diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index b731601..edf7a97 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -17,9 +17,9 @@ jobs: fail-fast: false matrix: python-version: - - 3.7 - - 3.8 - - 3.9 + - "3.8" + - "3.9" + - "3.10" os: - ubuntu-latest #- macOS-latest diff --git a/poetry.lock b/poetry.lock index 06dcac4..edee308 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. 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"more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] + [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<4.0" diff --git a/pyproject.toml b/pyproject.toml index 8eb3148..6a55ba9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "tanabesugano" -version = "1.3.1" +version = "1.4.0" description = "A python-solver for Tanabe-Sugano and Energy-Correlation diagrams" authors = ["Anselm Hahn "] maintainers = ["Anselm Hahn "] diff --git a/tanabesugano/__init__.py b/tanabesugano/__init__.py index 9c73af2..3e8d9f9 100644 --- a/tanabesugano/__init__.py +++ b/tanabesugano/__init__.py @@ -1 +1 @@ -__version__ = "1.3.1" +__version__ = "1.4.0" diff --git a/tanabesugano/batch.py b/tanabesugano/batch.py index 201530a..438347a 100644 --- a/tanabesugano/batch.py +++ b/tanabesugano/batch.py @@ -6,14 +6,13 @@ class Batch: - def __init__( - self, - Dq: List[float] = [4000.0, 4500.0, 10], - B: List[float] = [400.0, 4500.0, 10], - C: List[float] = [3600.0, 4000, 10], - d_count: int = 5, - slater: bool = False, - ): + def __init__(self, Dq: List[float] = None, B: List[float] = None, C: List[float] = None, d_count: int = 5, slater: bool = False): + if Dq is None: + Dq = [4000.0, 4500.0, 10] + if B is None: + B = [400.0, 4500.0, 10] + if C is None: + C = [3600.0, 4000, 10] if len(Dq) != 3: raise KeyError( "The range of `Dq` is based on the three values: start, stop, steps!" diff --git a/tanabesugano/cmd.py b/tanabesugano/cmd.py index 801baf9..15e944a 100644 --- a/tanabesugano/cmd.py +++ b/tanabesugano/cmd.py @@ -1,8 +1,11 @@ #!/usr/bin/env python import argparse +from logging import warning + import matplotlib.pyplot as plt import numpy as np +import pandas as pd from prettytable import PrettyTable from tanabesugano import matrices, tools @@ -17,17 +20,16 @@ def __init__( nroots: int = 100, d_count: int = 5, slater: bool = False, - ): + ) -> None: self.Dq = Dq # Oh-crystalfield-splitting self.B = B # Racah-Parameter B in wavenumbers self.C = C # Racah-Parameter C in wavenumbers if slater: - # Transformin Racah to Slater-Condon + # Transforming Racah to Slater-Condon self.B, self.C = tools.racah(B, C) self.nroot = nroots - self.e_range = np.linspace(0.0, self.Dq, nroots) - self.delta_B = self.e_range / self.B + energy = np.linspace(0.0, self.Dq, nroots) self.d_count = d_count if self.d_count in {4, 5, 6}: @@ -38,96 +40,133 @@ def __init__( self._size = 10 self.result = np.zeros((self._size + 1, nroots)) - def plot(self): + self.df = pd.DataFrame({"Energy": energy, "delta_B": energy / self.B}) + + def plot(self) -> None: # Figure one for classical Tanabe-Sugano-Diagram with B-dependency plt.figure(1) # Set Window Title - for i in range(self._size + 1): - plt.plot(self.delta_B, self.result[i, :] / self.B, ls="--") - plt.title("Tanabe-Sugano-Diagram") - plt.ylabel("$E/B$") - plt.xlabel("$\Delta/B$") - + plt.plot( + self.df["delta_B"], + # get the states from self.df + self.df.drop(["Energy", "delta_B"], axis=1).to_numpy() / self.B, + ls="--", + ) + self.label_plot("Tanabe-Sugano-Diagram", "$E/B$", "$\Delta/B$") # Figure one for Energy-Correlation-Diagram Dq-Energy versus State-Energy plt.figure(2) - for i in range(self._size + 1): - plt.plot(self.e_range * 10.0, self.result[i, :], ls="--") - plt.title("DD excitations -Diagram") - plt.ylabel("$dd-state-energy\,(1/cm)$") - plt.xlabel("$10Dq\,(1/cm)$") + plt.plot( + self.df["Energy"] * 10.0, + self.df.drop(["Energy", "delta_B"], axis=1).to_numpy(), + ls="--", + ) + self.label_plot( + "DD excitations -Diagram", "$dd-state-energy\,(1/cm)$", "$10Dq\,(1/cm)$" + ) plt.show() - def savetxt(self): + def label_plot(self, arg0: str, arg1: str, arg2: str) -> None: + """Labels the plot.""" + plt.title(arg0) + plt.ylabel(arg1) + plt.xlabel(arg2) - title_TS = "TS-diagram_d%i_10Dq_%i_B_%i_C_%i.txt" % ( - self.d_count, - self.Dq * 10.0, - self.B, - self.C, - ) - ts_states = np.concatenate( - (np.array([self.delta_B]), np.divide(self.result, self.B)) + def savetxt(self) -> None: + + title_TS = ( + f"TS-diagram_d{self.d_count}_10Dq_{self.Dq * 10.0}_" + f"B_{self.B}_C_{self.C}.csv" ) - np.savetxt(title_TS, ts_states.T, delimiter="\t", fmt="%.6f") - title_DD = "DD-energies_d%i_10Dq_%i_B_%i_C_%i.txt" % ( - self.d_count, - self.Dq * 10.0, - self.B, - self.C, + pd.concat( + [self.df["delta_B"], self.df.drop(["Energy", "delta_B"], axis=1) / self.B], + axis=1, + ).to_csv(title_TS, index=False) + + title_DD = ( + f"DD-energies_d{self.d_count}_10Dq_{self.Dq * 10.0}_" + f"B_{self.B}_C_{self.C}.csv" ) - dd_states = np.concatenate((np.array([self.e_range * 10.0]), self.result)) - np.savetxt(title_DD, dd_states.T, delimiter="\t", fmt="%.6f") - def calculation(self): + pd.concat( + [self.df["Energy"] * 10.0, self.df.drop(["Energy", "delta_B"], axis=1)], + axis=1, + ).to_csv(title_DD, index=False) + + def calculation(self) -> None: """ Is filling the self.result with the iTS states of over-iterated energy range """ - for i, dq in enumerate(self.e_range): - - if self.d_count == 2: # d3 - - states = matrices.d2(Dq=dq, B=self.B, C=self.C).solver() - self.result[:, i] = np.concatenate(list(states.values())) - + result = [] + for dq in self.df["Energy"]: + if self.d_count == 2: # d2 + result.append( + self.subsplit_states( + matrices.d2(Dq=dq, B=self.B, C=self.C).solver() + ) + ) elif self.d_count == 3: # d3 - - states = matrices.d3(Dq=dq, B=self.B, C=self.C).solver() - self.result[:, i] = np.concatenate(list(states.values())) - + result.append( + self.subsplit_states( + matrices.d3(Dq=dq, B=self.B, C=self.C).solver() + ) + ) elif self.d_count == 4: # d4 - - states = matrices.d4(Dq=dq, B=self.B, C=self.C).solver() - self.result[:, i] = np.concatenate(list(states.values())) - + result.append( + self.subsplit_states( + matrices.d4(Dq=dq, B=self.B, C=self.C).solver() + ) + ) elif self.d_count == 5: # d5 - states = matrices.d5(Dq=dq, B=self.B, C=self.C).solver() - self.result[:, i] = np.concatenate(list(states.values())) - + result.append( + self.subsplit_states( + matrices.d5(Dq=dq, B=self.B, C=self.C).solver() + ) + ) elif self.d_count == 6: # d6 - - states = matrices.d6(Dq=dq, B=self.B, C=self.C).solver() - self.result[:, i] = np.concatenate(list(states.values())) - + result.append( + self.subsplit_states( + matrices.d6(Dq=dq, B=self.B, C=self.C).solver() + ) + ) elif self.d_count == 7: # d7 - - states = matrices.d7(Dq=dq, B=self.B, C=self.C).solver() - self.result[:, i] = np.concatenate(list(states.values())) - + result.append( + self.subsplit_states( + matrices.d7(Dq=dq, B=self.B, C=self.C).solver() + ) + ) elif self.d_count == 8: # d8 - - states = matrices.d8(Dq=dq, B=self.B, C=self.C).solver() - self.result[:, i] = np.concatenate(list(states.values())) - + result.append( + self.subsplit_states( + matrices.d8(Dq=dq, B=self.B, C=self.C).solver() + ) + ) else: + raise ValueError("`d_count` must be in {2,3,4,5,6,7,8}") + + # Transform list of dictionaries to dictionary of arrays + result = { + key: np.array([d[key] for d in result]).flatten() for key in result[0] + } + self.df = pd.concat([self.df, pd.DataFrame(result)], axis=1) + + @staticmethod + def subsplit_states(states: dict) -> dict: + """Subsplitting the states for a better overview.""" + rearranged_states = {} + for key, value in states.items(): + if len(value) > 1: + for i, _value in enumerate(value): + rearranged_states[f"{key}_{i}"] = np.array([_value]) + else: + rearranged_states[key] = value + return rearranged_states - print("not a correct value!") - - def ci_cut(self, dq_ci=None): + def ci_cut(self, dq_ci=None) -> None: """ Extracting the atomic-termsymbols for a specific dq depending on the oxidation state """ @@ -166,7 +205,7 @@ def ci_cut(self, dq_ci=None): states = matrices.d8(Dq=dq_ci / 10.0, B=self.B, C=self.C).solver() self.ts_print(states, dq_ci=dq_ci) - def ts_print(self, states, dq_ci=None): + def ts_print(self, states, dq_ci=None) -> None: """ parameter @@ -211,7 +250,7 @@ def ts_print(self, states, dq_ci=None): x.align["cm"] = "r" x.align["eV"] = "r" print(x) - title = "TS_Cut_d%i_10Dq_%i_B_%i_C_%i.txt" % ( + title = "TS_Cut_d%i_10Dq_%i_B_%i_C_%i.csv" % ( self.d_count, dq_ci, self.B, @@ -221,9 +260,11 @@ def ts_print(self, states, dq_ci=None): np.savetxt( title, results.T, - delimiter="\t", - header="state\tcm\teV", - fmt="%s\t%i\t%.4f", + delimiter=",", + header="state,cm,eV", + fmt=r"%s,%i,%.4f", + # Remove # for comments + comments="", ) diff --git a/tanabesugano/test/test_front.py b/tanabesugano/test/test_front.py index 60dc7cb..ddf0935 100644 --- a/tanabesugano/test/test_front.py +++ b/tanabesugano/test/test_front.py @@ -1,6 +1,7 @@ -from tanabesugano import cmd as frontapp from typing import Any +from tanabesugano import cmd as frontapp + def test_frontapp(): return frontapp.CMDmain(