/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
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+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* Gromacs Runs On Most of All Computer Systems
*/
#include "types/commrec.h"
#ifdef __cplusplus
-extern "C" {
+extern "C" {
#endif
-#define TRICLINIC(box) (box[YY][XX]!=0 || box[ZZ][XX]!=0 || box[ZZ][YY]!=0)
+#define TRICLINIC(box) (box[YY][XX] != 0 || box[ZZ][XX] != 0 || box[ZZ][YY] != 0)
#define NTRICIMG 14
#define NCUCVERT 24
#define NCUCEDGE 36
- enum {
+enum {
ecenterTRIC, /* 0.5*(a+b+c) */
ecenterRECT, /* (0.5*a[x],0.5*b[y],0.5*c[z]) */
ecenterZERO, /* (0,0,0) */
ecenterDEF = ecenterTRIC
- };
-
- int ePBC2npbcdim(int ePBC);
- /* Returns the number of dimensions that use pbc, starting at X */
-
- int inputrec2nboundeddim(t_inputrec *ir);
- /* Returns the number of dimensions in which
- * the coordinates of the particles are bounded, starting at X.
- */
-
- void dump_pbc(FILE *fp,t_pbc *pbc);
- /* Dump the contents of the pbc structure to the file */
-
- const char *check_box(int ePBC,matrix box);
- /* Returns NULL if the box is supported by Gromacs.
- * Otherwise is returns a string with the problem.
- * When ePBC=-1, the type of pbc is guessed from the box matrix.
- */
-
- real max_cutoff2(int ePBC,matrix box);
- /* Returns the square of the maximum cut-off allowed for the box,
- * taking into account that the grid neighborsearch code and pbc_dx
- * only check combinations of single box-vector shifts.
- */
-
- int guess_ePBC(matrix box);
- /* Guesses the type of periodic boundary conditions using the box */
-
- gmx_bool correct_box(FILE *fplog,int step,tensor box,t_graph *graph);
- /* Checks for un-allowed box angles and corrects the box
- * and the integer shift vectors in the graph (if graph!=NULL) if necessary.
- * Returns TRUE when the box was corrected.
- */
-
- int ndof_com(t_inputrec *ir);
- /* Returns the number of degrees of freedom of the center of mass */
-
- void set_pbc(t_pbc *pbc,int ePBC,matrix box);
- /* Initiate the periodic boundary conditions.
- * pbc_dx will not use pbc and return the normal difference vector
- * when one or more of the diagonal elements of box are zero.
- * When ePBC=-1, the type of pbc is guessed from the box matrix.
- */
-
- t_pbc *set_pbc_dd(t_pbc *pbc,int ePBC,
- gmx_domdec_t *dd,gmx_bool bSingleDir,matrix box);
- /* As set_pbc, but additionally sets that correct distances can
- * be obtained using (combinations of) single box-vector shifts.
- * Should be used with pbc_dx_aiuc.
- * If dd!=NULL pbc is not used for directions
- * with dd->nc[i]==1 with bSingleDir==TRUE or
- * with dd->nc[i]<=2 with bSingleDir==FALSE.
- * Returns pbc when pbc operations are required, NULL otherwise.
- */
-
- void pbc_dx(const t_pbc *pbc,const rvec x1, const rvec x2, rvec dx);
- /* Calculate the correct distance vector from x2 to x1 and put it in dx.
- * set_pbc must be called before ever calling this routine.
- *
- * For triclinic boxes pbc_dx does not necessarily return the shortest
- * distance vector. If pbc->bLimitDistance=TRUE an atom pair with
- * distance vector dx with norm2(dx) > pbc->limit_distance2 could
- * have a shorter distance, but not shorter than sqrt(pbc->limit_distance2).
- * pbc->limit_distance2 is always larger than max_cutoff2(box).
- * For the standard rhombic dodecahedron and truncated octahedron
- * pbc->bLimitDistance=FALSE and thus all distances are correct.
- */
-
- int pbc_dx_aiuc(const t_pbc *pbc,const rvec x1,const rvec x2,rvec dx);
- /* Calculate the correct distance vector from x2 to x1 and put it in dx,
- * This function can only be used when all atoms are in the rectangular
- * or triclinic unit-cell.
- * Returns the ishift required to shift x1 at closest distance to x2;
- * i.e. if 0<=ishift<SHIFTS then x1 - x2 + shift_vec[ishift] = dx
- * (see calc_shifts below on how to obtain shift_vec)
- * set_pbc_dd or set_pbc must be called before ever calling this routine.
- */
- void pbc_dx_d(const t_pbc *pbc,const dvec x1, const dvec x2, dvec dx);
- /* As pbc_dx, but for double precision vectors.
- * set_pbc must be called before ever calling this routine.
- */
-
- gmx_bool image_rect(ivec xi,ivec xj,ivec box_size,
- real rlong2,int *shift,real *r2);
- /* Calculate the distance between xi and xj for a rectangular box.
- * When the distance is SMALLER than rlong2 return TRUE, return
- * the shift code in shift and the distance in r2. When the distance is
- * >= rlong2 return FALSE;
- * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
- */
-
- gmx_bool image_tri(ivec xi,ivec xj,imatrix box,
- real rlong2,int *shift,real *r2);
- /* Calculate the distance between xi and xj for a triclinic box.
- * When the distance is SMALLER than rlong2 return TRUE, return
- * the shift code in shift and the distance in r2. When the distance is
- * >= rlong2 return FALSE;
- * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
- */
-
- gmx_bool image_cylindric(ivec xi,ivec xj,ivec box_size,real rlong2,
- int *shift,real *r2);
- /* Calculate the distance between xi and xj for a rectangular box
- * using a cylindric cutoff for long-range only.
- * When the distance is SMALLER than rlong2 (in X and Y dir.)
- * return TRUE, return
- * the shift code in shift and the distance in r2. When the distance is
- * >= rlong2 return FALSE;
- * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
- */
-
- void calc_shifts(matrix box,rvec shift_vec[]);
- /* This routine calculates ths shift vectors necessary to use the
- * ns routine.
- */
-
- void calc_box_center(int ecenter,matrix box,rvec box_center);
- /* Calculates the center of the box.
- * See the description for the enum ecenter above.
- */
-
- void calc_triclinic_images(matrix box,rvec img[]);
- /* Calculates the NTRICIMG box images */
-
- void calc_compact_unitcell_vertices(int ecenter,matrix box,
- rvec vert[]);
- /* Calculates the NCUCVERT vertices of a compact unitcell */
-
- int *compact_unitcell_edges(void);
- /* Return an array of unitcell edges of length NCUCEDGE*2,
- * this is an index in vert[], which is calculated by calc_unitcell_vertices.
- * The index consists of NCUCEDGE pairs of vertex indices.
- * The index does not change, so it needs to be retrieved only once.
- */
-
- void put_atoms_in_box_omp(int ePBC,matrix box,int natoms,rvec x[]);
- /* This wrapper function around put_atoms_in_box() with the ugly manual
- * workload splitting is needed toavoid silently introducing multithreading
- * in tools.
- * */
-
-
- void put_atoms_in_box(int ePBC, matrix box,int natoms,rvec x[]);
- /* These routines puts ONE or ALL atoms in the box, not caring
- * about charge groups!
- * Also works for triclinic cells.
- */
-
- void put_atoms_in_triclinic_unitcell(int ecenter,matrix box,
- int natoms,rvec x[]);
- /* This puts ALL atoms in the triclinic unit cell, centered around the
- * box center as calculated by calc_box_center.
- */
-
- const char *put_atoms_in_compact_unitcell(int ePBC,int ecenter,
- matrix box,
- int natoms,rvec x[]);
- /* This puts ALL atoms at the closest distance for the center of the box
- * as calculated by calc_box_center.
- * Will return NULL is everything went ok and a warning string if not
- * all atoms could be placed in the unitcell. This can happen for some
- * triclinic unitcells, see the comment at pbc_dx above.
- * When ePBC=-1, the type of pbc is guessed from the box matrix.
- */
-
+};
+
+int ePBC2npbcdim(int ePBC);
+/* Returns the number of dimensions that use pbc, starting at X */
+
+int inputrec2nboundeddim(t_inputrec *ir);
+/* Returns the number of dimensions in which
+ * the coordinates of the particles are bounded, starting at X.
+ */
+
+void dump_pbc(FILE *fp, t_pbc *pbc);
+/* Dump the contents of the pbc structure to the file */
+
+const char *check_box(int ePBC, matrix box);
+/* Returns NULL if the box is supported by Gromacs.
+ * Otherwise is returns a string with the problem.
+ * When ePBC=-1, the type of pbc is guessed from the box matrix.
+ */
+
+real max_cutoff2(int ePBC, matrix box);
+/* Returns the square of the maximum cut-off allowed for the box,
+ * taking into account that the grid neighborsearch code and pbc_dx
+ * only check combinations of single box-vector shifts.
+ */
+
+int guess_ePBC(matrix box);
+/* Guesses the type of periodic boundary conditions using the box */
+
+gmx_bool correct_box(FILE *fplog, int step, tensor box, t_graph *graph);
+/* Checks for un-allowed box angles and corrects the box
+ * and the integer shift vectors in the graph (if graph!=NULL) if necessary.
+ * Returns TRUE when the box was corrected.
+ */
+
+int ndof_com(t_inputrec *ir);
+/* Returns the number of degrees of freedom of the center of mass */
+
+void set_pbc(t_pbc *pbc, int ePBC, matrix box);
+/* Initiate the periodic boundary conditions.
+ * pbc_dx will not use pbc and return the normal difference vector
+ * when one or more of the diagonal elements of box are zero.
+ * When ePBC=-1, the type of pbc is guessed from the box matrix.
+ */
+
+t_pbc *set_pbc_dd(t_pbc *pbc, int ePBC,
+ gmx_domdec_t *dd, gmx_bool bSingleDir, matrix box);
+/* As set_pbc, but additionally sets that correct distances can
+ * be obtained using (combinations of) single box-vector shifts.
+ * Should be used with pbc_dx_aiuc.
+ * If dd!=NULL pbc is not used for directions
+ * with dd->nc[i]==1 with bSingleDir==TRUE or
+ * with dd->nc[i]<=2 with bSingleDir==FALSE.
+ * Returns pbc when pbc operations are required, NULL otherwise.
+ */
+
+void pbc_dx(const t_pbc *pbc, const rvec x1, const rvec x2, rvec dx);
+/* Calculate the correct distance vector from x2 to x1 and put it in dx.
+ * set_pbc must be called before ever calling this routine.
+ *
+ * For triclinic boxes pbc_dx does not necessarily return the shortest
+ * distance vector. If pbc->bLimitDistance=TRUE an atom pair with
+ * distance vector dx with norm2(dx) > pbc->limit_distance2 could
+ * have a shorter distance, but not shorter than sqrt(pbc->limit_distance2).
+ * pbc->limit_distance2 is always larger than max_cutoff2(box).
+ * For the standard rhombic dodecahedron and truncated octahedron
+ * pbc->bLimitDistance=FALSE and thus all distances are correct.
+ */
+
+int pbc_dx_aiuc(const t_pbc *pbc, const rvec x1, const rvec x2, rvec dx);
+/* Calculate the correct distance vector from x2 to x1 and put it in dx,
+ * This function can only be used when all atoms are in the rectangular
+ * or triclinic unit-cell.
+ * Returns the ishift required to shift x1 at closest distance to x2;
+ * i.e. if 0<=ishift<SHIFTS then x1 - x2 + shift_vec[ishift] = dx
+ * (see calc_shifts below on how to obtain shift_vec)
+ * set_pbc_dd or set_pbc must be called before ever calling this routine.
+ */
+void pbc_dx_d(const t_pbc *pbc, const dvec x1, const dvec x2, dvec dx);
+/* As pbc_dx, but for double precision vectors.
+ * set_pbc must be called before ever calling this routine.
+ */
+
+gmx_bool image_rect(ivec xi, ivec xj, ivec box_size,
+ real rlong2, int *shift, real *r2);
+/* Calculate the distance between xi and xj for a rectangular box.
+ * When the distance is SMALLER than rlong2 return TRUE, return
+ * the shift code in shift and the distance in r2. When the distance is
+ * >= rlong2 return FALSE;
+ * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
+ */
+
+gmx_bool image_tri(ivec xi, ivec xj, imatrix box,
+ real rlong2, int *shift, real *r2);
+/* Calculate the distance between xi and xj for a triclinic box.
+ * When the distance is SMALLER than rlong2 return TRUE, return
+ * the shift code in shift and the distance in r2. When the distance is
+ * >= rlong2 return FALSE;
+ * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
+ */
+
+gmx_bool image_cylindric(ivec xi, ivec xj, ivec box_size, real rlong2,
+ int *shift, real *r2);
+/* Calculate the distance between xi and xj for a rectangular box
+ * using a cylindric cutoff for long-range only.
+ * When the distance is SMALLER than rlong2 (in X and Y dir.)
+ * return TRUE, return
+ * the shift code in shift and the distance in r2. When the distance is
+ * >= rlong2 return FALSE;
+ * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
+ */
+
+void calc_shifts(matrix box, rvec shift_vec[]);
+/* This routine calculates ths shift vectors necessary to use the
+ * ns routine.
+ */
+
+void calc_box_center(int ecenter, matrix box, rvec box_center);
+/* Calculates the center of the box.
+ * See the description for the enum ecenter above.
+ */
+
+void calc_triclinic_images(matrix box, rvec img[]);
+/* Calculates the NTRICIMG box images */
+
+void calc_compact_unitcell_vertices(int ecenter, matrix box,
+ rvec vert[]);
+/* Calculates the NCUCVERT vertices of a compact unitcell */
+
+int *compact_unitcell_edges(void);
+/* Return an array of unitcell edges of length NCUCEDGE*2,
+ * this is an index in vert[], which is calculated by calc_unitcell_vertices.
+ * The index consists of NCUCEDGE pairs of vertex indices.
+ * The index does not change, so it needs to be retrieved only once.
+ */
+
+void put_atoms_in_box_omp(int ePBC, matrix box, int natoms, rvec x[]);
+/* This wrapper function around put_atoms_in_box() with the ugly manual
+ * workload splitting is needed toavoid silently introducing multithreading
+ * in tools.
+ * */
+
+
+void put_atoms_in_box(int ePBC, matrix box, int natoms, rvec x[]);
+/* These routines puts ONE or ALL atoms in the box, not caring
+ * about charge groups!
+ * Also works for triclinic cells.
+ */
+
+void put_atoms_in_triclinic_unitcell(int ecenter, matrix box,
+ int natoms, rvec x[]);
+/* This puts ALL atoms in the triclinic unit cell, centered around the
+ * box center as calculated by calc_box_center.
+ */
+
+const char *put_atoms_in_compact_unitcell(int ePBC, int ecenter,
+ matrix box,
+ int natoms, rvec x[]);
+/* This puts ALL atoms at the closest distance for the center of the box
+ * as calculated by calc_box_center.
+ * Will return NULL is everything went ok and a warning string if not
+ * all atoms could be placed in the unitcell. This can happen for some
+ * triclinic unitcells, see the comment at pbc_dx above.
+ * When ePBC=-1, the type of pbc is guessed from the box matrix.
+ */
+
#ifdef __cplusplus
}
#endif
-#endif /* _pbc_h */
+#endif /* _pbc_h */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff