*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/ifunc.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
-typedef union t_iparams {
+struct gmx_ffparams_t;
+
+typedef union t_iparams
+{
/* Some parameters have A and B values for free energy calculations.
* The B values are not used for regular simulations of course.
* Free Energy for nonbondeds can be computed by changing the atom type.
} wpol;
struct
{
- real a, alpha1, alpha2, rfac;
+ real a, alpha1, alpha2;
} thole;
struct
{
struct InteractionList
{
/* Returns the total number of elements in iatoms */
- int size() const { return gmx::ssize(iatoms); }
+ int size() const { return static_cast<int>(iatoms.size()); }
+
+ /* Returns whether the list is empty */
+ bool empty() const { return iatoms.empty(); }
+
+ /* Adds one interaction to the list */
+ template<std::size_t numAtoms>
+ void push_back(const int parameterType, const std::array<int, numAtoms>& atoms)
+ {
+ const std::size_t oldSize = iatoms.size();
+ iatoms.resize(iatoms.size() + 1 + numAtoms);
+ iatoms[oldSize] = parameterType;
+ for (std::size_t i = 0; i < numAtoms; i++)
+ {
+ iatoms[oldSize + 1 + i] = atoms[i];
+ }
+ }
+
+ /* Adds one interaction to the list */
+ void push_back(const int parameterType, const int numAtoms, const int* atoms)
+ {
+ const std::size_t oldSize = iatoms.size();
+ iatoms.resize(iatoms.size() + 1 + numAtoms);
+ iatoms[oldSize] = parameterType;
+ for (int i = 0; i < numAtoms; i++)
+ {
+ iatoms[oldSize + 1 + i] = atoms[i];
+ }
+ }
+
+ /* Appends \p ilist at the back of the list */
+ void append(const InteractionList& ilist)
+ {
+ iatoms.insert(iatoms.end(), ilist.iatoms.begin(), ilist.iatoms.end());
+ }
+
+ /* Clears the list */
+ void clear() { iatoms.clear(); }
/* List of interactions, see explanation further down */
std::vector<int> iatoms;
*
* TODO: Consider only including entries in use instead of all F_NRE
*/
-typedef std::array<InteractionList, F_NRE> InteractionLists;
+using InteractionLists = std::array<InteractionList, F_NRE>;
-/* Deprecated list of listed interactions.
- *
- * The nonperturbed/perturbed interactions are now separated (sorted) in the
- * ilist, such that the first 0..(nr_nonperturbed-1) ones are exactly that, and
- * the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
- * interactions.
- */
+/* Deprecated list of listed interactions */
struct t_ilist
{
/* Returns the total number of elements in iatoms */
int size() const { return nr; }
+ /* Returns whether the list is empty */
+ bool empty() const { return nr == 0; }
+
int nr;
t_iatom* iatoms;
int nalloc;
};
-/* TODO: Replace t_ilist in gmx_localtop_t by InteractionList.
- * The nr_nonperturbed functionality needs to be ported.
- * Remove t_topology.
- * Remove t_ilist and remove templating on list type
- * in mshift.cpp, constr.cpp, vsite.cpp and domdec_topology.cpp.
- */
+/* TODO: Remove t_ilist and remove templating on list type in mshift.cpp */
/*
* The structs InteractionList and t_ilist defines a list of atoms with their interactions.
std::vector<InteractionListHandle> handles;
for (size_t ftype = 0; ftype < ilists.size(); ftype++)
{
- if ((interaction_function[ftype].flags & flags) && ilists[ftype].size() > 0)
+ if ((interaction_function[ftype].flags & flags) && !ilists[ftype].empty())
{
handles.push_back({ static_cast<int>(ftype), ilists[ftype].iatoms });
}
{
ilsortUNKNOWN,
ilsortNO_FE,
- ilsortFE_UNSORTED,
ilsortFE_SORTED
};
-typedef struct t_idef
+/* Struct with list of interaction parameters and lists of interactions
+ *
+ * TODO: Convert to a proper class with private data members so we can
+ * ensure that the free-energy sorting and sorting setting is consistent.
+ */
+class InteractionDefinitions
+{
+public:
+ /* Constructor
+ *
+ * \param[in] ffparams The interaction parameters, the lifetime of the created object should not exceed the lifetime of the passed parameters
+ */
+ InteractionDefinitions(const gmx_ffparams_t& ffparams);
+
+ // Clears data not read in from ffparams
+ void clear();
+
+ // The interaction parameters
+ const std::vector<t_iparams>& iparams;
+ // The function type per type
+ const std::vector<int>& functype;
+ // Position restraint interaction parameters
+ std::vector<t_iparams> iparams_posres;
+ // Flat-bottomed position restraint parameters
+ std::vector<t_iparams> iparams_fbposres;
+ // The list of interactions for each type. Note that some, such as LJ and COUL will have 0 entries.
+ std::array<InteractionList, F_NRE> il;
+ /* The number of non-perturbed interactions at the start of each entry in il */
+ std::array<int, F_NRE> numNonperturbedInteractions;
+ // The sorting state of interaction in il
+ int ilsort = ilsortUNKNOWN;
+ // The dihedral correction maps
+ gmx_cmap_t cmap_grid;
+};
+
+/* Deprecated interation definitions, used in t_topology */
+struct t_idef
{
int ntypes;
int atnr;
t_functype* functype;
t_iparams* iparams;
real fudgeQQ;
- gmx_cmap_t* cmap_grid;
t_iparams * iparams_posres, *iparams_fbposres;
- int iparams_posres_nalloc, iparams_fbposres_nalloc;
t_ilist il[F_NRE];
- /* The number of non-perturbed interactions at the start of each entry in il */
- int numNonperturbedInteractions[F_NRE];
- int ilsort;
-} t_idef;
+ int ilsort;
+};
/*
* The struct t_idef defines all the interactions for the complete
const char* title,
const t_functype* functype,
const InteractionList& ilist,
- gmx_bool bShowNumbers,
- gmx_bool bShowParameters,
+ bool bShowNumbers,
+ bool bShowParameters,
const t_iparams* iparams);
-void pr_idef(FILE* fp, int indent, const char* title, const t_idef* idef, gmx_bool bShowNumbers, gmx_bool bShowParameters);
+void pr_idef(FILE* fp, int indent, const char* title, const t_idef* idef, bool bShowNumbers, bool bShowParameters);
/*! \brief
* Properly initialize idef struct.
*/
void done_idef(t_idef* idef);
-void copy_ilist(const t_ilist* src, t_ilist* dst);
-
#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff