Bulk Modulus calculation:

- new bulk modulus analysis added
- some adaptation for io/input_file_reader
- tests for bulk modulus analysis added
- input file uses:
   - energy_perturbation_files: all energy files which show a small
     perturbations from the equilibrium volume, each file corrsponds to
     one perturbation.
   - volumes_perturbation: an array of all volumes that show a small
     perturbation from the equilibrium, each volume corrosponds with a
     energy file
  -  out_file: the name of the output file
  -  mode_file: is default simple. It is used to choose which kind of
     bulk modulus calculation is used:
        - simple: two point finite difference calculation (for 2 points)
        - BMEOS: Birch-Murnaghan equation of state fit (more than 2
          points)
        - MEOS: Murnaghan equation of state fit (more than 2 points) not
          implemented yet
  - info_file: filename for the info-file
  - log_file: filename for the log_file
- rudimentary tests are written

PQAnalysis/analysis/__init__.py

@@ -3,3 +3,4 @@
 """
 
 from .rdf import RDF, RDFInputFileReader, RDFDataWriter, RDFLogWriter, rdf
+from .bulk_modulus import BulkModulus, BulkModulusInputFileReader, BulkModulusDataWriter, BulkModulusLogWriter, bulk_modulus

PQAnalysis/analysis/bulk_modulus/__init__.py

@@ -0,0 +1,25 @@
+"""
+A package containing classes and functions to handle bulk modulus.
+
+Classes
+-------
+:py:class:`~PQAnalysis.analysis.bulk_modulus.bulk_modulus.BulkModulus`
+    A class to handle radial distribution functions.
+:py:class:`~PQAnalysis.analysis.bulk_modulus.bulk_modulusInputFileReader.BulkModulusInputFileReader`
+    A class to read bulk modulus from input files.
+:py:class:`~PQAnalysis.analysis.bulk_modulus.bulk_modulusOutputFileWriter.BulkModulusDataWriter`
+    A class to write bulk modulus to output files.
+:py:class:`~PQAnalysis.analysis.bulk_modulus.bulk_modulusOutputFileWriter.BulkModulusLogWriter`
+    A class to write log files.
+   
+Functions
+---------
+:py:func:`~PQAnalysis.analysis.bulk_modulus.bulk_modulus.bulk_modulus`
+    A function to create BulkModuluss from an input file. 
+"""
+
+from .api import bulk_modulus
+from .bulk_modulus import BulkModulus
+from .bulk_modulus_input_file_reader import BulkModulusInputFileReader
+from .bulk_modulus_output_file_writer import BulkModulusDataWriter, BulkModulusLogWriter
+from .exceptions import *

PQAnalysis/analysis/bulk_modulus/api.py

@@ -0,0 +1,134 @@
+"""
+This module provides API functions for bulk modulus analysis.
+"""
+import numpy as np
+from beartype.typing import List, Tuple
+
+from PQAnalysis.io.energy_file_reader import EnergyFileReader
+from PQAnalysis.traj import MDEngineFormat
+from PQAnalysis.type_checking import runtime_type_checking
+
+from PQAnalysis.types import Np1DNumberArray, Np2DNumberArray
+from .bulk_modulus import BulkModulus
+from .bulk_modulus_input_file_reader import BulkModulusInputFileReader
+from .bulk_modulus_output_file_writer import BulkModulusDataWriter
+from .bulk_modulus_output_file_writer import BulkModulusLogWriter
+
+
+@runtime_type_checking
+def bulk_modulus(input_file: str, md_format: MDEngineFormat | str = MDEngineFormat.PQ):
+    """
+    Calculates the bulk modulus using a given input file.
+
+    This is just a wrapper function combining the underlying classes and functions.
+
+    For more information on the input file keys please
+    visit
+    :py:mod:`~PQAnalysis.analysis.bulk_modulus.bulk_modulus_input_file_reader`.
+    For more information on the exact calculation of the thermal expansion coefficient please visit
+    :py:class:`~PQAnalysis.analysis.bulk_modulus.bulk_modulus.BulkModulus`.
+
+    Parameters
+    ----------
+    input_file : str
+        The input file. For more information on the input file
+        keys please visit
+        :py:mod:`~PQAnalysis.analysis.bulk_modulus.bulk_modulus_input_file_reader`.
+    md_format : MDEngineFormat | str, optional
+        the format of the input trajectory. Default is "PQ".
+        For more information on the supported formats please visit
+        :py:class:`~PQAnalysis.traj.formats.MDEngineFormat`.
+    """
+    md_format = MDEngineFormat(md_format)
+
+    input_reader = BulkModulusInputFileReader(input_file)
+    input_reader.read()
+
+    if input_reader.energy_perturbation_files is None:
+        raise ValueError(
+            "The energy perturbation files are required."
+        )
+
+    if md_format != MDEngineFormat.PQ:
+        use_info_file = True
+        info_file = input_reader.info_file
+
+    else:
+        info_file = input_reader.info_file
+        use_info_file = False
+
+    if (len(input_reader.energy_perturbation_files) == 0):
+        raise ValueError(
+            "The energy perturbation files are required."
+        )
+    if (len(input_reader.volumes_perturbation) == 0):
+        raise ValueError(
+            "The volumes perturbation are required."
+        )
+
+    if (len(input_reader.energy_perturbation_files) != len(input_reader.volumes_perturbation)):
+        raise ValueError(
+            "The number of energy perturbation files and volumes perturbation must be the same."
+        )
+
+    if (len(input_reader.energy_perturbation_files) == 1):
+        raise ValueError(
+            "At least two energy perturbation files are required."
+        )
+
+    if (len(input_reader.volumes_perturbation) == 1):
+        raise ValueError(
+            "At least two volumes perturbation are required."
+
+        )
+
+    pressures_perturbation = np.empty(
+        (len(input_reader.volumes_perturbation), 2))
+
+    for i, file in enumerate(input_reader.energy_perturbation_files):
+
+        energy_reader = EnergyFileReader(
+            filename=file,
+            info_filename=info_file,
+            use_info_file=use_info_file,
+            engine_format=md_format)
+        energy_data = energy_reader.read()
+        pressure_units = energy_data.units["PRESSURE"]
+        pressure_data = energy_data.data[energy_data.info["PRESSURE"]]
+        pressures_perturbation[i, 0] = np.average(pressure_data)
+        pressures_perturbation[i, 1] = np.std(pressure_data)
+
+    if input_reader.volumes_perturbation is None:
+        raise ValueError(
+            "The volumes perturbation must be provided."
+        )
+
+    if input_reader.volume_equilibrium is None:
+        raise ValueError(
+            "The equilibrium volume must be provided."
+        )
+
+    if input_reader.mode is None:
+        mode = "simple"
+    else:
+        mode = input_reader.mode
+
+    _bulk_modulus = BulkModulus(
+        pressures_perturbation=pressures_perturbation,
+        volumes_perturbation=np.array(input_reader.volumes_perturbation),
+        volume_equilibrium=input_reader.volume_equilibrium,
+        mode=mode
+    )
+
+    data_writer = BulkModulusDataWriter(
+        filename=input_reader.out_file_key
+    )
+
+    log_writer = BulkModulusLogWriter(filename=input_reader.log_file)
+
+    log_writer.write_before_run(_bulk_modulus)
+
+    bulk_modulus_data = _bulk_modulus.run()
+
+    data_writer.write(Tuple(bulk_modulus_data))
+    log_writer.write_after_run(_bulk_modulus, pressure_units)