Constructing local atom sets for density fitting

Constructs local atom sets for density fitting during simulation
setup.

refs #2282

Change-Id: I0300376a6818f3ad8bb6474b09a9b0f1cbb46eae

diff --git a/src/gromacs/applied_forces/densityfitting.cpp b/src/gromacs/applied_forces/densityfitting.cpp
index c098653eb0420c6265172801fe6421d54037bc91..f40fef3111121bcf1457178b80bf614599127117 100644 (file)
--- a/src/gromacs/applied_forces/densityfitting.cpp
+++ b/src/gromacs/applied_forces/densityfitting.cpp
@@ -45,8 +45,10 @@
 
 #include <memory>
 
+#include "gromacs/domdec/localatomsetmanager.h"
 #include "gromacs/mdrunutility/mdmodulenotification.h"
 #include "gromacs/mdtypes/imdmodule.h"
+#include "gromacs/utility/classhelpers.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/keyvaluetreebuilder.h"
 
@@ -67,6 +69,9 @@ namespace
 /*! \internal
  * \brief Collect density fitting parameters only available during simulation setup.
  *
+ * \todo Implement builder pattern that will not use unqiue_ptr to check if
+ *       parameters have been set or not.
+ *
  * To build the density fitting force provider during simulation setup,
  * the DensityFitting class needs access to parameters that become available
  * only during simulation setup.
@@ -78,6 +83,14 @@ namespace
 class DensityFittingSimulationParameterSetup
 {
     public:
+        DensityFittingSimulationParameterSetup() = default;
+        /*! \brief Set the local atom set for the density fitting.
+         * \param[in] localAtomSet of atoms to be fitted
+         */
+        void setLocalAtomSet(const LocalAtomSet &localAtomSet)
+        {
+            localAtomSet_ = std::make_unique<LocalAtomSet>(localAtomSet);
+        }
 
         /*! \brief Return local atom set for density fitting.
          * \throws InternalError if local atom set is not set
@@ -93,6 +106,7 @@ class DensityFittingSimulationParameterSetup
             }
             return *localAtomSet_;
         }
+
         /*! \brief Return transformation into density lattice.
          * \throws InternalError if transformation into density lattice is not set
          * \returns transormation into density lattice
@@ -126,6 +140,7 @@ class DensityFittingSimulationParameterSetup
         std::unique_ptr<TranslateAndScale> transformationToDensityLattice_;
         //! The local atom set to act on
         std::unique_ptr<LocalAtomSet>      localAtomSet_;
+        GMX_DISALLOW_COPY_AND_ASSIGN(DensityFittingSimulationParameterSetup);
 };
 
 /*! \internal
@@ -149,6 +164,8 @@ class DensityFitting final : public IMDModule
          *     KeyValueTreeObjectBuilder as parameter
          *   - reading its internal parameters from a key-value-tree during
          *     simulation setup by taking a const KeyValueTreeObject & parameter
+         *   - constructing local atom sets in the simulation parameter setup
+         *     by taking a LocalAtomSetManager * as parameter
          */
         explicit DensityFitting(MdModulesNotifier *notifier)
         {
@@ -173,6 +190,12 @@ class DensityFitting final : public IMDModule
                     densityFittingOptions_.readInternalParametersFromKvt(tree);
                 };
             notifier->notifier_.subscribe(readInternalParametersFunction);
+            // constructing local atom sets during simulation setup
+            const auto setLocalAtomSetFunction = [this](LocalAtomSetManager *localAtomSetManager) {
+                    this->constructLocalAtomSet(localAtomSetManager);
+                };
+            notifier->notifier_.subscribe(setLocalAtomSetFunction);
+
         }
 
         //! From IMDModule; this class provides the mdpOptions itself
@@ -196,6 +219,19 @@ class DensityFitting final : public IMDModule
         //! This MDModule provides its own output
         IMDOutputProvider *outputProvider() override { return &densityFittingOutputProvider_; }
 
+        /*! \brief Set up the local atom sets that are used by this module.
+         *
+         * \note When density fitting is set up with MdModuleNotification in
+         *       the constructor, this function is called back.
+         *
+         * \param[in] localAtomSetManager the manager to add local atom sets.
+         */
+        void constructLocalAtomSet(LocalAtomSetManager * localAtomSetManager)
+        {
+            LocalAtomSet atomSet = localAtomSetManager->add(densityFittingOptions_.buildParameters().indices_);
+            densityFittingSimulationParameters_.setLocalAtomSet(atomSet);
+        }
+
     private:
         //! The output provider
         DensityFittingOutputProvider                 densityFittingOutputProvider_;
@@ -207,6 +243,7 @@ class DensityFitting final : public IMDModule
          * simulation setup time.
          */
         DensityFittingSimulationParameterSetup       densityFittingSimulationParameters_;
+        GMX_DISALLOW_COPY_AND_ASSIGN(DensityFitting);
 };
 
 }   // namespace