Modify some logging levels.

Author: NikoOinonen

ppafm/chemistry.py

@@ -75,10 +75,10 @@ def findTris(bonds, neighs):
                 common.append(i)
         ncm = len(common)
         if ncm > 2:
-            logger.debug(f"WARNING: bond {b} common neighbors {common}")
+            logger.warning(f"bond {b} common neighbors {common}")
             continue
         elif ncm < 1:
-            logger.debug(f"WARNING: bond {b} common neighbors {common}")
+            logger.warning(f"bond {b} common neighbors {common}")
             continue
         tri0 = tuple(sorted(b + (common[0],)))
         tris.add(tri0)
@@ -147,6 +147,7 @@ def removeBorderAtoms(ps, cog, R):
 def validBonds(bonds, mask, na):
     a2a = np.cumsum(mask) - 1
     bonds_ = []
+    logger.debug(f"validBonds mask: {mask}")
     for i, j in bonds:
         if mask[i] and mask[j]:
             bonds_.append((a2a[i], a2a[j]))

ppafm/cli/generateElFF.py

@@ -121,15 +121,15 @@ def main(argv=None):
             if parameters.probeType == "8":
                 drho_kpfm = {"pz": 0.045}
                 sigma = 0.48
-                logger.debug("Select CO-tip polarization ")
+                logger.info("Select CO-tip polarization ")
             if parameters.probeType == "47":
                 drho_kpfm = {"pz": 0.21875}
                 sigma = 0.7
-                logger.debug(f"Select Ag polarization with decay sigma {sigma}")
+                logger.info(f"Select Ag polarization with decay sigma {sigma}")
             if parameters.probeType == "54":
                 drho_kpfm = {"pz": 0.250}
                 sigma = 0.67
-                logger.debug("Select Xe-tip polarization")
+                logger.info("Select Xe-tip polarization")
         else:
             logger.error(f'Neither is "{args.KPFM_sample}" a density file with an appropriate ("{input_format}") format nor is it a valid name of a tip polarizability model.')
             sys.exit(1)

ppafm/cli/relaxed_scan.py

@@ -102,7 +102,7 @@ def main(argv=None):
     ff_vdw = ff_pauli = ff_electrostatics = ff_boltzman = ff_kpfm_t0sv = ff_kpfm_tvs0 = None
 
     if args.noLJ:
-        logger.debug(f"Apauli {parameters.Apauli}")
+        logger.info(f"Using separate Pauli and vdW force fields. Apauli: {parameters.Apauli}")
 
         logger.info("Loading Pauli force field from FFpauli_{x,y,z}")
         ff_pauli, lvec, _, atomic_info_or_head = io.load_vec_field("FFpauli", data_format=args.output_format)

ppafm/common.py

@@ -525,9 +525,9 @@ def autoGridN(parameters):
 # load atoms species parameters form a file ( currently used to load Lennard-Jones parameters )
 def loadSpecies(fname=None):
     if fname is None or not os.path.exists(fname):
-        logger.debug("WARNING: loadSpecies(None) => load default atomtypes.ini")
+        logger.debug("loadSpecies(None) => load default atomtypes.ini")
         fname = cpp_utils.PACKAGE_PATH / "defaults" / "atomtypes.ini"
-    logger.debug(f"loadSpecies from {fname}")
+    logger.info(f"loadSpecies from {fname}")
     # FFparams=np.genfromtxt(fname,dtype=[('rmin',np.float64),('epsilon',np.float64),('atom',int),('symbol', '|S10')],usecols=[0,1,2,3])
     FFparams = np.genfromtxt(
         fname,
@@ -828,12 +828,12 @@ def atoms2iZs(names, elem_dict):
 def parseAtoms(atoms, elem_dict, PBC=True, autogeom=False, lvec=None, parameters=None):
     Rs = np.array([atoms[1], atoms[2], atoms[3]])
     if elem_dict is None:
-        logger.debug("WARNING: elem_dict is None => iZs are zero")
+        logger.warning("elem_dict is None => iZs are zero")
         iZs = np.zeros(len(atoms[0]))
     else:
         iZs = atoms2iZs(atoms[0], elem_dict)
     if autogeom:
-        logger.debug("WARNING: autoGeom shifts atoms")
+        logger.warning("autoGeom shifts atoms")
         autoGeom(Rs, shiftXY=True, fitCell=True, border=3.0)
     Rs = np.transpose(Rs, (1, 0)).copy()
     Qs = np.array(atoms[4])

ppafm/fitSpline.py

@@ -265,6 +265,7 @@ def imfig(data, title):
     coefs3 = np.array([1.0, 4.0, 1.0]) / 6
 
     coefs6 = np.array([7.14285714e-03, 8.57142857e-01, 8.50714286e00, 1.72571429e01, 8.50714286e00, 8.57142857e-01, 7.14285714e-03]) / (2 * 1.72571429e01)
+    logger.debug(f"coeffs6: {coefs6}")
 
     coefs5 = np.array([0.1, 0.2, 0.4, 0.2, 0.1])