Add feature flags and create CLAUDE.md for project guidance

Reviewed-on: #13

.gitea/scripts/code_review.py

@@ -1,5 +1,6 @@
 """Code Reviewer for Gitea."""
 
+import asyncio
 import fnmatch
 import json
 import os
@@ -7,6 +8,7 @@ import re
 from typing import Any
 
 import requests
+import aiohttp
 from model import Model
 
 ACCESS_TOKEN = os.getenv("ACCESS_TOKEN", "")
@@ -57,8 +59,8 @@ def parse_diff(diff: str) -> list[dict[str, Any]]:
         r"(?s)diff --git a/(.+?) b/(.*?)\r?\n(.*?)(?=diff --git a/|$)", re.S
     )
     old_new_pattern = re.compile(r"(?m)^(---|\+\+\+)\s+(.*)$")
-    hunk_pattern = re.compile(
-        r"^@@ -(\d+)(?:,(\d+))? \+(\d+)(?:,(\d+))? @@(.*?)(?=^@@ |$)",
+    chunk_range_pattern = re.compile(
+        r"@@ -(\d+)(?:,(\d+))? \+(\d+)(?:,(\d+))? @@(.*?)?(?=@@|\Z)",
         re.MULTILINE | re.DOTALL,
     )
     list_diff = []
@@ -77,33 +79,31 @@ def parse_diff(diff: str) -> list[dict[str, Any]]:
             print("Neglict deleted file")
             continue
         new_file = new_file.lstrip("b/")
-
-        hunk_match = hunk_pattern.search(diff_text)
-        if hunk_match is None:
-            continue
-        old_idx = int(hunk_match.group(1))
-        new_idx = int(hunk_match.group(3))
-        remain_text = diff_text[hunk_match.end() + 1 :]
-        diff_text = []
-        for line in remain_text.splitlines():
-            if line.startswith("-"):
-                diff_text.append(f"{old_idx} {line}")
-                old_idx += 1
-            elif line.startswith("+"):
-                diff_text.append(f"{new_idx} {line}")
-                new_idx += 1
-            else:
-                diff_text.append(line)
-        diff_text = "\n".join(diff_text)
-
         if any(fnmatch.fnmatch(new_file, pattern) for pattern in EXCLUDE_PATTERNS):
             print(f"Exclude file {new_file}")
             continue
 
+        output_diff_text = []
+        for chunk_range_match in chunk_range_pattern.finditer(diff_text):
+            old_idx = int(chunk_range_match.group(1))
+            new_idx = int(chunk_range_match.group(3))
+            for line in chunk_range_match.group(5).splitlines():
+                if line.startswith("-"):
+                    output_diff_text.append(f"{old_idx} None {line}")
+                    old_idx += 1
+                elif line.startswith("+"):
+                    output_diff_text.append(f"None {new_idx} {line}")
+                    new_idx += 1
+                else:
+                    output_diff_text.append(f"{old_idx} {new_idx} {line}")
+                    old_idx += 1
+                    new_idx += 1
+
+        output_diff_text = "\n".join(output_diff_text)
         list_diff.append(
             {
                 "file": new_file,
-                "chunk": diff_text,
+                "chunk": output_diff_text,
             }
         )
     return list_diff
@@ -133,7 +133,7 @@ def create_comment(
     return comments
 
 
-def analyze_single_chunks(
+async def analyze_single_chunks(
     single_chunk_model: Model, parsed_diff: list[dict[str, Any]]
 ) -> list[dict[str, Any]]:
     """Analyze single chunks and create comments.
@@ -145,29 +145,33 @@ def analyze_single_chunks(
     Returns:
         list[dict[str, Any]]: comments for single chunk review
     """
-    comments = []
-    title = EVENT_DATA["pull_request"]["title"]
-    description = EVENT_DATA["pull_request"]["body"]
-    for diff in parsed_diff:
+
+    async def process_single_chunk(diff: dict[str, Any]):
         file = diff["file"]
         chunk = diff["chunk"]
-        response = single_chunk_model.get_response_single_chunk(
+        response = await single_chunk_model.get_response_single_chunk(
             file, title, description, chunk
         )
         response = response.strip("`").lstrip("json").strip() or "[]"
 
         try:
             response_json = json.loads(response)
-            new_comments = create_comment(file, response_json)
-            comments.extend(new_comments)
+            return create_comment(file, response_json)
         except json.JSONDecodeError:
             print(f"Failed to parse response: {response}")
-            continue
+            return []
 
+    title = EVENT_DATA["pull_request"]["title"]
+    description = EVENT_DATA["pull_request"]["body"]
+    tasks = [process_single_chunk(diff) for diff in parsed_diff]
+    results = await asyncio.gather(*tasks)
+
+    # Flatten the list of comments
+    comments = [comment for result in results for comment in result]
     return comments
 
 
-def get_file_content(file: str) -> str | None:
+async def get_file_content(file: str) -> str | None:
     """Get file content from Gitea.
 
     Args:
@@ -183,15 +187,18 @@ def get_file_content(file: str) -> str | None:
     url = f"{repo_url}/raw/{branch}%2F{replaced_file}?ref={branch}"
 
     try:
-        response = requests.get(url, headers=HEADERS)
-        response.raise_for_status()
-        return response.text
-    except requests.RequestException as e:
-        print(f"Failed to get file content: {e}")
-        return None
+        async with aiohttp.ClientSession(headers=HEADERS) as session:
+            async with session.get(url) as response:
+                response.raise_for_status()
+                return await response.text()
+    except aiohttp.ClientError as e:  # More specific exception handling
+        print(f"Network error fetching {file}: {e}")
+    except asyncio.TimeoutError:
+        print(f"Timeout fetching {file}")
+    return None
 
 
-def analyze_full_context(
+async def analyze_full_context(
     full_context_model: Model, parsed_diff: list[dict[str, Any]]
 ) -> str:
     """Analyze full context and create review.
@@ -203,20 +210,26 @@ def analyze_full_context(
     Returns:
         str: review for full context
     """
-    file_contents = []
-    for diff in parsed_diff:
+
+    async def get_file_data(diff: dict[str, Any]):
         file = diff["file"]
         chunk = diff["chunk"]
         content = get_file_content(file)
         if content is None:
-            continue
-        file_contents.append(f"File: {file}")
-        file_contents.append(content)
-        file_contents.append(f"Diff: {chunk}")
+            return None
+        return f"File: {file}\n{content}\nDiff: {chunk}"
+
+    tasks = [get_file_data(diff) for diff in parsed_diff]
+    file_contents_list = await asyncio.gather(*tasks)
+
+    file_contents = [item for item in file_contents_list if item is not None]
+
+    if not file_contents:
+        return ""
 
     title = EVENT_DATA["pull_request"]["title"]
     description = EVENT_DATA["pull_request"]["body"]
-    response = full_context_model.get_response_full_context(
+    response = await full_context_model.get_response_full_context(
         title, description, file_contents
     )
     response = response.strip("`").lstrip("markdown").strip()
@@ -246,10 +259,10 @@ def post_review(
     response.raise_for_status()
 
 
-def main() -> None:
-    """Code Reviewer for Gitea."""
+async def main() -> None:
+    """Code Reviewer for Gitea: Asynchronous version."""
     if EVENT_DATA["action"] not in ["opened", "synchronized"]:
-        print("Unsupproted event.")
+        print("Unsupported event.")
         return
 
     diff = get_diff()
@@ -271,10 +284,21 @@ def main() -> None:
     )
 
     parsed_diff = parse_diff(diff)
-    comments = analyze_single_chunks(single_chunk_model, parsed_diff)
-    full_context_response = analyze_full_context(full_context_model, parsed_diff)
+    comments_task = asyncio.create_task(
+        analyze_single_chunks(single_chunk_model, parsed_diff)
+    )
+
+    if EVENT_DATA["action"] == "opened":
+        full_context_response_task = asyncio.create_task(
+            analyze_full_context(full_context_model, parsed_diff)
+        )
+        full_context_response = await full_context_response_task
+    else:
+        full_context_response = ""
+
+    comments = await comments_task
     post_review(full_context_response, comments)
 
 
 if __name__ == "__main__":
-    main()
+    asyncio.run(main())

.gitea/scripts/model.py

@@ -4,8 +4,16 @@ from enum import Enum
 from typing import Any
 
 import google.generativeai as genai
-from anthropic import Anthropic
-from openai import OpenAI
+import typing_extensions as typing
+from anthropic import AsyncAnthropic
+from openai import AsyncOpenAI
+
+
+class GoogleResponse(typing.TypedDict):
+    """The response from Google model."""
+
+    lineNumber: int
+    reviewComment: str
 
 
 class ModelProvider(Enum):
@@ -35,6 +43,7 @@ class ModelProvider(Enum):
 PREFIX_TO_MODEL = {
     "gpt": ModelProvider.OPENAI,
     "o1": ModelProvider.OPENAI,
+    "o3": ModelProvider.OPENAI,
     "claude": ModelProvider.ANTHROPIC,
     "gemini": ModelProvider.GOOGLE,
     "deepseek": ModelProvider.DEEPSEEK,
@@ -79,16 +88,18 @@ class Model:
         """
         match self.provider:
             case ModelProvider.OPENAI:
-                return OpenAI(api_key=api_key)
+                return AsyncOpenAI(api_key=api_key)
             case ModelProvider.ANTHROPIC:
-                return Anthropic(api_key=api_key)
+                return AsyncAnthropic(api_key=api_key)
             case ModelProvider.GOOGLE:
                 genai.configure(api_key=api_key)
-                return genai.GenerativeModel(model=self.model, api_key=api_key)
+                return genai.GenerativeModel(
+                    model_name=self.model, system_instruction=self.system_prompt
+                )
             case ModelProvider.DEEPSEEK:
-                return OpenAI(api_key=api_key, base_url="https://api.deepseek.com")
+                return AsyncOpenAI(api_key=api_key, base_url="https://api.deepseek.com")
 
-    def request(self, prompt: str) -> str:
+    async def request(self, prompt: str) -> str:
         """Request the model to generate a response.
 
         Args:
@@ -99,7 +110,7 @@ class Model:
         """
         match self.provider:
             case ModelProvider.OPENAI | ModelProvider.DEEPSEEK:
-                response = self.session.chat.completions.create(
+                response = await self.session.chat.completions.create(
                     model=self.model,
                     messages=[
                         {"role": "system", "content": self.system_prompt},
@@ -113,7 +124,7 @@ class Model:
                 )
                 return response.choices[0].message.content.strip()
             case ModelProvider.ANTHROPIC:
-                response = self.session.messages.create(
+                response = await self.session.messages.create(
                     model=self.model,
                     messages=[{"role": "user", "content": prompt}],
                     system=[
@@ -128,10 +139,16 @@ class Model:
                 )
                 return response.content[0].text.strip()
             case ModelProvider.GOOGLE:
-                response = self.session.generate_content(prompt)
+                response = await self.session.generate_content_async(
+                    prompt,
+                    generation_config=genai.GenerationConfig(
+                        response_mime_type="application/json",
+                        response_schema=list[GoogleResponse],
+                    ),
+                )
                 return response.text.strip()
 
-    def get_response_single_chunk(
+    async def get_response_single_chunk(
         self, file: str, title: str, description: str, chunk: str
     ) -> str:
         """Get the response for a single chunk.
@@ -146,9 +163,9 @@ class Model:
             str: The response.
         """
         prompt = SINGLE_CHUNK_USER_PROMPT.format(file, title, description, chunk)
-        return self.request(prompt)
+        return await self.request(prompt)
 
-    def get_response_full_context(
+    async def get_response_full_context(
         self, title: str, description: str, file_contents: list[str]
     ) -> str:
         """Get the response for full context.
@@ -165,7 +182,7 @@ class Model:
             prompt = FULL_CONTEXT_USER_PROMPT.format(
                 title, description, "\n".join(file_contents)
             )
-            return self.request(prompt)
+            return await self.request(prompt)
         except Exception as e:
             print(f"Error during full context response: {e}")
             print(prompt)
@@ -175,14 +192,21 @@ class Model:
 SINGLE_CHUNK_SYSTEM_PROMPT = (
     "Your task is to review pull requests. Instructions:\n"
     "- Provide the response in the following JSON format:  "
-    """[{{"lineNumber":  <line_number>, "reviewComment": "<review comment>"}}] \n"""
+    """[{{"lineNumber": int, "reviewComment": str}}] \n"""
     "- lineNumber is about the line number of the code that in new file. \n"
+    "- lineNumber can be found at the front of each line. \n"
+    "- At the first number is old line number, the second number is new line number. \n"
+    "- If the line starts with `+`, it means the line is added. \n"
+    "- If the line starts with `-`, it means the line is deleted. \n"
+    "- Evaluate whether the code changes and additions are appropriate "
+    "and if the new code structure is suitable. \n"
     "- Do not give positive comments or compliments. \n"
     "- Provide comments and suggestions ONLY if there is something to improve"
     "otherwise return an empty array. \n"
     "- Write the comment in GitHub Markdown format. \n"
     "- Use the given description only for the overall context "
     "and only comment the code. \n"
+    "- Do not suggest type hint or naming convention. \n"
     "- IMPORTANT: NEVER suggest adding comments to the code. \n"
 )
 SINGLE_CHUNK_USER_PROMPT = (

.gitea/workflows/ai-review.yml

@@ -21,15 +21,15 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install requests py-gitea openai anthropic google-generativeai          
+          pip install aiohttp requests py-gitea openai anthropic google-generativeai
 
       - name: Run Code Review
         env:
           ACCESS_TOKEN: ${{ secrets.ACCESS_TOKEN }}
-          FULL_CONTEXT_MODEL: deepseek-reasoner
-          FULL_CONTEXT_API_KEY: ${{ secrets.DEEPSEEK_API_KEY }}
-          SINGLE_CHUNK_MODEL: gpt-4o
-          SINGLE_CHUNK_API_KEY: ${{ secrets.OPENAI_API_KEY }}
+          FULL_CONTEXT_MODEL: o3-mini
+          FULL_CONTEXT_API_KEY: ${{ secrets.OPENAI_API_KEY }}
+          SINGLE_CHUNK_MODEL: gemini-2.0-flash-exp
+          SINGLE_CHUNK_API_KEY: ${{ secrets.GOOGLE_API_KEY }}
           EXCLUDE: "*.yml,*.yaml"
         run: python .gitea/scripts/code_review.py
 

CLAUDE.md

@@ -0,0 +1,564 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+Rust-OpenMM is a Rust port of the OpenMM molecular simulation toolkit. The project follows a test-driven development approach, converting C++ tests to Rust and implementing functionality to make them pass.
+
+## Key Directories
+
+- `openmm/` - Original C++ OpenMM library (reference implementation)
+- `rust-openmm/src/` - Rust implementation following the module structure:
+  - `system.rs` - Core molecular system representation
+  - `force/` - Force field components (trait-based)
+  - `integrator/` - Time integration algorithms
+  - `platform/` - Compute platform abstractions
+  - `context.rs` - Simulation context binding components
+  - `state.rs` - Simulation state management
+
+## Development Commands
+
+```bash
+# Build the project
+cargo build
+
+# Run tests (most are currently ignored)
+cargo test
+
+# Run tests including ignored ones
+cargo test -- --ignored
+
+# Generate documentation
+cargo doc --open
+
+# Check code without building
+cargo check
+
+# Format code
+cargo fmt
+
+# Run linter
+cargo clippy
+```
+
+## Development Strategy
+
+1. **Test-Driven Conversion**: Convert C++ tests first, then implement functionality
+2. **Progressive Implementation**: Use `unimplemented!()` placeholders for missing functionality
+3. **Test Organization**:
+   - Unit tests: In source files using `#[cfg(test)]` modules
+   - Integration tests: In `tests/` directory (for cross-module functionality)
+
+## Architecture Principles
+
+- **Trait-Based Design**: Forces and integrators use traits for extensibility
+- **Idiomatic Rust**: Prefer Rust patterns over direct C++ translation
+- **Modular Structure**: Each force type, integrator, and platform is a separate module
+- **Zero-Copy Where Possible**: Use references and borrowing to minimize allocations
+
+## Key Dependencies
+
+- `nalgebra`: Linear algebra operations (vectors, matrices)
+- `approx`: Floating-point comparisons in tests
+
+## Feature Flags
+
+- `cpu` (default): CPU compute platform
+- `vulkan`: Vulkan compute platform (not yet implemented)
+- 'cuda': Nvidia cuda platform
+- 'opencl': OpenCL platform
+
+## C++ Reference Locations
+
+When implementing new functionality, refer to:
+- Force implementations: `openmm/openmmapi/src/*Force.cpp`
+- Test cases: `openmm/tests/Test*.cpp`
+- Platform code: `openmm/platforms/*/src/`
+
+## Common Patterns
+
+### Adding a New Force Type
+1. Create `src/force/new_force.rs`
+2. Define struct implementing `Force` trait
+3. Add module declaration to `src/force/mod.rs`
+4. Convert corresponding C++ test from `openmm/tests/`
+
+### Implementing Placeholder Methods
+Replace `unimplemented!()` with actual implementation, ensuring:
+- Proper error handling with `Result` types
+- Efficient memory usage
+- Thread safety where applicable
+
+## Testing Approach
+
+- Tests should closely mirror C++ test structure for validation
+- Use `approx::assert_relative_eq!` for floating-point comparisons
+- Mark incomplete tests with `#[ignore]` until implementation is ready
+
+# TODO
+
+## API
+### Core Objects
+- [ ] System - `openmm/openmmapi/include/openmm/System.h`
+- [ ] Context - `openmm/openmmapi/include/openmm/Context.h`
+- [ ] Platform - `openmm/openmmapi/include/openmm/Platform.h`
+- [ ] State - `openmm/openmmapi/include/openmm/State.h`
+
+### Forces
+- [ ] The Force abstract class - `openmm/openmmapi/include/openmm/Force.h`
+- Common bonded and non-bonded forces
+  - [ ] CMAPTorsionForce - `openmm/openmmapi/include/openmm/CMAPTorsionForce.h`
+  - [ ] DrudeForce - `openmm/plugins/drude/openmmapi/include/openmm/DrudeForce.h`
+  - [ ] GBSAOBCForce - `openmm/openmmapi/include/openmm/GBSAOBCForce.h`
+  - [ ] GayBerneForce - `openmm/openmmapi/include/openmm/GayBerneForce.h`
+  - [ ] HarmonicAngleForce - `openmm/openmmapi/include/openmm/HarmonicAngleForce.h`
+  - [ ] HarmonicBondForce - `openmm/openmmapi/include/openmm/HarmonicBondForce.h`
+  - [ ] NonbondedForce - `openmm/openmmapi/include/openmm/NonbondedForce.h`
+  - [ ] PeriodicTorsionForce - `openmm/openmmapi/include/openmm/PeriodicTorsionForce.h`
+  - [ ] RBTorsionForce - `openmm/openmmapi/include/openmm/RBTorsionForce.h`
+
+- AMOEBA forces
+  - [ ] AmoebaGeneralizedKirkwoodForce - `openmm/plugins/amoeba/openmmapi/include/openmm/AmoebaGeneralizedKirkwoodForce.h`
+  - [ ] AmoebaMultipoleForce - `openmm/plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h`
+  - [ ] AmoebaTorsionTorsionForce - `openmm/plugins/amoeba/openmmapi/include/openmm/AmoebaTorsionTorsionForce.h`
+  - [ ] AmoebaVdwForce - `openmm/plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h`
+  - [ ] AmoebaWcaDispersionForce - `openmm/plugins/amoeba/openmmapi/include/openmm/AmoebaWcaDispersionForce.h`
+  - [ ] HippoNonbondedForce - `openmm/plugins/amoeba/openmmapi/include/openmm/HippoNonbondedForce.h`
+
+- Pseudo-forces
+  - [ ] AndersenThermostat - `openmm/openmmapi/include/openmm/AndersenThermostat.h`
+  - [ ] ATMForce - `openmm/openmmapi/include/openmm/ATMForce.h`
+  - [ ] CMMotionRemover - `openmm/openmmapi/include/openmm/CMMotionRemover.h`
+  - [ ] MonteCarloAnisotropicBarostat - `openmm/openmmapi/include/openmm/MonteCarloAnisotropicBarostat.h`
+  - [ ] MonteCarloBarostat - `openmm/openmmapi/include/openmm/MonteCarloBarostat.h`
+  - [ ] MonteCarloFlexibleBarostat - `openmm/openmmapi/include/openmm/MonteCarloFlexibleBarostat.h`
+  - [ ] MonteCarloMembraneBarostat - `openmm/openmmapi/include/openmm/MonteCarloMembraneBarostat.h`
+  - [ ] RMSDForce - `openmm/openmmapi/include/openmm/RMSDForce.h`
+  - [ ] RPMDMonteCarloBarostat - `openmm/plugins/rpmd/openmmapi/include/openmm/RPMDMonteCarloBarostat.h`
+
+- Customizing Force
+  - [ ] CustomAngleForce - `openmm/openmmapi/include/openmm/CustomAngleForce.h`
+  - [ ] CustomBondForce - `openmm/openmmapi/include/openmm/CustomBondForce.h`
+  - [ ] CustomCVForce - `openmm/openmmapi/include/openmm/CustomCVForce.h`
+  - [ ] CustomCentroidBondForce - `openmm/openmmapi/include/openmm/CustomCentroidBondForce.h`
+  - [ ] CustomCompoundBondForce - `openmm/openmmapi/include/openmm/CustomCompoundBondForce.h`
+  - [ ] CustomExternalForce - `openmm/openmmapi/include/openmm/CustomExternalForce.h`
+  - [ ] CustomGBForce - `openmm/openmmapi/include/openmm/CustomGBForce.h`
+  - [ ] CustomHbondForce - `openmm/openmmapi/include/openmm/CustomHbondForce.h`
+  - [ ] CustomManyParticleForce - `openmm/openmmapi/include/openmm/CustomManyParticleForce.h`
+  - [ ] CustomNonbondedForce - `openmm/openmmapi/include/openmm/CustomNonbondedForce.h`
+  - [ ] CustomTorsionForce - `openmm/openmmapi/include/openmm/CustomTorsionForce.h`
+
+### Integrators
+- [ ] The integrator abstract object - `openmm/openmmapi/include/openmm/Integrator.h`
+
+- General purpose integrators
+  - [ ] BrownianIntegrator - `openmm/openmmapi/include/openmm/BrownianIntegrator.h`
+  - [ ] LangevinIntegrator - `openmm/openmmapi/include/openmm/LangevinIntegrator.h`
+  - [ ] LangevinMiddleIntegrator - `openmm/openmmapi/include/openmm/LangevinMiddleIntegrator.h`
+  - [ ] NoseHooverIntegrator - `openmm/openmmapi/include/openmm/NoseHooverIntegrator.h`
+  - [ ] VariableLangevinIntegrator - `openmm/openmmapi/include/openmm/VariableLangevinIntegrator.h`
+  - [ ] VariableVerletIntegrator - `openmm/openmmapi/include/openmm/VariableVerletIntegrator.h`
+  - [ ] VerletIntegrator - `openmm/openmmapi/include/openmm/VerletIntegrator.h`
+
+- Drude integrators
+  - [ ] DrudeIntegrator - `openmm/plugins/drude/openmmapi/include/openmm/DrudeIntegrator.h`
+  - [ ] DrudeLangevinIntegrator - `openmm/plugins/drude/openmmapi/include/openmm/DrudeLangevinIntegrator.h`
+  - [ ] DrudeNoseHooverIntegrator - `openmm/plugins/drude/openmmapi/include/openmm/DrudeNoseHooverIntegrator.h`
+  - [ ] DrudeSCFIntegrator - `openmm/plugins/drude/openmmapi/include/openmm/DrudeSCFIntegrator.h`
+
+- Ring Polymer Molecular Dynamics integrators
+  - [ ] RPMDIntegrator - `openmm/plugins/rpmd/openmmapi/include/openmm/RPMDIntegrator.h`
+
+- Customizing Integrator
+  - [ ] CustomIntegrator - `openmm/openmmapi/include/openmm/CustomIntegrator.h`
+  - [ ] CompoundIntegrator - `openmm/openmmapi/include/openmm/CompoundIntegrator.h`
+
+### Extra classes
+- Tabulated functions
+  - [ ] TabulatedFunction - `openmm/openmmapi/include/openmm/TabulatedFunction.h`
+  - [ ] Continuous1DFunction - `openmm/openmmapi/include/openmm/TabulatedFunction.h`
+  - [ ] Continuous2DFunction - `openmm/openmmapi/include/openmm/TabulatedFunction.h`
+  - [ ] Continuous3DFunction - `openmm/openmmapi/include/openmm/TabulatedFunction.h`
+  - [ ] Discrete1DFunction - `openmm/openmmapi/include/openmm/TabulatedFunction.h`
+  - [ ] Discrete2DFunction - `openmm/openmmapi/include/openmm/TabulatedFunction.h`
+  - [ ] Discrete3DFunction - `openmm/openmmapi/include/openmm/TabulatedFunction.h`
+
+- Virtual Sites
+  - [ ] VirtualSite - `openmm/openmmapi/include/openmm/VirtualSite.h`
+  - [ ] LocalCoordinatesSite - `openmm/openmmapi/include/openmm/VirtualSite.h`
+  - [ ] OutOfPlaneSite - `openmm/openmmapi/include/openmm/VirtualSite.h`
+  - [ ] ThreeParticleAverageSite - `openmm/openmmapi/include/openmm/VirtualSite.h`
+  - [ ] TwoParticleAverageSite - `openmm/openmmapi/include/openmm/VirtualSite.h`
+
+- Serialization
+  - [ ] SerializationNode - `openmm/serialization/include/openmm/serialization/SerializationNode.h`
+  - [ ] SerializationProxy - `openmm/serialization/include/openmm/serialization/SerializationProxy.h`
+  - [ ] XmlSerializer - `openmm/serialization/include/openmm/serialization/XmlSerializer.h`
+
+- Other classes
+  - [ ] LocalEnergyMinimizer - `openmm/openmmapi/include/openmm/LocalEnergyMinimizer.h`
+  - [ ] MinimizationReporter - `openmm/openmmapi/include/openmm/MinimizationReporter.h`
+  - [ ] NoseHooverChain - `openmm/openmmapi/include/openmm/NoseHooverChain.h`
+  - [ ] OpenMMException - `openmm/openmmapi/include/openmm/OpenMMException.h`
+  - [ ] Vec3 - `openmm/openmmapi/include/openmm/Vec3.h`
+
+## Integrated Examples
+- Cookbook examples (Python-based, reference only)
+  - [ ] First Simulation
+  - [ ] Changing Temperature and Pressure
+  - [ ] Saving Systems to XML Files
+  - [ ] Merging Molecules in a Topology
+  - [ ] Adding Hydrogens to Nonstandard Molecules
+  - [ ] Applying a Fixed External Force
+  - [ ] Constraining Atom Positions
+  - [ ] Restraining Atom Positions
+  - [ ] Restraining Dihedrals
+  - [ ] Analyzing Energy Contributions
+  - [ ] Computing Interaction Energies
+  - [ ] Querying and Modifying Charges and Other Parameters
+
+- Examples
+  - [ ] HelloArgon - `openmm/examples/HelloArgon.cpp`
+  - [ ] HelloEthane - `openmm/examples/HelloEthane.cpp`
+  - [ ] HelloSodiumChloride - `openmm/examples/HelloSodiumChloride.cpp`
+  - [ ] HelloWaterBox - `openmm/examples/HelloWaterBox.cpp`
+  - [ ] simulateAmber - `openmm/examples/simulateAmber.py`
+  - [ ] simulateCharmm - `openmm/examples/simulateCharmm.py`
+  - [ ] simulateGromacs - `openmm/examples/simulateGromacs.py`
+  - [ ] simulatePdb - `openmm/examples/simulatePdb.py`
+
+- Test files
+  - **Core**
+    - [ ] TestATMForce - `openmm/tests/TestATMForce.h`
+    - [ ] TestAndersenThermostat - `openmm/tests/TestAndersenThermostat.h`
+    - [ ] TestBrownianIntegrator - `openmm/tests/TestBrownianIntegrator.h`
+    - [ ] TestCMAPTorsionForce - `openmm/tests/TestCMAPTorsionForce.h`
+    - [ ] TestCMMotionRemover - `openmm/tests/TestCMMotionRemover.h`
+    - [ ] TestCheckpoints - `openmm/tests/TestCheckpoints.h`
+    - [ ] TestCompoundIntegrator - `openmm/tests/TestCompoundIntegrator.h`
+    - [ ] TestCustomAngleForce - `openmm/tests/TestCustomAngleForce.h`
+    - [ ] TestCustomBondForce - `openmm/tests/TestCustomBondForce.h`
+    - [ ] TestCustomCPPForce - `openmm/tests/TestCustomCPPForce.h`
+    - [ ] TestCustomCVForce - `openmm/tests/TestCustomCVForce.h`
+    - [ ] TestCustomCentroidBondForce - `openmm/tests/TestCustomCentroidBondForce.h`
+    - [ ] TestCustomCompoundBondForce - `openmm/tests/TestCustomCompoundBondForce.h`
+    - [ ] TestCustomExternalForce - `openmm/tests/TestCustomExternalForce.h`
+    - [ ] TestCustomGBForce - `openmm/tests/TestCustomGBForce.h`
+    - [ ] TestCustomHbondForce - `openmm/tests/TestCustomHbondForce.h`
+    - [ ] TestCustomIntegrator - `openmm/tests/TestCustomIntegrator.h`
+    - [ ] TestCustomManyParticleForce - `openmm/tests/TestCustomManyParticleForce.h`
+    - [ ] TestCustomNonbondedForce - `openmm/tests/TestCustomNonbondedForce.h`
+    - [ ] TestCustomTorsionForce - `openmm/tests/TestCustomTorsionForce.h`
+    - [ ] TestDispersionPME - `openmm/tests/TestDispersionPME.h`
+    - [ ] TestEnforcePeriodicBox - `openmm/tests/TestEnforcePeriodicBox.cpp`
+    - [ ] TestEwald - `openmm/tests/TestEwald.h`
+    - [ ] TestFindExclusions - `openmm/tests/TestFindExclusions.cpp`
+    - [ ] TestFindMolecules - `openmm/tests/TestFindMolecules.cpp`
+    - [ ] TestGBSAOBCForce - `openmm/tests/TestGBSAOBCForce.h`
+    - [ ] TestGayBerneForce - `openmm/tests/TestGayBerneForce.h`
+    - [ ] TestHarmonicAngleForce - `openmm/tests/TestHarmonicAngleForce.h`
+      - [x] TestBonds - closed by #10 
+      - [x] TestPeriodic - closed by #10
+      - [ ] TestParallelComputation
+    - [ ] TestHarmonicBondForce - `openmm/tests/TestHarmonicBondForce.h`
+      - [x] TestBonds - closed by #8
+      - [x] TestPeriodic - closed by #8
+      - [ ] TestParallelComputation
+    - [ ] TestLangevinIntegrator - `openmm/tests/TestLangevinIntegrator.h`
+    - [ ] TestLangevinMiddleIntegrator - `openmm/tests/TestLangevinMiddleIntegrator.h`
+    - [ ] TestLocalEnergyMinimizer - `openmm/tests/TestLocalEnergyMinimizer.h`
+    - [ ] TestMonteCarloAnisotropicBarostat - `openmm/tests/TestMonteCarloAnisotropicBarostat.h`
+    - [ ] TestMonteCarloBarostat - `openmm/tests/TestMonteCarloBarostat.h`
+    - [ ] TestMonteCarloFlexibleBarostat - `openmm/tests/TestMonteCarloFlexibleBarostat.h`
+    - [ ] TestNonbondedForce - `openmm/tests/TestNonbondedForce.h`
+    - [ ] TestNoseHooverIntegrator - `openmm/tests/TestNoseHooverIntegrator.h`
+    - [ ] TestParser - `openmm/tests/TestParser.cpp`
+    - [ ] TestPeriodicTorsionForce - `openmm/tests/TestPeriodicTorsionForce.h`
+    - [ ] TestRBTorsionForce - `openmm/tests/TestRBTorsionForce.h`
+    - [ ] TestRMSDForce - `openmm/tests/TestRMSDForce.h`
+    - [ ] TestSettle - `openmm/tests/TestSettle.h`
+    - [ ] TestSplineFitter - `openmm/tests/TestSplineFitter.cpp`
+    - [x] TestSystem - `openmm/tests/TestSystem.cpp`
+      - closed by #6
+    - [ ] TestVariableLangevinIntegrator - `openmm/tests/TestVariableLangevinIntegrator.h`
+    - [ ] TestVariableVerletIntegrator - `openmm/tests/TestVariableVerletIntegrator.h`
+    - [ ] TestVectorExpression - `openmm/tests/TestVectorExpression.cpp`
+    - [ ] TestVectorize - `openmm/tests/TestVectorize.cpp`
+    - [ ] TestVectorizeAvx - `openmm/tests/TestVectorizeAvx.cpp`
+    - [ ] TestVectorizeAvx2 - `openmm/tests/TestVectorizeAvx2.cpp`
+    - [ ] TestVectorizeGeneric - `openmm/tests/TestVectorizeGeneric.h`
+    - [ ] TestVerletIntegrator - `openmm/tests/TestVerletIntegrator.h`
+    - [ ] TestVirtualSites - `openmm/tests/TestVirtualSites.h`
+
+  - **Serialization**
+    - [ ] TestSerializeAmoebaGeneralizedKirkwoodForce - `openmm/plugins/amoeba/serialization/tests/TestSerializeAmoebaGeneralizedKirkwoodForce.cpp`
+    - [ ] TestSerializeAmoebaMultipoleForce - `openmm/plugins/amoeba/serialization/tests/TestSerializeAmoebaMultipoleForce.cpp`
+    - [ ] TestSerializeAmoebaTorsionTorsionForce - `openmm/plugins/amoeba/serialization/tests/TestSerializeAmoebaTorsionTorsionForce.cpp`
+    - [ ] TestSerializeAmoebaVdwForce - `openmm/plugins/amoeba/serialization/tests/TestSerializeAmoebaVdwForce.cpp`
+    - [ ] TestSerializeAmoebaWcaDispersionForce - `openmm/plugins/amoeba/serialization/tests/TestSerializeAmoebaWcaDispersionForce.cpp`
+    - [ ] TestSerializeHippoNonbondedForce - `openmm/plugins/amoeba/serialization/tests/TestSerializeHippoNonbondedForce.cpp`
+    - [ ] TestSerializeDrudeForce - `openmm/plugins/drude/serialization/tests/TestSerializeDrudeForce.cpp`
+    - [ ] TestSerializeDrudeLangevinIntegrator - `openmm/plugins/drude/serialization/tests/TestSerializeDrudeLangevinIntegrator.cpp`
+    - [ ] TestSerializeDrudeNoseHooverIntegrator - `openmm/plugins/drude/serialization/tests/TestSerializeDrudeNoseHooverIntegrator.cpp`
+    - [ ] TestSerializationNode - `openmm/serialization/tests/TestSerializationNode.cpp`
+    - [ ] TestSerializeATMForce - `openmm/serialization/tests/TestSerializeATMForce.cpp`
+    - [ ] TestSerializeAndersenThermostat - `openmm/serialization/tests/TestSerializeAndersenThermostat.cpp`
+    - [ ] TestSerializeCMAPTorsion - `openmm/serialization/tests/TestSerializeCMAPTorsion.cpp`
+    - [ ] TestSerializeCMMotionRemover - `openmm/serialization/tests/TestSerializeCMMotionRemover.cpp`
+    - [ ] TestSerializeCustomAngleForce - `openmm/serialization/tests/TestSerializeCustomAngleForce.cpp`
+    - [ ] TestSerializeCustomBondForce - `openmm/serialization/tests/TestSerializeCustomBondForce.cpp`
+    - [ ] TestSerializeCustomCVForce - `openmm/serialization/tests/TestSerializeCustomCVForce.cpp`
+    - [ ] TestSerializeCustomCentroidBondForce - `openmm/serialization/tests/TestSerializeCustomCentroidBondForce.cpp`
+    - [ ] TestSerializeCustomCompoundBondForce - `openmm/serialization/tests/TestSerializeCustomCompoundBondForce.cpp`
+    - [ ] TestSerializeCustomExternalForce - `openmm/serialization/tests/TestSerializeCustomExternalForce.cpp`
+    - [ ] TestSerializeCustomGBForce - `openmm/serialization/tests/TestSerializeCustomGBForce.cpp`
+    - [ ] TestSerializeCustomHbondForce - `openmm/serialization/tests/TestSerializeCustomHbondForce.cpp`
+    - [ ] TestSerializeCustomManyParticleForce - `openmm/serialization/tests/TestSerializeCustomManyParticleForce.cpp`
+    - [ ] TestSerializeCustomNonbondedForce - `openmm/serialization/tests/TestSerializeCustomNonbondedForce.cpp`
+    - [ ] TestSerializeCustomTorsionForce - `openmm/serialization/tests/TestSerializeCustomTorsionForce.cpp`
+    - [ ] TestSerializeGBSAOBCForce - `openmm/serialization/tests/TestSerializeGBSAOBCForce.cpp`
+    - [ ] TestSerializeGayBerneForce - `openmm/serialization/tests/TestSerializeGayBerneForce.cpp`
+    - [ ] TestSerializeHarmonicAngleForce - `openmm/serialization/tests/TestSerializeHarmonicAngleForce.cpp`
+    - [ ] TestSerializeHarmonicBondForce - `openmm/serialization/tests/TestSerializeHarmonicBondForce.cpp`
+    - [ ] TestSerializeIntegrator - `openmm/serialization/tests/TestSerializeIntegrator.cpp`
+    - [ ] TestSerializeMonteCarloAnisotropicBarostat - `openmm/serialization/tests/TestSerializeMonteCarloAnisotropicBarostat.cpp`
+    - [ ] TestSerializeMonteCarloBarostat - `openmm/serialization/tests/TestSerializeMonteCarloBarostat.cpp`
+    - [ ] TestSerializeMonteCarloFlexibleBarostat - `openmm/serialization/tests/TestSerializeMonteCarloFlexibleBarostat.cpp`
+    - [ ] TestSerializeMonteCarloMembraneBarostat - `openmm/serialization/tests/TestSerializeMonteCarloMembraneBarostat.cpp`
+    - [ ] TestSerializeNonbondedForce - `openmm/serialization/tests/TestSerializeNonbondedForce.cpp`
+    - [ ] TestSerializeNoseHooverIntegrator - `openmm/serialization/tests/TestSerializeNoseHooverIntegrator.cpp`
+    - [ ] TestSerializePeriodicTorsionForce - `openmm/serialization/tests/TestSerializePeriodicTorsionForce.cpp`
+    - [ ] TestSerializeRBTorsionForce - `openmm/serialization/tests/TestSerializeRBTorsionForce.cpp`
+    - [ ] TestSerializeRMSDForce - `openmm/serialization/tests/TestSerializeRMSDForce.cpp`
+    - [ ] TestSerializeState - `openmm/serialization/tests/TestSerializeState.cpp`
+    - [ ] TestSerializeSystem - `openmm/serialization/tests/TestSerializeSystem.cpp`
+    - [ ] TestSerializeTabulatedFunctions - `openmm/serialization/tests/TestSerializeTabulatedFunctions.cpp`
+
+  - **Platforms**
+    - [ ] CPU
+      - [ ] TestCpuCheckpoints - `openmm/platforms/cpu/tests/TestCpuCheckpoints.cpp`
+      - [ ] TestCpuCompoundIntegrator - `openmm/platforms/cpu/tests/TestCpuCompoundIntegrator.cpp`
+      - [ ] TestCpuCustomCPPForce - `openmm/platforms/cpu/tests/TestCpuCustomCPPForce.cpp`
+      - [ ] TestCpuCustomGBForce - `openmm/platforms/cpu/tests/TestCpuCustomGBForce.cpp`
+      - [ ] TestCpuCustomManyParticleForce - `openmm/platforms/cpu/tests/TestCpuCustomManyParticleForce.cpp`
+      - [ ] TestCpuCustomNonbondedForce - `openmm/platforms/cpu/tests/TestCpuCustomNonbondedForce.cpp`
+      - [ ] TestCpuDispersionPME - `openmm/platforms/cpu/tests/TestCpuDispersionPME.cpp`
+      - [ ] TestCpuEwald - `openmm/platforms/cpu/tests/TestCpuEwald.cpp`
+      - [ ] TestCpuGBSAOBCForce - `openmm/platforms/cpu/tests/TestCpuGBSAOBCForce.cpp`
+      - [ ] TestCpuGayBerneForce - `openmm/platforms/cpu/tests/TestCpuGayBerneForce.cpp`
+      - [ ] TestCpuHarmonicAngleForce - `openmm/platforms/cpu/tests/TestCpuHarmonicAngleForce.cpp`
+      - [ ] TestCpuLangevinIntegrator - `openmm/platforms/cpu/tests/TestCpuLangevinIntegrator.cpp`
+      - [ ] TestCpuLangevinMiddleIntegrator - `openmm/platforms/cpu/tests/TestCpuLangevinMiddleIntegrator.cpp`
+      - [ ] TestCpuNeighborList - `openmm/platforms/cpu/tests/TestCpuNeighborList.cpp`
+      - [ ] TestCpuNonbondedForce - `openmm/platforms/cpu/tests/TestCpuNonbondedForce.cpp`
+      - [ ] TestCpuPeriodicTorsionForce - `openmm/platforms/cpu/tests/TestCpuPeriodicTorsionForce.cpp`
+      - [ ] TestCpuRBTorsionForce - `openmm/platforms/cpu/tests/TestCpuRBTorsionForce.cpp`
+      - [ ] TestCpuSettle - `openmm/platforms/cpu/tests/TestCpuSettle.cpp`
+    - [ ] CUDA
+      - [ ] TestCudaATMForce - `openmm/platforms/cuda/tests/TestCudaATMForce.cpp`
+      - [ ] TestCudaAndersenThermostat - `openmm/platforms/cuda/tests/TestCudaAndersenThermostat.cpp`
+      - [ ] TestCudaBrownianIntegrator - `openmm/platforms/cuda/tests/TestCudaBrownianIntegrator.cpp`
+      - [ ] TestCudaCMAPTorsionForce - `openmm/platforms/cuda/tests/TestCudaCMAPTorsionForce.cpp`
+      - [ ] TestCudaCMMotionRemover - `openmm/platforms/cuda/tests/TestCudaCMMotionRemover.cpp`
+      - [ ] TestCudaCheckpoints - `openmm/platforms/cuda/tests/TestCudaCheckpoints.cpp`
+      - [ ] TestCudaCompoundIntegrator - `openmm/platforms/cuda/tests/TestCudaCompoundIntegrator.cpp`
+      - [ ] TestCudaCustomAngleForce - `openmm/platforms/cuda/tests/TestCudaCustomAngleForce.cpp`
+      - [ ] TestCudaCustomBondForce - `openmm/platforms/cuda/tests/TestCudaCustomBondForce.cpp`
+      - [ ] TestCudaCustomCPPForce - `openmm/platforms/cuda/tests/TestCudaCustomCPPForce.cpp`
+      - [ ] TestCudaCustomCVForce - `openmm/platforms/cuda/tests/TestCudaCustomCVForce.cpp`
+      - [ ] TestCudaCustomCentroidBondForce - `openmm/platforms/cuda/tests/TestCudaCustomCentroidBondForce.cpp`
+      - [ ] TestCudaCustomCompoundBondForce - `openmm/platforms/cuda/tests/TestCudaCustomCompoundBondForce.cpp`
+      - [ ] TestCudaCustomExternalForce - `openmm/platforms/cuda/tests/TestCudaCustomExternalForce.cpp`
+      - [ ] TestCudaCustomGBForce - `openmm/platforms/cuda/tests/TestCudaCustomGBForce.cpp`
+      - [ ] TestCudaCustomHbondForce - `openmm/platforms/cuda/tests/TestCudaCustomHbondForce.cpp`
+      - [ ] TestCudaCustomIntegrator - `openmm/platforms/cuda/tests/TestCudaCustomIntegrator.cpp`
+      - [ ] TestCudaCustomManyParticleForce - `openmm/platforms/cuda/tests/TestCudaCustomManyParticleForce.cpp`
+      - [ ] TestCudaCustomNonbondedForce - `openmm/platforms/cuda/tests/TestCudaCustomNonbondedForce.cpp`
+      - [ ] TestCudaCustomTorsionForce - `openmm/platforms/cuda/tests/TestCudaCustomTorsionForce.cpp`
+      - [ ] TestCudaDispersionPME - `openmm/platforms/cuda/tests/TestCudaDispersionPME.cpp`
+      - [ ] TestCudaEwald - `openmm/platforms/cuda/tests/TestCudaEwald.cpp`
+      - [ ] TestCudaFFT3D - `openmm/platforms/cuda/tests/TestCudaFFT3D.cpp`
+      - [ ] TestCudaGBSAOBCForce - `openmm/platforms/cuda/tests/TestCudaGBSAOBCForce.cpp`
+      - [ ] TestCudaGayBerneForce - `openmm/platforms/cuda/tests/TestCudaGayBerneForce.cpp`
+      - [ ] TestCudaHarmonicAngleForce - `openmm/platforms/cuda/tests/TestCudaHarmonicAngleForce.cpp`
+      - [ ] TestCudaHarmonicBondForce - `openmm/platforms/cuda/tests/TestCudaHarmonicBondForce.cpp`
+      - [ ] TestCudaLangevinIntegrator - `openmm/platforms/cuda/tests/TestCudaLangevinIntegrator.cpp`
+      - [ ] TestCudaLangevinMiddleIntegrator - `openmm/platforms/cuda/tests/TestCudaLangevinMiddleIntegrator.cpp`
+      - [ ] TestCudaLocalEnergyMinimizer - `openmm/platforms/cuda/tests/TestCudaLocalEnergyMinimizer.cpp`
+      - [ ] TestCudaMonteCarloAnisotropicBarostat - `openmm/platforms/cuda/tests/TestCudaMonteCarloAnisotropicBarostat.cpp`
+      - [ ] TestCudaMonteCarloBarostat - `openmm/platforms/cuda/tests/TestCudaMonteCarloBarostat.cpp`
+      - [ ] TestCudaMonteCarloFlexibleBarostat - `openmm/platforms/cuda/tests/TestCudaMonteCarloFlexibleBarostat.cpp`
+      - [ ] TestCudaMultipleForces - `openmm/platforms/cuda/tests/TestCudaMultipleForces.cpp`
+      - [ ] TestCudaNonbondedForce - `openmm/platforms/cuda/tests/TestCudaNonbondedForce.cpp`
+      - [ ] TestCudaNoseHooverIntegrator - `openmm/platforms/cuda/tests/TestCudaNoseHooverIntegrator.cpp`
+      - [ ] TestCudaPeriodicTorsionForce - `openmm/platforms/cuda/tests/TestCudaPeriodicTorsionForce.cpp`
+      - [ ] TestCudaRBTorsionForce - `openmm/platforms/cuda/tests/TestCudaRBTorsionForce.cpp`
+      - [ ] TestCudaRMSDForce - `openmm/platforms/cuda/tests/TestCudaRMSDForce.cpp`
+      - [ ] TestCudaRandom - `openmm/platforms/cuda/tests/TestCudaRandom.cpp`
+      - [ ] TestCudaSettle - `openmm/platforms/cuda/tests/TestCudaSettle.cpp`
+      - [ ] TestCudaSort - `openmm/platforms/cuda/tests/TestCudaSort.cpp`
+      - [ ] TestCudaVariableLangevinIntegrator - `openmm/platforms/cuda/tests/TestCudaVariableLangevinIntegrator.cpp`
+      - [ ] TestCudaVariableVerletIntegrator - `openmm/platforms/cuda/tests/TestCudaVariableVerletIntegrator.cpp`
+      - [ ] TestCudaVerletIntegrator - `openmm/platforms/cuda/tests/TestCudaVerletIntegrator.cpp`
+      - [ ] TestCudaVirtualSites - `openmm/platforms/cuda/tests/TestCudaVirtualSites.cpp` 
+    - [ ] OpenCL
+      - [ ] TestOpenCLATMForce - `openmm/platforms/opencl/tests/TestOpenCLATMForce.cpp`
+      - [ ] TestOpenCLAndersenThermostat - `openmm/platforms/opencl/tests/TestOpenCLAndersenThermostat.cpp`
+      - [ ] TestOpenCLBrownianIntegrator - `openmm/platforms/opencl/tests/TestOpenCLBrownianIntegrator.cpp`
+      - [ ] TestOpenCLCMAPTorsionForce - `openmm/platforms/opencl/tests/TestOpenCLCMAPTorsionForce.cpp`
+      - [ ] TestOpenCLCMMotionRemover - `openmm/platforms/opencl/tests/TestOpenCLCMMotionRemover.cpp`
+      - [ ] TestOpenCLCheckpoints - `openmm/platforms/opencl/tests/TestOpenCLCheckpoints.cpp`
+      - [ ] TestOpenCLCompoundIntegrator - `openmm/platforms/opencl/tests/TestOpenCLCompoundIntegrator.cpp`
+      - [ ] TestOpenCLCustomAngleForce - `openmm/platforms/opencl/tests/TestOpenCLCustomAngleForce.cpp`
+      - [ ] TestOpenCLCustomBondForce - `openmm/platforms/opencl/tests/TestOpenCLCustomBondForce.cpp`
+      - [ ] TestOpenCLCustomCPPForce - `openmm/platforms/opencl/tests/TestOpenCLCustomCPPForce.cpp`
+      - [ ] TestOpenCLCustomCVForce - `openmm/platforms/opencl/tests/TestOpenCLCustomCVForce.cpp`
+      - [ ] TestOpenCLCustomCentroidBondForce - `openmm/platforms/opencl/tests/TestOpenCLCustomCentroidBondForce.cpp`
+      - [ ] TestOpenCLCustomCompoundBondForce - `openmm/platforms/opencl/tests/TestOpenCLCustomCompoundBondForce.cpp`
+      - [ ] TestOpenCLCustomExternalForce - `openmm/platforms/opencl/tests/TestOpenCLCustomExternalForce.cpp`
+      - [ ] TestOpenCLCustomGBForce - `openmm/platforms/opencl/tests/TestOpenCLCustomGBForce.cpp`
+      - [ ] TestOpenCLCustomHbondForce - `openmm/platforms/opencl/tests/TestOpenCLCustomHbondForce.cpp`
+      - [ ] TestOpenCLCustomIntegrator - `openmm/platforms/opencl/tests/TestOpenCLCustomIntegrator.cpp`
+      - [ ] TestOpenCLCustomManyParticleForce - `openmm/platforms/opencl/tests/TestOpenCLCustomManyParticleForce.cpp`
+      - [ ] TestOpenCLCustomNonbondedForce - `openmm/platforms/opencl/tests/TestOpenCLCustomNonbondedForce.cpp`
+      - [ ] TestOpenCLCustomTorsionForce - `openmm/platforms/opencl/tests/TestOpenCLCustomTorsionForce.cpp`
+      - [ ] TestOpenCLDeviceQuery - `openmm/platforms/opencl/tests/TestOpenCLDeviceQuery.cpp`
+      - [ ] TestOpenCLDispersionPME - `openmm/platforms/opencl/tests/TestOpenCLDispersionPME.cpp`
+      - [ ] TestOpenCLEwald - `openmm/platforms/opencl/tests/TestOpenCLEwald.cpp`
+      - [ ] TestOpenCLFFT - `openmm/platforms/opencl/tests/TestOpenCLFFT.cpp`
+      - [ ] TestOpenCLGBSAOBCForce - `openmm/platforms/opencl/tests/TestOpenCLGBSAOBCForce.cpp`
+      - [ ] TestOpenCLGayBerneForce - `openmm/platforms/opencl/tests/TestOpenCLGayBerneForce.cpp`
+      - [ ] TestOpenCLHarmonicAngleForce - `openmm/platforms/opencl/tests/TestOpenCLHarmonicAngleForce.cpp`
+      - [ ] TestOpenCLHarmonicBondForce - `openmm/platforms/opencl/tests/TestOpenCLHarmonicBondForce.cpp`
+      - [ ] TestOpenCLLangevinIntegrator - `openmm/platforms/opencl/tests/TestOpenCLLangevinIntegrator.cpp`
+      - [ ] TestOpenCLLangevinMiddleIntegrator - `openmm/platforms/opencl/tests/TestOpenCLLangevinMiddleIntegrator.cpp`
+      - [ ] TestOpenCLLocalEnergyMinimizer - `openmm/platforms/opencl/tests/TestOpenCLLocalEnergyMinimizer.cpp`
+      - [ ] TestOpenCLMonteCarloAnisotropicBarostat - `openmm/platforms/opencl/tests/TestOpenCLMonteCarloAnisotropicBarostat.cpp`
+      - [ ] TestOpenCLMonteCarloBarostat - `openmm/platforms/opencl/tests/TestOpenCLMonteCarloBarostat.cpp`
+      - [ ] TestOpenCLMonteCarloFlexibleBarostat - `openmm/platforms/opencl/tests/TestOpenCLMonteCarloFlexibleBarostat.cpp`
+      - [ ] TestOpenCLMultipleForces - `openmm/platforms/opencl/tests/TestOpenCLMultipleForces.cpp`
+      - [ ] TestOpenCLNonbondedForce - `openmm/platforms/opencl/tests/TestOpenCLNonbondedForce.cpp`
+      - [ ] TestOpenCLNoseHooverIntegrator - `openmm/platforms/opencl/tests/TestOpenCLNoseHooverIntegrator.cpp`
+      - [ ] TestOpenCLPeriodicTorsionForce - `openmm/platforms/opencl/tests/TestOpenCLPeriodicTorsionForce.cpp`
+      - [ ] TestOpenCLRBTorsionForce - `openmm/platforms/opencl/tests/TestOpenCLRBTorsionForce.cpp`
+      - [ ] TestOpenCLRMSDForce - `openmm/platforms/opencl/tests/TestOpenCLRMSDForce.cpp`
+      - [ ] TestOpenCLRandom - `openmm/platforms/opencl/tests/TestOpenCLRandom.cpp`
+      - [ ] TestOpenCLSettle - `openmm/platforms/opencl/tests/TestOpenCLSettle.cpp`
+      - [ ] TestOpenCLSort - `openmm/platforms/opencl/tests/TestOpenCLSort.cpp`
+      - [ ] TestOpenCLVariableLangevinIntegrator - `openmm/platforms/opencl/tests/TestOpenCLVariableLangevinIntegrator.cpp`
+      - [ ] TestOpenCLVariableVerletIntegrator - `openmm/platforms/opencl/tests/TestOpenCLVariableVerletIntegrator.cpp`
+      - [ ] TestOpenCLVerletIntegrator - `openmm/platforms/opencl/tests/TestOpenCLVerletIntegrator.cpp`
+      - [ ] TestOpenCLVirtualSites - `openmm/platforms/opencl/tests/TestOpenCLVirtualSites.cpp`
+    - [ ] Reference
+      - [ ] TestReferenceATMForce - `openmm/platforms/reference/tests/TestReferenceATMForce.cpp`
+      - [ ] TestReferenceAndersenThermostat - `openmm/platforms/reference/tests/TestReferenceAndersenThermostat.cpp`
+      - [ ] TestReferenceBrownianIntegrator - `openmm/platforms/reference/tests/TestReferenceBrownianIntegrator.cpp`
+      - [ ] TestReferenceCMAPTorsionForce - `openmm/platforms/reference/tests/TestReferenceCMAPTorsionForce.cpp`
+      - [ ] TestReferenceCMMotionRemover - `openmm/platforms/reference/tests/TestReferenceCMMotionRemover.cpp`
+      - [ ] TestReferenceCheckpoints - `openmm/platforms/reference/tests/TestReferenceCheckpoints.cpp`
+      - [ ] TestReferenceCompoundIntegrator - `openmm/platforms/reference/tests/TestReferenceCompoundIntegrator.cpp`
+      - [ ] TestReferenceCustomAngleForce - `openmm/platforms/reference/tests/TestReferenceCustomAngleForce.cpp`
+      - [ ] TestReferenceCustomBondForce - `openmm/platforms/reference/tests/TestReferenceCustomBondForce.cpp`
+      - [ ] TestReferenceCustomCPPForce - `openmm/platforms/reference/tests/TestReferenceCustomCPPForce.cpp`
+      - [ ] TestReferenceCustomCVForce - `openmm/platforms/reference/tests/TestReferenceCustomCVForce.cpp`
+      - [ ] TestReferenceCustomCentroidBondForce - `openmm/platforms/reference/tests/TestReferenceCustomCentroidBondForce.cpp`
+      - [ ] TestReferenceCustomCompoundBondForce - `openmm/platforms/reference/tests/TestReferenceCustomCompoundBondForce.cpp`
+      - [ ] TestReferenceCustomExternalForce - `openmm/platforms/reference/tests/TestReferenceCustomExternalForce.cpp`
+      - [ ] TestReferenceCustomGBForce - `openmm/platforms/reference/tests/TestReferenceCustomGBForce.cpp`
+      - [ ] TestReferenceCustomHbondForce - `openmm/platforms/reference/tests/TestReferenceCustomHbondForce.cpp`
+      - [ ] TestReferenceCustomIntegrator - `openmm/platforms/reference/tests/TestReferenceCustomIntegrator.cpp`
+      - [ ] TestReferenceCustomManyParticleForce - `openmm/platforms/reference/tests/TestReferenceCustomManyParticleForce.cpp`
+      - [ ] TestReferenceCustomNonbondedForce - `openmm/platforms/reference/tests/TestReferenceCustomNonbondedForce.cpp`
+      - [ ] TestReferenceCustomTorsionForce - `openmm/platforms/reference/tests/TestReferenceCustomTorsionForce.cpp`
+      - [ ] TestReferenceDispersionPME - `openmm/platforms/reference/tests/TestReferenceDispersionPME.cpp`
+      - [ ] TestReferenceEwald - `openmm/platforms/reference/tests/TestReferenceEwald.cpp`
+      - [ ] TestReferenceGBSAOBCForce - `openmm/platforms/reference/tests/TestReferenceGBSAOBCForce.cpp`
+      - [ ] TestReferenceGayBerneForce - `openmm/platforms/reference/tests/TestReferenceGayBerneForce.cpp`
+      - [ ] TestReferenceHarmonicAngleForce - `openmm/platforms/reference/tests/TestReferenceHarmonicAngleForce.cpp`
+      - [ ] TestReferenceHarmonicBondForce - `openmm/platforms/reference/tests/TestReferenceHarmonicBondForce.cpp`
+      - [ ] TestReferenceKineticEnergy - `openmm/platforms/reference/tests/TestReferenceKineticEnergy.cpp`
+      - [ ] TestReferenceLangevinIntegrator - `openmm/platforms/reference/tests/TestReferenceLangevinIntegrator.cpp`
+      - [ ] TestReferenceLangevinMiddleIntegrator - `openmm/platforms/reference/tests/TestReferenceLangevinMiddleIntegrator.cpp`
+      - [ ] TestReferenceLocalEnergyMinimizer - `openmm/platforms/reference/tests/TestReferenceLocalEnergyMinimizer.cpp`
+      - [ ] TestReferenceMonteCarloAnisotropicBarostat - `openmm/platforms/reference/tests/TestReferenceMonteCarloAnisotropicBarostat.cpp`
+      - [ ] TestReferenceMonteCarloBarostat - `openmm/platforms/reference/tests/TestReferenceMonteCarloBarostat.cpp`
+      - [ ] TestReferenceMonteCarloFlexibleBarostat - `openmm/platforms/reference/tests/TestReferenceMonteCarloFlexibleBarostat.cpp`
+      - [ ] TestReferenceMonteCarloMembraneBarostat - `openmm/platforms/reference/tests/TestReferenceMonteCarloMembraneBarostat.cpp`
+      - [ ] TestReferenceNeighborList - `openmm/platforms/reference/tests/TestReferenceNeighborList.cpp`
+      - [ ] TestReferenceNonbondedForce - `openmm/platforms/reference/tests/TestReferenceNonbondedForce.cpp`
+      - [ ] TestReferenceNoseHooverIntegrator - `openmm/platforms/reference/tests/TestReferenceNoseHooverIntegrator.cpp`
+      - [ ] TestReferencePeriodicTorsionForce - `openmm/platforms/reference/tests/TestReferencePeriodicTorsionForce.cpp`
+      - [ ] TestReferenceRBTorsionForce - `openmm/platforms/reference/tests/TestReferenceRBTorsionForce.cpp`
+      - [ ] TestReferenceRMSDForce - `openmm/platforms/reference/tests/TestReferenceRMSDForce.cpp`
+      - [ ] TestReferenceRandom - `openmm/platforms/reference/tests/TestReferenceRandom.cpp`
+      - [ ] TestReferenceSettle - `openmm/platforms/reference/tests/TestReferenceSettle.cpp`
+      - [ ] TestReferenceVariableLangevinIntegrator - `openmm/platforms/reference/tests/TestReferenceVariableLangevinIntegrator.cpp`
+      - [ ] TestReferenceVariableVerletIntegrator - `openmm/platforms/reference/tests/TestReferenceVariableVerletIntegrator.cpp`
+      - [ ] TestReferenceVerletIntegrator - `openmm/platforms/reference/tests/TestReferenceVerletIntegrator.cpp`
+      - [ ] TestReferenceVirtualSites - `openmm/platforms/reference/tests/TestReferenceVirtualSites.cpp`
+
+  - **Plugins**
+    - [ ] CUDA
+      - [ ] TestCudaAmoebaExtrapolatedPolarization - `openmm/plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaExtrapolatedPolarization.cpp`
+      - [ ] TestCudaAmoebaGeneralizedKirkwoodForce - `openmm/plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaGeneralizedKirkwoodForce.cpp`
+      - [ ] TestCudaAmoebaMultipoleForce - `openmm/plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaMultipoleForce.cpp`
+      - [ ] TestCudaAmoebaTorsionTorsionForce - `openmm/plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaTorsionTorsionForce.cpp`
+      - [ ] TestCudaAmoebaVdwForce - `openmm/plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaVdwForce.cpp`
+      - [ ] TestCudaHippoNonbondedForce - `openmm/plugins/amoeba/platforms/cuda/tests/TestCudaHippoNonbondedForce.cpp`
+      - [ ] TestCudaWcaDispersionForce - `openmm/plugins/amoeba/platforms/cuda/tests/TestCudaWcaDispersionForce.cpp`
+      - [ ] TestCudaDrudeForce - `openmm/plugins/drude/platforms/cuda/tests/TestCudaDrudeForce.cpp`
+      - [ ] TestCudaDrudeLangevinIntegrator - `openmm/plugins/drude/platforms/cuda/tests/TestCudaDrudeLangevinIntegrator.cpp`
+      - [ ] TestCudaDrudeNoseHoover - `openmm/plugins/drude/platforms/cuda/tests/TestCudaDrudeNoseHoover.cpp`
+      - [ ] TestCudaDrudeSCFIntegrator - `openmm/plugins/drude/platforms/cuda/tests/TestCudaDrudeSCFIntegrator.cpp`
+      - [ ] TestCudaRpmd - `openmm/plugins/rpmd/platforms/cuda/tests/TestCudaRpmd.cpp`
+    - [ ] OpenCL
+      - [ ] TestOpenCLAmoebaExtrapolatedPolarization - `openmm/plugins/amoeba/platforms/opencl/tests/TestOpenCLAmoebaExtrapolatedPolarization.cpp`
+      - [ ] TestOpenCLAmoebaGeneralizedKirkwoodForce - `openmm/plugins/amoeba/platforms/opencl/tests/TestOpenCLAmoebaGeneralizedKirkwoodForce.cpp`
+      - [ ] TestOpenCLAmoebaMultipoleForce - `openmm/plugins/amoeba/platforms/opencl/tests/TestOpenCLAmoebaMultipoleForce.cpp`
+      - [ ] TestOpenCLAmoebaTorsionTorsionForce - `openmm/plugins/amoeba/platforms/opencl/tests/TestOpenCLAmoebaTorsionTorsionForce.cpp`
+      - [ ] TestOpenCLAmoebaVdwForce - `openmm/plugins/amoeba/platforms/opencl/tests/TestOpenCLAmoebaVdwForce.cpp`
+      - [ ] TestOpenCLHippoNonbondedForce - `openmm/plugins/amoeba/platforms/opencl/tests/TestOpenCLHippoNonbondedForce.cpp`
+      - [ ] TestOpenCLWcaDispersionForce - `openmm/plugins/amoeba/platforms/opencl/tests/TestOpenCLWcaDispersionForce.cpp`
+      - [ ] TestOpenCLDrudeForce - `openmm/plugins/drude/platforms/opencl/tests/TestOpenCLDrudeForce.cpp`
+      - [ ] TestOpenCLDrudeLangevinIntegrator - `openmm/plugins/drude/platforms/opencl/tests/TestOpenCLDrudeLangevinIntegrator.cpp`
+      - [ ] TestOpenCLDrudeNoseHoover - `openmm/plugins/drude/platforms/opencl/tests/TestOpenCLDrudeNoseHoover.cpp`
+      - [ ] TestOpenCLDrudeSCFIntegrator - `openmm/plugins/drude/platforms/opencl/tests/TestOpenCLDrudeSCFIntegrator.cpp`
+      - [ ] TestOpenCLRpmd - `openmm/plugins/rpmd/platforms/opencl/tests/TestOpenCLRpmd.cpp`
+    - [ ] Reference
+      - [ ] TestReferenceAmoebaExtrapolatedPolarization - `openmm/plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaExtrapolatedPolarization.cpp`
+      - [ ] TestReferenceAmoebaGeneralizedKirkwoodForce - `openmm/plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaGeneralizedKirkwoodForce.cpp`
+      - [ ] TestReferenceAmoebaMultipoleForce - `openmm/plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaMultipoleForce.cpp`
+      - [ ] TestReferenceAmoebaTorsionTorsionForce - `openmm/plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaTorsionTorsionForce.cpp`
+      - [ ] TestReferenceAmoebaVdwForce - `openmm/plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaVdwForce.cpp`
+      - [ ] TestReferenceHippoNonbondedForce - `openmm/plugins/amoeba/platforms/reference/tests/TestReferenceHippoNonbondedForce.cpp`
+      - [ ] TestReferenceWcaDispersionForce - `openmm/plugins/amoeba/platforms/reference/tests/TestReferenceWcaDispersionForce.cpp`
+      - [ ] TestReferenceDrudeForce - `openmm/plugins/drude/platforms/reference/tests/TestReferenceDrudeForce.cpp`
+      - [ ] TestReferenceDrudeLangevinIntegrator - `openmm/plugins/drude/platforms/reference/tests/TestReferenceDrudeLangevinIntegrator.cpp`
+      - [ ] TestReferenceDrudeNoseHoover - `openmm/plugins/drude/platforms/reference/tests/TestReferenceDrudeNoseHoover.cpp`
+      - [ ] TestReferenceDrudeSCFIntegrator - `openmm/plugins/drude/platforms/reference/tests/TestReferenceDrudeSCFIntegrator.cpp`
+      - [ ] TestReferenceRpmd - `openmm/plugins/rpmd/platforms/reference/tests/TestReferenceRpmd.cpp`
+    - [ ] Serialization
+      - [ ] TestSerializeAmoebaGeneralizedKirkwoodForce - `openmm/plugins/amoeba/serialization/tests/TestSerializeAmoebaGeneralizedKirkwoodForce.cpp`
+      - [ ] TestSerializeAmoebaMultipoleForce - `openmm/plugins/amoeba/serialization/tests/TestSerializeAmoebaMultipoleForce.cpp`
+      - [ ] TestSerializeAmoebaTorsionTorsionForce - `openmm/plugins/amoeba/serialization/tests/TestSerializeAmoebaTorsionTorsionForce.cpp`
+      - [ ] TestSerializeAmoebaVdwForce - `openmm/plugins/amoeba/serialization/tests/TestSerializeAmoebaVdwForce.cpp`
+      - [ ] TestSerializeAmoebaWcaDispersionForce - `openmm/plugins/amoeba/serialization/tests/TestSerializeAmoebaWcaDispersionForce.cpp`
+      - [ ] TestSerializeHippoNonbondedForce - `openmm/plugins/amoeba/serialization/tests/TestSerializeHippoNonbondedForce.cpp`
+      - [ ] TestSerializeDrudeForce - `openmm/plugins/drude/serialization/tests/TestSerializeDrudeForce.cpp`
+      - [ ] TestSerializeDrudeLangevinIntegrator - `openmm/plugins/drude/serialization/tests/TestSerializeDrudeLangevinIntegrator.cpp`
+      - [ ] TestSerializeDrudeNoseHooverIntegrator - `openmm/plugins/drude/serialization/tests/TestSerializeDrudeNoseHooverIntegrator.cpp`
+    - [ ] TestAmoebaExtrapolatedPolarization - `openmm/plugins/amoeba/tests/TestAmoebaExtrapolatedPolarization.h`
+    - [ ] TestAmoebaGeneralizedKirkwoodForce - `openmm/plugins/amoeba/tests/TestAmoebaGeneralizedKirkwoodForce.h`
+    - [ ] TestAmoebaMultipoleForce - `openmm/plugins/amoeba/tests/TestAmoebaMultipoleForce.h`
+    - [ ] TestAmoebaTorsionTorsionForce - `openmm/plugins/amoeba/tests/TestAmoebaTorsionTorsionForce.h`
+    - [ ] TestAmoebaVdwForce - `openmm/plugins/amoeba/tests/TestAmoebaVdwForce.h`
+    - [ ] TestHippoNonbondedForce - `openmm/plugins/amoeba/tests/TestHippoNonbondedForce.h`
+    - [ ] TestWcaDispersionForce - `openmm/plugins/amoeba/tests/TestWcaDispersionForce.h`
+    - [ ] TestCpuPme - `openmm/plugins/cpupme/tests/TestCpuPme.cpp`
+    - [ ] TestDrudeForce - `openmm/plugins/drude/tests/TestDrudeForce.h`
+    - [ ] TestDrudeLangevinIntegrator - `openmm/plugins/drude/tests/TestDrudeLangevinIntegrator.h`
+    - [ ] TestDrudeNoseHoover - `openmm/plugins/drude/tests/TestDrudeNoseHoover.h`
+    - [ ] TestDrudeSCFIntegrator - `openmm/plugins/drude/tests/TestDrudeSCFIntegrator.h` 
+    - [ ] TestRpmd - `openmm/plugins/rpmd/tests/TestRpmd.h`

Cargo.toml

@@ -5,6 +5,13 @@ edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
+[features]
+default = ["cpu"]
+cpu = []
+vulkan = []
+cuda = []
+opencl = []
+
 [dependencies]
 nalgebra = "0.33.2"
-approx = "0.5"
+approx = "0.5"