pyphyschemtools 0.1.0__py3-none-any.whl

pyphyschemtools/spectra.py

@@ -0,0 +1,451 @@
+############################################################
+#                       Absorption spectra
+############################################################
+from .visualID_Eng import fg, bg, hl
+from .core import centerTitle, centertxt
+
+import numpy as np
+import matplotlib.pyplot as plt
+import scipy.constants as sc
+
+class SpectrumSimulator:
+
+    def __init__(self, sigma_ev=0.3, plotWH=(12,8), \
+                 fontSize_axisText=14, fontSize_axisLabels=14, fontSize_legends=12,
+                 fontsize_peaks=12,
+                 colorS='#3e89be',colorVT='#469cd6'
+                ):
+        """
+        Initializes the spectrum simulator
+
+        Args:
+            - sigma_ev (float): Gaussian half-width at half-maximum in electron-volts (eV).
+                                Default is 0.3 eV (GaussView default is 0.4 eV).
+            - plotWH (tuple(int,int)): Width and Height of the matplotlib figures in inches. Default is (12,8).
+            - colorS: color of the simulated spectrum (default ='#3e89be')
+            - colorVT: color of the vertical transition line (default = '#469cd6')
+
+        Returns:
+            None: This method initializes the instance attributes.
+        Calculates:
+            - sigmanm = half-width of the Gaussian band, in nm
+        """
+        self.sigma_ev = sigma_ev
+        # Conversion constante eV -> nm sigma
+        self.ev2nm_const = (sc.h * sc.c) * 1e9 / sc.e
+        self.sigmanm = self.ev2nm_const / self.sigma_ev
+        self.plotW = plotWH[0]
+        self.plotH = plotWH[1]
+        self.colorS = colorS
+        self.colorVT = colorVT
+        self.fig = None
+        self.graph = None
+        self.fontSize_axisText = fontSize_axisText
+        self.fontSize_axisLabels = fontSize_axisLabels
+        self.fontSize_legends = fontSize_legends
+        self.fontsize_peaks = fontsize_peaks
+
+        print(f"sigma = {sigma_ev} eV -> sigmanm = {self.sigmanm:.1f} nm")
+    
+    def _initializePlot(self):
+        fig, graph = plt.subplots(figsize=(self.plotW,self.plotH))
+        plt.subplots_adjust(wspace=0)
+        plt.xticks(fontsize=self.fontSize_axisText,fontweight='bold')
+        plt.yticks(fontsize=self.fontSize_axisText,fontweight='bold')
+        return fig, graph
+    
+    def _calc_epsiG(self,lambdaX,lambdai,fi):
+        '''
+        calculates a Gaussian band shape around a vertical transition
+        input:
+            - lambdaX = wavelength variable, in nm
+            - lambdai = vertical excitation wavelength for i_th state, in nm
+            - fi = oscillator strength for state i (dimensionless)
+        output :
+            molar absorption coefficient, in L mol-1 cm-1
+        '''
+        import scipy.constants as sc
+        import numpy as np
+        c = sc.c*1e2 #cm-1
+        NA = sc.N_A #mol-1
+        me = sc.m_e*1000 #g
+        e = sc.e*sc.c*10 #elementary charge in esu 
+        pf = np.sqrt(np.pi)*e**2*NA/(1000*np.log(10)*c**2*me)
+        nubarX = 1e7 / lambdaX # nm to cm-1
+        nubari = 1e7 / lambdai
+        sigmabar = 1e7 / self.sigmanm
+        epsi = pf * (fi / sigmabar) * np.exp(-((nubarX - nubari)/sigmabar)**2)
+        return epsi
+    
+    def _Absorbance(self,eps,opl,cc):
+        '''
+        Calculates the Absorbance with the Beer-Lambert law
+        input:
+            - eps = molar absorption coefficient, in L mol-1 cm-1
+            - opl = optical path length, in cm
+            - cc = concentration of the attenuating species, in mol.L-1
+        output :
+            Absorbance, A (dimensionless)
+        '''
+        return eps*opl*cc
+    
+    def _sumStatesWithGf(self,wavel,wavelTAB,feTAB):
+        '''
+        '''
+        import numpy as np
+        sumInt = np.zeros(len(wavel))
+        for l in wavel:
+            for i in range(len(wavelTAB)):
+                sumInt[np.argwhere(l==wavel)[0][0]] += self._calc_epsiG(l,wavelTAB[i],feTAB[i])
+        return sumInt
+    
+    def _FindPeaks(self,sumInt,height,prom=1):
+        '''
+        Finds local maxima within the spectrum based on height and prominence.
+        
+        Prominence is crucial when switching between linear and logarithmic scales:
+        - In Linear mode: A large prominence (e.g., 1 to 1000) filters out noise.
+        - In Log mode: Data is compressed into a range of ~0 to 5. A large 
+          prominence will 'hide' real peaks. A smaller value (0.01 to 0.1) 
+          is required to detect shoulders and overlapping bands.
+
+        Input:
+            - sumInt: Array of intensities (Epsilon or Absorbance).
+            - height: Minimum height a peak must reach to be considered.
+            - prom: Required vertical distance between the peak and its lowest contour line.
+        
+        Returns:
+            - PeakIndex: Indices of the detected peaks in the wavelength array.
+            - PeakHeight: The intensity values at these peak positions.
+        '''
+        from scipy.signal import find_peaks
+        peaks = find_peaks(sumInt, height = height, threshold = None, distance = 1, prominence=prom)
+        PeakIndex = peaks[0]
+        # Check if 'peak_heights' exists in the properties dictionary
+        if 'peak_heights' in peaks[1]:
+            PeakHeight = peaks[1]['peak_heights']
+        else:
+            # If height=None, we extract values manually from the input data
+            PeakHeight = sumInt[PeakIndex]
+        return PeakIndex,PeakHeight
+
+    def _FindShoulders(self, data, tP):
+        '''
+        ###not working
+        Detects shoulders using the second derivative.
+        A shoulder appears as a peak in the negative second derivative.
+        
+        Note on scales:
+        - If ylog is True: data should be log10(sumInt) and tP should be log10(tP).
+          The second derivative on log data is much more sensitive to subtle 
+          inflection points in weak transitions (like n -> pi*).
+        - If ylog is False: data is linear sumInt and tP is linear.
+        
+        Returns:
+            - shoulder_idx (ndarray): Array of indices where shoulders were found.
+            - shoulder_heights (ndarray): The intensity values at these positions 
+              extracted from the input data.
+        '''
+        import numpy as np
+        # Calculate the second derivative (rate of change of the slope)
+        d2 = np.gradient(np.gradient(data))
+        
+        # We search for peaks in the opposite of the second derivative (-d2).
+        # A local maximum in -d2 corresponds to a point of maximum curvature 
+        # (inflection), which identifies a shoulder.
+        # We use a very low prominence threshold to capture subtle inflections.
+        shoulder_idx, _ = self._FindPeaks(-d2, height=None, prom=0.0001)
+        shoulder_heights = data[shoulder_idx]
+        print(shoulder_idx, shoulder_heights )
+        
+        return shoulder_idx, shoulder_heights 
+    
+    def _pickPeak(self,wavel,peaksIndex,peaksH,color,\
+                  shift=500,height=500,posAnnotation=200, ylog=False):
+        '''
+        Annotates peaks with a small vertical tick and the wavelength value.
+        Adjusts offsets based on whether the plot is in log10 scale or linear.
+        In log mode, peaksH must already be log10 values.
+        '''
+        s=shift
+        h=height
+        a=posAnnotation
+        
+
+        for i in range(len(peaksIndex)):
+            x = wavel[peaksIndex[i]]
+            y = peaksH[i]
+            if ylog:
+                # In log scale, we use multipliers to keep the same visual distance
+                # 1.1 means "10% above the peak"
+                # Adjust these factors based on your preference
+                y_s = y * 1.1
+                y_h = y * 1.3
+                y_a = y * 1.5
+                self.graph.vlines(x, y_s, y_h, colors=color, linestyles='solid')
+                self.graph.annotate(f"{x:.1f}",xy=(x,y),xytext=(x,y_a),rotation=90,size=self.fontsize_peaks,ha='center',va='bottom', color=color)
+            else:
+                # Classic linear offsets
+                self.graph.vlines(x, y+s, y+s+h, colors=color, linestyles='solid')
+                self.graph.annotate(f"{x:.1f}",xy=(x,y),xytext=(x,y+s+h+a),rotation=90,size=self.fontsize_peaks,ha='center',va='bottom',color=color)
+        return
+
+    def _setup_axes(self, lambdamin, lambdamax, ymax, ylabel="Absorbance"):
+            self.graph.set_xlabel('wavelength / nm', size=self.fontSize_axisLabels, fontweight='bold', color='#2f6b91')
+            self.graph.set_ylabel(ylabel, size=self.fontSize_axisLabels, fontweight='bold', color='#2f6b91')
+            self.graph.set_xlim(lambdamin, lambdamax)
+            self.graph.set_ylim(0, ymax)
+            self.graph.tick_params(axis='both', labelsize=self.fontSize_axisText,labelcolor='black')
+            for tick in self.graph.xaxis.get_majorticklabels(): tick.set_fontweight('bold') #it is both powerful
+                                                # (you can specify the type of a specific tick) and annoying
+            for tick in self.graph.yaxis.get_majorticklabels(): tick.set_fontweight('bold')
+    
+    def plotTDDFTSpectrum(self,wavel,sumInt,wavelTAB,feTAB,tP,ylog,labelSpectrum,colorS='#0000ff',colorT='#0000cf'):
+        
+        '''
+        Called by plotEps_lambda_TDDFT. Plots a single simulated UV-Vis spectrum, i.e. after
+        gaussian broadening, together with the TDDFT vertical transitions (i.e. plotted as lines)
+        
+        input:
+            - wavel = array of gaussian-broadened wavelengths, in nm
+            - sumInt = corresponding molar absorptiopn coefficients, in L. mol-1 cm-1
+            - wavelTAB = wavelength of TDDFT, e.g. discretized, transitions
+            - ylog = log plot of epsilon
+            - tP: threshold for finding the peaks
+            - feTAB = TDDFT oscillator strength for each transition of wavelTAB
+            - labelSpectrum = title for the spectrum
+        '''
+
+        # # --- DEBUG START ---
+        # if ylog:
+        #     print(f"\n--- DEBUG LOG MODE ---")
+        #     print(f"Max sumInt (linear): {np.max(sumInt):.2f}")
+        #     print(f"Max sumInt (log10):  {np.log10(max(np.max(sumInt), 1e-5)):.2f}")
+        # # --- DEBUG END ---
+        if ylog:
+            # Apply safety floor to the entire array
+            self.graph.set_yscale('log')
+            ymin_val = 1.0 # Epsilon = 1
+        else:
+            self.graph.set_yscale('linear')
+            ymin_val = 0
+            
+        # vertical lines
+        for i in range(len(wavelTAB)):
+            val_eps = self._calc_epsiG(wavelTAB[i],wavelTAB[i],feTAB[i])
+            self.graph.vlines(x=wavelTAB[i], ymin=ymin_val, ymax=max(val_eps, ymin_val), colors=colorT)
+
+        self.graph.plot(wavel,sumInt,linewidth=3,linestyle='-',color=colorS,label=labelSpectrum)
+
+        self.graph.legend(fontsize=self.fontSize_legends)
+        if ylog:
+            # Use log-transformed data and log-transformed threshold
+            # Clipping tP to 1e-5 ensures we don't take log of 0 or negative
+            tPlog = np.log10(max(tP, 1e-5))
+            # prom=0.05 allows detection of peaks that are close in log-magnitude
+            peaks, peaksH_log = self._FindPeaks(np.log10(np.clip(sumInt, 1e-5, None)), tPlog, prom=0.05)
+            peaksH = 10**peaksH_log
+            # shoulders, shouldersH_log = self._FindShoulders(np.log10(np.clip(sumInt, 1e-5, None)), tPlog)
+            # all_idx = np.concatenate((peaks, shoulders))
+            # allH_log = np.concatenate((peaksH_log, shouldersH_log))
+            # allH = 10**allH_log
+        else:
+            peaks, peaksH = self._FindPeaks(sumInt,tP)
+            # shoulders, shouldersH = self._FindShoulders(wavel, sumInt, tP)
+            # all_idx = np.concatenate((peaks, shoulders))
+            # allH = np.concatenate((peaksH, shouldersH))
+        self._pickPeak(wavel,peaks,peaksH,colorS,500,500,200,ylog)
+        
+    
+    def plotEps_lambda_TDDFT(self,datFile,lambdamin=200,lambdamax=800,\
+                             epsMax=None, titles=None, tP = 10, \
+                             ylog=False,\
+                             filename=None):
+        '''
+        Plots a TDDFT VUV simulated spectrum (vertical transitions and transitions summed with gaussian functions)
+        between lambdamin and lambdamax (sum of states done in the range [lambdamin-50, lambdamlax+50] nm)
+        input:
+            - datFile: list of pathway/names to "XXX_ExcStab.dat" files generated by 'GParser Gaussian.log -S'
+            - lambdamin, lambdamax: plot range
+            - epsMax: y axis graph limit
+            - titles: list of titles (1 per spectrum plot)
+            - tP: threshold for finding the peaks (default = 10 L. mol-1 cm-1)
+            - ylog: y logarithmic axis (default: False).
+            - save: saves in a png file (300 dpi) if True (default = False)
+            - filename: saves figure in a 300 dpi png file if not None (default), with filename=full pathway
+        '''
+        if self.fig is not None:
+            graph = self.graph
+            fig = self.fig
+            lambdamin = self.lambdamin
+            lambdamax = self.lambdamax
+            epsMax = self.epsMax
+        else:
+            fig, graph = self._initializePlot()
+
+        graph.set_prop_cycle(None)
+
+        if self.fig is None:
+            self.fig = fig
+            self.graph = graph
+            self.lambdamin = lambdamin
+            self.lambdamax = lambdamax
+            self.epsMax = epsMax
+            
+            graph.set_xlabel('wavelength / nm',size=self.fontSize_axisLabels,fontweight='bold',color='#2f6b91')
+
+            graph.set_xlim(lambdamin,lambdamax)
+
+            import matplotlib.ticker as ticker
+            graph.xaxis.set_major_locator(ticker.MultipleLocator(50)) # sets a tick for every integer multiple of the base (here 250) within the view interval
+        
+        istate,state,wavel,fe,SSq = np.genfromtxt(datFile,skip_header=1,dtype="<U20,<U20,float,float,<U20",unpack=True)
+        wavel = np.array(wavel)
+        fe = np.array(fe)
+        if wavel.size == 1:
+            wavel = np.array([wavel])
+            fe = np.array([fe])
+        wvl = np.arange(lambdamin-50,lambdamax+50,1)
+        sumInt = self._sumStatesWithGf(wvl,wavel,fe)
+        self.plotTDDFTSpectrum(wvl,sumInt,wavel,fe,tP,ylog,titles,self.colorS,self.colorVT)
+        if ylog:
+            graph.set_ylabel('log(molar absorption coefficient / L mol$^{-1}$ cm$^{-1})$',size=self.fontSize_axisLabels,fontweight='bold',color='#2f6b91')
+            graph.set_ylim(1, epsMax * 5 if epsMax else None)
+        else:
+            graph.set_yscale('linear')
+            graph.set_ylabel('molar absorption coefficient / L mol$^{-1}$ cm$^{-1}$',size=self.fontSize_axisLabels,fontweight='bold',color='#2f6b91')
+            graph.set_ylim(0, epsMax if epsMax else np.max(sumInt)*1.18)
+        if filename is not None: self.fig.savefig(filename, dpi=300, bbox_inches='tight')
+        plt.show()
+
+        peaksI, peaksH = self._FindPeaks(sumInt,tP)
+        print(f"{bg.LIGHTREDB}{titles}{bg.OFF}")
+        for i in range(len(peaksI)):
+            print(f"peak {i:3}. {wvl[peaksI[i]]:4} nm. epsilon_max = {peaksH[i]:.1f} L mol-1 cm-1")
+        if ylog:
+            print()
+            # prom=0.05 allows detection of peaks that are close in log-magnitude
+            peaksI, peaksH = self._FindPeaks(np.log10(np.clip(sumInt, 1e-5, None)), np.log10(max(tP, 1e-5)), prom=0.05)
+            for i in range(len(peaksI)):
+                print(f"peak {i:3}. {wvl[peaksI[i]]:4} nm. log10(epsilon_max) = {peaksH[i]:.1f}")
+
+    def plotAbs_lambda_TDDFT(self, datFiles=None, C0=1e-5, lambdamin=200, lambdamax=800, Amax=2.0,\
+                             titles=None, linestyles=[], annotateP=[], tP = 0.1,\
+                             resetColors=False,\
+                             filename=None):
+        '''
+        Plots a simulated TDDFT VUV absorbance spectrum (transitions summed with gaussian functions)
+        between lambdamin and lambdamax (sum of states done in the range [lambdamin-50, lambdamlax+50] nm)
+        input:
+            - datFiles: list of pathway/name to files generated by 'GParser Gaussian.log -S'
+            - C0: list of concentrations needed to calculate A = epsilon x l x c (in mol.L-1)
+            - lambdamin, lambdamax: plot range (x axis)
+            - Amax: y axis graph limit
+            - titles: list of titles (1 per spectrum plot)
+            - linestyles: list of line styles(default = "-", i.e. a continuous line)
+            - annotateP: list of Boolean (annotate lambda max True or False. Default = True)
+            - tP: threshold for finding the peaks (default = 0.1)
+            - resetColors (bool): If True, resets the matplotlib color cycle 
+                                 to the first color. This allows different series 
+                                 (e.g., gas phase vs. solvent) to share the same 
+                                 color coding for each molecule across multiple calls. Default: False
+            - save: saves in a png file (300 dpi) if True (default = False)
+            - filename: saves figure in a 300 dpi png file if not None (default), with filename=full pathway
+        '''
+
+        if self.fig is None:
+            fig, graph = self._initializePlot()
+            self.fig = fig
+            self.graph = graph
+            self.lambdamin = lambdamin
+            self.lambdamax = lambdamax
+            self.Amax = Amax
+        else:
+            graph = self.graph
+            fig = self.fig
+            lambdamin = self.lambdamin
+            lambdamax = self.lambdamax
+            Amax = self.Amax
+            if resetColors: graph.set_prop_cycle(None)
+            
+        if linestyles == []: linestyles = len(datFiles)*['-']
+        if annotateP == []: annotateP = len(datFiles)*[True]
+
+        self._setup_axes(lambdamin, lambdamax, self.Amax, ylabel="Absorbance")
+        
+        wvl = np.arange(lambdamin-50,lambdamax+50,1)
+        for f in range(len(datFiles)):
+            istate,state,wavel,fe,SSq = np.genfromtxt(datFiles[f],skip_header=1,dtype="<U20,<U20,float,float,<U20",unpack=True)
+            sumInt = self._sumStatesWithGf(wvl,wavel,fe)
+            Abs = self._Absorbance(sumInt,1,C0[f])
+            plot=self.graph.plot(wvl,Abs,linewidth=3,linestyle=linestyles[f],label=f"{titles[f]}. TDDFT ($C_0$={C0[f]} mol/L)")
+            peaksI, peaksH = self._FindPeaks(Abs,tP,0.01)
+            if (annotateP[f]): self._pickPeak(wvl,peaksI,peaksH,plot[0].get_color(),0.01,0.04,0.02)
+            print(f"{bg.LIGHTREDB}TDDFT. {titles[f]}{bg.OFF}")
+            for i in range(len(peaksI)):
+                print(f"peak {i:3}. {wvl[peaksI[i]]:4} nm. A = {peaksH[i]:.2f}")
+                
+        self.graph.legend(fontsize=self.fontSize_legends)
+
+        if filename is not None: self.fig.savefig(filename, dpi=300, bbox_inches='tight')
+
+        return
+    
+    def plotAbs_lambda_exp(self, csvFiles, C0, lambdamin=200, lambdamax=800,\
+                             Amax=2.0, titles=None, linestyles=[], annotateP=[], tP = 0.1,\
+                             filename=None):
+        '''
+        Plots an experimental VUV absorbance spectrum read from a csv file between lambdamin and lambdamax
+        input:
+            - superpose: False = plots a new graph, otherwise the plot is superposed to a previously created one
+                         (probably with plotAbs_lambda_TDDFT())
+            - csvfiles: list of pathway/name to experimental csvFiles (see examples for the format)
+            - C0: list of experimental concentrations, i.e. for each sample
+            - lambdamin, lambdamax: plot range (x axis)
+            - Amax: graph limit (y axis)
+            - titles: list of titles (1 per spectrum plot)
+            - linestyles: list of line styles(default = "--", i.e. a dashed line)
+            - annotateP: list of Boolean (annotate lambda max True or False. Default = True)
+            - tP: threshold for finding the peaks (default = 0.1)
+            - save: saves in a png file (300 dpi) if True (default = False)
+            - filename: saves figure in a 300 dpi png file if not None (default), with filename=full pathway
+        '''
+        if linestyles == []: linestyles = len(csvFiles)*['--']
+        if annotateP == []: annotateP = len(csvFiles)*[True]
+
+        if self.fig is not None:
+            graph = self.graph
+            fig = self.fig
+            lambdamin = self.lambdamin
+            lambdamax = self.lambdamax
+            Amax = self.Amax
+        else:
+            fig, graph = self._initializePlot()
+            
+        graph.set_prop_cycle(None)
+        
+        if self.fig is None:
+            self.graph = graph
+            self.fig = fig
+            self.lambdamin = lambdamin
+            self.lambdamax = lambdamax
+            self.Amax = Amax
+            
+        self._setup_axes(lambdamin, lambdamax, self.Amax, ylabel="Absorbance")
+                
+        for f in range(len(csvFiles)):
+            wavel,Abs = np.genfromtxt(csvFiles[f],skip_header=1,unpack=True,delimiter=";")
+            wavel *= 1e9
+            plot=graph.plot(wavel,Abs,linewidth=3,linestyle=linestyles[f],label=f"{titles[f]}. exp ($C_0$={C0[f]} mol/L)")
+            peaksI, peaksH = self._FindPeaks(Abs,tP,0.01)
+            if (annotateP[f]): self._pickPeak(wavel,peaksI,peaksH,plot[0].get_color(),0.01,0.04,0.02)
+            print(f"{bg.LIGHTREDB}exp. {titles[f]}{bg.OFF}")
+            for i in range(len(peaksI)):
+                print(f"peak {i:3}. {wavel[peaksI[i]]:4} nm. A = {peaksH[i]:.2f}")
+
+        graph.legend(fontsize=self.fontSize_legends)
+
+        if filename is not None: self.fig.savefig(filename, dpi=300, bbox_inches='tight')
+    
+        return
+