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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 "../fileio/trx.h"
50 #include "types/topology.h"
51 #include "types/energy.h"
52 #include "types/inputrec.h"
53 #include "types/nrnb.h"
54 #include "types/nblist.h"
55 #include "types/nbnxn_pairlist.h"
56 #include "types/nsgrid.h"
57 #include "types/forcerec.h"
58 #include "types/fcdata.h"
59 #include "types/mdatom.h"
60 #include "types/ifunc.h"
61 #include "types/group.h"
62 #include "types/state.h"
63 #include "types/shellfc.h"
64 #include "types/constr.h"
65 #include "types/oenv.h"
66 #include "types/commrec_fwd.h"
73 * Memory (re)allocation can be VERY slow, especially with some
74 * MPI libraries that replace the standard malloc and realloc calls.
75 * To avoid slow memory allocation we use over_alloc to set the memory
76 * allocation size for large data blocks. Since this scales the size
77 * with a factor, we use log(n) realloc calls instead of n.
78 * This can reduce allocation times from minutes to seconds.
80 /* This factor leads to 4 realloc calls to double the array size */
81 #define OVER_ALLOC_FAC 1.19
83 void set_over_alloc_dd(gmx_bool set);
84 /* Turns over allocation for variable size atoms/cg/top arrays on or off,
88 int over_alloc_dd(int n);
89 /* Returns n when domain decomposition over allocation is off.
90 * Returns OVER_ALLOC_FAC*n + 100 when over allocation in on.
91 * This is to avoid frequent reallocation
92 * during domain decomposition in mdrun.
95 /* Over allocation for small data types: int, real etc. */
96 #define over_alloc_small(n) (int)(OVER_ALLOC_FAC*(n) + 8000)
98 /* Over allocation for large data types: complex structs */
99 #define over_alloc_large(n) (int)(OVER_ALLOC_FAC*(n) + 1000)
101 int gmx_int64_to_int(gmx_int64_t step, const char *warn);
102 /* Convert a gmx_int64_t value to int.
103 * If warn!=NULL a warning message will be written
104 * to stderr when step does not fit in an int,
106 * "WARNING during %s:", where warn is printed in %s.
109 #define STEPSTRSIZE 22
111 char *gmx_step_str(gmx_int64_t i, char *buf);
112 /* Prints a gmx_int64_t value in buf and returns the pointer to buf.
113 * buf should be large enough to contain i: STEPSTRSIZE (22) chars.
114 * When multiple gmx_int64_t values are printed in the same printf call,
115 * be sure to call gmx_step_str with different buffers.
118 /* Functions to initiate and delete structures *
119 * These functions are defined in gmxlib/typedefs.c
121 void init_mtop(gmx_mtop_t *mtop);
122 void init_top(t_topology *top);
123 void init_inputrec(t_inputrec *ir);
124 void init_energyhistory(energyhistory_t * enerhist);
125 void done_energyhistory(energyhistory_t * enerhist);
126 void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength);
127 void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int nlambda);
128 t_state *serial_init_local_state(t_state *state_global);
129 void init_df_history(df_history_t *dfhist, int nlambda);
130 void done_df_history(df_history_t *dfhist);
131 void copy_df_history(df_history_t * df_dest, df_history_t *df_source);
132 void done_moltype(gmx_moltype_t *molt);
133 void done_molblock(gmx_molblock_t *molb);
134 void done_mtop(gmx_mtop_t *mtop, gmx_bool bDoneSymtab);
135 void done_top(t_topology *top);
136 void done_inputrec(t_inputrec *ir);
137 void done_state(t_state *state);
139 void set_box_rel(t_inputrec *ir, t_state *state);
140 /* Set state->box_rel used in mdrun to preserve the box shape */
142 void preserve_box_shape(t_inputrec *ir, matrix box_rel, matrix b);
143 /* Preserve the box shape, b can be box or boxv */
145 t_atoms *mtop2atoms(gmx_mtop_t *mtop);
146 /* generate a t_atoms struct for the system from gmx_mtop_t */
148 real max_cutoff(real cutoff1, real cutoff2);
149 /* Returns the maximum of the cut-off's, taking into account that 0=inf. */
156 #endif /* _typedefs_h */