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42 #define BIG_STRLEN 1048576
44 #include <sys/types.h>
46 #include "types/simple.h"
47 #include "types/enums.h"
48 #include "types/block.h"
49 #include "types/symtab.h"
50 #include "types/idef.h"
51 #include "types/atoms.h"
52 #include "types/trx.h"
53 #include "types/topology.h"
54 #include "types/energy.h"
55 #include "types/inputrec.h"
56 #include "types/ishift.h"
57 #include "types/graph.h"
58 #include "types/nrnb.h"
59 #include "types/nblist.h"
60 #include "types/nsgrid.h"
61 #include "types/commrec.h"
62 #include "types/forcerec.h"
63 #include "types/fcdata.h"
64 #include "types/mdatom.h"
65 #include "types/pbc.h"
66 #include "types/ifunc.h"
67 #include "types/filenm.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"
80 * Memory (re)allocation can be VERY slow, especially with some
81 * MPI libraries that replace the standard malloc and realloc calls.
82 * To avoid slow memory allocation we use over_alloc to set the memory
83 * allocation size for large data blocks. Since this scales the size
84 * with a factor, we use log(n) realloc calls instead of n.
85 * This can reduce allocation times from minutes to seconds.
87 /* This factor leads to 4 realloc calls to double the array size */
88 #define OVER_ALLOC_FAC 1.19
90 void set_over_alloc_dd(gmx_bool set);
91 /* Turns over allocation for variable size atoms/cg/top arrays on or off,
95 int over_alloc_dd(int n);
96 /* Returns n when domain decomposition over allocation is off.
97 * Returns OVER_ALLOC_FAC*n + 100 when over allocation in on.
98 * This is to avoid frequent reallocation
99 * during domain decomposition in mdrun.
102 /* Over allocation for small data types: int, real etc. */
103 #define over_alloc_small(n) (OVER_ALLOC_FAC*(n) + 8000)
105 /* Over allocation for large data types: complex structs */
106 #define over_alloc_large(n) (OVER_ALLOC_FAC*(n) + 1000)
108 int gmx_large_int_to_int(gmx_large_int_t step,const char *warn);
109 /* Convert a gmx_large_int_t value to int.
110 * If warn!=NULL a warning message will be written
111 * to stderr when step does not fit in an int,
113 * "WARNING during %s:", where warn is printed in %s.
116 #define STEPSTRSIZE 22
118 char *gmx_step_str(gmx_large_int_t i,char *buf);
119 /* Prints a gmx_large_int_t value in buf and returns the pointer to buf.
120 * buf should be large enough to contain i: STEPSTRSIZE (22) chars.
121 * When multiple gmx_large_int_t values are printed in the same printf call,
122 * be sure to call gmx_step_str with different buffers.
125 /* Functions to initiate and delete structures *
126 * These functions are defined in gmxlib/typedefs.c
128 void init_block(t_block *block);
129 void init_blocka(t_blocka *block);
130 void init_atom (t_atoms *at);
131 void init_mtop(gmx_mtop_t *mtop);
132 void init_top (t_topology *top);
133 void init_inputrec(t_inputrec *ir);
134 void init_gtc_state(t_state *state,int ngtc, int nnhpres, int nhchainlength);
135 void init_state(t_state *state,int natoms,int ngtc, int nnhpres, int nhchainlength);
137 void copy_blocka(const t_blocka *src,t_blocka *dest);
139 void done_block(t_block *block);
140 void done_blocka(t_blocka *block);
141 void done_atom (t_atoms *at);
142 void done_moltype(gmx_moltype_t *molt);
143 void done_molblock(gmx_molblock_t *molb);
144 void done_mtop(gmx_mtop_t *mtop,gmx_bool bDoneSymtab);
145 void done_top(t_topology *top);
146 void done_inputrec(t_inputrec *ir);
147 void done_state(t_state *state);
149 void set_box_rel(t_inputrec *ir,t_state *state);
150 /* Set state->box_rel used in mdrun to preserve the box shape */
152 void preserve_box_shape(t_inputrec *ir,matrix box_rel,matrix b);
153 /* Preserve the box shape, b can be box or boxv */
155 void stupid_fill_block(t_block *grp, int natom,gmx_bool bOneIndexGroup);
156 /* Fill a block structure with numbers identical to the index
157 * (0, 1, 2, .. natom-1)
158 * If bOneIndexGroup, then all atoms are lumped in one index group,
159 * otherwise there is one atom per index entry
162 void stupid_fill_blocka(t_blocka *grp, int natom);
163 /* Fill a block structure with numbers identical to the index
164 * (0, 1, 2, .. natom-1)
165 * There is one atom per index entry
168 void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo);
169 /* allocate memory for the arrays, set nr to natoms and nres to 0
170 * set pdbinfo to NULL or allocate memory for it */
172 t_atoms *copy_t_atoms(t_atoms *src);
173 /* copy an atoms struct from src to a new one */
175 void add_t_atoms(t_atoms *atoms,int natom_extra,int nres_extra);
176 /* allocate extra space for more atoms and or residues */
178 void t_atoms_set_resinfo(t_atoms *atoms,int atom_ind,t_symtab *symtab,
179 const char *resname,int resnr,unsigned char ic,
180 int chainnum, char chainid);
181 /* Set the residue name, number, insertion code and chain identifier
182 * of atom index atom_ind.
185 void free_t_atoms(t_atoms *atoms,gmx_bool bFreeNames);
186 /* Free all the arrays and set the nr and nres to 0.
187 * bFreeNames tells if to free the atom and residue name strings,
188 * don't free them if they still need to be used in e.g. the topology struct.
191 t_atoms *mtop2atoms(gmx_mtop_t *mtop);
192 /* generate a t_atoms struct for the system from gmx_mtop_t */
194 real max_cutoff(real cutoff1,real cutoff2);
195 /* Returns the maximum of the cut-off's, taking into account that 0=inf. */
202 #endif /* _typedefs_h */