#define MAXPTR 254
#define NOGID 255
+using gmx::BasicVector;
+
/* Resource parameters
* Do not change any of these until you read the instruction
* in readinp.h. Some cpp's do not take spaces after the backslash
j = 0;
while ((j < nr)
&& gmx_strcasecmp(
- names[2 * i].c_str(),
- *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
+ names[2 * i].c_str(),
+ *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][j]])))
{
j++;
}
k = 0;
while ((k < nr)
&& gmx_strcasecmp(
- names[2 * i + 1].c_str(),
- *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
+ names[2 * i + 1].c_str(),
+ *(groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput][k]])))
{
k++;
}
}
}
-static bool absolute_reference(const t_inputrec* ir, const gmx_mtop_t& sys, const bool posres_only, ivec AbsRef)
+//! Returns whether dimensions have an absolute reference due to walls, pbc or freezing
+static BasicVector<bool> haveAbsoluteReference(const t_inputrec& ir)
{
- int d, g, i;
- const t_iparams* pr;
-
- clear_ivec(AbsRef);
+ BasicVector<bool> absRef = { false, false, false };
- if (!posres_only)
+ /* Check the degrees of freedom of the COM (not taking COMM removal into account) */
+ for (int d = 0; d < DIM; d++)
{
- /* Check the COM */
- for (d = 0; d < DIM; d++)
- {
- AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
- }
- /* Check for freeze groups */
- for (g = 0; g < ir->opts.ngfrz; g++)
+ absRef[d] = (d >= ndof_com(&ir));
+ }
+ /* Check for freeze groups */
+ for (int g = 0; g < ir.opts.ngfrz; g++)
+ {
+ for (int d = 0; d < DIM; d++)
{
- for (d = 0; d < DIM; d++)
+ if (ir.opts.nFreeze[g][d] != 0)
{
- if (ir->opts.nFreeze[g][d] != 0)
- {
- AbsRef[d] = 1;
- }
+ absRef[d] = true;
}
}
}
- /* Check for position restraints */
- for (const auto ilist : IListRange(sys))
+ return absRef;
+}
+
+//! Returns whether position restraints are used for dimensions
+static BasicVector<bool> havePositionRestraints(const gmx_mtop_t& sys)
+{
+ BasicVector<bool> havePosres = { false, false, false };
+
+ for (const auto ilists : IListRange(sys))
{
- if (ilist.nmol() > 0 && (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
+ const auto& posResList = ilists.list()[F_POSRES];
+ const auto& fbPosResList = ilists.list()[F_FBPOSRES];
+ if (ilists.nmol() > 0 && (!havePosres[XX] || !havePosres[YY] || !havePosres[ZZ]))
{
- for (int i = 0; i < ilist.list()[F_POSRES].size(); i += 2)
+ for (int i = 0; i < posResList.size(); i += 2)
{
- pr = &sys.ffparams.iparams[ilist.list()[F_POSRES].iatoms[i]];
- for (d = 0; d < DIM; d++)
+ const t_iparams& pr = sys.ffparams.iparams[posResList.iatoms[i]];
+ for (int d = 0; d < DIM; d++)
{
- if (pr->posres.fcA[d] != 0)
+ if (pr.posres.fcA[d] != 0)
{
- AbsRef[d] = 1;
+ havePosres[d] = true;
}
}
}
- for (i = 0; i < ilist.list()[F_FBPOSRES].size(); i += 2)
+ for (int i = 0; i < fbPosResList.size(); i += 2)
{
/* Check for flat-bottom posres */
- pr = &sys.ffparams.iparams[ilist.list()[F_FBPOSRES].iatoms[i]];
- if (pr->fbposres.k != 0)
+ const t_iparams& pr = sys.ffparams.iparams[fbPosResList.iatoms[i]];
+ if (pr.fbposres.k != 0)
{
- switch (pr->fbposres.geom)
+ switch (pr.fbposres.geom)
{
- case efbposresSPHERE: AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1; break;
- case efbposresCYLINDERX: AbsRef[YY] = AbsRef[ZZ] = 1; break;
- case efbposresCYLINDERY: AbsRef[XX] = AbsRef[ZZ] = 1; break;
+ case efbposresSPHERE: havePosres = { true, true, true }; break;
+ case efbposresCYLINDERX: havePosres[YY] = havePosres[ZZ] = true; break;
+ case efbposresCYLINDERY: havePosres[XX] = havePosres[ZZ] = true; break;
case efbposresCYLINDER:
/* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
- case efbposresCYLINDERZ: AbsRef[XX] = AbsRef[YY] = 1; break;
+ case efbposresCYLINDERZ: havePosres[XX] = havePosres[YY] = true; break;
case efbposresX: /* d=XX */
case efbposresY: /* d=YY */
case efbposresZ: /* d=ZZ */
- d = pr->fbposres.geom - efbposresX;
- AbsRef[d] = 1;
+ havePosres[pr.fbposres.geom - efbposresX] = true;
break;
default:
gmx_fatal(FARGS,
- " Invalid geometry for flat-bottom position restraint.\n"
+ "Invalid geometry for flat-bottom position restraint.\n"
"Expected nr between 1 and %d. Found %d\n",
efbposresNR - 1,
- pr->fbposres.geom);
+ pr.fbposres.geom);
}
}
}
}
}
- return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
+ return havePosres;
}
static void check_combination_rule_differences(const gmx_mtop_t& mtop,
ptr = getenv("GMX_LJCOMB_TOL");
if (ptr != nullptr)
{
- double dbl;
+ double dbl;
double gmx_unused canary;
if (sscanf(ptr, "%lf%lf", &dbl, &canary) != 1)
}
}
+static bool allTrue(const BasicVector<bool>& boolVector)
+{
+ return boolVector[0] && boolVector[1] && boolVector[2];
+}
+
void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
{
// Not meeting MTS requirements should have resulted in a fatal error, so we can assert here
int i, m, c, nmol;
bool bCharge;
gmx_mtop_atomloop_block_t aloopb;
- ivec AbsRef;
char warn_buf[STRLEN];
set_warning_line(wi, mdparin, -1);
- if (absolute_reference(ir, *sys, false, AbsRef))
+ if (allTrue(haveAbsoluteReference(*ir)) && allTrue(havePositionRestraints(*sys)))
{
warning_note(wi,
"Removing center of mass motion in the presence of position restraints might "
if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != IntegrationAlgorithm::BD
&& ir->comm_mode == ComRemovalAlgorithm::No
- && !(absolute_reference(ir, *sys, FALSE, AbsRef) || ir->nsteps <= 10) && !ETC_ANDERSEN(ir->etc))
+ && !(allTrue(haveAbsoluteReference(*ir)) || allTrue(havePositionRestraints(*sys)) || ir->nsteps <= 10)
+ && !ETC_ANDERSEN(ir->etc))
{
warning(wi,
"You are not using center of mass motion removal (mdp option comm-mode), numerical "
/* Check for pressure coupling with absolute position restraints */
if (ir->epc != PressureCoupling::No && ir->refcoord_scaling == RefCoordScaling::No)
{
- absolute_reference(ir, *sys, TRUE, AbsRef);
+ const BasicVector<bool> havePosres = havePositionRestraints(*sys);
{
for (m = 0; m < DIM; m++)
{
- if (AbsRef[m] && norm2(ir->compress[m]) > 0)
+ if (havePosres[m] && norm2(ir->compress[m]) > 0)
{
warning(wi,
"You are using pressure coupling with absolute position restraints, "
{
if (ir->pull->coord[i].group[0] == 0 || ir->pull->coord[i].group[1] == 0)
{
- absolute_reference(ir, *sys, FALSE, AbsRef);
+ const auto absRef = haveAbsoluteReference(*ir);
+ const auto havePosres = havePositionRestraints(*sys);
for (m = 0; m < DIM; m++)
{
- if (ir->pull->coord[i].dim[m] && !AbsRef[m])
+ if (ir->pull->coord[i].dim[m] && !(absRef[m] || havePosres[m]))
{
warning(wi,
"You are using an absolute reference for pulling, but the rest of "
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff