bandu 1.2.0__py3-none-any.whl → 1.3.0__py3-none-any.whl

bandu/bandu.py

@@ -123,7 +123,7 @@ class BandU():
             if self.grid:
                 wfk = wfk.GridWFK()
             if self.fft:
-                wfk = wfk.FFT()
+                wfk = wfk.IFFT()
             if self.norm:
                 wfk = wfk.Normalize()
             yield wfk
@@ -244,7 +244,7 @@ class BandU():
     ):
         total_states = self.found_states
         if nums is []:
-            nums = [0,total_states-1]
+            nums = [1,total_states]
         else:
             # check if list has only 2 elements
             if len(nums) != 2:
@@ -268,6 +268,6 @@ class BandU():
         for i in range(nums[0]-1, nums[1]):
             file_name = xsf_name + f'_{i+1}'
             wfk = copy(self.bandu_fxns[i])
-            wfk.wfk_coeffs = wfk.wfk_coeffs.reshape((z,y,x))
+            wfk.wfk_coeffs = wfk.wfk_coeffs.reshape((x,y,z))
             wfk = wfk.XSFFormat()
             wfk.WriteXSF(xsf_file=file_name)

bandu/wfk_class.py

@@ -138,16 +138,16 @@ class WFK():
             If nothing is passed, it is assumed the coefficients of a single band are supplied.
         '''
         # initialize 3D grid
-        gridded_wfk = np.zeros((self.ngfftz, self.ngffty, self.ngfftx), dtype=complex)
+        gridded_wfk = np.zeros((self.ngfftx, self.ngffty, self.ngfftz), dtype=complex)
         # update grid with wfk coefficients
         for k, kpt in enumerate(self.pw_indices):
             kx = kpt[0]
             ky = kpt[1]
             kz = kpt[2]
             if band_index >= 0:
-                gridded_wfk[kz, ky, kx] = self.wfk_coeffs[band_index][k]
+                gridded_wfk[kx, ky, kz] = self.wfk_coeffs[band_index][k]
             else:
-                gridded_wfk[kz, ky, kx] = self.wfk_coeffs[k]
+                gridded_wfk[kx, ky, kz] = self.wfk_coeffs[k]
         new_WFK = copy(self)
         new_WFK.wfk_coeffs = gridded_wfk
         return new_WFK
@@ -166,9 +166,9 @@ class WFK():
             If nothing is passed, it is assumed the coefficients of a single band are supplied.
         '''
         # check if coefficients are gridded before undoing grid format
-        if self.wfk_coeffs.shape != (self.ngfftz,self.ngffty,self.ngfftx):
+        if self.wfk_coeffs.shape != (self.ngfftx,self.ngffty,self.ngfftz):
             raise ValueError((
-                f'Plane wave coefficients must be in 3D grid with shape ({self.ngfftz}, {self.ngffty}, {self.ngfftx})'
+                f'Plane wave coefficients must be in 3D grid with shape ({self.ngfftx}, {self.ngffty}, {self.ngfftz})'
                 ' in order to remove the gridded format'
             ))
         if band_index >= 0:
@@ -192,7 +192,7 @@ class WFK():
         # Fourier transform reciprocal grid to real space grid
         real_coeffs = fftn(self.wfk_coeffs, norm='ortho')
         new_WFK = copy(self)
-        new_WFK.wfk_coeffs = np.array(real_coeffs).reshape((self.ngfftz, self.ngffty, self.ngfftx))
+        new_WFK.wfk_coeffs = np.array(real_coeffs).reshape((self.ngfftx, self.ngffty, self.ngfftz))
         return new_WFK
     #-----------------------------------------------------------------------------------------------------------------#
     # method transforming real space wfks to reciprocal space
@@ -206,7 +206,7 @@ class WFK():
         # Fourier transform real space grid to reciprocal space grid
         reciprocal_coeffs = ifftn(self.wfk_coeffs, norm='ortho')
         new_WFK = copy(self)
-        new_WFK.wfk_coeffs = np.array(reciprocal_coeffs).reshape((self.ngfftz,self.ngffty,self.ngfftx))
+        new_WFK.wfk_coeffs = np.array(reciprocal_coeffs).reshape((self.ngfftx,self.ngffty,self.ngfftz))
         return new_WFK
     #-----------------------------------------------------------------------------------------------------------------#
     # method for normalizing wfks
@@ -430,34 +430,34 @@ class WFK():
         # append zeros to ends of all axes in grid_wfk
         # zeros get replaced by values at beginning of each axis
         # this repetition is required by XSF format
-        if np.shape(self.wfk_coeffs) != (self.ngfftz, self.ngffty, self.ngfftx):
+        if np.shape(self.wfk_coeffs) != (self.ngfftx, self.ngffty, self.ngfftz):
             raise ValueError(
                 f'''Passed array is not the correct shape:
-                Expected: ({self.ngfftz}, {self.ngffty}, {self.ngfftx}),
+                Expected: ({self.ngfftx}, {self.ngffty}, {self.ngfftz}),
                 Received: {np.shape(self.wfk_coeffs)}
             ''')
         else:
             grid_wfk = self.wfk_coeffs
-        grid_wfk = np.append(grid_wfk, np.zeros((1, self.ngffty, self.ngfftx)), axis=0)
-        grid_wfk = np.append(grid_wfk, np.zeros((self.ngfftz+1, 1, self.ngfftx)), axis=1)
-        grid_wfk = np.append(grid_wfk, np.zeros((self.ngfftz+1, self.ngffty+1, 1)), axis=2)
+        grid_wfk = np.append(grid_wfk, np.zeros((1, self.ngffty, self.ngfftz)), axis=0)
+        grid_wfk = np.append(grid_wfk, np.zeros((self.ngfftx+1, 1, self.ngfftz)), axis=1)
+        grid_wfk = np.append(grid_wfk, np.zeros((self.ngfftx+1, self.ngffty+1, 1)), axis=2)
         for x in range(self.ngfftx+1):
             for y in range(self.ngffty+1):
                 for z in range(self.ngfftz+1):
                     if x == self.ngfftx:
-                        grid_wfk[z][y][x] = grid_wfk[z][y][0]
+                        grid_wfk[x,y,z] = grid_wfk[0,y,z]
                     if y == self.ngffty:
-                        grid_wfk[z][y][x] = grid_wfk[z][0][x]
+                        grid_wfk[x,y,z] = grid_wfk[x,0,z]
                     if z == self.ngfftz:
-                        grid_wfk[z][y][x] = grid_wfk[0][x][y]
+                        grid_wfk[x,y,z] = grid_wfk[x,y,0]
                     if x == self.ngfftx and y == self.ngffty:
-                        grid_wfk[z][y][x] = grid_wfk[z][0][0]
+                        grid_wfk[x,y,z] = grid_wfk[0,0,z]
                     if x == self.ngfftx and z == self.ngfftz:
-                        grid_wfk[z][y][x] = grid_wfk[0][y][0]
+                        grid_wfk[x,y,z] = grid_wfk[0,y,0]
                     if z == self.ngfftz and y == self.ngffty:
-                        grid_wfk[z][y][x] = grid_wfk[0][0][x]
+                        grid_wfk[x,y,z] = grid_wfk[x,0,0]
                     if x == self.ngfftx and y == self.ngffty and z == self.ngfftz:
-                        grid_wfk[z][y][x] = grid_wfk[0][0][0]
+                        grid_wfk[x,y,z] = grid_wfk[0,0,0]
         new_WFK = copy(self)
         new_WFK.wfk_coeffs = grid_wfk
         new_WFK.ngfftx += 1
@@ -474,18 +474,18 @@ class WFK():
         '''
         grid = self.wfk_coeffs
         # to_be_del will be used to remove all extra data points added for XSF formatting
-        to_be_del = np.ones((self.ngfftz, self.ngfftx, self.ngffty), dtype=bool)
+        to_be_del = np.ones((self.ngfftx, self.ngffty, self.ngfftz), dtype=bool)
         for z in range(self.ngfftz):
-            for x in range(self.ngffty):
-                for y in range(self.ngfftx):
+            for y in range(self.ngffty):
+                for x in range(self.ngfftx):
                     # any time you reach the last density point it is a repeat of the first point
                     # remove the end points along each axis
                     if y == self.ngffty - 1 or x == self.ngfftx - 1 or z == self.ngfftz - 1:
-                        to_be_del[z,y,x] = False
+                        to_be_del[x,y,z] = False
         # remove xsf entries from array
         grid = grid[to_be_del]
         # restore grid shape
-        grid = grid.reshape((self.ngfftz-1, self.ngffty-1, self.ngfftx-1))
+        grid = grid.reshape((self.ngfftx-1, self.ngffty-1, self.ngfftz-1))
         new_WFK = copy(self)
         new_WFK.wfk_coeffs = grid
         new_WFK.ngfftx -= 1
@@ -522,16 +522,16 @@ class WFK():
             print(f'{self.natom} 1', file=xsf)
             for i, coord in enumerate(self.xred):
                 atomic_num = int(self.znucltypat[self.typat[i] - 1])
-                cart_coord = np.dot(coord, self.lattice)
+                cart_coord = np.matmul(coord, self.lattice)
                 print(f'{atomic_num} {cart_coord[0]} {cart_coord[1]} {cart_coord[2]}', file=xsf)
             print('ATOMS', file=xsf)
             for i, coord in enumerate(self.xred):
                 atomic_num = int(self.znucltypat[self.typat[i] - 1])
-                cart_coord = np.dot(coord, self.lattice)
+                cart_coord = np.matmul(coord, self.lattice)
                 print(f'{atomic_num} {cart_coord[0]} {cart_coord[1]} {cart_coord[2]}', file=xsf)
-            print('BEGIN_BLOCK_DATAGRID3D', file=xsf)
+            print('BEGIN_BLOCK_DATAGRID_3D', file=xsf)
             print('datagrids', file=xsf)
-            print('DATAGRID_3D_DENSITY', file=xsf)
+            print('BEGIN_DATAGRID_3D_principal_orbital_component', file=xsf)
             print(f'{self.ngfftx} {self.ngffty} {self.ngfftz}', file=xsf)
             print('0.0 0.0 0.0', file=xsf)
             print(f'{self.lattice[0,0]} {self.lattice[0,1]} {self.lattice[0,2]}', file=xsf)
@@ -543,14 +543,14 @@ class WFK():
                     for x in range(self.ngfftx):
                         count += 1
                         if _component:
-                            print(self.wfk_coeffs[z,y,x].real, file=xsf, end=' ')
+                            print(self.wfk_coeffs[x,y,z].real, file=xsf, end=' ')
                         else:
-                            print(self.wfk_coeffs[z,y,x].imag, file=xsf, end=' ')
+                            print(self.wfk_coeffs[x,y,z].imag, file=xsf, end=' ')
                         if count == 6:
                             count = 0
                             print('\n', file=xsf, end='')
             print('END_DATAGRID_3D', file=xsf)
-            print('END_BLOCK_DATAGRID3D', file=xsf)
+            print('END_BLOCK_DATAGRID_3D', file=xsf)
         # rerun method to write out imaginary part
         if _component:
             xsf_file = xsf_file.split('_real')[0]

{bandu-1.2.0.dist-info → bandu-1.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bandu
-Version: 1.2.0
+Version: 1.3.0
 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-1.2.0.dist-info → bandu-1.3.0.dist-info}/RECORD

@@ -1,14 +1,14 @@
 bandu/abinit_reader.py,sha256=U4HUUTnju9MpyGtWMOedUQLln90k2F0XIv0Q0zcP05c,47704
-bandu/bandu.py,sha256=-gahVb8Eqx33RzcbYngzjDHmbMib6grRXEQE_fTgLWg,12786
+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=wSIA1TpwhioPUHpBe4_gc14e8K98fv3q0LwwD5NLboo,27725
 bandu/translate.py,sha256=YGTkwne4bdrw649OjRKBio7IBsCNVoa__rjkFZK6uRI,2217
-bandu/wfk_class.py,sha256=QchfEjqssSHbC3IcXrKNz3euFLR62WMj-ZPFd2m0mX0,26215
+bandu/wfk_class.py,sha256=ANpGtdB5DUJsUjs9804t6Vmoh5wtWGmAzelE-b57pWo,26221
 bandu/xsf_reader.py,sha256=gfv7LsTofWw4PrcOeqltOREJD6RLDq8CeFSsnlfohEw,4778
-bandu-1.2.0.dist-info/licenses/LICENSE,sha256=jk_B-WYDiyH9RtxC45pO6JUtBxmfX5i240dVzv1okCg,1088
-bandu-1.2.0.dist-info/METADATA,sha256=abHRtBrAvc6Vos3f5SwcvdOilNA4pu90mEVhK3nxapU,8945
-bandu-1.2.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-bandu-1.2.0.dist-info/top_level.txt,sha256=AxbMFU3BRdjCr75K9gAdblwlBMQ3qr9-AaCC-IS8OWs,6
-bandu-1.2.0.dist-info/RECORD,,
+bandu-1.3.0.dist-info/licenses/LICENSE,sha256=jk_B-WYDiyH9RtxC45pO6JUtBxmfX5i240dVzv1okCg,1088
+bandu-1.3.0.dist-info/METADATA,sha256=WivTIcB4CKkcOc5PySUPPT5f2RxhComT_qRhf2O_0fs,8945
+bandu-1.3.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+bandu-1.3.0.dist-info/top_level.txt,sha256=AxbMFU3BRdjCr75K9gAdblwlBMQ3qr9-AaCC-IS8OWs,6
+bandu-1.3.0.dist-info/RECORD,,