### start

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1internal_1_1OptionSectionImpl-members.xhtml

Initializes the option section, performing any necessary setup.

```APIDOC
## start

### Description
Initializes the option section.
```

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

### Get Kernel Setup

Source: https://manual.gromacs.org/2025.3/doxygen/html-lib/namespacegmx.xhtml

Returns the kernel setup based on benchmark options.

```cpp
static NbnxmKernelSetup getKernelSetup (const NbnxmKernelBenchOptions &options)
```

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

### elementSetup

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1MttkElement.xhtml

Performs any necessary setup for the MttkElement before the simulation starts. This implementation indicates no specific setup is required.

```APIDOC
## elementSetup

### Description
Performs setup for the MttkElement. This implementation requires no specific setup.

### Method
`void elementSetup()`
```

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

### setup

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1StatePropagatorData.xhtml

Performs the initial setup for the associated Element.

```APIDOC
## setup

### Description
Initial set up for the associated element.

### Signature
`void setup()`
```

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

### Example Test Parameterization and Naming Setup

Source: https://manual.gromacs.org/2025.3/doxygen/html-lib/naming_8h.xhtml

Demonstrates the setup for parameterized tests using `std::tuple` and custom naming functors. It includes defining test parameters, a test fixture, and the naming functors for both test cases and reference data filenames.

```cpp
//! Enumeration used as an element of the test parameter tuple
enum class : int Flavor { A, B, C, Count };
EnumerationArray<Flavor, const char*> sc_flavorName = { "A", "B", "C" };

//! The test-parameter tuple
std::tuple<int, std::string, Flavor, float> TestParameters;
//! Parameterized test fixture
class ExampleTest : public ::testing::TestWithParam<TestParameters> { };

//! Functor containing tuple for naming each test case
const NameOfTestFromTuple<TestParameters> sc_testNamer{
std::make_tuple(PrefixFormatter<int, intToString>{"i_"},
useString,
sc_flavorName,
doubleToString) };

// Extra functor for further customizing the filename used for the
// reference data, particularly useful when some parameters should
// not influence the name of the file. See below for details.
// This example makes reference-data filenames like
// Combinations_ExampleTest_i_0_foo_3_1416.xml
const RefDataFilenameMaker<TestParameters> sc_refDataFilenameMaker {
std::make_tuple(PrefixFormatter<int, intToString>{"i_"},
useString,
toEmptyString, // ignores the Flavor
doubleToString) };
```

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

### Setup

Source: https://manual.gromacs.org/2025.3/doxygen/html-lib/functions_func_0x73.xhtml

Performs setup operations for various components like HaloExchange, DomainCommForward, and ListedForces.

```APIDOC
## setup()

### Description
Performs setup operations for the component.

### Method
Not applicable (C++ method)

### Endpoint
Not applicable (C++ method)

### Parameters
None explicitly documented in this context.

### Request Example
Not applicable (C++ method)

### Response
This function is associated with `gmx::HaloExchange`, `gmx::DomainCommForward`, and `ListedForces`.

### Response Example
Not applicable (C++ method)
```

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

### elementSetup

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1StatePropagatorData_1_1Element.xhtml

Performs setup operations for the element, such as backing up starting velocities.

```APIDOC
## elementSetup

### Description
Performs setup operations for the element, including backing up starting velocities. This method is part of the `ISimulatorElement` interface.

### Method
`void elementSetup()`
```

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

### elementSetup()

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1CompositeSimulatorElement-members.xhtml

Performs setup operations for the simulator element. This method is called once before the simulation starts.

```APIDOC
## elementSetup()

### Description
Performs setup operations for the simulator element. This method is called once before the simulation starts.

### Method
`virtual`

### Endpoint
`elementSetup()`
```

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

### Check Kernel Setup

Source: https://manual.gromacs.org/2025.3/doxygen/html-lib/namespacegmx.xhtml

Checks the kernel setup. Returns an optional string with error information if setup fails.

```cpp
static std::optional< std::string > checkKernelSetup (const NbnxmKernelBenchOptions &options)
```

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

### Start Source

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1SelectionFileOptionStorage.xhtml

Starts adding values from a new source for the option.

```APIDOC
## startSource()

### Description
Starts adding values from a new source for the option.
```

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

### NeighborSearchSignaller::setup

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1NeighborSearchSignaller.xhtml

Placeholder method for setup, does nothing at setup time.

```APIDOC
## void gmx::NeighborSearchSignaller::setup()

### Description
Do nothing at setup time.

### Method
void

### Implements
gmx::ISignaller
```

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

### Install Build Tools

Source: https://manual.gromacs.org/2025.3/gmxapi/userguide/install.html

Install the necessary Python build tools before creating a source archive.

```bash
pip install --upgrade setuptools build
```

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

### setupAndRunInstance

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/namespacegmx.xhtml

Sets up and runs the requested benchmark instance and prints the results.

```APIDOC
## setupAndRunInstance

### Description
Sets up and runs the requested benchmark instance and prints the results.

### Signature
static void | setupAndRunInstance (const BenchmarkSystem &system, const NbnxmKernelBenchOptions &options, const bool doWarmup)
```

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

### Template C++ Example

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/examples.xhtml

A basic C++ template file for Gromacs examples. This serves as a starting point for developing new examples.

```cpp
// This is a template file for GROMACS examples.
// It is not intended to be compiled or run directly.
// Use it as a starting point for your own examples.

#include <iostream>

int main() {
    // TODO: Add your example code here
    std::cout << "Hello, GROMACS example!" << std::endl;
    return 0;
}

```

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

### Setup and Run Benchmark Instance

Source: https://manual.gromacs.org/2025.3/doxygen/html-lib/namespacegmx.xhtml

Sets up and runs the requested benchmark instance and prints the results.

```cpp
static void setupAndRunInstance (const BenchmarkSystem &system, const NbnxmKernelBenchOptions &options, const bool doWarmup)
```

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

### getKernelSetup

Source: https://manual.gromacs.org/2025.3/doxygen/html-user/namespacegmx.xhtml

Returns the kernel setup configuration. This function retrieves the current setup for NBNxM kernels based on provided options.

```APIDOC
## getKernelSetup

### Description
Returns the kernel setup configuration. This function retrieves the current setup for NBNxM kernels based on provided options.

### Signature
`static NbnxmKernelSetup getKernelSetup(const NbnxmKernelBenchOptions &options)`
```

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

### setup()

Source: https://manual.gromacs.org/2025.3/doxygen/html-user/functions_func_0x73.xhtml

Sets up domain communication or halo exchange.

```APIDOC
## setup()

### Description
Sets up domain communication or halo exchange.

### Method
N/A

### Endpoint
N/A

### Parameters
N/A

### Request Example
N/A

### Response
#### Success Response
Initializes the communication or exchange mechanism.

### Response Example
N/A
```

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

### gmx::setupAndRunInstance

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/bench__setup_8cpp.xhtml

Sets up and runs the requested benchmark instance, then prints the results. This function orchestrates the execution and reporting of a single benchmark run.

```APIDOC
## gmx::setupAndRunInstance

### Description
Sets up and runs the requested benchmark instance and prints the results.

### Signature
static void gmx::setupAndRunInstance(const BenchmarkSystem &system, const NbnxmKernelBenchOptions &options, const bool doWarmup)

### Parameters
* **system** (const BenchmarkSystem &) - The benchmark system configuration.
* **options** (const NbnxmKernelBenchOptions &) - The benchmark options for the instance.
* **doWarmup** (const bool) - Flag to indicate if a warmup run should be performed.
```

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

### Notify Callbacks During MD Run Setup

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/page_mdmodules.xhtml

Trigger notifications for subscribed callbacks during the setup phase of an MD run, for example, within Mdrunner.

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

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

### elementSetup

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1CheckpointHelper.xhtml

Placeholder method for element setup. The CheckpointHelper does not require any specific setup actions when it is initialized as part of the simulator loop.

```APIDOC
## void gmx::CheckpointHelper::elementSetup()

### Description
No element setup needed.
```

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

### Get DD Grid Setup

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/domdec__setup_8cpp.xhtml

Determines the domain decomposition (DD) grid setup. It can either implement user-specified settings or estimate optimal parameters like PME ranks, cell setup, and initial ddbox.

```cpp
DDGridSetup getDDGridSetup(
    const gmx::MDLogger& _mdlog_,
    DDRole _ddRole_,
    MPI_Comm _communicator_,
    int _numRanksRequested_,
    const gmx::DomdecOptions& _options_,
    const DDSettings& _ddSettings_,
    const DDSystemInfo& _systemInfo_,
    real _cellSizeLimit_,
    const gmx_mtop_t& _mtop_,
    const t_inputrec& _ir_,
    const gmx::SeparatePmeRanksPermitted& _separatePmeRanksPermitted_,
    const matrix _box_,
    gmx::ArrayRef< const gmx::RVec > _xGlobal_,
    gmx_ddbox_t* _ddbox_
);
```

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

### Initialize Input Options

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/page_analysistemplate.xhtml

Sets up tool description, output file name option, selection options, and a cutoff value option. It also indicates the requirement for topology information.

```cpp
void MyAnalysisTool::initOptions(gmx::IOptionsContainer& options)
{
    // Set description text for the tool
    options.description("A template for trajectory analysis tools.");

    // Declare an option for the output file name
    options.addOption(gmx::FileNameOption("o", "output.dat", "Output file name"));

    // Declare options for setting selections
    options.addOption(selectionOption_);

    // Declare an option to set a cutoff value, with a default
    options.addOption(gmx::DoubleOption("cutoff", &cutoff_, "Cutoff distance"));

    // Indicate that the tool requires topology information (for demonstration)
    options.requireTopology(true);
}
```

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

### getKernelSetup

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/namespacegmx.xhtml

Returns the kernel setup based on provided benchmark options.

```APIDOC
## getKernelSetup

### Description
Returns the kernel setup.

### Signature
static NbnxmKernelSetup | getKernelSetup (const NbnxmKernelBenchOptions &options)
```

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

### Start mdrun with external MPI

Source: https://manual.gromacs.org/2025.3/user-guide/mdrun-performance.html

Starts mdrun using an external MPI implementation, launching a specified number of ranks and allowing hardware/MPI setup to determine OpenMP threads.

```bash
mpirun -np 2 gmx_mpi mdrun

```

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

### Typical Usage of CommandLineModuleManager

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1CommandLineModuleManager.xhtml

Demonstrates the typical setup and execution flow for a CommandLineModuleManager, including initialization, module registration, and running the manager.

```cpp
#include <gromacs/commandline/cmdlinemodulemanager.h>

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);
    }
}
```

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

### elementSetup()

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1AndersenTemperatureCoupling-members.xhtml

Performs setup operations for the simulation element. This method is called once before the simulation starts to prepare the element.

```APIDOC
## elementSetup()

### Description
Performs setup operations for the simulation element. This method is called once before the simulation starts to prepare the element.

### Method
`override`
```

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

### setup

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1DomDecHelper.xhtml

Performs the initial domain decomposition partitioning.

```APIDOC
## setup

### Description
The initial domain decomposition partitioning.

### Method
void
```

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

### handleRestart

Source: https://manual.gromacs.org/2025.3/doxygen/html-user/namespacegmx.xhtml

Handles the startup of mdrun, particularly concerning checkpoint files (-cpi) and appending (-append). It determines the starting behavior and returns a log file pointer.

```APIDOC
## handleRestart

### Description
Handle startup of mdrun, particularly regarding -cpi and -append.

### Signature
std::tuple< StartingBehavior, LogFilePtr > handleRestart(bool isSimulationMain, MPI_Comm communicator, const gmx_multisim_t *ms, AppendingBehavior appendingBehavior, int nfile, t_filenm fnm[])
```

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

### setup

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/functions_func_0x73.xhtml

Sets up various components. Applies to StatePropagatorData, LastStepSignaller, DomainCommForward, HaloExchange, ListedForces, DomDecHelper, ISignaller, PmeLoadBalanceHelper, NeighborSearchSignaller, LoggingSignaller, and TrajectorySignaller.

```APIDOC
## setup()

### Description
Sets up various components.

### Applies to
gmx::StatePropagatorData, gmx::LastStepSignaller, gmx::DomainCommForward, gmx::HaloExchange, ListedForces, gmx::DomDecHelper, gmx::ISignaller, gmx::PmeLoadBalanceHelper, gmx::NeighborSearchSignaller, gmx::LoggingSignaller, gmx::TrajectorySignaller, gmx::EnergySignaller
```

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

### checkInputConsistencyInterval

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/namespacegmx.xhtml

Checks if the starting configuration is consistent with the specified interval. This function is likely used to validate simulation setup parameters related to intervals.

```APIDOC
## checkInputConsistencyInterval

### Description
Check if the starting configuration is consistent with the given interval.

### Signature
`static void checkInputConsistencyInterval(const AwhParams &awhParams, WarningHandler *wi)`
```

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

### setup

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1HaloExchange-members.xhtml

Sets up the HaloExchange object for a new simulation step.

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

### Description
Configures the HaloExchange object for the current simulation step. This function is called to prepare for communication based on domain decomposition, local state, box dimensions, and force records.

### Method
`setup`

### Parameters
#### Path Parameters
- **dd** (gmx_domdec_t *) - Required - Pointer to the domain decomposition structure.
- **localState** (t_state *) - Required - Pointer to the local state of the simulation.
- **ddbox** (const gmx_ddbox_t &) - Required - Constant reference to the domain decomposition box structure.
- **fr** (t_forcerec *) - Required - Pointer to the force record structure.
- **cellsChanged** (const bool) - Required - Boolean indicating if the simulation cells have changed.
```

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

### GROMACS Index File Example (ndx)

Source: https://manual.gromacs.org/2025.3/reference-manual/file-formats.html

Defines user-definable sets of atoms for GROMACS analysis and preprocessing. Atom numbering starts at 1.

```text
[ Oxygen ]
1  4  7
[ Hydrogen ]
2  3  5  6
8  9

```

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

### Start mdrun on Two Nodes with Shared GPU (Alternative)

Source: https://manual.gromacs.org/2025.3/user-guide/mdrun-performance.html

Starts gmx mdrun on two nodes using eight total ranks, each with three OpenMP threads. All four ranks on a node share GPU with ID 0. Performance may vary compared to other setups.

```bash
mpirun -np 8 gmx_mpi mdrun -ntomp 3 -gputasks 0000

```

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

### MTS Setup and Requirements

Source: https://manual.gromacs.org/2025.3/doxygen/html-user/namespacegmx.xhtml

Functions related to setting up and validating Multi-Time-Stepping (MTS) levels and requirements.

```APIDOC
## setupMtsLevels

### Description
Sets up and returns the MTS levels and checks requirements of MTS.

### Signature
```cpp
std::vector<MtsLevel> setupMtsLevels(const GromppMtsOpts &mtsOpts, std::vector<std::string> *errorMessages)
```

## haveValidMtsSetup

### Description
Returns whether MTS is used and its setup is internally valid.

### Signature
```cpp
bool haveValidMtsSetup(const t_inputrec &ir)
```

## checkMtsRequirements

### Description
Checks whether the MTS requirements on other algorithms and output frequencies are met.

### Signature
```cpp
std::vector<std::string> checkMtsRequirements(const t_inputrec &ir)
```

## forceGroupMtsLevel

### Description
Returns the MTS level at which a force group is to be computed.

### Signature
```cpp
static int forceGroupMtsLevel(ArrayRef<const MtsLevel> mtsLevels, const MtsForceGroups mtsForceGroup)
```
```

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

### Setup Nbnxm for Benchmark Instance

Source: https://manual.gromacs.org/2025.3/doxygen/html-lib/namespacegmx.xhtml

Sets up and returns a Nbnxm object for the given benchmark options and system.

```cpp
static std::unique_ptr< nonbonded_verlet_t > setupNbnxmForBenchInstance (const NbnxmKernelBenchOptions &options, const BenchmarkSystem &system)
```

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

### gmx make_ndx -twin option example

Source: https://manual.gromacs.org/2025.3/onlinehelp/gmx-make_ndx.html

The -twin switch duplicates all index groups with an offset of -natoms, which is useful for Computational Electrophysiology double-layer membrane setups.

```bash
gmx make_ndx -f conf.gro -o index.ndx -twin -natoms 10000
```

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

### Get Number of Grids Function

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/gridset_8cpp.xhtml

A static function within the GridSet class that returns the total number of search grids based on the provided domain setup.

```cpp
static int | gmx::numGrids (const GridSet::DomainSetup &domainSetup)
```

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

### InstallationPrefixInfo

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/structgmx_1_1InstallationPrefixInfo.xhtml

Initializes the InstallationPrefixInfo structure with the provided path and a boolean indicating if it's a source layout.

```APIDOC
## InstallationPrefixInfo

### Description
Initializes the structure with given values.

### Parameters
* **path** (std::filesystem::path) - Description of the installation prefix path.
* **bSource** (bool) - Indicates if the path points to a source tree-like layout.
```

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

### Get gmxapi Version using pkg_resources

Source: https://manual.gromacs.org/2025.3/gmxapi/userguide/pythonreference.html

Access the installed gmxapi package version using the pkg_resources module. This is a common way to retrieve package versions in Python.

```python
import pkg_resources

print(pkg_resources.get_distribution('gmxapi').version)

```

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

### setup_edi

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/namespaceanonymous__namespace_02edsam_8cpp_03.xhtml

Sets up essential dynamics work parameters.

```APIDOC
## setup_edi

### Description
Set up essential dynamics work parameters.

### Signature
void setup_edi (t_edpar *edi)

### Parameters
* **edi** (t_edpar *) - Essential dynamics parameters structure to set up.
```

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

### setup

Source: https://manual.gromacs.org/2025.3/doxygen/html-user/classgmx_1_1HaloExchange-members.xhtml

Sets up the HaloExchange object for a simulation run.

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

### Description
Sets up the HaloExchange object with necessary simulation parameters. This method configures the halo exchange for the current simulation state.

### Method
`setup`

### Parameters
#### Path Parameters
- **dd** (gmx_domdec_t *) - Pointer to the domain decomposition structure.
- **localState** (t_state *) - Pointer to the local state of the simulation.
- **ddbox** (const gmx_ddbox_t &) - The domain decomposition box information.
- **fr** (t_forcerec *) - Pointer to the force record.
- **cellsChanged** (const bool) - Flag indicating if the simulation cells have changed.
```

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

### Accessing Custom Data in analyzeFrame

Source: https://manual.gromacs.org/2025.3/doxygen/html-user/page_analysistemplate.xhtml

In analyzeFrame, custom data structures (if used) can be accessed via a static_cast for shorthand. This example shows how to get data from a custom structure.

```cpp
const auto& data = static_cast<const MyModuleData*>(pdata)->data();
```

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

### chooseStartingBehavior

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/namespacegmx_1_1anonymous__namespace_02handlerestart_8cpp_03.xhtml

Determines the appropriate starting behavior for a Gromacs simulation based on appending behavior and existing files. It handles cases where different simulations in a multi-simulation setup might have different restart conditions.

```APIDOC
## chooseStartingBehavior

### Description
Choose the starting behaviour for this simulation.

This routine cannot print tons of data, since it is called before the log file is opened.
Note that different simulations in a multi-simulation can return values that depend on whether the respective checkpoint files are found (and other files found, when appending), and so can differ between multi-simulations. It is the caller's responsibility to detect this and react accordingly.

### Signature
StartingBehaviorHandler chooseStartingBehavior(const AppendingBehavior appendingBehavior, const int nfile, t_filenm fnm[])
```

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

### StringOption Constructors and Basic Configuration

Source: https://manual.gromacs.org/2025.3/doxygen/html-user/classgmx_1_1StringOption.xhtml

Demonstrates the initialization of a StringOption and setting basic properties like description and requirement.

```APIDOC
## StringOption(const char *name)

### Description
Initializes an option with the given name.

### Method
Constructor

### Parameters
* **name** (const char *) - The name of the option.

## StringOption::description

### Description
Sets a description for the option.

### Method
Setter

### Parameters
* **descr** (const char *) - The description string for the option.

## StringOption::required

### Description
Requires the option to be specified explicitly.

### Method
Setter

### Parameters
* **bRequired** (bool) - If true, the option is required. Defaults to true.
```

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

### Configuring GROMACS with CMake Command-Line Options

Source: https://manual.gromacs.org/2025.3/install-guide/index.html

Specify build options directly on the CMake command line using the -D flag. This example configures GROMACS for CUDA GPUs, MPI, and a custom installation prefix.

```bash
cmake .. -DGMX_GPU=CUDA -DGMX_MPI=ON \
         -DCMAKE_INSTALL_PREFIX=/home/marydoe/programs
```

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

### Typical Usage of CommandLineModuleManager

Source: https://manual.gromacs.org/2025.3/doxygen/html-lib/classgmx_1_1CommandLineModuleManager.xhtml

Demonstrates the typical setup and execution flow for a command-line application using CommandLineModuleManager. This includes initialization, module registration (commented out), running the manager, and exception handling.

```cpp
#include <gromacs/commandline/cmdlinemodulemanager.h>

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);
}
}
```

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

### nbnxmKernelSimd (EwaldAnalytical, LorentzBerthelot, PotShift, VdwCutoffCheck::Yes)

Source: https://manual.gromacs.org/2025.3/doxygen/html-user/namespacegmx.xhtml

This overload computes analytical Ewald Coulomb interactions with Lorentz-Berthelot LJ combination rules, potential shifting, and a Van der Waals cutoff check. This configuration is for specific simulation setups.

```APIDOC
## nbnxmKernelSimd < KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs >

### Description
This function computes non-bonded interactions using a SIMD-optimized kernel. It is specialized for analytical Ewald Coulomb interactions, a cutoff check for Van der Waals forces, Lorentz-Berthelot combination rules for LJ potentials, and applies a potential shift.

### Parameters
- **nbl** (const NbnxnPairlistCpu *): Pointer to the non-bonded pairlist structure.
- **nbat** (const nbnxn_atomdata_t *): Pointer to the atom data for non-bonded interactions.
- **ic** (const interaction_const_t *): Pointer to interaction constants.
- **shift_vec** (const rvec *): Vector for potential shifting.
- **out** (nbxn_atomdata_output_t *): Output structure for interaction data.
```

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

### Typical Usage of TextTableFormatter

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1TextTableFormatter.xhtml

Demonstrates the basic setup and usage of TextTableFormatter to add columns, add text to columns, and format a row. This example shows a simple row with text that fits within the defined column widths.

```cpp
#include <gromacs/onlinehelp/helpformat.h>
#include <cstdio>
#include <string>

// Assuming gmx::TextTableFormatter is available
// For demonstration purposes, we'll use a placeholder if not directly available in this context.

// Placeholder for the actual class if not in scope for a standalone example
namespace gmx {
class TextTableFormatter {
public:
    TextTableFormatter() {}
    void addColumn(const char* title, int width, bool bWrap) {}
    void clear() {}
    void addColumnLine(int index, const std::string& text) {}
    void setColumnFirstLineOffset(int index, int firstLine) {}
    std::string formatRow() { return ""; } // Placeholder return
};
}

int main() {
    gmx::TextTableFormatter formatter;
    formatter.addColumn("Name", 10, false);
    formatter.addColumn("Type", 10, false);
    formatter.addColumn("Description", 50, true);
    formatter.clear();
    formatter.addColumnLine(0, "name");
    formatter.addColumnLine(1, "type");
    formatter.addColumnLine(2, "Description for name");
    printf("%s", formatter.formatRow().c_str());
    return 0;
}

```

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

### SetUp

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/functions_func_0x73.xhtml

Sets up the test environment for Shake. Applies to ShakeTest.

```APIDOC
## SetUp()

### Description
Sets up the test environment for Shake.

### Applies to
gmx::test::anonymous_namespace{shake.cpp}::ShakeTest
```

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

### Interpolating a Specific Function's Derivative

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1QuadraticSplineTable.xhtml

Interpolate the derivative of a specific function within a multi-function table. This example shows how to get the derivative of the second function (index 1) from a table containing three functions in total.

```cpp
double x = 0.5; // The point at which to evaluate the derivative
double der;

// Interpolate the derivative of the second function (index 1) from a table with 3 functions total.
// table.evaluateDerivative<TotalFunctions, FunctionIndex>(x, &output_derivative_pointer);
table.evaluateDerivative<3, 1>(x, &der);

```

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

### setup

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1PmeLoadBalanceHelper.xhtml

Initializes the PME load balancing object before simulation steps.

```APIDOC
## void setup ()

### Description
Initializes the load balancing object.

### Method
void
```

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

### elementSetup

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1ComputeGlobalsElement.xhtml

Performs the initial setup for the element, which includes the first call to compute_globals.

```APIDOC
## elementSetup()

### Description
Element setup - first call to compute_globals.

### Method
override
```

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

### Get Base PME GPU Spline Parameter Index

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/pme__gpu__calculate__splines__sycl_8h.xhtml

Calculates the base index for PME GPU spline parameter buffers. This function is a prerequisite for getSplineParamIndex() and is used to determine the starting point for accessing spline parameters within a sub-group.

```cpp
template<int order, int atomsPerSubGroup>
static int getSplineParamIndexBase(
    int _subGroupIndex_,
    int _atomSubGroupIndex_
)
```

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

### setupNbnxmForBenchInstance

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/namespacegmx.xhtml

Sets up and returns a Nbnxm object for the given benchmark options and system.

```APIDOC
## setupNbnxmForBenchInstance

### Description
Sets up and returns a Nbnxm object for the given benchmark options and system.

### Signature
static std::unique_ptr < nonbonded_verlet_t > | setupNbnxmForBenchInstance (const NbnxmKernelBenchOptions &options, const BenchmarkSystem &system)
```

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

### TextTableFormatter with Text Wrapping and Line Offset

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1TextTableFormatter.xhtml

Illustrates how TextTableFormatter handles text that might overflow columns by using text wrapping and how to control the starting line for column output using setColumnFirstLineOffset. This example shows a row with a long name that requires careful formatting.

```cpp
#include <gromacs/onlinehelp/helpformat.h>
#include <cstdio>
#include <string>

// Assuming gmx::TextTableFormatter is available
// For demonstration purposes, we'll use a placeholder if not directly available in this context.

// Placeholder for the actual class if not in scope for a standalone example
namespace gmx {
class TextTableFormatter {
public:
    TextTableFormatter() {}
    void addColumn(const char* title, int width, bool bWrap) {}
    void clear() {}
    void addColumnLine(int index, const std::string& text) {}
    void setColumnFirstLineOffset(int index, int firstLine) {}
    std::string formatRow() { return ""; } // Placeholder return
};
}

int main() {
    gmx::TextTableFormatter formatter;
    formatter.addColumn("Name", 10, false);
    formatter.addColumn("Type", 10, false);
    formatter.addColumn("Description", 50, true);
    formatter.clear();
    formatter.addColumnLine(0, "averylongname");
    formatter.addColumnLine(1, "type");
    formatter.setColumnFirstLineOffset(1, 1);
    formatter.addColumnLine(2, "Description for name");
    printf("%s", formatter.formatRow().c_str());
    // format other rows by repeating the above code
    return 0;
}

```

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

### Install gmxapi with Verbose Output

Source: https://manual.gromacs.org/2025.3/gmxapi/userguide/install.html

Install gmxapi, specifying the GROMACS installation path and enabling verbose output to help diagnose installation issues.

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

```

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

### Setting Up Input Options

Source: https://manual.gromacs.org/2025.3/doxygen/html-user/page_analysistemplate.xhtml

Configures tool-specific options, including output file, selections, and cutoff values. Requires topology information.

```cpp
void MyAnalysisTool::initOptions(gmx::TrajectoryAnalysisSettings &settings)
{
    settings.setToolBoxDescription("My custom trajectory analysis tool.");

    // Option for output file name
    settings.addOption("o", "output", "Output file name", &outputFileName_);

    // Options for selections
    settings.addOption(selectionOption_, "sel", "Selection for analysis");

    // Option for cutoff value, with default from constructor
    settings.addOption("c", "cutoff", "Cutoff distance", &cutoff_, gmx::IOptionsContainer::Optional);

    // Indicate that topology is required (for demonstration)
    settings.forceRequiresTopology();
}

```

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

### Install gmxapi from a downloaded source archive

Source: https://manual.gromacs.org/2025.3/gmxapi/userguide/install.html

Download the gmxapi source distribution archive and then install it from the local file. This method is useful for installing specific versions or when direct PyPI installation is not preferred.

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

```

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

### elementSetup

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1PullElement.xhtml

Performs initial setup for the PullElement.

```APIDOC
## elementSetup

### Description
Sets the initial annealing temperature. This method is part of the ISimulatorElement interface.

### Method
void
```

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

### Set Start Time

Source: https://manual.gromacs.org/2025.3/doxygen/html-lib/functions_func_0x73.xhtml

Sets the start time for a simulation or analysis. This function is part of a utility for setting the start time.

```APIDOC
## SetStartTime()

### Description
Sets the start time for the simulation or analysis.

### Method
Not applicable (C++ method)

### Endpoint
Not applicable (C++ method)

### Parameters
None explicitly documented in this context.

### Request Example
Not applicable (C++ method)

### Response
This function is part of the `gmx::SetStartTime` utility.

### Response Example
Not applicable (C++ method)
```

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

### Setup and Run Simple Simulation with gmxapi

Source: https://manual.gromacs.org/2025.3/gmxapi/userguide/usage.html

Sets up a simulation using a TPR file and prepares it for execution. The simulation is triggered explicitly by calling .run().

```python
import gmxapi as gmx
simulation_input = gmx.read_tpr(tpr_filename)
md = gmx.mdrun(simulation_input)
```

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

### Perform Offline gmxapi Installation

Source: https://manual.gromacs.org/2025.3/gmxapi/userguide/install.html

Install gmxapi using pre-downloaded wheel files from a local directory, ensuring no internet connection is required during installation.

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

```

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

### start()

Source: https://manual.gromacs.org/2025.3/doxygen/html-user/functions_func_0x73.xhtml

Initiates a process, such as histogram settings initialization or a simulation cycle.

```APIDOC
## start()

### Description
Initiates a process, such as histogram settings initialization or a simulation cycle.

### Method
N/A

### Endpoint
N/A

### Parameters
N/A

### Request Example
N/A

### Response
#### Success Response
Begins the execution of the specified process.

### Response Example
N/A
```

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

### setupForceOutputs

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/namespacegmx.xhtml

Set up the different force buffers; also does clearing.

```APIDOC
## setupForceOutputs

### Description
Set up the different force buffers; also does clearing.

### Method
static ForceOutputs

### Endpoint
setupForceOutputs
```

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

### Specify GROMACS Installation Path

Source: https://manual.gromacs.org/2025.3/gmxapi/userguide/install.html

When GROMACS is not sourced via GMXRC, set the gmxapi_ROOT environment variable to point to the GROMACS installation directory before installing gmxapi.

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

```

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

### kernelSetup

Source: https://manual.gromacs.org/2025.3/doxygen/html-lib/functions_func_0x6b.xhtml

Initializes the kernel setup for nonbonded Verlet interactions.

```APIDOC
## kernelSetup

### Description
Initializes the kernel setup for nonbonded Verlet interactions.

### Method
(Not specified in source)

### Endpoint
(Not specified in source)

### Parameters
(No parameters specified in source)

### Response
#### Success Response
- **gmx::nonbonded_verlet_t**: The type returned by the kernel setup function.

#### Response Example
(No response example specified in source)
```

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

### Install gmxapi Python Package

Source: https://manual.gromacs.org/2025.3/gmxapi/userguide/install.html

Sources the GROMACS environment script and then installs the gmxapi Python package from PyPI. This command assumes GROMACS is installed in `/path/to/gromacs`.

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

```

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

### checkKernelSetup

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/namespacegmx.xhtml

Checks the kernel setup based on provided benchmark options.

```APIDOC
## checkKernelSetup

### Description
Checks the kernel setup.

### Signature
static std::optional< std::string > | checkKernelSetup (const NbnxmKernelBenchOptions &options)
```

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

### gmx::SelectionPosition::refId

Source: https://manual.gromacs.org/2025.3/doxygen/html-user/classgmx_1_1SelectionPosition.xhtml

Returns the reference ID for this position. For dynamic selections, this ID helps associate positions across frames. After compilation, these IDs are sequentially numbered starting from zero. In each frame, the ID reflects the position's location in the original array. If SelectionOption::dynamicMask() is set, positions not in the current selection get an ID of -1; otherwise, they are removed. Default values are zero-based.

```APIDOC
## gmx::SelectionPosition::refId

### Description
Returns the reference ID for this position. For dynamic selections, this ID helps associate positions across frames. After compilation, these IDs are sequentially numbered starting from zero. In each frame, the ID reflects the position's location in the original array. If SelectionOption::dynamicMask() is set, positions not in the current selection get an ID of -1; otherwise, they are removed. Default values are zero-based.

### Method
const

### Return Value
int - The reference ID of the position.
```

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

### Kernel Setup Access

Source: https://manual.gromacs.org/2025.3/doxygen/html-lib/structgmx_1_1nonbonded__verlet__t.xhtml

Provides access to the kernel setup configuration.

```APIDOC
## Kernel Setup Access

### `const NbnxmKernelSetup &kernelSetup() const`

**Description**: Return the kernel setup.
```

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

### BenchmarkSystem()

Source: https://manual.gromacs.org/2025.3/doxygen/html-user/functions_func_0x62.xhtml

Initializes the benchmarking system.

```APIDOC
## BenchmarkSystem()

### Description
Initializes the benchmarking system.

### Method
N/A

### Endpoint
N/A

### Parameters
N/A

### Request Example
N/A

### Response
N/A

### Response Example
N/A
```

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

### Example Usage of makeSimulationInput

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/group__module__mdrun.xhtml

Demonstrates how to prepare LegacyMdrunOptions, create a SimulationInputHandle using makeSimulationInput, and add it to a SimulationInputBuilder. This function is not yet part of the public API and is subject to change.

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

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

### Start Set

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1SelectionFileOptionStorage.xhtml

Starts adding a new set of values for the option.

```APIDOC
## startSet()

### Description
Starts adding a new set of values for the option.
```

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

### QMMMSimulationParameterSetup Methods

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1anonymous__namespace_02qmmm_8cpp_03_1_1QMMMSimulationParameterSetup.xhtml

Provides access to methods for managing QMMM simulation parameters, including setting and retrieving atom sets, periodic boundary conditions, and logger instances.

```APIDOC
## Class: gmx::anonymous_namespace{qmmm.cpp}::QMMMSimulationParameterSetup

### Description
Helper class that holds simulation data and callback functions for simulation setup time notifications.

### Public Member Functions

#### `void setLocalQMAtomSet(const LocalAtomSet &localAtomSet)`
Set the local atom set for the QM atoms.

#### `void setLocalMMAtomSet(const LocalAtomSet &localAtomSet)`
Set the local atom set for the MM atoms.

#### `const LocalAtomSet& localQMAtomSet() const`
Return local atom set for QM atoms.

* **Exceptions**: `InternalError` if local atom set is not set.

#### `const LocalAtomSet& localMMAtomSet() const`
Return local atom set for MM atoms.

* **Exceptions**: `InternalError` if local atom set is not set.

#### `void setPeriodicBoundaryConditionType(const PbcType &pbc)`
Set the periodic boundary condition via MdModuleNotifier.

#### `PbcType periodicBoundaryConditionType()`
Get the periodic boundary conditions.

#### `void setLogger(const MDLogger &logger)`
Set the logger for QMMM during mdrun.

#### `const MDLogger& logger() const`
Get the logger instance.
```

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

### start

Source: https://manual.gromacs.org/2025.3/doxygen/html-full/classgmx_1_1OptionsAssigner.xhtml

Starts the process of assigning values. This method does not throw any exceptions.

```APIDOC
## start

### Description
Starts assigning values.

### Does Not Throw
```