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38 #include "wholemoleculetransform.h"
40 #include "gromacs/domdec/ga2la.h"
41 #include "gromacs/topology/mtop_util.h"
46 WholeMoleculeTransform::WholeMoleculeTransform(const gmx_mtop_t& mtop,
47 const PbcType pbcType,
48 const bool useAtomReordering) :
51 gmx_localtop_t localTop(mtop.ffparams);
53 gmx_mtop_generate_local_top(mtop, &localTop, false);
55 graph_ = mk_graph(localTop.idef, mtop.natoms);
57 wholeMoleculeCoordinates_.resize(mtop.natoms);
59 if (useAtomReordering)
61 // Store a copy of the global edges
62 globalEdgeAtomBegin_ = graph_.edgeAtomBegin;
63 graphGlobalAtomOrderEdges_ = graph_.edges;
64 // Reset the graph range to cover the whole system
65 graph_.edgeAtomBegin = 0;
66 graph_.edgeAtomEnd = graph_.shiftAtomEnd;
68 // Resize the edge color list for potential addition of non-connected atoms
69 graph_.edgeColor.resize(graph_.edgeAtomEnd);
73 void WholeMoleculeTransform::updateAtomOrder(ArrayRef<const int> globalAtomIndices, const gmx_ga2la_t& ga2la)
75 GMX_RELEASE_ASSERT(!graphGlobalAtomOrderEdges_.empty(),
76 "We need the edges in the global atom order");
78 GMX_RELEASE_ASSERT(globalAtomIndices.ssize() == graph_.shiftAtomEnd,
79 "The number of indices should match the number of atoms we shift");
81 const int globalEdgeAtomEnd = globalEdgeAtomBegin_ + graphGlobalAtomOrderEdges_.size();
83 for (const int globalAtomIndex : globalAtomIndices)
85 if (globalAtomIndex >= globalEdgeAtomBegin_ && globalAtomIndex < globalEdgeAtomEnd)
87 // Get the list of global atoms linked to this atom and add their local indices
88 const ArrayRef<const int> globalList =
89 graphGlobalAtomOrderEdges_[globalAtomIndex - globalEdgeAtomBegin_];
90 graph_.edges.pushBackListOfSize(globalList.size());
91 ArrayRef<int> lastList = graph_.edges.back();
92 std::transform(globalList.begin(), globalList.end(), lastList.begin(), [&ga2la](int i) -> int {
93 return ga2la.find(i)->la;
98 // The atom has no edges, push back an empty list
99 graph_.edges.pushBackListOfSize(0);
103 GMX_RELEASE_ASSERT(int(graph_.edges.size()) == graph_.shiftAtomEnd,
104 "We should have as many lists of edges as the system (shift) size");
107 void WholeMoleculeTransform::updateForAtomPbcJumps(ArrayRef<const RVec> x, const matrix box)
109 mk_mshift(nullptr, &graph_, pbcType_, box, as_rvec_array(x.data()));
112 ArrayRef<const RVec> WholeMoleculeTransform::wholeMoleculeCoordinates(ArrayRef<const RVec> x, const matrix box)
114 shift_x(&graph_, box, as_rvec_array(x.data()), as_rvec_array(wholeMoleculeCoordinates_.data()));
116 return wholeMoleculeCoordinates_;