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43 /* DEPRECATED! value for signaling unitialized variables */
46 #include <sys/types.h>
47 #include "visibility.h"
49 #include "types/simple.h"
50 #include "types/enums.h"
51 #include "types/block.h"
52 #include "types/symtab.h"
53 #include "types/idef.h"
54 #include "types/atoms.h"
55 #include "types/trx.h"
56 #include "types/topology.h"
57 #include "types/energy.h"
58 #include "types/inputrec.h"
59 #include "types/ishift.h"
60 #include "types/graph.h"
61 #include "types/nrnb.h"
62 #include "types/nblist.h"
63 #include "types/nbnxn_pairlist.h"
64 #include "types/nsgrid.h"
65 #include "types/forcerec.h"
66 #include "types/fcdata.h"
67 #include "types/mdatom.h"
68 #include "types/pbc.h"
69 #include "types/ifunc.h"
70 #include "types/filenm.h"
71 #include "types/group.h"
72 #include "types/state.h"
73 #include "types/shellfc.h"
74 #include "types/constr.h"
75 #include "types/matrix.h"
76 #include "types/oenv.h"
83 * Memory (re)allocation can be VERY slow, especially with some
84 * MPI libraries that replace the standard malloc and realloc calls.
85 * To avoid slow memory allocation we use over_alloc to set the memory
86 * allocation size for large data blocks. Since this scales the size
87 * with a factor, we use log(n) realloc calls instead of n.
88 * This can reduce allocation times from minutes to seconds.
90 /* This factor leads to 4 realloc calls to double the array size */
91 #define OVER_ALLOC_FAC 1.19
94 void set_over_alloc_dd(gmx_bool set
);
95 /* Turns over allocation for variable size atoms/cg/top arrays on or off,
100 int over_alloc_dd(int n
);
101 /* Returns n when domain decomposition over allocation is off.
102 * Returns OVER_ALLOC_FAC*n + 100 when over allocation in on.
103 * This is to avoid frequent reallocation
104 * during domain decomposition in mdrun.
107 /* Over allocation for small data types: int, real etc. */
108 #define over_alloc_small(n) (OVER_ALLOC_FAC*(n) + 8000)
110 /* Over allocation for large data types: complex structs */
111 #define over_alloc_large(n) (OVER_ALLOC_FAC*(n) + 1000)
114 int gmx_large_int_to_int(gmx_large_int_t step
, const char *warn
);
115 /* Convert a gmx_large_int_t value to int.
116 * If warn!=NULL a warning message will be written
117 * to stderr when step does not fit in an int,
119 * "WARNING during %s:", where warn is printed in %s.
122 #define STEPSTRSIZE 22
125 char *gmx_step_str(gmx_large_int_t i
, char *buf
);
126 /* Prints a gmx_large_int_t value in buf and returns the pointer to buf.
127 * buf should be large enough to contain i: STEPSTRSIZE (22) chars.
128 * When multiple gmx_large_int_t values are printed in the same printf call,
129 * be sure to call gmx_step_str with different buffers.
132 /* Functions to initiate and delete structures *
133 * These functions are defined in gmxlib/typedefs.c
136 void init_block(t_block
*block
);
138 void init_blocka(t_blocka
*block
);
140 void init_atom (t_atoms
*at
);
142 void init_mtop(gmx_mtop_t
*mtop
);
144 void init_top (t_topology
*top
);
145 void init_inputrec(t_inputrec
*ir
);
147 void init_energyhistory(energyhistory_t
* enerhist
);
149 void done_energyhistory(energyhistory_t
* enerhist
);
151 void init_gtc_state(t_state
*state
, int ngtc
, int nnhpres
, int nhchainlength
);
153 void init_state(t_state
*state
, int natoms
, int ngtc
, int nnhpres
, int nhchainlength
, int nlambda
);
155 void init_df_history(df_history_t
*dfhist
, int nlambda
);
157 void done_df_history(df_history_t
*dfhist
);
159 void copy_df_history(df_history_t
* df_dest
, df_history_t
*df_source
);
162 void copy_blocka(const t_blocka
*src
, t_blocka
*dest
);
165 void done_block(t_block
*block
);
167 void done_blocka(t_blocka
*block
);
169 void done_atom (t_atoms
*at
);
170 void done_moltype(gmx_moltype_t
*molt
);
171 void done_molblock(gmx_molblock_t
*molb
);
172 void done_mtop(gmx_mtop_t
*mtop
, gmx_bool bDoneSymtab
);
173 void done_top(t_topology
*top
);
174 void done_inputrec(t_inputrec
*ir
);
176 void done_state(t_state
*state
);
179 void set_box_rel(t_inputrec
*ir
, t_state
*state
);
180 /* Set state->box_rel used in mdrun to preserve the box shape */
183 void preserve_box_shape(t_inputrec
*ir
, matrix box_rel
, matrix b
);
184 /* Preserve the box shape, b can be box or boxv */
187 void stupid_fill_block(t_block
*grp
, int natom
, gmx_bool bOneIndexGroup
);
188 /* Fill a block structure with numbers identical to the index
189 * (0, 1, 2, .. natom-1)
190 * If bOneIndexGroup, then all atoms are lumped in one index group,
191 * otherwise there is one atom per index entry
195 void stupid_fill_blocka(t_blocka
*grp
, int natom
);
196 /* Fill a block structure with numbers identical to the index
197 * (0, 1, 2, .. natom-1)
198 * There is one atom per index entry
202 void init_t_atoms(t_atoms
*atoms
, int natoms
, gmx_bool bPdbinfo
);
203 /* allocate memory for the arrays, set nr to natoms and nres to 0
204 * set pdbinfo to NULL or allocate memory for it */
206 t_atoms
*copy_t_atoms(t_atoms
*src
);
207 /* copy an atoms struct from src to a new one */
209 void add_t_atoms(t_atoms
*atoms
, int natom_extra
, int nres_extra
);
210 /* allocate extra space for more atoms and or residues */
213 void t_atoms_set_resinfo(t_atoms
*atoms
, int atom_ind
, t_symtab
*symtab
,
214 const char *resname
, int resnr
, unsigned char ic
,
215 int chainnum
, char chainid
);
216 /* Set the residue name, number, insertion code and chain identifier
217 * of atom index atom_ind.
221 void free_t_atoms(t_atoms
*atoms
, gmx_bool bFreeNames
);
222 /* Free all the arrays and set the nr and nres to 0.
223 * bFreeNames tells if to free the atom and residue name strings,
224 * don't free them if they still need to be used in e.g. the topology struct.
227 t_atoms
*mtop2atoms(gmx_mtop_t
*mtop
);
228 /* generate a t_atoms struct for the system from gmx_mtop_t */
231 real
max_cutoff(real cutoff1
, real cutoff2
);
232 /* Returns the maximum of the cut-off's, taking into account that 0=inf. */
239 #endif /* _typedefs_h */