ENH:Add 3D PDF calculator support

README.md

@@ -149,6 +149,7 @@ construction environment can be further customized in a `sconscript.local`
 script.  The library integrity can be verified by executing unit tests with
 `scons -j4 test` (requires the CxxTest framework).
 
+[Instructions for compiling and modifying source code in development mode](docs/development_instructions.md)
 
 ## CONTACTS
 

SConstruct

@@ -66,7 +66,7 @@ vars.Add(PathVariable(
 vars.Add(EnumVariable(
     'build',
     'compiler settings',
-    'fast', allowed_values=('fast', 'debug', 'coverage')))
+    'fast', allowed_values=('fast', 'debug', 'develop', 'coverage')))
 vars.Add(EnumVariable(
     'tool',
     'C++ compiler toolkit to be used',

docs/development_instructions.md

@@ -0,0 +1,242 @@
+# Compile and Modify diffpy Source Code
+
+---
+
+## I. Prerequisites
+
+### 1) Install System Dependencies
+
+Open a terminal and run the following commands in order:
+
+```bash
+# Update package list
+sudo apt update
+
+# Install build toolchain, CMake, Git, Python development headers, etc.
+sudo apt install -y build-essential cmake git python3-dev
+
+# Install SCons (used to build libdiffpy)
+sudo apt install -y scons
+
+# Install GSL (GNU Scientific Library) and ObjCryst (X-ray crystallography library)
+sudo apt install -y libgsl-dev libobjcryst-dev
+```
+
+---
+
+### 2) Create a Conda Virtual Environment
+
+> If you haven't installed Miniconda, please download and install it first
+
+```bash
+# Create your environment (e.g., named your_env_name) with Python 3.11
+conda create -n your_env_name python=3.11 -y
+
+# Activate the environment (shell prompt will show (your_env_name))
+conda activate your_env_name
+
+# Install Python dependencies
+conda install -y numpy
+
+# Install additional scientific libraries
+conda install -c conda-forge boost-cpp gsl pyobjcryst
+```
+
+All subsequent operations should be performed within the (your_env_name) environment!
+
+---
+
+## II. Get the Source Code
+
+Assume our working directory is `~/workspace` (adjust to your actual setup):
+
+```bash
+# Switch to the working directory
+cd ~/workspace
+
+# Clone the two core repositories
+git clone https://github.com/diffpy/libdiffpy.git diffpy.libdiffpy
+git clone https://github.com/diffpy/diffpy.srreal.git diffpy.srreal
+```
+
+> The directory structure should be: `~/workspace/`
+>
+> ```
+> ~/workspace/
+> ├── diffpy.libdiffpy/   ← C++ core library
+> └── diffpy.srreal/      ← Python interface layer
+> ```
+
+---
+
+## III. Initial Build (Developer Mode)
+
+> We use `--inplace` so after modifying code you only need to recompile, no `pip install` required.
+
+---
+
+### Step 1: Build libdiffpy (C++ Library)
+
+```bash
+# Enter the libdiffpy directory
+cd ~/workspace/diffpy.libdiffpy
+
+# Clean old builds (optional but recommended)
+rm -rf build/
+
+# Build the C++ library with SCons
+scons
+```
+
+Success indicators:
+
+- `build/fast-x86_64/libdiffpy.so` is generated
+- No errors in terminal output; warnings can be ignored
+
+Verify it was generated:
+
+```bash
+ls -l build/fast-x86_64/libdiffpy.so
+```
+
+> If you see `ObjCryst not found` or `gsl-config not found`, make sure you ran the `apt install` commands in Step 1.
+
+---
+
+### Step 2: Set Environment Variables
+
+To allow srreal to find the newly built `libdiffpy.so`, set the following variables and replace the paths with your actual paths:
+
+```bash
+# Set the libdiffpy build path
+export DIFFPY_LIBDIFFPY_BUILD="$HOME/workspace/diffpy.libdiffpy/build/fast-x86_64"
+
+# Tell the linker and runtime where to find .so files
+export LD_LIBRARY_PATH="$DIFFPY_LIBDIFFPY_BUILD:$LD_LIBRARY_PATH"
+export LIBRARY_PATH="$DIFFPY_LIBDIFFPY_BUILD:$LIBRARY_PATH"
+
+# Let Python import srreal source directly (developer mode)
+export PYTHONPATH="$HOME/workspace/diffpy.srreal/src:$PYTHONPATH"
+```
+
+---
+
+### Step 3: Build diffpy.srreal (Python Extension)
+
+```bash
+# Enter the srreal directory
+cd ~/workspace/diffpy.srreal
+
+# Clean old builds
+rm -rf build/
+
+# Build the Python extension (generate .so in place)
+python setup.py build_ext --inplace
+```
+
+Success indicators:
+
+- `diffpy/srreal/srreal_ext.cpython-*.so` is generated
+- No `cannot find -ldiffpy` errors
+
+---
+
+### Step 4: Verify the Installation
+
+```bash
+# Test whether it can be imported
+python -c "from diffpy.srreal.pdfcalculator import PDFCalculator; print('srreal Success！')"
+```
+
+If you see `srreal Success！`, everything is working!
+
+---
+
+## IV. Daily Development: Modify Code + Rebuild
+
+### Scenario A: Only Modified diffpy.srreal Python or C++ Code
+
+```bash
+# 1. Activate your Conda environment
+conda activate your_env_name
+
+# 2. Enter the srreal directory
+cd ~/workspace/diffpy.srreal
+
+# 3. Clean and rebuild
+rm -rf build/
+python setup.py build_ext --inplace
+```
+
+No need to rebuild libdiffpy
+
+---
+
+### Scenario B: Modified diffpy.libdiffpy C++ Code
+
+```bash
+# 1. Activate your Conda environment
+conda activate your_env_name
+
+# 2. Rebuild libdiffpy
+cd ~/workspace/diffpy.libdiffpy
+rm -rf build/
+scons
+
+# 3. Update environment variables (ensure they point to the latest .so)
+export DIFFPY_LIBDIFFPY_BUILD="$HOME/workspace/diffpy.libdiffpy/build/fast-x86_64"
+export LD_LIBRARY_PATH="$DIFFPY_LIBDIFFPY_BUILD:$LD_LIBRARY_PATH"
+
+# 4. Rebuild srreal (since it depends on libdiffpy)
+cd ~/workspace/diffpy.srreal
+rm -rf build/
+python setup.py build_ext --inplace
+```
+
+Key point: if you change the underlying C++ library, you must rebuild the Python extension
+
+---
+
+## V. Common Issues and Fixes
+
+### Issue 1: ModuleNotFoundError: No module named 'numpy'
+
+→ Fix: run `conda install numpy` in your Conda environment
+
+### Issue 2: cannot find -ldiffpy
+
+→ Fix:
+
+1. Confirm `libdiffpy.so` has been generated
+2. Confirm `LD_LIBRARY_PATH` and `LIBRARY_PATH` are set correctly
+
+### Issue 3: gsl-config: not found
+
+→ Fix: run `sudo apt install libgsl-dev`
+
+### Issue 4: Checking for C++ library ObjCryst... no
+
+→ Fix: run `sudo apt install libobjcryst-dev`
+
+If you encounter other issues, you can search relevant forums or contact qiaohai@tongji.edu.cn
+
+---
+
+## VI. Appendix: One-Click Environment Variable Setup
+
+You can append the following to `~/.bashrc` so you don't have to set environment variables every time:
+
+```bash
+# diffpy development environment
+export DIFFPY_WORKSPACE="$HOME/workspace"
+export DIFFPY_LIBDIFFPY_BUILD="$DIFFPY_WORKSPACE/diffpy.libdiffpy/build/fast-x86_64"
+export LD_LIBRARY_PATH="$DIFFPY_LIBDIFFPY_BUILD:$LD_LIBRARY_PATH"
+export LIBRARY_PATH="$DIFFPY_LIBDIFFPY_BUILD:$LIBRARY_PATH"
+export PYTHONPATH="$DIFFPY_WORKSPACE/diffpy.srreal/src:$PYTHONPATH"
+```
+
+Then run:
+
+```bash
+source ~/.bashrc
+```