiyH9RtxC45pO6JUtBxmfX5i240dVzv1okCg,1088
+bandu-1.3.3.dist-info/METADATA,sha256=w1VzntS0rWvnJzXJvFI1sRBTZYDZiguMscJNY9CZPf8,8945
+bandu-1.3.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+bandu-1.3.3.dist-info/top_level.txt,sha256=AxbMFU3BRdjCr75K9gAdblwlBMQ3qr9-AaCC-IS8OWs,6
+bandu-1.3.3.dist-info/RECORD,,

bandu-1.3.1.dist-info/RECORD

@@ -1,14 +0,0 @@
-bandu/abinit_reader.py,sha256=U4HUUTnju9MpyGtWMOedUQLln90k2F0XIv0Q0zcP05c,47704
-bandu/bandu.py,sha256=1B7FZb3eYNm9JhPzEwZoGCAUNZpPD9Oux79eVCwSopE,12785
-bandu/brillouin_zone.py,sha256=-SarCuvUthk5h_sFHM6KDHLns1eCWGk_v5fHngWFu08,7997
-bandu/colors.py,sha256=OcIBwVh9ieu04n1cruRgyoYslKsdfJKf-u4oWMd3CwQ,2316
-bandu/isosurface_class.py,sha256=M6XAuy89uyX3v_JX3wYd5VqAWel9JiMQ7wRBhFhhn3A,10236
-bandu/plotter.py,sha256=jvxsvabzTxgWUZxX2XtO1VFoMdiu0C_qXdODJqpBfrA,27718
-bandu/translate.py,sha256=YGTkwne4bdrw649OjRKBio7IBsCNVoa__rjkFZK6uRI,2217
-bandu/wfk_class.py,sha256=j7bvEAb9eUU77mHGNLGdPpmpgVBb6bsKQqej9n0cANc,26203
-bandu/xsf_reader.py,sha256=JegYFLXFaijR09qUauFzQ1IqOcgxxBXx4gfBPtooZfU,4860
-bandu-1.3.1.dist-info/licenses/LICENSE,sha256=jk_B-WYDiyH9RtxC45pO6JUtBxmfX5i240dVzv1okCg,1088
-bandu-1.3.1.dist-info/METADATA,sha256=WjYkKWHlGeMcrXkolD6uQnDZKIGcAEZEpDcW5XJ5q8A,8945
-bandu-1.3.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-bandu-1.3.1.dist-info/top_level.txt,sha256=AxbMFU3BRdjCr75K9gAdblwlBMQ3qr9-AaCC-IS8OWs,6
-bandu-1.3.1.dist-info/RECORD,,