src/gromacs/coordinateio/outputadapters/outputselector.cpp

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  35 /*!\internal
  36  * \file
  37  * \brief
  38  * Implements outputselector class.
  39  *
  40  * \author Paul Bauer <paul.bauer.q@gmail.com>
  41  * \ingroup module_coordinateio
  42  */
  43
  44 #include "gmxpre.h"
  45
  46 #include "outputselector.h"
  47
  48 #include <algorithm>
  49
  50 #include "gromacs/math/vec.h"
  51 #include "gromacs/trajectory/trajectoryframe.h"
  52 #include "gromacs/utility/smalloc.h"
  53
  54 namespace gmx
  55 {
  56
  57 /*! \brief
  58  * Modify atoms information in coordinate frame to fit output selection.
  59  *
  60  * Changes the information contained in the coordinate frame t_atoms struct to match
  61  * the selection provided to the module.
  62  *
  63  * \param[in] atoms Pointer to original t_atoms.
  64  * \param[in] selectionAtoms Pointer to local atoms.
  65  * \param[in]     sel   Reference to selection.
  66  */
  67 static void adjustAtomInformation(t_atoms* atoms, t_atoms* selectionAtoms, const Selection& sel)
  68 {
  69     int natoms = sel.atomCount();
  70
  71     selectionAtoms->nr   = natoms;
  72     selectionAtoms->nres = atoms->nres;
  73
  74     srenew(selectionAtoms->resinfo, atoms->nres);
  75     srenew(selectionAtoms->atom, natoms);
  76     srenew(selectionAtoms->atomname, natoms);
  77
  78     selectionAtoms->haveType    = atoms->haveType;
  79     selectionAtoms->haveBState  = atoms->haveBState;
  80     selectionAtoms->haveMass    = atoms->haveMass;
  81     selectionAtoms->haveCharge  = atoms->haveCharge;
  82     selectionAtoms->havePdbInfo = atoms->havePdbInfo;
  83
  84     if (atoms->haveType)
  85     {
  86         srenew(selectionAtoms->atomtype, natoms);
  87     }
  88     if (atoms->haveBState)
  89     {
  90         srenew(selectionAtoms->atomtypeB, natoms);
  91     }
  92     if (atoms->havePdbInfo)
  93     {
  94         srenew(selectionAtoms->pdbinfo, natoms);
  95     }
  96
  97     for (int i = 0; i < natoms; i++)
  98     {
  99         int pos                     = sel.position(i).refId();
 100         selectionAtoms->atom[i]     = atoms->atom[pos];
 101         selectionAtoms->atomname[i] = atoms->atomname[pos];
 102         if (selectionAtoms->haveType)
 103         {
 104             selectionAtoms->atomtype[i] = atoms->atomtype[pos];
 105         }
 106         if (selectionAtoms->haveBState)
 107         {
 108             selectionAtoms->atomtypeB[i] = atoms->atomtypeB[pos];
 109         }
 110         if (selectionAtoms->havePdbInfo)
 111         {
 112             selectionAtoms->pdbinfo[i] = atoms->pdbinfo[pos];
 113         }
 114     }
 115     // Copy residue information unconditionally.
 116     for (int i = 0; i < atoms->nres; i++)
 117     {
 118         selectionAtoms->resinfo[i] = atoms->resinfo[i];
 119     }
 120 }
 121
 122 void OutputSelector::processFrame(const int /*framenumber*/, t_trxframe* input)
 123 {
 124     size_t natoms = sel_.atomCount();
 125
 126     input->natoms = natoms;
 127
 128     localX_.resize(natoms);
 129     if (input->bV)
 130     {
 131         localV_.resize(natoms);
 132     }
 133     if (input->bF)
 134     {
 135         localF_.resize(natoms);
 136     }
 137     if (input->index)
 138     {
 139         localIndex_.resize(natoms);
 140     }
 141
 142     for (size_t i = 0; i < natoms; i++)
 143     {
 144         int pos = sel_.position(i).refId();
 145
 146         copy_rvec(input->x[pos], localX_[i]);
 147         if (input->bV)
 148         {
 149             copy_rvec(input->v[pos], localV_[i]);
 150         }
 151         if (input->bF)
 152         {
 153             copy_rvec(input->f[pos], localF_[i]);
 154         }
 155         if (input->index)
 156         {
 157             localIndex_[i] = input->index[pos];
 158         }
 159     }
 160     input->x = as_rvec_array(localX_.data());
 161
 162     input->index = localIndex_.data();
 163
 164     if (input->bV)
 165     {
 166         input->v = as_rvec_array(localV_.data());
 167     }
 168     if (input->bF)
 169     {
 170         input->f = as_rvec_array(localF_.data());
 171     }
 172
 173     if (input->bAtoms)
 174     {
 175         if (selectionAtoms_ == nullptr)
 176         {
 177             selectionAtoms_.reset(new t_atoms);
 178             init_t_atoms(selectionAtoms_.get(), natoms, false);
 179         }
 180         adjustAtomInformation(input->atoms, selectionAtoms_.get(), sel_);
 181         input->atoms = selectionAtoms_.get();
 182     }
 183 }
 184
 185 } // namespace gmx