fixes in user doc

src/colvar/ERMSD.cpp

@@ -55,7 +55,7 @@ eRMSD measures the distance between structures by considering only the relative
 
 2. Calculate all pairwise distance vectors \f$ \vec{r}_{i,j} \f$ among base centers.
 
-3. Rescale distance vectors as \f$ \tilde{\vec{r}}_{i,j} = (r_x/a,r_y/a,r_z/b) \f$, where  a=b=5 \AA, c= 3 \AA. This rescaling has the effect of weghting more deviations on the z-axis with respect to the x/y directions.
+3. Rescale distance vectors as \f$ \tilde{\vec{r}}_{i,j} = (r_x/a,r_y/a,r_z/b) \f$, where  a=b=5 \r{A}, c=3 \r{A}. This rescaling has the effect of weghting more deviations on the z-axis with respect to the x/y directions.
 
 4. Calculate the G vectors
 

src/dimred/OutputPCAProjections.cpp

@@ -33,7 +33,7 @@
 namespace PLMD {
 namespace dimred {
 
-//+PLUMEDOC ANALYSIS OUTPUT_PCA_PROJECTION
+//+PLUMEDOC DIMRED OUTPUT_PCA_PROJECTION
 /*
 This is used to output the projection calculated by principle component analysis
 

src/dimred/SketchMap.cpp

@@ -25,7 +25,7 @@
 namespace PLMD {
 namespace dimred {
 
-//+PLUMEDOC ANALYSIS SKETCH_MAP
+//+PLUMEDOC DIMRED SKETCH_MAP
 /*
 This can be used to output the data that has been stored in an Analysis object.
 

src/generic/Plumed.cpp

@@ -35,8 +35,7 @@
 
 using namespace std;
 
-namespace PLMD
-{
+namespace PLMD {
 namespace generic {
 
 //+PLUMEDOC GENERIC PLUMED

src/pamm/PAMM.cpp

@@ -88,7 +88,7 @@ we use to calculate our PAMM components are thus:
 In the above \f$N_k\f$ is a normalisation factor that is calculated based on \f$\Sigma\f$.  The vector \f$\mathbf{s}\f$ is a vector of quantities
 that are calculated by the \ref TORSIONS actions.  This vector must be two dimensional and in this case each component is the value of a
 torsion angle.  If we look at the two \ref TORSIONS actions in the above we are calculating the \f$\phi\f$ and \f$\psi\f$ backbone torsional
-angles in a protein (Note the use of \ref MOLFINTO to make specification of atoms straightforward).  We thus calculate the values of our
+angles in a protein (Note the use of \ref MOLINFO to make specification of atoms straightforward).  We thus calculate the values of our
 2 \f$ \{ \phi \} \f$  kernels 3 times.  The first time we use the \f$\phi\f$ and \f$\psi\f$ angles in the 2nd resiude of the protein,
 the second time it is the \f$\phi\f$ and \f$\psi\f$ angles of the 3rd residue of the protein and the third time it is the \f$\phi\f$ and \f$\psi\f$ angles
 of the 4th residue in the protein.  The final two quantities that are output by the print command, p.mean-1 and p.mean-2, are the averages

user-doc/Analysis.md

@@ -178,7 +178,7 @@ OUTPUT_COLVAR_FILE USE_OUTPUT_DATA_FROM=ll2 FILE=mylandmarks
 When landmark selection is performed in this way a weight is ascribed to each of the landmark configurations.  This weight is
 calculated by summing the weights of all the trajectory frames in each of the landmarks Voronoi polyhedra 
 (https://en.wikipedia.org/wiki/Voronoi_diagram).  The weight of each trajectory frame is one unless you are reweighting using the
-formula described in the \ref analysisbas to counteract the fact of a simulation bias or an elevated temperature.  If you are reweighting
+formula described in the \ref analysisbias to counteract the fact of a simulation bias or an elevated temperature.  If you are reweighting
 using these formula the weight of each of the points is equal to the exponential term in the numerator of these expressions.
 
 \section dimred Dimensionality Reduction

user-doc/CollectiveVariables.md

@@ -181,7 +181,7 @@ forcefield.
 \section usingbase Extracting all the base quantities
 
 There may be occasions where you want to get information on all the individual colvar values that you have calculated.
-For example you might want to output the values of all the coordination numbers calculated by a \ref COORDINATIONNUMERS 
+For example you might want to output the values of all the coordination numbers calculated by a \ref COORDINATIONNUMBER 
 action.  You can thus use the following commands to extract this sort of information.
 
 @MCOLVARA@ 

user-doc/Installation.md

@@ -370,7 +370,7 @@ possible kinds of innocuous errors:
   some feature introduced in PLUMED in a newer version.
 - If `plumed` executable is newer than the test suite, the tests might fail since some
   non-backward compatible change was made in PLUMED. We try to keep the number
-  of non-backward compatible changes small, but as you can see in the \ref Changelog there
+  of non-backward compatible changes small, but as you can see in the \ref ChangeLog there
   are typically a few of them at every new major release.
 
 \attention

user-doc/Performances.md

@@ -267,7 +267,7 @@ PLUMED: 4A  2 dfast                                      108     0.135210     0.
 ...
 \endverbatim
 
-Notice the usage of `x2` as a variable for the switching function (see \switchingfunction).
+Notice the usage of `x2` as a variable for the switching function (see \ref switchingfunction).
 
 \page Time Time your Input
 

user-doc/tutorials/others/ves-lugano2017-01-metad.txt

@@ -36,7 +36,7 @@ parameters corrected to be used with long-range Coulomb solvers \cite Price-JCP-
 The system contains 1 Na, 1 Cl, and 106 water molecules (total 320 atoms).
 
 \anchor ves-school-2017-metad-NaCl
-\image html ves-lugano2017-metad_nacl.png "NaCl in water"
+\image html ves-lugano2017-metad_NaCl.png "NaCl in water"
 
 
 \subsection ves-lugano2017-metad-subsection-2 Perform an unbiased simulation and control the distance Na-Cl