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/imd/imd.h"
  43 #include "gromacs/mdtypes/iforceprovider.h"
  44 #include "gromacs/mdtypes/imdmodule.h"
  45 #include "gromacs/mdtypes/imdoutputprovider.h"
  46 #include "gromacs/mdtypes/imdpoptionprovider.h"
  47 #include "gromacs/mdtypes/inputrec.h"
  48 #include "gromacs/options/options.h"
  49 #include "gromacs/options/optionsection.h"
  50 #include "gromacs/options/treesupport.h"
  51 #include "gromacs/swap/swapcoords.h"
  52 #include "gromacs/utility/keyvaluetree.h"
  53 #include "gromacs/utility/keyvaluetreebuilder.h"
  54 #include "gromacs/utility/keyvaluetreetransform.h"
  55 #include "gromacs/utility/smalloc.h"
  56
  57 namespace gmx
  58 {
  59
  60 class MDModules::Impl : public IMDOutputProvider
  61 {
  62     public:
  63
  64         Impl()
  65             : field_(createElectricFieldModule()),
  66               imd_(createInteractiveMolecularDynamicsModule()),
  67               swapCoordinates_(createSwapCoordinatesModule())
  68         {
  69         }
  70
  71         void makeModuleOptions(Options *options)
  72         {
  73             // Create a section for applied-forces modules
  74             auto appliedForcesOptions = options->addSection(OptionSection("applied-forces"));
  75             field_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions);
  76             // In future, other sections would also go here.
  77         }
  78
  79         // From IMDOutputProvider
  80         void initOutput(FILE *fplog, int nfile, const t_filenm fnm[],
  81                         bool bAppendFiles, const gmx_output_env_t *oenv) override
  82         {
  83             field_->outputProvider()->initOutput(fplog, nfile, fnm, bAppendFiles, oenv);
  84         }
  85         void finishOutput() override
  86         {
  87             field_->outputProvider()->finishOutput();
  88         }
  89
  90         std::unique_ptr<IMDModule>      field_;
  91         std::unique_ptr<ForceProviders> forceProviders_;
  92         std::unique_ptr<IMDModule>      imd_;
  93         std::unique_ptr<IMDModule>      swapCoordinates_;
  94
  95         /*! \brief List of registered MDModules
  96          *
  97          * Note that MDModules::Impl owns this container, but it is only used by
  98          * the MDModules::initForceProviders() function. To be consistent with
  99          * IMDModule's vision, as indicated by its docs, we should
 100          * \todo update IMDModule docs to allow nullptr return values
 101          * \todo check for nullptr returned by IMDModule methods.
 102          * \todo include field_ in modules_
 103          */
 104         std::vector< std::shared_ptr<IMDModule> > modules_;
 105 };
 106
 107 MDModules::MDModules() : impl_(new Impl)
 108 {
 109 }
 110
 111 MDModules::~MDModules()
 112 {
 113 }
 114
 115 void MDModules::initMdpTransform(IKeyValueTreeTransformRules *rules)
 116 {
 117     auto appliedForcesScope = rules->scopedTransform("/applied-forces");
 118     impl_->field_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules());
 119 }
 120
 121 void MDModules::buildMdpOutput(KeyValueTreeObjectBuilder *builder)
 122 {
 123     impl_->field_->mdpOptionProvider()->buildMdpOutput(builder);
 124 }
 125
 126 void MDModules::assignOptionsToModules(const KeyValueTreeObject  &params,
 127                                        IKeyValueTreeErrorHandler *errorHandler)
 128 {
 129     Options moduleOptions;
 130     impl_->makeModuleOptions(&moduleOptions);
 131     // The actual output is in the data fields of the modules that
 132     // were set up in the module options.
 133     assignOptionsFromKeyValueTree(&moduleOptions, params, errorHandler);
 134 }
 135
 136 void MDModules::adjustInputrecBasedOnModules(t_inputrec *ir)
 137 {
 138     Options moduleOptions;
 139     impl_->makeModuleOptions(&moduleOptions);
 140
 141     checkForUnknownOptionsInKeyValueTree(*ir->params, moduleOptions);
 142
 143     std::unique_ptr<KeyValueTreeObject> params(
 144             new KeyValueTreeObject(
 145                     adjustKeyValueTreeFromOptions(*ir->params, moduleOptions)));
 146     delete ir->params;
 147     ir->params = params.release();
 148 }
 149
 150 IMDOutputProvider *MDModules::outputProvider()
 151 {
 152     return impl_.get();
 153 }
 154
 155 ForceProviders *MDModules::initForceProviders()
 156 {
 157     GMX_RELEASE_ASSERT(impl_->forceProviders_ == nullptr,
 158                        "Force providers initialized multiple times");
 159     impl_->forceProviders_ = std::make_unique<ForceProviders>();
 160     impl_->field_->initForceProviders(impl_->forceProviders_.get());
 161     for (auto && module : impl_->modules_)
 162     {
 163         module->initForceProviders(impl_->forceProviders_.get());
 164     }
 165     return impl_->forceProviders_.get();
 166 }
 167
 168 void MDModules::add(std::shared_ptr<gmx::IMDModule> module)
 169 {
 170     impl_->modules_.emplace_back(std::move(module));
 171 }
 172
 173 } // namespace gmx