/* calculate charge density */
static void calc_q2all(
gmx_mtop_t *mtop, /* molecular topology */
real *q2all, real *q2allnr)
{
int imol,iatom; /* indices for loops */
real q2_all=0; /* Sum of squared charges */
int nrq_mol; /* Number of charges in a single molecule */
int nrq_all; /* Total number of charges in the MD system */
real nrq_all_r; /* No of charges in real format */
real qi,q2_mol;
gmx_moltype_t *molecule;
gmx_molblock_t *molblock;
#ifdef DEBUG
fprintf(stderr, "\nCharge density:\n");
#endif
q2_all = 0.0; /* total q squared */
nrq_all = 0; /* total number of charges in the system */
for (imol=0; imol<mtop->nmolblock; imol++) /* Loop over molecule types */
{
q2_mol=0.0; /* q squared value of this molecule */
nrq_mol=0; /* number of charges this molecule carries */
molecule = &(mtop->moltype[imol]);
molblock = &(mtop->molblock[imol]);
for (iatom=0; iatom<molblock->natoms_mol; iatom++) /* Loop over atoms in this molecule */
{
qi = molecule->atoms.atom[iatom].q; /* Charge of this atom */
/* Is this charge worth to be considered? */
if (is_charge(qi))
{
q2_mol += qi*qi;
nrq_mol++;
}
}
/* Multiply with the number of molecules present of this type and add */
q2_all += q2_mol*molblock->nmol;
nrq_all += nrq_mol*molblock->nmol;
#ifdef DEBUG
fprintf(stderr, "Molecule %2d (%5d atoms) q2_mol=%10.3e nr.mol.charges=%5d (%6dx) q2_all=%10.3e tot.charges=%d\n",
imol,molblock->natoms_mol,q2_mol,nrq_mol,molblock->nmol,q2_all,nrq_all);
#endif
}
nrq_all_r = nrq_all;
*q2all=q2_all;
*q2allnr=nrq_all;
}
/* Allocate and fill an array with coordinates and charges,
* returns the number of charges found
*/
static int prepare_x_q(real *q[], rvec *x[], gmx_mtop_t *mtop, rvec x_orig[], t_commrec *cr)
{
int i;
int nq; /* number of charged particles */
gmx_mtop_atomloop_all_t aloop;
t_atom *atom;
if (MASTER(cr))
{
snew(*q, mtop->natoms);
snew(*x, mtop->natoms);
nq = 0;
aloop = gmx_mtop_atomloop_all_init(mtop);
while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
{
if (is_charge(atom->q))
{
(*q)[nq] = atom->q;
(*x)[nq][XX] = x_orig[i][XX];
(*x)[nq][YY] = x_orig[i][YY];
(*x)[nq][ZZ] = x_orig[i][ZZ];
nq++;
}
}
/* Give back some unneeded memory */
srenew(*q, nq);
srenew(*x, nq);
}
/* Broadcast x and q in the parallel case */
if (PAR(cr))
{
/* Transfer the number of charges */
block_bc(cr, nq);
snew_bc(cr, *x, nq);
snew_bc(cr, *q, nq);
nblock_bc(cr, nq, *x);
nblock_bc(cr, nq, *q);
}
return nq;
}
/* Allocate and fill an array with coordinates and charges,
* returns the number of charges found
*/
static int prepare_x_q(real *q[], rvec *x[], gmx_mtop_t *mtop, rvec x_orig[], t_commrec *cr)
{
int i,anr_global;
int nq; /* number of charged particles */
t_atom *atom;
if (MASTER(cr))
{
snew(*q, mtop->natoms);
snew(*x, mtop->natoms);
nq=0;
for (i=0; i<mtop->natoms; i++)
{
anr_global = i;
gmx_mtop_atomnr_to_atom(mtop,anr_global,&atom);
if (is_charge(atom->q))
{
(*q)[nq] = atom->q;
(*x)[nq][XX] = x_orig[i][XX];
(*x)[nq][YY] = x_orig[i][YY];
(*x)[nq][ZZ] = x_orig[i][ZZ];
nq++;
}
}
/* Give back some unneeded memory */
srenew(*q, nq);
srenew(*x, nq);
}
/* Broadcast x and q in the parallel case */
if (PAR(cr))
{
/* Transfer the number of charges */
block_bc(cr,nq);
snew_bc(cr, *x, nq);
snew_bc(cr, *q, nq);
nblock_bc(cr,nq,*x);
nblock_bc(cr,nq,*q);
}
return nq;
}