src/gromacs/mdlib/qmmm.h

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  37 #ifndef GMX_MDLIB_QMMM_H
  38 #define GMX_MDLIB_QMMM_H
  39
  40 #include "gromacs/math/vectypes.h"
  41 #include "gromacs/mdlib/tgroup.h"
  42
  43 struct gmx_localtop_t;
  44 struct gmx_mtop_t;
  45 struct t_commrec;
  46 struct t_forcerec;
  47 struct t_inputrec;
  48 struct t_mdatoms;
  49 struct t_QMMMrec;
  50
  51 typedef struct {
  52     int                nrQMatoms;      /* total nr of QM atoms              */
  53     rvec              *xQM;            /* shifted to center of box          */
  54     int               *indexQM;        /* atom i = atom indexQM[i] in mdrun */
  55     int               *atomicnumberQM; /* atomic numbers of QM atoms        */
  56     real              *QMcharges;      /* atomic charges of QM atoms(ONIOM) */
  57     int               *shiftQM;
  58     int                QMcharge;       /* charge of the QM system           */
  59     int                multiplicity;   /* multipicity (no of unpaired eln)  */
  60     int                QMmethod;       /* see enums.h for all methods       */
  61     int                QMbasis;        /* see enums.h for all bases         */
  62     int                nelectrons;     /* total number of elecs in QM region*/
  63     gmx_bool           bTS;            /* Optimize a TS, only steep, no md  */
  64     gmx_bool           bOPT;           /* Optimize QM subsys, only steep, no md  */
  65     gmx_bool          *frontatoms;     /* qm atoms on the QM side of a QM-MM bond */
  66     /* Gaussian specific stuff */
  67     int                nQMcpus;        /* no. of CPUs used for the QM calc. */
  68     int                QMmem;          /* memory for the gaussian calc.     */
  69     int                accuracy;       /* convergence criterium (E(-x))     */
  70     gmx_bool           cpmcscf;        /* using cpmcscf(l1003)*/
  71     char              *gauss_dir;
  72     char              *gauss_exe;
  73     char              *devel_dir;
  74     char              *orca_basename; /* basename for I/O with orca        */
  75     char              *orca_dir;      /* directory for ORCA                */
  76     real              *c6;
  77     real              *c12;
  78     /* Surface hopping stuff */
  79     gmx_bool           bSH;     /* surface hopping (diabatic only)   */
  80     real               SAon;    /* at which energy gap the SA starts */
  81     real               SAoff;   /* at which energy gap the SA stops  */
  82     int                SAsteps; /* stepwise switchinng on the SA     */
  83     int                SAstep;  /* current state of SA               */
  84     int                CIdim;
  85     real              *CIvec1;
  86     real              *CIvec2;
  87     real              *CIvec1old;
  88     real              *CIvec2old;
  89     ivec               SHbasis;
  90     int                CASelectrons;
  91     int                CASorbitals;
  92 } t_QMrec;
  93
  94 typedef struct {
  95     int            nrMMatoms;   /* nr of MM atoms, updated every step*/
  96     rvec          *xMM;         /* shifted to center of box          */
  97     int           *indexMM;     /* atom i = atom indexMM[I] in mdrun */
  98     real          *MMcharges;   /* MM point charges in std QMMM calc.*/
  99     int           *shiftMM;
 100     int           *MMatomtype;  /* only important for semi-emp.      */
 101     real           scalefactor;
 102     /* gaussian specific stuff */
 103     real          *c6;
 104     real          *c12;
 105 } t_MMrec;
 106
 107
 108 typedef struct t_QMMMrec {
 109     int             QMMMscheme; /* ONIOM (multi-layer) or normal          */
 110     int             nrQMlayers; /* number of QM layers (total layers +1 (MM)) */
 111     t_QMrec       **qm;         /* atoms and run params for each QM group */
 112     t_MMrec        *mm;         /* there can only be one MM subsystem !   */
 113 } t_QMMMrec;
 114
 115 void atomic_number(int nr, char ***atomtype, int *nucnum);
 116
 117 t_QMMMrec *mk_QMMMrec(void);
 118 /* allocates memory for QMMMrec */
 119
 120 void init_QMMMrec(t_commrec  *cr,
 121                   gmx_mtop_t *mtop,
 122                   t_inputrec *ir,
 123                   t_forcerec *fr);
 124
 125 /* init_QMMMrec initializes the QMMM record. From
 126  * topology->atoms.atomname and topology->atoms.atomtype the atom
 127  * names and types are read; from inputrec->QMcharge
 128  * resp. inputrec->QMmult the nelecs and multiplicity are determined
 129  * and md->cQMMM gives numbers of the MM and QM atoms
 130  */
 131
 132 void update_QMMMrec(t_commrec      *cr,
 133                     t_forcerec     *fr,
 134                     rvec            x[],
 135                     t_mdatoms      *md,
 136                     matrix          box,
 137                     gmx_localtop_t *top);
 138
 139 /* update_QMMMrec fills the MM stuff in QMMMrec. The MM atoms are
 140  * taken froom the neighbourlists of the QM atoms. In a QMMM run this
 141  * routine should be called at every step, since it updates the MM
 142  * elements of the t_QMMMrec struct.
 143  */
 144
 145 real calculate_QMMM(t_commrec *cr,
 146                     rvec x[], rvec f[],
 147                     t_forcerec *fr);
 148
 149 /* QMMM computes the QM forces. This routine makes either function
 150  * calls to gmx QM routines (derived from MOPAC7 (semi-emp.) and MPQC
 151  * (ab initio)) or generates input files for an external QM package
 152  * (listed in QMMMrec.QMpackage). The binary of the QM package is
 153  * called by system().
 154  */
 155
 156 #endif