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42 /* DEPRECATED! value for signaling unitialized variables */
45 #include <sys/types.h>
47 #include "types/simple.h"
48 #include "types/enums.h"
49 #include "types/idef.h"
50 #include "types/atoms.h"
51 #include "../fileio/trx.h"
52 #include "types/topology.h"
53 #include "types/energy.h"
54 #include "types/inputrec.h"
55 #include "types/nrnb.h"
56 #include "types/nblist.h"
57 #include "types/nbnxn_pairlist.h"
58 #include "types/nsgrid.h"
59 #include "types/forcerec.h"
60 #include "types/fcdata.h"
61 #include "types/mdatom.h"
62 #include "types/ifunc.h"
63 #include "types/group.h"
64 #include "types/state.h"
65 #include "types/shellfc.h"
66 #include "types/constr.h"
67 #include "types/oenv.h"
68 #include "types/commrec_fwd.h"
75 * Memory (re)allocation can be VERY slow, especially with some
76 * MPI libraries that replace the standard malloc and realloc calls.
77 * To avoid slow memory allocation we use over_alloc to set the memory
78 * allocation size for large data blocks. Since this scales the size
79 * with a factor, we use log(n) realloc calls instead of n.
80 * This can reduce allocation times from minutes to seconds.
82 /* This factor leads to 4 realloc calls to double the array size */
83 #define OVER_ALLOC_FAC 1.19
85 void set_over_alloc_dd(gmx_bool set);
86 /* Turns over allocation for variable size atoms/cg/top arrays on or off,
90 int over_alloc_dd(int n);
91 /* Returns n when domain decomposition over allocation is off.
92 * Returns OVER_ALLOC_FAC*n + 100 when over allocation in on.
93 * This is to avoid frequent reallocation
94 * during domain decomposition in mdrun.
97 /* Over allocation for small data types: int, real etc. */
98 #define over_alloc_small(n) (int)(OVER_ALLOC_FAC*(n) + 8000)
100 /* Over allocation for large data types: complex structs */
101 #define over_alloc_large(n) (int)(OVER_ALLOC_FAC*(n) + 1000)
103 int gmx_int64_to_int(gmx_int64_t step, const char *warn);
104 /* Convert a gmx_int64_t value to int.
105 * If warn!=NULL a warning message will be written
106 * to stderr when step does not fit in an int,
108 * "WARNING during %s:", where warn is printed in %s.
111 #define STEPSTRSIZE 22
113 char *gmx_step_str(gmx_int64_t i, char *buf);
114 /* Prints a gmx_int64_t value in buf and returns the pointer to buf.
115 * buf should be large enough to contain i: STEPSTRSIZE (22) chars.
116 * When multiple gmx_int64_t values are printed in the same printf call,
117 * be sure to call gmx_step_str with different buffers.
120 /* Functions to initiate and delete structures *
121 * These functions are defined in gmxlib/typedefs.c
123 void init_atom (t_atoms *at);
124 void init_mtop(gmx_mtop_t *mtop);
125 void init_top(t_topology *top);
126 void init_inputrec(t_inputrec *ir);
127 void init_energyhistory(energyhistory_t * enerhist);
128 void done_energyhistory(energyhistory_t * enerhist);
129 void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength);
130 void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int nlambda);
131 t_state *serial_init_local_state(t_state *state_global);
132 void init_df_history(df_history_t *dfhist, int nlambda);
133 void done_df_history(df_history_t *dfhist);
134 void copy_df_history(df_history_t * df_dest, df_history_t *df_source);
135 void done_atom (t_atoms *at);
136 void done_moltype(gmx_moltype_t *molt);
137 void done_molblock(gmx_molblock_t *molb);
138 void done_mtop(gmx_mtop_t *mtop, gmx_bool bDoneSymtab);
139 void done_top(t_topology *top);
140 void done_inputrec(t_inputrec *ir);
141 void done_state(t_state *state);
143 void set_box_rel(t_inputrec *ir, t_state *state);
144 /* Set state->box_rel used in mdrun to preserve the box shape */
146 void preserve_box_shape(t_inputrec *ir, matrix box_rel, matrix b);
147 /* Preserve the box shape, b can be box or boxv */
149 void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo);
150 /* allocate memory for the arrays, set nr to natoms and nres to 0
151 * set pdbinfo to NULL or allocate memory for it */
153 t_atoms *copy_t_atoms(t_atoms *src);
154 /* copy an atoms struct from src to a new one */
156 void add_t_atoms(t_atoms *atoms, int natom_extra, int nres_extra);
157 /* allocate extra space for more atoms and or residues */
159 void t_atoms_set_resinfo(t_atoms *atoms, int atom_ind, struct t_symtab *symtab,
160 const char *resname, int resnr, unsigned char ic,
161 int chainnum, char chainid);
162 /* Set the residue name, number, insertion code and chain identifier
163 * of atom index atom_ind.
166 void free_t_atoms(t_atoms *atoms, gmx_bool bFreeNames);
167 /* Free all the arrays and set the nr and nres to 0.
168 * bFreeNames tells if to free the atom and residue name strings,
169 * don't free them if they still need to be used in e.g. the topology struct.
172 t_atoms *mtop2atoms(gmx_mtop_t *mtop);
173 /* generate a t_atoms struct for the system from gmx_mtop_t */
175 real max_cutoff(real cutoff1, real cutoff2);
176 /* Returns the maximum of the cut-off's, taking into account that 0=inf. */
183 #endif /* _typedefs_h */