Fix issues that occured when running ppafm-generate-elff with tip's d…

…ensity.

ppafm/HighLevel.py

@@ -295,15 +295,15 @@ def computeDFTD3(input_file, df_params="PBE", geometry_format=None, save_format=
     # Load atomic geometry
     atoms, nDim, lvec = io.loadGeometry(input_file, format=geometry_format, parameters=parameters)
     elem_dict = PPU.getFFdict(PPU.loadSpecies())
-    iZs, Rs, _ = PPU.parseAtoms(atoms, elem_dict, autogeom=False, PBC=parameters.PBC, lvec=lvec)
+    iZs, Rs, _ = PPU.parseAtoms(atoms, elem_dict, autogeom=False, PBC=parameters.PBC, lvec=lvec, parameters=parameters)
     iPP = PPU.atom2iZ(parameters.probeType, elem_dict)
 
     # Compute coefficients for each atom
     df_params = d3.get_df_params(df_params)
     coeffs = core.computeD3Coeffs(Rs, iZs, iPP, df_params)
 
     # Compute the force field
-    FF, V = prepareArrays(None, compute_energy)
+    FF, V = prepareArrays(None, compute_energy, parameters=parameters)
     core.setFF_shape(np.shape(FF), lvec, parameters=parameters)
     core.getDFTD3FF(shift_positions(Rs, -lvec[0]), coeffs)
 
@@ -364,15 +364,13 @@ def computeELFF_pointCharge(geomFile, geometry_format=None, tip="s", save_format
 
 
 def computeElFF(V, lvec, nDim, tip, computeVpot=False, tilt=0.0, sigma=None, deleteV=True, parameters=None):
-    if verbose > 0:
-        print(" ========= get electrostatic forcefiled from hartree ")
     rho = None
     multipole = None
     if sigma is None:
         sigma = parameters.sigma
-    if type(tip) is np.ndarray:
+    if isinstance(tip, (list, np.ndarray)):
         rho = tip
-    elif type(tip) is dict:
+    elif isinstance(tip, dict):
         multipole = tip
     else:
         if tip in {"s", "px", "py", "pz", "dx2", "dy2", "dz2", "dxy", "dxz", "dyz"}:
@@ -383,8 +381,6 @@ def computeElFF(V, lvec, nDim, tip, computeVpot=False, tilt=0.0, sigma=None, del
             if any(nDim_tip != nDim):
                 sys.exit("Error: Input file for tip charge density has been specified, but the dimensions are incompatible with the Hartree potential file!")
             rho *= -1  # Negative charge density from positive electron density
-    if verbose > 0:
-        print(" computing convolution with tip by FFT ")
     Fel_x, Fel_y, Fel_z, Vout = fFFT.potential2forces_mem(V, lvec, nDim, rho=rho, sigma=sigma, multipole=multipole, doPot=computeVpot, tilt=tilt, deleteV=deleteV)
     FFel = io.packVecGrid(Fel_x, Fel_y, Fel_z)
     del Fel_x, Fel_y, Fel_z
@@ -423,7 +419,7 @@ def _getAtomsWhichTouchPBCcell(Rs, elems, nDim, lvec, Rcut, bSaveDebug, fname=No
     return Rs_, elems
 
 
-def getAtomsWhichTouchPBCcell(fname, Rcut=1.0, bSaveDebug=True, geometry_format=None):
+def getAtomsWhichTouchPBCcell(fname, Rcut=1.0, bSaveDebug=True, geometry_format=None, parameters=None):
     atoms, nDim, lvec = io.loadGeometry(fname, format=geometry_format, parameters=parameters)
     Rs = np.array(atoms[1:4])  # get just positions x,y,z
     elems = np.array(atoms[0])

ppafm/cli/generateDFTD3.py

@@ -48,7 +48,7 @@ def main():
             sys.exit(1)
         df_params = args.df_name
 
-    computeDFTD3(args.input, df_params=df_params, geometry_format=args.input_format, save_format=args.output_format, compute_energy=args.energy)
+    computeDFTD3(args.input, df_params=df_params, geometry_format=args.input_format, save_format=args.output_format, compute_energy=args.energy, parameters=parameters)
 
 
 if __name__ == "__main__":

ppafm/cli/generateElFF.py

@@ -44,7 +44,7 @@ def main(argv=None):
         if args.tip_dens is None:
             raise Exception("Rcore>0 but no tip density provided!")
         valence_electrons_dictionary = loadValenceElectronDict()
-        rs_tip, elems_tip = getAtomsWhichTouchPBCcell(args.tip_dens, Rcut=args.Rcore)
+        rs_tip, elems_tip = getAtomsWhichTouchPBCcell(args.tip_dens, Rcut=args.Rcore, parameters=parameters)
 
     atoms_samp, _, lvec_samp = io.loadGeometry(args.input, format=args.input_format, parameters=parameters)
     head_samp = io.primcoords2Xsf(atoms_samp[0], [atoms_samp[1], atoms_samp[2], atoms_samp[3]], lvec_samp)