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36 * \brief Defines the constraint element for the modular simulator
38 * \author Pascal Merz <pascal.merz@me.com>
39 * \ingroup module_modularsimulator
44 #include "constraintelement.h"
46 #include "gromacs/math/vec.h"
47 #include "gromacs/mdtypes/enerdata.h"
48 #include "gromacs/mdtypes/inputrec.h"
49 #include "gromacs/mdtypes/state.h"
50 #include "gromacs/utility/fatalerror.h"
52 #include "energyelement.h"
53 #include "freeenergyperturbationelement.h"
54 #include "statepropagatordata.h"
58 template<ConstraintVariable variable>
59 ConstraintsElement<variable>::ConstraintsElement(Constraints* constr,
60 StatePropagatorData* statePropagatorData,
61 EnergyElement* energyElement,
62 FreeEnergyPerturbationElement* freeEnergyPerturbationElement,
65 const t_inputrec* inputrec,
66 const t_mdatoms* mdAtoms) :
67 nextVirialCalculationStep_(-1),
68 nextEnergyWritingStep_(-1),
69 nextLogWritingStep_(-1),
70 isMasterRank_(isMaster),
71 statePropagatorData_(statePropagatorData),
72 energyElement_(energyElement),
73 freeEnergyPerturbationElement_(freeEnergyPerturbationElement),
79 GMX_ASSERT(constr_, "Constraint element created but constr == nullptr");
82 template<ConstraintVariable variable>
83 void ConstraintsElement<variable>::elementSetup()
85 if (!inputrec_->bContinuation
86 && ((variable == ConstraintVariable::Positions && inputrec_->eI == eiMD)
87 || (variable == ConstraintVariable::Velocities && inputrec_->eI == eiVV)))
89 const real lambdaBonded = freeEnergyPerturbationElement_
90 ? freeEnergyPerturbationElement_->constLambdaView()[efptBONDED]
92 // Constrain the initial coordinates and velocities
93 do_constrain_first(fplog_, constr_, inputrec_, mdAtoms_, statePropagatorData_->localNumAtoms(),
94 statePropagatorData_->positionsView(), statePropagatorData_->velocitiesView(),
95 statePropagatorData_->box(), lambdaBonded);
99 if (inputrec_->eConstrAlg == econtLINCS)
101 fprintf(fplog_, "RMS relative constraint deviation after constraining: %.2e\n",
108 template<ConstraintVariable variable>
109 void ConstraintsElement<variable>::scheduleTask(Step step,
110 Time gmx_unused time,
111 const RegisterRunFunctionPtr& registerRunFunction)
113 bool calculateVirial = (step == nextVirialCalculationStep_);
114 bool writeLog = (step == nextLogWritingStep_);
115 bool writeEnergy = (step == nextEnergyWritingStep_);
117 // register constraining
118 (*registerRunFunction)(std::make_unique<SimulatorRunFunction>(
119 [this, step, calculateVirial, writeLog, writeEnergy]() {
120 apply(step, calculateVirial, writeLog, writeEnergy);
124 template<ConstraintVariable variable>
125 void ConstraintsElement<variable>::apply(Step step, bool calculateVirial, bool writeLog, bool writeEnergy)
129 rvec *x, *xprime, *min_proj, *v;
131 const real lambdaBonded = freeEnergyPerturbationElement_
132 ? freeEnergyPerturbationElement_->constLambdaView()[efptBONDED]
138 case ConstraintVariable::Positions:
139 x = as_rvec_array(statePropagatorData_->previousPositionsView().paddedArrayRef().data());
140 xprime = as_rvec_array(statePropagatorData_->positionsView().paddedArrayRef().data());
142 v = as_rvec_array(statePropagatorData_->velocitiesView().paddedArrayRef().data());
144 case ConstraintVariable::Velocities:
145 x = as_rvec_array(statePropagatorData_->positionsView().paddedArrayRef().data());
146 xprime = as_rvec_array(statePropagatorData_->velocitiesView().paddedArrayRef().data());
147 min_proj = as_rvec_array(statePropagatorData_->velocitiesView().paddedArrayRef().data());
150 default: gmx_fatal(FARGS, "Constraint algorithm not implemented for modular simulator.");
153 constr_->apply(writeLog, writeEnergy, step, 1, 1.0, x, xprime, min_proj, statePropagatorData_->box(),
154 lambdaBonded, &dvdlambda, v, calculateVirial ? &vir_con : nullptr, variable);
158 if (inputrec_->eI == eiVV)
160 // For some reason, the shake virial in VV is reset twice a step.
161 // Energy element will only do this once per step.
162 // TODO: Investigate this
163 clear_mat(energyElement_->constraintVirial(step));
165 energyElement_->addToConstraintVirial(vir_con, step);
168 /* The factor of 2 correction is necessary because half of the constraint
169 * force is removed in the VV step. This factor is either exact or a very
170 * good approximation, statistically insignificant in any real free energy
171 * calculation. Any possible error is not a simulation propagation error,
172 * but a potential reporting error in the data that goes to dh/dlambda.
173 * Cf. redmine issue #1255
175 const real c_dvdlConstraintCorrectionFactor = EI_VV(inputrec_->eI) ? 2.0 : 1.0;
176 energyElement_->enerdata()->term[F_DVDL_CONSTR] += c_dvdlConstraintCorrectionFactor * dvdlambda;
179 template<ConstraintVariable variable>
180 SignallerCallbackPtr ConstraintsElement<variable>::registerEnergyCallback(EnergySignallerEvent event)
182 if (event == EnergySignallerEvent::VirialCalculationStep)
184 return std::make_unique<SignallerCallback>(
185 [this](Step step, Time /*unused*/) { nextVirialCalculationStep_ = step; });
190 template<ConstraintVariable variable>
191 SignallerCallbackPtr ConstraintsElement<variable>::registerTrajectorySignallerCallback(TrajectoryEvent event)
193 if (event == TrajectoryEvent::EnergyWritingStep)
195 return std::make_unique<SignallerCallback>(
196 [this](Step step, Time /*unused*/) { nextEnergyWritingStep_ = step; });
201 template<ConstraintVariable variable>
202 SignallerCallbackPtr ConstraintsElement<variable>::registerLoggingCallback()
204 return std::make_unique<SignallerCallback>(
205 [this](Step step, Time /*unused*/) { nextLogWritingStep_ = step; });
208 //! Explicit template initialization
210 template class ConstraintsElement<ConstraintVariable::Positions>;
211 template class ConstraintsElement<ConstraintVariable::Velocities>;