#include "gromacs/utility/snprintf.h"
/* TODO The implementation details should move to their own source file. */
-InteractionType::InteractionType(gmx::ArrayRef<const int> atoms,
- gmx::ArrayRef<const real> params,
- const std::string &name)
+InteractionOfType::InteractionOfType(gmx::ArrayRef<const int> atoms,
+ gmx::ArrayRef<const real> params,
+ const std::string &name)
: atoms_(atoms.begin(), atoms.end()),
interactionTypeName_(name)
{
}
}
-const int &InteractionType::ai() const
+const int &InteractionOfType::ai() const
{
GMX_RELEASE_ASSERT(!atoms_.empty(), "Need to have at least one atom set");
return atoms_[0];
}
-const int &InteractionType::aj() const
+const int &InteractionOfType::aj() const
{
GMX_RELEASE_ASSERT(atoms_.size() > 1, "Need to have at least two atoms set");
return atoms_[1];
}
-const int &InteractionType::ak() const
+const int &InteractionOfType::ak() const
{
GMX_RELEASE_ASSERT(atoms_.size() > 2, "Need to have at least three atoms set");
return atoms_[2];
}
-const int &InteractionType::al() const
+const int &InteractionOfType::al() const
{
GMX_RELEASE_ASSERT(atoms_.size() > 3, "Need to have at least four atoms set");
return atoms_[3];
}
-const int &InteractionType::am() const
+const int &InteractionOfType::am() const
{
GMX_RELEASE_ASSERT(atoms_.size() > 4, "Need to have at least five atoms set");
return atoms_[4];
}
-const real &InteractionType::c0() const
+const real &InteractionOfType::c0() const
{
return forceParam_[0];
}
-const real &InteractionType::c1() const
+const real &InteractionOfType::c1() const
{
return forceParam_[1];
}
-const real &InteractionType::c2() const
+const real &InteractionOfType::c2() const
{
return forceParam_[2];
}
-const std::string &InteractionType::interactionTypeName() const
+const std::string &InteractionOfType::interactionTypeName() const
{
return interactionTypeName_;
}
-void InteractionType::sortBondAtomIds()
+void InteractionOfType::sortBondAtomIds()
{
if (aj() < ai())
{
}
}
-void InteractionType::sortAngleAtomIds()
+void InteractionOfType::sortAngleAtomIds()
{
if (ak() < ai())
{
}
}
-void InteractionType::sortDihedralAtomIds()
+void InteractionOfType::sortDihedralAtomIds()
{
if (al() < ai())
{
}
}
-void InteractionType::sortAtomIds()
+void InteractionOfType::sortAtomIds()
{
if (isBond())
{
}
};
-void InteractionType::setForceParameter(int pos, real value)
+void InteractionOfType::setForceParameter(int pos, real value)
{
GMX_RELEASE_ASSERT(pos < MAXFORCEPARAM, "Can't set parameter beyond the maximum number of parameters");
forceParam_[pos] = value;
/* For all the molecule types */
for (auto &mol : mols)
{
- n += mol.plist[ifunc].size();
- mol.plist[ifunc].interactionTypes.clear();
+ n += mol.interactions[ifunc].size();
+ mol.interactions[ifunc].interactionTypes.clear();
}
return n;
}
int nint = 0;
for (const gmx_molblock_t &molb : mtop->molblock)
{
- nint += molb.nmol*mi[molb.type].plist[ftype].size();
+ nint += molb.nmol*mi[molb.type].interactions[ftype].size();
}
return nint;
PreprocessingAtomTypes *atypes, gmx_mtop_t *sys,
std::vector<MoleculeInformation> *mi,
std::unique_ptr<MoleculeInformation> *intermolecular_interactions,
- gmx::ArrayRef<InteractionTypeParameters> plist,
+ gmx::ArrayRef<InteractionsOfType> interactions,
int *comb, double *reppow, real *fudgeQQ,
gmx_bool bMorse,
warninp *wi)
/* TOPOLOGY processing */
sys->name = do_top(bVerbose, topfile, topppfile, opts, bZero, &(sys->symtab),
- plist, comb, reppow, fudgeQQ,
+ interactions, comb, reppow, fudgeQQ,
atypes, mi, intermolecular_interactions,
ir,
&molblock,
for (gmx_molblock_t &molb : mtop->molblock)
{
nat_molb = molb.nmol*mtop->moltype[molb.type].atoms.nr;
- const InteractionTypeParameters *pr = &(molinfo[molb.type].plist[F_POSRES]);
- const InteractionTypeParameters *prfb = &(molinfo[molb.type].plist[F_FBPOSRES]);
+ const InteractionsOfType *pr = &(molinfo[molb.type].interactions[F_POSRES]);
+ const InteractionsOfType *prfb = &(molinfo[molb.type].interactions[F_FBPOSRES]);
if (pr->size() > 0 || prfb->size() > 0)
{
atom = mtop->moltype[molb.type].atoms.atom;
for (const gmx_molblock_t &molb : mtop->molblock)
{
count_mol = 0;
- gmx::ArrayRef<const InteractionTypeParameters> plist = mi[molb.type].plist;
+ gmx::ArrayRef<const InteractionsOfType> interactions = mi[molb.type].interactions;
for (int i = 0; i < F_NRE; i++)
{
if (i == F_SETTLE)
{
- count_mol += 3*plist[i].size();
+ count_mol += 3*interactions[i].size();
}
else if (interaction_function[i].flags & IF_CONSTRAINT)
{
- count_mol += plist[i].size();
+ count_mol += interactions[i].size();
}
}
warning_error(wi, warn_buf);
}
- std::array<InteractionTypeParameters, F_NRE> plist;
- gmx_mtop_t sys;
- PreprocessingAtomTypes atypes;
+ std::array<InteractionsOfType, F_NRE> interactions;
+ gmx_mtop_t sys;
+ PreprocessingAtomTypes atypes;
if (debug)
{
pr_symtab(debug, 0, "Just opened", &sys.symtab);
new_status(fn, opt2fn_null("-pp", NFILE, fnm), opt2fn("-c", NFILE, fnm),
opts, ir, bZero, bGenVel, bVerbose, &state,
&atypes, &sys, &mi, &intermolecular_interactions,
- plist, &comb, &reppow, &fudgeQQ,
+ interactions, &comb, &reppow, &fudgeQQ,
opts->bMorse,
wi);
for (size_t mt = 0; mt < sys.moltype.size(); mt++)
{
nvsite +=
- set_vsites(bVerbose, &sys.moltype[mt].atoms, &atypes, mi[mt].plist);
+ set_vsites(bVerbose, &sys.moltype[mt].atoms, &atypes, mi[mt].interactions);
}
/* now throw away all obsolete bonds, angles and dihedrals: */
/* note: constraints are ALWAYS removed */
{
for (size_t mt = 0; mt < sys.moltype.size(); mt++)
{
- clean_vsite_bondeds(mi[mt].plist, sys.moltype[mt].atoms.nr, bRmVSBds);
+ clean_vsite_bondeds(mi[mt].interactions, sys.moltype[mt].atoms.nr, bRmVSBds);
}
}
}
/* If we are using CMAP, setup the pre-interpolation grid */
- if (plist[F_CMAP].ncmap() > 0)
+ if (interactions[F_CMAP].ncmap() > 0)
{
- init_cmap_grid(&sys.ffparams.cmap_grid, plist[F_CMAP].cmapAngles, plist[F_CMAP].cmakeGridSpacing);
- setup_cmap(plist[F_CMAP].cmakeGridSpacing, plist[F_CMAP].cmapAngles, plist[F_CMAP].cmap, &sys.ffparams.cmap_grid);
+ init_cmap_grid(&sys.ffparams.cmap_grid, interactions[F_CMAP].cmapAngles, interactions[F_CMAP].cmakeGridSpacing);
+ setup_cmap(interactions[F_CMAP].cmakeGridSpacing, interactions[F_CMAP].cmapAngles, interactions[F_CMAP].cmap, &sys.ffparams.cmap_grid);
}
set_wall_atomtype(&atypes, opts, ir, wi);
if (bRenum)
{
- atypes.renumberTypes(plist, &sys, ir->wall_atomtype, bVerbose);
+ atypes.renumberTypes(interactions, &sys, ir->wall_atomtype, bVerbose);
}
if (ir->implicit_solvent)
}
const int ntype = atypes.size();
- convertInteractionTypeParameters(ntype, plist, mi, intermolecular_interactions.get(),
- comb, reppow, fudgeQQ, &sys);
+ convertInteractionsOfType(ntype, interactions, mi, intermolecular_interactions.get(),
+ comb, reppow, fudgeQQ, &sys);
if (debug)
{
- pr_symtab(debug, 0, "After converInteractionTypeParameters", &sys.symtab);
+ pr_symtab(debug, 0, "After converInteractionsOfType", &sys.symtab);
}
/* set ptype to VSite for virtual sites */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff