api/gmxapi/include/gmxapi/system.h

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  35 #ifndef GMXAPI_SYSTEM_H
  36 #define GMXAPI_SYSTEM_H
  37 /*! \file
  38  * \brief Declare container for molecular systems
  39  *
  40  * \ingroup gmxapi
  41  */
  42 #include <memory>
  43 #include <string>
  44
  45 #include "gmxapi/gmxapi.h"
  46 #include "gmxapi/status.h"
  47
  48 namespace gmxapi
  49 {
  50
  51 // Forward declarations.
  52 class Context; // full specification in gmxapi/context.h
  53 class Session; // full specification in gmxapi/session.h
  54
  55 /*!
  56  * \brief Deprecated: A wrapper for gmx::Mdrunner
  57  *
  58  * Container for molecular model and simulation parameters.
  59  *
  60  * \internal
  61  * It was not intended as such, but gmxapi::System has ended up as basically a
  62  * wrapper for the gmx::Mdrunner simulator object and serves as the aspect of a
  63  * gmxapi Session that performs simulation work. As such, this class does not fit the
  64  * current gmxapi paradigm and will be removed, reworked, or renamed soon.
  65  *
  66  * # Protocol
  67  *
  68  * As of gmxapi 0.0.6, a simulation is configured and launched as follows.
  69  *
  70  * 1. Caller gets a System handle with gmxapi::fromTprFile().
  71  * 2. Caller optionally attaches additional MD Modules with
  72  *    getSpec()->addModule(std::shared_ptr<gmxapi::MDModule> module).
  73  *    See gmxapi::MDHolder
  74  * 3. Caller gets a runnable object by passing a Context to System::launch()
  75  *
  76  * During launch() configured gmxapi::MDModules are attached to the simulator, which is
  77  * then run by calling run() on the object returned by launch().
  78  *
  79  * \ingroup gmxapi
  80  */
  81 class System final
  82 {
  83 public:
  84     /*! \brief Private implementation class.
  85      *
  86      * System::Impl does not have a public interface and is only exposed in opaque pointers.
  87      */
  88     class Impl;
  89
  90     /*! \brief No copy.
  91      *
  92      * The semantics of copying a System are ambiguous, so disallow implicit
  93      * copy.
  94      * \{
  95      * \internal
  96      * Some sort of prototype or clone idiom could be useful, but
  97      * needs to explicitly identify any expensive operations.
  98      */
  99     System(const System&) = delete;
 100     System& operator=(const System&) = delete;
 101     /*! \} */
 102
 103     /*! \brief Allow move.
 104      *
 105      * \{
 106      */
 107     System(System&& /*unused*/) noexcept;
 108     System& operator=(System&& /*unused*/) noexcept;
 109     /*! \} */
 110
 111     /*!
 112      * \brief Create by taking ownership of an implementation object.
 113      *
 114      * \param implementation
 115      */
 116     explicit System(std::unique_ptr<Impl> implementation);
 117
 118     /*! \cond internal
 119      *  Destructor defined later to allow unique_ptr members of partially-defined types.
 120      */
 121     ~System();
 122     /*! \endcond */
 123
 124     /*!
 125      * \brief Configure the computing environment for the specified workflow.
 126      *
 127      * \return Ownership of a ready-to-run workflow or nullptr if there were errors.
 128      *
 129      * If errors occur, they will be stored in the context object. If run without
 130      * an argument, launch() uses the current context of the System object. If a
 131      * context argument is given, the system and its configured workflow are
 132      * translated to the provided context and launched.
 133      *
 134      * \param context (optional) execution context in which to launch.
 135      *
 136      * \note The Session object does not "own" the Context, but must be able
 137      * to extend the lifetime of the Context in which it is running.
 138      *
 139      * \todo Policy: does System then track the (potentially remote) context or should
 140      * it be considered to have "forked", and the new session object retrieved from
 141      * the session handle if needed?
 142      *
 143      * \cond internal
 144      * # Protocol
 145      *
 146      * The current implementation of System::launch() performs the following actions.
 147      *
 148      * When launch() is called, a new gmxapi::Session is created by passing a
 149      * gmxapi::Workflow to context->launch().
 150      * The Workflow basically just contains the TPR filename.
 151      * 1. A new Mdrunner is created from the information in the gmxapi::Workflow
 152      * 2. A new Session is created using the ContextImpl and the runner
 153      *
 154      * Then, for each module available through getSpec()->getModules(),
 155      * the session and module are passed to gmxapi::setSessionRestraint().
 156      * 1. A gmx::IRestraintPotential is retrieved from the module.
 157      * 2. A unique, named SessionResources is created for the module and attached to the SessionImpl.
 158      *     1. The module is added as a signaller to the session SignalManager
 159      *        with getSignalManager()->addSignaller(module->name())
 160      *     2. The SessionResources is passed to IRestraintPotential::bindSession().
 161      *        Currently, the only thing the restraint could do at this point is to
 162      *        save a copy of the pointer and later pass it to gmxapi::getMdrunnerSignal().
 163      *     3. The restraint is passed to gmx::Mdrunner::addPullPotential(),
 164      *        which adds the restraint to the global gmx::restraint::Manager,
 165      *        which then needs to be `clear()`ed after the runner completes.
 166      *
 167      * Shared ownership of the Session is returned to the caller of launch().
 168      *
 169      * \endcond
 170      */
 171     std::shared_ptr<Session> launch(const std::shared_ptr<Context>& context);
 172
 173 private:
 174     /*!
 175      * \brief Opaque pointer to implementation.
 176      */
 177     std::unique_ptr<Impl> impl_;
 178 };
 179
 180
 181 /*! \brief Defines an MD workflow from a TPR file.
 182  *
 183  * The TPR file has sufficient information to fully specify an MD run, though
 184  * various parameters are implicit until the work is launched. The TPR filename
 185  * provided must refer to identical TPR files at the API client and at the
 186  * master rank of the execution host.
 187  *
 188  * \param filename Filesystem path of TPR file.
 189  * \returns gmxapi::System object with the specified workflow.
 190  * \ingroup gmxapi
 191  */
 192 System fromTprFile(const std::string& filename);
 193
 194 } // end namespace gmxapi
 195
 196 #endif // include guard