* the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "thread_mpi/threads.h"
+#include "gromacs/legacyheaders/typedefs.h"
-#include "smalloc.h"
-#include "symtab.h"
-#include "vec.h"
-#include "pbc.h"
-#include "macros.h"
#include <string.h>
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/random/random.h"
+#include "gromacs/utility/smalloc.h"
/* The source code in this file should be thread-safe.
Please keep it that way. */
-
-
-static gmx_bool bOverAllocDD = FALSE;
-static tMPI_Thread_mutex_t over_alloc_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
-
-
-void set_over_alloc_dd(gmx_bool set)
-{
- tMPI_Thread_mutex_lock(&over_alloc_mutex);
- /* we just make sure that we don't set this at the same time.
- We don't worry too much about reading this rarely-set variable */
- bOverAllocDD = set;
- tMPI_Thread_mutex_unlock(&over_alloc_mutex);
-}
-
-int over_alloc_dd(int n)
-{
- if (bOverAllocDD)
- {
- return OVER_ALLOC_FAC*n + 100;
- }
- else
- {
- return n;
- }
-}
-
int gmx_int64_to_int(gmx_int64_t step, const char *warn)
{
int i;
return i;
}
-char *gmx_step_str(gmx_int64_t i, char *buf)
-{
- sprintf(buf, "%"GMX_PRId64, i);
-
- return buf;
-}
-
-void init_block(t_block *block)
-{
- int i;
-
- block->nr = 0;
- block->nalloc_index = 1;
- snew(block->index, block->nalloc_index);
- block->index[0] = 0;
-}
-
-void init_blocka(t_blocka *block)
-{
- int i;
-
- block->nr = 0;
- block->nra = 0;
- block->nalloc_index = 1;
- snew(block->index, block->nalloc_index);
- block->index[0] = 0;
- block->nalloc_a = 0;
- block->a = NULL;
-}
-
-void init_atom(t_atoms *at)
-{
- int i;
-
- at->nr = 0;
- at->nres = 0;
- at->atom = NULL;
- at->resinfo = NULL;
- at->atomname = NULL;
- at->atomtype = NULL;
- at->atomtypeB = NULL;
- at->pdbinfo = NULL;
-}
-
-void init_atomtypes(t_atomtypes *at)
-{
- at->nr = 0;
- at->radius = NULL;
- at->vol = NULL;
- at->atomnumber = NULL;
- at->gb_radius = NULL;
- at->S_hct = NULL;
-}
-
-void init_groups(gmx_groups_t *groups)
-{
- int g;
-
- groups->ngrpname = 0;
- groups->grpname = NULL;
- for (g = 0; (g < egcNR); g++)
- {
- groups->grps[g].nm_ind = NULL;
- groups->ngrpnr[g] = 0;
- groups->grpnr[g] = NULL;
- }
-
-}
-
-void init_mtop(gmx_mtop_t *mtop)
-{
- mtop->name = NULL;
- mtop->nmoltype = 0;
- mtop->moltype = NULL;
- mtop->nmolblock = 0;
- mtop->molblock = NULL;
- mtop->maxres_renum = 0;
- mtop->maxresnr = -1;
- init_groups(&mtop->groups);
- init_block(&mtop->mols);
- open_symtab(&mtop->symtab);
-}
-
-void init_top(t_topology *top)
-{
- int i;
-
- top->name = NULL;
- init_atom (&(top->atoms));
- init_atomtypes(&(top->atomtypes));
- init_block(&top->cgs);
- init_block(&top->mols);
- init_blocka(&top->excls);
- open_symtab(&top->symtab);
-}
-
void init_inputrec(t_inputrec *ir)
{
memset(ir, 0, (size_t)sizeof(*ir));
snew(ir->simtempvals, 1);
}
-void stupid_fill_block(t_block *grp, int natom, gmx_bool bOneIndexGroup)
-{
- int i;
-
- if (bOneIndexGroup)
- {
- grp->nalloc_index = 2;
- snew(grp->index, grp->nalloc_index);
- grp->index[0] = 0;
- grp->index[1] = natom;
- grp->nr = 1;
- }
- else
- {
- grp->nalloc_index = natom+1;
- snew(grp->index, grp->nalloc_index);
- snew(grp->index, natom+1);
- for (i = 0; (i <= natom); i++)
- {
- grp->index[i] = i;
- }
- grp->nr = natom;
- }
-}
-
-void stupid_fill_blocka(t_blocka *grp, int natom)
-{
- int i;
-
- grp->nalloc_a = natom;
- snew(grp->a, grp->nalloc_a);
- for (i = 0; (i < natom); i++)
- {
- grp->a[i] = i;
- }
- grp->nra = natom;
-
- grp->nalloc_index = natom + 1;
- snew(grp->index, grp->nalloc_index);
- for (i = 0; (i <= natom); i++)
- {
- grp->index[i] = i;
- }
- grp->nr = natom;
-}
-
-void copy_blocka(const t_blocka *src, t_blocka *dest)
-{
- int i;
-
- dest->nr = src->nr;
- dest->nalloc_index = dest->nr + 1;
- snew(dest->index, dest->nalloc_index);
- for (i = 0; i < dest->nr+1; i++)
- {
- dest->index[i] = src->index[i];
- }
- dest->nra = src->nra;
- dest->nalloc_a = dest->nra + 1;
- snew(dest->a, dest->nalloc_a);
- for (i = 0; i < dest->nra+1; i++)
- {
- dest->a[i] = src->a[i];
- }
-}
-
-void done_block(t_block *block)
-{
- block->nr = 0;
- sfree(block->index);
- block->nalloc_index = 0;
-}
-
-void done_blocka(t_blocka *block)
-{
- block->nr = 0;
- block->nra = 0;
- sfree(block->index);
- sfree(block->a);
- block->index = NULL;
- block->a = NULL;
- block->nalloc_index = 0;
- block->nalloc_a = 0;
-}
-
-void done_atom (t_atoms *at)
-{
- at->nr = 0;
- at->nres = 0;
- sfree(at->atom);
- sfree(at->resinfo);
- sfree(at->atomname);
- sfree(at->atomtype);
- sfree(at->atomtypeB);
- if (at->pdbinfo)
- {
- sfree(at->pdbinfo);
- }
-}
-
-void done_atomtypes(t_atomtypes *atype)
-{
- atype->nr = 0;
- sfree(atype->radius);
- sfree(atype->vol);
- sfree(atype->surftens);
- sfree(atype->atomnumber);
- sfree(atype->gb_radius);
- sfree(atype->S_hct);
-}
-
-void done_moltype(gmx_moltype_t *molt)
-{
- int f;
-
- done_atom(&molt->atoms);
- done_block(&molt->cgs);
- done_blocka(&molt->excls);
-
- for (f = 0; f < F_NRE; f++)
- {
- sfree(molt->ilist[f].iatoms);
- molt->ilist[f].nalloc = 0;
- }
-}
-
-void done_molblock(gmx_molblock_t *molb)
-{
- if (molb->nposres_xA > 0)
- {
- molb->nposres_xA = 0;
- free(molb->posres_xA);
- }
- if (molb->nposres_xB > 0)
- {
- molb->nposres_xB = 0;
- free(molb->posres_xB);
- }
-}
-
-void done_mtop(gmx_mtop_t *mtop, gmx_bool bDoneSymtab)
-{
- int i;
-
- if (bDoneSymtab)
- {
- done_symtab(&mtop->symtab);
- }
-
- sfree(mtop->ffparams.functype);
- sfree(mtop->ffparams.iparams);
-
- for (i = 0; i < mtop->nmoltype; i++)
- {
- done_moltype(&mtop->moltype[i]);
- }
- sfree(mtop->moltype);
- for (i = 0; i < mtop->nmolblock; i++)
- {
- done_molblock(&mtop->molblock[i]);
- }
- sfree(mtop->molblock);
- done_block(&mtop->mols);
-}
-
-void done_top(t_topology *top)
-{
- int f;
-
- sfree(top->idef.functype);
- sfree(top->idef.iparams);
- for (f = 0; f < F_NRE; ++f)
- {
- sfree(top->idef.il[f].iatoms);
- top->idef.il[f].iatoms = NULL;
- top->idef.il[f].nalloc = 0;
- }
-
- done_atom (&(top->atoms));
-
- /* For GB */
- done_atomtypes(&(top->atomtypes));
-
- done_symtab(&(top->symtab));
- done_block(&(top->cgs));
- done_block(&(top->mols));
- done_blocka(&(top->excls));
-}
-
static void done_pull_group(t_pull_group *pgrp)
{
if (pgrp->nat > 0)
}
}
-void add_t_atoms(t_atoms *atoms, int natom_extra, int nres_extra)
-{
- int i;
-
- if (natom_extra > 0)
- {
- srenew(atoms->atomname, atoms->nr+natom_extra);
- srenew(atoms->atom, atoms->nr+natom_extra);
- if (NULL != atoms->pdbinfo)
- {
- srenew(atoms->pdbinfo, atoms->nr+natom_extra);
- }
- if (NULL != atoms->atomtype)
- {
- srenew(atoms->atomtype, atoms->nr+natom_extra);
- }
- if (NULL != atoms->atomtypeB)
- {
- srenew(atoms->atomtypeB, atoms->nr+natom_extra);
- }
- for (i = atoms->nr; (i < atoms->nr+natom_extra); i++)
- {
- atoms->atomname[i] = NULL;
- memset(&atoms->atom[i], 0, sizeof(atoms->atom[i]));
- if (NULL != atoms->pdbinfo)
- {
- memset(&atoms->pdbinfo[i], 0, sizeof(atoms->pdbinfo[i]));
- }
- if (NULL != atoms->atomtype)
- {
- atoms->atomtype[i] = NULL;
- }
- if (NULL != atoms->atomtypeB)
- {
- atoms->atomtypeB[i] = NULL;
- }
- }
- atoms->nr += natom_extra;
- }
- if (nres_extra > 0)
- {
- srenew(atoms->resinfo, atoms->nres+nres_extra);
- for (i = atoms->nres; (i < atoms->nres+nres_extra); i++)
- {
- memset(&atoms->resinfo[i], 0, sizeof(atoms->resinfo[i]));
- }
- atoms->nres += nres_extra;
- }
-}
-
-void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo)
-{
- atoms->nr = natoms;
- atoms->nres = 0;
- snew(atoms->atomname, natoms);
- atoms->atomtype = NULL;
- atoms->atomtypeB = NULL;
- snew(atoms->resinfo, natoms);
- snew(atoms->atom, natoms);
- if (bPdbinfo)
- {
- snew(atoms->pdbinfo, natoms);
- }
- else
- {
- atoms->pdbinfo = NULL;
- }
-}
-
-t_atoms *copy_t_atoms(t_atoms *src)
-{
- t_atoms *dst;
- int i;
-
- snew(dst, 1);
- init_t_atoms(dst, src->nr, (NULL != src->pdbinfo));
- dst->nr = src->nr;
- if (NULL != src->atomname)
- {
- snew(dst->atomname, src->nr);
- }
- if (NULL != src->atomtype)
- {
- snew(dst->atomtype, src->nr);
- }
- if (NULL != src->atomtypeB)
- {
- snew(dst->atomtypeB, src->nr);
- }
- for (i = 0; (i < src->nr); i++)
- {
- dst->atom[i] = src->atom[i];
- if (NULL != src->pdbinfo)
- {
- dst->pdbinfo[i] = src->pdbinfo[i];
- }
- if (NULL != src->atomname)
- {
- dst->atomname[i] = src->atomname[i];
- }
- if (NULL != src->atomtype)
- {
- dst->atomtype[i] = src->atomtype[i];
- }
- if (NULL != src->atomtypeB)
- {
- dst->atomtypeB[i] = src->atomtypeB[i];
- }
- }
- dst->nres = src->nres;
- for (i = 0; (i < src->nres); i++)
- {
- dst->resinfo[i] = src->resinfo[i];
- }
- return dst;
-}
-
-void t_atoms_set_resinfo(t_atoms *atoms, int atom_ind, t_symtab *symtab,
- const char *resname, int resnr, unsigned char ic,
- int chainnum, char chainid)
-{
- t_resinfo *ri;
-
- ri = &atoms->resinfo[atoms->atom[atom_ind].resind];
- ri->name = put_symtab(symtab, resname);
- ri->rtp = NULL;
- ri->nr = resnr;
- ri->ic = ic;
- ri->chainnum = chainnum;
- ri->chainid = chainid;
-}
-
-void free_t_atoms(t_atoms *atoms, gmx_bool bFreeNames)
-{
- int i;
-
- if (bFreeNames && atoms->atomname != NULL)
- {
- for (i = 0; i < atoms->nr; i++)
- {
- if (atoms->atomname[i] != NULL)
- {
- sfree(*atoms->atomname[i]);
- *atoms->atomname[i] = NULL;
- }
- }
- }
- if (bFreeNames && atoms->resinfo != NULL)
- {
- for (i = 0; i < atoms->nres; i++)
- {
- if (atoms->resinfo[i].name != NULL)
- {
- sfree(*atoms->resinfo[i].name);
- *atoms->resinfo[i].name = NULL;
- }
- }
- }
- if (bFreeNames && atoms->atomtype != NULL)
- {
- for (i = 0; i < atoms->nr; i++)
- {
- if (atoms->atomtype[i] != NULL)
- {
- sfree(*atoms->atomtype[i]);
- *atoms->atomtype[i] = NULL;
- }
- }
- }
- if (bFreeNames && atoms->atomtypeB != NULL)
- {
- for (i = 0; i < atoms->nr; i++)
- {
- if (atoms->atomtypeB[i] != NULL)
- {
- sfree(*atoms->atomtypeB[i]);
- *atoms->atomtypeB[i] = NULL;
- }
- }
- }
- sfree(atoms->atomname);
- sfree(atoms->atomtype);
- sfree(atoms->atomtypeB);
- sfree(atoms->resinfo);
- sfree(atoms->atom);
- sfree(atoms->pdbinfo);
- atoms->nr = 0;
- atoms->nres = 0;
- atoms->atomname = NULL;
- atoms->atomtype = NULL;
- atoms->atomtypeB = NULL;
- atoms->resinfo = NULL;
- atoms->atom = NULL;
- atoms->pdbinfo = NULL;
-}
-
real max_cutoff(real cutoff1, real cutoff2)
{
if (cutoff1 == 0 || cutoff2 == 0)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff