add readme

GIT_WORKFLOW.md

@@ -1,238 +0,0 @@
-# Git Workflow for Hugging Face Repository
-
-Your Hugging Face repository is now cloned and works **exactly like GitHub**! You can use all the standard git commands.
-
-## 📍 Repository Location
-```
-/Users/liliana/Research/CMU/Isayev/Projects/Collaborations/Bernhard_Amide-coupling/Publish/prism_hf_repo
-```
-
-## 🚀 Basic Workflow (Just Like GitHub)
-
-### 1. Check Status
-See what files have changed:
-```bash
-cd prism_hf_repo
-git status
-```
-
-### 2. Add Files
-Stage files for commit (like `git add` in GitHub):
-
-**Add a specific file:**
-```bash
-git add qm_calculations/new_file.xyz
-```
-
-**Add all files in a directory:**
-```bash
-git add qm_calculations/
-```
-
-**Add all changes:**
-```bash
-git add .
-```
-
-### 3. Commit Changes
-Save your changes with a message:
-```bash
-git commit -m "Add new quantum calculations"
-```
-
-### 4. Push to Hugging Face
-Upload your changes (like `git push` in GitHub):
-```bash
-git push
-```
-
-That's it! Your changes are now live on Hugging Face! 🎉
-
----
-
-## 📝 Common Operations
-
-### Add a New File
-```bash
-cd prism_hf_repo
-cp ~/my_new_file.xyz qm_calculations/
-git add qm_calculations/my_new_file.xyz
-git commit -m "Add new XYZ structure"
-git push
-```
-
-### Add Multiple Files
-```bash
-cd prism_hf_repo
-cp -r ~/new_data_folder qm_calculations/
-git add qm_calculations/new_data_folder/
-git commit -m "Add new data folder"
-git push
-```
-
-### Edit a File
-```bash
-cd prism_hf_repo
-nano qm_calculations/README.md  # or use any editor
-git add qm_calculations/README.md
-git commit -m "Update README"
-git push
-```
-
-### Delete a File
-```bash
-cd prism_hf_repo
-git rm qm_calculations/old_file.xyz
-git commit -m "Remove old file"
-git push
-```
-
-### Delete a Folder
-```bash
-cd prism_hf_repo
-git rm -r qm_calculations/old_folder/
-git commit -m "Remove old folder"
-git push
-```
-
-### Rename/Move Files
-```bash
-cd prism_hf_repo
-git mv qm_calculations/old_name.xyz qm_calculations/new_name.xyz
-git commit -m "Rename file"
-git push
-```
-
----
-
-## 🔄 Syncing Changes
-
-### Pull Latest Changes
-If someone else made changes, or you edited on the web:
-```bash
-cd prism_hf_repo
-git pull
-```
-
-### See What Changed
-```bash
-git log                    # See commit history
-git log --oneline          # Compact view
-git diff                   # See unstaged changes
-git diff --staged          # See staged changes
-```
-
----
-
-## 🎯 Example Workflow
-
-Let's say you want to add a new XYZ file:
-
-```bash
-# 1. Navigate to the repo
-cd /Users/liliana/Research/CMU/Isayev/Projects/Collaborations/Bernhard_Amide-coupling/Publish/prism_hf_repo
-
-# 2. Copy your file
-cp ~/my_calculation.xyz qm_calculations/hammett_XYZs/
-
-# 3. Check status (optional but recommended)
-git status
-
-# 4. Stage the file
-git add qm_calculations/hammett_XYZs/my_calculation.xyz
-
-# 5. Commit
-git commit -m "Add new Hammett calculation for compound X"
-
-# 6. Push to Hugging Face
-git push
-
-# Done! View at: https://huggingface.co/datasets/gomesgroup/prism
-```
-
----
-
-## 🔧 Advanced Operations
-
-### Undo Uncommitted Changes
-```bash
-git checkout -- file.xyz          # Discard changes to a file
-git reset --hard                  # Discard all uncommitted changes (careful!)
-```
-
-### Undo Last Commit (Before Push)
-```bash
-git reset --soft HEAD~1           # Undo commit, keep changes staged
-git reset --mixed HEAD~1          # Undo commit, unstage changes
-git reset --hard HEAD~1           # Undo commit and discard changes (careful!)
-```
-
-### View File History
-```bash
-git log qm_calculations/file.xyz  # See commits affecting this file
-git show <commit-hash>:file.xyz   # View file at specific commit
-```
-
-### Create a Branch (Optional)
-```bash
-git checkout -b new-feature       # Create and switch to branch
-git add .
-git commit -m "Add feature"
-git push origin new-feature       # Push branch
-```
-
----
-
-## 📊 Quick Reference Table
-
-| Git Command | What It Does | Like GitHub? |
-|-------------|--------------|--------------|
-| `git status` | Check what changed | ✅ Yes |
-| `git add <file>` | Stage file for commit | ✅ Yes |
-| `git commit -m "msg"` | Save changes locally | ✅ Yes |
-| `git push` | Upload to Hugging Face | ✅ Yes, exactly! |
-| `git pull` | Download latest changes | ✅ Yes |
-| `git rm <file>` | Delete file | ✅ Yes |
-| `git mv <old> <new>` | Rename/move file | ✅ Yes |
-| `git log` | View history | ✅ Yes |
-
----
-
-## 💡 Tips
-
-1. **Always `git pull` before making changes** if you might have edited on the web
-2. **Use descriptive commit messages** so you know what changed later
-3. **Commit often** - small, frequent commits are better than large ones
-4. **Check `git status`** before committing to see what will be included
-5. **Large files**: Hugging Face uses Git LFS automatically for large files
-
----
-
-## 🌐 View Your Repository Online
-
-After pushing, view your changes at:
-**https://huggingface.co/datasets/gomesgroup/prism**
-
----
-
-## 🆘 Troubleshooting
-
-### Push Rejected?
-```bash
-git pull --rebase      # Get latest changes first
-git push               # Try again
-```
-
-### Accidentally Added Wrong File?
-```bash
-git reset HEAD file.xyz   # Unstage file before commit
-git rm --cached file.xyz  # Remove from staging, keep local copy
-```
-
-### Want to Start Fresh?
-```bash
-cd /Users/liliana/Research/CMU/Isayev/Projects/Collaborations/Bernhard_Amide-coupling/Publish
-rm -rf prism_hf_repo
-git clone https://gomesgroup:YOUR_TOKEN@huggingface.co/datasets/gomesgroup/prism prism_hf_repo
-```
-

qm_calculations/README.md

@@ -1,3 +1,29 @@
 # QM Calculations
 
-This directory contains quantum mechanical calculations for the amide coupling project.
+This directory contains the XYZ structures of the DFT calculations for the amide coupling project.
+It contains the tabulated free-energies for the reaction mechanism in `all_investigated_rxn_mechanisms.dat` and
+for the hammett study in `hammett_analysis_summarized.xlsx`.
+
+Free-energies were calculated using [GoodVibes](https://github.com/patonlab/GoodVibes). 
+
+## Data
+```bash
+qm_calculations/
+├── README.md
+├── hammett_XYZs/
+│   ├── hammett_analysis_summarized.xlsx    # Tabulated free energies for Hammett study
+│   ├── *_acid_chloride_wb97xd.xyz          # Acid chloride structures (14 files)
+│   ├── *_amine_wb97xd.xyz                  # Amine structures (11 files)
+│   ├── amine_*-base_wb97xd.xyz             # Amine base structures (10 files)
+│   ├── TSA_amide_*_wb97xd.xyz              # Transition states A (27 files)
+│   └── TSB_gen-base_*_wb97xd.xyz           # Transition states B (26 files)
+└── reaction_mechanism_XYZs/
+    ├── all_investigated_rxn_mechanisms.dat # Tabulated free energies for reaction mechanisms
+    ├── ints/                               # Intermediate structures (34 files)
+    ├── products/                           # Product structures (8 files)
+    ├── reactants/                          # Reactant structures (30 files)
+    └── ts/                                 # Transition state structures (31 files)
+```
+
+
+