/* calculates center of mass of selection index from all coordinates x */
void pull_calc_coms(t_commrec *cr,
t_pull *pull, t_mdatoms *md, t_pbc *pbc, double t,
rvec x[], rvec *xp)
{
int g, i, ii, m;
real mass, w, wm, twopi_box = 0;
double wmass, wwmass, invwmass;
dvec com, comp;
double cm, sm, cmp, smp, ccm, csm, ssm, csw, snw;
rvec *xx[2], x_pbc = {0, 0, 0}, dx;
t_pull_group *pgrp;
if (pull->rbuf == NULL)
{
snew(pull->rbuf, pull->ngroup);
}
if (pull->dbuf == NULL)
{
snew(pull->dbuf, 3*pull->ngroup);
}
if (pull->bRefAt)
{
pull_set_pbcatoms(cr, pull, md, x, pull->rbuf);
}
if (pull->cosdim >= 0)
{
for (m = pull->cosdim+1; m < pull->npbcdim; m++)
{
if (pbc->box[m][pull->cosdim] != 0)
{
gmx_fatal(FARGS, "Can not do cosine weighting for trilinic dimensions");
}
}
twopi_box = 2.0*M_PI/pbc->box[pull->cosdim][pull->cosdim];
}
for (g = 0; g < pull->ngroup; g++)
{
pgrp = &pull->group[g];
clear_dvec(com);
clear_dvec(comp);
wmass = 0;
wwmass = 0;
cm = 0;
sm = 0;
cmp = 0;
smp = 0;
ccm = 0;
csm = 0;
ssm = 0;
if (!(g == 0 && PULL_CYL(pull)))
{
if (pgrp->epgrppbc == epgrppbcREFAT)
{
/* Set the pbc atom */
copy_rvec(pull->rbuf[g], x_pbc);
}
w = 1;
for (i = 0; i < pgrp->nat_loc; i++)
{
ii = pgrp->ind_loc[i];
mass = md->massT[ii];
if (pgrp->epgrppbc != epgrppbcCOS)
{
if (pgrp->weight_loc)
{
w = pgrp->weight_loc[i];
}
wm = w*mass;
wmass += wm;
wwmass += wm*w;
if (pgrp->epgrppbc == epgrppbcNONE)
{
/* Plain COM: sum the coordinates */
for (m = 0; m < DIM; m++)
{
com[m] += wm*x[ii][m];
}
if (xp)
{
for (m = 0; m < DIM; m++)
{
comp[m] += wm*xp[ii][m];
}
}
}
else
{
/* Sum the difference with the reference atom */
pbc_dx(pbc, x[ii], x_pbc, dx);
for (m = 0; m < DIM; m++)
{
com[m] += wm*dx[m];
}
if (xp)
{
/* For xp add the difference between xp and x to dx,
* such that we use the same periodic image,
* also when xp has a large displacement.
*/
for (m = 0; m < DIM; m++)
{
comp[m] += wm*(dx[m] + xp[ii][m] - x[ii][m]);
}
}
}
}
else
{
/* Determine cos and sin sums */
csw = cos(x[ii][pull->cosdim]*twopi_box);
snw = sin(x[ii][pull->cosdim]*twopi_box);
cm += csw*mass;
sm += snw*mass;
ccm += csw*csw*mass;
csm += csw*snw*mass;
ssm += snw*snw*mass;
if (xp)
{
csw = cos(xp[ii][pull->cosdim]*twopi_box);
snw = sin(xp[ii][pull->cosdim]*twopi_box);
cmp += csw*mass;
smp += snw*mass;
}
}
}
}
/* Copy local sums to a buffer for global summing */
switch (pgrp->epgrppbc)
{
case epgrppbcNONE:
case epgrppbcREFAT:
copy_dvec(com, pull->dbuf[g*3]);
copy_dvec(comp, pull->dbuf[g*3+1]);
pull->dbuf[g*3+2][0] = wmass;
pull->dbuf[g*3+2][1] = wwmass;
pull->dbuf[g*3+2][2] = 0;
break;
case epgrppbcCOS:
pull->dbuf[g*3 ][0] = cm;
pull->dbuf[g*3 ][1] = sm;
pull->dbuf[g*3 ][2] = 0;
pull->dbuf[g*3+1][0] = ccm;
pull->dbuf[g*3+1][1] = csm;
pull->dbuf[g*3+1][2] = ssm;
pull->dbuf[g*3+2][0] = cmp;
pull->dbuf[g*3+2][1] = smp;
pull->dbuf[g*3+2][2] = 0;
break;
}
}
if (cr && PAR(cr))
{
/* Sum the contributions over the nodes */
gmx_sumd(pull->ngroup*3*DIM, pull->dbuf[0], cr);
}
for (g = 0; g < pull->ngroup; g++)
{
pgrp = &pull->group[g];
if (pgrp->nat > 0 && !(g == 0 && PULL_CYL(pull)))
{
if (pgrp->epgrppbc != epgrppbcCOS)
{
/* Determine the inverse mass */
wmass = pull->dbuf[g*3+2][0];
wwmass = pull->dbuf[g*3+2][1];
invwmass = 1/wmass;
/* invtm==0 signals a frozen group, so then we should keep it zero */
if (pgrp->invtm > 0)
{
pgrp->wscale = wmass/wwmass;
pgrp->invtm = 1.0/(pgrp->wscale*wmass);
}
/* Divide by the total mass */
for (m = 0; m < DIM; m++)
{
pgrp->x[m] = pull->dbuf[g*3 ][m]*invwmass;
if (xp)
{
pgrp->xp[m] = pull->dbuf[g*3+1][m]*invwmass;
}
if (pgrp->epgrppbc == epgrppbcREFAT)
{
pgrp->x[m] += pull->rbuf[g][m];
if (xp)
{
pgrp->xp[m] += pull->rbuf[g][m];
}
}
}
}
else
{
/* Determine the optimal location of the cosine weight */
csw = pull->dbuf[g*3][0];
snw = pull->dbuf[g*3][1];
pgrp->x[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
/* Set the weights for the local atoms */
wmass = sqrt(csw*csw + snw*snw);
wwmass = (pull->dbuf[g*3+1][0]*csw*csw +
pull->dbuf[g*3+1][1]*csw*snw +
pull->dbuf[g*3+1][2]*snw*snw)/(wmass*wmass);
pgrp->wscale = wmass/wwmass;
pgrp->invtm = 1.0/(pgrp->wscale*wmass);
/* Set the weights for the local atoms */
csw *= pgrp->invtm;
snw *= pgrp->invtm;
for (i = 0; i < pgrp->nat_loc; i++)
{
ii = pgrp->ind_loc[i];
pgrp->weight_loc[i] = csw*cos(twopi_box*x[ii][pull->cosdim]) +
snw*sin(twopi_box*x[ii][pull->cosdim]);
}
if (xp)
{
csw = pull->dbuf[g*3+2][0];
snw = pull->dbuf[g*3+2][1];
pgrp->xp[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
}
}
if (debug)
{
fprintf(debug, "Pull group %d wmass %f wwmass %f invtm %f\n",
g, wmass, wwmass, pgrp->invtm);
}
}
}
if (PULL_CYL(pull))
{
/* Calculate the COMs for the cyclinder reference groups */
make_cyl_refgrps(cr, pull, md, pbc, t, x, xp);
}
}
/* calculates center of mass of selection index from all coordinates x */
void pull_calc_coms(t_commrec *cr,
struct pull_t *pull, t_mdatoms *md, t_pbc *pbc, double t,
rvec x[], rvec *xp)
{
int g;
real twopi_box = 0;
pull_comm_t *comm;
comm = &pull->comm;
if (comm->rbuf == NULL)
{
snew(comm->rbuf, pull->ngroup);
}
if (comm->dbuf == NULL)
{
snew(comm->dbuf, 3*pull->ngroup);
}
if (pull->bRefAt && pull->bSetPBCatoms)
{
pull_set_pbcatoms(cr, pull, x, comm->rbuf);
if (cr != NULL && DOMAINDECOMP(cr))
{
/* We can keep these PBC reference coordinates fixed for nstlist
* steps, since atoms won't jump over PBC.
* This avoids a global reduction at the next nstlist-1 steps.
* Note that the exact values of the pbc reference coordinates
* are irrelevant, as long all atoms in the group are within
* half a box distance of the reference coordinate.
*/
pull->bSetPBCatoms = FALSE;
}
}
if (pull->cosdim >= 0)
{
int m;
assert(pull->npbcdim <= DIM);
for (m = pull->cosdim+1; m < pull->npbcdim; m++)
{
if (pbc->box[m][pull->cosdim] != 0)
{
gmx_fatal(FARGS, "Can not do cosine weighting for trilinic dimensions");
}
}
twopi_box = 2.0*M_PI/pbc->box[pull->cosdim][pull->cosdim];
}
for (g = 0; g < pull->ngroup; g++)
{
pull_group_work_t *pgrp;
pgrp = &pull->group[g];
if (pgrp->bCalcCOM)
{
if (pgrp->epgrppbc != epgrppbcCOS)
{
dvec com, comp;
double wmass, wwmass;
rvec x_pbc = { 0, 0, 0 };
int i;
clear_dvec(com);
clear_dvec(comp);
wmass = 0;
wwmass = 0;
if (pgrp->epgrppbc == epgrppbcREFAT)
{
/* Set the pbc atom */
copy_rvec(comm->rbuf[g], x_pbc);
}
for (i = 0; i < pgrp->nat_loc; i++)
{
int ii, m;
real mass, wm;
ii = pgrp->ind_loc[i];
mass = md->massT[ii];
if (pgrp->weight_loc == NULL)
{
wm = mass;
wmass += wm;
}
else
{
real w;
w = pgrp->weight_loc[i];
wm = w*mass;
wmass += wm;
wwmass += wm*w;
}
if (pgrp->epgrppbc == epgrppbcNONE)
{
/* Plain COM: sum the coordinates */
for (m = 0; m < DIM; m++)
{
com[m] += wm*x[ii][m];
}
if (xp)
{
for (m = 0; m < DIM; m++)
{
comp[m] += wm*xp[ii][m];
}
}
}
else
{
rvec dx;
/* Sum the difference with the reference atom */
pbc_dx(pbc, x[ii], x_pbc, dx);
for (m = 0; m < DIM; m++)
{
com[m] += wm*dx[m];
}
if (xp)
{
/* For xp add the difference between xp and x to dx,
* such that we use the same periodic image,
* also when xp has a large displacement.
*/
for (m = 0; m < DIM; m++)
{
comp[m] += wm*(dx[m] + xp[ii][m] - x[ii][m]);
}
}
}
}
/* We do this check after the loop above to avoid more nesting.
* If we have a single-atom group the mass is irrelevant, so
* we can remove the mass factor to avoid division by zero.
* Note that with constraint pulling the mass does matter, but
* in that case a check group mass != 0 has been done before.
*/
if (pgrp->params.nat == 1 && pgrp->nat_loc == 1 && wmass == 0)
{
int m;
/* Copy the single atom coordinate */
for (m = 0; m < DIM; m++)
{
com[m] = x[pgrp->ind_loc[0]][m];
}
/* Set all mass factors to 1 to get the correct COM */
wmass = 1;
wwmass = 1;
}
if (pgrp->weight_loc == NULL)
{
wwmass = wmass;
}
/* Copy local sums to a buffer for global summing */
copy_dvec(com, comm->dbuf[g*3]);
copy_dvec(comp, comm->dbuf[g*3 + 1]);
comm->dbuf[g*3 + 2][0] = wmass;
comm->dbuf[g*3 + 2][1] = wwmass;
comm->dbuf[g*3 + 2][2] = 0;
}
else
{
/* Cosine weighting geometry */
double cm, sm, cmp, smp, ccm, csm, ssm, csw, snw;
int i;
cm = 0;
sm = 0;
cmp = 0;
smp = 0;
ccm = 0;
csm = 0;
ssm = 0;
for (i = 0; i < pgrp->nat_loc; i++)
{
int ii;
real mass;
ii = pgrp->ind_loc[i];
mass = md->massT[ii];
/* Determine cos and sin sums */
csw = cos(x[ii][pull->cosdim]*twopi_box);
snw = sin(x[ii][pull->cosdim]*twopi_box);
cm += csw*mass;
sm += snw*mass;
ccm += csw*csw*mass;
csm += csw*snw*mass;
ssm += snw*snw*mass;
if (xp)
{
csw = cos(xp[ii][pull->cosdim]*twopi_box);
snw = sin(xp[ii][pull->cosdim]*twopi_box);
cmp += csw*mass;
smp += snw*mass;
}
}
/* Copy local sums to a buffer for global summing */
comm->dbuf[g*3 ][0] = cm;
comm->dbuf[g*3 ][1] = sm;
comm->dbuf[g*3 ][2] = 0;
comm->dbuf[g*3+1][0] = ccm;
comm->dbuf[g*3+1][1] = csm;
comm->dbuf[g*3+1][2] = ssm;
comm->dbuf[g*3+2][0] = cmp;
comm->dbuf[g*3+2][1] = smp;
comm->dbuf[g*3+2][2] = 0;
}
}
}
pull_reduce_double(cr, comm, pull->ngroup*3*DIM, comm->dbuf[0]);
for (g = 0; g < pull->ngroup; g++)
{
pull_group_work_t *pgrp;
pgrp = &pull->group[g];
if (pgrp->params.nat > 0 && pgrp->bCalcCOM)
{
if (pgrp->epgrppbc != epgrppbcCOS)
{
double wmass, wwmass;
int m;
/* Determine the inverse mass */
wmass = comm->dbuf[g*3+2][0];
wwmass = comm->dbuf[g*3+2][1];
pgrp->mwscale = 1.0/wmass;
/* invtm==0 signals a frozen group, so then we should keep it zero */
if (pgrp->invtm != 0)
{
pgrp->wscale = wmass/wwmass;
pgrp->invtm = wwmass/(wmass*wmass);
}
/* Divide by the total mass */
for (m = 0; m < DIM; m++)
{
pgrp->x[m] = comm->dbuf[g*3 ][m]*pgrp->mwscale;
if (xp)
{
pgrp->xp[m] = comm->dbuf[g*3+1][m]*pgrp->mwscale;
}
if (pgrp->epgrppbc == epgrppbcREFAT)
{
pgrp->x[m] += comm->rbuf[g][m];
if (xp)
{
pgrp->xp[m] += comm->rbuf[g][m];
}
}
}
}
else
{
/* Cosine weighting geometry */
double csw, snw, wmass, wwmass;
int i, ii;
/* Determine the optimal location of the cosine weight */
csw = comm->dbuf[g*3][0];
snw = comm->dbuf[g*3][1];
pgrp->x[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
/* Set the weights for the local atoms */
wmass = sqrt(csw*csw + snw*snw);
wwmass = (comm->dbuf[g*3+1][0]*csw*csw +
comm->dbuf[g*3+1][1]*csw*snw +
comm->dbuf[g*3+1][2]*snw*snw)/(wmass*wmass);
pgrp->mwscale = 1.0/wmass;
pgrp->wscale = wmass/wwmass;
pgrp->invtm = wwmass/(wmass*wmass);
/* Set the weights for the local atoms */
csw *= pgrp->invtm;
snw *= pgrp->invtm;
for (i = 0; i < pgrp->nat_loc; i++)
{
ii = pgrp->ind_loc[i];
pgrp->weight_loc[i] = csw*cos(twopi_box*x[ii][pull->cosdim]) +
snw*sin(twopi_box*x[ii][pull->cosdim]);
}
if (xp)
{
csw = comm->dbuf[g*3+2][0];
snw = comm->dbuf[g*3+2][1];
pgrp->xp[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
}
}
if (debug)
{
fprintf(debug, "Pull group %d wmass %f invtm %f\n",
g, 1.0/pgrp->mwscale, pgrp->invtm);
}
}
}
if (pull->bCylinder)
{
/* Calculate the COMs for the cyclinder reference groups */
make_cyl_refgrps(cr, pull, md, pbc, t, x);
}
}
