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Some fixes in documentation
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GiovanniBussi committed Jan 29, 2025
1 parent f843963 commit 7ec974d
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6 changes: 3 additions & 3 deletions src/generic/MolInfo.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -49,11 +49,11 @@ generated with `gmx editconf -f topol.tpr -o reference.pdb`.
More information of the PDB parser implemented in PLUMED can be found \ref pdbreader "at this page".
If the flag `WHOLE` is used, the reference structure is assumed to be whole, i.e. not broken by PBC.
**This will impact PDB calculations in all the actions following the MOLINFO action!**.
**This will impact PBC calculations in all the actions following the MOLINFO action!**.
In particular, actions that reconstruct molecules locally will do the reconstruction using a
minimum spanning tree rather than the order in which atoms are provided.
Notice that PLUMED 2.8 and 2.9 this would only have affected the behavior of \ref WHOLEMOLECULES
actions, whereas starting with PLUMED 2.10 all actions that reconstruct PBCs are affected.
Notice that in PLUMED 2.8, 2.9, and 2.10 this would only have affected the behavior of \ref WHOLEMOLECULES
actions, whereas starting with PLUMED 2.11 all actions that reconstruct PBCs are affected.
If you want a variable to ignore this, you can just repeate the MOLINFO action without
the `WHOLE` flag: all the following actions will use the traditional reconstruction algorithm,
based on the order in which atoms are listed.
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4 changes: 2 additions & 2 deletions src/generic/WholeMolecules.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -137,7 +137,7 @@ void WholeMolecules::registerKeywords( Keywords& keys ) {
"specifying all. Alternatively, if you wish to use a subset of the residues you can specify the particular residues "
"you are interested in as a list of numbers");
keys.add("optional","MOLTYPE","the type of molecule that is under study. This is used to define the backbone atoms");
keys.addFlag("EMST", false, "only for backward compatibility, as of PLUMED 2.10 this is the default when using MOLINFO with WHOLE");
keys.addFlag("EMST", false, "only for backward compatibility, as of PLUMED 2.11 this is the default when using MOLINFO with WHOLE");
keys.addFlag("ADDREFERENCE", false, "Define the reference position of the first atom of each entity using a PDB file");
}

Expand All @@ -151,7 +151,7 @@ WholeMolecules::WholeMolecules(const ActionOptions&ao):
// parse optional flags
bool doemst_tmp;
parseFlag("EMST", doemst_tmp);
if(doemst_tmp) log << "EMST option is not needed any more as of PLUMED 2.10\n";
if(doemst_tmp) log << "EMST option is not needed any more as of PLUMED 2.11\n";
parseFlag("ADDREFERENCE", addref);

auto* moldat=plumed.getActionSet().selectLatest<GenericMolInfo*>(this);
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Found broken examples in automatic/ANGLES.tmp
Found broken examples in automatic/ANN.tmp
Found broken examples in automatic/CAVITY.tmp
Found broken examples in automatic/CLASSICAL_MDS.tmp
Found broken examples in automatic/CLUSTER_DIAMETER.tmp
Found broken examples in automatic/CLUSTER_DISTRIBUTION.tmp
Found broken examples in automatic/CLUSTER_PROPERTIES.tmp
Found broken examples in automatic/CONSTANT.tmp
Found broken examples in automatic/CONTACT_MATRIX.tmp
Found broken examples in automatic/CONTACT_MATRIX_PROPER.tmp
Found broken examples in automatic/CONVERT_TO_FES.tmp
Found broken examples in automatic/COORDINATIONNUMBER.tmp
Found broken examples in automatic/DFSCLUSTERING.tmp
Found broken examples in automatic/DISTANCE_FROM_CONTOUR.tmp
Found broken examples in automatic/DUMPCUBE.tmp
Found broken examples in automatic/DUMPGRID.tmp
Found broken examples in automatic/EDS.tmp
Found broken examples in automatic/EMMI.tmp
Found broken examples in automatic/ENVIRONMENTSIMILARITY.tmp
Found broken examples in automatic/FIND_CONTOUR.tmp
Found broken examples in automatic/FIND_CONTOUR_SURFACE.tmp
Found broken examples in automatic/FIND_SPHERICAL_CONTOUR.tmp
Found broken examples in automatic/FOURIER_TRANSFORM.tmp
Found broken examples in automatic/FUNCPATHGENERAL.tmp
Found broken examples in automatic/FUNCPATHMSD.tmp
Found broken examples in automatic/FUNNEL.tmp
Found broken examples in automatic/FUNNEL_PS.tmp
Found broken examples in automatic/GHBFIX.tmp
Found broken examples in automatic/GPROPERTYMAP.tmp
Found broken examples in automatic/HBOND_MATRIX.tmp
Found broken examples in automatic/HISTOGRAM.tmp
Found broken examples in automatic/INCLUDE.tmp
Found broken examples in automatic/INCYLINDER.tmp
Found broken examples in automatic/INENVELOPE.tmp
Found broken examples in automatic/INTERPOLATE_GRID.tmp
Found broken examples in automatic/LOCAL_AVERAGE.tmp
Found broken examples in automatic/MAZE_OPTIMIZER_BIAS.tmp
Found broken examples in automatic/MAZE_RANDOM_ACCELERATION_MD.tmp
Found broken examples in automatic/MAZE_SIMULATED_ANNEALING.tmp
Found broken examples in automatic/MAZE_STEERED_MD.tmp
Found broken examples in automatic/METATENSOR.tmp
Found broken examples in automatic/MULTICOLVARDENS.tmp
Found broken examples in automatic/OUTPUT_CLUSTER.tmp
Found broken examples in automatic/PAMM.tmp
Found broken examples in automatic/PCA.tmp
Found broken examples in automatic/PCAVARS.tmp
Found broken examples in automatic/PIV.tmp
Found broken examples in automatic/PLUMED.tmp
Found broken examples in automatic/Q3.tmp
Found broken examples in automatic/Q4.tmp
Found broken examples in automatic/Q6.tmp
Found broken examples in automatic/QUATERNION.tmp
Found broken examples in automatic/REWEIGHT_BIAS.tmp
Found broken examples in automatic/REWEIGHT_METAD.tmp
Found broken examples in automatic/SIZESHAPE_POSITION_LINEAR_PROJ.tmp
Found broken examples in automatic/SIZESHAPE_POSITION_MAHA_DIST.tmp
Found broken examples in automatic/SPRINT.tmp
Found broken examples in automatic/TETRAHEDRALPORE.tmp
Found broken examples in automatic/TORSIONS.tmp
Found broken examples in automatic/WHAM_HISTOGRAM.tmp
Found broken examples in automatic/WHAM_WEIGHTS.tmp
Found broken examples in AnalysisPP.md
Found broken examples in CollectiveVariablesPP.md
Found broken examples in MiscelaneousPP.md

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