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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/block.h"
50 #include "types/symtab.h"
51 #include "types/idef.h"
52 #include "types/atoms.h"
53 #include "../fileio/trx.h"
54 #include "types/topology.h"
55 #include "types/energy.h"
56 #include "types/inputrec.h"
57 #include "types/ishift.h"
58 #include "types/graph.h"
59 #include "types/nrnb.h"
60 #include "types/nblist.h"
61 #include "types/nbnxn_pairlist.h"
62 #include "types/nsgrid.h"
63 #include "types/forcerec.h"
64 #include "types/fcdata.h"
65 #include "types/mdatom.h"
66 #include "types/pbc.h"
67 #include "types/ifunc.h"
68 #include "types/group.h"
69 #include "types/state.h"
70 #include "types/shellfc.h"
71 #include "types/constr.h"
72 #include "types/matrix.h"
73 #include "types/oenv.h"
74 #include "types/commrec_fwd.h"
81 * Memory (re)allocation can be VERY slow, especially with some
82 * MPI libraries that replace the standard malloc and realloc calls.
83 * To avoid slow memory allocation we use over_alloc to set the memory
84 * allocation size for large data blocks. Since this scales the size
85 * with a factor, we use log(n) realloc calls instead of n.
86 * This can reduce allocation times from minutes to seconds.
88 /* This factor leads to 4 realloc calls to double the array size */
89 #define OVER_ALLOC_FAC 1.19
91 void set_over_alloc_dd(gmx_bool set);
92 /* Turns over allocation for variable size atoms/cg/top arrays on or off,
96 int over_alloc_dd(int n);
97 /* Returns n when domain decomposition over allocation is off.
98 * Returns OVER_ALLOC_FAC*n + 100 when over allocation in on.
99 * This is to avoid frequent reallocation
100 * during domain decomposition in mdrun.
103 /* Over allocation for small data types: int, real etc. */
104 #define over_alloc_small(n) (int)(OVER_ALLOC_FAC*(n) + 8000)
106 /* Over allocation for large data types: complex structs */
107 #define over_alloc_large(n) (int)(OVER_ALLOC_FAC*(n) + 1000)
109 int gmx_int64_to_int(gmx_int64_t step, const char *warn);
110 /* Convert a gmx_int64_t value to int.
111 * If warn!=NULL a warning message will be written
112 * to stderr when step does not fit in an int,
114 * "WARNING during %s:", where warn is printed in %s.
117 #define STEPSTRSIZE 22
119 char *gmx_step_str(gmx_int64_t i, char *buf);
120 /* Prints a gmx_int64_t value in buf and returns the pointer to buf.
121 * buf should be large enough to contain i: STEPSTRSIZE (22) chars.
122 * When multiple gmx_int64_t values are printed in the same printf call,
123 * be sure to call gmx_step_str with different buffers.
126 /* Functions to initiate and delete structures *
127 * These functions are defined in gmxlib/typedefs.c
129 void init_block(t_block *block);
130 void init_blocka(t_blocka *block);
131 void init_atom (t_atoms *at);
132 void init_mtop(gmx_mtop_t *mtop);
133 void init_top(t_topology *top);
134 void init_inputrec(t_inputrec *ir);
135 void init_energyhistory(energyhistory_t * enerhist);
136 void done_energyhistory(energyhistory_t * enerhist);
137 void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength);
138 void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int nlambda);
139 t_state *serial_init_local_state(t_state *state_global);
140 void init_df_history(df_history_t *dfhist, int nlambda);
141 void done_df_history(df_history_t *dfhist);
142 void copy_df_history(df_history_t * df_dest, df_history_t *df_source);
144 void copy_blocka(const t_blocka *src, t_blocka *dest);
146 void done_block(t_block *block);
147 void done_blocka(t_blocka *block);
148 void done_atom (t_atoms *at);
149 void done_moltype(gmx_moltype_t *molt);
150 void done_molblock(gmx_molblock_t *molb);
151 void done_mtop(gmx_mtop_t *mtop, gmx_bool bDoneSymtab);
152 void done_top(t_topology *top);
153 void done_inputrec(t_inputrec *ir);
154 void done_state(t_state *state);
156 void set_box_rel(t_inputrec *ir, t_state *state);
157 /* Set state->box_rel used in mdrun to preserve the box shape */
159 void preserve_box_shape(t_inputrec *ir, matrix box_rel, matrix b);
160 /* Preserve the box shape, b can be box or boxv */
162 void stupid_fill_block(t_block *grp, int natom, gmx_bool bOneIndexGroup);
163 /* Fill a block structure with numbers identical to the index
164 * (0, 1, 2, .. natom-1)
165 * If bOneIndexGroup, then all atoms are lumped in one index group,
166 * otherwise there is one atom per index entry
169 void stupid_fill_blocka(t_blocka *grp, int natom);
170 /* Fill a block structure with numbers identical to the index
171 * (0, 1, 2, .. natom-1)
172 * There is one atom per index entry
175 void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo);
176 /* allocate memory for the arrays, set nr to natoms and nres to 0
177 * set pdbinfo to NULL or allocate memory for it */
179 t_atoms *copy_t_atoms(t_atoms *src);
180 /* copy an atoms struct from src to a new one */
182 void add_t_atoms(t_atoms *atoms, int natom_extra, int nres_extra);
183 /* allocate extra space for more atoms and or residues */
185 void t_atoms_set_resinfo(t_atoms *atoms, int atom_ind, t_symtab *symtab,
186 const char *resname, int resnr, unsigned char ic,
187 int chainnum, char chainid);
188 /* Set the residue name, number, insertion code and chain identifier
189 * of atom index atom_ind.
192 void free_t_atoms(t_atoms *atoms, gmx_bool bFreeNames);
193 /* Free all the arrays and set the nr and nres to 0.
194 * bFreeNames tells if to free the atom and residue name strings,
195 * don't free them if they still need to be used in e.g. the topology struct.
198 t_atoms *mtop2atoms(gmx_mtop_t *mtop);
199 /* generate a t_atoms struct for the system from gmx_mtop_t */
201 real max_cutoff(real cutoff1, real cutoff2);
202 /* Returns the maximum of the cut-off's, taking into account that 0=inf. */
209 #endif /* _typedefs_h */