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);
}
}
pull_t *set_pull_init(t_inputrec *ir, const gmx_mtop_t *mtop,
rvec *x, matrix box, real lambda,
const gmx_output_env_t *oenv)
{
pull_params_t *pull;
pull_t *pull_work;
t_mdatoms *md;
t_pbc pbc;
int c;
double t_start;
pull = ir->pull;
pull_work = init_pull(NULL, pull, ir, 0, NULL, mtop, NULL, oenv, lambda, FALSE, 0);
md = init_mdatoms(NULL, mtop, ir->efep);
atoms2md(mtop, ir, -1, NULL, mtop->natoms, md);
if (ir->efep)
{
update_mdatoms(md, lambda);
}
set_pbc(&pbc, ir->ePBC, box);
t_start = ir->init_t + ir->init_step*ir->delta_t;
pull_calc_coms(NULL, pull_work, 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++)
{
t_pull_coord *pcrd;
t_pull_group *pgrp0, *pgrp1;
double value;
real init = 0;
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);
if (pcrd->bStart)
{
init = pcrd->init;
pcrd->init = 0;
}
get_pull_coord_value(pull_work, c, &pbc, &value);
value *= pull_conversion_factor_internal2userinput(pcrd);
fprintf(stderr, " %10.3f %s", value, pull_coordinate_units(pcrd));
if (pcrd->bStart)
{
pcrd->init = value + init;
}
if (pcrd->eGeom == epullgDIST)
{
if (pcrd->init < 0)
{
gmx_fatal(FARGS, "The initial pull distance (%g) needs to be non-negative with geometry %s. If you want a signed distance, use geometry %s instead.",
pcrd->init, EPULLGEOM(pcrd->eGeom), EPULLGEOM(epullgDIR));
}
/* TODO: With a positive init but a negative rate things could still
* go wrong, but it might be fine if you don't pull too far.
* We should give a warning or note when there is only one pull dim
* active, since that is usually the problematic case when you should
* be using direction. We will do this later, since an already planned
* generalization of the pull code makes pull dim available here.
*/
}
else if (pcrd->eGeom == epullgANGLE || pcrd->eGeom == epullgANGLEAXIS)
{
if (pcrd->init < 0 || pcrd->init > 180)
{
gmx_fatal(FARGS, "The initial pull reference angle (%g) is outside of the allowed range [0, 180] degrees.", pcrd->init);
}
}
else if (pcrd->eGeom == epullgDIHEDRAL)
{
if (pcrd->init < -180 || pcrd->init > 180)
{
gmx_fatal(FARGS, "The initial pull reference angle (%g) is outside of the allowed range [-180, 180] degrees.",
pcrd->init);
}
}
fprintf(stderr, " %10.3f %s\n", pcrd->init, pull_coordinate_units(pcrd));
}
return pull_work;
}
