Update README.md

Author: Kalpa08

README.md

@@ -20,13 +20,14 @@
 **ConeZen** is a lightweight, open-source Python package designed to characterize and visualize the branching plane topology at a conical intersection (CI). The shape and orientation of a CI's potential energy surfaces dictate the pathways for ultrafast, non-radiative electronic transitions, which are fundamental to processes like vision, photosynthesis, and DNA photostability.
 
 Using output from standard quantum chemistry programs (tested on SHARC-OpenMolcas), **ConeZen** computes key topological descriptors and renders intuitive 3D potential energy surfaces. This allows researchers to move from raw numerical data to an intuitive, quantitative understanding of the CI landscape, helping to predict the outcomes of photochemical reactions.
-- 📝Note: ConeZen was tested with the gradients and NAC obtained from SHARC-OpenMolcas interface. (see [SHARC Manual](https://sharc-md.org/?page_id=1454))
+- 📝Note: ConeZen was tested with the gradients and NAC obtained from SHARC-OpenMolcas interface. The automated extraction feature is specifically designed for the QM.out file generated by this interface. (see [SHARC Manual](https://sharc-md.org/?page_id=1454))
 ---
 
 ## ✨ Key Features
 
-- **Automated Analysis**  
-	Computes key CI descriptors:  
+- **Automated Analysis**
+  -  **Direct QM Output Parsing**  Automatically extracts the required gradients and nonadiabatic coupling (NAC) vectors directly from sharc-molcas QM.out files. Just specify the file and the states of interest (e.g., S1, T2), and ConeZen handles the rest.
+  - **Topological Analysis**  Computes key CI descriptors from the vector data:  
  	- The strength or pitch ( $\delta_{gh}$ )  
  	- The asymmetry ( $$\Delta_{gh}$$ )  
  	- The relative tilt and tilt heading ( σ ), $\theta_s$ respectively.   
@@ -109,6 +110,36 @@ conezen
 ```
 The interactive session will look like this:
 
+### New Automated Extraction Workflow:
+
+This is the recommended and easiest workflow.
+
+```
+============================================================
+    ConeZen: Conical Intersection Branching Plane Visualization
+============================================================
+...
+(Do you want to automatically extract gradients and NACs from a QM output file? (only for sharc-molcas output QM.out file) [y/n]: y
+Enter the source QM file name (default: QM.out):
+Enter the total number of singlet states (default: 20): 5
+Enter the total number of triplet states (default: 20): 5
+Enter the lower state (e.g., S2): s2
+Enter the upper state (e.g., S3): s3
+✅ Successfully extracted and saved 'S2_gradient.out'
+✅ Successfully extracted and saved 'S3_gradient.out'
+✅ Automatically extracted and saved 'NAC_S2_S3.out'
+Enter the energy of the intersection point (Hartree) (default: 0):
+...
+✅ Key quantities calculated.
+Save branching plane key quantities to a file? [y/n]: y
+Enter filename for parameters (default: ci_parameters.txt):
+...
+Show 3D surface plot now? [y/n]: y
+```
+### Manual Input Workflow:
+
+If you choose not to use the automated extractor or have your gradient/NAC files prepared separately, you can provide them manually.
+
 ```bash
 ============================================================
     ConeZen: Conical Intersection Branching Plane Visualization
@@ -182,14 +213,21 @@ plt.show()
 
 ## 📄 Input File Format
 
+ConeZen can now work directly with QM.out files from SHARC-OpenMolcas, but it also supports manually prepared text files.
+- Source Quantum Chemistry File (`QM.out`):
+	-  This is the primary input for the new automated workflow.
+ 	-  ConeZen searches this file for the specific headers corresponding to the requested electronic states (e.g., m1 1 s1 3 ms1 0 for the S2 gradient) to extract gradient and NAC vectors.
+  -  
+
 ConeZen expects simple text files for the gradients, nonadiabatic coupling (NAC) vectors, and geometry. The format is designed for easy generation from post-processing scripts and is directly compatible with output from programs like SHARC-OpenMolcas.
 
 - Gradient and NAC Files (```gradientA.out```, ```gradientB.out```, ```NAC.out```):
-	- The first line is treated as a header and is skipped.
-	- Subsequent lines should contain the Cartesian vector components (x, y, z) for each atom, typically in units of Hartree/Bohr.
+	- These files are generated automatically when using the extraction workflow or can be provided manually.
+ 	- The first line is treated as a header and is skipped.
+	- Subsequent lines should contain the Cartesian vector components (x, y, z) for each atom.
 	- The script reads the first three numeric values on each line. Any additional text (like atom symbols) is ignored.
-- Geometry File (.xyz):
-	- A standard XYZ file format is expected. This is used to correctly label the atoms in the output vector files.
+- Geometry File (```.xyz```):
+	- A standard XYZ file format is used to add atom labels to the output vector files.
 	- The first two lines (number of atoms and a comment line) are skipped as per the standard.
 
 Example ```gradientA.out```:
@@ -218,6 +256,7 @@ Coordinates from ORCA-job orca
 ```
 ## 📤 Output
 The CLI tool can generate several useful output files in your working directory:
+- ```S2_gradient.out```, ```NAC_S2_S3.out```, etc.: The gradient and NAC files automatically extracted from the source QM.out file.
 - ```ci_parameters.txt```: A text file containing the calculated topological quantities ($\delta_{gh}$, $$\Delta_{gh}$$ , σ , $\theta_s$). This provides a quick human-readable summary of the CI's characters.
 - ```x_vectors.out```, ```y_vectors.out```:  The orthonormal branching plane vectors $\hat{x}$ and $\hat{y}$.
 - ```conical_intersection.png```: A high-resolution image of the 3D plot. The plot is saved with a transparent background and tight bounding box, making it easy to incorporate into other documents.
@@ -227,8 +266,7 @@ The CLI tool can generate several useful output files in your working directory:
 If you use ConeZen in your research, please cite the accompanying paper. Your citation allows us to track the software's impact and helps support its continued development.
 
 ```
-Kalpajyoti Dihingia & Biswajit Maiti, ConeZen: A Python Package for Visualizing Conical Intersection Branching Planes, journal name (2025).
-
+To be updated
 Zenodo DOI: [Zenodo DOI will go here]
 
 ```
@@ -245,23 +283,18 @@ Zenodo DOI: [Zenodo DOI will go here]
 ```
 
 ---
-### 🙏 Acknowledgments
-
-Developed as part of my Ph.D. research at *Banaras Hindu University (BHU)*.
-
-Special thanks to **Prof. Biswajit Maiti** and **Dr. Sebastian** for their guidance and support.
 
 ## ⚖️ License
 
 Distributed under the **GNU GPL v3.0**. See the [LICENSE](LICENSE) file for details.
 
 ---
+## 🙏 Acknowledgments
 
-## References
-
-  > Ignacio Fdez. Galván, Mickaël G. Delcey, Thomas Bondo Pedersen, Francesco Aquilante, and Roland Lindh,  
-  > "Analytical State-Average Complete-Active-Space Self-Consistent Field Nonadiabatic Coupling Vectors: Implementation with Density-Fitted Two-Electron Integrals",  
-  > *J. Chem. Theory Comput.* 2016, **12(8)**, 3636–3653. DOI: [10.1021/acs.jctc.6b00384](https://doi.org/10.1021/acs.jctc.6b00384)
+- Developed at *Banaras Hindu University (BHU)*.
+- Based on the theoretical framework described in:
+  	```J. Chem. Theory Comput. 2016, 12(8), 3636–3653. DOI: 10.1021/acs.jctc.6b00384```
+---
 
 For full metadata and citation, see [`CITATION.cff`](CITATION.cff) and [`.zenodo.json`](.zenodo.json).