init

electrochemistry/echem/io_data/gas_sensor.py

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+import numpy as np
+from typing import Union, List, Iterable
+from monty.re import regrep
+import re
+from echem.io_data.ddec import AtomicNetCharges
+
+
+
+
+class GasSensor:
+    def __init__(self):
+        pass
+
+    @staticmethod
+    def read_OUTCAR(filepath) -> float:
+        """
+        This function reads your OUTCAR file to get the final Energy of the system.
+        """
+
+        file = open(filepath, 'r')
+        data = file.readlines()
+        file.close()
+
+        patterns = {'energy_ionic': r'free  energy\s+TOTEN\s+=\s+(.\d+\.\d+)\s+eV'}
+        matches = regrep(filepath, patterns)
+
+        end_energy = np.array([float(i[0][0]) for i in matches['energy_ionic']])
+        
+        return end_energy[-1]
+
+    @staticmethod   
+    def sort_DDEC_output(filepath, k: int) -> list[int]:
+        """
+        This function sorts atoms in your system to get atoms related to your molecule
+        k - number of atoms consisting in your molecule
+        """
+
+        z_coords = {}
+
+        idx = 1
+
+        with open(filepath, 'r') as file:
+            while True:
+                line = file.readline()
+                if re.search('\sChargemol', line) is not None:
+                    break
+
+                list_of_substrings = line.split('    ')
+                if re.search('^\s|^j', list_of_substrings[0]) is None:
+                    z_coords[idx] = list_of_substrings[-2]
+                    idx += 1
+                    continue
+
+        sorted_z_coords = dict(sorted(z_coords.items(), key = lambda item: item[1], reverse = True))
+
+        result = []
+        counter = 0
+        for item in sorted_z_coords:
+            if counter < k:
+                result.append(item)
+                counter += 1
+            else:
+                break
+
+        return result
+
+    @staticmethod   
+    def get_chrg_mol(filepath, k: int or list[int]) -> float:
+        """
+        This function can help you to get the molecule charge.
+        filepath - DDEC6 output file: DDEC_even_tempered_net_atomic_charges.xyz
+        k - the number of atoms, consisting in molecule. Besides, your can write the ordinal number of an atom in your molecule.
+        """
+
+        atomic_charges = AtomicNetCharges.from_file(filepath)
+        net_charges = atomic_charges.net_charges
+
+
+        if type(k) == int:
+            chrg_molecule = 0       
+            targets = GasSensor.sort_DDEC_output(filepath, k)
+            for i in targets:
+                chrg_molecule += net_charges[i - 1]
+            return chrg_molecule
+        elif isinstance(k, list):
+            targets = k
+            chrg_molecule = 0       
+            for i in targets:
+                chrg_molecule += net_charges[i - 1]
+            return chrg_molecule
+            
+    @staticmethod       
+    def get_Ead(filepath, E_surface, E_molecule) -> float:
+        """ 
+        This function can help you to get the adsorption energy, using energy of whole system, energy of the surface and energy of your         molecule.
+        filepath - your OUTCAR file obtained as a result of VASP optimization.
+        """
+        E_system = GasSensor.read_OUTCAR(filepath)
+        E_ad = E_system - E_surface - E_molecule
+        #print(E_ad) 
+        return E_ad
+    
+    @staticmethod   
+    def get_energy_in_meV(filepath):
+        """ 
+        This function can help you to get energies in meV.
+        filepath - your .txt file, consisting of energies in eV.
+        """
+        X = np.genfromtxt(filepath)
+        X_new = []
+        for i in X:
+            X_new = X * 1000
+        return f'Your energies in meV: {X_new}'
+