Updating minushalf to pass tests

minushalf/commands/band_character.py

@@ -4,7 +4,7 @@
 """
 import click
 from minushalf.data.softwares import Softwares
-from minushalf.softwares.vasp import Vasp
+from minushalf.softwares.vasp_factory import Vasp
 from minushalf.utils.cli_messages import welcome_message,end_message
 from minushalf.utils.projection_to_df import projection_to_df
 from minushalf.utils.band_structure import  BandStructure

minushalf/commands/band_gap.py

@@ -3,7 +3,7 @@
 """
 
 import click
-from minushalf.softwares.vasp import Vasp
+from minushalf.softwares.vasp_factory import Vasp
 from minushalf.data.softwares import Softwares
 from minushalf.utils.cli_messages import welcome_message,end_message
 from minushalf.utils.band_structure import  BandStructure

minushalf/commands/cbm_character.py

@@ -4,7 +4,7 @@
 """
 import click
 from minushalf.data.softwares import Softwares
-from minushalf.softwares.vasp import Vasp
+from minushalf.softwares.vasp_factory import Vasp
 from minushalf.utils.cli_messages import welcome_message,end_message
 from minushalf.utils.projection_to_df import projection_to_df
 from minushalf.utils.band_structure import  BandStructure

minushalf/commands/correct_potfile.py

@@ -4,7 +4,7 @@
 import sys
 import click
 from loguru import logger
-from minushalf.softwares.vasp import Vasp
+from minushalf.softwares.vasp_factory import Vasp
 from minushalf.data.softwares import Softwares
 from minushalf.io.vtotal import (Vtotal)
 from minushalf.utils.cli_messages import welcome_message,end_message

minushalf/commands/execute.py

@@ -14,7 +14,7 @@
 from minushalf.utils.cli_messages import welcome_message,end_message
 from minushalf.utils.get_correction_params import get_valence_correction_params, get_conduction_correction_params
 
-from minushalf.softwares.vasp import (Vasp)
+from minushalf.softwares.vasp_factory import (Vasp)
 from minushalf.corrections.correction import (DFTCorrection)
 from minushalf.data.minushalf_yaml_default_configuration import CorrectionDefaultParams
 from minushalf.data.softwares import (Softwares)

minushalf/commands/vbm_character.py

@@ -2,7 +2,7 @@
 Aims to show how the last valence band are composed by the orbitals of each atom.
 """
 import click
-from minushalf.softwares.vasp import Vasp
+from minushalf.softwares.vasp_factory import Vasp
 from minushalf.data.softwares import Softwares
 from minushalf.utils.cli_messages import welcome_message,end_message
 from minushalf.utils.projection_to_df import projection_to_df

minushalf/data/constants.py

@@ -20,30 +20,8 @@ class Constants:
                  Johannes Rydberg, is a physical constant relating to the
                  electromagnetic spectra of an atom
     """
-    @property
-    def pi_constant(self):
-        """
-        Constant PI
-        """
-        return 3.1415926548
-
-    @property
-    def trimming_exponent(self):
-        """
-        Expoent for trimming function
-        """
-        return 8
-
-    @property
-    def bohr_radius(self):
-        """
-        Bohr radius
-        """
-        return 0.529177068
-
-    @property
-    def rydberg(self):
-        """
-        Rydberg constant
-        """
-        return 13.6058038
+    def __init__(self) -> None:
+        self.pi_constant = 3.1415926548
+        self.trimming_exponent = 8
+        self.bohr_radius = 0.529177068
+        self.rydberg = 13.6058038

minushalf/utils/correct_potential_fourier_transform.py

@@ -12,63 +12,17 @@ def correct_potential_fourier_transform(
     occupation_potential: np.array,
     cut: float,
 ) -> np.array:
-    r"""
-    The pseudopotential is given in terms of the radial distance, and is only defined for r >= 0,
-    as expected. Since it is only evaluated inside an integral from 0 to infinity, it does not
-    matter what values it assumes for r < 0. A natural choice is to define the function to be
-    zero for negative values, but a more convenient choice is to choose
-    v(-r)=-v(r) and n(-r)=-n(r), since purely real and odd functions have purely imaginary Fourier transforms.
-    Let v' and n' be the odd extensions of the potential and the number density, respectively.
-
-    .. math::
-        E_{v} = \int_{0}^{\infty}v(r)n(r)dr = \int_{0}^{\infty}v'(r)n'(r)dr =
-        \frac{1}{2}\cdot\int_{-\infty}^{\infty}v'(r)n'(r)dr = -\frac{1}{2}\cdot\int_{-\infty}^{\infty}V(k)N(k)dk
-
-
-    On the third equalitty, we used the fact that the product of two odd
-    functions is even, and in the last step we have applied Parseval's theorem,
-    considering that the Fourier transforms are purely imaginary. Even though
-    the function may not pass through the origin, we can still make an odd extension, by making it discontinuous.
-
-    The data stored on POTCAR corresponds to the Fourier transform of the odd extension of v. It can be approximated
-    by the summation on the right, where the prefactors were ommited.
-
-    .. math::
-        V(k) = i\cdot \sqrt{\frac{2}{\pi}}\cdot\int_{0}^{\infty}v(r)sin(b\cdot k\cdot r)dr
-        \Rightarrow V(k)\sim \sum^{N_{r}}_{i=1}
-        \frac{(v[i]\cdot sin(b\cdot k\cdot r[i])+v[i-1]\cdot sin(b\cdot k\cdot r[i-1]))}{2\cdot (r[i]-r[i-1])}
-
-    Computes the opposite of the imaginary part of the j-th fourier transform coefficient
-    through numerical integrationIndex zero stands for the r=DeltaR, and the function is
-    assumed to be zero at the origin. Thus, the first trapezium of the numerical integration is
-    degenerated to a triangulum, and its area must be calculated as so.
-
-        Args:
-            coefficient (np.array): Fourier transform of the potential for the atom in its ground state
-
-            k (np.array): The wave vector in reciprocal space
-
-            rays(np.array): List of rays on which pseudopotential calculations were made
-
-            occupation_potential (np.arraygit): Potential of fractional electron occupation at the exact level to be corrected
-
-            cut(float): Cutting parameter to cancel the potential
-
-        Returns:
-            Fourier transform of the potential for the state with fractional occupation of the crystal
-    """
     const = Constants()
+
     k = np.reshape(k, (len(k), 1))
-
+    
     if not k[0][0]:
         k[0][0] = 10**(-12)
-
     try:
         filter_rays = rays[np.where(rays < cut)]
     except ValueError as cut_error:
         raise ValueError(
             "the cut is smaller than all the rays passed") from cut_error
-
     radius = filter_rays[1:].astype(float)
     lazy_radius = filter_rays[:-1].astype(float)
     potential = occupation_potential[1:len(filter_rays)].astype(float)

minushalf/utils/get_correction_params.py

@@ -5,7 +5,8 @@
 from minushalf.interfaces.minushalf_yaml import MinushalfYaml
 from minushalf.interfaces.software_abstract_factory import SoftwaresAbstractFactory
 from minushalf.utils.cut_initial_guess import CutInitialGuess
-from minushalf.utils.get_correction_params import get_fractionary_correction_indexes,get_simple_correction_indexes
+from minushalf.utils.fractionary_correction_indexes import get_fractionary_correction_indexes
+from minushalf.utils.simple_correction_indexes import get_simple_correction_indexes
 from minushalf.data.cut_initial_guess_methods import (CutInitialGuessMethods)
 from minushalf.utils.band_structure import BandStructure
 from minushalf.utils.projection_to_df import projection_to_df

pyproject.toml

@@ -25,16 +25,16 @@ install_command = python -m pip install .
 deps=
     pytest==6.2.1
     pytest-mock==3.0.0
-    pandas==1.3.4
+    pandas==1.4.0
     fortranformat==0.2.5
     Click==7.1.2
     pyfiglet==0.8.post1 
     loguru==0.5.3
-    tabulate==0.8.7
+    tabulate==0.9.0
     pyyaml
     scipy==1.7.3
     aenum==3.0.0
-    numpy==1.21.0
+    numpy==1.22.0
 usedevelop=False
 commands=
     python -m pytest

requirements.txt

@@ -1,10 +1,10 @@
-pandas==1.3.4
+pandas==1.4.0
 fortranformat==0.2.5
 Click==7.1.2
 pyfiglet==0.8.post1 
 loguru==0.5.3
-tabulate==0.8.7
+tabulate==0.9.0
 pyyaml
 scipy==1.7.3
 aenum==3.0.0
-numpy==1.21.0
+numpy==1.22.0

setup.py

@@ -28,13 +28,13 @@
     long_description=long_description,
     license="GPL",
     install_requires=[
-        "pandas==1.3.4",
+        "pandas==1.4.0",
         "fortranformat==0.2.5",
         "Click==7.1.2",
         "pyfiglet==0.8.post1",
         "loguru==0.5.3",
-        "tabulate==0.8.7",
-        "numpy==1.21.0",
+        "tabulate==0.9.0",
+        "numpy==1.22.0",
         "pyyaml",
         "scipy==1.7.3",
         "aenum==3.0.0",

tests/cli/test_band_character.py

@@ -2,7 +2,7 @@
 Test band character command
 """
 from click.testing import CliRunner
-from minushalf.commands import band_character
+from minushalf.commands.band_character import band_character
 
 
 def test_band_character_gan_3d(file_path):

tests/cli/test_band_gap.py

@@ -2,7 +2,7 @@
 Test band gap command
 """
 from click.testing import CliRunner
-from minushalf.commands import band_gap
+from minushalf.commands.band_gap import band_gap
 
 
 def test_band_gap_gan_3d(file_path):

tests/cli/test_cbm_character.py

@@ -2,7 +2,7 @@
 Test cbm character command
 """
 from click.testing import CliRunner
-from minushalf.commands import cbm_character
+from minushalf.commands.cbm_character import cbm_character
 
 
 def test_cbm_character_gan_3d(file_path):
@@ -14,7 +14,9 @@ def test_cbm_character_gan_3d(file_path):
     result_path = file_path("/gan-3d/result_cbm_character.txt")
     runner = CliRunner()
     result = runner.invoke(cbm_character, ['-b', base_path])
-
+    print(result.output)
+    import os
+    os.system(f"echo {result.output} > a.txt")
     with open(result_path) as file:
         assert file.read() == result.output
 

tests/cli/test_correct_potfile.py

@@ -4,7 +4,7 @@
 import os
 import numpy as np
 from click.testing import CliRunner
-from minushalf.commands import correct_potfile
+from minushalf.commands.correct_potfile import correct_potfile
 
 
 def test_correct_potfile_ga_first(file_path):

tests/cli/test_create_input.py

@@ -4,9 +4,9 @@
 import os
 from click.testing import CliRunner
 from minushalf import atomic_program
-from minushalf.commands import create_input
-from minushalf.data import ElectronicDistribution
-from minushalf.io import InputFile
+from minushalf.commands.create_input import create_input
+from minushalf.data.electronic_distribution import ElectronicDistribution
+from minushalf.io.input_file import InputFile
 
 
 def test_create_input_with_all_elements():

tests/cli/test_occupation.py

@@ -5,8 +5,8 @@
 import pytest
 from click.testing import CliRunner
 from minushalf import atomic_program
-from minushalf.io import InputFile
-from minushalf.commands import occupation
+from minushalf.io.input_file import InputFile
+from minushalf.commands.fractional_occupation import occupation
 
 
 def test_occupation_with_default_params_O():

tests/cli/test_run_atomic.py

@@ -5,9 +5,9 @@
 from unittest import mock
 from click.testing import CliRunner
 from minushalf import atomic_program
-from minushalf.commands import run_atomic
-from minushalf.data import ElectronicDistribution
-from minushalf.io import InputFile
+from minushalf.commands.run_atomic_program import run_atomic
+from minushalf.data.electronic_distribution import ElectronicDistribution
+from minushalf.io.input_file import InputFile
 
 
 def test_atomic_run_workflow():

tests/cli/test_vbm_character.py

@@ -2,7 +2,7 @@
 Test vbm character command
 """
 from click.testing import CliRunner
-from minushalf.commands import vbm_character
+from minushalf.commands.vbm_character import vbm_character
 
 
 def test_vbm_character_gan_3d(file_path):