include/pbc.h

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  38
  39 #ifndef _types_pbc_h
  40 #define _types_pbc_h
  41 #include "visibility.h"
  42 #include "sysstuff.h"
  43 #include "typedefs.h"
  44 #include "types/commrec.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 GMX_LIBGMX_EXPORT
  64 int ePBC2npbcdim(int ePBC);
  65 /* Returns the number of dimensions that use pbc, starting at X */
  66
  67 GMX_LIBGMX_EXPORT
  68 int inputrec2nboundeddim(t_inputrec *ir);
  69 /* Returns the number of dimensions in which
  70  * the coordinates of the particles are bounded, starting at X.
  71  */
  72
  73 void dump_pbc(FILE *fp, t_pbc *pbc);
  74 /* Dump the contents of the pbc structure to the file */
  75
  76 GMX_LIBGMX_EXPORT
  77 const char *check_box(int ePBC, matrix box);
  78 /* Returns NULL if the box is supported by Gromacs.
  79  * Otherwise is returns a string with the problem.
  80  * When ePBC=-1, the type of pbc is guessed from the box matrix.
  81  */
  82
  83 GMX_LIBGMX_EXPORT
  84 real max_cutoff2(int ePBC, matrix box);
  85 /* Returns the square of the maximum cut-off allowed for the box,
  86  * taking into account that the grid neighborsearch code and pbc_dx
  87  * only check combinations of single box-vector shifts.
  88  */
  89
  90 GMX_LIBGMX_EXPORT
  91 int guess_ePBC(matrix box);
  92 /* Guesses the type of periodic boundary conditions using the box */
  93
  94 GMX_LIBGMX_EXPORT
  95 gmx_bool correct_box(FILE *fplog, int step, tensor box, t_graph *graph);
  96 /* Checks for un-allowed box angles and corrects the box
  97  * and the integer shift vectors in the graph (if graph!=NULL) if necessary.
  98  * Returns TRUE when the box was corrected.
  99  */
 100
 101 GMX_LIBGMX_EXPORT
 102 int ndof_com(t_inputrec *ir);
 103 /* Returns the number of degrees of freedom of the center of mass */
 104
 105 GMX_LIBGMX_EXPORT
 106 void set_pbc(t_pbc *pbc, int ePBC, matrix box);
 107 /* Initiate the periodic boundary conditions.
 108  * pbc_dx will not use pbc and return the normal difference vector
 109  * when one or more of the diagonal elements of box are zero.
 110  * When ePBC=-1, the type of pbc is guessed from the box matrix.
 111  */
 112
 113 GMX_LIBGMX_EXPORT
 114 t_pbc *set_pbc_dd(t_pbc *pbc, int ePBC,
 115                   gmx_domdec_t *dd, gmx_bool bSingleDir, matrix box);
 116 /* As set_pbc, but additionally sets that correct distances can
 117  * be obtained using (combinations of) single box-vector shifts.
 118  * Should be used with pbc_dx_aiuc.
 119  * If dd!=NULL pbc is not used for directions
 120  * with dd->nc[i]==1 with bSingleDir==TRUE or
 121  * with dd->nc[i]<=2 with bSingleDir==FALSE.
 122  * Returns pbc when pbc operations are required, NULL otherwise.
 123  */
 124
 125 GMX_LIBGMX_EXPORT
 126 void pbc_dx(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  * set_pbc must be called before ever calling this routine.
 129  *
 130  * For triclinic boxes pbc_dx does not necessarily return the shortest
 131  * distance vector. If pbc->bLimitDistance=TRUE an atom pair with
 132  * distance vector dx with norm2(dx) > pbc->limit_distance2 could
 133  * have a shorter distance, but not shorter than sqrt(pbc->limit_distance2).
 134  * pbc->limit_distance2 is always larger than max_cutoff2(box).
 135  * For the standard rhombic dodecahedron and truncated octahedron
 136  * pbc->bLimitDistance=FALSE and thus all distances are correct.
 137  */
 138
 139 GMX_LIBGMX_EXPORT
 140 int pbc_dx_aiuc(const t_pbc *pbc, const rvec x1, const rvec x2, rvec dx);
 141 /* Calculate the correct distance vector from x2 to x1 and put it in dx,
 142  * This function can only be used when all atoms are in the rectangular
 143  * or triclinic unit-cell.
 144  * Returns the ishift required to shift x1 at closest distance to x2;
 145  * i.e. if 0<=ishift<SHIFTS then x1 - x2 + shift_vec[ishift] = dx
 146  * (see calc_shifts below on how to obtain shift_vec)
 147  * set_pbc_dd or set_pbc must be called before ever calling this routine.
 148  */
 149 GMX_LIBGMX_EXPORT
 150 void pbc_dx_d(const t_pbc *pbc, const dvec x1, const dvec x2, dvec dx);
 151 /* As pbc_dx, but for double precision vectors.
 152  * set_pbc must be called before ever calling this routine.
 153  */
 154
 155 gmx_bool image_rect(ivec xi, ivec xj, ivec box_size,
 156                     real rlong2, int *shift, real *r2);
 157 /* Calculate the distance between xi and xj for a rectangular box.
 158  * When the distance is SMALLER than rlong2 return TRUE, return
 159  * the shift code in shift and the distance in r2. When the distance is
 160  * >= rlong2 return FALSE;
 161  * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
 162  */
 163
 164 gmx_bool image_tri(ivec xi, ivec xj, imatrix box,
 165                    real rlong2, int *shift, real *r2);
 166 /* Calculate the distance between xi and xj for a triclinic box.
 167  * When the distance is SMALLER than rlong2 return TRUE, return
 168  * the shift code in shift and the distance in r2. When the distance is
 169  * >= rlong2 return FALSE;
 170  * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
 171  */
 172
 173 gmx_bool image_cylindric(ivec xi, ivec xj, ivec box_size, real rlong2,
 174                          int *shift, real *r2);
 175 /* Calculate the distance between xi and xj for a rectangular box
 176  * using a cylindric cutoff for long-range only.
 177  * When the distance is SMALLER than rlong2 (in X and Y dir.)
 178  * return TRUE, return
 179  * the shift code in shift and the distance in r2. When the distance is
 180  * >= rlong2 return FALSE;
 181  * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
 182  */
 183
 184 GMX_LIBGMX_EXPORT
 185 void calc_shifts(matrix box, rvec shift_vec[]);
 186 /* This routine calculates ths shift vectors necessary to use the
 187  * ns routine.
 188  */
 189
 190 GMX_LIBGMX_EXPORT
 191 void calc_box_center(int ecenter, matrix box, rvec box_center);
 192 /* Calculates the center of the box.
 193  * See the description for the enum ecenter above.
 194  */
 195
 196 GMX_LIBGMX_EXPORT
 197 void calc_triclinic_images(matrix box, rvec img[]);
 198 /* Calculates the NTRICIMG box images */
 199
 200 GMX_LIBGMX_EXPORT
 201 void calc_compact_unitcell_vertices(int ecenter, matrix box,
 202                                     rvec vert[]);
 203 /* Calculates the NCUCVERT vertices of a compact unitcell */
 204
 205 GMX_LIBGMX_EXPORT
 206 int *compact_unitcell_edges(void);
 207 /* Return an array of unitcell edges of length NCUCEDGE*2,
 208  * this is an index in vert[], which is calculated by calc_unitcell_vertices.
 209  * The index consists of NCUCEDGE pairs of vertex indices.
 210  * The index does not change, so it needs to be retrieved only once.
 211  */
 212
 213 GMX_LIBGMX_EXPORT
 214 void put_atoms_in_box_omp(int ePBC, matrix box, int natoms, rvec x[]);
 215 /* This wrapper function around put_atoms_in_box() with the ugly manual
 216  * workload splitting is needed toavoid silently introducing multithreading
 217  * in tools.
 218  * */
 219
 220
 221 GMX_LIBGMX_EXPORT
 222 void put_atoms_in_box(int ePBC, matrix box, int natoms, rvec x[]);
 223 /* These routines puts ONE or ALL atoms in the box, not caring
 224  * about charge groups!
 225  * Also works for triclinic cells.
 226  */
 227
 228 GMX_LIBGMX_EXPORT
 229 void put_atoms_in_triclinic_unitcell(int ecenter, matrix box,
 230                                      int natoms, rvec x[]);
 231 /* This puts ALL atoms in the triclinic unit cell, centered around the
 232  * box center as calculated by calc_box_center.
 233  */
 234
 235 GMX_LIBGMX_EXPORT
 236 const char *put_atoms_in_compact_unitcell(int ePBC, int ecenter,
 237                                           matrix box,
 238                                           int natoms, rvec x[]);
 239 /* This puts ALL atoms at the closest distance for the center of the box
 240  * as calculated by calc_box_center.
 241  * Will return NULL is everything went ok and a warning string if not
 242  * all atoms could be placed in the unitcell. This can happen for some
 243  * triclinic unitcells, see the comment at pbc_dx above.
 244  * When ePBC=-1, the type of pbc is guessed from the box matrix.
 245  */
 246
 247 #ifdef __cplusplus
 248 }
 249 #endif
 250
 251 #endif  /* _pbc_h */