src/gromacs/trajectory/trajectoryframe.cpp

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  35 #include "gmxpre.h"
  36
  37 #include "trajectoryframe.h"
  38
  39 #include <cstdio>
  40
  41 #include <algorithm>
  42
  43 #include "gromacs/math/veccompare.h"
  44 #include "gromacs/topology/atoms.h"
  45 #include "gromacs/utility/compare.h"
  46 #include "gromacs/utility/exceptions.h"
  47 #include "gromacs/utility/smalloc.h"
  48 #include "gromacs/utility/stringutil.h"
  49
  50 void comp_frame(FILE *fp, t_trxframe *fr1, t_trxframe *fr2,
  51                 gmx_bool bRMSD, real ftol, real abstol)
  52 {
  53     fprintf(fp, "\n");
  54     cmp_int(fp, "not_ok", -1, fr1->not_ok, fr2->not_ok);
  55     cmp_int(fp, "natoms", -1, fr1->natoms, fr2->natoms);
  56     if (cmp_bool(fp, "bStep", -1, fr1->bStep, fr2->bStep))
  57     {
  58         cmp_int(fp, "step", -1, fr1->step, fr2->step);
  59     }
  60     cmp_int(fp, "step", -1, fr1->step, fr2->step);
  61     if (cmp_bool(fp, "bTime", -1, fr1->bTime, fr2->bTime))
  62     {
  63         cmp_real(fp, "time", -1, fr1->time, fr2->time, ftol, abstol);
  64     }
  65     if (cmp_bool(fp, "bLambda", -1, fr1->bLambda, fr2->bLambda))
  66     {
  67         cmp_real(fp, "lambda", -1, fr1->lambda, fr2->lambda, ftol, abstol);
  68     }
  69     if (cmp_bool(fp, "bAtoms", -1, fr1->bAtoms, fr2->bAtoms))
  70     {
  71         cmp_atoms(fp, fr1->atoms, fr2->atoms, ftol, abstol);
  72     }
  73     if (cmp_bool(fp, "bPrec", -1, fr1->bPrec, fr2->bPrec))
  74     {
  75         cmp_real(fp, "prec", -1, fr1->prec, fr2->prec, ftol, abstol);
  76     }
  77     if (cmp_bool(fp, "bX", -1, fr1->bX, fr2->bX))
  78     {
  79         cmp_rvecs(fp, "x", std::min(fr1->natoms, fr2->natoms), fr1->x, fr2->x, bRMSD, ftol, abstol);
  80     }
  81     if (cmp_bool(fp, "bV", -1, fr1->bV, fr2->bV))
  82     {
  83         cmp_rvecs(fp, "v", std::min(fr1->natoms, fr2->natoms), fr1->v, fr2->v, bRMSD, ftol, abstol);
  84     }
  85     if (cmp_bool(fp, "bF", -1, fr1->bF, fr2->bF))
  86     {
  87         cmp_rvecs(fp, "f", std::min(fr1->natoms, fr2->natoms), fr1->f, fr2->f, bRMSD, ftol, abstol);
  88     }
  89     if (cmp_bool(fp, "bBox", -1, fr1->bBox, fr2->bBox))
  90     {
  91         cmp_rvecs(fp, "box", 3, fr1->box, fr2->box, FALSE, ftol, abstol);
  92     }
  93 }
  94
  95 void done_frame(t_trxframe *frame)
  96 {
  97     if (frame->atoms)
  98     {
  99         done_atom(frame->atoms);
 100         sfree(frame->atoms);
 101     }
 102     sfree(frame->x);
 103     sfree(frame->v);
 104     sfree(frame->f);
 105 }
 106
 107 namespace gmx
 108 {
 109
 110 TrajectoryFrame::TrajectoryFrame(const t_trxframe &frame)
 111     : frame_(frame)
 112 {
 113     // This would be nicer as an initializer, but once uncrustify is
 114     // happy, Doxygen can't parse it.
 115     box_ = {{{{0}}}};
 116
 117     if (!frame.bStep)
 118     {
 119         GMX_THROW(APIError("Cannot handle trajectory frame that lacks a step number"));
 120     }
 121     if (!frame.bTime)
 122     {
 123         GMX_THROW(APIError("Cannot handle trajectory frame that lacks a time"));
 124     }
 125     if (frame.bBox)
 126     {
 127         for (int d = 0; d < DIM; ++d)
 128         {
 129             for (int dd = 0; dd < DIM; ++dd)
 130             {
 131                 box_[d][dd] = frame.box[d][dd];
 132             }
 133         }
 134     }
 135 }
 136
 137 std::string TrajectoryFrame::frameName() const
 138 {
 139     return formatString("Time %f Step %" PRId64, frame_.time, frame_.step);
 140 }
 141
 142 std::int64_t TrajectoryFrame::step() const
 143 {
 144     return frame_.step;
 145 }
 146
 147 double TrajectoryFrame::time() const
 148 {
 149     return frame_.time;
 150 }
 151
 152 int TrajectoryFrame::pbc() const
 153 {
 154     return frame_.ePBC;
 155 }
 156
 157 ArrayRef<const RVec> TrajectoryFrame::x() const
 158 {
 159     return arrayRefFromArray(reinterpret_cast<RVec *>(frame_.x),
 160                              frame_.natoms);
 161 }
 162
 163 ArrayRef<const RVec> TrajectoryFrame::v() const
 164 {
 165     if (frame_.bV)
 166     {
 167         return arrayRefFromArray(reinterpret_cast<RVec *>(frame_.v),
 168                                  frame_.natoms);
 169     }
 170     else
 171     {
 172         return EmptyArrayRef();
 173     }
 174 }
 175
 176 ArrayRef<const RVec> TrajectoryFrame::f() const
 177 {
 178     if (frame_.bF)
 179     {
 180         return arrayRefFromArray(reinterpret_cast<RVec *>(frame_.f),
 181                                  frame_.natoms);
 182     }
 183     else
 184     {
 185         return EmptyArrayRef();
 186     }
 187 }
 188
 189 bool TrajectoryFrame::hasBox() const
 190 {
 191     return frame_.bBox;
 192 }
 193
 194 const BoxMatrix &TrajectoryFrame::box() const
 195 {
 196     return box_;
 197 }
 198
 199 } // namespace gmx