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/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"
  54
  55 namespace gmx
  56 {
  57
  58 class MDModules::Impl : public IMDOutputProvider
  59 {
  60     public:
  61
  62         Impl()
  63             : field_(createElectricFieldModule())
  64         {
  65         }
  66
  67         void makeModuleOptions(Options *options)
  68         {
  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.
  73         }
  74
  75         // From IMDOutputProvider
  76         virtual void initOutput(FILE *fplog, int nfile, const t_filenm fnm[],
  77                                 bool bAppendFiles, const gmx_output_env_t *oenv)
  78         {
  79             field_->outputProvider()->initOutput(fplog, nfile, fnm, bAppendFiles, oenv);
  80         }
  81         virtual void finishOutput()
  82         {
  83             field_->outputProvider()->finishOutput();
  84         }
  85
  86         std::unique_ptr<IMDModule>      field_;
  87         std::unique_ptr<ForceProviders> forceProviders_;
  88 };
  89
  90 MDModules::MDModules() : impl_(new Impl)
  91 {
  92 }
  93
  94 MDModules::~MDModules()
  95 {
  96 }
  97
  98 void MDModules::initMdpTransform(IKeyValueTreeTransformRules *rules)
  99 {
 100     auto appliedForcesScope = rules->scopedTransform("/applied-forces");
 101     impl_->field_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules());
 102 }
 103
 104 void MDModules::buildMdpOutput(KeyValueTreeObjectBuilder *builder)
 105 {
 106     impl_->field_->mdpOptionProvider()->buildMdpOutput(builder);
 107 }
 108
 109 void MDModules::assignOptionsToModules(const KeyValueTreeObject  &params,
 110                                        IKeyValueTreeErrorHandler *errorHandler)
 111 {
 112     Options moduleOptions;
 113     impl_->makeModuleOptions(&moduleOptions);
 114     // The actual output is in the data fields of the modules that
 115     // were set up in the module options.
 116     assignOptionsFromKeyValueTree(&moduleOptions, params, errorHandler);
 117 }
 118
 119 void MDModules::adjustInputrecBasedOnModules(t_inputrec *ir)
 120 {
 121     Options moduleOptions;
 122     impl_->makeModuleOptions(&moduleOptions);
 123
 124     checkForUnknownOptionsInKeyValueTree(*ir->params, moduleOptions);
 125
 126     std::unique_ptr<KeyValueTreeObject> params(
 127             new KeyValueTreeObject(
 128                     adjustKeyValueTreeFromOptions(*ir->params, moduleOptions)));
 129     delete ir->params;
 130     ir->params = params.release();
 131 }
 132
 133 IMDOutputProvider *MDModules::outputProvider()
 134 {
 135     return impl_.get();
 136 }
 137
 138 ForceProviders *MDModules::initForceProviders()
 139 {
 140     GMX_RELEASE_ASSERT(impl_->forceProviders_ == nullptr,
 141                        "Force providers initialized multiple times");
 142     impl_->forceProviders_.reset(new ForceProviders);
 143     impl_->field_->initForceProviders(impl_->forceProviders_.get());
 144     return impl_->forceProviders_.get();
 145 }
 146
 147 } // namespace gmx