src/gromacs/pbcutil/pbc.h

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  37 #ifndef GMX_PBCUTIL_PBC_H
  38 #define GMX_PBCUTIL_PBC_H
  39
  40 #include <stdio.h>
  41
  42 #include "gromacs/math/vectypes.h"
  43 #include "gromacs/utility/arrayref.h"
  44 #include "gromacs/utility/basedefinitions.h"
  45 #include "gromacs/utility/real.h"
  46
  47 struct gmx_domdec_t;
  48 struct gmx_mtop_t;
  49
  50 enum {
  51     epbcXYZ, epbcNONE, epbcXY, epbcSCREW, epbcNR
  52 };
  53
  54 //! Strings corresponding to epbc enum values.
  55 extern const char *epbc_names[epbcNR+1];
  56
  57 /* Maximum number of combinations of single triclinic box vectors
  58  * required to shift atoms that are within a brick of the size of
  59  * the diagonal of the box to within the maximum cut-off distance.
  60  */
  61 #define MAX_NTRICVEC 12
  62
  63 /*! \brief Structure containing info on periodic boundary conditions */
  64 typedef struct t_pbc {
  65     //! The PBC type
  66     int        ePBC;
  67     //! Number of dimensions in which PBC is exerted
  68     int        ndim_ePBC;
  69     /*! \brief Determines how to compute distance vectors.
  70      *
  71      *  Indicator of how to compute distance vectors, depending
  72      *  on PBC type (depends on ePBC and dimensions with(out) DD)
  73      *  and the box angles.
  74      */
  75     int        ePBCDX;
  76     /*! \brief Used for selecting which dimensions to use in PBC.
  77      *
  78      *  In case of 1-D PBC this indicates which dimension is used,
  79      *  in case of 2-D PBC this indicates the opposite
  80      */
  81     int        dim;
  82     //! The simulation box
  83     matrix     box;
  84     //! The lengths of the diagonal of the full box
  85     rvec       fbox_diag;
  86     //! Halve of the above
  87     rvec       hbox_diag;
  88     //! Negative of the above
  89     rvec       mhbox_diag;
  90     //! Maximum allowed cutoff squared for the box and PBC used
  91     real       max_cutoff2;
  92     /*! \brief Number of triclinic shift vectors.
  93      *
  94      *  Number of triclinic shift vectors depends on the skewedness
  95      *  of the box, that is mostly on the angles. For triclinic boxes
  96      *  we first take the closest image along each Cartesian dimension
  97      *  independently. When the resulting distance^2 is larger than
  98      *  max_cutoff2, up to ntric_vec triclinic shift vectors need to
  99      *  be tried. Because of the restrictions imposed on the unit-cell
 100      *  by GROMACS, ntric_vec <= MAX_NTRICVEC = 12.
 101      */
 102     int        ntric_vec;
 103     //! The triclinic shift vectors in grid cells. Internal use only.
 104     ivec       tric_shift[MAX_NTRICVEC];
 105     //!  The triclinic shift vectors in length units
 106     rvec       tric_vec[MAX_NTRICVEC];
 107 } t_pbc;
 108
 109 #define TRICLINIC(box) ((box)[YY][XX] != 0 || (box)[ZZ][XX] != 0 || (box)[ZZ][YY] != 0)
 110
 111 #define NTRICIMG 14
 112 #define NCUCVERT 24
 113 #define NCUCEDGE 36
 114
 115 enum {
 116     ecenterTRIC, /* 0.5*(a+b+c)                  */
 117     ecenterRECT, /* (0.5*a[x],0.5*b[y],0.5*c[z]) */
 118     ecenterZERO, /* (0,0,0)                      */
 119     ecenterDEF = ecenterTRIC
 120 };
 121
 122 struct t_graph;
 123
 124 /*! \brief Returns the number of dimensions that use pbc
 125  *
 126  * \param[in] ePBC The periodic boundary condition type
 127  * \return the number of dimensions that use pbc, starting at X
 128  */
 129 int ePBC2npbcdim(int ePBC);
 130
 131 /*! \brief Dump the contents of the pbc structure to the file
 132  *
 133  * \param[in] fp  The file pointer to write to
 134  * \param[in] pbc The periodic boundary condition information structure
 135  */
 136 void dump_pbc(FILE *fp, t_pbc *pbc);
 137
 138 /*! \brief Check the box for consistency
 139  *
 140  * \param[in] ePBC The pbc identifier
 141  * \param[in] box  The box matrix
 142  * \return NULL if the box is supported by Gromacs.
 143  * Otherwise returns a string with the problem.
 144  * When ePBC=-1, the type of pbc is guessed from the box matrix.
 145  */
 146 const char *check_box(int ePBC, const matrix box);
 147
 148 /*! \brief Creates box matrix from edge lengths and angles.
 149  *
 150  * \param[in,out] box         The box matrix
 151  * \param[in] vec            The edge lengths
 152  * \param[in] angleInDegrees The angles
 153  */
 154 void matrix_convert(matrix box, const rvec vec, const rvec angleInDegrees);
 155
 156 /*! \brief Compute the maximum cutoff for the box
 157
 158  * Returns the square of the maximum cut-off allowed for the box,
 159  * taking into account that the grid neighborsearch code and pbc_dx
 160  * only check combinations of single box-vector shifts.
 161  * \param[in] ePBC The pbc identifier
 162  * \param[in] box  The box matrix
 163  * \return the maximum cut-off.
 164  */
 165 real max_cutoff2(int ePBC, const matrix box);
 166
 167 /*! \brief Guess PBC typr
 168  *
 169  * Guesses the type of periodic boundary conditions using the box
 170  * \param[in] box  The box matrix
 171  * \return The pbc identifier
 172  */
 173 int guess_ePBC(const matrix box);
 174
 175 /*! \brief Corrects the box if necessary
 176  *
 177  * Checks for un-allowed box angles and corrects the box
 178  * and the integer shift vectors in the graph (if graph!=NULL) if necessary.
 179  * \param[in] fplog File for debug output
 180  * \param[in] step  The MD step number
 181  * \param[in] box   The simulation cell
 182  * \param[in] graph Information about molecular connectivity
 183  * \return TRUE when the box was corrected.
 184  */
 185 gmx_bool correct_box(FILE *fplog, int step, tensor box, struct t_graph *graph);
 186
 187 /*! \brief Initiate the periodic boundary condition algorithms.
 188  *
 189  * pbc_dx will not use pbc and return the normal difference vector
 190  * when one or more of the diagonal elements of box are zero.
 191  * When ePBC=-1, the type of pbc is guessed from the box matrix.
 192  * \param[in,out] pbc The pbc information structure
 193  * \param[in] ePBC The PBC identifier
 194  * \param[in] box  The box tensor
 195  */
 196 void set_pbc(t_pbc *pbc, int ePBC, const matrix box);
 197
 198 /*! \brief Initiate the periodic boundary condition algorithms.
 199  *
 200  * As set_pbc, but additionally sets that correct distances can
 201  * be obtained using (combinations of) single box-vector shifts.
 202  * Should be used with pbc_dx_aiuc.
 203  * If domdecCells!=NULL pbc is not used for directions
 204  * with dd->nc[i]==1 with bSingleDir==TRUE or
 205  * with dd->nc[i]<=2 with bSingleDir==FALSE.
 206  * Note that when no PBC is required only pbc->ePBC is set,
 207  * the rest of the struct will be invalid.
 208  * \param[in,out] pbc The pbc information structure
 209  * \param[in] ePBC        The PBC identifier
 210  * \param[in] domdecCells 3D integer vector describing the number of DD cells
 211  *                        or nullptr if not using DD.
 212  * \param[in] bSingleDir  TRUE if DD communicates only in one direction along dimensions
 213  * \param[in] box         The box tensor
 214  * \return the pbc structure when pbc operations are required, NULL otherwise.
 215  */
 216 t_pbc *set_pbc_dd(t_pbc *pbc, int ePBC,
 217                   const ivec domdecCells, gmx_bool bSingleDir,
 218                   const matrix box);
 219
 220 /*! \brief Compute distance with PBC
 221  *
 222  * Calculate the correct distance vector from x2 to x1 and put it in dx.
 223  * set_pbc must be called before ever calling this routine.
 224  *
 225  * Note that for triclinic boxes that do not obey the GROMACS unit-cell
 226  * restrictions, pbc_dx and pbc_dx_aiuc will not correct for PBC.
 227  * \param[in,out] pbc The pbc information structure
 228  * \param[in]    x1  Coordinates for particle 1
 229  * \param[in]    x2  Coordinates for particle 2
 230  * \param[out]   dx  Distance vector
 231  */
 232 void pbc_dx(const t_pbc *pbc, const rvec x1, const rvec x2, rvec dx);
 233
 234 /*! \brief Compute distance vector for simple PBC types
 235  *
 236  * Calculate the correct distance vector from x2 to x1 and put it in dx,
 237  * This function can only be used when all atoms are in the rectangular
 238  * or triclinic unit-cell.
 239  * set_pbc_dd or set_pbc must be called before ever calling this routine.
 240  * \param[in,out] pbc The pbc information structure
 241  * \param[in]    x1  Coordinates for particle 1
 242  * \param[in]    x2  Coordinates for particle 2
 243  * \param[out]   dx  Distance vector
 244  * \return the ishift required to shift x1 at closest distance to x2;
 245  * i.e. if 0<=ishift<SHIFTS then x1 - x2 + shift_vec[ishift] = dx
 246  * (see calc_shifts below on how to obtain shift_vec)
 247  */
 248 int pbc_dx_aiuc(const t_pbc *pbc, const rvec x1, const rvec x2, rvec dx);
 249
 250 /*! \brief Compute distance with PBC
 251  *
 252  * As pbc_dx, but for double precision vectors.
 253  * set_pbc must be called before ever calling this routine.
 254  * \param[in,out] pbc The pbc information structure
 255  * \param[in]    x1  Coordinates for particle 1
 256  * \param[in]    x2  Coordinates for particle 2
 257  * \param[out]   dx  Distance vector
 258  */
 259 void pbc_dx_d(const t_pbc *pbc, const dvec x1, const dvec x2, dvec dx);
 260
 261 /*! \brief Computes shift vectors
 262  *
 263  * This routine calculates ths shift vectors necessary to use the
 264  * neighbor searching routine.
 265  * \param[in]  box       The simulation box
 266  * \param[out] shift_vec The shifting vectors
 267  */
 268 void calc_shifts(const matrix box, rvec shift_vec[]);
 269
 270 /*! \brief Calculates the center of the box.
 271  *
 272  * See the description for the enum ecenter above.
 273  * \param[in]  ecenter    Description of center type
 274  * \param[in]  box        The simulation box
 275  * \param[out] box_center The center of the box
 276  */
 277 void calc_box_center(int ecenter, const matrix box, rvec box_center);
 278
 279 /*! \brief Calculates the NTRICIMG box images
 280  *
 281  * \param[in]  box The simulation box
 282  * \param[out] img The triclinic box images
 283  */
 284 void calc_triclinic_images(const matrix box, rvec img[]);
 285
 286 /*! \brief Calculates the NCUCVERT vertices of a compact unitcell
 287  *
 288  * \param[in]  ecenter The center type
 289  * \param[in]  box     The simulation box
 290  * \param[out] vert    The vertices
 291  */
 292 void calc_compact_unitcell_vertices(int ecenter, const matrix box,
 293                                     rvec vert[]);
 294
 295 /*! \brief Compute unitcell edges
 296  *
 297  * \return an array of unitcell edges of length NCUCEDGE*2,
 298  * this is an index in vert[], which is calculated by calc_unitcell_vertices.
 299  * The index consists of NCUCEDGE pairs of vertex indices.
 300  * The index does not change, so it needs to be retrieved only once.
 301  */
 302 int *compact_unitcell_edges();
 303
 304 /*! \brief Put atoms inside the simulations box
 305  *
 306  * These routines puts ONE or ALL atoms in the box, not caring
 307  * about charge groups!
 308  * Also works for triclinic cells.
 309  * \param[in]     ePBC   The pbc type
 310  * \param[in]     box    The simulation box
 311  * \param[in,out] x      The coordinates of the atoms
 312  */
 313 void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x);
 314
 315 /*! \brief Parallellizes put_atoms_in_box()
 316  *
 317  * This wrapper function around put_atoms_in_box() with the ugly manual
 318  * workload splitting is needed to avoid silently introducing multithreading
 319  * in tools.
 320  * \param[in]     ePBC       The pbc type
 321  * \param[in]     box        The simulation box
 322  * \param[in,out] x          The coordinates of the atoms
 323  * \param[in]     nth        number of threads to be used in the given module
 324  */
 325 void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_unused int nth);
 326
 327 /*! \brief Put atoms inside triclinic box
 328  *
 329  * This puts ALL atoms in the triclinic unit cell, centered around the
 330  * box center as calculated by calc_box_center.
 331  * \param[in]    ecenter The pbc center type
 332  * \param[in]    box     The simulation box
 333  * \param[in,out] x       The coordinates of the atoms
 334  */
 335 void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box,
 336                                      gmx::ArrayRef<gmx::RVec> x);
 337
 338 /*! \brief Put atoms inside the unitcell
 339  *
 340  * This puts ALL atoms at the closest distance for the center of the box
 341  * as calculated by calc_box_center.
 342  * When ePBC=-1, the type of pbc is guessed from the box matrix.
 343  * \param[in]    ePBC    The pbc type
 344  * \param[in]    ecenter The pbc center type
 345  * \param[in]    box     The simulation box
 346  * \param[in,out] x       The coordinates of the atoms
 347  */
 348 void put_atoms_in_compact_unitcell(int ePBC, int ecenter,
 349                                    const matrix box,
 350                                    gmx::ArrayRef<gmx::RVec> x);
 351
 352 /*! \brief Make all molecules whole by shifting positions
 353  *
 354  * \param[in]     fplog     Log file
 355  * \param[in]     ePBC      The PBC type
 356  * \param[in]     box       The simulation box
 357  * \param[in]     mtop      System topology definition
 358  * \param[in,out] x         The coordinates of the atoms
 359  */
 360 void do_pbc_first_mtop(FILE *fplog, int ePBC, const matrix box,
 361                        const gmx_mtop_t *mtop, rvec x[]);
 362
 363 /*! \brief Make molecules consisting of multiple charge groups whole by shifting positions
 364  *
 365  * \param[in]     ePBC      The PBC type
 366  * \param[in]     box       The simulation box
 367  * \param[in]     mtop      System topology definition
 368  * \param[in,out] x         The coordinates of the atoms
 369  */
 370 void do_pbc_mtop(int ePBC, const matrix box,
 371                  const gmx_mtop_t *mtop, rvec x[]);
 372
 373 #endif