/* Pulling with a harmonic umbrella potential or constant force */
static void do_pull_pot(int ePull,
t_pull *pull, t_pbc *pbc, double t, real lambda,
real *V, tensor vir, real *dVdl)
{
int g,j,m;
dvec dev;
double ndr,invdr;
real k,dkdl;
t_pullgrp *pgrp;
/* loop over the groups that are being pulled */
*V = 0;
*dVdl = 0;
for(g=1; g<1+pull->ngrp; g++)
{
pgrp = &pull->grp[g];
get_pullgrp_distance(pull,pbc,g,t,pgrp->dr,dev);
k = (1.0 - lambda)*pgrp->k + lambda*pgrp->kB;
dkdl = pgrp->kB - pgrp->k;
switch (pull->eGeom)
{
case epullgDIST:
ndr = dnorm(pgrp->dr);
invdr = 1/ndr;
if (ePull == epullUMBRELLA)
{
pgrp->f_scal = -k*dev[0];
*V += 0.5* k*dsqr(dev[0]);
*dVdl += 0.5*dkdl*dsqr(dev[0]);
}
else
{
pgrp->f_scal = -k;
*V += k*ndr;
*dVdl += dkdl*ndr;
}
for(m=0; m<DIM; m++)
{
pgrp->f[m] = pgrp->f_scal*pgrp->dr[m]*invdr;
}
break;
case epullgDIR:
case epullgDIRPBC:
case epullgCYL:
if (ePull == epullUMBRELLA)
{
pgrp->f_scal = -k*dev[0];
*V += 0.5* k*dsqr(dev[0]);
*dVdl += 0.5*dkdl*dsqr(dev[0]);
}
else
{
ndr = 0;
for(m=0; m<DIM; m++)
{
ndr += pgrp->vec[m]*pgrp->dr[m];
}
pgrp->f_scal = -k;
*V += k*ndr;
*dVdl += dkdl*ndr;
}
for(m=0; m<DIM; m++)
{
pgrp->f[m] = pgrp->f_scal*pgrp->vec[m];
}
break;
case epullgPOS:
for(m=0; m<DIM; m++)
{
if (ePull == epullUMBRELLA)
{
pgrp->f[m] = -k*dev[m];
*V += 0.5* k*dsqr(dev[m]);
*dVdl += 0.5*dkdl*dsqr(dev[m]);
}
else
{
pgrp->f[m] = -k*pull->dim[m];
*V += k*pgrp->dr[m]*pull->dim[m];
*dVdl += dkdl*pgrp->dr[m]*pull->dim[m];
}
}
break;
}
if (vir)
{
/* Add the pull contribution to the virial */
for(j=0; j<DIM; j++)
{
for(m=0;m<DIM;m++)
{
vir[j][m] -= 0.5*pgrp->f[j]*pgrp->dr[m];
}
}
}
}
}
void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real lambda,
const output_env_t oenv, gmx_bool bStart)
{
t_mdatoms *md;
t_pull *pull;
t_pullgrp *pgrp;
t_pbc pbc;
int ndim, g, m;
double t_start, tinvrate;
rvec init;
dvec dr, dev;
init_pull(NULL, ir, 0, NULL, mtop, NULL, oenv, lambda, FALSE, 0);
md = init_mdatoms(NULL, mtop, ir->efep);
atoms2md(mtop, ir, 0, NULL, 0, mtop->natoms, md);
if (ir->efep)
{
update_mdatoms(md, lambda);
}
pull = ir->pull;
if (pull->eGeom == epullgPOS)
{
ndim = 3;
}
else
{
ndim = 1;
}
set_pbc(&pbc, ir->ePBC, box);
t_start = ir->init_t + ir->init_step*ir->delta_t;
pull_calc_coms(NULL, pull, md, &pbc, t_start, x, NULL);
fprintf(stderr, "Pull group natoms pbc atom distance at start reference at t=0\n");
for (g = 0; g < pull->ngrp+1; g++)
{
pgrp = &pull->grp[g];
fprintf(stderr, "%8d %8d %8d ", g, pgrp->nat, pgrp->pbcatom+1);
copy_rvec(pgrp->init, init);
clear_rvec(pgrp->init);
if (g > 0)
{
if (pgrp->rate == 0)
{
tinvrate = 0;
}
else
{
tinvrate = t_start/pgrp->rate;
}
get_pullgrp_distance(pull, &pbc, g, 0, dr, dev);
for (m = 0; m < DIM; m++)
{
if (m < ndim)
{
fprintf(stderr, " %6.3f", dev[m]);
}
else
{
fprintf(stderr, " ");
}
}
fprintf(stderr, " ");
for (m = 0; m < DIM; m++)
{
if (bStart)
{
pgrp->init[m] = init[m] + dev[m]
- tinvrate*(pull->eGeom == epullgPOS ? pgrp->vec[m] : 1);
}
else
{
pgrp->init[m] = init[m];
}
if (m < ndim)
{
fprintf(stderr, " %6.3f", pgrp->init[m]);
}
else
{
fprintf(stderr, " ");
}
}
}
fprintf(stderr, "\n");
}
}
