src/gromacs/mdrun/mdmodules.cpp

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  35 #include "gmxpre.h"
  36
  37 #include "mdmodules.h"
  38
  39 #include <memory>
  40
  41 #include "gromacs/applied_forces/electricfield.h"
  42 #include "gromacs/applied_forces/densityfitting/densityfitting.h"
  43 #include "gromacs/imd/imd.h"
  44 #include "gromacs/mdtypes/iforceprovider.h"
  45 #include "gromacs/mdtypes/imdmodule.h"
  46 #include "gromacs/mdtypes/imdoutputprovider.h"
  47 #include "gromacs/mdtypes/imdpoptionprovider.h"
  48 #include "gromacs/mdtypes/inputrec.h"
  49 #include "gromacs/options/options.h"
  50 #include "gromacs/options/optionsection.h"
  51 #include "gromacs/options/treesupport.h"
  52 #include "gromacs/swap/swapcoords.h"
  53 #include "gromacs/utility/keyvaluetree.h"
  54 #include "gromacs/utility/keyvaluetreebuilder.h"
  55 #include "gromacs/utility/keyvaluetreetransform.h"
  56 #include "gromacs/utility/mdmodulenotification.h"
  57 #include "gromacs/utility/smalloc.h"
  58
  59 namespace gmx
  60 {
  61
  62 class MDModules::Impl : public IMDOutputProvider
  63 {
  64 public:
  65     Impl() :
  66         densityFitting_(DensityFittingModuleInfo::create()),
  67         field_(createElectricFieldModule()),
  68         imd_(createInteractiveMolecularDynamicsModule()),
  69         swapCoordinates_(createSwapCoordinatesModule())
  70     {
  71     }
  72
  73     void makeModuleOptions(Options* options)
  74     {
  75         // Create a section for applied-forces modules
  76         auto appliedForcesOptions = options->addSection(OptionSection("applied-forces"));
  77         field_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions);
  78         densityFitting_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions);
  79         // In future, other sections would also go here.
  80     }
  81
  82     // From IMDOutputProvider
  83     void initOutput(FILE* fplog, int nfile, const t_filenm fnm[], bool bAppendFiles, const gmx_output_env_t* oenv) override
  84     {
  85         field_->outputProvider()->initOutput(fplog, nfile, fnm, bAppendFiles, oenv);
  86         densityFitting_->outputProvider()->initOutput(fplog, nfile, fnm, bAppendFiles, oenv);
  87     }
  88     void finishOutput() override
  89     {
  90         field_->outputProvider()->finishOutput();
  91         densityFitting_->outputProvider()->finishOutput();
  92     }
  93
  94     /*! \brief Manages callbacks and notifies the MD modules.
  95      *
  96      * \note The notifier must be constructed before the modules and shall
  97      *       not be destructed before the modules are destructed.
  98      */
  99     MdModulesNotifier notifier_;
 100
 101     std::unique_ptr<IMDModule>      densityFitting_;
 102     std::unique_ptr<IMDModule>      field_;
 103     std::unique_ptr<ForceProviders> forceProviders_;
 104     std::unique_ptr<IMDModule>      imd_;
 105     std::unique_ptr<IMDModule>      swapCoordinates_;
 106
 107     /*! \brief List of registered MDModules
 108      *
 109      * Note that MDModules::Impl owns this container, but it is only used by
 110      * the MDModules::initForceProviders() function. To be consistent with
 111      * IMDModule's vision, as indicated by its docs, we should
 112      * \todo update IMDModule docs to allow nullptr return values
 113      * \todo check for nullptr returned by IMDModule methods.
 114      * \todo include field_ in modules_
 115      */
 116     std::vector<std::shared_ptr<IMDModule>> modules_;
 117 };
 118
 119 MDModules::MDModules() : impl_(new Impl) {}
 120
 121 MDModules::~MDModules() {}
 122
 123 void MDModules::initMdpTransform(IKeyValueTreeTransformRules* rules)
 124 {
 125     auto appliedForcesScope = rules->scopedTransform("/applied-forces");
 126     impl_->field_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules());
 127     impl_->densityFitting_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules());
 128 }
 129
 130 void MDModules::buildMdpOutput(KeyValueTreeObjectBuilder* builder)
 131 {
 132     impl_->field_->mdpOptionProvider()->buildMdpOutput(builder);
 133     impl_->densityFitting_->mdpOptionProvider()->buildMdpOutput(builder);
 134 }
 135
 136 void MDModules::assignOptionsToModules(const KeyValueTreeObject& params, IKeyValueTreeErrorHandler* errorHandler)
 137 {
 138     Options moduleOptions;
 139     impl_->makeModuleOptions(&moduleOptions);
 140     // The actual output is in the data fields of the modules that
 141     // were set up in the module options.
 142     assignOptionsFromKeyValueTree(&moduleOptions, params, errorHandler);
 143 }
 144
 145 void MDModules::adjustInputrecBasedOnModules(t_inputrec* ir)
 146 {
 147     Options moduleOptions;
 148     impl_->makeModuleOptions(&moduleOptions);
 149
 150     checkForUnknownOptionsInKeyValueTree(*ir->params, moduleOptions);
 151
 152     std::unique_ptr<KeyValueTreeObject> params(
 153             new KeyValueTreeObject(adjustKeyValueTreeFromOptions(*ir->params, moduleOptions)));
 154     delete ir->params;
 155     ir->params = params.release();
 156 }
 157
 158 IMDOutputProvider* MDModules::outputProvider()
 159 {
 160     return impl_.get();
 161 }
 162
 163 ForceProviders* MDModules::initForceProviders()
 164 {
 165     GMX_RELEASE_ASSERT(impl_->forceProviders_ == nullptr,
 166                        "Force providers initialized multiple times");
 167     impl_->forceProviders_ = std::make_unique<ForceProviders>();
 168     impl_->field_->initForceProviders(impl_->forceProviders_.get());
 169     impl_->densityFitting_->initForceProviders(impl_->forceProviders_.get());
 170     for (auto&& module : impl_->modules_)
 171     {
 172         module->initForceProviders(impl_->forceProviders_.get());
 173     }
 174     return impl_->forceProviders_.get();
 175 }
 176
 177 void MDModules::subscribeToPreProcessingNotifications()
 178 {
 179     impl_->densityFitting_->subscribeToPreProcessingNotifications(&impl_->notifier_);
 180 }
 181
 182 void MDModules::subscribeToSimulationSetupNotifications()
 183 {
 184     impl_->densityFitting_->subscribeToSimulationSetupNotifications(&impl_->notifier_);
 185 }
 186
 187 void MDModules::add(std::shared_ptr<gmx::IMDModule> module)
 188 {
 189     impl_->modules_.emplace_back(std::move(module));
 190 }
 191
 192 const MdModulesNotifier& MDModules::notifier()
 193 {
 194     return impl_->notifier_;
 195 }
 196
 197 } // namespace gmx