include/pbc.h

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  35
  36 #ifndef _pbc_h
  37 #define _pbc_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include "sysstuff.h"
  44 #include "typedefs.h"
  45
  46 #ifdef __cplusplus
  47 extern "C" {
  48 #endif
  49
  50 #define TRICLINIC(box) (box[YY][XX]!=0 || box[ZZ][XX]!=0 || box[ZZ][YY]!=0)
  51
  52 #define NTRICIMG 14
  53 #define NCUCVERT 24
  54 #define NCUCEDGE 36
  55
  56   enum {
  57     ecenterTRIC, /* 0.5*(a+b+c)                  */
  58     ecenterRECT, /* (0.5*a[x],0.5*b[y],0.5*c[z]) */
  59     ecenterZERO, /* (0,0,0)                      */
  60     ecenterDEF = ecenterTRIC
  61   };
  62
  63   extern int ePBC2npbcdim(int ePBC);
  64   /* Returns the number of dimensions that use pbc, starting at X */
  65
  66   extern int inputrec2nboundeddim(t_inputrec *ir);
  67   /* Returns the number of dimensions in which
  68    * the coordinates of the particles are bounded, starting at X.
  69    */
  70
  71   extern void dump_pbc(FILE *fp,t_pbc *pbc);
  72   /* Dump the contents of the pbc structure to the file */
  73
  74   extern const char *check_box(int ePBC,matrix box);
  75   /* Returns NULL if the box is supported by Gromacs.
  76    * Otherwise is returns a string with the problem.
  77    * When ePBC=-1, the type of pbc is guessed from the box matrix.
  78    */
  79
  80   extern real max_cutoff2(int ePBC,matrix box);
  81   /* Returns the square of the maximum cut-off allowed for the box,
  82    * taking into account that the grid neighborsearch code and pbc_dx
  83    * only check combinations of single box-vector shifts.
  84    */
  85
  86   int guess_ePBC(matrix box);
  87   /* Guesses the type of periodic boundary conditions using the box */
  88
  89   extern bool correct_box(FILE *fplog,int step,tensor box,t_graph *graph);
  90   /* Checks for un-allowed box angles and corrects the box
  91    * and the integer shift vectors in the graph (if graph!=NULL) if necessary.
  92    * Returns TRUE when the box was corrected.
  93    */
  94
  95   extern int ndof_com(t_inputrec *ir);
  96   /* Returns the number of degrees of freedom of the center of mass */
  97
  98   extern void set_pbc(t_pbc *pbc,int ePBC,matrix box);
  99   /* Initiate the periodic boundary conditions.
 100    * pbc_dx will not use pbc and return the normal difference vector
 101    * when one or more of the diagonal elements of box are zero.
 102    * When ePBC=-1, the type of pbc is guessed from the box matrix.
 103    */
 104
 105   extern t_pbc *set_pbc_dd(t_pbc *pbc,int ePBC,
 106                            gmx_domdec_t *dd,bool bSingleDir,matrix box);
 107   /* As set_pbc, but additionally sets that correct distances can
 108    * be obtained using (combinations of) single box-vector shifts.
 109    * Should be used with pbc_dx_aiuc.
 110    * If dd!=NULL pbc is not used for directions
 111    * with dd->nc[i]==1 with bSingleDir==TRUE or
 112    * with dd->nc[i]<=2 with bSingleDir==FALSE.
 113    * Returns pbc when pbc operations are required, NULL otherwise.
 114    */
 115
 116   extern void pbc_dx(const t_pbc *pbc,const rvec x1, const rvec x2, rvec dx);
 117   /* Calculate the correct distance vector from x2 to x1 and put it in dx.
 118    * set_pbc must be called before ever calling this routine.
 119    *
 120    * For triclinic boxes pbc_dx does not necessarily return the shortest
 121    * distance vector. If pbc->bLimitDistance=TRUE an atom pair with
 122    * distance vector dx with norm2(dx) > pbc->limit_distance2 could
 123    * have a shorter distance, but not shorter than sqrt(pbc->limit_distance2).
 124    * pbc->limit_distance2 is always larger than max_cutoff2(box).
 125    * For the standard rhombic dodecahedron and truncated octahedron
 126    * pbc->bLimitDistance=FALSE and thus all distances are correct.
 127    */
 128
 129   extern int pbc_dx_aiuc(const t_pbc *pbc,const rvec x1,const rvec x2,rvec dx);
 130   /* Calculate the correct distance vector from x2 to x1 and put it in dx,
 131    * This function can only be used when all atoms are in the rectangular
 132    * or triclinic unit-cell.
 133    * Returns the ishift required to shift x1 at closest distance to x2;
 134    * i.e. if 0<=ishift<SHIFTS then x1 - x2 + shift_vec[ishift] = dx
 135    * (see calc_shifts below on how to obtain shift_vec)
 136    * set_pbc_dd or set_pbc must be called before ever calling this routine.
 137    */
 138   extern void pbc_dx_d(const t_pbc *pbc,const dvec x1, const dvec x2, dvec dx);
 139   /* As pbc_dx, but for double precision vectors.
 140    * set_pbc must be called before ever calling this routine.
 141    */
 142
 143   extern bool image_rect(ivec xi,ivec xj,ivec box_size,
 144                          real rlong2,int *shift,real *r2);
 145   /* Calculate the distance between xi and xj for a rectangular box.
 146    * When the distance is SMALLER than rlong2 return TRUE, return
 147    * the shift code in shift and the distance in r2. When the distance is
 148    * >= rlong2 return FALSE;
 149    * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
 150    */
 151
 152   extern bool image_tri(ivec xi,ivec xj,imatrix box,
 153                         real rlong2,int *shift,real *r2);
 154   /* Calculate the distance between xi and xj for a triclinic box.
 155    * When the distance is SMALLER than rlong2 return TRUE, return
 156    * the shift code in shift and the distance in r2. When the distance is
 157    * >= rlong2 return FALSE;
 158    * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
 159    */
 160
 161   extern bool image_cylindric(ivec xi,ivec xj,ivec box_size,real rlong2,
 162                               int *shift,real *r2);
 163   /* Calculate the distance between xi and xj for a rectangular box
 164    * using a cylindric cutoff for long-range only.
 165    * When the distance is SMALLER than rlong2 (in X and Y dir.)
 166    * return TRUE, return
 167    * the shift code in shift and the distance in r2. When the distance is
 168    * >= rlong2 return FALSE;
 169    * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
 170    */
 171
 172   extern void calc_shifts(matrix box,rvec shift_vec[]);
 173   /* This routine calculates ths shift vectors necessary to use the
 174    * ns routine.
 175    */
 176
 177   extern void calc_cgcm(FILE *log,int cg0,int cg1,t_block *cgs,
 178                         rvec pos[],rvec cg_cm[]);
 179   /* Routine to compute centers of geometry of charge groups. No periodicity
 180    * is used.
 181    */
 182
 183   extern void put_charge_groups_in_box (FILE *log,int cg0,int cg1,
 184                                         int ePBC,matrix box,t_block *cgs,
 185                                         rvec pos[],
 186                                         rvec cg_cm[]);
 187
 188   /* This routine puts charge groups in the periodic box, keeping them
 189    * together.
 190    */
 191
 192   extern void calc_box_center(int ecenter,matrix box,rvec box_center);
 193   /* Calculates the center of the box.
 194    * See the description for the enum ecenter above.
 195    */
 196
 197   extern void calc_triclinic_images(matrix box,rvec img[]);
 198   /* Calculates the NTRICIMG box images */
 199
 200   extern void calc_compact_unitcell_vertices(int ecenter,matrix box,
 201                                              rvec vert[]);
 202   /* Calculates the NCUCVERT vertices of a compact unitcell */
 203
 204   extern int *compact_unitcell_edges(void);
 205   /* Return an array of unitcell edges of length NCUCEDGE*2,
 206    * this is an index in vert[], which is calculated by calc_unitcell_vertices.
 207    * The index consists of NCUCEDGE pairs of vertex indices.
 208    * The index does not change, so it needs to be retrieved only once.
 209    */
 210   extern void put_atom_in_box(matrix box,rvec x);
 211
 212   extern void put_atoms_in_box(matrix box,int natoms,rvec x[]);
 213   /* These routines puts ONE or ALL atoms in the box, not caring
 214    * about charge groups!
 215    * Also works for triclinic cells.
 216    */
 217
 218   extern void put_atoms_in_triclinic_unitcell(int ecenter,matrix box,
 219                                               int natoms,rvec x[]);
 220   /* This puts ALL atoms in the triclinic unit cell, centered around the
 221    * box center as calculated by calc_box_center.
 222    */
 223
 224   extern const char *put_atoms_in_compact_unitcell(int ePBC,int ecenter,
 225                                                    matrix box,
 226                                                    int natoms,rvec x[]);
 227   /* This puts ALL atoms at the closest distance for the center of the box
 228    * as calculated by calc_box_center.
 229    * Will return NULL is everything went ok and a warning string if not
 230    * all atoms could be placed in the unitcell. This can happen for some
 231    * triclinic unitcells, see the comment at pbc_dx above.
 232    * When ePBC=-1, the type of pbc is guessed from the box matrix.
 233    */
 234
 235 #ifdef __cplusplus
 236 }
 237 #endif
 238
 239 #endif  /* _pbc_h */