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37 * Implements classes in topologyinformation.h.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_trajectoryanalysis
44 #include "topologyinformation.h"
48 #include "gromacs/fileio/confio.h"
49 #include "gromacs/math/vec.h"
50 #include "gromacs/pbcutil/rmpbc.h"
51 #include "gromacs/topology/mtop_util.h"
52 #include "gromacs/topology/topology.h"
53 #include "gromacs/utility/arrayref.h"
54 #include "gromacs/utility/exceptions.h"
55 #include "gromacs/utility/gmxassert.h"
56 #include "gromacs/utility/smalloc.h"
57 #include "gromacs/utility/unique_cptr.h"
62 TopologyInformation::TopologyInformation()
63 : hasLoadedMtop_(false),
64 expandedTopology_(nullptr),
66 bTop_(false), ePBC_(-1)
71 TopologyInformation::~TopologyInformation()
75 void TopologyInformation::fillFromInputFile(const std::string &filename)
77 mtop_ = std::make_unique<gmx_mtop_t>();
78 // TODO When filename is not a .tpr, then using readConfAndAtoms
79 // would be efficient for not doing multiple conversions for
80 // makeAtomsData. However we'd also need to be able to copy the
81 // t_atoms that we'd keep, which we currently can't do.
82 // TODO Once there are fewer callers of the file-reading
83 // functionality, make them read directly into std::vector.
85 readConfAndTopology(filename.c_str(), &bTop_, mtop_.get(),
88 xtop_.assign(x, x + mtop_->natoms);
89 vtop_.assign(v, v + mtop_->natoms);
92 hasLoadedMtop_ = true;
93 // TODO: Only load this here if the tool actually needs it; selections
94 // take care of themselves.
95 for (gmx_moltype_t &moltype : mtop_->moltype)
97 if (!moltype.atoms.haveMass)
99 // Try to read masses from database, be silent about missing masses
100 atomsSetMassesBasedOnNames(&moltype.atoms, FALSE);
105 const gmx_localtop_t *TopologyInformation::expandedTopology() const
107 // Do lazy initialization
108 if (expandedTopology_ == nullptr && hasTopology())
110 expandedTopology_ = std::make_unique<gmx_localtop_t>();
111 gmx_mtop_generate_local_top(*mtop_, expandedTopology_.get(), false);
114 return expandedTopology_.get();
120 //! Helps implement lazy initialization.
121 AtomsDataPtr makeAtoms(const TopologyInformation &top_)
123 AtomsDataPtr atoms(new t_atoms);
124 if (top_.hasTopology())
126 *atoms = gmx_mtop_global_atoms(top_.mtop());
130 init_atom(atoms.get());
137 const t_atoms *TopologyInformation::atoms() const
139 // Do lazy initialization
140 if (atoms_ == nullptr)
142 atoms_ = makeAtoms(*this);
148 AtomsDataPtr TopologyInformation::copyAtoms() const
150 // Note that we do not return atoms_, so that regardless of
151 // whether the user has already used it, or will use it in the
152 // future, any transformation operations on the data structure
153 // returned here cannot have unintended effects.
154 return makeAtoms(*this);
158 TopologyInformation::x() const
162 GMX_THROW(APIError("Topology coordinates requested without setting efUseTopX"));
168 TopologyInformation::v() const
172 GMX_THROW(APIError("Topology coordinates requested without setting efUseTopV"));
178 TopologyInformation::getBox(matrix box) const
180 GMX_RELEASE_ASSERT(box != nullptr, "Must have valid box to fill");
181 copy_mat(const_cast<rvec *>(boxtop_), box);
185 TopologyInformation::name() const
187 if (hasTopology() && mtop_->name)
194 gmx_rmpbc_t gmx_rmpbc_init(const gmx::TopologyInformation &topInfo)
196 GMX_RELEASE_ASSERT(topInfo.hasTopology(), "Cannot remove PBC without a topology");
198 return gmx_rmpbc_init(&topInfo.expandedTopology()->idef, topInfo.ePBC(), topInfo.mtop()->natoms);