#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
-typedef union t_iparams
-{
+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 {
+ struct
+ {
real a, b, c;
} bham;
- struct {
+ struct
+ {
real rA, krA, rB, krB;
} harmonic;
- struct {
+ struct
+ {
real klinA, aA, klinB, aB;
} linangle;
- struct {
+ struct
+ {
real lowA, up1A, up2A, kA, lowB, up1B, up2B, kB;
} restraint;
/* No free energy supported for cubic bonds, FENE, WPOL or cross terms */
- struct {
+ struct
+ {
real b0, kb, kcub;
} cubic;
- struct {
+ struct
+ {
real bm, kb;
} fene;
- struct {
+ struct
+ {
real r1e, r2e, krr;
} cross_bb;
- struct {
+ struct
+ {
real r1e, r2e, r3e, krt;
} cross_ba;
- struct {
+ struct
+ {
real thetaA, kthetaA, r13A, kUBA, thetaB, kthetaB, r13B, kUBB;
} u_b;
- struct {
+ struct
+ {
real theta, c[5];
} qangle;
- struct {
+ struct
+ {
real alpha;
} polarize;
- struct {
+ struct
+ {
real alpha, drcut, khyp;
} anharm_polarize;
- struct {
+ struct
+ {
real al_x, al_y, al_z, rOH, rHH, rOD;
} wpol;
- struct {
+ struct
+ {
real a, alpha1, alpha2, rfac;
} thole;
- struct {
+ struct
+ {
real c6, c12;
} lj;
- struct {
+ struct
+ {
real c6A, c12A, c6B, c12B;
} lj14;
- struct {
+ struct
+ {
real fqq, qi, qj, c6, c12;
} ljc14;
- struct {
+ 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;
+ struct
+ {
+ real phiA, cpA;
+ int mult;
+ real phiB, cpB;
} pdihs;
- struct {
+ 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 {
+ struct
+ {
real doh, dhh;
} settle;
- struct {
+ struct
+ {
real b0A, cbA, betaA, b0B, cbB, betaB;
} morse;
- struct {
+ struct
+ {
real pos0A[DIM], fcA[DIM], pos0B[DIM], fcB[DIM];
} posres;
- struct {
- real pos0[DIM], r, k; int geom;
+ struct
+ {
+ real pos0[DIM], r, k;
+ int geom;
} fbposres;
- struct {
+ struct
+ {
real rbcA[NR_RBDIHS], rbcB[NR_RBDIHS];
} rbdihs;
- struct {
+ struct
+ {
real cbtcA[NR_CBTDIHS], cbtcB[NR_CBTDIHS];
} cbtdihs;
- struct {
+ struct
+ {
real a, b, c, d, e, f;
} vsite;
- struct {
- int n; real a;
+ 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;
+ struct
+ {
+ real low, up1, up2, kfac;
+ int type, label, npair;
} disres;
- struct {
+ struct
+ {
real phiA, dphiA, kfacA, phiB, dphiB, kfacB;
} dihres;
- struct {
- int ex, power, label; real c, obs, kfac;
+ struct
+ {
+ int ex, power, label;
+ real c, obs, kfac;
} orires;
- struct {
- int table; real kA; real kB;
+ struct
+ {
+ int table;
+ real kA;
+ real kB;
} tab;
- struct {
+ struct
+ {
int cmapA, cmapB;
} cmap;
- struct {
+ struct
+ {
real buf[MAXFORCEPARAM];
- } generic; /* Conversion */
+ } generic; /* Conversion */
} t_iparams;
typedef int t_functype;
struct InteractionList
{
/* Returns the total number of elements in iatoms */
- int size() const
- {
- return gmx::ssize(iatoms);
- }
+ int size() const { return gmx::ssize(iatoms); }
/* List of interactions, see explanation further down */
std::vector<int> iatoms;
struct t_ilist
{
/* Returns the total number of elements in iatoms */
- int size() const
- {
- return nr;
- }
+ int size() const { return nr; }
int nr;
int nr_nonperturbed;
- t_iatom *iatoms;
+ t_iatom* iatoms;
int nalloc;
};
struct InteractionListHandle
{
const int functionType; //!< The function type
- const std::vector<int> &iatoms; //!< Reference to interaction list
+ 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)
+static inline std::vector<InteractionListHandle> extractILists(const InteractionLists& ilists, int flags)
{
std::vector<InteractionListHandle> handles;
for (size_t ftype = 0; ftype < ilists.size(); ftype++)
*
* \param[in] ilistHandle The ilist to return the stride for
*/
-static inline int ilistStride(const InteractionListHandle &ilistHandle)
+static inline int ilistStride(const InteractionListHandle& ilistHandle)
{
return 1 + NRAL(ilistHandle.functionType);
}
struct gmx_cmap_t
{
int grid_spacing = 0; /* Grid spacing */
- std::vector<gmx_cmapdata_t> cmapdata; /* Lists of grids with actual, pre-interpolated data */
+ std::vector<gmx_cmapdata_t> cmapdata; /* Lists of grids with actual, pre-interpolated data */
};
-enum {
- ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
+enum
+{
+ ilsortUNKNOWN,
+ ilsortNO_FE,
+ ilsortFE_UNSORTED,
+ ilsortFE_SORTED
};
typedef struct t_idef
{
int ntypes;
int atnr;
- t_functype *functype;
- t_iparams *iparams;
+ t_functype* functype;
+ t_iparams* iparams;
real fudgeQQ;
- gmx_cmap_t *cmap_grid;
- t_iparams *iparams_posres, *iparams_fbposres;
+ gmx_cmap_t* cmap_grid;
+ t_iparams * iparams_posres, *iparams_fbposres;
int iparams_posres_nalloc, iparams_fbposres_nalloc;
- t_ilist il[F_NRE];
- int ilsort;
+ t_ilist il[F_NRE];
+ int ilsort;
} t_idef;
/*
* The state of the sorting of il, values are provided above.
*/
-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);
+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);
+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);
+void done_idef(t_idef* idef);
-void copy_ilist(const t_ilist *src, t_ilist *dst);
+void copy_ilist(const t_ilist* src, t_ilist* dst);
#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff