include/pbc.h

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  35
  36 #ifndef _types_pbc_h
  37 #define _types_pbc_h
  38
  39 #include "sysstuff.h"
  40 #include "typedefs.h"
  41 #include "types/commrec.h"
  42
  43 #ifdef __cplusplus
  44 extern "C" {
  45 #endif
  46
  47 #define TRICLINIC(box) (box[YY][XX]!=0 || box[ZZ][XX]!=0 || box[ZZ][YY]!=0)
  48
  49 #define NTRICIMG 14
  50 #define NCUCVERT 24
  51 #define NCUCEDGE 36
  52
  53   enum {
  54     ecenterTRIC, /* 0.5*(a+b+c)                  */
  55     ecenterRECT, /* (0.5*a[x],0.5*b[y],0.5*c[z]) */
  56     ecenterZERO, /* (0,0,0)                      */
  57     ecenterDEF = ecenterTRIC
  58   };
  59
  60   int ePBC2npbcdim(int ePBC);
  61   /* Returns the number of dimensions that use pbc, starting at X */
  62
  63   int inputrec2nboundeddim(t_inputrec *ir);
  64   /* Returns the number of dimensions in which
  65    * the coordinates of the particles are bounded, starting at X.
  66    */
  67
  68   void dump_pbc(FILE *fp,t_pbc *pbc);
  69   /* Dump the contents of the pbc structure to the file */
  70
  71   const char *check_box(int ePBC,matrix box);
  72   /* Returns NULL if the box is supported by Gromacs.
  73    * Otherwise is returns a string with the problem.
  74    * When ePBC=-1, the type of pbc is guessed from the box matrix.
  75    */
  76
  77   real max_cutoff2(int ePBC,matrix box);
  78   /* Returns the square of the maximum cut-off allowed for the box,
  79    * taking into account that the grid neighborsearch code and pbc_dx
  80    * only check combinations of single box-vector shifts.
  81    */
  82
  83   int guess_ePBC(matrix box);
  84   /* Guesses the type of periodic boundary conditions using the box */
  85
  86   gmx_bool correct_box(FILE *fplog,int step,tensor box,t_graph *graph);
  87   /* Checks for un-allowed box angles and corrects the box
  88    * and the integer shift vectors in the graph (if graph!=NULL) if necessary.
  89    * Returns TRUE when the box was corrected.
  90    */
  91
  92   int ndof_com(t_inputrec *ir);
  93   /* Returns the number of degrees of freedom of the center of mass */
  94
  95   void set_pbc(t_pbc *pbc,int ePBC,matrix box);
  96   /* Initiate the periodic boundary conditions.
  97    * pbc_dx will not use pbc and return the normal difference vector
  98    * when one or more of the diagonal elements of box are zero.
  99    * When ePBC=-1, the type of pbc is guessed from the box matrix.
 100    */
 101
 102   t_pbc *set_pbc_dd(t_pbc *pbc,int ePBC,
 103                            gmx_domdec_t *dd,gmx_bool bSingleDir,matrix box);
 104   /* As set_pbc, but additionally sets that correct distances can
 105    * be obtained using (combinations of) single box-vector shifts.
 106    * Should be used with pbc_dx_aiuc.
 107    * If dd!=NULL pbc is not used for directions
 108    * with dd->nc[i]==1 with bSingleDir==TRUE or
 109    * with dd->nc[i]<=2 with bSingleDir==FALSE.
 110    * Returns pbc when pbc operations are required, NULL otherwise.
 111    */
 112
 113   void pbc_dx(const t_pbc *pbc,const rvec x1, const rvec x2, rvec dx);
 114   /* Calculate the correct distance vector from x2 to x1 and put it in dx.
 115    * set_pbc must be called before ever calling this routine.
 116    *
 117    * For triclinic boxes pbc_dx does not necessarily return the shortest
 118    * distance vector. If pbc->bLimitDistance=TRUE an atom pair with
 119    * distance vector dx with norm2(dx) > pbc->limit_distance2 could
 120    * have a shorter distance, but not shorter than sqrt(pbc->limit_distance2).
 121    * pbc->limit_distance2 is always larger than max_cutoff2(box).
 122    * For the standard rhombic dodecahedron and truncated octahedron
 123    * pbc->bLimitDistance=FALSE and thus all distances are correct.
 124    */
 125
 126   int pbc_dx_aiuc(const t_pbc *pbc,const rvec x1,const rvec x2,rvec dx);
 127   /* Calculate the correct distance vector from x2 to x1 and put it in dx,
 128    * This function can only be used when all atoms are in the rectangular
 129    * or triclinic unit-cell.
 130    * Returns the ishift required to shift x1 at closest distance to x2;
 131    * i.e. if 0<=ishift<SHIFTS then x1 - x2 + shift_vec[ishift] = dx
 132    * (see calc_shifts below on how to obtain shift_vec)
 133    * set_pbc_dd or set_pbc must be called before ever calling this routine.
 134    */
 135   void pbc_dx_d(const t_pbc *pbc,const dvec x1, const dvec x2, dvec dx);
 136   /* As pbc_dx, but for double precision vectors.
 137    * set_pbc must be called before ever calling this routine.
 138    */
 139
 140   gmx_bool image_rect(ivec xi,ivec xj,ivec box_size,
 141                          real rlong2,int *shift,real *r2);
 142   /* Calculate the distance between xi and xj for a rectangular box.
 143    * When the distance is SMALLER than rlong2 return TRUE, return
 144    * the shift code in shift and the distance in r2. When the distance is
 145    * >= rlong2 return FALSE;
 146    * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
 147    */
 148
 149   gmx_bool image_tri(ivec xi,ivec xj,imatrix box,
 150                         real rlong2,int *shift,real *r2);
 151   /* Calculate the distance between xi and xj for a triclinic box.
 152    * When the distance is SMALLER than rlong2 return TRUE, return
 153    * the shift code in shift and the distance in r2. When the distance is
 154    * >= rlong2 return FALSE;
 155    * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
 156    */
 157
 158   gmx_bool image_cylindric(ivec xi,ivec xj,ivec box_size,real rlong2,
 159                               int *shift,real *r2);
 160   /* Calculate the distance between xi and xj for a rectangular box
 161    * using a cylindric cutoff for long-range only.
 162    * When the distance is SMALLER than rlong2 (in X and Y dir.)
 163    * return TRUE, return
 164    * the shift code in shift and the distance in r2. When the distance is
 165    * >= rlong2 return FALSE;
 166    * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
 167    */
 168
 169   void calc_shifts(matrix box,rvec shift_vec[]);
 170   /* This routine calculates ths shift vectors necessary to use the
 171    * ns routine.
 172    */
 173
 174   void calc_box_center(int ecenter,matrix box,rvec box_center);
 175   /* Calculates the center of the box.
 176    * See the description for the enum ecenter above.
 177    */
 178
 179   void calc_triclinic_images(matrix box,rvec img[]);
 180   /* Calculates the NTRICIMG box images */
 181
 182   void calc_compact_unitcell_vertices(int ecenter,matrix box,
 183                                              rvec vert[]);
 184   /* Calculates the NCUCVERT vertices of a compact unitcell */
 185
 186   int *compact_unitcell_edges(void);
 187   /* Return an array of unitcell edges of length NCUCEDGE*2,
 188    * this is an index in vert[], which is calculated by calc_unitcell_vertices.
 189    * The index consists of NCUCEDGE pairs of vertex indices.
 190    * The index does not change, so it needs to be retrieved only once.
 191    */
 192
 193   void put_atoms_in_box_omp(int ePBC,matrix box,int natoms,rvec x[]);
 194   /* This wrapper function around put_atoms_in_box() with the ugly manual
 195    * workload splitting is needed toavoid silently introducing multithreading
 196    * in tools.
 197    * */
 198
 199
 200   void put_atoms_in_box(int ePBC, matrix box,int natoms,rvec x[]);
 201   /* These routines puts ONE or ALL atoms in the box, not caring
 202    * about charge groups!
 203    * Also works for triclinic cells.
 204    */
 205
 206   void put_atoms_in_triclinic_unitcell(int ecenter,matrix box,
 207                                               int natoms,rvec x[]);
 208   /* This puts ALL atoms in the triclinic unit cell, centered around the
 209    * box center as calculated by calc_box_center.
 210    */
 211
 212   const char *put_atoms_in_compact_unitcell(int ePBC,int ecenter,
 213                                                    matrix box,
 214                                                    int natoms,rvec x[]);
 215   /* This puts ALL atoms at the closest distance for the center of the box
 216    * as calculated by calc_box_center.
 217    * Will return NULL is everything went ok and a warning string if not
 218    * all atoms could be placed in the unitcell. This can happen for some
 219    * triclinic unitcells, see the comment at pbc_dx above.
 220    * When ePBC=-1, the type of pbc is guessed from the box matrix.
 221    */
 222
 223 #ifdef __cplusplus
 224 }
 225 #endif
 226
 227 #endif  /* _pbc_h */