class ForceWithShiftForces;
}
-typedef struct {
- int nrQMatoms; /* total nr of QM atoms */
- rvec *xQM; /* shifted to center of box */
- int *indexQM; /* atom i = atom indexQM[i] in mdrun */
- int *atomicnumberQM; /* atomic numbers of QM atoms */
- real *QMcharges; /* atomic charges of QM atoms(ONIOM) */
- int *shiftQM;
- int QMcharge; /* charge of the QM system */
- int multiplicity; /* multipicity (no of unpaired eln) */
- int QMmethod; /* see enums.h for all methods */
- int QMbasis; /* see enums.h for all bases */
- int nelectrons; /* total number of elecs in QM region*/
+typedef struct
+{
+ int nrQMatoms; /* total nr of QM atoms */
+ rvec* xQM; /* shifted to center of box */
+ int* indexQM; /* atom i = atom indexQM[i] in mdrun */
+ int* atomicnumberQM; /* atomic numbers of QM atoms */
+ real* QMcharges; /* atomic charges of QM atoms(ONIOM) */
+ int* shiftQM;
+ int QMcharge; /* charge of the QM system */
+ int multiplicity; /* multipicity (no of unpaired eln) */
+ int QMmethod; /* see enums.h for all methods */
+ int QMbasis; /* see enums.h for all bases */
+ int nelectrons; /* total number of elecs in QM region*/
/* Gaussian specific stuff */
- int nQMcpus; /* no. of CPUs used for the QM calc. */
- int QMmem; /* memory for the gaussian calc. */
- int accuracy; /* convergence criterium (E(-x)) */
- gmx_bool cpmcscf; /* using cpmcscf(l1003)*/
- char *gauss_dir;
- char *gauss_exe;
- char *devel_dir;
- char *orca_basename; /* basename for I/O with orca */
- char *orca_dir; /* directory for ORCA */
+ int nQMcpus; /* no. of CPUs used for the QM calc. */
+ int QMmem; /* memory for the gaussian calc. */
+ int accuracy; /* convergence criterium (E(-x)) */
+ gmx_bool cpmcscf; /* using cpmcscf(l1003)*/
+ char* gauss_dir;
+ char* gauss_exe;
+ char* devel_dir;
+ char* orca_basename; /* basename for I/O with orca */
+ char* orca_dir; /* directory for ORCA */
/* Surface hopping stuff */
- gmx_bool bSH; /* surface hopping (diabatic only) */
- real SAon; /* at which energy gap the SA starts */
- real SAoff; /* at which energy gap the SA stops */
- int SAsteps; /* stepwise switchinng on the SA */
- int SAstep; /* current state of SA */
- int CIdim;
- real *CIvec1;
- real *CIvec2;
- real *CIvec1old;
- real *CIvec2old;
- ivec SHbasis;
- int CASelectrons;
- int CASorbitals;
+ gmx_bool bSH; /* surface hopping (diabatic only) */
+ real SAon; /* at which energy gap the SA starts */
+ real SAoff; /* at which energy gap the SA stops */
+ int SAsteps; /* stepwise switchinng on the SA */
+ int SAstep; /* current state of SA */
+ int CIdim;
+ real* CIvec1;
+ real* CIvec2;
+ real* CIvec1old;
+ real* CIvec2old;
+ ivec SHbasis;
+ int CASelectrons;
+ int CASorbitals;
} t_QMrec;
-typedef struct {
- int nrMMatoms; /* nr of MM atoms, updated every step*/
- rvec *xMM; /* shifted to center of box */
- int *indexMM; /* atom i = atom indexMM[I] in mdrun */
- real *MMcharges; /* MM point charges in std QMMM calc.*/
- int *shiftMM;
- int *MMatomtype; /* only important for semi-emp. */
- real scalefactor;
+typedef struct
+{
+ int nrMMatoms; /* nr of MM atoms, updated every step*/
+ rvec* xMM; /* shifted to center of box */
+ int* indexMM; /* atom i = atom indexMM[I] in mdrun */
+ real* MMcharges; /* MM point charges in std QMMM calc.*/
+ int* shiftMM;
+ int* MMatomtype; /* only important for semi-emp. */
+ real scalefactor;
} t_MMrec;
-typedef struct t_QMMMrec {
- int QMMMscheme; /* ONIOM (multi-layer) or normal */
- int nrQMlayers; /* number of QM layers (total layers +1 (MM)) */
- t_QMrec **qm; /* atoms and run params for each QM group */
- t_MMrec *mm; /* there can only be one MM subsystem ! */
+typedef struct t_QMMMrec
+{
+ int QMMMscheme; /* ONIOM (multi-layer) or normal */
+ int nrQMlayers; /* number of QM layers (total layers +1 (MM)) */
+ t_QMrec** qm; /* atoms and run params for each QM group */
+ t_MMrec* mm; /* there can only be one MM subsystem ! */
} t_QMMMrec;
-void atomic_number(int nr, char ***atomtype, int *nucnum);
+void atomic_number(int nr, char*** atomtype, int* nucnum);
-t_QMMMrec *mk_QMMMrec();
+t_QMMMrec* mk_QMMMrec();
/* allocates memory for QMMMrec */
-void init_QMMMrec(const t_commrec *cr,
- const gmx_mtop_t *mtop,
- const t_inputrec *ir,
- const t_forcerec *fr);
+void init_QMMMrec(const t_commrec* cr, const gmx_mtop_t* mtop, const t_inputrec* ir, const t_forcerec* fr);
/* init_QMMMrec initializes the QMMM record. From
* topology->atoms.atomname and topology->atoms.atomtype the atom
* resp. inputrec->QMmult the nelecs and multiplicity are determined
* and md->cQMMM gives numbers of the MM and QM atoms
*/
-void update_QMMMrec(const t_commrec *cr,
- const t_forcerec *fr,
- const rvec *x,
- const t_mdatoms *md,
- const matrix box);
+void update_QMMMrec(const t_commrec* cr, const t_forcerec* fr, const rvec* x, const t_mdatoms* md, const matrix box);
/* update_QMMMrec fills the MM stuff in QMMMrec. The MM atoms are
* taken froom the neighbourlists of the QM atoms. In a QMMM run this
* routine should be called at every step, since it updates the MM
* elements of the t_QMMMrec struct.
*/
-real calculate_QMMM(const t_commrec *cr,
- gmx::ForceWithShiftForces *forceWithShiftForces,
- const t_forcerec *fr);
+real calculate_QMMM(const t_commrec* cr, gmx::ForceWithShiftForces* forceWithShiftForces, const t_forcerec* fr);
/* QMMM computes the QM forces. This routine makes either function
* calls to gmx QM routines (derived from MOPAC7 (semi-emp.) and MPQC
* \param[in] ir Inputrec used in simulation.
* \returns Vector of atoms.
*/
-std::vector<int> qmmmAtomIndices(const t_inputrec &ir, const gmx_mtop_t &mtop);
+std::vector<int> qmmmAtomIndices(const t_inputrec& ir, const gmx_mtop_t& mtop);
/*! \brief
* Remove charges from QMMM atoms.
* \param[in] mtop Topology used for removing atoms.
* \param[in] qmmmAtoms ArrayRef to vector conatining qmmm atom indices.
*/
-void removeQmmmAtomCharges(gmx_mtop_t *mtop, gmx::ArrayRef<const int> qmmmAtoms);
+void removeQmmmAtomCharges(gmx_mtop_t* mtop, gmx::ArrayRef<const int> qmmmAtoms);
#endif
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