static real ektrans(rvec v[], real mass[], int isize, int index[])
{
dvec mvcom;
double mtot;
int i, j, d;
clear_dvec(mvcom);
mtot = 0;
for (i = 0; i < isize; i++)
{
j = index[i];
for (d = 0; d < DIM; d++)
{
mvcom[d] += mass[j]*v[j][d];
}
mtot += mass[j];
}
return dnorm2(mvcom)/(mtot*2);
}
static void init_pull_coord(t_pull_coord *pcrd, int coord_index_for_output,
char *dim_buf,
const char *origin_buf, const char *vec_buf,
warninp_t wi)
{
int m;
dvec origin, vec;
char buf[STRLEN];
if (pcrd->eType == epullCONSTRAINT && (pcrd->eGeom == epullgCYL ||
pcrd->eGeom == epullgDIRRELATIVE ||
pcrd->eGeom == epullgANGLE ||
pcrd->eGeom == epullgANGLEAXIS ||
pcrd->eGeom == epullgDIHEDRAL))
{
gmx_fatal(FARGS, "Pulling of type %s can not be combined with geometry %s. Consider using pull type %s.",
epull_names[pcrd->eType],
epullg_names[pcrd->eGeom],
epull_names[epullUMBRELLA]);
}
if (pcrd->eType == epullEXTERNAL)
{
if (pcrd->externalPotentialProvider[0] == '\0')
{
sprintf(buf, "The use of pull type '%s' for pull coordinate %d requires that the name of the module providing the potential external is set with the option %s%d%s",
epull_names[pcrd->eType], coord_index_for_output,
"pull-coord", coord_index_for_output, "-potential-provider");
warning_error(wi, buf);
}
if (pcrd->rate != 0)
{
sprintf(buf, "The use of pull type '%s' for pull coordinate %d requires that the pull rate is zero",
epull_names[pcrd->eType], coord_index_for_output);
warning_error(wi, buf);
}
if (pcrd->eGeom == epullgCYL)
{
/* Warn the user of a PBC restriction, caused by the fact that
* there is no reference value with an external pull potential.
*/
sprintf(buf, "With pull type '%s' and geometry '%s', the distance component along the cylinder axis between atoms in the cylinder group and the COM of the pull group should be smaller than half the box length",
epull_names[pcrd->eType], epullg_names[pcrd->eGeom]);
warning_note(wi, buf);
}
}
process_pull_dim(dim_buf, pcrd->dim, pcrd);
string2dvec(origin_buf, origin);
if (pcrd->group[0] != 0 && dnorm(origin) > 0)
{
gmx_fatal(FARGS, "The pull origin can only be set with an absolute reference");
}
/* Check the given initial reference value and warn for dangerous values */
if (pcrd->eGeom == epullgDIST)
{
if (pcrd->bStart && pcrd->init < 0)
{
sprintf(buf, "The initial reference distance set by pull-coord-init is set to a negative value (%g) with geometry %s while distances need to be non-negative. "
"This may work, since you have set pull-coord-start to 'yes' which modifies this value, but only for certain starting distances. "
"If this is a mistake you may want to use geometry %s instead.",
pcrd->init, EPULLGEOM(pcrd->eGeom), EPULLGEOM(epullgDIR));
warning(wi, buf);
}
}
else if (pcrd->eGeom == epullgANGLE || pcrd->eGeom == epullgANGLEAXIS)
{
if (pcrd->bStart && (pcrd->init < 0 || pcrd->init > 180))
{
/* This value of pcrd->init may be ok depending on pcrd->bStart which modifies pcrd->init later on */
sprintf(buf, "The initial reference angle set by pull-coord-init (%g) is outside of the allowed range [0, 180] degrees for geometry (%s). "
"This may work, since you have set pull-coord-start to 'yes' which modifies this value, but only for certain starting angles.",
pcrd->init, EPULLGEOM(pcrd->eGeom));
warning(wi, buf);
}
}
else if (pcrd->eGeom == epullgDIHEDRAL)
{
if (pcrd->bStart && (pcrd->init < -180 || pcrd->init > 180))
{
sprintf(buf, "The initial reference angle set by pull-coord-init (%g) is outside of the allowed range [-180, 180] degrees for geometry (%s). "
"This may work, since you have set pull-coord-start to 'yes' which modifies this value, but only for certain starting angles.",
pcrd->init, EPULLGEOM(pcrd->eGeom));
warning(wi, buf);
}
}
/* Check and set the pull vector */
clear_dvec(vec);
string2dvec(vec_buf, vec);
if (pcrd->eGeom == epullgDIR || pcrd->eGeom == epullgCYL || pcrd->eGeom == epullgDIRPBC || pcrd->eGeom == epullgANGLEAXIS)
{
if (dnorm2(vec) == 0)
{
gmx_fatal(FARGS, "With pull geometry %s the pull vector can not be 0,0,0",
epullg_names[pcrd->eGeom]);
}
for (int d = 0; d < DIM; d++)
{
if (vec[d] != 0 && pcrd->dim[d] == 0)
{
gmx_fatal(FARGS, "pull-coord-vec has non-zero %c-component while pull_dim for the %c-dimension is set to N", 'x'+d, 'x'+d);
}
}
/* Normalize the direction vector */
dsvmul(1/dnorm(vec), vec, vec);
}
else /* This case is for are all the geometries where the pull vector is not used */
{
if (dnorm2(vec) > 0)
{
sprintf(buf, "A pull vector is given (%g %g %g) but will not be used with geometry %s. If you really want to use this "
"vector, consider using geometry %s instead.",
vec[0], vec[1], vec[2], EPULLGEOM(pcrd->eGeom),
pcrd->eGeom == epullgANGLE ? EPULLGEOM(epullgANGLEAXIS) : EPULLGEOM(epullgDIR));
warning(wi, buf);
}
}
for (m = 0; m < DIM; m++)
{
pcrd->origin[m] = origin[m];
pcrd->vec[m] = vec[m];
}
}
static void init_pull_coord(t_pull_coord *pcrd,
char *dim_buf,
const char *origin_buf, const char *vec_buf,
warninp_t wi)
{
int m;
dvec origin, vec;
char buf[STRLEN];
if (pcrd->eType == epullCONSTRAINT && (pcrd->eGeom == epullgCYL ||
pcrd->eGeom == epullgDIRRELATIVE))
{
gmx_fatal(FARGS, "Pulling of type %s can not be combined with geometry %s. Consider using pull type %s.",
epull_names[pcrd->eType],
epullg_names[pcrd->eGeom],
epull_names[epullUMBRELLA]);
}
process_pull_dim(dim_buf, pcrd->dim);
string2dvec(origin_buf, origin);
if (pcrd->group[0] != 0 && dnorm(origin) > 0)
{
gmx_fatal(FARGS, "The pull origin can only be set with an absolute reference");
}
/* Check and set the pull vector */
clear_dvec(vec);
if (pcrd->eGeom == epullgDIST)
{
if (pcrd->init < 0)
{
sprintf(buf, "The initial pull distance is negative with geometry %s, while a distance can not be negative. Use geometry %s instead.",
EPULLGEOM(pcrd->eGeom), EPULLGEOM(epullgDIR));
warning_error(wi, buf);
}
/* 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 != epullgDIRRELATIVE)
{
string2dvec(vec_buf, vec);
if (dnorm2(vec) == 0)
{
gmx_fatal(FARGS, "With pull geometry %s the pull vector can not be 0,0,0",
epullg_names[pcrd->eGeom]);
}
if (pcrd->eGeom == epullgDIR || pcrd->eGeom == epullgCYL)
{
/* Normalize the direction vector */
dsvmul(1/dnorm(vec), vec, vec);
}
}
for (m = 0; m < DIM; m++)
{
pcrd->origin[m] = origin[m];
pcrd->vec[m] = vec[m];
}
}