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36 * \brief Declares the element performing first-order pressure coupling for the modular simulator
38 * \author Pascal Merz <pascal.merz@me.com>
39 * \ingroup module_modularsimulator
41 * This header is only used within the modular simulator module
44 #ifndef GMX_MODULARSIMULATOR_FIRSTORDERPRESSURECOUPLING_H
45 #define GMX_MODULARSIMULATOR_FIRSTORDERPRESSURECOUPLING_H
47 #include "modularsimulatorinterfaces.h"
52 enum class PressureCoupling;
57 class FreeEnergyPerturbationData;
58 class GlobalCommunicationHelper;
59 class LegacySimulatorData;
61 class ModularSimulatorAlgorithmBuilderHelper;
62 class StatePropagatorData;
65 * \brief Element performing first-order pressure coupling
67 * This element implements the first-order pressure coupling algorithms
68 * (Berendesen, c-rescale).
70 class FirstOrderPressureCoupling final : public ISimulatorElement, public ICheckpointHelperClient
74 FirstOrderPressureCoupling(int couplingFrequency,
76 real couplingTimeStep,
77 StatePropagatorData* statePropagatorData,
78 EnergyData* energyData,
80 const t_inputrec* inputrec,
81 const MDAtoms* mdAtoms,
83 ReportPreviousStepConservedEnergy reportPreviousStepConservedEnergy);
85 void scheduleTask(Step step, Time time, const RegisterRunFunction& function) override;
86 //! Setup - initialize relative box matrix
87 void elementSetup() override;
88 //! No teardown needed
89 void elementTeardown() override{};
91 //! ICheckpointHelperClient write checkpoint implementation
92 void saveCheckpointState(std::optional<WriteCheckpointData> checkpointData, const t_commrec* cr) override;
93 //! ICheckpointHelperClient read checkpoint implementation
94 void restoreCheckpointState(std::optional<ReadCheckpointData> checkpointData, const t_commrec* cr) override;
95 //! ICheckpointHelperClient key implementation
96 const std::string& clientID() override;
98 /*! \brief Factory method implementation
100 * \param legacySimulatorData Pointer allowing access to simulator level data
101 * \param builderHelper ModularSimulatorAlgorithmBuilder helper object
102 * \param statePropagatorData Pointer to the \c StatePropagatorData object
103 * \param energyData Pointer to the \c EnergyData object
104 * \param freeEnergyPerturbationData Pointer to the \c FreeEnergyPerturbationData object
105 * \param globalCommunicationHelper Pointer to the \c GlobalCommunicationHelper object
106 * \param offset The step offset at which the barostat is applied
107 * \param reportPreviousStepConservedEnergy Report the previous or the current step conserved energy
109 * \return Pointer to the element to be added. Element needs to have been stored using \c storeElement
111 static ISimulatorElement*
112 getElementPointerImpl(LegacySimulatorData* legacySimulatorData,
113 ModularSimulatorAlgorithmBuilderHelper* builderHelper,
114 StatePropagatorData* statePropagatorData,
115 EnergyData* energyData,
116 FreeEnergyPerturbationData gmx_unused* freeEnergyPerturbationData,
117 GlobalCommunicationHelper gmx_unused* globalCommunicationHelper,
119 ReportPreviousStepConservedEnergy reportPreviousStepConservedEnergy);
122 //! Calculate the scaling matrix
123 template<PressureCoupling pressureCouplingType>
124 void calculateScalingMatrix(Step step);
125 //! Scale the box and coordinates according to the current scaling matrix
126 template<PressureCoupling pressureCouplingType>
127 void scaleBoxAndCoordinates();
128 //! Helper function returning the conserved energy contribution
129 real conservedEnergyContribution(Step step);
131 //! The pressure coupling type required
132 const PressureCoupling pressureCouplingType_;
133 //! The coupling time step (simulation time step x coupling frequency)
134 const real couplingTimeStep_;
135 //! The frequency at which pressure coupling is applied
136 const int couplingFrequency_;
137 //! The offset at which pressure coupling is applied
138 const int couplingOffset_;
140 //! The current box scaling matrix
141 tensor boxScalingMatrix_;
142 //! Relative box shape
144 //! Contribution to the conserved energy
145 double conservedEnergyContribution_;
146 //! Contribution to the conserved energy
147 double previousStepConservedEnergyContribution_;
148 //! Current step of the conserved energy contribution
149 Step conservedEnergyContributionStep_;
150 //! Whether we're reporting current step or previous step conserved energy
151 const ReportPreviousStepConservedEnergy reportPreviousStepConservedEnergy_;
153 // TODO: Clarify relationship to data objects and find a more robust alternative to raw pointers (#3583)
154 //! Pointer to the micro state
155 StatePropagatorData* statePropagatorData_;
156 //! Pointer to the energy data
157 EnergyData* energyData_;
159 // Access to ISimulator data
162 //! Contains user input mdp options.
163 const t_inputrec* inputrec_;
164 //! Atom parameters for this domain.
165 const MDAtoms* mdAtoms_;
166 //! Manages flop accounting.
169 //! CheckpointHelper identifier
170 const std::string identifier_;
171 //! Helper function to read from / write to CheckpointData
172 template<CheckpointDataOperation operation>
173 void doCheckpointData(CheckpointData<operation>* checkpointData);
178 #endif // GMX_MODULARSIMULATOR_FIRSTORDERPRESSURECOUPLING_H