Fix pre-commit errors

.editorconfig

@@ -1,4 +1,4 @@
-# EditorConfig is awesome: https://EditorConfig.org
+# EditorConfig: https://EditorConfig.org
 
 root = true
 

gbasis/base_four_symm.py

@@ -2,9 +2,10 @@
 import abc
 import itertools as it
 
+import numpy as np
+
 from gbasis.base import BaseGaussianRelatedArray
 from gbasis.spherical import generate_transformation
-import numpy as np
 
 
 # pylint: disable=W0235

gbasis/base_one.py

@@ -1,9 +1,10 @@
 """Base class for arrays that depend on one contracted Gaussian."""
 import abc
 
+import numpy as np
+
 from gbasis.base import BaseGaussianRelatedArray
 from gbasis.spherical import generate_transformation
-import numpy as np
 
 
 # pylint: disable=W0235

gbasis/base_two_asymm.py

@@ -1,9 +1,10 @@
 """Base class for arrays that depend on two contracted Gaussians."""
 import abc
 
+import numpy as np
+
 from gbasis.base import BaseGaussianRelatedArray
 from gbasis.spherical import generate_transformation
-import numpy as np
 
 
 # pylint: disable=W0235

gbasis/base_two_symm.py

@@ -2,9 +2,10 @@
 
 import abc
 
+import numpy as np
+
 from gbasis.base import BaseGaussianRelatedArray
 from gbasis.spherical import generate_transformation
-import numpy as np
 
 
 # pylint: disable=W0235

gbasis/contractions.py

@@ -1,7 +1,9 @@
 """Data class for contractions of Gaussian-type primitives."""
 
 from numbers import Integral
+
 import numpy as np
+
 from gbasis.utils import factorial2
 
 
@@ -31,7 +33,8 @@ class GeneralizedContractionShell:
  .. math::
 
  \phi (\mathbf{r} | \mathbf{R}_A, \mathbf{a}, \mathbf{d}, \boldsymbol{\alpha}) =
- N_{\phi} (\mathbf{R}_A, \mathbf{a}, \mathbf{d}, \boldsymbol{\alpha}) \sum_i d_i g_i (\mathbf{r} | \mathbf{R}_A, \mathbf{a})
+ N_{\phi} (\mathbf{R}_A, \mathbf{a}, \mathbf{d}, \boldsymbol{\alpha})
+ \sum_i d_i g_i (\mathbf{r} | \mathbf{R}_A, \mathbf{a})
 
  where :math:`d_i` is the contraction coefficient of the primitive and :math:`N_{\phi}` is the
  normalization constant of the contraction.
@@ -63,7 +66,8 @@ class GeneralizedContractionShell:
  .. math::
 
  \phi_j (\mathbf{r} | \mathbf{R}_A, \mathbf{a}, \mathbf{d}, \boldsymbol{\alpha}) =
- N_{\phi} (\mathbf{R}_A, \mathbf{a}, \mathbf{d}, \boldsymbol{\alpha}) \sum_i d_{ij} g_i (\mathbf{r} | \mathbf{R}_A, \mathbf{a})
+ N_{\phi} (\mathbf{R}_A, \mathbf{a}, \mathbf{d}, \boldsymbol{\alpha})
+ \sum_i d_{ij} g_i (\mathbf{r} | \mathbf{R}_A, \mathbf{a})
 
  Attributes
  ----------
@@ -427,8 +431,8 @@ def angmom_components_sph(self):
  return tuple(["c1", "s1", "c0"])
  else:
  return tuple(
- ["s{}".format(m) for m in range(self.angmom, 0, -1)]
- + ["c{}".format(m) for m in range(self.angmom + 1)]
+ [f"s{m}" for m in range(self.angmom, 0, -1)]
+ + [f"c{m}" for m in range(self.angmom + 1)]
  )
 
  @property

gbasis/evals/density.py

@@ -1,9 +1,10 @@
 """Density Evaluation."""
-from gbasis.evals.eval import evaluate_basis
-from gbasis.evals.eval_deriv import evaluate_deriv_basis
 import numpy as np
 from scipy.special import comb
 
+from gbasis.evals.eval import evaluate_basis
+from gbasis.evals.eval_deriv import evaluate_deriv_basis
+
 
 def evaluate_density_using_evaluated_orbs(one_density_matrix, orb_eval):
  """Return the evaluation of the density given the evaluated orbitals.
@@ -218,15 +219,16 @@ def evaluate_deriv_density(
  \sum_{l_x=0}^{L_x} \sum_{l_y=0}^{L_y} \sum_{l_z=0}^{L_z}
  \binom{L_x}{l_x} \binom{L_y}{l_y} \binom{L_z}{l_z}
  \sum_{ij} \gamma_{ij}
- \frac{\partial^{l_x + l_y + l_z} \rho(\mathbf{r})}{\partial x^{l_x} \partial y^{l_y} \partial z^{l_z}}
+ \frac{\partial^{l_x + l_y + l_z}
+ \rho(\mathbf{r})}{\partial x^{l_x} \partial y^{l_y} \partial z^{l_z}}
  \frac{
  \partial^{L_x + L_y + L_z - l_x - l_y - l_z} \rho(\mathbf{r})
  }{
  \partial x^{L_x - l_x} \partial y^{L_y - l_y} \partial z^{L_z - l_z}
  }
 
- where :math:`L_x, L_y, L_z` are the orders of the derivative relative to the :math:`x, y, \text{and} z` components,
- respectively.
+ where :math:`L_x, L_y, L_z` are the orders of the derivative relative to the
+ :math:`x, y, \text{and} z` components, respectively.
 
  Parameters
  ----------
@@ -320,7 +322,7 @@ def evaluate_density_gradient(
  \frac{\partial}{\partial x} \rho(\mathbf{r})\\\\
  \frac{\partial}{\partial y} \rho(\mathbf{r})\\\\
  \frac{\partial}{\partial z} \rho(\mathbf{r})
- \end{bmatrix} 
+ \end{bmatrix}
 
  Parameters
  ----------
@@ -489,7 +491,7 @@ def evaluate_density_hessian(
  r"""Return the Hessian of the density evaluated at the given points.
 
  .. math::
- 
+
  H[\rho(\mathbf{r})]
  =
  \begin{bmatrix}

gbasis/evals/electrostatic_potential.py

@@ -1,7 +1,8 @@
 """Module for computing electrostatic potential integrals."""
-from gbasis.integrals.point_charge import point_charge_integral
 import numpy as np
 
+from gbasis.integrals.point_charge import point_charge_integral
+
 
 def electrostatic_potential(
  basis,
@@ -18,12 +19,13 @@ def electrostatic_potential(
 
  - \left(
  - \sum_A \frac{Z_A}{|\mathbf{R}_C - \mathbf{R}_A|}
- + \sum_{ab} \gamma_{ab} \int \phi_a(\mathbf{r}) \frac{-1}{|\mathbf{r} - \mathbf{R}_C|} \phi_b(\mathbf{r}) d\mathbf{r}
+ + \sum_{ab} \gamma_{ab} \int \phi_a(\mathbf{r}) \frac{-1}{|\mathbf{r}
+ - \mathbf{R}_C|} \phi_b(\mathbf{r}) d\mathbf{r}
  \right)
 
- where :math:`\mathbf{R}_C` is the coordinate of a unitary point charge, :math:`\mathbf{R}_A` is the
- coordinate of the nucleus :math:`A`, :math:`Z_A` its charge, and :math:`\gamma_{ab}` is the
- one-electron density matrix.
+ where :math:`\mathbf{R}_C` is the coordinate of a unitary point charge, :math:`\mathbf{R}_A`
+ is the coordinate of the nucleus :math:`A`, :math:`Z_A` its charge, and :math:`\gamma_{ab}`
+ is the one-electron density matrix.
 
  Parameters
  ----------

gbasis/evals/eval.py

@@ -1,8 +1,9 @@
 """Functions for evaluating Gaussian contractions."""
+import numpy as np
+
 from gbasis.base_one import BaseOneIndex
 from gbasis.contractions import GeneralizedContractionShell
 from gbasis.evals._deriv import _eval_deriv_contractions
-import numpy as np
 
 
 class Eval(BaseOneIndex):

gbasis/evals/eval_deriv.py

@@ -1,9 +1,12 @@
 """Functions for evaluating Gaussian primitives."""
+import numpy as np
+
 from gbasis.base_one import BaseOneIndex
 from gbasis.contractions import GeneralizedContractionShell
-from gbasis.evals._deriv import _eval_deriv_contractions
-from gbasis.evals._deriv import _eval_first_second_order_deriv_contractions
-import numpy as np
+from gbasis.evals._deriv import (
+ _eval_deriv_contractions,
+ _eval_first_second_order_deriv_contractions,
+)
 
 
 class EvalDeriv(BaseOneIndex):
@@ -150,13 +153,13 @@ def evaluate_deriv_basis(
  The derivative (to arbitrary orders) of a basis function is given by:
 
  .. math::
- 
+
  \frac{\partial^{m_x + m_y + m_z}}{\partial x^{m_x} \partial y^{m_y} \partial z^{m_z}}
  \phi (\mathbf{r})
- 
- where :math:`m_x, m_y, m_z` are the orders of the derivative with respect to x, y, and z, 
- :math:`\phi` is the basis function (a generalized contraction shell), and :math:`\mathbf{r}_n` are
- the coordinate of the points in space where the basis function is evaluated.
+
+ where :math:`m_x, m_y, m_z` are the orders of the derivative with respect to x, y, and z,
+ :math:`\phi` is the basis function (a generalized contraction shell), and :math:`\mathbf{r}_n`
+ are the coordinate of the points in space where the basis function is evaluated.
 
  Parameters
  ----------

gbasis/evals/stress_tensor.py

@@ -1,10 +1,11 @@
 """Module for computing properties related to the stress tensor."""
+import numpy as np
+
 from gbasis.evals.density import (
  evaluate_density_laplacian,
  evaluate_deriv_density,
  evaluate_deriv_reduced_density_matrix,
 )
-import numpy as np
 
 
 # TODO: need to be tested against reference
@@ -132,31 +133,31 @@ def evaluate_ehrenfest_force(one_density_matrix, basis, points, alpha=1, beta=0,
 
  .. math::
 
-  F_{j}(\mathbf{r} | \alpha, \beta)
-  =&- \sum_i \frac{\partial}{\partial r_i} \boldsymbol{\sigma}_{ij}\\
-  =&
-  \alpha
-  \sum_i
-  \left.
-  \frac{\partial^3}{\partial r^2_i \partial r'_j} \gamma(\mathbf{r}, \mathbf{r}')
-  \right|_{\mathbf{r} = \mathbf{r}'}\\
-  &- (1 - \alpha)
-  \sum_i
-  \left.
-  \frac{\partial^3}{\partial r^2_i \partial r_j} \gamma(\mathbf{r}, \mathbf{r})
-  \right|_{\mathbf{r} = \mathbf{r}'}
-  - (1 - 2\alpha)
-  \sum_i
-  \left.
-  \frac{\partial^3}{\partial r_i \partial r_j \partial r'_i} \gamma(\mathbf{r}, \mathbf{r})
-  \right|_{\mathbf{r} = \mathbf{r}'}\\
-  &+ \frac{1}{2} \beta
-  \left(
-  \frac{\partial^3}{\partial r_j \partial x^2}
-  + \frac{\partial^3}{\partial r_j \partial y^2}
-  + \frac{\partial^3}{\partial r_j \partial z^2}
-  \right)
-  \rho(\mathbf{r})
+ F_{j}(\mathbf{r} | \alpha, \beta)
+ =&- \sum_i \frac{\partial}{\partial r_i} \boldsymbol{\sigma}_{ij}\\
+ =&
+ \alpha
+ \sum_i
+ \left.
+ \frac{\partial^3}{\partial r^2_i \partial r'_j} \gamma(\mathbf{r}, \mathbf{r}')
+ \right|_{\mathbf{r} = \mathbf{r}'}\\
+ &- (1 - \alpha)
+ \sum_i
+ \left.
+ \frac{\partial^3}{\partial r^2_i \partial r_j} \gamma(\mathbf{r}, \mathbf{r})
+ \right|_{\mathbf{r} = \mathbf{r}'}
+ - (1 - 2\alpha)
+ \sum_i
+ \left.
+ \frac{\partial^3}{\partial r_i \partial r_j \partial r'_i} \gamma(\mathbf{r}, \mathbf{r})
+ \right|_{\mathbf{r} = \mathbf{r}'}\\
+ &+ \frac{1}{2} \beta
+ \left(
+ \frac{\partial^3}{\partial r_j \partial x^2}
+ + \frac{\partial^3}{\partial r_j \partial y^2}
+ + \frac{\partial^3}{\partial r_j \partial z^2}
+ \right)
+ \rho(\mathbf{r})
 
  Parameters
  ----------

gbasis/integrals/_diff_operator_int.py

@@ -1,9 +1,10 @@
 """Integrals over differential operator involving contracted Cartesian Gaussians."""
+import numpy as np
+
 from gbasis.integrals._moment_int import (
  _cleanup_intermediate_integrals,
  _compute_multipole_moment_integrals_intermediate,
 )
-import numpy as np
 
 
 # FIXME: returns nan when exponent is zero

gbasis/integrals/_one_elec_int.py

@@ -1,5 +1,6 @@
 """One-electron integrals involving Contracted Cartesian Gaussians."""
 import numpy as np
+
 from gbasis.utils import factorial2
 
 

gbasis/integrals/_two_elec_int.py

@@ -1,5 +1,6 @@
 """Two-electron integrals involving Contracted Cartesian Gaussians."""
 import numpy as np
+
 from gbasis.utils import factorial2
 
 # pylint: disable=C0103,R0914,R0915

gbasis/integrals/angular_momentum.py

@@ -1,11 +1,12 @@
 """Module for evaluating the integral over the angular momentum operator."""
+import numpy as np
+
 from gbasis.base_two_symm import BaseTwoIndexSymmetric
 from gbasis.contractions import GeneralizedContractionShell
 from gbasis.integrals._diff_operator_int import (
  _compute_differential_operator_integrals_intermediate,
 )
 from gbasis.integrals._moment_int import _compute_multipole_moment_integrals_intermediate
-import numpy as np
 
 
 # TODO: need to test against reference
@@ -161,17 +162,18 @@ def angular_momentum_integral(basis, transform=None):
 
  .. math::
 
- \left< \hat{\mathbf{L}} \right>
- &= \int \phi_a(\mathbf{r}) \left( -i \mathbf{r} \times \nabla \right) \phi_b(\mathbf{r}) d\mathbf{r}\\
- &= -i
- \begin{bmatrix}
- \int \phi_a(\mathbf{r}) y\frac{\partial}{\partial z} \phi_b(\mathbf{r}) d\mathbf{r}
- - \int \phi_a(\mathbf{r}) z\frac{\partial}{\partial y} \phi_b(\mathbf{r}) d\mathbf{r}\\\\
- \int \phi_a(\mathbf{r}) z\frac{\partial}{\partial x} \phi_b(\mathbf{r}) d\mathbf{r}
- - \int \phi_a(\mathbf{r}) x\frac{\partial}{\partial z} \phi_b(\mathbf{r}) d\mathbf{r}\\\\
- \int \phi_a(\mathbf{r}) x\frac{\partial}{\partial y} \phi_b(\mathbf{r}) d\mathbf{r}
- - \int \phi_a(\mathbf{r}) y\frac{\partial}{\partial x} \phi_b(\mathbf{r}) d\mathbf{r}\\\\
- \end{bmatrix}
+ \left< \hat{\mathbf{L}} \right>
+ &= \int \phi_a(\mathbf{r}) \left( -i \mathbf{r} \times \nabla \right) \phi_b(\mathbf{r})
+ d\mathbf{r}\\
+ &= -i
+ \begin{bmatrix}
+ \int \phi_a(\mathbf{r}) y\frac{\partial}{\partial z} \phi_b(\mathbf{r}) d\mathbf{r}
+ - \int \phi_a(\mathbf{r}) z\frac{\partial}{\partial y} \phi_b(\mathbf{r}) d\mathbf{r}\\\\
+ \int \phi_a(\mathbf{r}) z\frac{\partial}{\partial x} \phi_b(\mathbf{r}) d\mathbf{r}
+ - \int \phi_a(\mathbf{r}) x\frac{\partial}{\partial z} \phi_b(\mathbf{r}) d\mathbf{r}\\\\
+ \int \phi_a(\mathbf{r}) x\frac{\partial}{\partial y} \phi_b(\mathbf{r}) d\mathbf{r}
+ - \int \phi_a(\mathbf{r}) y\frac{\partial}{\partial x} \phi_b(\mathbf{r}) d\mathbf{r}\\\\
+ \end{bmatrix}
 
  Parameters
  ----------

gbasis/integrals/electron_repulsion.py

@@ -1,12 +1,13 @@
 """Electron-electron repulsion integral."""
+import numpy as np
+
 from gbasis.base_four_symm import BaseFourIndexSymmetric
 from gbasis.contractions import GeneralizedContractionShell
 from gbasis.integrals._two_elec_int import (
  _compute_two_elec_integrals,
  _compute_two_elec_integrals_angmom_zero,
 )
 from gbasis.integrals.point_charge import PointChargeIntegral
-import numpy as np
 
 
 class ElectronRepulsionIntegral(BaseFourIndexSymmetric):

gbasis/integrals/kinetic_energy.py

@@ -1,8 +1,9 @@
 """Module for evaluating the kinetic energy integral."""
+import numpy as np
+
 from gbasis.base_two_symm import BaseTwoIndexSymmetric
 from gbasis.contractions import GeneralizedContractionShell
 from gbasis.integrals._diff_operator_int import _compute_differential_operator_integrals
-import numpy as np
 
 
 class KineticEnergyIntegral(BaseTwoIndexSymmetric):
@@ -126,7 +127,8 @@ def kinetic_energy_integral(basis, transform=None):
 
  \begin{split}
  \left< \hat{T} \right>
- &= \int \phi_a(\mathbf{r}) \left( -\frac{1}{2} \nabla^2 \right) \phi_b(\mathbf{r}) d\mathbf{r}\\
+ &= \int \phi_a(\mathbf{r}) \left( -\frac{1}{2} \nabla^2 \right) \phi_b(\mathbf{r})
+ d\mathbf{r}\\
  &= -\frac{1}{2}
  \left(
  \int \phi_a(\mathbf{r}) \frac{\partial^2}{\partial x^2} \phi_b(\mathbf{r}) d\mathbf{r}