/* 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 c, j, m;
double dev, ndr, invdr;
real k, dkdl;
t_pull_coord *pcrd;
/* loop over the pull coordinates */
*V = 0;
*dVdl = 0;
for (c = 0; c < pull->ncoord; c++)
{
pcrd = &pull->coord[c];
get_pull_coord_distance(pull, c, pbc, t, pcrd->dr, &dev);
k = (1.0 - lambda)*pcrd->k + lambda*pcrd->kB;
dkdl = pcrd->kB - pcrd->k;
switch (pull->eGeom)
{
case epullgDIST:
ndr = dnorm(pcrd->dr);
invdr = 1/ndr;
if (ePull == epullUMBRELLA)
{
pcrd->f_scal = -k*dev;
*V += 0.5* k*dsqr(dev);
*dVdl += 0.5*dkdl*dsqr(dev);
}
else
{
pcrd->f_scal = -k;
*V += k*ndr;
*dVdl += dkdl*ndr;
}
for (m = 0; m < DIM; m++)
{
pcrd->f[m] = pcrd->f_scal*pcrd->dr[m]*invdr;
}
break;
case epullgDIR:
case epullgDIRPBC:
case epullgCYL:
if (ePull == epullUMBRELLA)
{
pcrd->f_scal = -k*dev;
*V += 0.5* k*dsqr(dev);
*dVdl += 0.5*dkdl*dsqr(dev);
}
else
{
ndr = 0;
for (m = 0; m < DIM; m++)
{
ndr += pcrd->vec[m]*pcrd->dr[m];
}
pcrd->f_scal = -k;
*V += k*ndr;
*dVdl += dkdl*ndr;
}
for (m = 0; m < DIM; m++)
{
pcrd->f[m] = pcrd->f_scal*pcrd->vec[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*pcrd->f[j]*pcrd->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_pull_coord *pcrd;
t_pull_group *pgrp0, *pgrp1;
t_pbc pbc;
int c, m;
double t_start, tinvrate;
real init;
dvec dr;
double 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, mtop->natoms, md);
if (ir->efep)
{
update_mdatoms(md, lambda);
}
pull = ir->pull;
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 (c = 0; c < pull->ncoord; c++)
{
pcrd = &pull->coord[c];
pgrp0 = &pull->group[pcrd->group[0]];
pgrp1 = &pull->group[pcrd->group[1]];
fprintf(stderr, "%8d %8d %8d\n",
pcrd->group[0], pgrp0->nat, pgrp0->pbcatom+1);
fprintf(stderr, "%8d %8d %8d ",
pcrd->group[1], pgrp1->nat, pgrp1->pbcatom+1);
init = pcrd->init;
pcrd->init = 0;
if (pcrd->rate == 0)
{
tinvrate = 0;
}
else
{
tinvrate = t_start/pcrd->rate;
}
get_pull_coord_distance(pull, c, &pbc, 0, dr, &dev);
fprintf(stderr, " %6.3f ", dev);
if (bStart)
{
pcrd->init = init + dev - tinvrate;
}
else
{
pcrd->init = init;
}
fprintf(stderr, " %6.3f\n", pcrd->init);
}
}
