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[gromacs.git] / src / gromacs / topology / idef.h

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
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 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
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 */
#ifndef GMX_TOPOLOGY_IDEF_H
#define GMX_TOPOLOGY_IDEF_H

#include <cstdio>

#include <array>
#include <vector>

#include "gromacs/math/vectypes.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"

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.
     * The harmonic type is used for all harmonic potentials:
     * bonds, angles and improper dihedrals
     */
    struct
    {
        real a, b, c;
    } bham;
    struct
    {
        real rA, krA, rB, krB;
    } harmonic;
    struct
    {
        real klinA, aA, klinB, aB;
    } linangle;
    struct
    {
        real lowA, up1A, up2A, kA, lowB, up1B, up2B, kB;
    } restraint;
    /* No free energy supported for cubic bonds, FENE, WPOL or cross terms */
    struct
    {
        real b0, kb, kcub;
    } cubic;
    struct
    {
        real bm, kb;
    } fene;
    struct
    {
        real r1e, r2e, krr;
    } cross_bb;
    struct
    {
        real r1e, r2e, r3e, krt;
    } cross_ba;
    struct
    {
        real thetaA, kthetaA, r13A, kUBA, thetaB, kthetaB, r13B, kUBB;
    } u_b;
    struct
    {
        real theta, c[5];
    } qangle;
    struct
    {
        real alpha;
    } polarize;
    struct
    {
        real alpha, drcut, khyp;
    } anharm_polarize;
    struct
    {
        real al_x, al_y, al_z, rOH, rHH, rOD;
    } wpol;
    struct
    {
        real a, alpha1, alpha2, rfac;
    } thole;
    struct
    {
        real c6, c12;
    } lj;
    struct
    {
        real c6A, c12A, c6B, c12B;
    } lj14;
    struct
    {
        real fqq, qi, qj, c6, c12;
    } ljc14;
    struct
    {
        real qi, qj, c6, c12;
    } ljcnb;
    /* Proper dihedrals can not have different multiplicity when
     * doing free energy calculations, because the potential would not
     * be periodic anymore.
     */
    struct
    {
        real phiA, cpA;
        int  mult;
        real phiB, cpB;
    } pdihs;
    struct
    {
        real dA, dB;
    } constr;
    /* Settle can not be used for Free energy calculations of water bond geometry.
     * Use shake (or lincs) instead if you have to change the water bonds.
     */
    struct
    {
        real doh, dhh;
    } settle;
    struct
    {
        real b0A, cbA, betaA, b0B, cbB, betaB;
    } morse;
    struct
    {
        real pos0A[DIM], fcA[DIM], pos0B[DIM], fcB[DIM];
    } posres;
    struct
    {
        real pos0[DIM], r, k;
        int  geom;
    } fbposres;
    struct
    {
        real rbcA[NR_RBDIHS], rbcB[NR_RBDIHS];
    } rbdihs;
    struct
    {
        real cbtcA[NR_CBTDIHS], cbtcB[NR_CBTDIHS];
    } cbtdihs;
    struct
    {
        real a, b, c, d, e, f;
    } vsite;
    struct
    {
        int  n;
        real a;
    } vsiten;
    /* NOTE: npair is only set after reading the tpx file */
    struct
    {
        real low, up1, up2, kfac;
        int  type, label, npair;
    } disres;
    struct
    {
        real phiA, dphiA, kfacA, phiB, dphiB, kfacB;
    } dihres;
    struct
    {
        int  ex, power, label;
        real c, obs, kfac;
    } orires;
    struct
    {
        int  table;
        real kA;
        real kB;
    } tab;
    struct
    {
        int cmapA, cmapB;
    } cmap;
    struct
    {
        real buf[MAXFORCEPARAM];
    } generic; /* Conversion */
} t_iparams;

typedef int t_functype;

/* List of listed interactions, see description further down.
 *
 * TODO: Consider storing the function type as well.
 * TODO: Consider providing per interaction access.
 */
struct InteractionList
{
    /* Returns the total number of elements in 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;
};

/* List of interaction lists, one list for each interaction type
 *
 * TODO: Consider only including entries in use instead of all F_NRE
 */
using InteractionLists = std::array<InteractionList, F_NRE>;

/* 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: 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.
 * General field description:
 *   int nr
 *      the size (nr elements) of the interactions array (iatoms[]).
 *   t_iatom *iatoms
 *  specifies which atoms are involved in an interaction of a certain
 *       type. The layout of this array is as follows:
 *
 *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 *        |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
 *        +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
 *
 *  So for interaction type type1 3 atoms are needed, and for type2 and
 *      type3 only 2. The type identifier is used to select the function to
 *      calculate the interaction and its actual parameters. This type
 *      identifier is an index in a params[] and functype[] array.
 */

/*! \brief Type for returning a list of InteractionList references
 *
 * TODO: Remove when the function type is made part of InteractionList
 */
struct InteractionListHandle
{
    const int               functionType; //!< The function type
    const std::vector<int>& iatoms;       //!< Reference to interaction list
};

/*! \brief Returns a list of all non-empty InteractionList entries with any of the interaction flags in \p flags set
 *
 * \param[in] ilists  Set of interaction lists
 * \param[in] flags   Bit mask with one or more IF_... bits set
 */
static inline std::vector<InteractionListHandle> extractILists(const InteractionLists& ilists, int flags)
{
    std::vector<InteractionListHandle> handles;
    for (size_t ftype = 0; ftype < ilists.size(); ftype++)
    {
        if ((interaction_function[ftype].flags & flags) && !ilists[ftype].empty())
        {
            handles.push_back({ static_cast<int>(ftype), ilists[ftype].iatoms });
        }
    }
    return handles;
}

/*! \brief Returns the stride for the iatoms array in \p ilistHandle
 *
 * \param[in] ilistHandle  The ilist to return the stride for
 */
static inline int ilistStride(const InteractionListHandle& ilistHandle)
{
    return 1 + NRAL(ilistHandle.functionType);
}

struct gmx_cmapdata_t
{
    std::vector<real> cmap; /* Has length 4*grid_spacing*grid_spacing, */
    /* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
};

struct gmx_cmap_t
{
    int                         grid_spacing = 0; /* Grid spacing */
    std::vector<gmx_cmapdata_t> cmapdata; /* Lists of grids with actual, pre-interpolated data */
};


enum
{
    ilsortUNKNOWN,
    ilsortNO_FE,
    ilsortFE_UNSORTED,
    ilsortFE_SORTED
};

/* 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;
    t_iparams * iparams_posres, *iparams_fbposres;

    t_ilist il[F_NRE];
    int     ilsort;
};

/*
 * The struct t_idef defines all the interactions for the complete
 * simulation. The structure is setup in such a way that the multinode
 * version of the program  can use it as easy as the single node version.
 * General field description:
 *   int ntypes
 *      defines the number of elements in functype[] and param[].
 *   int nodeid
 *      the node id (if parallel machines)
 *   int atnr
 *      the number of atomtypes
 *   t_functype *functype
 *      array of length ntypes, defines for every force type what type of
 *      function to use. Every "bond" with the same function but different
 *      force parameters is a different force type. The type identifier in the
 *      forceatoms[] array is an index in this array.
 *   t_iparams *iparams
 *      array of length ntypes, defines the parameters for every interaction
 *      type. The type identifier in the actual interaction list
 *      (ilist[ftype].iatoms[]) is an index in this array.
 *   gmx_cmap_t cmap_grid
 *      the grid for the dihedral pair correction maps.
 *   t_iparams *iparams_posres, *iparams_fbposres
 *      defines the parameters for position restraints only.
 *      Position restraints are the only interactions that have different
 *      parameters (reference positions) for different molecules
 *      of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
 *   t_ilist il[F_NRE]
 *      The list of interactions for each type. Note that some,
 *      such as LJ and COUL will have 0 entries.
 *   int ilsort
 *      The state of the sorting of il, values are provided above.
 */

namespace gmx
{
class TextWriter;
} // namespace gmx

void printInteractionParameters(gmx::TextWriter* writer, t_functype ftype, const t_iparams& iparams);
void pr_iparams(FILE* fp, t_functype ftype, const t_iparams& iparams);
void pr_ilist(FILE*                  fp,
              int                    indent,
              const char*            title,
              const t_functype*      functype,
              const InteractionList& ilist,
              gmx_bool               bShowNumbers,
              gmx_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);

/*! \brief
 * Properly initialize idef struct.
 *
 * \param[in] idef Pointer to idef struct to initialize.
 */
void init_idef(t_idef* idef);

/*! \brief
 * Properly clean up idef struct.
 *
 * \param[in] idef Pointer to idef struct to clean up.
 */
void done_idef(t_idef* idef);

#endif