Oscillator strength direct additions

repsample_acetylcall.py

@@ -30,18 +30,11 @@
 
 oscillator_strengths_array = np.array(oscillator_strengths)
 excitation_energies_cm_array = np.array(excitation_energies_cm)
-excitation_energies_ev_array = excitation_energies_cm_array*(0.0001239841984)
+excitation_energies_ev_array = excitation_energies_cm_array * 0.0001239841984
 
-excitation_energies_help_array = excitation_energies_ev_array/27.211396
-tdpx = np.sqrt((3*oscillator_strengths_array)/(2*excitation_energies_help_array))
-
-trans_dip_mom_y = np.zeros((2000,3))
-trans_dip_mom_z = np.zeros((2000,3))
-
-MYGEOM = rstd.GeomReduction(2000, 3, 20, 1000, 8, 16, weighted=True, pdfcomp = "KLdiv", intweights=False, verbose=False, dim1=False) #create an instance of GeomReduction with specified parameters: 500 samples, 3 states, 20 representative molecules, 100 cycles, 1 core, 1 job, without weighting, using KL divergence for PDF comparison, no integer weights, and verbose off
+MYGEOM = rstd.GeomReduction(2000, 3, 5, 1000, 8, 16, weighted=True, pdfcomp = "KLdiv", intweights=False, verbose=False, dim1=False) #create an instance of GeomReduction with specified parameters: 500 samples, 3 states, 20 representative molecules, 100 cycles, 1 core, 1 job, without weighting, using KL divergence for PDF comparison, no integer weights, and verbose off
 
 np.random.seed(42) #set the seed for reproducibility
 
-
-MYGEOM.read_data_direct(excitation_energies_ev_array, tdpx, trans_dip_mom_y, trans_dip_mom_z) #directly feed the generated data into the GeomReduction instance
+MYGEOM.read_data_direct_osc(excitation_energies_ev_array, oscillator_strengths_array) #directly feed the generated data into the GeomReduction instance
 MYGEOM.reduce_geoms() #start the geometry reduction process to select representative geometries

src/pyneapples/rep_sampler_2d.py

@@ -212,6 +212,19 @@ def read_data_direct(self, excitation_energies, transition_dipole_moments_x, tra
         self.weights = self.exc*self.trans   #calculate the weight for each transition as the product of excitation energy and the (summed) dipole moment
         self.wnorms = np.sum(self.weights, axis=0)/np.sum(self.weights) #provides a normalization factor for each state, ensuring that the weights are comparable across states
 
+    def read_data_direct_osc(self, excitation_energies, oscillator_stregths):
+
+        evs_in_au = 27.211396 # Conversion factor from electronvolts to atomic units
+
+        self.infile = "Test_Filename"   #stores the filename
+        self.exc = excitation_energies # Assign excitation energies in eV units
+        self.time = datetime.datetime.now() #records the current date and time
+
+        self.trans = abs((3*oscillator_stregths)/(2*(self.exc/evs_in_au)))  # Calculate transition dipole moment scaler value (as above) using energy in a.u.
+
+        self.weights = self.exc*self.trans   #calculate the weight for each transition as the product of excitation energy and the (summed) dipole moment
+        self.wnorms = np.sum(self.weights, axis=0)/np.sum(self.weights) #provides a normalization factor for each state, ensuring that the weights are comparable across states
+
 
     def read_data(self, infile):
         """Reads and parses input data from given input file."""