void update_adress_weights_atom_per_atom(
int cg0,
int cg1,
t_block * cgs,
rvec x[],
t_forcerec * fr,
t_mdatoms * mdatoms,
t_pbc * pbc)
{
int icg, k, k0, k1;
atom_id * cgindex;
int adresstype;
real adressr, adressw;
rvec * ref;
real * wf;
int n_hyb, n_ex, n_cg;
n_hyb = 0;
n_cg = 0;
n_ex = 0;
adresstype = fr->adress_type;
adressr = fr->adress_ex_width;
adressw = fr->adress_hy_width;
wf = mdatoms->wf;
ref = &(fr->adress_refs);
cgindex = cgs->index;
/* Weighting function is determined for each atom individually.
* This is an approximation
* as in the theory requires an interpolation based on the center of masses.
* Should be used with caution */
for (icg = cg0; (icg < cg1); icg++)
{
k0 = cgindex[icg];
k1 = cgindex[icg + 1];
for (k = (k0); (k < k1); k++)
{
wf[k] = adress_weight(x[k], adresstype, adressr, adressw, ref, pbc, fr);
if (wf[k] == 0)
{
n_cg++;
}
else if (wf[k] == 1)
{
n_ex++;
}
else
{
n_hyb++;
}
}
}
}
void
update_adress_weights_atom(int cg0,
int cg1,
t_block * cgs,
rvec x[],
t_forcerec * fr,
t_mdatoms * mdatoms,
t_pbc * pbc)
{
int icg,k,k0,k1;
atom_id * cgindex;
int adresstype;
real adressr,adressw;
rvec * ref;
rvec * ref_2;
real * massT;
real * wf;
real * wfprime;
adresstype = fr->adress_type;
adressr = fr->adress_ex_width;
adressw = fr->adress_hy_width;
massT = mdatoms->massT;
wf = mdatoms->wf;
ref = &(fr->adress_refs);
ref_2 = &(fr->adress_refs_2);
cgindex = cgs->index;
wfprime = mdatoms->wfprime;
/* Only use first atom in charge group.
* We still can't be sure that the vsite and constructing
* atoms are on the same processor, so we must calculate
* in the same way as com adress. */
for(icg=cg0; (icg<cg1); icg++)
{
k0 = cgindex[icg];
k1 = cgindex[icg+1];
wf[k0] = adress_weight(x[k0],adresstype,adressr,adressw,ref,ref_2,pbc,fr);
wfprime[k0] = Dadress_weight(x[k0],adresstype,adressr,adressw,ref,ref_2,pbc,fr);
/* Set wf of all atoms in charge group equal to wf of first atom in charge group*/
for(k=(k0+1); (k<k1); k++)
{
wf[k] = wf[k0];
wfprime[k] = wfprime[k0];
}
}
}
void
update_adress_weights_cog(t_iparams ip[],
t_ilist ilist[],
rvec x[],
t_forcerec * fr,
t_mdatoms * mdatoms,
t_pbc * pbc)
{
int i, j, k, nr, nra, inc;
int ftype, adresstype;
t_iatom avsite, ai, aj, ak, al;
t_iatom * ia;
real adressr, adressw;
rvec * ref;
real * wf;
int n_hyb, n_ex, n_cg;
adresstype = fr->adress_type;
adressr = fr->adress_ex_width;
adressw = fr->adress_hy_width;
wf = mdatoms->wf;
ref = &(fr->adress_refs);
n_hyb = 0;
n_cg = 0;
n_ex = 0;
/* Since this is center of geometry AdResS, we know the vsite
* is in the same charge group node as the constructing atoms.
* Loop over vsite types, calculate the weight of the vsite,
* then assign that weight to the constructing atoms. */
for (ftype = 0; (ftype < F_NRE); ftype++)
{
if (interaction_function[ftype].flags & IF_VSITE)
{
nra = interaction_function[ftype].nratoms;
nr = ilist[ftype].nr;
ia = ilist[ftype].iatoms;
for (i = 0; (i < nr); )
{
/* The vsite and first constructing atom */
avsite = ia[1];
ai = ia[2];
wf[avsite] = adress_weight(x[avsite], adresstype, adressr, adressw, ref, pbc, fr);
wf[ai] = wf[avsite];
if (wf[ai] == 0)
{
n_cg++;
}
else if (wf[ai] == 1)
{
n_ex++;
}
else
{
n_hyb++;
}
/* Assign the vsite wf to rest of constructing atoms depending on type */
inc = nra+1;
switch (ftype)
{
case F_VSITE2:
aj = ia[3];
wf[aj] = wf[avsite];
break;
case F_VSITE3:
aj = ia[3];
wf[aj] = wf[avsite];
ak = ia[4];
wf[ak] = wf[avsite];
break;
case F_VSITE3FD:
aj = ia[3];
wf[aj] = wf[avsite];
ak = ia[4];
wf[ak] = wf[avsite];
break;
case F_VSITE3FAD:
aj = ia[3];
wf[aj] = wf[avsite];
ak = ia[4];
wf[ak] = wf[avsite];
break;
case F_VSITE3OUT:
aj = ia[3];
wf[aj] = wf[avsite];
ak = ia[4];
wf[ak] = wf[avsite];
break;
case F_VSITE4FD:
aj = ia[3];
wf[aj] = wf[avsite];
ak = ia[4];
wf[ak] = wf[avsite];
al = ia[5];
wf[al] = wf[avsite];
break;
case F_VSITE4FDN:
aj = ia[3];
wf[aj] = wf[avsite];
ak = ia[4];
wf[ak] = wf[avsite];
al = ia[5];
wf[al] = wf[avsite];
break;
case F_VSITEN:
inc = 3*ip[ia[0]].vsiten.n;
for (j = 3; j < inc; j += 3)
{
ai = ia[j+2];
wf[ai] = wf[avsite];
}
break;
default:
gmx_fatal(FARGS, "No such vsite type %d in %s, line %d",
ftype, __FILE__, __LINE__);
}
/* Increment loop variables */
i += inc;
ia += inc;
}
}
}
}
void
update_adress_weights_com(FILE gmx_unused * fplog,
int cg0,
int cg1,
t_block * cgs,
rvec x[],
t_forcerec * fr,
t_mdatoms * mdatoms,
t_pbc * pbc)
{
int icg, k, k0, k1, d;
real nrcg, inv_ncg, mtot, inv_mtot;
atom_id * cgindex;
rvec ix;
int adresstype;
real adressr, adressw;
rvec * ref;
real * massT;
real * wf;
int n_hyb, n_ex, n_cg;
n_hyb = 0;
n_cg = 0;
n_ex = 0;
adresstype = fr->adress_type;
adressr = fr->adress_ex_width;
adressw = fr->adress_hy_width;
massT = mdatoms->massT;
wf = mdatoms->wf;
ref = &(fr->adress_refs);
/* Since this is center of mass AdResS, the vsite is not guaranteed
* to be on the same node as the constructing atoms. Therefore we
* loop over the charge groups, calculate their center of mass,
* then use this to calculate wf for each atom. This wastes vsite
* construction, but it's the only way to assure that the explicit
* atoms have the same wf as their vsite. */
#ifdef DEBUG
fprintf(fplog, "Calculating center of mass for charge groups %d to %d\n",
cg0, cg1);
#endif
cgindex = cgs->index;
/* Compute the center of mass for all charge groups */
for (icg = cg0; (icg < cg1); icg++)
{
k0 = cgindex[icg];
k1 = cgindex[icg+1];
nrcg = k1-k0;
if (nrcg == 1)
{
wf[k0] = adress_weight(x[k0], adresstype, adressr, adressw, ref, pbc, fr);
if (wf[k0] == 0)
{
n_cg++;
}
else if (wf[k0] == 1)
{
n_ex++;
}
else
{
n_hyb++;
}
}
else
{
mtot = 0.0;
for (k = k0; (k < k1); k++)
{
mtot += massT[k];
}
if (mtot > 0.0)
{
inv_mtot = 1.0/mtot;
clear_rvec(ix);
for (k = k0; (k < k1); k++)
{
for (d = 0; (d < DIM); d++)
{
ix[d] += x[k][d]*massT[k];
}
}
for (d = 0; (d < DIM); d++)
{
ix[d] *= inv_mtot;
}
}
/* Calculate the center of gravity if the charge group mtot=0 (only vsites) */
else
{
inv_ncg = 1.0/nrcg;
clear_rvec(ix);
for (k = k0; (k < k1); k++)
{
for (d = 0; (d < DIM); d++)
{
ix[d] += x[k][d];
}
}
for (d = 0; (d < DIM); d++)
{
ix[d] *= inv_ncg;
}
}
/* Set wf of all atoms in charge group equal to wf of com */
wf[k0] = adress_weight(ix, adresstype, adressr, adressw, ref, pbc, fr);
if (wf[k0] == 0)
{
n_cg++;
}
else if (wf[k0] == 1)
{
n_ex++;
}
else
{
n_hyb++;
}
for (k = (k0+1); (k < k1); k++)
{
wf[k] = wf[k0];
}
}
}
}