Merge pull request #36 from sgoodlett/sgoodlett

Tests and CI updates. Also Ih fix
NASymmetry · Nov 20, 2024 · 07f6b5e · 07f6b5e
2 parents 99aa8cf + aaba50c
commit 07f6b5e
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diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
@@ -6,12 +6,16 @@ jobs:
     strategy:
       matrix:
         cfg:
-          - conda-env: base
-            python-version: 3.8
           - conda-env: base
             python-version: 3.9
           - conda-env: base
             python-version: "3.10"
+          - conda-env: base
+            python-version: "3.11"
+          - conda-env: base
+            python-version: "3.12"
+          - conda-env: base
+            python-version: "3.13"
     env:
       PYVER: ${{ matrix.cfg.python-version }}
       CONDA_ENV: ${{ matrix.cfg.conda-env }}
@@ -36,3 +40,12 @@ jobs:
         pytest --cov="molsym" --color=yes --cov-report=xml test/
     - name: Upload Coverage to Codecov
       uses: codecov/codecov-action@v2
+      with:
+        directory: ./coverage/reports/
+        env_vars: OS,PYTHON
+        fail_ci_if_error: false
+        files: ./coverage.xml
+        flags: unittests
+        name: codecov-umbrella
+        token: ${{ secrets.CODECOV_TOKEN }}
+        verbose: true
diff --git a/LICENSE.txt b/LICENSE.txt
diff --git a/PsiCon_2023.ipynb b/PsiCon_2023.ipynb
diff --git a/README.md b/README.md
@@ -19,8 +19,8 @@
       </a>
     </td>
     <td align="center">
-      <a href=https://codecov.io/gh/CCQC/MolSym>
-      <img src=https://codecov.io/gh/CCQC/MolSym/branch/main/graph/badge.svg?token=NQDJ0QYLB0>
+      <a href=https://codecov.io/gh/NASymmetry/MolSym>
+      <img src=https://codecov.io/gh/NASymmetry/MolSym/branch/main/graph/badge.svg?token=NQDJ0QYLB0>
       </a> 
     </td>
   </tr>
@@ -42,7 +42,7 @@ Create a new conda environment with:
 
   `conda create -n "NameYourEnvironment" python=3.X`
 
-MolSym is tested with Python 3.8, 3.9, and 3.10 but should work for more recent versions as well.
+MolSym is tested with Python 3.9-3.13, but should work for more recent versions and some older versions as well.
 
   `git clone git@github.com:NASymmetry/MolSym.git`
 

diff --git a/acetylene.xyz b/acetylene.xyz
diff --git a/base.yaml b/base.yaml
@@ -1,12 +1,13 @@
 name: test
 channels:
   - defaults
+  - conda-forge
   - psi4
 dependencies:
     # Base
-  - numpy
+  - numpy>=2.0.0
   - python
-  - qcelemental
+  - qcelemental>=0.28.0
   #- psi4
   - pytest
   - pytest-cov

diff --git a/docs/Makefile b/docs/Makefile
diff --git a/docs/SI/irrep_mats_SI.pdf b/docs/SI/irrep_mats_SI.pdf
diff --git a/docs/_templates/class.rst b/docs/_templates/class.rst
@@ -0,0 +1,19 @@
+{{ fullname | escape | underline}}
+
+{{ module }}
+
+{{ objname }}
+
+{% block attributes %} {% if attributes %} .. rubric:: Attributes
+
+{% for item in attributes %}
+~{{ fullname }}.{{ item }}
+
+{%- endfor %} {% endif %} {% endblock %}
+
+{% block methods %} {% if methods %} .. rubric:: Methods
+
+{% for item in methods %}
+{%- if item != '__init__' %} ~{{ fullname }}.{{ item }} {%- endif -%}
+
+{%- endfor %} {% endif %} {% endblock %}
diff --git a/docs/api.rst b/docs/api.rst
diff --git a/docs/conf.py b/docs/conf.py
@@ -37,7 +37,7 @@
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ['docs/_templates']
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

diff --git a/docs/generated/molsym.molecule.rst b/docs/generated/molsym.molecule.rst
diff --git a/docs/generated/molsym.pgdetect.flowchart.rst b/docs/generated/molsym.pgdetect.flowchart.rst
diff --git a/docs/generated/molsym.pgdetect.flowchart_helper.rst b/docs/generated/molsym.pgdetect.flowchart_helper.rst
diff --git a/docs/generated/molsym.pgdetect.rst b/docs/generated/molsym.pgdetect.rst
diff --git a/docs/generated/molsym.rst b/docs/generated/molsym.rst
diff --git a/docs/generated/molsym.salcs.SymmetryEquivalentIC.rst b/docs/generated/molsym.salcs.SymmetryEquivalentIC.rst
diff --git a/docs/generated/molsym.salcs.cartesian_coordinates.rst b/docs/generated/molsym.salcs.cartesian_coordinates.rst
diff --git a/docs/generated/molsym.salcs.function_set.rst b/docs/generated/molsym.salcs.function_set.rst
diff --git a/docs/generated/molsym.salcs.internal_coordinates.rst b/docs/generated/molsym.salcs.internal_coordinates.rst
diff --git a/docs/generated/molsym.salcs.linear_functions.rst b/docs/generated/molsym.salcs.linear_functions.rst
diff --git a/docs/generated/molsym.salcs.projection_op.rst b/docs/generated/molsym.salcs.projection_op.rst
diff --git a/docs/generated/molsym.salcs.rst b/docs/generated/molsym.salcs.rst
diff --git a/docs/generated/molsym.salcs.salc.rst b/docs/generated/molsym.salcs.salc.rst
diff --git a/docs/generated/molsym.salcs.spherical_harmonics.rst b/docs/generated/molsym.salcs.spherical_harmonics.rst
diff --git a/docs/generated/molsym.symmetrize.rst b/docs/generated/molsym.symmetrize.rst
diff --git a/docs/generated/molsym.symtext.Ih_irrep_mats.rst b/docs/generated/molsym.symtext.Ih_irrep_mats.rst
diff --git a/docs/generated/molsym.symtext.character_table.rst b/docs/generated/molsym.symtext.character_table.rst
diff --git a/docs/generated/molsym.symtext.general_irrep_mats.rst b/docs/generated/molsym.symtext.general_irrep_mats.rst
diff --git a/docs/generated/molsym.symtext.goat.rst b/docs/generated/molsym.symtext.goat.rst
diff --git a/docs/generated/molsym.symtext.irrep_mats.rst b/docs/generated/molsym.symtext.irrep_mats.rst
diff --git a/docs/generated/molsym.symtext.linear_helper.rst b/docs/generated/molsym.symtext.linear_helper.rst
diff --git a/docs/generated/molsym.symtext.multiplication_table.rst b/docs/generated/molsym.symtext.multiplication_table.rst
diff --git a/docs/generated/molsym.symtext.point_group.rst b/docs/generated/molsym.symtext.point_group.rst
diff --git a/docs/generated/molsym.symtext.rst b/docs/generated/molsym.symtext.rst
diff --git a/docs/generated/molsym.symtext.symel.rst b/docs/generated/molsym.symtext.symel.rst
diff --git a/docs/generated/molsym.symtext.symtext.rst b/docs/generated/molsym.symtext.symtext.rst
diff --git a/docs/generated/molsym.symtext.symtext_helper.rst b/docs/generated/molsym.symtext.symtext_helper.rst
diff --git a/docs/generated/molsym.symtools.rst b/docs/generated/molsym.symtools.rst
diff --git a/docs/index.md b/docs/index.md
diff --git a/docs/index.rst b/docs/index.rst
diff --git a/docs/make.bat b/docs/make.bat
diff --git a/docs/usage.rst b/docs/usage.rst
@@ -1,4 +1,23 @@
 Usage
 =====
 
-How to use MolSym.
+MolSym is an open-source Python package for handling molecular symmetry.
+Features of MolSym include:
+
+*   Point group detection
+*   Molecule symmetrization
+*   Symmetry element, irreducible representation, irreducible representation matrices, and character table generation for arbitrary point groups
+*   Symmetry adapted linear combinations for internal coordinates, Cartesian nuclear coordinates, spherical harmonic basis functions, and Cartesian basis functions
+
+Point Group detection
+---------------------
+
+
+Symmetrization
+--------------
+
+Symtext generation
+------------------
+
+SALCs
+-----
diff --git a/environment.yml b/environment.yml
@@ -3,7 +3,7 @@ channels:
   - defaults
   - conda-forge
 dependencies:
-  - numpy>=1.23.4
-  - qcelemental >= 0.25.1
+  - numpy>=2.0.0
+  - qcelemental >= 0.28.0
   - sphinx >= 7.3.7
   - sphinx_rtd_theme >= 2.0.0
diff --git a/input.py b/input.py
diff --git a/molsym.png b/molsym.png
diff --git a/molsym/__init__.py b/molsym/__init__.py
diff --git a/molsym/molecule.py b/molsym/molecule.py
@@ -6,17 +6,42 @@
 
 @dataclass
 class Atom():
+    """
+    Dataclass for storing atom information
+
+    :param Z: Atomic number of atom.
+    :param mass: Mass of atom in amu as defined by QCElemental.
+    :param xyz: Position vector of atom in Cartesian coordinates.
+    :type Z: int 
+    :type mass: float
+    :type xyz: NumPy array of shape (3,)
+    """
     Z:int
     mass:float
     xyz:np.array
 
 @dataclass
 class SEA():
+    """
+    SEA: symmetry equivalent atoms.
+    SEAs are atoms that can be swapped with no distinguishable change in the molecule.
+
+    :param label: Optionally defines rotor type of SEA set (e.g. Single Atom, Linear, Spherical, Regular Polygon, Oblate Symmetric Top, etc.)
+    :param subset: Sublist of atom indices in molecule that constitute the SEA set
+    :param axis: Optionally defines possible rotational symmetry vector
+    :type label: str or None
+    :type subset: NumPy array of integers
+    :type axis: NumPy array of shape (3,) or None
+    """
     label:str
     subset:np.array
     axis:np.array
 
 class Molecule():
+    """
+    Class dealing with molecule relevant information.
+    Typically initiated from a QCSchema object.
+    """
     def __init__(self, atoms, coords, masses) -> None:
         self.tol = 1e-5
         self.atoms = np.asarray(atoms)
@@ -29,6 +54,13 @@ def __init__(self, atoms, coords, masses) -> None:
 
     @classmethod
     def from_schema(cls, schema):
+        """
+        Class method for constructing a Molecule from a QCSchema object
+
+        :param schema: Schema dictionary to be converted to Molecule
+        :type schema: dict
+        :rtype: molsym.Molecule
+        """
         atoms = schema["symbols"]
         natoms = len(atoms)
         coords = np.reshape(schema["geometry"], (natoms,3))
@@ -40,6 +72,13 @@ def from_schema(cls, schema):
 
     @classmethod
     def from_file(cls, fn):
+        """
+        Class method for constructing a Molecule from an *.xyz file
+
+        :param fn: Filename
+        :type fn: str
+        :rtype: molsym.Molecule
+        """
         with open(fn, "r") as lfn:
             strang = lfn.read()
         strang = "units bohr\n"+strang
@@ -48,7 +87,14 @@ def from_file(cls, fn):
 
     @classmethod
     def from_psi4_schema(cls, schema):
-        # Schemas coming from Psi4 are different for some reason?
+        """
+        Class method for constructing a Molecule from a QCSchema object generated in Psi4.
+        Schemas coming from Psi4 are different for some reason?
+
+        :param schema: Schema dictionary to be converted to Molecule
+        :type schema: dict
+        :rtype: molsym.Molecule
+        """
         atoms = schema["elem"] # was symbols
         natoms = len(atoms)
         coords = np.reshape(schema["geom"], (natoms,3)) # was geometry
@@ -87,27 +133,58 @@ def __eq__(self, other):
             return c1 and c2 and c3
 
     def find_com(self):
+        """
+        Get center of mass of molecule.
+
+        :return: Center of mass
+        :rtype: NumPy array of shape (3,)
+        """
         com = np.zeros(3)
         for i in range(self.natoms):
             com += self.masses[i]*self.coords[i,:]
         return com / sum(self.masses)
 
     def is_at_com(self):
+        """
+        Checks if molecule is at center of mass already.
+
+        :rtype: bool
+        """
         if sum(abs(self.find_com())) < self.tol:
             return True
         else:
             return False
 
     def translate(self, r):
+        """
+        Translates Cartesian positions of all atoms in molecule in place by vector r.
+
+        :param r: Translation vector
+        :type r: NumPy array of shape (3,)
+        """
         for i in range(self.natoms):
             self.coords[i,:] -= r
 
     def transform(self, M):
+        """
+        Transform coordinates of molecule by matrix M and return new molecule.
+
+        :param M: Transformation matrix (e.g. rotation, reflection, etc.)
+        :type M: NumPy array (3,3)
+        :return: Molecule with transformed atom coordinates
+        :rtype: molsym.Molecule
+        """
         new_mol = deepcopy(self)
         new_mol.coords = np.dot(new_mol.coords,np.transpose(M))
         return new_mol
 
     def distance_matrix(self):
+        """
+        Calculates the interatomic distance matrix as all pairwise distances between atoms.
+
+        :return: Interatomic distance matrix
+        :rtype: NumPy array of shape (self.natoms,self.natoms)
+        """
         dm = np.zeros((self.natoms,self.natoms))
         for i in range(self.natoms):
             for j in range(i,self.natoms):
@@ -116,6 +193,13 @@ def distance_matrix(self):
         return dm
 
     def find_SEAs(self):
+        """
+        Find sets of symmetry equivalent atoms.
+        Permutations of the distance matrix reveal which atoms form symmetry equivalent sets.
+
+        :return: List of symmetry equivalent atom sets
+        :rtype: List[molsym.SEA]
+        """
         dm = self.distance_matrix()
         out = []
         for i in range(self.natoms):
@@ -151,7 +235,12 @@ def find_SEAs(self):
         return SEAs
 
     def symmetrize(self, asym_tol=0.05):
-        # This code might be bad. Consider removing. Interatomic distances ---> Cart. not always well defined
+        """
+        Symmetrizes molecule.
+        This code might be bad. Consider removing. Interatomic distances ---> Cart. not always well defined
+        
+        :deprecated:
+        """
         print("Warning! Using this symmetrize (the one in Molecule) may fail!")
         dm = self.distance_matrix()
         SEAs = self.find_SEAs()

diff --git a/molsym/pgdetect/__init__.py b/molsym/pgdetect/__init__.py
diff --git a/molsym/pgdetect/flowchart.py b/molsym/pgdetect/flowchart.py
@@ -3,12 +3,25 @@
 from .flowchart_helper import *
 
 def find_point_group(mol):
+    """
+    Find the point group of a molecule.
+    Bases on the algorithm developed by:
+        Beruski, Otávio; Vidal, Luciano N. Algorithms for computer detection of 
+        symmetry elements in molecular systems, J. Comp. Chem, 2013 doi:10.1002/jcc.23493
+    Returns a primary and secondary axis in order to define an orienation of the molecule
+    with resepct to the symmetry elements generated later.
+    
+    :type mol: molsym.Molecule
+    :return: Schoenflies point group string, primary axis, and secondary axis
+    :rtype: (str, NumPy array of shape (3,), NumPy array of shape (3,))
+    """
+
     paxis = [0,0,0]
     saxis = [0,0,0]
     moit = calcmoit(mol)
     Ia_mol, Ib_mol, Ic_mol = np.sort(np.linalg.eigh(moit)[0])
     # Linear tops
-    if Ia_mol == 0.0:
+    if np.isclose(Ia_mol, 0.0, atol=mol.tol):
         if isequivalent(mol, mol.transform(inversion_matrix())):
             pg = "D0h"
         else:
@@ -32,7 +45,7 @@ def find_point_group(mol):
             # Reorienting vectors such that one face is on the z-axis with "pentagon" pointing at the POSITIVE y-axis
             phi = (1+np.sqrt(5.0))/2
             # Weirdness here, negative or positive???
-            theta =-np.arccos(phi/np.sqrt(1+(phi**2)))
+            theta = np.arccos(phi/np.sqrt(1+(phi**2)))
             rmat = rotation_matrix(saxis, theta)
             paxis = np.dot(rmat, tempaxis)
             taxis = np.dot(rmat, paxis)