Add README and Git workflow guide

GIT_WORKFLOW.md

@@ -0,0 +1,238 @@
+# 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

@@ -0,0 +1,3 @@
+# QM Calculations
+
+This directory contains quantum mechanical calculations for the amide coupling project.