aton 0.2.2__tar.gz → 0.2.3__tar.gz

{aton-0.2.2 → aton-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aton
-Version: 0.2.2
+Version: 0.2.3
 Summary: The Ab-iniTiO & Neutron research toolbox, or ATON, provides powerful and comprehensive tools for cutting-edge materials research, focused on (but not limited to) neutron science.
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus
@@ -41,9 +41,11 @@ or [ATON](https://pablogila.github.io/ATON/),
 provides powerful and comprehensive tools
 for cutting-edge materials research,
 focused on (but not limited to) neutron science.
+Designed to bridge the gap between theoretical modeling and experimental validation,
+ATON allows researchers to streamline and simplify workflows in the study of advanced materials.
 
 Just like its [ancient Egyptian deity](https://en.wikipedia.org/wiki/Aten) counterpart,
-this all-in-one Python package contains a range of tools
+this all-in-one Python package comprises a range of utility tools
 from INS spectra analysis to *ab-initio* interfaces
 for [Quantum ESPRESSO](https://www.quantum-espresso.org/),
 [Phonopy](https://phonopy.github.io/phonopy/) and

{aton-0.2.2 → aton-0.2.3}/README.md

@@ -8,9 +8,11 @@ or [ATON](https://pablogila.github.io/ATON/),
 provides powerful and comprehensive tools
 for cutting-edge materials research,
 focused on (but not limited to) neutron science.
+Designed to bridge the gap between theoretical modeling and experimental validation,
+ATON allows researchers to streamline and simplify workflows in the study of advanced materials.
 
 Just like its [ancient Egyptian deity](https://en.wikipedia.org/wiki/Aten) counterpart,
-this all-in-one Python package contains a range of tools
+this all-in-one Python package comprises a range of utility tools
 from INS spectra analysis to *ab-initio* interfaces
 for [Quantum ESPRESSO](https://www.quantum-espresso.org/),
 [Phonopy](https://phonopy.github.io/phonopy/) and

{aton-0.2.2 → aton-0.2.3}/aton/_version.py

@@ -10,5 +10,5 @@ https://semver.org/
 
 """
 
-__version__ = 'v0.2.2'
+__version__ = 'v0.2.3'
 

{aton-0.2.2 → aton-0.2.3}/aton/qrotor/rotate.py

@@ -51,6 +51,11 @@ def structure_qe(
     To override this and instead use the vector between the first two atoms
     as the rotation axis, set `use_centroid = False`.
 
+    **WARNING: The `positions` list is order-sensitive**.
+    If you rotate more than one chemical group in a structure,
+    be sure to follow the same direction for each group (e.g. all clockwise)
+    to ensure that all axes of rotation point in the same direction.
+
     To debug, `show_axis = True` adds two additional helium atoms as the rotation vector.
     """
     print('Rotating Quantum ESPRESSO input structure with QRotor...')
@@ -106,13 +111,21 @@ def rotate_coords(
     Then rotates said coordinates by a given `angle` in degrees.
     Returns a list with the updated positions.
 
-    By default, the rotation axis is defined by the perpendicular vector
+    By default, the rotation vector is defined by the perpendicular
     passing through the geometrical center of the first three points.
     To override this and use the vector between the first two atoms
     as the rotation axis, set `use_centroid = False`.
 
+    **WARNING: The `positions` list is order-sensitive**.
+    If you rotate more than one chemical group in a structure,
+    be sure to follow the same direction for each group (e.g. all clockwise)
+    to ensure that all rotation vectors point in the same direction.
+
     If `show_axis = True` it returns two additional coordinates at the end of the list,
     with the centroid and the rotation vector. Only works with `use_centroid = True`.
+
+    The rotation uses Rodrigues' rotation formula,
+    powered by [`scipy.spatial.transform.Rotation.from_rotvec`](https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.transform.Rotation.from_rotvec.html#scipy.spatial.transform.Rotation.from_rotvec).
     """
     if len(positions) < 3:
         raise ValueError("At least three atoms must be rotated.")

{aton-0.2.2 → aton-0.2.3}/aton/qrotor/system.py

@@ -129,10 +129,8 @@ class System:
         # Check that the grid is still within -2pi and 2pi, otherwise normalise it for a final time
         while self.grid[0] <= (-2 * np.pi + 0.1):  # With a small tolerance
             self.grid = self.grid + 2 * np.pi
-            print('plus 2')
         while self.grid[-1] >= 2.5 * np.pi:  # It was not a problem until reaching 5/2 pi
             self.grid = self.grid -2 * np.pi
-            print('minus 2')
         print(f'Potential shifted by {phase}π')
         if calculate:
             self.solve()

{aton-0.2.2 → aton-0.2.3}/aton/txt/__init__.py

@@ -26,7 +26,7 @@ alat_lines = txt.find.lines('relax.out', 'Lattice parameter =')
 # Extract the numerical value of the last match
 alat = txt.extract.number(alat_lines[-1], 'Lattice parameter')
 # Paste it into another file
-txt.edit.replace_line('scf.in', 'Lattice parameter =', f'Lattice parameter ='{alat})
+txt.edit.replace_line('scf.in', 'Lattice parameter =', f'Lattice parameter = {alat}')
 ```
 
 Advanced usage such as regular expression matching or

{aton-0.2.2 → aton-0.2.3}/aton.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aton
-Version: 0.2.2
+Version: 0.2.3
 Summary: The Ab-iniTiO & Neutron research toolbox, or ATON, provides powerful and comprehensive tools for cutting-edge materials research, focused on (but not limited to) neutron science.
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus
@@ -41,9 +41,11 @@ or [ATON](https://pablogila.github.io/ATON/),
 provides powerful and comprehensive tools
 for cutting-edge materials research,
 focused on (but not limited to) neutron science.
+Designed to bridge the gap between theoretical modeling and experimental validation,
+ATON allows researchers to streamline and simplify workflows in the study of advanced materials.
 
 Just like its [ancient Egyptian deity](https://en.wikipedia.org/wiki/Aten) counterpart,
-this all-in-one Python package contains a range of tools
+this all-in-one Python package comprises a range of utility tools
 from INS spectra analysis to *ab-initio* interfaces
 for [Quantum ESPRESSO](https://www.quantum-espresso.org/),
 [Phonopy](https://phonopy.github.io/phonopy/) and