include/pbc.h

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