static void get_vsite_masses(const gmx_moltype_t *moltype,
const gmx_ffparams_t *ffparams,
real *vsite_m,
int *n_nonlin_vsite)
{
int ft, i;
const t_ilist *il;
*n_nonlin_vsite = 0;
/* Check for virtual sites, determine mass from constructing atoms */
for (ft = 0; ft < F_NRE; ft++)
{
if (IS_VSITE(ft))
{
il = &moltype->ilist[ft];
for (i = 0; i < il->nr; i += 1+NRAL(ft))
{
const t_iparams *ip;
real cam[5] = {0}, inv_mass, coeff, m_aj;
int a1, j, aj;
ip = &ffparams->iparams[il->iatoms[i]];
a1 = il->iatoms[i+1];
if (ft != F_VSITEN)
{
for (j = 1; j < NRAL(ft); j++)
{
cam[j] = moltype->atoms.atom[il->iatoms[i+1+j]].m;
if (cam[j] == 0)
{
cam[j] = vsite_m[il->iatoms[i+1+j]];
}
if (cam[j] == 0)
{
gmx_fatal(FARGS, "In molecule type '%s' %s construction involves atom %d, which is a virtual site of equal or high complexity. This is not supported.",
*moltype->name,
interaction_function[ft].longname,
il->iatoms[i+1+j]+1);
}
}
}
switch (ft)
{
case F_VSITE2:
/* Exact */
vsite_m[a1] = (cam[1]*cam[2])/(cam[2]*sqr(1-ip->vsite.a) + cam[1]*sqr(ip->vsite.a));
break;
case F_VSITE3:
/* Exact */
vsite_m[a1] = (cam[1]*cam[2]*cam[3])/(cam[2]*cam[3]*sqr(1-ip->vsite.a-ip->vsite.b) + cam[1]*cam[3]*sqr(ip->vsite.a) + cam[1]*cam[2]*sqr(ip->vsite.b));
break;
case F_VSITEN:
/* Exact */
inv_mass = 0;
for (j = 0; j < 3*ffparams->iparams[il->iatoms[i]].vsiten.n; j += 3)
{
aj = il->iatoms[i+j+2];
coeff = ffparams->iparams[il->iatoms[i+j]].vsiten.a;
if (moltype->atoms.atom[aj].ptype == eptVSite)
{
m_aj = vsite_m[aj];
}
else
{
m_aj = moltype->atoms.atom[aj].m;
}
if (m_aj <= 0)
{
gmx_incons("The mass of a vsiten constructing atom is <= 0");
}
inv_mass += coeff*coeff/m_aj;
}
vsite_m[a1] = 1/inv_mass;
/* Correct for loop increment of i */
i += j - 1 - NRAL(ft);
break;
default:
/* Use the mass of the lightest constructing atom.
* This is an approximation.
* If the distance of the virtual site to the
* constructing atom is less than all distances
* between constructing atoms, this is a safe
* over-estimate of the displacement of the vsite.
* This condition holds for all H mass replacement
* vsite constructions, except for SP2/3 groups.
* In SP3 groups one H will have a F_VSITE3
* construction, so even there the total drift
* estimate shouldn't be far off.
*/
assert(j >= 1);
vsite_m[a1] = cam[1];
for (j = 2; j < NRAL(ft); j++)
{
vsite_m[a1] = min(vsite_m[a1], cam[j]);
}
(*n_nonlin_vsite)++;
break;
}
if (gmx_debug_at)
{
fprintf(debug, "atom %4d %-20s mass %6.3f\n",
a1, interaction_function[ft].longname, vsite_m[a1]);
}
}
}
}
}
static void get_verlet_buffer_atomtypes(const gmx_mtop_t *mtop,
verletbuf_atomtype_t **att_p,
int *natt_p,
int *n_nonlin_vsite)
{
verletbuf_atomtype_t *att;
int natt;
int mb, nmol, ft, i, j, a1, a2, a3, a;
const t_atoms *atoms;
const t_ilist *il;
const t_atom *at;
const t_iparams *ip;
real *con_m, *vsite_m, cam[5];
att = NULL;
natt = 0;
if (n_nonlin_vsite != NULL)
{
*n_nonlin_vsite = 0;
}
for (mb = 0; mb < mtop->nmolblock; mb++)
{
nmol = mtop->molblock[mb].nmol;
atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
/* Check for constraints, as they affect the kinetic energy */
snew(con_m, atoms->nr);
snew(vsite_m, atoms->nr);
for (ft = F_CONSTR; ft <= F_CONSTRNC; ft++)
{
il = &mtop->moltype[mtop->molblock[mb].type].ilist[ft];
for (i = 0; i < il->nr; i += 1+NRAL(ft))
{
a1 = il->iatoms[i+1];
a2 = il->iatoms[i+2];
con_m[a1] += atoms->atom[a2].m;
con_m[a2] += atoms->atom[a1].m;
}
}
il = &mtop->moltype[mtop->molblock[mb].type].ilist[F_SETTLE];
for (i = 0; i < il->nr; i += 1+NRAL(F_SETTLE))
{
a1 = il->iatoms[i+1];
a2 = il->iatoms[i+2];
a3 = il->iatoms[i+3];
con_m[a1] += atoms->atom[a2].m + atoms->atom[a3].m;
con_m[a2] += atoms->atom[a1].m + atoms->atom[a3].m;
con_m[a3] += atoms->atom[a1].m + atoms->atom[a2].m;
}
/* Check for virtual sites, determine mass from constructing atoms */
for (ft = 0; ft < F_NRE; ft++)
{
if (IS_VSITE(ft))
{
il = &mtop->moltype[mtop->molblock[mb].type].ilist[ft];
for (i = 0; i < il->nr; i += 1+NRAL(ft))
{
ip = &mtop->ffparams.iparams[il->iatoms[i]];
a1 = il->iatoms[i+1];
for (j = 1; j < NRAL(ft); j++)
{
cam[j] = atoms->atom[il->iatoms[i+1+j]].m;
if (cam[j] == 0)
{
cam[j] = vsite_m[il->iatoms[i+1+j]];
}
if (cam[j] == 0)
{
gmx_fatal(FARGS, "In molecule type '%s' %s construction involves atom %d, which is a virtual site of equal or high complexity. This is not supported.",
*mtop->moltype[mtop->molblock[mb].type].name,
interaction_function[ft].longname,
il->iatoms[i+1+j]+1);
}
}
switch (ft)
{
case F_VSITE2:
/* Exact except for ignoring constraints */
vsite_m[a1] = (cam[2]*sqr(1-ip->vsite.a) + cam[1]*sqr(ip->vsite.a))/(cam[1]*cam[2]);
break;
case F_VSITE3:
/* Exact except for ignoring constraints */
vsite_m[a1] = (cam[2]*cam[3]*sqr(1-ip->vsite.a-ip->vsite.b) + cam[1]*cam[3]*sqr(ip->vsite.a) + cam[1]*cam[2]*sqr(ip->vsite.b))/(cam[1]*cam[2]*cam[3]);
break;
default:
/* Use the mass of the lightest constructing atom.
* This is an approximation.
* If the distance of the virtual site to the
* constructing atom is less than all distances
* between constructing atoms, this is a safe
* over-estimate of the displacement of the vsite.
* This condition holds for all H mass replacement
* replacement vsite constructions, except for SP2/3
* groups. In SP3 groups one H will have a F_VSITE3
* construction, so even there the total drift
* estimation shouldn't be far off.
*/
assert(j >= 1);
vsite_m[a1] = cam[1];
for (j = 2; j < NRAL(ft); j++)
{
vsite_m[a1] = min(vsite_m[a1], cam[j]);
}
if (n_nonlin_vsite != NULL)
{
*n_nonlin_vsite += nmol;
}
break;
}
}
}
}
for (a = 0; a < atoms->nr; a++)
{
at = &atoms->atom[a];
/* We consider an atom constrained, #DOF=2, when it is
* connected with constraints to one or more atoms with
* total mass larger than 1.5 that of the atom itself.
*/
add_at(&att, &natt,
at->m, at->type, at->q, con_m[a] > 1.5*at->m, nmol);
}
sfree(vsite_m);
sfree(con_m);
}
if (gmx_debug_at)
{
for (a = 0; a < natt; a++)
{
fprintf(debug, "type %d: m %5.2f t %d q %6.3f con %d n %d\n",
a, att[a].mass, att[a].type, att[a].q, att[a].con, att[a].n);
}
}
*att_p = att;
*natt_p = natt;
}
