Make loadParams part of the PpafmParameters dataclass

Also, implement `from_file` class method.

ppafm/cli/fitting/fitting.py

@@ -61,9 +61,8 @@ def getFzlist(BIGarray, MIN, MAX, points):
     raise ValueError('Please provide the file "atomtypes.ini"')
 
 
-parameters = common.PpafmParameters()
+parameters = common.PpafmParameters.from_file("params.ini")
 print(" >> OVEWRITING SETTINGS by params.ini  ")
-common.loadParams("params.ini", parameters=parameters)
 scan_min = parameters.scanMin
 scan_max = parameters.scanMax
 atoms, nDim, lvec = io.loadGeometry("p_eq.xyz", parameters=parameters)

ppafm/cli/fitting/plotLine.py

@@ -59,8 +59,7 @@ def selectLine(BIGarray, MIN, MAX, startingPoint, endPoint, nsteps):
 if options.points == []:
     sys.exit("Error!! The '-p' or '--points' argument is required\npython plotLine.py -p XMINxYMINxZMIN XMAXxYMAXxZMAX")
 
-parameters = common.PpafmParameters()
-common.loadParams("params.ini", parameters=parameters)
+parameters = common.PpafmParameters.from_file("params.ini")
 if os.path.isfile("atomtypes.ini"):
     print(">> LOADING LOCAL atomtypes.ini")
     FFparams = common.loadSpecies("atomtypes.ini")

ppafm/cli/fitting/plotZ.py

@@ -54,9 +54,7 @@ def find_minimum(array, precision=0.0001):
     sys.exit(HELP_MSG)
 
 print(" >> OVEWRITING SETTINGS by params.ini  ")
-parameters = common.PpafmParameters()
-
-common.loadParams("params.ini", parameters=parameters)
+parameters = common.PpafmParameters.from_file("params.ini")
 dz = parameters.scanStep[2]
 Amp = [parameters.Amplitude]
 scan_max = parameters.scanMax[2]

ppafm/cli/generateDFTD3.py

@@ -34,14 +34,10 @@ def main():
     )
     args = parser.parse_args()
 
-    try:
-        # Try overwriting global parameters with params.ini file.
-        common.loadParams("params.ini")
-    except Exception:
-        print("No params.ini provided => using default parameters.")
+    parameters = common.PpafmParameters.from_file("params.ini")
 
     # Overwrite global parameters with command line arguments.
-    common.apply_options(vars(args))
+    common.apply_options(vars(args), parameters=parameters)
 
     if args.df_params is not None:
         p = args.df_params

ppafm/cli/generateElFF.py

@@ -32,8 +32,7 @@ def main(argv=None):
     args = parser.parse_args(argv)
 
     # Load parameters.
-    parameters = common.PpafmParameters()
-    common.loadParams("params.ini", parameters)
+    parameters = common.PpafmParameters.from_file("params.ini")
     common.apply_options(vars(args), parameters)
 
     # Load species.

ppafm/cli/generateElFF_point_charges.py

@@ -8,8 +8,7 @@ def main(argv=None):
     parser = common.CLIParser(description="Generate electrostatic force field by Coulomb interaction of point charges. The generated force field is saved to FFel_{x,y,z}.[ext].")
     parser.add_arguments(["input", "input_format", "output_format", "tip", "energy", "noPBC"])
     args = parser.parse_args(argv)
-    parameters = common.PpafmParameters()
-    common.loadParams("params.ini", parameters=parameters)
+    parameters = common.PpafmParameters.from_file("params.ini")
     common.apply_options(vars(args), parameters=parameters)
 
     computeELFF_pointCharge(args.input, geometry_format=args.input_format, tip=args.tip, save_format=args.output_format, computeVpot=args.energy, parameters=parameters)

ppafm/cli/generateLJFF.py

@@ -9,8 +9,7 @@ def main(argv=None):
     parser = common.CLIParser(description="Generate a Lennard-Jones, Morse, or vdW force field. The generated force field is saved to FFLJ_{x,y,z}.[ext].")
     parser.add_arguments(["input", "input_format", "output_format", "ffModel", "energy", "noPBC"])
     args = parser.parse_args(argv)
-    parameters = common.PpafmParameters()
-    common.loadParams("params.ini", parameters)
+    parameters = common.PpafmParameters.from_file("params.ini")
     common.apply_options(vars(args), parameters)
     species_file = "atomtypes.ini" if Path("atomtypes.ini").is_file() else None
     computeLJ(

ppafm/cli/generateTraining_PVE.py

@@ -13,10 +13,7 @@
 
 file_format = "xsf"
 
-parameters = common.PpafmParameters()
-
-# Arguments definition.
-common.loadParams("params.ini", parameters)
+parameters = common.PpafmParameters.from_file("params.ini")
 
 if os.path.isfile("atomtypes.ini"):
     print(">> LOADING LOCAL atomtypes.ini")

ppafm/cli/plot_results.py

@@ -36,12 +36,11 @@ def main(argv=None):
     parser.add_argument( "--bI",        action="store_true",                           help="Plot images for Boltzmann current"    )
     # fmt: on
 
-    parameters = common.PpafmParameters()
+    parameters = common.PpafmParameters.from_file("params.ini")
 
     args = parser.parse_args(argv)
     opt_dict = vars(args)
 
-    common.loadParams("params.ini", parameters)
     common.apply_options(opt_dict, parameters)
 
     if opt_dict["Laplace"]:

ppafm/cli/relaxed_scan.py

@@ -47,11 +47,10 @@ def main(argv=None):
     parser.add_argument("--pol_s",          action="store",      type=float, default=1.0, help="Scaling factor for sample polarization")
     # fmt: on
 
-    parameters = common.PpafmParameters()
+    parameters = common.PpafmParameters.from_file("params.ini")
 
     args = parser.parse_args(argv)
     opt_dict = vars(args)
-    common.loadParams("params.ini", parameters)
     common.apply_options(opt_dict, parameters)
 
     # =============== Setup

ppafm/cli/utilities/evalFFLine.py

@@ -77,9 +77,7 @@ def getLines(lst, atoms):
 
 # ======== main
 
-parameters = common.PpafmParameters()
-
-PPU.loadParams("params.ini")
+parameters = common.PpafmParameters.from_file("params.ini")
 FFparams = PPU.loadSpecies("atomtypes.ini", parameters=parameters)
 elem_dict = PPU.getFFdict(FFparams)
 print(elem_dict)

ppafm/common.py

@@ -3,9 +3,12 @@
 import os
 import typing
 from argparse import ArgumentParser
+from pathlib import Path
 
 import numpy as np
 import pydantic
+import toml
+import yaml
 
 from . import cpp_utils
 
@@ -75,6 +78,98 @@ class Config:
         arbitrary_types_allowed = True
         validate_assignment = True
 
+    @classmethod
+    def from_file(cls, file_path: typing.Union[str, Path] = Path("params.ini")):
+        """Load parameters from a file."""
+        file_path = Path(file_path)
+        object = cls()
+        suffix = file_path.suffix
+        try:
+            with open(file_path) as file:
+                if suffix == ".ini":
+                    lines = file.readlines()
+                    object.load_ini(lines)
+                elif suffix == ".yaml":
+                    object.parse_obj(yaml.safe_load(file))
+                elif suffix == ".toml":
+                    object.parse_obj(toml.load(file))
+                else:
+                    raise ValueError(f"Unsupported file extension: {suffix}")
+        except FileNotFoundError:
+            raise ValueError(f"File {file_path} not found")
+        return object
+
+    def parse_obj(self, obj):
+        for key, value in obj.items():
+            setattr(self, key, value)
+
+    def dump_parameters(self, file_path: typing.Union[str, Path] = Path("params.ini")):
+        """Save parameters to a file."""
+        file_path = Path(file_path)
+        suffix = file_path.suffix
+        try:
+            with open(file_path, "w") as file:
+                if suffix == ".yaml":
+                    yaml.dump(self.model_dump(), file, default_flow_style=False, indent=4)
+                elif suffix == ".toml":
+                    toml.dump(self.model_dump(), file)
+                else:
+                    raise ValueError(f"Unsupported file extension: {suffix}")
+        except FileNotFoundError:
+            raise ValueError(f"File {file_path} not found")
+
+    def load_ini(self, lines):
+        for line in lines:
+            words = line.split()
+            if len(words) >= 2:
+                key = words[0]
+                if hasattr(self, key):
+                    val = getattr(self, key)
+                    if key[0][0] == "#":
+                        continue
+                    if verbose > 0:
+                        print(key, " is class ", val.__class__)
+                    if isinstance(val, bool):
+                        word = words[1].strip()
+                        setattr(self, key, word[0] == "T" or word[0] == "t")
+                        if verbose > 0:
+                            print(key, getattr(self, key), ">>", word, "<<")
+                    elif isinstance(val, float):
+                        setattr(self, key, float(words[1]))
+                        if verbose > 0:
+                            print(key, getattr(self, key), words[1])
+                    elif isinstance(val, int):
+                        setattr(self, key, int(words[1]))
+                        if verbose > 0:
+                            print(key, getattr(self, key), words[1])
+                    elif isinstance(val, str):
+                        setattr(self, key, words[1])
+                    elif isinstance(val, list):
+                        if isinstance(val[0], float):
+                            setattr(self, key, [float(words[1]), float(words[2]), float(words[3])])
+                            if verbose > 0:
+                                print(key, getattr(self, key), words[1], words[2], words[3])
+                        elif isinstance(val[0], int):
+                            if verbose > 0:
+                                print(key)
+                            setattr(self, key, [int(words[1]), int(words[2]), int(words[3])])
+                            if verbose > 0:
+                                print(key, getattr(self, key), words[1], words[2], words[3])
+                        else:
+                            setattr(self, key, [str(words[1]), float(words[2])])
+                            if verbose > 0:
+                                print(key, getattr(self, key), words[1], words[2])
+                else:
+                    raise ValueError(f"Parameter {key} is not known")
+        if self.gridN[0] <= 0:
+            autoGridN(parameters=self)
+
+        self.tip = self.tip.replace('"', "")
+        self.tip = self.tip.replace("'", "")
+        # Necessary for working even with quotemarks in params.ini
+        self.tip_base[0] = self.tip_base[0].replace('"', "")
+        self.tip_base[0] = self.tip_base[0].replace("'", "")
+
 
 class CLIParser(ArgumentParser):
     """
@@ -436,66 +531,6 @@ def autoGridN(parameters):
     return parameters.gridN
 
 
-# overide default parameters by parameters read from a file
-def loadParams(fname, parameters):
-    if verbose > 0:
-        print(" >> OVERWRITING SETTINGS by " + fname)
-    fin = open(fname)
-    for line in fin:
-        words = line.split()
-        if len(words) >= 2:
-            key = words[0]
-            if hasattr(parameters, key):
-                val = getattr(parameters, key)
-                if key[0][0] == "#":
-                    continue
-                if verbose > 0:
-                    print(key, " is class ", val.__class__)
-                if isinstance(val, bool):
-                    word = words[1].strip()
-                    setattr(parameters, key, word[0] == "T" or word[0] == "t")
-                    if verbose > 0:
-                        print(key, getattr(parameters, key), ">>", word, "<<")
-                elif isinstance(val, float):
-                    setattr(parameters, key, float(words[1]))
-                    if verbose > 0:
-                        print(key, getattr(parameters, key), words[1])
-                elif isinstance(val, int):
-                    setattr(parameters, key, int(words[1]))
-                    if verbose > 0:
-                        print(key, getattr(parameters, key), words[1])
-                elif isinstance(val, str):
-                    setattr(parameters, key, words[1])
-                elif isinstance(val, list):
-                    if isinstance(val[0], float):
-                        setattr(parameters, key, [float(words[1]), float(words[2]), float(words[3])])
-                        if verbose > 0:
-                            print(key, getattr(parameters, key), words[1], words[2], words[3])
-                    elif isinstance(val[0], int):
-                        if verbose > 0:
-                            print(key)
-                        setattr(parameters, key, [int(words[1]), int(words[2]), int(words[3])])
-                        if verbose > 0:
-                            print(key, getattr(parameters, key), words[1], words[2], words[3])
-                    else:
-                        setattr(parameters, key, [str(words[1]), float(words[2])])
-                        if verbose > 0:
-                            print(key, getattr(parameters, key), words[1], words[2])
-            else:
-                raise ValueError(f"Parameter {key} is not known")
-    fin.close()
-    if parameters.gridN[0] <= 0:
-        autoGridN(parameters=parameters)
-
-    parameters.tip = parameters.tip.replace('"', "")
-    parameters.tip = parameters.tip.replace("'", "")
-    # Necessary for working even with quotemarks in params.ini
-    parameters.tip_base[0] = parameters.tip_base[0].replace('"', "")
-    parameters.tip_base[0] = parameters.tip_base[0].replace("'", "")
-    if verbose > 0:
-        print("Loaded parameters from ", fname)
-
-
 def apply_options(opt, parameters):
     if verbose > 0:
         print("!!!! OVERRIDE parameters !!!! in Apply options:")

ppafm/ocl/AFMulator.py

@@ -657,8 +657,7 @@ def plot_images(self, X, outdir="afm_images", prefix="df"):
 
 def _get_params(file_path):
     """Get AFMulator arguments from a params.ini file."""
-    parameters = common.PpafmParameters()
-    common.loadParams(file_path, parameters=parameters)
+    parameters = common.PpafmParameters.from_file(file_path)
     lvec = np.array(
         [
             parameters.FFgrid0,