[feat]: Integrating the io module

minushalf/commands/correct_potfile.py

@@ -6,8 +6,9 @@
 from loguru import logger
 from minushalf.softwares import Vasp
 from minushalf.data import Softwares
-from minushalf.utils import (welcome_message, end_message, Vtotal,
-                             AtomicPotential, parse_cut)
+from minushalf.io import (Vtotal)
+from minushalf.utils import (welcome_message, end_message, AtomicPotential,
+                             parse_cut)
 
 
 @click.command()

minushalf/commands/create_input.py

@@ -5,7 +5,8 @@
 import click
 from loguru import logger
 from minushalf.data import (CalculationCode, ExchangeCorrelation)
-from minushalf.utils import (welcome_message, end_message, InputFile)
+from minushalf.io import (InputFile)
+from minushalf.utils import (welcome_message, end_message)
 
 
 @click.command()

minushalf/commands/execute.py

@@ -10,13 +10,12 @@
 import pandas as pd
 import click
 from loguru import logger
+from minushalf.io import (MinushalfYaml, make_minushalf_results)
 from minushalf.utils import (
-    MinushalfYaml,
     BandStructure,
     projection_to_df,
     welcome_message,
     end_message,
-    make_minushalf_results,
     get_fractionary_correction_indexes,
     get_simple_correction_indexes,
 )

minushalf/commands/fractional_occupation.py

@@ -6,7 +6,8 @@
 import click
 import numpy as np
 from loguru import logger
-from minushalf.utils import (welcome_message, end_message, InputFile)
+from minushalf.io import (InputFile)
+from minushalf.utils import (welcome_message, end_message)
 from minushalf import atomic_program
 
 

minushalf/corrections/vasp_correction.py

@@ -11,9 +11,9 @@
 from minushalf.data import (CorrectionDefaultParams,
                             AtomicProgramDefaultParams, OrbitalType,
                             CutInitialGuessMethods)
-from minushalf.utils import (InputFile, Vtotal, MinushalfYaml, AtomicPotential,
-                             BandStructure, find_negative_band_gap,
-                             CutInitialGuess)
+from minushalf.io import (InputFile, Vtotal, MinushalfYaml)
+from minushalf.utils import (AtomicPotential, BandStructure,
+                             find_negative_band_gap, CutInitialGuess)
 from minushalf.interfaces import (Correction, Runner, SoftwaresAbstractFactory)
 
 

minushalf/io/__init__.py

@@ -7,3 +7,4 @@
 from .minushalf_yaml import MinushalfYaml
 from .input_file import InputFile
 from .vtotal import Vtotal
+from .make_minushalf_results import make_minushalf_results

minushalf/io/correction.py

@@ -122,6 +122,58 @@ def replace_cbm(self, characters: list) -> None:
 
         self._replace_cbm = characters
 
+    @property
+    def valence_cut_guess(self) -> list:
+        """
+        Returns:
+            CUT guess for nelder mead algorithm
+        """
+        return self._valence_cut_guess
+
+    @valence_cut_guess.setter
+    def valence_cut_guess(self, cut_guess: list) -> None:
+        """
+        Set valence_cut_guess
+        """
+
+        try:
+            if cut_guess != None:
+                for element in cut_guess:
+                    element[0] = element[0].capitalize()
+                    element[1] = element[1].lower()
+                    element[2] = float(element[2])
+        except:
+            loguru.logger.error("valence_cut_guess incorrectly specified")
+            raise Error("valence_cut_guess incorrectly specified")
+
+        self._valence_cut_guess = cut_guess
+
+    @property
+    def conduction_cut_guess(self) -> list:
+        """
+        Returns:
+            CUT guess for nelder mead algorithm
+        """
+        return self._conduction_cut_guess
+
+    @conduction_cut_guess.setter
+    def conduction_cut_guess(self, cut_guess: list) -> None:
+        """
+        Set conduction_cut_guess
+        """
+
+        try:
+            if cut_guess != None:
+                for element in cut_guess:
+                    element[0] = element[0].capitalize()
+                    element[1] = element[1].lower()
+                    element[2] = float(element[2])
+        except:
+            loguru.logger.error("conduction_cut_guess incorrectly specified")
+            raise Error("conduction_cut_guess incorrectly specified")
+
+        self._conduction_cut_guess = cut_guess
+
     @property
     def correction_code(self) -> dict:
         """
@@ -204,5 +256,9 @@ def to_dict(self):
             "_replace_cbm", None)
         parameters_dict["divide_character"] = parameters_dict.pop(
             "_divide_character", None)
+        parameters_dict["valence_cut_guess"] = parameters_dict.pop(
+            "_valence_cut_guess", None)
+        parameters_dict["conduction_cut_guess"] = parameters_dict.pop(
+            "_conduction_cut_guess", None)
 
         return parameters_dict

minushalf/utils/__init__.py

@@ -1,8 +1,6 @@
 """
 Init file for utils module
 """
-from .input_file import InputFile
-from .vtotal import Vtotal
 from .cli_messages import welcome_message, end_message
 from .drop_comments import drop_comments
 from .parse_valence_orbital_line import parse_valence_orbitals
@@ -15,8 +13,6 @@
                                 check_procar_exists, check_potcar_exists,
                                 check_outcar_exists)
 from .parse_cut import parse_cut
-from .minushalf_yaml import MinushalfYaml
-from .make_minushalf_results import make_minushalf_results
 from .negative_band_gap import find_negative_band_gap
 from .fractionary_correction_indexes import get_fractionary_correction_indexes
 from .simple_correction_indexes import get_simple_correction_indexes

minushalf/utils/atomic_potential.py

@@ -5,7 +5,7 @@
 import copy
 import numpy as np
 from minushalf.interfaces import PotentialFile
-from .vtotal import Vtotal
+from minushalf.io import Vtotal
 from .trimming_function import trimming_function
 from .correct_potential_fourier_transform import correct_potential_fourier_transform