src/gromacs/gmxpreprocess/read-conformation.cpp

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  35 #include "gmxpre.h"
  36
  37 #include "read-conformation.h"
  38
  39 #include <vector>
  40
  41 #include "gromacs/fileio/confio.h"
  42 #include "gromacs/topology/atomprop.h"
  43 #include "gromacs/topology/atoms.h"
  44 #include "gromacs/topology/mtop_util.h"
  45 #include "gromacs/topology/topology.h"
  46 #include "gromacs/utility/cstringutil.h"
  47 #include "gromacs/utility/smalloc.h"
  48 #include "gromacs/utility/unique_cptr.h"
  49
  50 using gmx::RVec;
  51
  52 std::vector<real>
  53 makeExclusionDistances(const t_atoms *a, gmx_atomprop_t aps,
  54                        real defaultDistance, real scaleFactor)
  55 {
  56     std::vector<real> exclusionDistances;
  57
  58     exclusionDistances.reserve(a->nr);
  59     for (int i = 0; i < a->nr; ++i)
  60     {
  61         real value;
  62         if (!gmx_atomprop_query(aps, epropVDW,
  63                                 *(a->resinfo[a->atom[i].resind].name),
  64                                 *(a->atomname[i]), &value))
  65         {
  66             value = defaultDistance;
  67         }
  68         else
  69         {
  70             value *= scaleFactor;
  71         }
  72         exclusionDistances.push_back(value);
  73     }
  74     return exclusionDistances;
  75 }
  76
  77 void readConformation(const char *confin, gmx_mtop_t *top,
  78                       std::vector<RVec> *x, std::vector<RVec> *v,
  79                       int *ePBC, matrix box, const char *statusTitle)
  80 {
  81     fprintf(stderr, "Reading %s configuration%s\n", statusTitle,
  82             v ? " and velocities" : "");
  83     rvec                   *x_tmp = nullptr, *v_tmp = nullptr;
  84     bool                    dummy;
  85     readConfAndTopology(confin, &dummy, top, ePBC, x ? &x_tmp : nullptr, v ? &v_tmp : nullptr, box);
  86     const gmx::sfree_guard  xguard(x_tmp);
  87     const gmx::sfree_guard  vguard(v_tmp);
  88     if (x && x_tmp)
  89     {
  90         *x = std::vector<RVec>(x_tmp, x_tmp + top->natoms);
  91     }
  92     if (v && v_tmp)
  93     {
  94         *v = std::vector<RVec>(v_tmp, v_tmp + top->natoms);
  95     }
  96     fprintf(stderr, "%s\nContaining %d atoms in %d residues\n",
  97             *top->name, top->natoms, gmx_mtop_nres(top));
  98 }
  99
 100 void readConformation(const char *confin, t_topology *top,
 101                       std::vector<RVec> *x, std::vector<RVec> *v,
 102                       int *ePBC, matrix box, const char *statusTitle)
 103 {
 104     fprintf(stderr, "Reading %s configuration%s\n", statusTitle,
 105             v ? " and velocities" : "");
 106     rvec                   *x_tmp = nullptr, *v_tmp = nullptr;
 107     read_tps_conf(confin, top, ePBC, x ? &x_tmp : nullptr, v ? &v_tmp : nullptr, box, FALSE);
 108     const gmx::sfree_guard  xguard(x_tmp);
 109     const gmx::sfree_guard  vguard(v_tmp);
 110     if (x && x_tmp)
 111     {
 112         *x = std::vector<RVec>(x_tmp, x_tmp + top->atoms.nr);
 113     }
 114     if (v && v_tmp)
 115     {
 116         *v = std::vector<RVec>(v_tmp, v_tmp + top->atoms.nr);
 117     }
 118     fprintf(stderr, "%s\nContaining %d atoms in %d residues\n",
 119             *top->name, top->atoms.nr, top->atoms.nres);
 120 }