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### void setup()

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1LoggingSignaller.xhtml

Performs necessary setup checks for the signaller.

```APIDOC
## void setup()

### Description
Validates that the necessary registration for the signaller has been completed.
```

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

### Install gmxapi from source distribution

Source: https://manual.gromacs.org/current/gmxapi/userguide/install.html

Download the source distribution and install it manually.

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

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

### void start()

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1nbnxn__cycle__t.xhtml

Starts the cycle counting process.

```APIDOC
### void start()

Starts the cycle counting process for profiling.
```

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

### Set Help Text Example

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1ICommandLineOptionsModuleSettings.xhtml

Example demonstrating how to define and set help text for a module using an array of strings.

```cpp
const char *const desc[] = {
"This is the description",
"for the options"
};
settings->setHelpText(desc);
```

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

### Install and Run Black

Source: https://manual.gromacs.org/current/dev-manual/code-formatting.html

Install the Black formatter and execute it using the repository's .black.toml configuration.

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

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

### Install gmxapi from PyPI

Source: https://manual.gromacs.org/current/gmxapi/userguide/install.html

Fetch and install the latest official release of gmxapi.

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

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

### start()

Source: https://manual.gromacs.org/current/doxygen/html-lib/classgmx_1_1OptionsAssigner.xhtml

Initializes the assignment process.

```APIDOC
### Method
void start()

### Description
Starts assigning values.
```

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

### Install gmxapi including pre-releases

Source: https://manual.gromacs.org/current/gmxapi/userguide/install.html

Use the --pre flag to include pre-release versions during installation.

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

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

### void setup()

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1ISignaller.xhtml

Initializes the signaller after construction and before the simulator run begins.

```APIDOC
### Method
`virtual void setup() = 0`

### Description
Method guaranteed to be called after construction, before simulator run.
```

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

### gmx::OptionsAssigner::start

Source: https://manual.gromacs.org/current/doxygen/html-lib/classgmx_1_1OptionsAssigner.xhtml

Starts the overall assignment process.

```APIDOC
### Method
void start()

### Description
Initializes the assignment process. Does not throw.
```

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

### writeOptionListStart

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1HelpWriterContext.xhtml

Starts writing a list of options by printing necessary headers.

```APIDOC
### void gmx::HelpWriterContext::writeOptionListStart() const

Starts writing a list of options. Prints any necessary headers for a list of options formatted with writeOptionItem().
```

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

### Execute quick installation sequence

Source: https://manual.gromacs.org/current/install-guide/index.html

A standard sequence of commands to unpack, configure, build, and install GROMACS with automatic FFTW download and regression testing.

```bash
tar xfz gromacs-2026.3.tar.gz
cd gromacs-2026.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC
```

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

### Install gmxapi from GROMACS source

Source: https://manual.gromacs.org/current/gmxapi/userguide/install.html

Commands to install the gmxapi package directly from the GROMACS source tree.

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

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

### Install the gmxapi Python package

Source: https://manual.gromacs.org/current/gmxapi/userguide/install.html

Commands to source the GROMACS environment and install the gmxapi package from PyPI.

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

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

### Constructing SimulationInput

Source: https://manual.gromacs.org/current/doxygen/html-full/group__module__mdrun.xhtml

Example usage of makeSimulationInput for setting up simulation input resources.

```cpp
// After preparing a LegacyMdrunOptions and calling handleRestart()... SimulationInputBuilder builder; auto simulationInputHandle = makeSimulationInput(options, &builder);
// In addition to MdrunnerBuilder::addFiles(), mdrunnerBuilder.addInput(simulationInputHandle.get());
```

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

### installationPrefix()

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1IProgramContext.xhtml

Returns the installation prefix for GROMACS, used to locate data files.

```APIDOC
### Method
`InstallationPrefixInfo installationPrefix() const`

### Description
Returns the installation prefix for GROMACS. This path is used to locate data files (e.g., `share/top/`).
```

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

### startFrame(const AnalysisDataFrameHeader &header)

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1AnalysisDataStorage.xhtml

Starts storing a new frame.

```APIDOC
## AnalysisDataStorage::startFrame

### Description
Starts storing a new frame.

### Parameters
- **header** (const AnalysisDataFrameHeader&) - Required - Header for the new frame.

### Returns
- **Frame** - Object corresponding to the started frame.
```

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

### Run mdrun with default settings

Source: https://manual.gromacs.org/current/user-guide/mdrun-performance.html

Starts a simulation using all available resources with automatic resource allocation.

```bash
gmx mdrun
```

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

### Triggering a notification

Source: https://manual.gromacs.org/current/doxygen/html-full/page_mdmodules.xhtml

Invoke the notification during setup, for example within Mdrunner.

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

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

### Find GROMACS package

Source: https://manual.gromacs.org/current/api/gmxlibs.html

Example of finding a specific suffixed GROMACS installation.

```cmake
find_package(gromacs_d)
```

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

### gmx::AbstractPlotModule::dataStarted

Source: https://manual.gromacs.org/current/doxygen/html-user/classgmx_1_1AnalysisDataPlotModule.xhtml

Initializes the module when data setup is complete.

```APIDOC
## void gmx::AbstractPlotModule::dataStarted(AbstractAnalysisData * data)

### Description
Called once when the data has been set up properly. This method provides access to the data object for initialization and validation.

### Parameters
- **data** (AbstractAnalysisData*) - Required - Data object to which the module is added.
```

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

### gmxSetUp

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1test_1_1TestHardwareEnvironment.xhtml

Initializes the test hardware environment.

```APIDOC
### Method
static void gmxSetUp()

### Description
Performs one-time setup of the test hardware environment. This should be called once per test binary before any tests requiring hardware information are executed.
```

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

### Execute MiMiC QM/MM Job Script

Source: https://manual.gromacs.org/current/reference-manual/special/mimic-qmmm.html

Example srun commands for launching GROMACS and CPMD concurrently in a QM/MM setup.

```bash
srun -N2 --ntasks-per-node=6 --cpus-per-task=4 -r0 gmx_mpi_d mdrun -deffnm mimic -ntomp 4 &
srun -N240 --ntasks-per-node=6 --cpus-per-task=4 -r2 cpmd.x benchmark.inp <path_to_pp_folder> > benchmark-240-4.out &
wait
```

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

### Install mpi4py

Source: https://manual.gromacs.org/current/gmxapi/userguide/install.html

Install mpi4py using the same MPI installation used for GROMACS.

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

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

### gmx::InstallationPrefixInfo::InstallationPrefixInfo

Source: https://manual.gromacs.org/current/doxygen/html-user/structgmx_1_1InstallationPrefixInfo.xhtml

Constructor for initializing the InstallationPrefixInfo structure with a path and layout type.

```APIDOC
## Constructor: gmx::InstallationPrefixInfo::InstallationPrefixInfo

### Description
Initializes the structure with the provided installation path and layout configuration.

### Signature
`InstallationPrefixInfo(const std::filesystem::path &path, bool bSource)`

### Parameters
- **path** (const std::filesystem::path&) - The path to the installation prefix or source tree root.
- **bSource** (bool) - Set to true if the path points to a source tree-like layout, false for a standard installation.
```

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

### Install gmxapi with CMake hint

Source: https://manual.gromacs.org/current/gmxapi/userguide/install.html

Use the gmxapi_ROOT environment variable to point to the GROMACS installation directory during package installation.

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

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

### gmx::HaloExchange::setup

Source: https://manual.gromacs.org/current/doxygen/html-user/classgmx_1_1HaloExchange.xhtml

Sets up the halo communication. This should be called after (re)partitioning.

```APIDOC
### void setup(gmx_domdec_t *dd, t_state *localState, const gmx_ddbox_t &ddbox, t_forcerec *fr, bool cellsChanged)

Sets up the halo communication. This method must be called after (re)partitioning of the domain decomposition.
```

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

### Include benchmark setup headers

Source: https://manual.gromacs.org/current/doxygen/html-lib/bench__setup_8h.xhtml

Required headers for utilizing the benchmark setup functionality.

```cpp
#include <string>
#include "gromacs/utility/real.h"
```

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

### Basic CommandLineParser Usage

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1CommandLineParser.xhtml

Demonstrates the standard workflow for initializing the parser, processing arguments, and finalizing the options.

```cpp
gmx::Options options("name", "description");
// Fill up options
gmx::CommandLineParser(&options).parse(&argc, argv);
options.finish();
```

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

### ListedForces::setup

Source: https://manual.gromacs.org/current/doxygen/html-lib/classListedForces.xhtml

Initializes the listed interactions and thread parallelization.

```APIDOC
## void ListedForces::setup(const InteractionDefinitions &domainIdef, int numAtomsForce, bool useGpu, gmx::ArrayRef< const unsigned short > restraintComIndices)

### Description
Copies the listed interactions from idef and sets up the thread parallelization.

### Parameters
- **domainIdef** (const InteractionDefinitions &) - Interaction definitions for all listed interactions to be computed on this domain/rank.
- **numAtomsForce** (int) - Force are, potentially, computed for atoms 0 to numAtomsForce.
- **useGpu** (bool) - Whether a GPU is used to compute (part of) the listed interactions.
- **restraintComIndices** (gmx::ArrayRef< const unsigned short >) - Reference to COM groups indices (needed for posres calculation).
```

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

### Install pybind11 dependency

Source: https://manual.gromacs.org/current/gmxapi/userguide/install.html

Explicitly install or upgrade pybind11 to resolve build-time dependency errors.

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

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

### Run mdrun with fixed thread count

Source: https://manual.gromacs.org/current/user-guide/mdrun-performance.html

Starts a simulation using a specific number of threads.

```bash
gmx mdrun -nt 8
```

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

### Configure GPU task mapping with mdrun

Source: https://manual.gromacs.org/current/user-guide/mdrun-performance.html

Example of mapping GPU tasks to specific GPU IDs using the -gputasks flag.

```bash
gmx mdrun -gputasks 0001 -nb gpu -pme gpu -npme 1 -ntmpi 4
```

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

### Install gmxapi build dependencies

Source: https://manual.gromacs.org/current/gmxapi/userguide/install.html

Install cmake and pybind11 required for building the gmxapi package.

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

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

### Set up a Python virtual environment

Source: https://manual.gromacs.org/current/gmxapi/userguide/install.html

Commands to create a virtual environment, activate it, and install essential build tools and MPI support.

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

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

### Configure CPU thread usage for mdrun

Source: https://manual.gromacs.org/current/user-guide/mdrun-performance.html

Example command to leave one CPU hardware thread unused to minimize interference between the GPU driver and CPU computation.

```bash
gmx mdrun -ntomp 31 -pin on
```

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

### gmx::AnalysisDataStorage::startDataStorage

Source: https://manual.gromacs.org/current/doxygen/html-lib/classgmx_1_1AnalysisDataStorage.xhtml

Initializes the storage process.

```APIDOC
## AnalysisDataStorage::startDataStorage(AbstractAnalysisData *data, AnalysisDataModuleManager *modules)

### Description
Starts storing data. The storage object takes responsibility for calling module notification methods.

### Parameters
- **data** (AbstractAnalysisData*) - Required - The data object containing this storage.
- **modules** (AnalysisDataModuleManager*) - Required - Module manager for the data.
```

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

### Perform offline installation of gmxapi

Source: https://manual.gromacs.org/current/gmxapi/userguide/install.html

Commands to download dependencies and install gmxapi in an environment without internet access.

```bash
# 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
```

```bash
# if in the GROMACS source repository
cd python_packaging/gmxapi
# or download and expand the archive
pip download --destination-directory DIR gmxapi
tar xf DIR/gmxapi*
cd gmxapi*

# Pre-fetch dependencies to DIR
pip download --destination-directory DIR .

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

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

### run

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1CommandLineHelpModule.xhtml

Executes the help module with the provided command-line arguments.

```APIDOC
### Method: int gmx::CommandLineHelpModule::run

#### Description
Runs the help module with the given command-line arguments.

#### Parameters
- **argc** (int) - Number of elements in argv.
- **argv** (char *[]) - Command-line arguments.

#### Returns
- **int** - Exit code for the program (0 on success).
```

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

### Install Python package dependencies

Source: https://manual.gromacs.org/current/dev-manual/documentation-generation.html

Install the necessary Python dependencies required for building the full package documentation.

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

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

### Using OptionsAssigner to set option values

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1OptionsAssigner.xhtml

Demonstrates the typical workflow for initializing an assigner, navigating sections, and appending values to options.

```cpp
gmx::Options options("name", "Title");
// Set up options
gmx::OptionsAssigner assigner(&options);
assigner.start();
assigner.startOption("opt1");
assigner.appendValue("3");
assigner.finishOption();
assigner.startSection("section");
assigner.startOption("opt2"); // Now in the subsection
assigner.appendValue("yes");
assigner.finishOption();
assigner.finishSection()
assigner.startOption("opt3"); // Again in the main options
assigner.appendValue("2");
assigner.finishOption();
assigner.finish();
```

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

### startOption(const char *name)

Source: https://manual.gromacs.org/current/doxygen/html-lib/classgmx_1_1OptionsAssigner.xhtml

Begins the assignment process for a specific option.

```APIDOC
### Method
void startOption(const char *name)

### Description
Starts assigning values for an option.
```

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

### Force Field Include File Example

Source: https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html

Example content of a forcefield.itp file, showing default settings and inclusion of non-bonded and bonded parameter files.

```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"
```

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

### void gmx::AnalysisDataHandle::startFrame(size_t index, real x, real dx = 0.0)

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1AnalysisDataHandle.xhtml

Starts data for a new frame. Each frame index must be started exactly once.

```APIDOC
### Method
`void startFrame(size_t index, real x, real dx = 0.0)`

### Description
Starts data for a new frame. Each index value 0, 1, ..., N should be started exactly once.

### Parameters
- **index** (size_t) - Required - Zero-based index for the frame to start.
- **x** (real) - Required - x value for the frame.
- **dx** (real) - Optional - Error in x for the frame if applicable.
```

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

### Example Urea Topology File

Source: https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html

A complete example of a .top file defining a urea molecule, including force field inclusions, atom definitions, bonds, dihedrals, 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
```

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

### void startContext(const char *name)

Source: https://manual.gromacs.org/current/doxygen/html-lib/classgmx_1_1MessageStringCollector.xhtml

Starts a new context for subsequent messages. This allows grouping messages under a specific label.

```APIDOC
## void startContext(const char *name)

### Description
Starts a context for messages. This helps in organizing collected strings under a specific context name.

### Parameters
- **name** (const char *) - Required - Short description of the context.
```

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

### Initialize SimulationState

Source: https://manual.gromacs.org/current/nblib/guide-to-writing-MD-programs.html

Creates a snapshot of the system state using topology, box dimensions, coordinates, velocities, and forces.

```cpp
SimulationState simulationState(coordinates, velocities, forces, box, topology);
```

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

### Equivalent atoms file format example

Source: https://manual.gromacs.org/current/onlinehelp/gmx-rmsdist.html

Example format for the optional -equiv input file, where each line specifies equivalent atoms by residue number, residue name, and atom name.

```text
HB* 3 SER  HB1 3 SER  HB2
```

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

### virtual void gmx::ICommandLineModule::writeHelp(const CommandLineHelpContext &context) const

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1ICommandLineModule.xhtml

Generates and prints help documentation for the module.

```APIDOC
### Method
`void writeHelp(const CommandLineHelpContext &context) const`

### Description
Prints help information for the module. In MPI-enabled builds, this is invoked only on the main rank.

### Parameters
- **context** (const CommandLineHelpContext &) - The context object used for formatting and writing the help output.

### Exceptions
- **std::bad_alloc** - Thrown if the system is out of memory.
- **FileIOError** - Thrown on any I/O error during help generation.
```

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

### startFrames

Source: https://manual.gromacs.org/current/doxygen/html-user/classgmx_1_1TrajectoryAnalysisModule.xhtml

Starts the analysis of frames.

```APIDOC
## TrajectoryAnalysisModuleDataPointer gmx::TrajectoryAnalysisModule::startFrames(const AnalysisDataParallelOptions &opt, const SelectionCollection &selections)

### Description
Starts the analysis of frames.

### Parameters
- **opt** (const AnalysisDataParallelOptions&) - Required - Parallelization options.
- **selections** (const SelectionCollection&) - Required - Selection collection.
```

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

### Run make-release-build.py

Source: https://manual.gromacs.org/current/dev-manual/gitlab-ci.html

Displays the command-line usage and available arguments for the release build automation script.

```text
usage: make-release-build.py [-h] (--local | --server) [--token TOKEN]
                             [--ssh-key SSH_KEY] [--release | --no-release]
                             [--dry-run | --no-dry-run] [--branch BRANCH]
```

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

### void ListedForces::setup

Source: https://manual.gromacs.org/current/doxygen/html-full/classListedForces.xhtml

Copies listed interactions from idef and sets up thread parallelization.

```APIDOC
## void ListedForces::setup

### Description
Copy the listed interactions from idef and set up the thread parallelization.

### Parameters
- **domainIdef** (const InteractionDefinitions &) - Interaction definitions for all listed interactions to be computed on this domain/rank
- **numAtomsForce** (int) - Force are, potentially, computed for atoms 0 to numAtomsForce
- **useGpu** (bool) - Whether a GPU is used to compute (part of) the listed interactions
- **restraintComIndices** (gmx::ArrayRef< const unsigned short >) - Reference to COM groups indices (needed for posres calculation)
```

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

### gmx_fft_init_2d_real

Source: https://manual.gromacs.org/current/doxygen/html-full/fft_8h.xhtml

Setup a 2-dimensional real-to-complex transform.

```APIDOC
## int gmx_fft_init_2d_real(gmx_fft_t *fft, int nx, int ny, gmx_fft_flag flags)

### Description
Setup a 2-dimensional real-to-complex transform. The normal space is assumed to be real, while the values in frequency space are complex.

### Parameters
- **fft** (gmx_fft_t *) - Pointer to opaque Gromacs FFT datatype
- **nx** (int) - Length of transform in first dimension
- **ny** (int) - Length of transform in second dimension
- **flags** (gmx_fft_flag) - FFT options

### Returns
- **status** (int) - 0 or a standard error message.
```

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

### gmx_fft_destroy

Source: https://manual.gromacs.org/current/doxygen/html-full/fft_8h.xhtml

Releases an FFT setup structure.

```APIDOC
## void gmx_fft_destroy(gmx_fft_t setup)

### Description
Destroy setup and release all allocated memory associated with the FFT plan.

### Parameters
- **setup** (gmx_fft_t) - Required - Setup returned from an initializer function.
```

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

### init

Source: https://manual.gromacs.org/current/doxygen/html-user/classgmx_1_1ICommandLineOptionsModule.xhtml

Initializes the module and provides settings for the runner.

```APIDOC
## virtual void init(CommandLineModuleSettings *settings)

### Description
Initializes the module and provides settings for the runner.
```

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

### Define String Options

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1StringOption.xhtml

Examples demonstrating how to define a simple string option and an option restricted to a set of predefined values.

```cpp
using gmx::StringOption;
// Simple option
std::string str;
options.addOption(StringOption("str").store(&str));
// Option that only accepts predefined values
const char * const allowed[] = { "atom", "residue", "molecule" };
std::string str;
options.addOption(StringOption("type").enumValue(allowed).store(&str));
```

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

### gmx_fft_init_many_1d_real

Source: https://manual.gromacs.org/current/doxygen/html-full/fft_8h.xhtml

Setup multiple 1-dimensional real-to-complex transforms.

```APIDOC
## int gmx_fft_init_many_1d_real(gmx_fft_t *fft, int nx, int howmany, gmx_fft_flag flags)

### Description
Setup multiple 1-dimensional real-to-complex transforms.

### Parameters
- **fft** (gmx_fft_t *) - Pointer to opaque Gromacs FFT datatype
- **nx** (int) - Length of transform in real space
- **howmany** (int) - Homany 1D FFTs
- **flags** (gmx_fft_flag) - FFT options

### Returns
- **status** (int) - 0 or a standard error message.
```

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

### gmx_fft_init_many_1d

Source: https://manual.gromacs.org/current/doxygen/html-full/fft_8h.xhtml

Setup multiple 1-dimensional complex-to-complex transforms.

```APIDOC
## int gmx_fft_init_many_1d(gmx_fft_t *fft, int nx, int howmany, gmx_fft_flag flags)

### Description
Setup multiple 1-dimensional complex-to-complex transforms.

### Parameters
- **fft** (gmx_fft_t *) - Pointer to opaque Gromacs FFT datatype
- **nx** (int) - Length of transform
- **howmany** (int) - Howmany 1D FFT
- **flags** (gmx_fft_flag) - FFT options

### Returns
- **status** (int) - 0 or a standard error message.
```

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

### Typical usage of CommandLineModuleManager

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1CommandLineModuleManager.xhtml

Demonstrates the standard initialization, module registration, and execution flow for a command-line program using the manager.

```cpp
int main(int argc, char *argv[])
{
gmx::CommandLineProgramContext &programContext = gmx::initForCommandLine(&argc, &argv);
try
{
gmx::CommandLineModuleManager manager("gmx", &programContext);
// <register all necessary modules>
int rc = manager.run(argc, argv);
gmx::finalizeForCommandLine();
return rc;
}
catch (const std::exception &ex)
{
gmx::printFatalErrorMessage(stderr, ex);
return gmx::processExceptionAtExitForCommandLine(ex);
}
}
```

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

### IMDModule::subscribeToSimulationSetupNotifications

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1IMDModule.xhtml

Subscribe to simulation setup notifications.

```APIDOC
## virtual void subscribeToSimulationSetupNotifications(MDModulesNotifiers* notifiers) = 0

### Description
Subscribe to simulation setup notifications.
```

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

### startData(const AnalysisDataParallelOptions &opt)

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1AnalysisData.xhtml

Creates a handle for adding data.

```APIDOC
### startData(const AnalysisDataParallelOptions &opt)

Creates a handle for adding data.

#### Parameters
- **opt** (AnalysisDataParallelOptions) - Parallel options for the data addition.
```

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

### void gmx::AbstractOptionStorage::startSource()

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1AbstractOptionStorage.xhtml

Starts adding values from a new source for the option, marking current values as defaults.

```APIDOC
## void gmx::AbstractOptionStorage::startSource()

### Description
Starts adding values from a new source for the option. This marks the current value of the option as a default value, causing the next call to startSet() to clear it, allowing values from the new source to overwrite old values.

### Guarantees
- This method does not throw.
```

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

### FMA Operation

Source: https://manual.gromacs.org/current/doxygen/html-full/gpu__kernel__utils_8h.xhtml

Example of a fused multiply-add operation.

```cpp
{
return __fma(valueOne, valueTwo, valueThree)
}
```

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

### gmx::nbnxn_cycle_t::start

Source: https://manual.gromacs.org/current/doxygen/html-user/classgmx_1_1nbnxn__cycle__t.xhtml

Starts the cycle counting process.

```APIDOC
### void start()

Starts the cycle counting process.
```

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

### startDataStorage(AbstractAnalysisData *data, AnalysisDataModuleManager *modules)

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1AnalysisDataStorage.xhtml

Initializes data storage with the provided data object and module manager.

```APIDOC
## AnalysisDataStorage::startDataStorage

### Description
Start storing data. The storage object will take responsibility of calling all module notification methods in AnalysisDataModuleManager.

### Parameters
- **data** (AbstractAnalysisData*) - Required - AbstractAnalysisData object containing this storage.
- **modules** (AnalysisDataModuleManager*) - Required - Module manager for `data`.
```

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

### void initManager(const CommandLine &args, const char *realBinaryName)

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1test_1_1CommandLineModuleManagerTestBase.xhtml

Initializes the command-line module manager with the provided arguments and binary name.

```APIDOC
### void initManager(const CommandLine &args, const char *realBinaryName)

Creates the manager to run the given command line.
```

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

### gmx::startsWith

Source: https://manual.gromacs.org/current/doxygen/html-lib/group__module__utility.xhtml

Checks if a string starts with a specific prefix.

```APIDOC
## bool gmx::startsWith(const std::string &str, const std::string &prefix)
## bool gmx::startsWith(const char *str, const char *prefix)

### Description
Tests whether a string starts with another string.
```

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

### setupGpuDevicePeerAccess

Source: https://manual.gromacs.org/current/doxygen/html-full/gpu__utils_8h.xhtml

Enable peer access between GPUs where supported.

```APIDOC
void setupGpuDevicePeerAccess(gmx::ArrayRef< const int > gpuIdsToUse, const gmx::MDLogger &mdlog)
```

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

### gmx::AnalysisDataStorage::startFrame

Source: https://manual.gromacs.org/current/doxygen/html-lib/classgmx_1_1AnalysisDataStorage.xhtml

Starts storing a new frame.

```APIDOC
## AnalysisDataStorage::startFrame(const AnalysisDataFrameHeader &header)

### Description
Starts storing a new frame using the provided header.

### Parameters
- **header** (AnalysisDataFrameHeader) - Required - Header for the new frame.

### Returns
- **Frame** - The frame object corresponding to the started frame.
```

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

### void gmx::OptionsAssigner::startOption(const char *name)

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1OptionsAssigner.xhtml

Starts assigning values for a specific option by name.

```APIDOC
## void gmx::OptionsAssigner::startOption(const char *name)

### Description
Starts assigning values for an option identified by its name.

### Parameters
- **name** (const char *) - Required - Name of the option to start assigning to.

### Exceptions
- **InvalidInputError** - Thrown if the option is not found, or if the option is specified more than once but does not support it.
```

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

### notifyParallelFrameStart

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1AnalysisDataModuleManager.xhtml

Notifies attached parallel modules of the start of a frame.

```APIDOC
## void notifyParallelFrameStart(const AnalysisDataFrameHeader &header) const

### Description
Notifies attached parallel modules of the start of a frame. It is allowed to call this method in any order for the frames, but should be called exactly once for each frame.

### Parameters
- **header** (const AnalysisDataFrameHeader&) - Required - Header information for the frame that is starting.

### Exceptions
- **unspecified** - Any exception thrown by attached data modules in IAnalysisDataModule::frameStarted().
```

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

### gmx::ICommandLineModule::writeHelp

Source: https://manual.gromacs.org/current/doxygen/html-user/classgmx_1_1ICommandLineModule.xhtml

Prints help information for the module.

```APIDOC
## virtual void writeHelp(const CommandLineHelpContext &context) const

### Description
Prints help for the module using the provided context. In MPI-enabled builds, this is called only on the main rank.

### Parameters
- **context** (const CommandLineHelpContext&) - Required - Context object used for formatting and writing the help output.
```

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

### init()

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1ICommandLineOptionsModule.xhtml

Allows for interaction between the module and the framework during initialization.

```APIDOC
### virtual void init(int *argc, char ***argv)

Initializes the module. This method is called by the framework to allow for customization. If no specific initialization is required, an empty implementation is sufficient.
```

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

### notifyFrameStart

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1AnalysisDataModuleManager.xhtml

Notifies attached serial modules of the start of a frame.

```APIDOC
void notifyFrameStart(const AnalysisDataFrameHeader &header) const
```

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

### gmx::HelpWriterContext::HelpWriterContext

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1HelpWriterContext.xhtml

Initializes a new HelpWriterContext instance with a writer and format, optionally including help links.

```APIDOC
## Constructor: gmx::HelpWriterContext::HelpWriterContext

### Description
Initializes a context with the given output writer and format. A version with links is also available where the links object must remain valid for the lifetime of the context.

### Parameters
- **writer** (TextWriter*) - Required - The output writer.
- **format** (HelpOutputFormat) - Required - The output format.
- **links** (const HelpLinks*) - Optional - Links to be used in the context.
```

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

### notifyParallelDataStart

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1AnalysisDataModuleManager.xhtml

Notifies attached modules of the start of parallel data.

```APIDOC
## void notifyParallelDataStart(AbstractAnalysisData *data, const AnalysisDataParallelOptions &options)

### Description
Notifies attached modules of the start of parallel data.

### Parameters
- **data** (AbstractAnalysisData*) - The data object.
- **options** (const AnalysisDataParallelOptions&) - Parallel processing options.
```

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

### notifyDataStart

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1AnalysisDataModuleManager.xhtml

Notifies attached modules of the start of serial data.

```APIDOC
## void notifyDataStart(AbstractAnalysisData *data)

### Description
Notifies attached modules of the start of serial data.

### Parameters
- **data** (AbstractAnalysisData*) - The data object.
```

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

### gmx::setupStepWorkload

Source: https://manual.gromacs.org/current/doxygen/html-full/decidesimulationworkload_8h.xhtml

Sets up force flag structure from the force bitmask for a specific simulation step.

```APIDOC
## Function: gmx::setupStepWorkload

### Description
Sets up force flag structure from the force bitmask for a specific simulation step, incorporating domain lifetime workload and general simulation workload settings.

### Signature
StepWorkload gmx::setupStepWorkload(const int legacyFlags, ArrayRef< const gmx::MtsLevel > mtsLevels, const int64_t step, const DomainLifetimeWorkload &domainWork, const SimulationWorkload &simulationWork)
```

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

### frameStarted

Source: https://manual.gromacs.org/current/doxygen/html-full/classgmx_1_1AnalysisDataFrameAverageModule.xhtml

Notifies the module that a new data frame has started.

```APIDOC
## void gmx::AnalysisDataFrameAverageModule::frameStarted(const AnalysisDataFrameHeader &frame)

### Description
Called at the start of each data frame.

### Parameters
- **frame** (const AnalysisDataFrameHeader&) - Required - Header information for the frame that is starting.
```
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