void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real lambda,
const output_env_t oenv)
{
pull_params_t *pull;
struct 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, 0, 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);
fprintf(stderr, " %10.3f nm", value);
if (pcrd->bStart)
{
pcrd->init = value + init;
}
fprintf(stderr, " %10.3f nm\n", pcrd->init);
}
finish_pull(pull_work);
}
void setStateDependentAwhParams(AwhParams *awhParams,
const pull_params_t *pull_params, pull_t *pull_work,
const matrix box, int ePBC,
const t_grpopts *inputrecGroupOptions, warninp_t wi)
{
/* The temperature is not really state depenendent but is not known
* when read_awhParams is called (in get ir).
* It is known first after do_index has been called in grompp.cpp.
*/
if (inputrecGroupOptions->ref_t == NULL ||
inputrecGroupOptions->ref_t[0] <= 0)
{
gmx_fatal(FARGS, "AWH biasing is only supported for temperatures > 0");
}
for (int i = 1; i < inputrecGroupOptions->ngtc; i++)
{
if (inputrecGroupOptions->ref_t[i] != inputrecGroupOptions->ref_t[0])
{
gmx_fatal(FARGS, "AWH biasing is currently only supported for identical temperatures for all temperature coupling groups");
}
}
t_pbc pbc;
set_pbc(&pbc, ePBC, box);
for (int k = 0; k < awhParams->numBias; k++)
{
AwhBiasParams *awhBiasParams = &awhParams->awhBiasParams[k];
for (int d = 0; d < awhBiasParams->ndim; d++)
{
AwhDimParams *dimParams = &awhBiasParams->dimParams[d];
/* The periodiciy of the AWH grid in certain cases depends on the simulation box */
dimParams->period = get_pull_coord_period(pull_params, dimParams->coordIndex, box);
/* The initial coordinate value, converted to external user units. */
dimParams->coordValueInit =
get_pull_coord_value(pull_work, dimParams->coordIndex, &pbc);
t_pull_coord *pullCoord = &pull_params->coord[dimParams->coordIndex];
dimParams->coordValueInit *= pull_conversion_factor_internal2userinput(pullCoord);
}
}
checkInputConsistencyInterval(awhParams, wi);
/* Register AWH as external potential with pull to check consistency. */
Awh::registerAwhWithPull(*awhParams, pull_work);
}
pull_t *set_pull_init(t_inputrec *ir, const gmx_mtop_t *mtop,
rvec *x, matrix box, real lambda,
warninp_t wi)
{
pull_params_t *pull;
pull_t *pull_work;
t_pbc pbc;
int c;
double t_start;
pull = ir->pull;
gmx::LocalAtomSetManager atomSets;
pull_work = init_pull(nullptr, pull, ir, mtop, nullptr, &atomSets, lambda);
auto mdAtoms = gmx::makeMDAtoms(nullptr, *mtop, *ir, false);
auto md = mdAtoms->mdatoms();
atoms2md(mtop, ir, -1, nullptr, mtop->natoms, mdAtoms.get());
if (ir->efep)
{
update_mdatoms(md, lambda);
}
set_pbc(&pbc, ir->ePBC, box);
t_start = ir->init_t + ir->init_step*ir->delta_t;
if (pull->bSetPbcRefToPrevStepCOM)
{
initPullComFromPrevStep(nullptr, pull_work, md, &pbc, x);
}
pull_calc_coms(nullptr, pull_work, md, &pbc, t_start, x, nullptr);
for (int g = 0; g < pull->ngroup; g++)
{
bool groupObeysPbc =
pullCheckPbcWithinGroup(*pull_work,
gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec *>(x),
mtop->natoms),
pbc, g, c_pullGroupSmallGroupThreshold);
if (!groupObeysPbc)
{
char buf[STRLEN];
if (pull->group[g].pbcatom_input == 0)
{
sprintf(buf, "When the maximum distance from a pull group reference atom to other atoms in the "
"group is larger than %g times half the box size a centrally placed "
"atom should be chosen as pbcatom. Pull group %d is larger than that and does not have "
"a specific atom selected as reference atom.", c_pullGroupSmallGroupThreshold, g);
warning_error(wi, buf);
}
else if (!pull->bSetPbcRefToPrevStepCOM)
{
sprintf(buf, "The maximum distance from the chosen PBC atom (%d) of pull group %d to other "
"atoms in the group is larger than %g times half the box size. "
"Set the pull-pbc-ref-prev-step-com option to yes.", pull->group[g].pbcatom + 1,
g, c_pullGroupSmallGroupThreshold);
warning_error(wi, buf);
}
}
if (groupObeysPbc)
{
groupObeysPbc =
pullCheckPbcWithinGroup(*pull_work,
gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec *>(x),
mtop->natoms),
pbc, g, c_pullGroupPbcMargin);
if (!groupObeysPbc)
{
char buf[STRLEN];
sprintf(buf,
"Pull group %d has atoms at a distance larger than %g times half the box size from the PBC atom (%d). "
"If atoms are or will more beyond half the box size from the PBC atom, the COM will be ill defined.",
g, c_pullGroupPbcMargin, pull->group[g].pbcatom + 1);
set_warning_line(wi, nullptr, -1);
warning(wi, buf);
}
}
}
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;
}
value = get_pull_coord_value(pull_work, c, &pbc);
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;
}
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;
}