Remove params dictionary from common.py, continue replacements.

ppafm/HighLevel.py

@@ -167,7 +167,7 @@ def perform_relaxation(lvec, FFLJ, FFel=None, FFpauli=None, FFboltz=None, FFkpfm
         FF += FFboltz
     if bFFtotDebug:
         io.save_vec_field("FFtotDebug", FF, lvec)
-    core.setFF_shape(np.shape(FF), lvec)
+    core.setFF_shape(np.shape(FF), lvec, parameters=parameters)
     core.setFF_Fpointer(FF)
     if (np.array(parameters.stiffness) < 0.0).any():
         parameters.stiffness = np.array([parameters.klat, parameters.klat, parameters.krad])
@@ -237,7 +237,7 @@ def computeLJ(geomFile, speciesFile, geometry_format=None, save_format=None, com
     FF, V = prepareArrays(None, computeVpot, parameters=parameters)
     if verbose > 0:
         print("FFLJ.shape", FF.shape)
-    core.setFF_shape(np.shape(FF), lvec)
+    core.setFF_shape(np.shape(FF), lvec, parameters=parameters)
 
     # shift atoms to the coordinate system in which the grid origin is zero
     Rs0 = shift_positions(Rs, -lvec[0])
@@ -308,7 +308,7 @@ def computeDFTD3(input_file, df_params="PBE", geometry_format=None, save_format=
 
     # Compute the force field
     FF, V = prepareArrays(None, compute_energy)
-    core.setFF_shape(np.shape(FF), lvec)
+    core.setFF_shape(np.shape(FF), lvec, parameters=parameters)
     core.getDFTD3FF(shift_positions(Rs, -lvec[0]), coeffs)
 
     # Save to file
@@ -340,7 +340,7 @@ def computeELFF_pointCharge(geomFile, geometry_format=None, tip="s", save_format
         print(parameters.gridN, parameters.gridA, parameters.gridB, parameters.gridC)
     _, Rs, Qs = PPU.parseAtoms(atoms, elem_dict=elem_dict, autogeom=False, PBC=parameters.PBC, lvec=lvec, parameters=parameters)
     FF, V = prepareArrays(None, computeVpot, parameters=parameters)
-    core.setFF_shape(np.shape(FF), lvec)
+    core.setFF_shape(np.shape(FF), lvec, parameters=parameters)
 
     # shift atoms to the coordinate system in which the grid origin is zero
     Rs0 = shift_positions(Rs, -lvec[0])
@@ -435,7 +435,9 @@ def getAtomsWhichTouchPBCcell(fname, Rcut=1.0, bSaveDebug=True, geometry_format=
     return Rs, elems
 
 
-def subtractCoreDensities(rho, lvec, elems=None, Rs=None, fname=None, valElDict=None, Rcore=0.7, bSaveDebugDens=False, bSaveDebugGeom=True, head=io.XSF_HEAD_DEFAULT):
+def subtractCoreDensities(
+    rho, lvec, elems=None, Rs=None, fname=None, valElDict=None, Rcore=0.7, bSaveDebugDens=False, bSaveDebugGeom=True, head=io.XSF_HEAD_DEFAULT, parameters=None
+):
     nDim = rho.shape
     if fname is not None:
         elems, Rs = getAtomsWhichTouchPBCcell(fname, Rcut=Rcore, bSaveDebug=bSaveDebugDens)
@@ -451,7 +453,7 @@ def subtractCoreDensities(rho, lvec, elems=None, Rs=None, fname=None, valElDict=
         print("V : ", V, " N: ", N, " dV: ", dV)
     if verbose > 0:
         print("sum(RHO): ", rho.sum(), " Nelec: ", rho.sum() * dV, " voxel volume: ", dV)  # check sum
-    core.setFF_shape(rho.shape, lvec)  # set grid sampling dimension and shape
+    core.setFF_shape(rho.shape, lvec, parameters=parameters)  # set grid sampling dimension and shape
     core.setFF_Epointer(rho)  # set pointer to array with density data (to write into)
     if verbose > 0:
         print(">>> Projecting Core Densities ... ")

ppafm/cli/generateTraining_PVE.py

@@ -40,7 +40,7 @@
 force_field, _ = prepareArrays(None, False)
 
 print("FFLJ.shape", force_field.shape)
-core.setFF_shape(np.shape(force_field), lvec_t)
+core.setFF_shape(np.shape(force_field), lvec_t, parameters=parameters)
 
 base_dir = os.getcwd()
 paths = ["out1", "out2"]

ppafm/common.py

@@ -76,58 +76,6 @@ class Config:
         validate_assignment = True
 
 
-# fmt: off
-# default parameters of simulation
-params = {
-    "PBC": True,
-    "nPBC": np.array([1, 1, 1]),
-    "gridN": np.array([-1, -1, -1]).astype(int),
-    "gridO": np.array([0.0, 0.0, 0.0]),
-    "gridA": np.array([0.0, 0.0, 0.0]),
-    "gridB": np.array([0.0, 0.0, 0.0]),
-    "gridC": np.array([0.0, 0.0, 0.0]),
-    "FFgrid0": np.array([-1.0, -1.0, -1.0]),
-    "FFgridA": np.array([-1.0, -1.0, -1.0]),
-    "FFgridB": np.array([-1.0, -1.0, -1.0]),
-    "FFgridC": np.array([-1.0, -1.0, -1.0]),
-    "moleculeShift": np.array([0.0, 0.0, 0.0]),
-    "probeType": "O",
-    "charge": 0.00,
-    "Apauli": 18.0,
-    "Bpauli": 1.0,
-    "ffModel": "LJ",
-    "Rcore": 0.7,
-    "r0Probe": np.array([0.00, 0.00, 4.00]),
-    "stiffness": np.array([-1.0, -1.0, -1.0]),
-    "klat": 0.5,
-    "krad": 20.00,
-    "tip": "s",
-    "sigma": 0.7,
-    "scanStep": np.array([0.10, 0.10, 0.10]),
-    "scanMin": np.array([0.0, 0.0, 5.0]),
-    "scanMax": np.array([20.0, 20.0, 8.0]),
-    "scanTilt": np.array([0.0, 0.0, -0.1]),
-    "tiltedScan": False,
-    "kCantilever": 1800.0,
-    "f0Cantilever": 30300.0,
-    "Amplitude": 1.0,
-    "plotSliceFrom": 16,
-    "plotSliceTo": 22,
-    "plotSliceBy": 1,
-    "imageInterpolation": "bicubic",
-    "colorscale": "gray",
-    "colorscale_kpfm": "seismic",
-    "ddisp": 0.05,
-    "aMorse": -1.6,
-    "tip_base": np.array(["None", 0.00]),
-    "Rtip": 30.0,
-    "permit": 0.00552634959,
-    "vdWDampKind": 2,
-    "#": None,
-}
-# fmt: on
-
-
 class CLIParser(ArgumentParser):
     """
     Subclass from the built-in ArgumentParser with functionality to easily add arguments commonly used in ppafm scripts.
@@ -163,7 +111,7 @@ class CLIParser(ArgumentParser):
         "Rcore": {
             "action": "store",
             "type": float,
-            "default": params["Rcore"],
+            "default": 0.7,
             "help": "Width of nuclear charge density blob to achieve charge neutrality [Å]",
         },
         "sigma": {
@@ -261,7 +209,7 @@ class CLIParser(ArgumentParser):
 
     def _check_params_args(self):
         for arg in self._params_args:
-            if arg not in params:
+            if arg not in PpafmParameters.model_filds:
                 raise ValueError(f"Argument name `{arg}` does not match with any parameter in global parameters dictionary.")
 
     @property
@@ -555,11 +503,11 @@ def loadParams(fname, parameters):
 
     parameters.tip = parameters.tip.replace('"', "")
     parameters.tip = parameters.tip.replace("'", "")
-    ### necessary for working even with quotemarks in params.ini
+    # 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("'", "")
-    ### necessary for working even with quotemarks in params.ini
-    print("Loaded parameters from ", fname)
+    if verbose > 0:
+        print("Loaded parameters from ", fname)
 
 
 def apply_options(opt, parameters):
@@ -572,7 +520,7 @@ def apply_options(opt, parameters):
             continue
         if hasattr(parameters, key):
             setattr(parameters, key, value)
-            if key == "klat" and params["stiffness"][0] > 0.0:
+            if key == "klat" and parameters.stiffness[0] > 0.0:
                 print("Overriding stiffness parameter with klat")
                 parameters.stiffness = np.array([-1.0, -1.0, -1.0])  # klat overrides stiffness
             if verbose > 0:
@@ -604,14 +552,14 @@ def loadSpecies(fname=None):
 
 # load atoms species parameters form a file ( currently used to load Lennard-Jones parameters )
 def loadSpeciesLines(lines):
-    params = []
+    parameters = []
     for l in lines:
         l = l.split()
         if len(l) >= 5:
             # print l
-            params.append((float(l[0]), float(l[1]), float(l[2]), int(l[3]), l[4]))
+            parameters.append((float(l[0]), float(l[1]), float(l[2]), int(l[3]), l[4]))
     return np.array(
-        params,
+        parameters,
         dtype=[
             ("rmin", np.float64),
             ("epsilon", np.float64),

ppafm/core.py

@@ -41,13 +41,13 @@ def setGridN(n):
 lib.setGridCell.restype = None
 
 
-def setGridCell(cell=None):
+def setGridCell(cell=None, parameters=None):
     if cell is None:
         cell = np.array(
             [
-                PPU.params["gridA"],
-                PPU.params["gridB"],
-                PPU.params["gridC"],
+                parameters.gridA,
+                parameters.gridB,
+                parameters.gridC,
             ],
             dtype=np.float64,
         ).copy()
@@ -63,10 +63,10 @@ def setGridCell(cell=None):
     lib.setGridCell(cell)
 
 
-def setFF_shape(n_, cell):
+def setFF_shape(n_, cell, parameters=None):
     n = np.array(n_).astype(np.int32)
     lib.setGridN(n)
-    setGridCell(cell)
+    setGridCell(cell, parameters=parameters)
 
 
 # void setFF_pointer( double * gridF, double * gridE  )
@@ -87,7 +87,7 @@ def setFF_Epointer(gridE):
     lib.setFF_Epointer(gridE)
 
 
-def setFF(cell=None, gridF=None, gridE=None):
+def setFF(cell=None, gridF=None, gridE=None, parameters=None):
     n_ = None
     if gridF is not None:
         setFF_Fpointer(gridF)
@@ -98,14 +98,14 @@ def setFF(cell=None, gridF=None, gridE=None):
     if cell is None:
         cell = np.array(
             [
-                PPU.params["gridA"],
-                PPU.params["gridB"],
-                PPU.params["gridC"],
+                parameters.gridA,
+                parameters.gridB,
+                parameters.gridC,
             ]
         ).copy()
     if n_ is not None:
         print("setFF() n_ : ", n_)
-        setFF_shape(n_, cell)
+        setFF_shape(n_, cell, parameters=parameters)
     else:
         "Warrning : setFF shape not set !!!"
 
@@ -133,15 +133,15 @@ def setFIRE(finc=1.1, fdec=0.5, falpha=0.99):
 lib.setTip.restype = None
 
 
-def setTip(lRadial=None, kRadial=None, rPP0=None, kSpring=None):
+def setTip(lRadial=None, kRadial=None, rPP0=None, kSpring=None, parameters=None):
     if lRadial is None:
-        lRadial = PPU.params["r0Probe"][2]
+        lRadial = parameters.r0Probe[2]
     if kRadial is None:
-        kRadial = PPU.params["krad"] / -PPU.eVA_Nm
+        kRadial = parameters.krad / -PPU.eVA_Nm
     if rPP0 is None:
-        rPP0 = np.array((PPU.params["r0Probe"][0], PPU.params["r0Probe"][1], 0.0))
+        rPP0 = np.array((parameters.r0Probe[0], parameters.r0Probe[1], 0.0))
     if kSpring is None:
-        kSpring = np.array((PPU.params["klat"], PPU.params["klat"], 0.0)) / -PPU.eVA_Nm
+        kSpring = np.array((parameters.klat, parameters.klat, 0.0)) / -PPU.eVA_Nm
     print(" IN setTip !!!!!!!!!!!!!! ")
     print(" lRadial ", lRadial)
     print(" kRadial ", kRadial)
@@ -259,10 +259,10 @@ def computeD3Coeffs(Rs, iZs, iZPP, df_params):
 lib.getMorseFF.restype = None
 
 
-def getMorseFF(Rs, REs, alpha=None):
+def getMorseFF(Rs, REs, alpha=None, parameters=None):
     if alpha is None:
-        alpha = PPU.params["aMorse"]
-    print("getMorseFF: alpha: %g [1/A] ", alpha)
+        alpha = parameters.aMorse
+    print(f"getMorseFF: alpha: {alpha} [1/A] ")
     natom = len(Rs)
     lib.getMorseFF(natom, Rs, REs, alpha)
 

tests/human_eye/test_TipForce.py

@@ -5,7 +5,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
-import ppafm.core as PPC
+from ppafm import common, core
 
 spline_ini = """
 0.0   0.4 -0.1
@@ -17,16 +17,18 @@
 # S = np.genfromtxt('TipRSpline.ini')
 S = np.genfromtxt(StringIO(spline_ini), skip_header=1)
 
+parameters = common.PppParameters()
+
 print("TipRSpline.ini overrides harmonic tip")
 xs = S[:, 0].copy()
 print("xs: ", xs)
 ydys = S[:, 1:].copy()
 print("ydys: ", ydys)
 plt.plot(xs, ydys[:, 0], "o")
 plt.plot(xs, ydys[:, 0] + ydys[:, 1], ".")
-PPC.setTipSpline(xs, ydys)
+core.setTipSpline(xs, ydys)
 
-PPC.setTip()
+core.setTip()
 
 fs = np.zeros((60, 3))
 r0 = np.array([0.0, 0.0, 0.5])
@@ -35,12 +37,12 @@
 xs = np.array(list(range(len(fs)))) * dr[2] + r0[2]
 # print "xs=",xs
 
-print(">>>  PPC.test_force( 1, r0, dr, R, fs )")
-PPC.test_force(1, r0, dr, R, fs)
+print(">>>  core.test_force( 1, r0, dr, R, fs )")
+core.test_force(1, r0, dr, R, fs)
 plt.plot(xs, fs[:, 2])
 
-print(">>>  PPC.test_force( 2, r0, dr, R, fs )")
-PPC.test_force(2, r0, dr, R, fs)
+print(">>>  core.test_force( 2, r0, dr, R, fs )")
+core.test_force(2, r0, dr, R, fs)
 plt.plot(xs, fs[:, 2])
 
 # print "fs:", fs

tests/test_io.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-
 import os
 
 import numpy as np
@@ -61,9 +60,10 @@ def test_parse_comment_ase():
 
 
 def test_load_aims():
-    from ppafm.common import params
+    from ppafm import common
     from ppafm.io import loadGeometry
 
+    parameters = common.PpafmParameters()
     temp_file = "temp_geom.in"
     geometry_str = """
         lattice_vector 4.0 0.0 0.0
@@ -76,7 +76,7 @@ def test_load_aims():
     with open(temp_file, "w") as f:
         f.write(geometry_str)
 
-    atoms, nDim, lvec = loadGeometry(temp_file, params=params)
+    atoms, nDim, lvec = loadGeometry(temp_file, parameters=parameters)
 
     assert np.allclose(
         atoms,
@@ -90,7 +90,7 @@ def test_load_aims():
             ]
         ),
     )
-    assert np.allclose(nDim, params["gridN"])
+    assert np.allclose(nDim, parameters.gridN)
     assert np.allclose(lvec, np.array([[0.0, 0.0, 0.0], [4.0, 0.0, 0.0], [1.0, 5.0, 0.0], [0.0, 0.0, 6.0]]))
 
     os.remove(temp_file)