#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strconvert.h"
+#include "hackblock.h"
#include "resall.h"
typedef struct {
struct VsiteBondParameter
{
- VsiteBondParameter(int ftype, const InteractionType &type)
- : ftype_(ftype), type_(type)
+ VsiteBondParameter(int ftype, const InteractionOfType &vsiteInteraction)
+ : ftype_(ftype), vsiteInteraction_(vsiteInteraction)
{}
- int ftype_;
- const InteractionType &type_;
+ int ftype_;
+ const InteractionOfType &vsiteInteraction_;
};
struct Atom2VsiteBond
}
static void enter_bonded(int nratoms, int *nrbonded, t_mybonded **bondeds,
- const InteractionType &type)
+ const InteractionOfType &type)
{
srenew(*bondeds, *nrbonded+1);
{
for (auto &vsite : at2vb[atoms[k]].vSiteBondedParameters)
{
- int ftype = vsite.ftype_;
- const InteractionType &type = vsite.type_;
- int nrcheck = vsite_bond_nrcheck(ftype);
+ int ftype = vsite.ftype_;
+ const InteractionOfType &type = vsite.vsiteInteraction_;
+ int nrcheck = vsite_bond_nrcheck(ftype);
/* abuse nrcheck to see if we're adding bond, angle or idih */
switch (nrcheck)
{
}
static std::vector<Atom2VsiteBond>
-make_at2vsitebond(int natoms, gmx::ArrayRef<InteractionTypeParameters> plist)
+make_at2vsitebond(int natoms, gmx::ArrayRef<InteractionsOfType> plist)
{
bool *bVSI;
}
static std::vector<Atom2VsiteConnection>
-make_at2vsitecon(int natoms, gmx::ArrayRef<InteractionTypeParameters> plist)
+make_at2vsitecon(int natoms, gmx::ArrayRef<InteractionsOfType> plist)
{
std::vector<bool> bVSI(natoms);
std::vector<Atom2VsiteConnection> at2vc(natoms);
}
}
-static void printInteractionType(FILE *fp, int ftype, int i, const InteractionType &type)
+static void printInteractionOfType(FILE *fp, int ftype, int i, const InteractionOfType &type)
{
static int pass = 0;
static int prev_ftype = NOTSET;
}
static bool calc_vsite3_param(PreprocessingAtomTypes *atypes,
- InteractionType *param, t_atoms *at,
+ InteractionOfType *param, t_atoms *at,
int nrbond, t_mybonded *bonds,
int nrang, t_mybonded *angles )
{
return bError;
}
-static bool calc_vsite3fd_param(InteractionType *param,
+static bool calc_vsite3fd_param(InteractionOfType *param,
int nrbond, t_mybonded *bonds,
int nrang, t_mybonded *angles)
{
return bError;
}
-static bool calc_vsite3fad_param(InteractionType *param,
+static bool calc_vsite3fad_param(InteractionOfType *param,
int nrbond, t_mybonded *bonds,
int nrang, t_mybonded *angles)
{
}
static bool calc_vsite3out_param(PreprocessingAtomTypes *atypes,
- InteractionType *param, t_atoms *at,
+ InteractionOfType *param, t_atoms *at,
int nrbond, t_mybonded *bonds,
int nrang, t_mybonded *angles)
{
return bError;
}
-static bool calc_vsite4fd_param(InteractionType *param,
+static bool calc_vsite4fd_param(InteractionOfType *param,
int nrbond, t_mybonded *bonds,
int nrang, t_mybonded *angles)
{
static bool
-calc_vsite4fdn_param(InteractionType *param,
+calc_vsite4fdn_param(InteractionOfType *param,
int nrbond, t_mybonded *bonds,
int nrang, t_mybonded *angles)
{
int set_vsites(bool bVerbose, t_atoms *atoms, PreprocessingAtomTypes *atypes,
- gmx::ArrayRef<InteractionTypeParameters> plist)
+ gmx::ArrayRef<InteractionsOfType> plist)
{
int ftype;
int nvsite, nrbond, nrang, nridih, nrset;
if (debug)
{
fprintf(debug, "bSet=%s ", gmx::boolToString(bSet));
- printInteractionType(debug, ftype, i, plist[ftype].interactionTypes[i]);
+ printInteractionOfType(debug, ftype, i, plist[ftype].interactionTypes[i]);
}
if (!bSet)
{
}
-typedef struct {
- int ftype, parnr;
-} t_pindex;
+/*! \brief
+ * Convenience typedef for linking function type to parameter numbers.
+ *
+ * The entries in this datastructure are valid if the particle participates in
+ * a virtual site interaction and has a valid vsite function type other than VSITEN.
+ * \todo Change to remove empty constructor when gmx::compat::optional is available.
+ */
+class VsiteAtomMapping
+{
+ public:
+ //! Only construct with all information in place or nothing
+ VsiteAtomMapping(int functionType, int interactionIndex)
+ : functionType_(functionType), interactionIndex_(interactionIndex)
+ {}
+ VsiteAtomMapping()
+ : functionType_(-1), interactionIndex_(-1)
+ {}
+ //! Get function type.
+ const int &functionType() const { return functionType_; }
+ //! Get parameter number.
+ const int &interactionIndex() const { return interactionIndex_; };
+ private:
+ //! Function type for the linked parameter.
+ int functionType_;
+ //! The linked parameter.
+ int interactionIndex_;
+};
-static void check_vsite_constraints(gmx::ArrayRef<InteractionTypeParameters> plist,
+static void check_vsite_constraints(gmx::ArrayRef<InteractionsOfType> plist,
int cftype, const int vsite_type[])
{
int n = 0;
}
}
-static void clean_vsite_bonds(gmx::ArrayRef<InteractionTypeParameters> plist, t_pindex pindex[],
+static void clean_vsite_bonds(gmx::ArrayRef<InteractionsOfType> plist,
+ gmx::ArrayRef<const VsiteAtomMapping> pindex,
int cftype, const int vsite_type[])
{
int ftype, nOut;
int nconverted, nremoved;
int oatom, at1, at2;
bool bKeep, bRemove, bAllFD;
- InteractionTypeParameters *ps;
+ InteractionsOfType *ps;
if (cftype == F_CONNBONDS)
{
if (vsite_type[atom] != NOTSET && vsite_type[atom] != F_VSITEN)
{
nvsite++;
- bool bThisFD = ( (pindex[atom].ftype == F_VSITE3FD ) ||
- (pindex[atom].ftype == F_VSITE3FAD) ||
- (pindex[atom].ftype == F_VSITE4FD ) ||
- (pindex[atom].ftype == F_VSITE4FDN ) );
- bool bThisOUT = ( (pindex[atom].ftype == F_VSITE3OUT) &&
+ bool bThisFD = ( (pindex[atom].functionType() == F_VSITE3FD ) ||
+ (pindex[atom].functionType() == F_VSITE3FAD) ||
+ (pindex[atom].functionType() == F_VSITE4FD ) ||
+ (pindex[atom].functionType() == F_VSITE4FDN ) );
+ bool bThisOUT = ( (pindex[atom].functionType() == F_VSITE3OUT) &&
((interaction_function[cftype].flags & IF_CONSTRAINT) != 0u) );
bAllFD = bAllFD && bThisFD;
if (bThisFD || bThisOUT)
{
oatom = atoms[1-k]; /* the other atom */
if (vsite_type[oatom] == NOTSET &&
- oatom == plist[pindex[atom].ftype].interactionTypes[pindex[atom].parnr].aj())
+ oatom == plist[pindex[atom].functionType()].interactionTypes[pindex[atom].interactionIndex()].aj())
{
/* if the other atom isn't a vsite, and it is AI */
bRemove = true;
/* TODO This would be nicer to implement with
a C++ "vector view" class" with an
STL-container-like interface. */
- vsnral = NRAL(pindex[atom].ftype) - 1;
- first_atoms = plist[pindex[atom].ftype].interactionTypes[pindex[atom].parnr].atoms().data() + 1;
+ vsnral = NRAL(pindex[atom].functionType()) - 1;
+ first_atoms = plist[pindex[atom].functionType()].interactionTypes[pindex[atom].interactionIndex()].atoms().data() + 1;
}
else
{
GMX_ASSERT(first_atoms != nullptr, "nvsite > 1 must have first_atoms != NULL");
/* if it is not the first then
check if this vsite is constructed from the same atoms */
- if (vsnral == NRAL(pindex[atom].ftype)-1)
+ if (vsnral == NRAL(pindex[atom].functionType())-1)
{
for (int m = 0; (m < vsnral) && !bKeep; m++)
{
const int *atoms;
bool bPresent = false;
- atoms = plist[pindex[atom].ftype].interactionTypes[pindex[atom].parnr].atoms().data() + 1;
+ atoms = plist[pindex[atom].functionType()].interactionTypes[pindex[atom].interactionIndex()].atoms().data() + 1;
for (int n = 0; (n < vsnral) && !bPresent; n++)
{
if (atoms[m] == first_atoms[n])
}
}
-static void clean_vsite_angles(gmx::ArrayRef<InteractionTypeParameters> plist, t_pindex pindex[],
+static void clean_vsite_angles(gmx::ArrayRef<InteractionsOfType> plist,
+ gmx::ArrayRef<VsiteAtomMapping> pindex,
int cftype, const int vsite_type[],
gmx::ArrayRef<const Atom2VsiteConnection> at2vc)
{
int atom, at1, at2;
- InteractionTypeParameters *ps;
+ InteractionsOfType *ps;
ps = &(plist[cftype]);
int oldSize = ps->size();
if (vsite_type[atom] != NOTSET && vsite_type[atom] != F_VSITEN)
{
nvsite++;
- bAll3FAD = bAll3FAD && (pindex[atom].ftype == F_VSITE3FAD);
+ bAll3FAD = bAll3FAD && (pindex[atom].functionType() == F_VSITE3FAD);
if (nvsite == 1)
{
/* store construction atoms of first vsite */
- vsnral = NRAL(pindex[atom].ftype) - 1;
- first_atoms = plist[pindex[atom].ftype].interactionTypes[pindex[atom].parnr].atoms().data() + 1;
+ vsnral = NRAL(pindex[atom].functionType()) - 1;
+ first_atoms = plist[pindex[atom].functionType()].interactionTypes[pindex[atom].interactionIndex()].atoms().data() + 1;
}
else
{
GMX_ASSERT(vsnral != 0, "If we've seen a vsite before, we know how many constructing atoms it had");
GMX_ASSERT(first_atoms != nullptr, "If we've seen a vsite before, we know what its first atom index was");
/* check if this vsite is constructed from the same atoms */
- if (vsnral == NRAL(pindex[atom].ftype)-1)
+ if (vsnral == NRAL(pindex[atom].functionType())-1)
{
for (int m = 0; (m < vsnral) && !bKeep; m++)
{
const int *subAtoms;
bool bPresent = false;
- subAtoms = plist[pindex[atom].ftype].interactionTypes[pindex[atom].parnr].atoms().data() + 1;
+ subAtoms = plist[pindex[atom].functionType()].interactionTypes[pindex[atom].interactionIndex()].atoms().data() + 1;
for (int n = 0; (n < vsnral) && !bPresent; n++)
{
if (subAtoms[m] == first_atoms[n])
}
}
-static void clean_vsite_dihs(gmx::ArrayRef<InteractionTypeParameters> plist, t_pindex pindex[],
+static void clean_vsite_dihs(gmx::ArrayRef<InteractionsOfType> plist,
+ gmx::ArrayRef<const VsiteAtomMapping> pindex,
int cftype, const int vsite_type[])
{
- InteractionTypeParameters *ps;
+ InteractionsOfType *ps;
ps = &(plist[cftype]);
if (nvsite == 0)
{
/* store construction atoms of first vsite */
- vsnral = NRAL(pindex[atom].ftype) - 1;
- first_atoms = plist[pindex[atom].ftype].interactionTypes[pindex[atom].parnr].atoms().data() + 1;
+ vsnral = NRAL(pindex[atom].functionType()) - 1;
+ first_atoms = plist[pindex[atom].functionType()].interactionTypes[pindex[atom].interactionIndex()].atoms().data() + 1;
}
else
{
GMX_ASSERT(vsnral != 0, "If we've seen a vsite before, we know how many constructing atoms it had");
GMX_ASSERT(first_atoms != nullptr, "If we've seen a vsite before, we know what its first atom index was");
/* check if this vsite is constructed from the same atoms */
- if (vsnral == NRAL(pindex[atom].ftype)-1)
+ if (vsnral == NRAL(pindex[atom].functionType())-1)
{
for (int m = 0; (m < vsnral) && !bKeep; m++)
{
const int *subAtoms;
bool bPresent = false;
- subAtoms = plist[pindex[atom].ftype].interactionTypes[pindex[atom].parnr].atoms().data() + 1;
+ subAtoms = plist[pindex[atom].functionType()].interactionTypes[pindex[atom].interactionIndex()].atoms().data() + 1;
for (int n = 0; (n < vsnral) && !bPresent; n++)
{
if (subAtoms[m] == first_atoms[n])
}
}
-void clean_vsite_bondeds(gmx::ArrayRef<InteractionTypeParameters> plist, int natoms, bool bRmVSiteBds)
+// TODO use gmx::compat::optional for pindex.
+void clean_vsite_bondeds(gmx::ArrayRef<InteractionsOfType> plist, int natoms, bool bRmVSiteBds)
{
- int nvsite, vsite;
- int *vsite_type;
- t_pindex *pindex;
- std::vector<Atom2VsiteConnection> at2vc;
+ int nvsite, vsite;
+ int *vsite_type;
+ std::vector<VsiteAtomMapping> pindex;
+ std::vector<Atom2VsiteConnection> at2vc;
- pindex = nullptr; /* avoid warnings */
/* make vsite_type array */
snew(vsite_type, natoms);
for (int i = 0; i < natoms; i++)
/* Make a reverse list to avoid ninteractions^2 operations */
at2vc = make_at2vsitecon(natoms, plist);
- snew(pindex, natoms);
+ pindex.resize(natoms);
for (int ftype = 0; ftype < F_NRE; ftype++)
{
/* Here we skip VSITEN. In neary all practical use cases this
if ((interaction_function[ftype].flags & IF_VSITE) &&
ftype != F_VSITEN)
{
- for (int parnr = 0; (parnr < gmx::ssize(plist[ftype])); parnr++)
+ for (int interactionIndex = 0;
+ interactionIndex < gmx::ssize(plist[ftype]);
+ interactionIndex++)
{
- int k = plist[ftype].interactionTypes[parnr].ai();
- pindex[k].ftype = ftype;
- pindex[k].parnr = parnr;
+ int k = plist[ftype].interactionTypes[interactionIndex].ai();
+ pindex[k] = VsiteAtomMapping(ftype, interactionIndex);
}
}
}
}
}
- sfree(pindex);
sfree(vsite_type);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff