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37 #include "mdmodules.h"
41 #include "gromacs/applied_forces/electricfield.h"
42 #include "gromacs/mdtypes/iforceprovider.h"
43 #include "gromacs/mdtypes/imdmodule.h"
44 #include "gromacs/mdtypes/imdoutputprovider.h"
45 #include "gromacs/mdtypes/imdpoptionprovider.h"
46 #include "gromacs/mdtypes/inputrec.h"
47 #include "gromacs/options/options.h"
48 #include "gromacs/options/optionsection.h"
49 #include "gromacs/options/treesupport.h"
50 #include "gromacs/utility/keyvaluetree.h"
51 #include "gromacs/utility/keyvaluetreebuilder.h"
52 #include "gromacs/utility/keyvaluetreetransform.h"
53 #include "gromacs/utility/smalloc.h"
58 class MDModules::Impl : public IMDOutputProvider
63 : field_(createElectricFieldModule())
67 void makeModuleOptions(Options *options)
69 // Create a section for applied-forces modules
70 auto appliedForcesOptions = options->addSection(OptionSection("applied-forces"));
71 field_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions);
72 // In future, other sections would also go here.
75 // From IMDOutputProvider
76 void initOutput(FILE *fplog, int nfile, const t_filenm fnm[],
77 bool bAppendFiles, const gmx_output_env_t *oenv) override
79 field_->outputProvider()->initOutput(fplog, nfile, fnm, bAppendFiles, oenv);
81 void finishOutput() override
83 field_->outputProvider()->finishOutput();
86 std::unique_ptr<IMDModule> field_;
87 std::unique_ptr<ForceProviders> forceProviders_;
89 /*! \brief List of registered MDModules
91 * Note that MDModules::Impl owns this container, but it is only used by
92 * the MDModules::initForceProviders() function. To be consistent with
93 * IMDModule's vision, as indicated by its docs, we should
94 * \todo update IMDModule docs to allow nullptr return values
95 * \todo check for nullptr returned by IMDModule methods.
96 * \todo include field_ in modules_
98 std::vector< std::shared_ptr<IMDModule> > modules_;
101 MDModules::MDModules() : impl_(new Impl)
105 MDModules::~MDModules()
109 void MDModules::initMdpTransform(IKeyValueTreeTransformRules *rules)
111 auto appliedForcesScope = rules->scopedTransform("/applied-forces");
112 impl_->field_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules());
115 void MDModules::buildMdpOutput(KeyValueTreeObjectBuilder *builder)
117 impl_->field_->mdpOptionProvider()->buildMdpOutput(builder);
120 void MDModules::assignOptionsToModules(const KeyValueTreeObject ¶ms,
121 IKeyValueTreeErrorHandler *errorHandler)
123 Options moduleOptions;
124 impl_->makeModuleOptions(&moduleOptions);
125 // The actual output is in the data fields of the modules that
126 // were set up in the module options.
127 assignOptionsFromKeyValueTree(&moduleOptions, params, errorHandler);
130 void MDModules::adjustInputrecBasedOnModules(t_inputrec *ir)
132 Options moduleOptions;
133 impl_->makeModuleOptions(&moduleOptions);
135 checkForUnknownOptionsInKeyValueTree(*ir->params, moduleOptions);
137 std::unique_ptr<KeyValueTreeObject> params(
138 new KeyValueTreeObject(
139 adjustKeyValueTreeFromOptions(*ir->params, moduleOptions)));
141 ir->params = params.release();
144 IMDOutputProvider *MDModules::outputProvider()
149 ForceProviders *MDModules::initForceProviders()
151 GMX_RELEASE_ASSERT(impl_->forceProviders_ == nullptr,
152 "Force providers initialized multiple times");
153 impl_->forceProviders_ = std::make_unique<ForceProviders>();
154 impl_->field_->initForceProviders(impl_->forceProviders_.get());
155 for (auto && module : impl_->modules_)
157 module->initForceProviders(impl_->forceProviders_.get());
159 return impl_->forceProviders_.get();
162 void MDModules::add(std::shared_ptr<gmx::IMDModule> module)
164 impl_->modules_.emplace_back(std::move(module));