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Fixed a couple of small things in manual pages for symfunc actions
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Gareth Aneurin Tribello committed Jan 31, 2025
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2 changes: 1 addition & 1 deletion src/symfunc/CoordinationNumbers.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ one hundred atoms with themselves:
```plumed
c: COORDINATIONNUMBER SPECIES=1-100 R_0=1.0
DUMPXYZ ATOMS=c ARG=c FILE=coords.xyz
DUMPATOMS ATOMS=c ARG=c FILE=coords.xyz
```
This input will produce an output file called coords that contains the coordination numbers of the 100 input atoms. The cutoff
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24 changes: 12 additions & 12 deletions src/symfunc/Steinhardt.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -53,9 +53,9 @@ As discussed on [this page](https://www.plumed-tutorials.org/lessons/23/001/data
be used to measure the degree of order in the system in a variety of different ways. The
simplest way of measuring whether or not the coordination sphere is ordered is to simply take the norm of the above vector i.e.
\f[
$$
Q_1(i) = \sqrt{ \sum_{m=-1}^1 q_{1m}(i)^{*} q_{1m}(i) }
\f]
$$
This norm is small when the coordination shell is disordered and larger when the coordination shell is ordered. Furthermore, in inputs like
the one shown below where the keywords LESS_THAN, MIN, MAX, HISTOGRAM, MEAN and so on are used with it is the distribution of these normed quantities
Expand Down Expand Up @@ -92,7 +92,7 @@ atoms, columns 2-4 will then contain the x, y and z positions of the atoms, colu
```plumed
q1: Q1 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN
DUMPATOMS ATOMS=q1 ARG=q1_anorm FILE=q1.xyz
DUMPATOMS ATOMS=q1 ARG=q1 FILE=q1.xyz
```
*/
Expand All @@ -119,9 +119,9 @@ As discussed on [this page](https://www.plumed-tutorials.org/lessons/23/001/data
be used to measure the degree of order in the system in a variety of different ways. The
simplest way of measuring whether or not the coordination sphere is ordered is to simply take the norm of the above vector i.e.
\f[
$$
Q_3(i) = \sqrt{ \sum_{m=-3}^3 q_{3m}(i)^{*} q_{3m}(i) }
\f]
$$
This norm is small when the coordination shell is disordered and larger when the coordination shell is ordered. Furthermore, in inputs like
the one shown below where the keywords LESS_THAN, MIN, MAX, HISTOGRAM, MEAN and so on are used with it is the distribution of these normed quantities
Expand Down Expand Up @@ -158,7 +158,7 @@ atoms, columns 2-4 will then contain the x, y and z positions of the atoms, colu
```plumed
q3: Q3 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN
DUMPATOMS ATOMS=q3 ARG=q3_anorm FILE=q3.xyz
DUMPATOMS ATOMS=q3 ARG=q3 FILE=q3.xyz
```
*/
Expand All @@ -185,9 +185,9 @@ As discussed on [this page](https://www.plumed-tutorials.org/lessons/23/001/data
be used to measure the degree of order in the system in a variety of different ways. The
simplest way of measuring whether or not the coordination sphere is ordered is to simply take the norm of the above vector i.e.
\f[
$$
Q_4(i) = \sqrt{ \sum_{m=-4}^4 q_{4m}(i)^{*} q_{4m}(i) }
\f]
$$
This norm is small when the coordination shell is disordered and larger when the coordination shell is ordered. Furthermore, in inputs like
the one shown below where the keywords LESS_THAN, MIN, MAX, HISTOGRAM, MEAN and so on are used with it is the distribution of these normed quantities
Expand Down Expand Up @@ -224,7 +224,7 @@ atoms, columns 2-4 will then contain the x, y and z positions of the atoms, colu
```plumed
q4: Q4 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN
DUMPATOMS ATOMS=q4 ARG=q4_anorm FILE=q4.xyz
DUMPATOMS ATOMS=q4 ARG=q4 FILE=q4.xyz
```
*/
Expand All @@ -251,9 +251,9 @@ As discussed on [this page](https://www.plumed-tutorials.org/lessons/23/001/data
be used to measure the degree of order in the system in a variety of different ways. The
simplest way of measuring whether or not the coordination sphere is ordered is to simply take the norm of the above vector i.e.
\f[
$$
Q_6(i) = \sqrt{ \sum_{m=-6}^6 q_{6m}(i)^{*} q_{6m}(i) }
\f]
$$
This norm is small when the coordination shell is disordered and larger when the coordination shell is ordered. Furthermore, in inputs like
the one shown below where the keywords LESS_THAN, MIN, MAX, HISTOGRAM, MEAN and so on are used with it is the distribution of these normed quantities
Expand Down Expand Up @@ -290,7 +290,7 @@ atoms, columns 2-4 will then contain the x, y and z positions of the atoms, colu
```plumed
q6: Q6 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN
DUMPATOMS ATOMS=q6 ARG=q6_anorm FILE=q6.xyz
DUMPATOMS ATOMS=q6 ARG=q6 FILE=q6.xyz
```
*/
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Found broken examples in automatic/ANN.tmp
Found broken examples in automatic/CLASSICAL_MDS.tmp
Found broken examples in automatic/CONVERT_TO_FES.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/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/FUNNEL.tmp
Found broken examples in automatic/FUNNEL_PS.tmp
Found broken examples in automatic/GPROPERTYMAP.tmp
Found broken examples in automatic/HISTOGRAM.tmp
Found broken examples in automatic/INTERPOLATE_GRID.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/PCA.tmp
Found broken examples in automatic/PCAVARS.tmp
Found broken examples in automatic/PIV.tmp
Found broken examples in automatic/PYCVINTERFACE.tmp
Found broken examples in automatic/PYTHONFUNCTION.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 AnalysisPP.md
Found broken examples in CollectiveVariablesPP.md
Found broken examples in MiscelaneousPP.md

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