/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
}
-/*! \brief Constructs and returns an atom constraint adjacency list
- *
- * Each constraint will be represented as a tuple, containing index of the second
- * constrained atom, index of the constraint and a sign that indicates the order of atoms in
- * which they are listed. Sign is needed to compute the mass factors.
- */
-static std::vector<std::vector<std::tuple<int, int, int>>>
+//! Helper type for discovering coupled constraints
+struct AtomsAdjacencyListElement
+{
+ AtomsAdjacencyListElement(const int indexOfSecondConstrainedAtom,
+ const int indexOfConstraint,
+ const int signFactor) :
+ indexOfSecondConstrainedAtom_(indexOfSecondConstrainedAtom),
+ indexOfConstraint_(indexOfConstraint),
+ signFactor_(signFactor)
+ {
+ }
+ //! The index of the other atom constrained to this atom.
+ int indexOfSecondConstrainedAtom_;
+ //! The index of this constraint in the container of constraints.
+ int indexOfConstraint_;
+ /*! \brief A multiplicative factor that indicates the relative
+ * order of the atoms in the atom list.
+ *
+ * Used for computing the mass factor of this constraint
+ * relative to any coupled constraints. */
+ int signFactor_;
+};
+//! Constructs and returns an atom constraint adjacency list
+static std::vector<std::vector<AtomsAdjacencyListElement>>
constructAtomsAdjacencyList(const int numAtoms, ArrayRef<const int> iatoms)
{
const int stride = 1 + NRAL(F_CONSTR);
const int numConstraints = iatoms.ssize() / stride;
- std::vector<std::vector<std::tuple<int, int, int>>> atomsAdjacencyList(numAtoms);
+ std::vector<std::vector<AtomsAdjacencyListElement>> atomsAdjacencyList(numAtoms);
for (int c = 0; c < numConstraints; c++)
{
int a1 = iatoms[stride * c + 1];
// Each constraint will be represented as a tuple, containing index of the second
// constrained atom, index of the constraint and a sign that indicates the order of atoms in
// which they are listed. Sign is needed to compute the mass factors.
- atomsAdjacencyList[a1].push_back(std::make_tuple(a2, c, +1));
- atomsAdjacencyList[a2].push_back(std::make_tuple(a1, c, -1));
+ atomsAdjacencyList[a1].emplace_back(a2, c, +1);
+ atomsAdjacencyList[a2].emplace_back(a1, c, -1);
}
return atomsAdjacencyList;
*/
inline int countCoupled(int a,
ArrayRef<int> numCoupledConstraints,
- ArrayRef<const std::vector<std::tuple<int, int, int>>> atomsAdjacencyList)
+ ArrayRef<const std::vector<AtomsAdjacencyListElement>> atomsAdjacencyList)
{
int counted = 0;
for (const auto& adjacentAtom : atomsAdjacencyList[a])
{
- const int c2 = std::get<1>(adjacentAtom);
+ const int c2 = adjacentAtom.indexOfConstraint_;
if (numCoupledConstraints[c2] == -1)
{
numCoupledConstraints[c2] = 0; // To indicate we've been here
- counted += 1 + countCoupled(std::get<0>(adjacentAtom), numCoupledConstraints, atomsAdjacencyList);
+ counted += 1
+ + countCoupled(adjacentAtom.indexOfSecondConstrainedAtom_,
+ numCoupledConstraints, atomsAdjacencyList);
}
}
return counted;
*/
inline void addWithCoupled(ArrayRef<const int> iatoms,
const int stride,
- ArrayRef<const std::vector<std::tuple<int, int, int>>> atomsAdjacencyList,
+ ArrayRef<const std::vector<AtomsAdjacencyListElement>> atomsAdjacencyList,
ArrayRef<int> splitMap,
const int c,
int* currentMapIndex)
const int a1 = iatoms[stride * c + 1 + atomIndexInConstraint];
for (const auto& adjacentAtom : atomsAdjacencyList[a1])
{
- const int c2 = std::get<1>(adjacentAtom);
+ const int c2 = adjacentAtom.indexOfConstraint_;
if (c2 != c)
{
addWithCoupled(iatoms, stride, atomsAdjacencyList, splitMap, c2, currentMapIndex);
* numCoupledConstraints vector is also used to keep track if the constrain was already counted.
*/
static std::vector<int> countNumCoupledConstraints(ArrayRef<const int> iatoms,
- ArrayRef<const std::vector<std::tuple<int, int, int>>> atomsAdjacencyList)
+ ArrayRef<const std::vector<AtomsAdjacencyListElement>> atomsAdjacencyList)
{
const int stride = 1 + NRAL(F_CONSTR);
const int numConstraints = iatoms.ssize() / stride;
coupledConstraintsCountsHost.at(splitMap.at(c1)) = 0;
int c1a1 = iatoms[stride * c1 + 1];
int c1a2 = iatoms[stride * c1 + 2];
- int c2;
- int c2a1;
- int c2a2;
- int sign;
-
- // Constraints, coupled trough the first atom.
- c2a1 = c1a1;
- for (unsigned j = 0; j < atomsAdjacencyList.at(c1a1).size(); j++)
+ // Constraints, coupled through the first atom.
+ int c2a1 = c1a1;
+ for (const auto& atomAdjacencyList : atomsAdjacencyList[c1a1])
{
-
- std::tie(c2a2, c2, sign) = atomsAdjacencyList.at(c1a1).at(j);
+ int c2 = atomAdjacencyList.indexOfConstraint_;
if (c1 != c2)
{
+ int c2a2 = atomAdjacencyList.indexOfSecondConstrainedAtom_;
+ int sign = atomAdjacencyList.signFactor_;
int index = kernelParams_.numConstraintsThreads
* coupledConstraintsCountsHost.at(splitMap.at(c1))
+ splitMap.at(c1);
// Constraints, coupled through the second atom.
c2a1 = c1a2;
- for (unsigned j = 0; j < atomsAdjacencyList.at(c1a2).size(); j++)
+ for (const auto& atomAdjacencyList : atomsAdjacencyList[c1a2])
{
-
- std::tie(c2a2, c2, sign) = atomsAdjacencyList.at(c1a2).at(j);
+ int c2 = atomAdjacencyList.indexOfConstraint_;
if (c1 != c2)
{
+ int c2a2 = atomAdjacencyList.indexOfSecondConstrainedAtom_;
+ int sign = atomAdjacencyList.signFactor_;
int index = kernelParams_.numConstraintsThreads
* coupledConstraintsCountsHost.at(splitMap.at(c1))
+ splitMap.at(c1);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff