src/gromacs/trajectoryanalysis/topologyinformation.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements classes in topologyinformation.h.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_trajectoryanalysis
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "topologyinformation.h"
  45
  46 #include "gromacs/compat/make_unique.h"
  47 #include "gromacs/fileio/confio.h"
  48 #include "gromacs/math/vec.h"
  49 #include "gromacs/pbcutil/rmpbc.h"
  50 #include "gromacs/topology/mtop_util.h"
  51 #include "gromacs/topology/topology.h"
  52 #include "gromacs/utility/arrayref.h"
  53 #include "gromacs/utility/exceptions.h"
  54 #include "gromacs/utility/gmxassert.h"
  55 #include "gromacs/utility/smalloc.h"
  56 #include "gromacs/utility/unique_cptr.h"
  57
  58 namespace gmx
  59 {
  60
  61 TopologyInformation::TopologyInformation()
  62     : mtop_(compat::make_unique<gmx_mtop_t>()),
  63       hasLoadedMtop_(false),
  64       expandedTopology_(nullptr),
  65       atoms_ (nullptr),
  66       bTop_(false), ePBC_(-1)
  67 {
  68 }
  69
  70
  71 TopologyInformation::~TopologyInformation()
  72 {
  73 }
  74
  75 void TopologyInformation::fillFromInputFile(const std::string &filename)
  76 {
  77     mtop_ = gmx::compat::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.
  84     rvec *x, *v;
  85     readConfAndTopology(filename.c_str(), &bTop_, mtop_.get(),
  86                         &ePBC_, &x, &v,
  87                         boxtop_);
  88     xtop_.assign(x, x + mtop_->natoms);
  89     vtop_.assign(v, v + mtop_->natoms);
  90     sfree(x);
  91     sfree(v);
  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)
  96     {
  97         if (!moltype.atoms.haveMass)
  98         {
  99             // Try to read masses from database, be silent about missing masses
 100             atomsSetMassesBasedOnNames(&moltype.atoms, FALSE);
 101         }
 102     }
 103 }
 104
 105 const gmx_localtop_t *TopologyInformation::expandedTopology() const
 106 {
 107     // Do lazy initialization
 108     if (expandedTopology_ == nullptr && hasTopology())
 109     {
 110         expandedTopology_.reset(gmx_mtop_generate_local_top(mtop_.get(), false));
 111     }
 112
 113     return expandedTopology_.get();
 114 }
 115
 116 namespace
 117 {
 118
 119 //! Helps implement lazy initialization.
 120 AtomsDataPtr makeAtoms(const TopologyInformation &top_)
 121 {
 122     AtomsDataPtr atoms(new t_atoms);
 123     if (top_.hasTopology())
 124     {
 125         *atoms = gmx_mtop_global_atoms(top_.mtop());
 126     }
 127     else
 128     {
 129         init_atom(atoms.get());
 130     }
 131     return atoms;
 132 }
 133
 134 }   // namespace
 135
 136 const t_atoms *TopologyInformation::atoms() const
 137 {
 138     // Do lazy initialization
 139     if (atoms_ == nullptr)
 140     {
 141         atoms_ = makeAtoms(*this);
 142     }
 143
 144     return atoms_.get();
 145 }
 146
 147 AtomsDataPtr TopologyInformation::copyAtoms() const
 148 {
 149     // Note that we do not return atoms_, so that regardless of
 150     // whether the user has already used it, or will use it in the
 151     // future, any transformation operations on the data structure
 152     // returned here cannot have unintended effects.
 153     return makeAtoms(*this);
 154 }
 155
 156 ArrayRef<const RVec>
 157 TopologyInformation::x() const
 158 {
 159     if (xtop_.empty())
 160     {
 161         GMX_THROW(APIError("Topology coordinates requested without setting efUseTopX"));
 162     }
 163     return xtop_;
 164 }
 165
 166 ArrayRef<const RVec>
 167 TopologyInformation::v() const
 168 {
 169     if (vtop_.empty())
 170     {
 171         GMX_THROW(APIError("Topology coordinates requested without setting efUseTopV"));
 172     }
 173     return vtop_;
 174 }
 175
 176 void
 177 TopologyInformation::getBox(matrix box) const
 178 {
 179     GMX_RELEASE_ASSERT(box != nullptr, "Must have valid box to fill");
 180     copy_mat(const_cast<rvec *>(boxtop_), box);
 181 }
 182
 183 const char *
 184 TopologyInformation::name() const
 185 {
 186     if (hasTopology() && mtop_->name)
 187     {
 188         return *mtop_->name;
 189     }
 190     return nullptr;
 191 }
 192
 193 gmx_rmpbc_t gmx_rmpbc_init(const gmx::TopologyInformation &topInfo)
 194 {
 195     GMX_RELEASE_ASSERT(topInfo.hasTopology(), "Cannot remove PBC without a topology");
 196
 197     return gmx_rmpbc_init(&topInfo.expandedTopology()->idef, topInfo.ePBC(), topInfo.mtop()->natoms);
 198 }
 199
 200 } // namespace gmx