### Run muParser Example

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/muparser/Install.txt

Navigate to the samples directory and execute the example binary to test the installation.

```bash
cd samples/example1
./example1
```

--------------------------------

### Install Project Rules

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/googletest/googlemock/CMakeLists.txt

Defines the installation rules for the project.

```cmake
install_project(gmock gmock_main)
```

--------------------------------

### Install muParser

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/muparser/Install.txt

Compile and install the muParser library and its components. 'sudo' is required for system-wide installation.

```bash
make
[sudo*] make install
[sudo*] ldconfig
```

--------------------------------

### Install gmxapi from Local Source Archive

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/gmxapi/userguide/install.rst

Download the gmxapi source distribution and install it from the local archive file. This is an alternative to installing directly from PyPI.

```bash
pip download gmxapi
pip install gmxapi-<version>.tar.gz
```

--------------------------------

### Configure and install pkg-config file

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/muparser/CMakeLists.txt

Sets up variables and installs the .pc file for system-wide package discovery.

```cmake
set(PACKAGE_NAME muparser)
if(ENABLE_WIDE_CHAR)
  set(PKG_CONFIG_FLAGS "-D_UNICODE")
endif(ENABLE_WIDE_CHAR)
configure_file(
    muparser.pc.in
    ${CMAKE_BINARY_DIR}/muparser.pc
    @ONLY
)
install(
    FILES ${CMAKE_BINARY_DIR}/muparser.pc
    DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig
    EXCLUDE_FROM_ALL
)
```

--------------------------------

### Install CMake and Pybind11

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/gmxapi/userguide/install.rst

Install essential build tools required by the gmxapi installer.

```bash
pip install --upgrade cmake pybind11
```

--------------------------------

### Set up Python virtual environment and install dependencies

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/gmxapi/userguide/install.rst

This command sequence sets up a Python virtual environment, activates it, ensures pip is up-to-date, and installs the mpi4py package. This is a prerequisite for installing gmxapi.

```bash
python3 -m venv $HOME/myvenv
. $HOME/myvenv/bin/activate
python -m ensurepip --default-pip
pip install --upgrade pip setuptools wheel
pip install mpi4py
```

--------------------------------

### Install and Run Black

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/dev-manual/code-formatting.rst

Install the Black formatter and run it using the repository's configuration file.

```bash
pip install black
black --config .black.toml .
```

--------------------------------

### Build OpenMP Examples

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/tng_io/src/tests/CMakeLists.txt

Configures the build to include OpenMP support for examples if found.

```cmake
if(TNG_BUILD_EXAMPLES)
    find_package(OpenMP)
    if(OPENMP_FOUND)
        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
        set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")

        add_executable(md_openmp md_openmp.c)
        target_link_libraries(md_openmp tng_io ${OpenMP_LIBS})
        if(UNIX)
            target_link_libraries(md_openmp m)
        endif()
        set_property(TARGET md_openmp PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/examples)
        set_property(TARGET md_openmp APPEND PROPERTY COMPILE_DEFINITIONS TNG_BUILD_OPENMP_EXAMPLES)


        add_executable(md_openmp_util md_openmp_util.c)
        target_link_libraries(md_openmp_util tng_io ${OpenMP_LIBS})
        if(UNIX)
            target_link_libraries(md_openmp_util m)
        endif()
        set_property(TARGET md_openmp_util PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/examples)
        set_property(TARGET md_openmp_util APPEND PROPERTY COMPILE_DEFINITIONS TNG_BUILD_OPENMP_EXAMPLES)

        add_executable(tng_parallel_read tng_parallel_read.c)
        target_link_libraries(tng_parallel_read tng_io)
        if(UNIX)
            target_link_libraries(tng_parallel_read m)
        endif()
        set_property(TARGET tng_parallel_read PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/examples)
        set_property(TARGET tng_parallel_read APPEND PROPERTY COMPILE_DEFINITIONS TNG_BUILD_OPENMP_EXAMPLES)
    endif()

    add_executable(tng_io_read_pos tng_io_read_pos.c)
    target_link_libraries(tng_io_read_pos tng_io)
    if(UNIX)
        target_link_libraries(tng_io_read_pos m)
    endif()
    if(HAVE_INTTYPES_H)
      set_property(TARGET tng_io_read_pos APPEND PROPERTY COMPILE_DEFINITIONS USE_STD_INTTYPES_H=1)
    endif()
    set_property(TARGET tng_io_read_pos PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/examples)

    add_executable(tng_io_read_pos_util tng_io_read_pos_util.c)
    target_link_libraries(tng_io_read_pos_util tng_io)
    if(UNIX)
        target_link_libraries(tng_io_read_pos_util m)
    endif()
    if(HAVE_INTTYPES_H)
      set_property(TARGET tng_io_read_pos_util APPEND PROPERTY COMPILE_DEFINITIONS USE_STD_INTTYPES_H=1)
    endif()
    set_property(TARGET tng_io_read_pos_util PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/examples)

    if(TNG_BUILD_FORTRAN)
        # This does not work due to a bug in CMake. Remove lines below if no fortran compiler is found.
        enable_language(Fortran OPTIONAL)
        if(${CMAKE_Fortran_COMPILER_WORKS})
            get_filename_component (Fortran_COMPILER_NAME ${CMAKE_Fortran_COMPILER} NAME)
            if (Fortran_COMPILER_NAME STREQUAL "gfortran")
                set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fcray-pointer ${OpenMP_C_FLAGS} -std=legacy -cpp -ffixed-line-length-none")
            endif()
            if(OPENMP_FOUND)

```

--------------------------------

### Include Sphinx Macros and Setup

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/CMakeLists.txt

Includes necessary Sphinx macros and initializes the Sphinx setup for documentation generation.

```cmake
include(SphinxMacros.cmake)
gmx_init_sphinx_setup(${SPHINX_INPUT_DIR})
```

--------------------------------

### Download and Install gmxapi from Source

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/gmxapi/userguide/install.rst

Use these commands to download the package to a directory and install it without index lookups.

```bash
pip download --destination-directory DIR .

# Build and install from the source directory.
pip install --no-index --find-links=DIR .
```

--------------------------------

### Build and Install GoogleTest

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/googletest/googletest/README.md

Compiles the generated build scripts and installs the resulting binaries to the system.

```bash
make
sudo make install    # Install in /usr/local/ by default
```

--------------------------------

### Install gmxapi from Source

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/gmxapi/userguide/install.rst

Installs the package from the local GROMACS source repository.

```shell
cd python_packaging/gmxapi
pip install -r requirements.txt
pip install .
```

--------------------------------

### Install template files

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/share/template/CMakeLists.txt

Defines installation rules for the template source files, README, and CMake helper files.

```cmake
install(FILES CMakeLists.txt.template
        DESTINATION ${GMX_INSTALL_GMXDATADIR}/template
        RENAME CMakeLists.txt
        COMPONENT development)

    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/README template.cpp Makefile.pkg
        DESTINATION ${GMX_INSTALL_GMXDATADIR}/template
        COMPONENT development)

install(FILES cmake/FindGROMACS.cmake
        DESTINATION ${GMX_INSTALL_GMXDATADIR}/template/cmake
        COMPONENT development)
```

--------------------------------

### Install Copying File

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/CMakeLists.txt

Installs the COPYING file to the data destination. This is typically necessary for binary distributions.

```cmake
#COPYING file: Only necessary for binary distributions.
#Simpler to always install.
install(FILES COPYING DESTINATION ${GMX_INSTALL_GMXDATADIR} COMPONENT data)
```

--------------------------------

### Install OpenCL utility and kernel files

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/gromacs/CMakeLists.txt

Deploys OpenCL headers and kernel source files to the installation directory when GMX_GPU_OPENCL is enabled.

```cmake
if(GMX_GPU_OPENCL)
    # Install the utility headers
    file(GLOB OPENCL_INSTALLED_FILES
        gpu_utils/vectype_ops.clh
        gpu_utils/device_utils.clh
        )
    install(FILES ${OPENCL_INSTALLED_FILES}
        DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/gpu_utils
        COMPONENT libraries)
    file(GLOB OPENCL_INSTALLED_FILES
        pbcutil/ishift.h
        )
    install(FILES ${OPENCL_INSTALLED_FILES}
        DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/pbcutil
        COMPONENT libraries)

    # Install the NBNXM source and headers
    file(GLOB OPENCL_INSTALLED_FILES
        nbnxm/constants.h
        )
    install(FILES ${OPENCL_INSTALLED_FILES}
        DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm
        COMPONENT libraries)
    file(GLOB OPENCL_INSTALLED_FILES
        nbnxm/opencl/nbnxm_ocl_kernels.cl
        nbnxm/opencl/nbnxm_ocl_kernel.clh
        nbnxm/opencl/nbnxm_ocl_kernel_pruneonly.clh
        nbnxm/opencl/nbnxm_ocl_kernels.clh
        nbnxm/opencl/nbnxm_ocl_kernels_fastgen.clh
        nbnxm/opencl/nbnxm_ocl_kernels_fastgen_add_twincut.clh
        nbnxm/opencl/nbnxm_ocl_kernel_utils.clh
        nbnxm/opencl/nbnxm_ocl_consts.h
        )
    install(FILES ${OPENCL_INSTALLED_FILES}
        DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm/opencl
        COMPONENT libraries)

    # Install the PME source and headers
    file(GLOB OPENCL_INSTALLED_FILES
        ewald/pme_spread.clh
        ewald/pme_solve.clh
        ewald/pme_gather.clh
        ewald/pme_gpu_calculate_splines.clh
        ewald/pme_program.cl
        ewald/pme_gpu_types.h
        )
    install(FILES ${OPENCL_INSTALLED_FILES}
        DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/ewald
        COMPONENT libraries)
endif()
```

--------------------------------

### Install Python documentation dependencies

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/dev-manual/documentation-generation.rst

Install the required Python packages for building the full documentation set.

```bash
pip install -r python_packaging/gmxapi/requirements.txt
```

--------------------------------

### Install gmxapi Python package

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/gmxapi/userguide/install.rst

After setting up the environment and sourcing the Gromacs installation, this command installs the gmxapi package from PyPI. Use --no-cache-dir to ensure a fresh build.

```bash
. /path/to/gromacs/bin/GMXRC
pip install --no-cache-dir gmxapi
```

--------------------------------

### Offline Installation via Wheels

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/gmxapi/userguide/install.rst

Commands to download or build wheels for offline installation.

```shell
# Remove any locally cached (previously built) wheels.
pip cache remove gmxapi

# Download gmxapi and dependencies from pypi.
pip wheel --wheel-dir DIR gmxapi
# or, using package source from the GROMACS repository
cd python_packaging/gmxapi
pip wheel --wheel-dir DIR .

# Later, install.
pip install --no-index --find-links=DIR DIR/gmxapi*whl
```

--------------------------------

### PDB File Format Example

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/reference-manual/file-formats.rst

Example of a PDB file structure showing atom records with coordinates and occupancy/temperature factors.

```text
ATOM      1  H1  LYS     1      14.260   6.590  34.480  1.00  0.00
    ATOM      2  H2  LYS     1      13.760   5.000  34.340  1.00  0.00
    ATOM      3  N   LYS     1      14.090   5.850  33.800  1.00  0.00
    ATOM      4  H3  LYS     1      14.920   5.560  33.270  1.00  0.00
    ...
    ...
```

--------------------------------

### Force Field Include File Example

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/reference-manual/topologies/topology-file-formats.rst

Example content of a force field .itp file, showing preprocessor definitions and the [ defaults ] directive.

```text
#define _FF_AMBER
#define _FF_AMBER99

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
1               2               yes             0.5     0.8333

#include "ffnonbonded.itp"
#include "ffbonded.itp"
```

--------------------------------

### Register NbLib Setup Tests

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/api/nblib/tests/CMakeLists.txt

Configures the NbLib setup test executable and registers it as an integration test.

```cmake
set(testname "NbLibSetupTests")
set(exename "nblib-setup-test")

gmx_add_gtest_executable(
    ${exename}
    HARDWARE_DETECTION
    CPP_SOURCE_FILES
    # files with code for tests
        box.cpp
        interactions.cpp
        particletype.cpp
        pbcholder.cpp
        molecules.cpp
        nbnxmsetup.cpp
        topology.cpp
        virials.cpp
    )
target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
target_link_libraries(${exename} PRIVATE nblib_test_infrastructure nblib)
target_include_directories(${exename} PRIVATE ${PROJECT_SOURCE_DIR}/api)
gmx_register_gtest_test(${testname} ${exename} INTEGRATION_TEST)
add_dependencies(nblib-tests ${exename})
```

--------------------------------

### Fallback Target: INSTALL Guide Unavailable

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/CMakeLists.txt

This target is created when Sphinx is not available, informing the user that the INSTALL guide cannot be built.

```cmake
add_custom_target(install-guide
    COMMAND ${CMAKE_COMMAND} -E echo
        "INSTALL cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available"
    VERBATIM)
```

--------------------------------

### Example pkg-config file content

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/googletest/docs/pkgconfig.md

A sample .pc file structure for GoogleTest.

```text
libdir=/usr/lib64
includedir=/usr/include

Name: gtest
Description: GoogleTest (without main() function)
Version: 1.11.0
URL: https://github.com/google/googletest
Libs: -L${libdir} -lgtest -lpthread
Cflags: -I${includedir} -DGTEST_HAS_PTHREAD=1 -lpthread
```

--------------------------------

### UnitTest::start_timestamp

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/googletest/docs/reference/testing.md

Gets the time of the test program start, in milliseconds from the start of the UNIX epoch.

```APIDOC
## UnitTest::start_timestamp

### Description
Gets the time of the test program start, in ms from the start of the UNIX epoch.

### Method
`TimeInMillis UnitTest::start_timestamp() const`
```

--------------------------------

### Initialize Input Options for Analysis Tool

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/doxygen/user/analysistemplate.md

Sets up options for the analysis tool, including description, output file name, selections, and a cutoff value. Requires topology information.

```cpp
void AnalysisTemplate::initOptions(gmx::TrajectoryAnalysisSettings& settings)
{
    settings.setToolDescription("Example trajectory analysis tool.");
    settings.addOutputFileOption("o", 'o', "output.dat", "Output file name.");
    settings.addSelectionOption("sel", 's', "all", "Atoms to analyze.");
    settings.addOption("cutoff", 'c', "0.5", "Cutoff distance.", &cutoff_);
    settings.setRequiresTopology(true);
}

```

--------------------------------

### TestSuite::start_timestamp

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/googletest/docs/reference/testing.md

Gets the time of the test suite start, in ms from the start of the UNIX epoch.

```APIDOC
## TestSuite::start_timestamp

### Description
Gets the time of the test suite start, in ms from the start of the UNIX epoch.

### Method
`TimeInMillis TestSuite::start_timestamp() const`
```

--------------------------------

### Notify MDModulesNotifier in Mdrunner Setup

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/doxygen/lib/mdmodules.md

Trigger notifications from the MDModulesNotifier during the Mdrunner setup phase. This example shows how to call the notify method with a callback argument.

```C++
YourCallbackSignature argument();
    mdModules_.notifier().notifier_.notify(argument);
```

--------------------------------

### Get muParser linker flags

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/muparser/Install.txt

Use pkg-config to retrieve the necessary linker flags for linking against the installed muParser library.

```bash
pkg-config muparser --libs
```

--------------------------------

### Get muParser compiler flags

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/muparser/Install.txt

Use pkg-config to retrieve the necessary compiler flags for linking against the installed muParser library.

```bash
pkg-config muparser --cflags
```

--------------------------------

### Minimalist Test Event Listener Example

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/googletest/docs/advanced.md

A basic implementation of a test event listener that prints messages when a test starts, ends, or a test assertion results in a failure or success.

```c++
  class MinimalistPrinter : public testing::EmptyTestEventListener {
    // Called before a test starts.
    void OnTestStart(const testing::TestInfo& test_info) override {
      printf("*** Test %s.%s starting.\n",
             test_info.test_suite_name(), test_info.name());
    }

    // Called after a failed assertion or a SUCCESS().
    void OnTestPartResult(const testing::TestPartResult& test_part_result) override {
      printf("%s in %s:%d\n%s\n",
             test_part_result.failed() ? "*** Failure" : "Success",
             test_part_result.file_name(),
             test_part_result.line_number(),
             test_part_result.summary());
    }

    // Called after a test ends.
    void OnTestEnd(const testing::TestInfo& test_info) override {
      printf("*** Test %s.%s ending.\n",
             test_info.test_suite_name(), test_info.name());
    }
  };
```

--------------------------------

### Set Example Files Directory

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/tng_io/src/tests/CMakeLists.txt

Defines a preprocessor macro for the directory containing test files.

```cmake
add_definitions(-DTNG_EXAMPLE_FILES_DIR="${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/tests/example_files/")
```

--------------------------------

### Install gmxapi with CMake Hints

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/gmxapi/userguide/install.rst

Uses configuration settings to define the root path and provide a CMake cache file for build hints.

```shell
pip install gmxapi \
  --config-settings=cmake.define.gmxapi_ROOT=${UNIQUE_PREFIX} \
  --config-settings=cmake.args=-C${UNIQUE_PREFIX}/share/cmake/gromacs${SUFFIX}/gromacs-hints${SUFFIX}.cmake
```

--------------------------------

### Basic mdrun with MPI and OpenMP

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/user-guide/mdrun-performance.rst

Starts mdrun with a specified number of MPI ranks and OpenMP threads per rank. Suitable for setups where CPU cores are evenly distributed across ranks for threading.

```bash
mpirun -np 20 gmx_mpi mdrun -ntomp 4 -gputasks 00
```

--------------------------------

### Per-Test-Suite Setup and Teardown Example

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/googletest/docs/advanced.md

Demonstrates how to declare and define static members and SetUpTestSuite/TearDownTestSuite methods for sharing resources across tests in a fixture. Ensure proper cleanup in TearDownTestSuite to prevent memory leaks, especially with derived classes.

```C++
class FooTest : public testing::Test {
 protected:
  // Per-test-suite set-up.
  // Called before the first test in this test suite.
  // Can be omitted if not needed.
  static void SetUpTestSuite() {
    shared_resource_ = new ...;

    // If `shared_resource_` is **not deleted** in `TearDownTestSuite()`,
    // reallocation should be prevented because `SetUpTestSuite()` may be called
    // in subclasses of FooTest and lead to memory leak.
    //
    // if (shared_resource_ == nullptr) {
    //   shared_resource_ = new ...;
    // }
  }

  // Per-test-suite tear-down.
  // Called after the last test in this test suite.
  // Can be omitted if not needed.
  static void TearDownTestSuite() {
    delete shared_resource_;
    shared_resource_ = nullptr;
  }

  // You can define per-test set-up logic as usual.
  void SetUp() override { ... }

  // You can define per-test tear-down logic as usual.
  void TearDown() override { ... }

  // Some expensive resource shared by all tests.
  static T* shared_resource_;
};

T* FooTest::shared_resource_ = nullptr;

TEST_F(FooTest, Test1) {
  ... you can refer to shared_resource_ here ...
}

TEST_F(FooTest, Test2) {
  ... you can refer to shared_resource_ here ...
}
```

--------------------------------

### mdrun with external MPI

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/user-guide/mdrun-performance.rst

Starts mdrun compiled with an external MPI library, launching multiple ranks. The number of OpenMP threads per rank is determined by hardware and MPI setup. This is typically used for multi-node or advanced single-node MPI configurations.

```bash
mpirun -np 2 gmx_mpi mdrun
```

--------------------------------

### Install gmxapi Including Pre-release Versions

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/gmxapi/userguide/install.rst

Install the latest version of gmxapi, including any pre-release versions. Use --no-cache-dir to ensure a fresh build.

```bash
# Get the latest version, including pre-release versions.
pip install --no-cache-dir --pre gmxapi
```

--------------------------------

### Install Gromacs

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/install-guide/index.rst

Installs Gromacs to the directory specified by CMAKE_INSTALL_PREFIX. Super-user privileges may be required if installing to a system directory.

```bash
make install
```

--------------------------------

### Build Docker Image for Sample Restraint

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/python_packaging/sample_restraint/README.md

Build a Docker image named 'samplerestraint' using the provided Dockerfile. This is an alternative to setting up MPI locally.

```bash
docker build -t samplerestraint . Dockerfile
```

--------------------------------

### Enable Install RPATH

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/python_packaging/sample_restraint/src/pythonmodule/CMakeLists.txt

Configures the extension to link against an installed GROMACS and use the install RPATH for dynamic linking at runtime.

```cmake
set_target_properties(gmxapi_extension PROPERTIES BUILD_WITH_INSTALL_RPATH TRUE)
```

```cmake
set_target_properties(gmxapi_extension PROPERTIES INSTALL_RPATH_USE_LINK_PATH TRUE)
```

--------------------------------

### Install Public Header Directories

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/api/gmxapi/CMakeLists.txt

Installs the public header directories for the gmxapi. This makes the API headers available to users after installation.

```cmake
install(DIRECTORY include/gmxapi
        DESTINATION include)
```

--------------------------------

### Install Package Config Files

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/googletest/googletest/CMakeLists.txt

Installs the generated version and configuration files for the CMake package. These files are placed in the installation directory for CMake to find.

```cmake
install(FILES ${version_file} ${config_file}
  COMPONENT "${PROJECT_NAME}"
  DESTINATION ${cmake_files_install_dir})
```

--------------------------------

### gMock Action Factory Example (Different Counters)

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/googletest/docs/gmock_cook_book.md

Demonstrates how an action factory creates distinct actions, leading to separate internal states when used repeatedly with different `EXPECT_CALL`s.

```cpp
  EXPECT_CALL(foo, DoThis())
      .WillRepeatedly(IncrementCounter(0));
  EXPECT_CALL(foo, DoThat())
      .WillRepeatedly(IncrementCounter(0));
  foo.DoThis();  // Returns 1.
  foo.DoThis();  // Returns 2.
  foo.DoThat();  // Returns 1 - DoThat() uses a different
                 // counter than DoThis()'s.
```

--------------------------------

### Create Project Directory

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/googletest/docs/quickstart-cmake.md

Use this command to create a new directory for your project and navigate into it.

```bash
$ mkdir my_project && cd my_project
```

--------------------------------

### Install Configured Resource Assignment Header

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/api/gmxapi/CMakeLists.txt

Installs the configured resource assignment header file for MPI. This is necessary for the correct functioning of MPI-related features in the installed API.

```cmake
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/include/gmxapi/mpi/resourceassignment.h
        DESTINATION include/gmxapi/mpi)
```

--------------------------------

### Install Configured API Version Header

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/api/gmxapi/CMakeLists.txt

Installs the configured API version header file from the build tree. This ensures the installed API has the correct version information.

```cmake
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/include/gmxapi/version.h
        DESTINATION include/gmxapi)
```

--------------------------------

### Specify Gromacs Installation Path for gmxapi

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/gmxapi/userguide/install.rst

If gmxapi cannot find the Gromacs installation, you can specify its location using the 'gmxapi_ROOT' environment variable during installation. This is an alternative to sourcing the GMXRC file.

```bash
gmxapi_ROOT=/path/to/gromacs pip install .
```

```bash
gmxapi_ROOT=/Users/eric/gromacs pip install --verbose gmxapi
```

--------------------------------

### Initialize Hermetic Build

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/googletest/googlemock/CMakeLists.txt

Includes and executes hermetic build setup functions if available.

```cmake
# Defines pre_project_set_up_hermetic_build() and set_up_hermetic_build().
include("${gtest_dir}/cmake/hermetic_build.cmake" OPTIONAL)

if (COMMAND pre_project_set_up_hermetic_build)
  # Google Test also calls hermetic setup functions from add_subdirectory,
  # although its changes will not affect things at the current scope.
  pre_project_set_up_hermetic_build()
endif()
```

--------------------------------

### Example Urea Topology File

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/reference-manual/topologies/topology-file-formats.rst

A complete example of a .top file defining a urea molecule, including atoms, bonds, dihedrals, restraints, and system composition.

```text
;
;       Example topology file
;
; The force-field files to be included
#include "amber99.ff/forcefield.itp"

[ moleculetype ]
; name  nrexcl
Urea         3

[ atoms ]
   1  C  1  URE      C      1     0.880229  12.01000   ; amber C  type
   2  O  1  URE      O      2    -0.613359  16.00000   ; amber O  type
   3  N  1  URE     N1      3    -0.923545  14.01000   ; amber N  type
   4  H  1  URE    H11      4     0.395055   1.00800   ; amber H  type
   5  H  1  URE    H12      5     0.395055   1.00800   ; amber H  type
   6  N  1  URE     N2      6    -0.923545  14.01000   ; amber N  type
   7  H  1  URE    H21      7     0.395055   1.00800   ; amber H  type
   8  H  1  URE    H22      8     0.395055   1.00800   ; amber H  type

[ bonds ]
    1    2
    1    3
    1    6
    3    4
    3    5
    6    7
    6    8

[ dihedrals ]
;   ai    aj    ak    al funct  definition
     2     1     3     4   9
     2     1     3     5   9
     2     1     6     7   9
     2     1     6     8   9
     3     1     6     7   9
     3     1     6     8   9
     6     1     3     4   9
     6     1     3     5   9

[ dihedrals ]
     3     6     1     2   4
     1     4     3     5   4
     1     7     6     8   4

[ position_restraints ]
; you wouldn't normally use this for a molecule like Urea,
; but we include it here for didactic purposes
; ai   funct    fc
   1     1     1000    1000    1000 ; Restrain to a point
   2     1     1000       0    1000 ; Restrain to a line (Y-axis)
   3     1     1000       0       0 ; Restrain to a plane (Y-Z-plane)

[ dihedral_restraints ]
; ai   aj    ak    al  type  phi  dphi  fc
    3    6     1    2     1  180     0  10
    1    4     3    5     1  180     0  10

; Include TIP3P water topology
#include "amber99.ff/tip3p.itp"

[ system ]
Urea in Water

[ molecules ]
;molecule name   nr.
Urea             1
SOL              1000
```

--------------------------------

### Install or Upgrade mpi4py

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/gmxapi/userguide/install.rst

Install or upgrade mpi4py, ensuring it is compatible with your MPI installation. Use MPICC to specify the MPI compiler if needed. The --no-cache-dir flag forces a rebuild.

```bash
MPICC=`which mpicc` pip install --no-cache-dir --upgrade mpi4py
```

--------------------------------

### Install Google Test

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/googletest/googletest/CMakeLists.txt

Installs the gtest and gtest_main targets as part of the project.

```cmake
install_project(gtest gtest_main)
```

--------------------------------

### Initialize Lambda Weights

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/share/README_FreeEnergyModifications.txt

Example of loading initial weights for lambda states, where the first entry is typically 0.00.

```text
init-lambda-weights =  0.00  0.54  1.45 3.45 6.78
```

--------------------------------

### Install Latest gmxapi from PyPI

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/gmxapi/userguide/install.rst

Fetch and install the latest official release of gmxapi from the Python Packaging Index. Use --no-cache-dir to avoid using potentially incompatible cached wheel packages.

```bash
# Get the latest official release.
pip install --no-cache-dir gmxapi
```

--------------------------------

### EXPECT_CALL with Return Actions Example

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/googletest/docs/gmock_for_dummies.md

This example demonstrates setting expectations on the turtle's GetX() method, specifying it will be called five times with specific return values for the first two calls and a repeated value for subsequent calls.

```cpp
using ::testing::Return;
...
EXPECT_CALL(turtle, GetX())
    .Times(5)
    .WillOnce(Return(100))
    .WillOnce(Return(150))
    .WillRepeatedly(Return(200));
```

--------------------------------

### Check Pytest Installation and Version

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/python_packaging/sample_restraint/tests/CMakeGROMACS.txt

Verifies if pytest is installed and meets the minimum version requirement (>= 3.0). If not found or an older version is detected, it prints a fatal error message with installation instructions.

```cmake
if(NOT GMXAPI_PYTEST_FOUND)
    execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "import pytest; print(pytest.__version__)"
                    RESULT_VARIABLE pytest_not_found OUTPUT_VARIABLE pytest_version ERROR_QUIET)
    if(pytest_not_found)
        message(FATAL_ERROR "Running the tests requires pytest. Please install it manually"
                " (try: ${PYTHON_EXECUTABLE} -m pip install pytest)")
    elseif(pytest_version VERSION_LESS 3.0)
        message(FATAL_ERROR "Running the tests requires pytest >= 3.0. Found: ${pytest_version}"
                "Please update it (try: ${PYTHON_EXECUTABLE} -m pip install -U pytest)")
    endif()
    set(GMXAPI_PYTEST_FOUND TRUE CACHE INTERNAL "Suppress checking for Python pytest module.")
endif()
```

--------------------------------

### Build and Run Tests with CMake

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/googletest/docs/quickstart-cmake.md

These commands demonstrate how to configure the build using CMake, build the project, and then run the discovered tests using ctest from the build directory.

```bash
my_project$ cmake -S . -B build
-- Build files have been written to: .../my_project/build

my_project$ cmake --build build
Scanning dependencies of target gtest
... (build output)
[100%] Built target gmock_main

my_project$ cd build && ctest
Test project .../my_project/build
    Start 1: HelloTest.BasicAssertions
1/1 Test #1: HelloTest.BasicAssertions ........   Passed    0.00 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) =   0.01 sec
```

--------------------------------

### Build and Install GROMACS Plugin

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/python_packaging/sample_restraint/README.md

Build the GROMACS plugin using make, run C++ tests, and optionally install the plugin. The PYTHONPATH environment variable can be set to locate the plugin if not installed.

```bash
make
# build and run C++ tests
make tests
make test
# optionally, install
make install
```

```bash
export PYTHONPATH=`pwd`/src/pythonmodule
```

--------------------------------

### Import gmxapi and sample_restraint modules

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/python_packaging/sample_restraint/examples/example.ipynb

Import the necessary gmxapi and sample_restraint modules. Ensure these modules are built and installed.

```python
# module built and installed with https://github.com/kassonlab/gmxapi
import gmx
# module built and installed with https://github.com/kassonlab/sample_restraint
import myplugin
```

--------------------------------

### Build and run tests

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/src/external/googletest/CONTRIBUTING.md

Standard commands to compile and execute the test suite on *nix systems.

```bash
make
```

```bash
make test
```

--------------------------------

### GROMACS Orientation Restraints Section Example

Source: https://gitlab.com/gromacs/gromacs/-/blob/main/docs/reference-manual/functions/restraints.rst

Example of how to define orientation restraints in a GROMACS topology file within the [ orientation_restraints ] section. This example shows five N-H residual dipolar coupling restraints.

```ini
[ orientation_restraints ]
```