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