/*
- *
+ *
* 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.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* Gromacs Runs On Most of All Computer Systems
*/
extern "C" {
#endif
-/*
+/*
* Memory (re)allocation can be VERY slow, especially with some
* MPI libraries that replace the standard malloc and realloc calls.
* To avoid slow memory allocation we use over_alloc to set the memory
#define OVER_ALLOC_FAC 1.19
void set_over_alloc_dd(gmx_bool set);
- /* Turns over allocation for variable size atoms/cg/top arrays on or off,
- * default is off.
- */
-
+/* Turns over allocation for variable size atoms/cg/top arrays on or off,
+ * default is off.
+ */
+
int over_alloc_dd(int n);
- /* Returns n when domain decomposition over allocation is off.
- * Returns OVER_ALLOC_FAC*n + 100 when over allocation in on.
- * This is to avoid frequent reallocation
- * during domain decomposition in mdrun.
- */
+/* Returns n when domain decomposition over allocation is off.
+ * Returns OVER_ALLOC_FAC*n + 100 when over allocation in on.
+ * This is to avoid frequent reallocation
+ * during domain decomposition in mdrun.
+ */
/* Over allocation for small data types: int, real etc. */
#define over_alloc_small(n) (OVER_ALLOC_FAC*(n) + 8000)
/* Over allocation for large data types: complex structs */
#define over_alloc_large(n) (OVER_ALLOC_FAC*(n) + 1000)
-int gmx_large_int_to_int(gmx_large_int_t step,const char *warn);
+int gmx_large_int_to_int(gmx_large_int_t step, const char *warn);
/* Convert a gmx_large_int_t value to int.
* If warn!=NULL a warning message will be written
* to stderr when step does not fit in an int,
#define STEPSTRSIZE 22
-char *gmx_step_str(gmx_large_int_t i,char *buf);
+char *gmx_step_str(gmx_large_int_t i, char *buf);
/* Prints a gmx_large_int_t value in buf and returns the pointer to buf.
* buf should be large enough to contain i: STEPSTRSIZE (22) chars.
* When multiple gmx_large_int_t values are printed in the same printf call,
*/
/* Functions to initiate and delete structures *
- * These functions are defined in gmxlib/typedefs.c
+ * These functions are defined in gmxlib/typedefs.c
*/
void init_block(t_block *block);
void init_blocka(t_blocka *block);
void init_inputrec(t_inputrec *ir);
void init_energyhistory(energyhistory_t * enerhist);
void done_energyhistory(energyhistory_t * enerhist);
-void init_gtc_state(t_state *state,int ngtc, int nnhpres, int nhchainlength);
-void init_state(t_state *state,int natoms,int ngtc, int nnhpres, int nhchainlength, int nlambda);
+void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength);
+void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int nlambda);
void init_df_history(df_history_t *dfhist, int nlambda, real wl_delta);
void copy_df_history(df_history_t * df_dest, df_history_t *df_source);
-void copy_blocka(const t_blocka *src,t_blocka *dest);
+void copy_blocka(const t_blocka *src, t_blocka *dest);
void done_block(t_block *block);
void done_blocka(t_blocka *block);
void done_atom (t_atoms *at);
void done_moltype(gmx_moltype_t *molt);
void done_molblock(gmx_molblock_t *molb);
-void done_mtop(gmx_mtop_t *mtop,gmx_bool bDoneSymtab);
+void done_mtop(gmx_mtop_t *mtop, gmx_bool bDoneSymtab);
void done_top(t_topology *top);
void done_inputrec(t_inputrec *ir);
void done_state(t_state *state);
-void set_box_rel(t_inputrec *ir,t_state *state);
+void set_box_rel(t_inputrec *ir, t_state *state);
/* Set state->box_rel used in mdrun to preserve the box shape */
-void preserve_box_shape(t_inputrec *ir,matrix box_rel,matrix b);
+void preserve_box_shape(t_inputrec *ir, matrix box_rel, matrix b);
/* Preserve the box shape, b can be box or boxv */
-void stupid_fill_block(t_block *grp, int natom,gmx_bool bOneIndexGroup);
+void stupid_fill_block(t_block *grp, int natom, gmx_bool bOneIndexGroup);
/* Fill a block structure with numbers identical to the index
* (0, 1, 2, .. natom-1)
* If bOneIndexGroup, then all atoms are lumped in one index group,
void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo);
/* allocate memory for the arrays, set nr to natoms and nres to 0
- * set pdbinfo to NULL or allocate memory for it */
+ * set pdbinfo to NULL or allocate memory for it */
t_atoms *copy_t_atoms(t_atoms *src);
/* copy an atoms struct from src to a new one */
-
-void add_t_atoms(t_atoms *atoms,int natom_extra,int nres_extra);
+
+void add_t_atoms(t_atoms *atoms, int natom_extra, int nres_extra);
/* allocate extra space for more atoms and or residues */
-
-void t_atoms_set_resinfo(t_atoms *atoms,int atom_ind,t_symtab *symtab,
- const char *resname,int resnr,unsigned char ic,
- int chainnum, char chainid);
+
+void t_atoms_set_resinfo(t_atoms *atoms, int atom_ind, t_symtab *symtab,
+ const char *resname, int resnr, unsigned char ic,
+ int chainnum, char chainid);
/* Set the residue name, number, insertion code and chain identifier
* of atom index atom_ind.
*/
-void free_t_atoms(t_atoms *atoms,gmx_bool bFreeNames);
+void free_t_atoms(t_atoms *atoms, gmx_bool bFreeNames);
/* Free all the arrays and set the nr and nres to 0.
* bFreeNames tells if to free the atom and residue name strings,
* don't free them if they still need to be used in e.g. the topology struct.
*/
t_atoms *mtop2atoms(gmx_mtop_t *mtop);
-/* generate a t_atoms struct for the system from gmx_mtop_t */
+/* generate a t_atoms struct for the system from gmx_mtop_t */
-real max_cutoff(real cutoff1,real cutoff2);
+real max_cutoff(real cutoff1, real cutoff2);
/* Returns the maximum of the cut-off's, taking into account that 0=inf. */
#ifdef __cplusplus
#endif
-#endif /* _typedefs_h */
+#endif /* _typedefs_h */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff