From 8c0b1386be6c5afbb5238f1dc26a87dbb3d55cce Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Mon, 24 Apr 2017 11:12:10 +0200
Subject: [PATCH] Syntax highlight in doc
I replaced
verbatim
endverbatim
with
plumedfile
endplumedfile
in (hopefully) all the places where it was appropriate.
---
src/adjmat/ClusterDiameter.cpp | 4 +-
src/adjmat/ClusterDistribution.cpp | 4 +-
src/adjmat/ClusterProperties.cpp | 4 +-
src/adjmat/ClusterSize.cpp | 4 +-
src/adjmat/ClusterWithSurface.cpp | 4 +-
src/adjmat/ContactAlignedMatrix.cpp | 4 +-
src/adjmat/ContactMatrix.cpp | 4 +-
src/adjmat/DFSClustering.cpp | 4 +-
src/adjmat/HbondMatrix.cpp | 4 +-
src/adjmat/MatrixColumnSums.cpp | 8 +--
src/adjmat/MatrixRowSums.cpp | 8 +--
src/adjmat/OutputCluster.cpp | 4 +-
src/adjmat/SMACMatrix.cpp | 4 +-
src/adjmat/Sprint.cpp | 8 +--
src/analysis/Average.cpp | 12 ++--
.../ClassicalMultiDimensionalScaling.cpp | 4 +-
src/analysis/Commit.cpp | 4 +-
src/analysis/Histogram.cpp | 16 ++---
src/analysis/PCA.cpp | 8 +--
src/bias/ABMD.cpp | 5 +-
src/bias/BiasValue.cpp | 11 ++--
src/bias/ExtendedLagrangian.cpp | 10 ++-
src/bias/External.cpp | 9 ++-
src/bias/LWalls.cpp | 4 +-
src/bias/MetaD.cpp | 36 +++++-----
src/bias/Metainference.cpp | 10 ++-
src/bias/MovingRestraint.cpp | 12 ++--
src/bias/PBMetaD.cpp | 16 ++---
src/bias/Restraint.cpp | 5 +-
src/bias/ReweightBias.cpp | 4 +-
src/bias/ReweightMetad.cpp | 5 +-
src/bias/UWalls.cpp | 5 +-
src/colvar/Angle.cpp | 5 +-
src/colvar/CS2Backbone.cpp | 8 +--
src/colvar/Cell.cpp | 5 +-
src/colvar/Constant.cpp | 9 ++-
src/colvar/ContactMap.cpp | 15 ++---
src/colvar/Coordination.cpp | 13 ++--
src/colvar/DHEnergy.cpp | 5 +-
src/colvar/DRMSD.cpp | 8 +--
src/colvar/Dimer.cpp | 20 +++---
src/colvar/Dipole.cpp | 5 +-
src/colvar/Distance.cpp | 23 +++----
src/colvar/ERMSD.cpp | 4 +-
src/colvar/Energy.cpp | 5 +-
src/colvar/Fake.cpp | 5 +-
src/colvar/FretEfficiency.cpp | 10 ++-
src/colvar/Gyration.cpp | 5 +-
src/colvar/Implicit.cpp | 5 +-
src/colvar/Jcoupling.cpp | 8 +--
src/colvar/MultiRMSD.cpp | 8 +--
src/colvar/NOE.cpp | 5 +-
src/colvar/PCARMSD.cpp | 4 +-
src/colvar/PRE.cpp | 4 +-
src/colvar/PathMSD.cpp | 4 +-
src/colvar/Position.cpp | 6 +-
src/colvar/PropertyMap.cpp | 4 +-
src/colvar/Puckering.cpp | 4 +-
src/colvar/RDC.cpp | 5 +-
src/colvar/RMSD.cpp | 4 +-
src/colvar/Template.cpp | 4 +-
src/colvar/Torsion.cpp | 8 +--
src/colvar/Volume.cpp | 5 +-
src/crystallization/Fccubic.cpp | 4 +-
src/crystallization/Gradient.cpp | 8 +--
.../InterMolecularTorsions.cpp | 4 +-
src/crystallization/MoleculeOrientation.cpp | 4 +-
src/crystallization/Q3.cpp | 24 +++----
src/crystallization/Q4.cpp | 24 +++----
src/crystallization/Q6.cpp | 24 +++----
src/crystallization/SMAC.cpp | 8 +--
src/crystallization/SimpleCubic.cpp | 8 +--
src/crystallization/Tetrahedral.cpp | 8 +--
src/eds/EDS.cpp | 12 ++--
src/function/Combine.cpp | 8 +--
src/function/Ensemble.cpp | 5 +-
src/function/FuncPathMSD.cpp | 8 +--
src/function/LocalEnsemble.cpp | 4 +-
src/function/Matheval.cpp | 16 ++---
src/function/Piecewise.cpp | 5 +-
src/function/Sort.cpp | 5 +-
src/function/Stats.cpp | 4 +-
src/function/Target.cpp | 4 +-
src/generic/Debug.cpp | 4 +-
src/generic/DumpAtoms.cpp | 10 ++-
src/generic/DumpDerivatives.cpp | 4 +-
src/generic/DumpForces.cpp | 6 +-
src/generic/DumpMassCharge.cpp | 9 ++-
src/generic/DumpProjections.cpp | 4 +-
src/generic/EffectiveEnergyDrift.cpp | 8 +--
src/generic/FitToTemplate.cpp | 5 +-
src/generic/Flush.cpp | 4 +-
src/generic/Group.cpp | 24 +++----
src/generic/Include.cpp | 12 ++--
src/generic/Print.cpp | 5 +-
src/generic/RandomExchanges.cpp | 12 ++--
src/generic/Read.cpp | 4 +-
src/generic/ResetCell.cpp | 5 +-
src/generic/Time.cpp | 5 +-
src/generic/UpdateIf.cpp | 5 +-
src/generic/WholeMolecules.cpp | 15 ++---
src/generic/WrapAround.cpp | 20 +++---
src/gridtools/ConvertToFES.cpp | 4 +-
src/gridtools/DumpCube.cpp | 4 +-
src/gridtools/DumpGrid.cpp | 16 ++---
src/gridtools/FindContour.cpp | 4 +-
src/gridtools/FindSphericalContour.cpp | 4 +-
src/gridtools/FourierTransform.cpp | 4 +-
src/gridtools/InterpolateGrid.cpp | 4 +-
src/maketools/plumedcheck | 6 ++
src/manyrestraints/LWalls.cpp | 4 +-
src/manyrestraints/UWalls.cpp | 4 +-
src/mapping/PCAVars.cpp | 4 +-
src/mapping/Path.cpp | 16 ++---
src/mapping/PropertyMap.cpp | 4 +-
src/multicolvar/AlphaBeta.cpp | 12 ++--
src/multicolvar/Angles.cpp | 12 ++--
src/multicolvar/Bridge.cpp | 4 +-
src/multicolvar/CenterOfMultiColvar.cpp | 8 +--
src/multicolvar/CoordinationNumbers.cpp | 8 +--
src/multicolvar/Density.cpp | 4 +-
src/multicolvar/DihedralCorrelation.cpp | 8 +--
src/multicolvar/DistanceFromContour.cpp | 4 +-
src/multicolvar/Distances.cpp | 24 +++----
src/multicolvar/DumpMultiColvar.cpp | 4 +-
src/multicolvar/FilterBetween.cpp | 16 ++---
src/multicolvar/FilterLessThan.cpp | 12 ++--
src/multicolvar/FilterMoreThan.cpp | 16 ++---
src/multicolvar/InPlaneDistances.cpp | 4 +-
src/multicolvar/LocalAverage.cpp | 8 +--
src/multicolvar/MultiColvarDensity.cpp | 8 +--
src/multicolvar/NumberOfLinks.cpp | 8 +--
src/multicolvar/Torsions.cpp | 8 +--
src/multicolvar/VolumeAround.cpp | 4 +-
src/multicolvar/VolumeCavity.cpp | 8 +--
src/multicolvar/VolumeInCylinder.cpp | 4 +-
src/multicolvar/VolumeInSphere.cpp | 4 +-
src/multicolvar/VolumeTetrapore.cpp | 8 +--
src/multicolvar/XAngle.cpp | 12 ++--
src/multicolvar/XDistances.cpp | 48 +++++++-------
src/multicolvar/XYDistances.cpp | 12 ++--
src/multicolvar/XYTorsion.cpp | 24 +++----
src/secondarystructure/AlphaRMSD.cpp | 5 +-
src/secondarystructure/AntibetaRMSD.cpp | 5 +-
src/secondarystructure/ParabetaRMSD.cpp | 5 +-
src/setup/Load.cpp | 12 ++--
src/setup/MolInfo.cpp | 10 ++-
src/setup/Restart.cpp | 15 ++---
src/setup/Units.cpp | 9 ++-
src/vatom/COM.cpp | 5 +-
src/vatom/Center.cpp | 5 +-
src/vatom/FixedAtom.cpp | 10 ++-
src/vatom/Ghost.cpp | 5 +-
user-doc/Analysis.txt | 8 +--
user-doc/Colvar.txt | 8 +--
user-doc/Files.txt | 10 ++-
user-doc/Functions.txt | 4 +-
user-doc/Group.txt | 16 ++---
user-doc/Misc.txt | 65 +++++++++----------
user-doc/Performances.txt | 12 ++--
user-doc/Regex.txt | 16 ++---
user-doc/Syntax.txt | 14 ++--
162 files changed, 675 insertions(+), 749 deletions(-)
diff --git a/src/adjmat/ClusterDiameter.cpp b/src/adjmat/ClusterDiameter.cpp
index ec26f2eeb..8bebeab92 100644
--- a/src/adjmat/ClusterDiameter.cpp
+++ b/src/adjmat/ClusterDiameter.cpp
@@ -40,7 +40,7 @@ than 2.0 and if they are within 6.0 nm of each other. Depth first search cluste
between every pair of atoms that are within the largest of the clusters found is then calculated and the largest of these distances is output to a file named
colvar.
-\verbatim
+\plumedfile
# Calculate coordination numbers
c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}
# Select coordination numbers that are more than 2.0
@@ -52,7 +52,7 @@ dfs: DFSCLUSTERING MATRIX=mat
clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1
dia: CLUSTER_DIAMETER CLUSTERS=dfs CLUSTER=1
PRINT ARG=dia FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/ClusterDistribution.cpp b/src/adjmat/ClusterDistribution.cpp
index 93f12fb04..afd7c956e 100644
--- a/src/adjmat/ClusterDistribution.cpp
+++ b/src/adjmat/ClusterDistribution.cpp
@@ -44,7 +44,7 @@ algorithm on the corresponding graph. The number of componets in this graph that
As discussed in \cite tribello-clustering this input was used to analyse the formation of a polycrystal of GeTe from amorphous
GeTe.
-\verbatim
+\plumedfile
q6: Q6 SPECIES=1-32768 SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3} LOWMEM
lq6: LOCAL_Q6 SPECIES=q6 SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3} LOWMEM
flq6: MFILTER_MORE DATA=lq6 SWITCH={GAUSSIAN D_0=0.19 R_0=0.01 D_MAX=0.2}
@@ -54,7 +54,7 @@ mat: CONTACT_MATRIX ATOMS=fcc SWITCH={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}
dfs: DFSCLUSTERING MATRIX=mat
nclust: CLUSTER_DISTRIBUTION CLUSTERS=dfs TRANSFORM={GAUSSIAN D_0=5.99 R_0=0.01 D_MAX=6.0} MORE_THAN={GAUSSIAN D_0=26.99 R_0=0.01 D_MAX=27}
PRINT ARG=nclust.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/ClusterProperties.cpp b/src/adjmat/ClusterProperties.cpp
index 9a0d38e5b..b1d891fe0 100644
--- a/src/adjmat/ClusterProperties.cpp
+++ b/src/adjmat/ClusterProperties.cpp
@@ -42,13 +42,13 @@ a graph. This dfs action then finds the largest connected component in this gra
numbers for the atoms in this largest connected component are then computed and this quantity is output to a colvar
file. The way this input can be used is described in detail in \cite tribello-clustering.
-\verbatim
+\plumedfile
lq: COORDINATIONNUMBER SPECIES=1-100 SWITCH={CUBIC D_0=0.45 D_MAX=0.55} LOWMEM
cm: CONTACT_MATRIX ATOMS=lq SWITCH={CUBIC D_0=0.45 D_MAX=0.55}
dfs: DFSCLUSTERING MATRIX=cm
clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1 SUM
PRINT ARG=clust1.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/ClusterSize.cpp b/src/adjmat/ClusterSize.cpp
index b0b22621d..4ae18bb49 100644
--- a/src/adjmat/ClusterSize.cpp
+++ b/src/adjmat/ClusterSize.cpp
@@ -39,7 +39,7 @@ The following input uses PLUMED to calculate a adjacency matrix that connects a
than 2.0 and if they are within 6.0 nm of each other. Depth first search clustering is used to find the connected components in this matrix and then
the number of atoms in the largest cluster is found. This quantity is then output to a file called colvar
-\verbatim
+\plumedfile
# Calculate coordination numbers
c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}
# Select coordination numbers that are more than 2.0
@@ -51,7 +51,7 @@ dfs: DFSCLUSTERING MATRIX=mat
clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1
nat: CLUSTER_NATOMS CLUSTERS=dfs CLUSTER=1
PRINT ARG=nat FILE=COLVAR
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/ClusterWithSurface.cpp b/src/adjmat/ClusterWithSurface.cpp
index ab472eee5..1042accd0 100644
--- a/src/adjmat/ClusterWithSurface.cpp
+++ b/src/adjmat/ClusterWithSurface.cpp
@@ -44,7 +44,7 @@ number of atoms with indices that are between 1 and 1996 and that are either in
atoms within the the second largest cluster are then counted and this number of atoms is output to a file called size. In addition the indices of the atoms
that were counted are output to a file called dfs2.dat.
-\verbatim
+\plumedfile
c1: COORDINATIONNUMBER SPECIES=1-1996 SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
cf: MFILTER_LESS DATA=c1 SWITCH={CUBIC D_0=13 D_MAX=13.5}
mat: CONTACT_MATRIX ATOMS=cf SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
@@ -53,7 +53,7 @@ clust2a: CLUSTER_WITHSURFACE CLUSTERS=dfs RCUT_SURF=0.3
size2a: CLUSTER_NATOMS CLUSTERS=clust2a CLUSTER=2
PRINT ARG=size2a FILE=size FMT=%8.4f
OUTPUT_CLUSTER CLUSTERS=clust2a CLUSTER=2 FILE=dfs2.dat
-\endverbatim
+\endplumedfile
*/
diff --git a/src/adjmat/ContactAlignedMatrix.cpp b/src/adjmat/ContactAlignedMatrix.cpp
index e1bdfcdba..d00542aea 100644
--- a/src/adjmat/ContactAlignedMatrix.cpp
+++ b/src/adjmat/ContactAlignedMatrix.cpp
@@ -57,12 +57,12 @@ is greater than 0.5. The sum of the rows of this matrix are then computed. The
many of the molecules that are within the first coordination sphere of molecule \f$i\f$ have an orientation that is similar to that of
molecule \f$i\f$. We thus calculate the number of these "coordination numbers" that are greater than 1.0 and output this quantity to a file.
-\verbatim
+\plumedfile
m1: MOLECULES MOL1=1,2 MOL2=3,4 MOL3=5,6 MOL4=7,8
mat: ALIGNED_MATRIX ATOMS=m1 SWITCH={RATIONAL R_0=0.1} ORIENTATION_SWITCH={RATIONAL R_0=0.1 D_MAX=0.5}
rr: ROWSUMS MATRIX=mat MORE_THAN={RATIONAL D_0=1.0 R_0=0.1}
PRINT ARG=rr.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/ContactMatrix.cpp b/src/adjmat/ContactMatrix.cpp
index 1105a1aa2..e1a332a2a 100644
--- a/src/adjmat/ContactMatrix.cpp
+++ b/src/adjmat/ContactMatrix.cpp
@@ -48,11 +48,11 @@ The input shown below calculates a \f$6 \times 6\f$ matrix whose elements are eq
of each other and which is zero otherwise. The columns in this matrix are then summed so as to give the coordination number for each atom.
The final quantity output in the colvar file is thus the average coordination number.
-\verbatim
+\plumedfile
aa: CONTACT_MATRIX ATOMS=1-6 SWITCH={EXP D_0=0.2 R_0=0.1 D_MAX=0.66}
COLUMNSUMS MATRIX=mat MEAN LABEL=csums
PRINT ARG=csums.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/DFSClustering.cpp b/src/adjmat/DFSClustering.cpp
index af0dc327e..23bf5c592 100644
--- a/src/adjmat/DFSClustering.cpp
+++ b/src/adjmat/DFSClustering.cpp
@@ -53,13 +53,13 @@ a graph. This dfs action then finds the largest connected component in this gra
numbers for the atoms in this largest connected component are then computed and this quantity is output to a colvar
file. The way this input can be used is described in detail in \cite tribello-clustering.
-\verbatim
+\plumedfile
lq: COORDINATIONNUMBER SPECIES=1-100 SWITCH={CUBIC D_0=0.45 D_MAX=0.55} LOWMEM
cm: CONTACT_MATRIX ATOMS=lq SWITCH={CUBIC D_0=0.45 D_MAX=0.55}
dfs: DFSCLUSTERING MATRIX=cm
clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1 SUM
PRINT ARG=clust1.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/HbondMatrix.cpp b/src/adjmat/HbondMatrix.cpp
index f75e95754..32e7989de 100644
--- a/src/adjmat/HbondMatrix.cpp
+++ b/src/adjmat/HbondMatrix.cpp
@@ -66,13 +66,13 @@ on the number of hydrogen bonds each of the water molecules donates and accepts.
five columns of data. The first four of these columns are a label for the atom and the x, y and z position of the oxygen. The last column is then
the number of accepted/donated hydrogen bonds.
-\verbatim
+\plumedfile
mat: HBOND_MATRIX ATOMS=1-192:3 HYDROGENS=2-192:3,3-192:3 SWITCH={RATIONAL R_0=3.20} HSWITCH={RATIONAL R_0=2.30} ASWITCH={RATIONAL R_0=0.167pi} SUM
rsums: ROWSUMS MATRIX=mat MEAN
csums: COLUMNSUMS MATRIX=mat MEAN
DUMPMULTICOLVAR DATA=rsums FILE=donors.xyz
DUMPMULTICOLVAR DATA=csums FILE=acceptors.x
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/MatrixColumnSums.cpp b/src/adjmat/MatrixColumnSums.cpp
index 773502349..cae24fcec 100644
--- a/src/adjmat/MatrixColumnSums.cpp
+++ b/src/adjmat/MatrixColumnSums.cpp
@@ -43,21 +43,21 @@ tells you whether atoms \f$i\f$ and \f$j\f$ are within 1.0 nm of each other. Th
and the average value is computed. As such the following input provides an alternative method for calculating the coordination numbers
of atoms 1 to 10.
-\verbatim
+\plumedfile
mat: CONTACT_MATRIX ATOMS=1-10 SWITCH={RATIONAL R_0=1.0}
rsums: COLUMNSUMS MATRIX=mat MEAN
PRINT ARG=rsums.* FILE=colvar
-\endverbatim
+\endplumedfile
The following input demonstrates another way that an average coordination number can be computed. This input calculates the number of atoms
with indices between 1 and 5 that are within the first coordination spheres of each of the atoms within indices between 6 and 15. The average
coordination number is then calculated from these fifteen coordination numbers and this quantity is output to a file.
-\verbatim
+\plumedfile
mat2: CONTACT_MATRIX ATOMSA=1-5 ATOMSB=6-15 SWITCH={RATIONAL R_0=1.0}
rsums: COLUMNSUMS MATRIX=mat2 MEAN
PRINT ARG=rsums.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/MatrixRowSums.cpp b/src/adjmat/MatrixRowSums.cpp
index 038aa89a7..6ef15fb28 100644
--- a/src/adjmat/MatrixRowSums.cpp
+++ b/src/adjmat/MatrixRowSums.cpp
@@ -43,21 +43,21 @@ tells you whether atoms \f$i\f$ and \f$j\f$ are within 1.0 nm of each other. Th
and the average value is computed. As such the following input provides an alternative method for calculating the coordination numbers
of atoms 1 to 10.
-\verbatim
+\plumedfile
mat: CONTACT_MATRIX ATOMS=1-10 SWITCH={RATIONAL R_0=1.0}
rsums: ROWSUMS MATRIX=mat MEAN
PRINT ARG=rsums.* FILE=colvar
-\endverbatim
+\endplumedfile
The following input demonstrates another way that an average coordination number can be computed. This input calculates the number of atoms
with indices between 6 and 15 that are within the first coordination spheres of each of the atoms within indices between 1 and 5. The average
coordination number is then calculated from these five coordination numbers and this quantity is output to a file.
-\verbatim
+\plumedfile
mat2: CONTACT_MATRIX ATOMSA=1-5 ATOMSB=6-15 SWITCH={RATIONAL R_0=1.0}
rsums: ROWSUMS MATRIX=mat2 MEAN
PRINT ARG=rsums.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/OutputCluster.cpp b/src/adjmat/OutputCluster.cpp
index c2b752f0d..4dd430f3c 100644
--- a/src/adjmat/OutputCluster.cpp
+++ b/src/adjmat/OutputCluster.cpp
@@ -47,13 +47,13 @@ that satisfy this criteria. The DFS algorithm is then used to find the connecte
in this matrix and the indices of the atoms in the largest connected component are then output
to a file.
-\verbatim
+\plumedfile
c1: COORDINATIONNUMBER SPECIES=1-1996 SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
cf: MFILTER_LESS DATA=c1 SWITCH={CUBIC D_0=13 D_MAX=13.5}
mat: CONTACT_MATRIX ATOMS=cf SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
dfs: DFSCLUSTERING MATRIX=mat
OUTPUT_CLUSTER CLUSTERS=dfs CLUSTER=1 FILE=dfs.dat
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/SMACMatrix.cpp b/src/adjmat/SMACMatrix.cpp
index ac433076b..a4e8288f4 100644
--- a/src/adjmat/SMACMatrix.cpp
+++ b/src/adjmat/SMACMatrix.cpp
@@ -49,7 +49,7 @@ molecules \f$i\f$ and \f$j\f$ are within 6 angstroms of each other and if the to
of these molecules is close to 0 or \f$\pi\f$. The various connected components of this matrix are determined using the
\ref DFSCLUSTERING algorithm and then the size of the largest cluster of connectes molecules is output to a colvar file
-\verbatim
+\plumedfile
UNITS LENGTH=A
MOLECULES ...
@@ -70,7 +70,7 @@ SMAC_MATRIX ...
dfs1: DFSCLUSTERING MATRIX=smacm
cc2: CLUSTER_NATOMS CLUSTERS=dfs1 CLUSTER=1
PRINT ARG=smac.*,cc1.*,cc2 FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/Sprint.cpp b/src/adjmat/Sprint.cpp
index f7e0a0da8..3e90100e8 100644
--- a/src/adjmat/Sprint.cpp
+++ b/src/adjmat/Sprint.cpp
@@ -46,17 +46,17 @@ This example input calculates the 7 SPRINT coordinates for a 7 atom cluster of L
atoms and prints their values to a file. In this input the SPRINT coordinates are calculated
in the manner described in ?? so two atoms are adjacent if they are within a cutoff:
-\verbatim
+\plumedfile
DENSITY SPECIES=1-7 LABEL=d1
CONTACT_MATRIX ATOMS=d1 SWITCH={RATIONAL R_0=0.1} LABEL=mat
SPRINT MATRIX=mat LABEL=ss
PRINT ARG=ss.* FILE=colvar
-\endverbatim
+\endplumedfile
This example input calculates the 14 SPRINT coordinates foa a molecule composed of 7 hydrogen and
7 carbon atoms. Once again two atoms are adjacent if they are within a cutoff:
-\verbatim
+\plumedfile
DENSITY SPECIES=1-7 LABEL=c
DENSITY SPECIES=8-14 LABEL=h
@@ -71,7 +71,7 @@ CONTACT_MATRIX ...
SPRINT MATRIX=mat LABEL=ss
PRINT ARG=ss.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/analysis/Average.cpp b/src/analysis/Average.cpp
index c96b2556b..9d0566da8 100644
--- a/src/analysis/Average.cpp
+++ b/src/analysis/Average.cpp
@@ -51,11 +51,11 @@ and output this to a file called COLVAR. In this example it is assumed that no
on the system and that the weights, \f$w(t')\f$ in the formulae above can thus all be set equal
to one.
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=1,2
d1a: AVERAGE ARG=d1
PRINT ARG=d1a FILE=colvar STRIDE=100
-\endverbatim
+\endplumedfile
The following example calculates the ensemble average for the torsional angle involving atoms 1, 2, 3 and 4.
At variance with the previous example this quantity is periodic so the second formula in the above introduction
@@ -65,23 +65,23 @@ forgotten and the process of averaging is begun again. The quantities output in
block averages taken over the first 100 frames of the trajectory, the block average over the second 100 frames
of trajectory and so on.
-\verbatim
+\plumedfile
t1: TORSION ATOMS=1,2,3,4
t1a: AVERAGE ARG=t1 CLEAR=100
PRINT ARG=t1a FILE=colvar STRIDE=100
-\endverbatim
+\endplumedfile
This third example incorporates a bias. Notice that the effect the bias has on the ensemble average is removed by taking
advantage of the \ref REWEIGHT_BIAS method. The final ensemble averages output to the file are thus block ensemble averages for the
unbiased canononical ensemble at a temperature of 300 K.
-\verbatim
+\plumedfile
t1: TORSION ATOMS=1,2,3,4
RESTRAINT ARG=t1 AT=pi KAPPA=100.
ww: REWEIGHT_BIAS TEMP=300
t1a: AVERAGE ARG=t1 LOGWEIGHTS=ww CLEAR=100
PRINT ARG=t1a FILE=colvar STRIDE=100
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/analysis/ClassicalMultiDimensionalScaling.cpp b/src/analysis/ClassicalMultiDimensionalScaling.cpp
index 93bb25f1d..68ac6aeae 100644
--- a/src/analysis/ClassicalMultiDimensionalScaling.cpp
+++ b/src/analysis/ClassicalMultiDimensionalScaling.cpp
@@ -55,7 +55,7 @@ can be found in the tutorial \ref belfast-3 and in the following <a href="https:
The following command instructs plumed to construct a classical multidimensional scaling projection of a trajectory.
The RMSD distance between atoms 1-256 have moved is used to measure the distances in the high-dimensional space.
-\verbatim
+\plumedfile
CLASSICAL_MDS ...
ATOMS=1-256
METRIC=OPTIMAL-FAST
@@ -63,7 +63,7 @@ CLASSICAL_MDS ...
NLOW_DIM=2
OUTPUT_FILE=rmsd-embed
... CLASSICAL_MDS
-\endverbatim
+\endplumedfile
The following section is for people who are interested in how this method works in detail. A solid understanding of this material is
not necessary to use MDS.
diff --git a/src/analysis/Commit.cpp b/src/analysis/Commit.cpp
index 5cbacf4db..d51d6b9e5 100644
--- a/src/analysis/Commit.cpp
+++ b/src/analysis/Commit.cpp
@@ -37,7 +37,7 @@ The following input monitors two torsional angles during a simulation,
defines two basins (A and B) as a function of the two torsions and
stops the simulation when it falls in one of the two. In the log
file will be shown the latest values for the CVs and the basin reached.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
COMMITTOR ...
@@ -48,7 +48,7 @@ COMMITTOR ...
BASIN_LL2=-0.15,-0.20
BASIN_UL2=-0.25,-0.40
... COMMITTOR
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/analysis/Histogram.cpp b/src/analysis/Histogram.cpp
index b8a74c797..16abb4a6d 100644
--- a/src/analysis/Histogram.cpp
+++ b/src/analysis/Histogram.cpp
@@ -84,7 +84,7 @@ Additional material and examples can be also found in the tutorial \ref belfast-
The following input monitors two torsional angles during a simulation
and outputs a continuos histogram as a function of them at the end of the simulation.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
@@ -97,11 +97,11 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hh FILE=histo
-\endverbatim
+\endplumedfile
The following input monitors two torsional angles during a simulation
and outputs a discrete histogram as a function of them at the end of the simulation.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
@@ -115,11 +115,11 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hh FILE=histo
-\endverbatim
+\endplumedfile
The following input monitors two torsional angles during a simulation
and outputs the histogram accumulated thus far every 100000 steps.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
@@ -132,14 +132,14 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hh FILE=histo STRIDE=100000
-\endverbatim
+\endplumedfile
The following input monitors two torsional angles during a simulation
and outputs a separate histogram for each 100000 steps worth of trajectory.
Notice how the CLEAR keyword is used here and how it is not used in the
previous example.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
@@ -153,7 +153,7 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hh FILE=histo STRIDE=100000
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/analysis/PCA.cpp b/src/analysis/PCA.cpp
index 5b31a04fa..528c6290b 100644
--- a/src/analysis/PCA.cpp
+++ b/src/analysis/PCA.cpp
@@ -63,9 +63,9 @@ of the first 22 atoms. The TYPE=OPTIMAL instruction ensures that translational
The first two principal components will be output to a file called pca-comp.pdb. Trajectory frames will be collected on every step and the PCA calculation
will be performed at the end of the simulation.
-\verbatim
+\plumedfile
PCA METRIC=OPTIMAL ATOMS=1-22 STRIDE=1 USE_ALL_DATA NLOW_DIM=2 OFILE=pca-comp.pdb
-\endverbatim
+\endplumedfile
The following input instructs PLUMED to perform a principal component analysis in which the covariance matrix is calculated from chnages in the six distances
seen in the previous lines. Notice that here the TYPE=EUCLIDEAN keyword is used to indicate that no alighment has to be done when calculating the various
@@ -75,7 +75,7 @@ PCA analysis will be performed twice. The REWEIGHT_BIAS keyword in this input t
when calculating averages and covariances a reweighting should be performed based and each frames' weight in these calculations should be determined based on
the current value of the instantaneous bias (see \ref REWEIGHT_BIAS).
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=1,2
d2: DISTANCE ATOMS=1,3
d3: DISTANCE ATOMS=1,4
@@ -84,7 +84,7 @@ d5: DISTANCE ATOMS=2,4
d6: DISTANCE ATOMS=3,4
PCA ARG=d1,d2,d3,d4,d5,d6 METRIC=EUCLIDEAN STRIDE=5 RUN=1000 NLOW_DIM=2 REWEIGHT_BIAS OFILE=pca-comp.pdb
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/bias/ABMD.cpp b/src/bias/ABMD.cpp
index 5e8bef344..a76c5341c 100644
--- a/src/bias/ABMD.cpp
+++ b/src/bias/ABMD.cpp
@@ -70,13 +70,12 @@ an additional white noise acting on the minimum position of the bias.
The following input sets up two biases, one on the distance between atoms 3 and 5
and another on the distance between atoms 2 and 4. The two target values are defined
using TO and the two strength using KAPPA. The total energy of the bias is printed.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
ABMD ARG=d1,d2 TO=1.0,1.5 KAPPA=5.0,5.0 LABEL=abmd
PRINT ARG=abmd.bias,abmd.d1_min,abmd.d2_min
-\endverbatim
-(See also \ref DISTANCE and \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/bias/BiasValue.cpp b/src/bias/BiasValue.cpp
index 3e77621a5..ff741a6c0 100644
--- a/src/bias/BiasValue.cpp
+++ b/src/bias/BiasValue.cpp
@@ -42,18 +42,17 @@ to some collective variable then using the value of this function directly as a
The following input tells plumed to use the value of the distance between atoms 3 and 5
and the value of the distance between atoms 2 and 4 as biases.
It then tells plumed to print the energy of the restraint
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=3,6 LABEL=d2
BIASVALUE ARG=d1,d2 LABEL=b
PRINT ARG=d1,d2,b.d1,b.d2
-\endverbatim
-(See also \ref DISTANCE and \ref PRINT).
+\endplumedfile
Another thing one can do is asking one system to follow
a circle in sin/cos according a time dependence
-\verbatim
+\plumedfile
t: TIME
# this just print cos and sin of time
cos: MATHEVAL ARG=t VAR=t FUNC=cos(t) PERIODIC=NO
@@ -72,9 +71,7 @@ vv1: MATHEVAL ARG=mycos,mysin,cos,sin VAR=mc,ms,c,s FUNC=100*((mc-c)^2+(ms-s)^
cc: BIASVALUE ARG=vv1
# some printout
PRINT ARG=t,cos,sin,d.x,d.y,d.z,mycos,mysin,cc.bias.vv1 STRIDE=1 FILE=colvar FMT=%8.4f
-\endverbatim
-(see also \ref TIME, \ref MATHEVAL, \ref COM, \ref DISTANCE, and \ref PRINT).
-
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/bias/ExtendedLagrangian.cpp b/src/bias/ExtendedLagrangian.cpp
index 85de570dd..ee3d3ada0 100644
--- a/src/bias/ExtendedLagrangian.cpp
+++ b/src/bias/ExtendedLagrangian.cpp
@@ -88,28 +88,26 @@ and many shorter runs.
The following input tells plumed to perform a metadynamics
with an extended Lagrangian on two torsional angles.
-\verbatim
+\plumedfile
phi: TORSION ATOMS=5,7,9,15
psi: TORSION ATOMS=7,9,15,17
ex: EXTENDED_LAGRANGIAN ARG=phi,psi KAPPA=20,20.0 TAU=0.1,0.1
METAD ARG=ex.phi_fict,ex.psi_fict PACE=100 SIGMA=0.35,0.35 HEIGHT=0.1
# monitor the two variables
PRINT STRIDE=10 ARG=phi,psi,ex.phi_fict,ex.psi_fict FILE=COLVAR
-\endverbatim
-(See also \ref TORSION, \ref METAD, and \ref PRINT).
+\endplumedfile
The following input tells plumed to perform a TAMD (or dAFED)
calculation on two torsional angles, keeping the two variables
at a fictitious temperature of 3000K with a Langevin thermostat
with friction 10
-\verbatim
+\plumedfile
phi: TORSION ATOMS=5,7,9,15
psi: TORSION ATOMS=7,9,15,17
ex: EXTENDED_LAGRANGIAN ARG=phi,psi KAPPA=20,20.0 TAU=0.1,0.1 FRICTION=10,10 TEMP=3000
# monitor the two variables
PRINT STRIDE=10 ARG=phi,psi,ex.phi_fict,ex.psi_fict FILE=COLVAR
-\endverbatim
-(See also \ref TORSION and \ref PRINT)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/bias/External.cpp b/src/bias/External.cpp
index 62bc54cf9..7c714efae 100644
--- a/src/bias/External.cpp
+++ b/src/bias/External.cpp
@@ -39,11 +39,10 @@ Calculate a restraint that is defined on a grid that is read during start up
\par Examples
The following is an input for a calculation with an external potential that is
defined in the file bias.dat and that acts on the distance between atoms 3 and 5.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
EXTERNAL ARG=d1 FILE=bias.dat LABEL=external
-\endverbatim
-(See also \ref DISTANCE \ref PRINT).
+\endplumedfile
The header in the file bias.dat should read:
\verbatim
@@ -61,11 +60,11 @@ with NOSPLINE you do not need to provide derivative information.
You can also include grids that are a function of more than one collective
variable. For instance the following would be the input for an external
potential acting on two torsional angles:
-\verbatim
+\plumedfile
TORSION ATOMS=4,5,6,7 LABEL=t1
TORSION ATOMS=6,7,8,9 LABEL=t2
EXTERNAL ARG=t1,t2 FILE=bias.dat LABEL=ext
-\endverbatim
+\endplumedfile
The header in the file bias.dat for this calculation would read:
\verbatim
diff --git a/src/bias/LWalls.cpp b/src/bias/LWalls.cpp
index 33d7f7c04..26bb720f1 100644
--- a/src/bias/LWalls.cpp
+++ b/src/bias/LWalls.cpp
@@ -52,13 +52,13 @@ The following input tells plumed to add both a lower and an upper walls on the d
between atoms 3 and 5 and the distance between atoms 2 and 4. The lower and upper limits
are defined at different values. The strength of the walls is the same for the four cases.
It also tells plumed to print the energy of the walls.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
UPPER_WALLS ARG=d1,d2 AT=1.0,1.5 KAPPA=150.0,150.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=uwall
LOWER_WALLS ARG=d1,d2 AT=0.0,1.0 KAPPA=150.0,150.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=lwall
PRINT ARG=uwall.bias,lwall.bias
-\endverbatim
+\endplumedfile
(See also \ref DISTANCE and \ref PRINT).
*/
diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
index b58618570..5023c38f2 100644
--- a/src/bias/MetaD.cpp
+++ b/src/bias/MetaD.cpp
@@ -163,35 +163,35 @@ The following input is for a standard metadynamics calculation using as
collective variables the distance between atoms 3 and 5
and the distance between atoms 2 and 4. The value of the CVs and
the metadynamics bias potential are written to the COLVAR file every 100 steps.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
METAD ARG=d1,d2 SIGMA=0.2,0.2 HEIGHT=0.3 PACE=500 LABEL=restraint
PRINT ARG=d1,d2,restraint.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
(See also \ref DISTANCE \ref PRINT).
\par
If you use adaptive Gaussians, with diffusion scheme where you use
a Gaussian that should cover the space of 20 timesteps in collective variables.
Note that in this case the histogram correction is needed when summing up hills.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
METAD ARG=d1,d2 SIGMA=20 HEIGHT=0.3 PACE=500 LABEL=restraint ADAPTIVE=DIFF
PRINT ARG=d1,d2,restraint.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
\par
If you use adaptive Gaussians, with geometrical scheme where you use
a Gaussian that should cover the space of 0.05 nm in Cartesian space.
Note that in this case the histogram correction is needed when summing up hills.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
METAD ARG=d1,d2 SIGMA=0.05 HEIGHT=0.3 PACE=500 LABEL=restraint ADAPTIVE=GEOM
PRINT ARG=d1,d2,restraint.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
\par
When using adaptive Gaussians you might want to limit how the hills width can change.
@@ -199,7 +199,7 @@ You can use SIGMA_MIN and SIGMA_MAX keywords.
The sigmas should specified in terms of CV so you should use the CV units.
Note that if you use a negative number, this means that the limit is not set.
Note also that in this case the histogram correction is needed when summing up hills.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
METAD ...
@@ -207,7 +207,7 @@ METAD ...
SIGMA_MIN=0.2,0.1 SIGMA_MAX=0.5,1.0
... METAD
PRINT ARG=d1,d2,restraint.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
\par
Multiple walkers can be also use as in \cite multiplewalkers
@@ -215,7 +215,7 @@ These are enabled by setting the number of walker used, the id of the
current walker which interprets the input file, the directory where the
hills containing files resides, and the frequency to read the other walkers.
Here is an example
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
METAD ...
ARG=d1 SIGMA=0.05 HEIGHT=0.3 PACE=500 LABEL=restraint
@@ -224,7 +224,7 @@ METAD ...
WALKERS_DIR=../
WALKERS_RSTRIDE=100
... METAD
-\endverbatim
+\endplumedfile
where WALKERS_N is the total number of walkers, WALKERS_ID is the
id of the present walker (starting from 0 ) and the WALKERS_DIR is the directory
where all the walkers are located. WALKERS_RSTRIDE is the number of step between
@@ -237,7 +237,7 @@ presented in \cite Tiwary_jp504920s as described above.
This is enabled by using the keyword REWEIGHTING_NGRID where the grid used for
the calculation is set. The number of grid points given in REWEIGHTING_NGRID
should be equal or larger than the number of grid points given in GRID_BIN.
-\verbatim
+\plumedfile
METAD ...
LABEL=metad
ARG=phi,psi SIGMA=0.20,0.20 HEIGHT=1.20 BIASFACTOR=5 TEMP=300.0 PACE=500
@@ -245,7 +245,7 @@ METAD ...
REWEIGHTING_NGRID=150,150
REWEIGHTING_NHILLS=20
... METAD
-\endverbatim
+\endplumedfile
Here we have asked that the calculation is performed every 20 hills by using
REWEIGHTING_NHILLS keyword. If this keyword is not given the calculation will
by default be performed every 50 hills. The c(t) reweighting factor will be given
@@ -285,7 +285,7 @@ Alternatively, if you use a BIASFACTOR yout simulation will converge to a free
energy that is a linear combination of the target free energy and of the intrinsic free energy
determined by the original force field.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
METAD ...
LABEL=t1
@@ -295,7 +295,7 @@ METAD ...
... METAD
PRINT ARG=d1,t1.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
The header in the file dist.dat for this calculation would read:
@@ -309,19 +309,19 @@ The header in the file dist.dat for this calculation would read:
Notice that BIASFACTOR can also be chosen as equal to 1. In this case one will perform
unbiased sampling. Instead of using HEIGHT, one should provide the TAU parameter.
-\verbatim
+\plumedfile
d: DISTANCE ATOMS=3,5
METAD ARG=d SIGMA=0.1 TAU=4.0 TEMP=300 PACE=100 BIASFACTOR=1.0
-\endverbatim
+\endplumedfile
The HILLS file obtained will still work with `plumed sum_hills` so as to plot a free-energy.
The case where this makes sense is probably that of RECT simulations.
Regarding RECT simulations, you can also use the RECT keyword so as to avoid using multiple input files.
For instance, a single input file will be
-\verbatim
+\plumedfile
d: DISTANCE ATOMS=3,5
METAD ARG=d SIGMA=0.1 TAU=4.0 TEMP=300 PACE=100 RECT=1.0,1.5,2.0,3.0
-\endverbatim
+\endplumedfile
The number of elements in the RECT array should be equal to the number of replicas.
diff --git a/src/bias/Metainference.cpp b/src/bias/Metainference.cpp
index e4d3e8b94..3953c436d 100644
--- a/src/bias/Metainference.cpp
+++ b/src/bias/Metainference.cpp
@@ -58,7 +58,7 @@ them and comparing them with a set of experimental values. RDCs are compared wit
the experimental data but for a multiplication factor SCALE that is also sampled by
MC on-the-fly
-\verbatim
+\plumedfile
RDC ...
LABEL=rdc
SCALE=0.0001
@@ -83,12 +83,12 @@ LABEL=spe
... METAINFERENCE
PRINT ARG=spe.bias FILE=BIAS STRIDE=1
-\endverbatim
+\endplumedfile
in the following example instead of using one uncertainty parameter per data point we use
a single uncertainty value in a long-tailed gaussian to take into account for outliers.
-\verbatim
+\plumedfile
METAINFERENCE ...
ARG=ardc.*
NOISETYPE=OUTLIERS
@@ -99,9 +99,7 @@ SIGMA_MEAN=0.001
TEMP=300
LABEL=spe
... METAINFERENCE
-\endverbatim
-
-(See also \ref RDC and \ref ENSEMBLE).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/bias/MovingRestraint.cpp b/src/bias/MovingRestraint.cpp
index 13cafce97..d5317af1d 100644
--- a/src/bias/MovingRestraint.cpp
+++ b/src/bias/MovingRestraint.cpp
@@ -53,7 +53,7 @@ Additional material and examples can be also found in the tutorial \ref belfast-
The following input is dragging the distance between atoms 2 and 4
from 1 to 2 in the first 1000 steps, then back in the next 1000 steps.
In the following 500 steps the restraint is progressively switched off.
-\verbatim
+\plumedfile
DISTANCE ATOMS=2,4 LABEL=d
MOVINGRESTRAINT ...
ARG=d
@@ -62,12 +62,12 @@ MOVINGRESTRAINT ...
STEP2=2000 AT2=1.0
STEP3=2500 KAPPA3=0.0
... MOVINGRESTRAINT
-\endverbatim
+\endplumedfile
The following input is progressively building restraints
distances between atoms 1 and 5 and between atoms 2 and 4
in the first 1000 steps. Afterwards, the restraint is kept
static.
-\verbatim
+\plumedfile
DISTANCE ATOMS=1,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
MOVINGRESTRAINT ...
@@ -75,10 +75,10 @@ MOVINGRESTRAINT ...
STEP0=0 AT0=1.0,1.5 KAPPA0=0.0,0.0
STEP1=1000 AT1=1.0,1.5 KAPPA1=1.0,1.0
... MOVINGRESTRAINT
-\endverbatim
+\endplumedfile
The following input is progressively bringing atoms 1 and 2
close to each other with an upper wall
-\verbatim
+\plumedfile
DISTANCE ATOMS=1,2 LABEL=d1
MOVINGRESTRAINT ...
ARG=d1
@@ -86,7 +86,7 @@ MOVINGRESTRAINT ...
STEP0=0 AT0=1.0 KAPPA0=10.0
STEP1=1000 AT1=0.0
... MOVINGRESTRAINT
-\endverbatim
+\endplumedfile
By default the Action is issuing some values which are
the work on each degree of freedom, the center of the harmonic potential,
diff --git a/src/bias/PBMetaD.cpp b/src/bias/PBMetaD.cpp
index b50557f7d..76c35154b 100644
--- a/src/bias/PBMetaD.cpp
+++ b/src/bias/PBMetaD.cpp
@@ -150,18 +150,18 @@ The following input is for PBMetaD calculation using as
collective variables the distance between atoms 3 and 5
and the distance between atoms 2 and 4. The value of the CVs and
the PBMetaD bias potential are written to the COLVAR file every 100 steps.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
PBMETAD ARG=d1,d2 SIGMA=0.2,0.2 HEIGHT=0.3 PACE=500 LABEL=pb FILE=HILLS_d1,HILLS_d2
PRINT ARG=d1,d2,pb.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
(See also \ref DISTANCE and \ref PRINT).
\par
If you use well-tempered metadynamics, you should specify a single biasfactor and initial
Gaussian height.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
PBMETAD ...
@@ -170,11 +170,11 @@ PACE=500 BIASFACTOR=8 LABEL=pb
FILE=HILLS_d1,HILLS_d2
... PBMETAD
PRINT ARG=d1,d2,pb.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
\par
The following input enables the MPI version of multiple-walkers.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
PBMETAD ...
@@ -184,7 +184,7 @@ FILE=HILLS_d1,HILLS_d2
WALKERS_MPI
... PBMETAD
PRINT ARG=d1,d2,pb.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
\par
The disk version of multiple-walkers can be
@@ -192,7 +192,7 @@ enabled by setting the number of walker used, the id of the
current walker which interprets the input file, the directory where the
hills containing files resides, and the frequency to read the other walkers.
Here is an example
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
PBMETAD ...
@@ -205,7 +205,7 @@ WALKERS_DIR=../
WALKERS_RSTRIDE=100
... PBMETAD
PRINT ARG=d1,d2,pb.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
where WALKERS_N is the total number of walkers, WALKERS_ID is the
id of the present walker (starting from 0 ) and the WALKERS_DIR is the directory
where all the walkers are located. WALKERS_RSTRIDE is the number of step between
diff --git a/src/bias/Restraint.cpp b/src/bias/Restraint.cpp
index 8bb3df202..85208d35b 100644
--- a/src/bias/Restraint.cpp
+++ b/src/bias/Restraint.cpp
@@ -49,13 +49,12 @@ Additional material and examples can be also found in the tutorial \ref belfast-
The following input tells plumed to restrain the distance between atoms 3 and 5
and the distance between atoms 2 and 4, at different equilibrium
values, and to print the energy of the restraint
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
RESTRAINT ARG=d1,d2 AT=1.0,1.5 KAPPA=150.0,150.0 LABEL=restraint
PRINT ARG=restraint.bias
-\endverbatim
-(See also \ref DISTANCE and \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/bias/ReweightBias.cpp b/src/bias/ReweightBias.cpp
index d0b2d90a3..60976e644 100644
--- a/src/bias/ReweightBias.cpp
+++ b/src/bias/ReweightBias.cpp
@@ -43,7 +43,7 @@ restraint will have an effect on the region of phase space that will be sampled
run using this variable. Consequently, when the histogram as a function of the distance, \f$x\f$, is accumulated,
we use reweighting into order to discount the effect of the bias from our final histogram.
-\verbatim
+\plumedfile
x: DISTANCE ATOMS=1,2
RESTRAINT ARG=x SLOPE=1.0 AT=0.0
as: REWEIGHT_BIAS TEMP=300
@@ -59,7 +59,7 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hB FILE=histoB STRIDE=1 FMT=%8.4f
-\endverbatim
+\endplumedfile
*/
diff --git a/src/bias/ReweightMetad.cpp b/src/bias/ReweightMetad.cpp
index 766ed40df..42a4855c2 100644
--- a/src/bias/ReweightMetad.cpp
+++ b/src/bias/ReweightMetad.cpp
@@ -39,7 +39,7 @@ we use reweighting into order to discount the effect of the bias from our final
metadynamics instead. Notice also that we have to specify how often we would like to calculate the c(t) reweighting
factor and the grid over which we calculate c(t) in the input to the METAD command.
-\verbatim
+\plumedfile
a: ANGLE ATOMS=1,2,3
x: DISTANCE ATOMS=1,2
METAD ARG=x PACE=100 SIGMA=0.1 HEIGHT=1.5 BIASFACTOR=5 GRID_MIN=0 GRID_MAX=10 GRID_BIN=100 REWEIGHTING_NGRID=100 REWEIGHTING_NHILLS=50
@@ -57,8 +57,7 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hB FILE=histoB STRIDE=1 FMT=%8.4f
-
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/bias/UWalls.cpp b/src/bias/UWalls.cpp
index 0f096f11b..bfe4d8929 100644
--- a/src/bias/UWalls.cpp
+++ b/src/bias/UWalls.cpp
@@ -52,14 +52,13 @@ The following input tells plumed to add both a lower and an upper walls on the d
between atoms 3 and 5 and the distance between atoms 2 and 4. The lower and upper limits
are defined at different values. The strength of the walls is the same for the four cases.
It also tells plumed to print the energy of the walls.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
UPPER_WALLS ARG=d1,d2 AT=1.0,1.5 KAPPA=150.0,150.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=uwall
LOWER_WALLS ARG=d1,d2 AT=0.0,1.0 KAPPA=150.0,150.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=lwall
PRINT ARG=uwall.bias,lwall.bias
-\endverbatim
-(See also \ref DISTANCE and \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/Angle.cpp b/src/colvar/Angle.cpp
index ed57d03ea..285d6fa50 100644
--- a/src/colvar/Angle.cpp
+++ b/src/colvar/Angle.cpp
@@ -67,7 +67,7 @@ This command tells plumed to calculate the angle between the vector connecting a
the vector connecting atom 2 to atom 3 and to print it on file COLVAR1. At the same time,
the angle between vector connecting atom 1 to atom 2 and the vector connecting atom 3 to atom 4 is printed
on file COLVAR2.
-\verbatim
+\plumedfile
a: ANGLE ATOMS=1,2,3
# equivalently one could state:
@@ -77,8 +77,7 @@ b: ANGLE ATOMS=1,2,3,4
PRINT ARG=a FILE=COLVAR1
PRINT ARG=b FILE=COLVAR2
-\endverbatim
-(see also \ref PRINT)
+\endplumedfile
*/
diff --git a/src/colvar/CS2Backbone.cpp b/src/colvar/CS2Backbone.cpp
index 040e0dfad..6c606e4e5 100644
--- a/src/colvar/CS2Backbone.cpp
+++ b/src/colvar/CS2Backbone.cpp
@@ -116,17 +116,17 @@ Additional material and examples can be also found in the tutorial \ref belfast-
In this first example the chemical shifts are used to calculate a scoring function to be used
in NMR driven Metadynamics \cite Granata:2013dk :
-\verbatim
+\plumedfile
whole: GROUP ATOMS=2612-2514:-1,961-1:-1,2466-962:-1,2513-2467:-1
WHOLEMOLECULES ENTITY0=whole
cs: CS2BACKBONE ATOMS=1-2612 NRES=176 DATA=../data/ TEMPLATE=template.pdb CAMSHIFT NOPBC
metad: METAD ARG=cs HEIGHT=0.5 SIGMA=0.1 PACE=200 BIASFACTOR=10
PRINT ARG=cs,metad.bias FILE=COLVAR STRIDE=100
-\endverbatim
+\endplumedfile
In this second example the chemical shifts are used as replica-averaged restrained as in \cite Camilloni:2012je \cite Camilloni:2013hs.
-\verbatim
+\plumedfile
cs: CS2BACKBONE ATOMS=1-174 DATA=data/ NRES=13
encs: ENSEMBLE ARG=(cs\.hn_.*),(cs\.nh_.*)
stcs: STATS ARG=encs.* SQDEVSUM PARARG=(cs\.exphn_.*),(cs\.expnh_.*)
@@ -134,7 +134,7 @@ RESTRAINT ARG=stcs.sqdevsum AT=0 KAPPA=0 SLOPE=24
PRINT ARG=(cs\.hn_.*),(cs\.nh_.*) FILE=RESTRAINT STRIDE=100
-\endverbatim
+\endplumedfile
(See also \ref WHOLEMOLECULES, \ref STATS, \ref METAD, \ref RESTRAINT and \ref PRINT)
diff --git a/src/colvar/Cell.cpp b/src/colvar/Cell.cpp
index 5c59e9f49..082fa237d 100644
--- a/src/colvar/Cell.cpp
+++ b/src/colvar/Cell.cpp
@@ -36,14 +36,13 @@ Calculate the components of the simulation cell
\par Examples
The following input tells plumed to print the squared modulo of each of the three lattice vectors
-\verbatim
+\plumedfile
cell: CELL
aaa: COMBINE ARG=cell.ax,cell.ay,cell.az POWERS=2,2,2 PERIODIC=NO
bbb: COMBINE ARG=cell.bx,cell.by,cell.bz POWERS=2,2,2 PERIODIC=NO
ccc: COMBINE ARG=cell.cx,cell.cy,cell.cz POWERS=2,2,2 PERIODIC=NO
PRINT ARG=aaa,bbb,ccc
-\endverbatim
-(See also \ref COMBINE and \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/Constant.cpp b/src/colvar/Constant.cpp
index 49423413d..247f9ac6d 100644
--- a/src/colvar/Constant.cpp
+++ b/src/colvar/Constant.cpp
@@ -44,21 +44,20 @@ The following input instructs plumed to compute the distance
between atoms 1 and 2. If this distance is between 1.0 and 2.0, it is
printed. If it is lower than 1.0 (larger than 2.0), 1.0 (2.0) is printed
-\verbatim
+\plumedfile
cn: CONSTANT VALUES=1.0,2.0
dis: DISTANCE ATOMS=1,2
sss: SORT ARG=cn.v_0,dis,cn.v_1
PRINT ARG=sss.2
-\endverbatim
-(See also \ref DISTANCE, \ref SORT, and \ref PRINT).
+\endplumedfile
In case you want to pass a single value you can use VALUE:
-\verbatim
+\plumedfile
cn: CONSTANT VALUE=1.0
dis: DISTANCE ATOMS=1
sss: SORT ARG=cn,dis
PRINT ARG=sss.1
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/ContactMap.cpp b/src/colvar/ContactMap.cpp
index 9405f172f..9fe8f82c9 100644
--- a/src/colvar/ContactMap.cpp
+++ b/src/colvar/ContactMap.cpp
@@ -45,17 +45,17 @@ The following example calculates switching functions based on the distances betw
1 and 2, 3 and 4 and 4 and 5. The values of these three switching functions are then output
to a file named colvar.
-\verbatim
+\plumedfile
CONTACTMAP ATOMS1=1,2 ATOMS2=3,4 ATOMS3=4,5 ATOMS4=5,6 SWITCH={RATIONAL R_0=1.5} LABEL=f1
PRINT ARG=f1.* FILE=colvar
-\endverbatim
+\endplumedfile
The following example calculates the difference of the current contact map with respect
to a reference provided. In this case REFERENCE is the fraction of contact that is formed
(i.e. the distance between two atoms transformed with the SWITH), while R_0 is the contact
distance. WEIGHT gives the relative weight of each contact to the final distance measure.
-\verbatim
+\plumedfile
CONTACTMAP ...
ATOMS1=1,2 REFERENCE1=0.1 WEIGHT1=0.5
ATOMS2=3,4 REFERENCE2=0.5 WEIGHT2=1.0
@@ -67,7 +67,7 @@ CMDIST
... CONTACTMAP
PRINT ARG=cmap FILE=colvar
-\endverbatim
+\endplumedfile
The next example calculates calculates fraction of native contacts (Q)
for Trp-cage mini-protein. R_0 is the distance at which the switch function is guaranteed to
@@ -80,7 +80,7 @@ WEIGHT is the 1/(number of contacts) giving equal weight to each contact.
When using native contact Q switch function, please cite \cite best2013
-\verbatim
+\plumedfile
# Full example available in regtest/basic/rt72/
CONTACTMAP ...
@@ -97,9 +97,8 @@ SUM
... CONTACTMAP
PRINT ARG=cmap FILE=colvar
-\endverbatim
-
-(See also \ref PRINT and \ref switchingfunction)
+\endplumedfile
+(See also \ref switchingfunction)
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/Coordination.cpp b/src/colvar/Coordination.cpp
index c1aa2da4f..fe0a8b08d 100644
--- a/src/colvar/Coordination.cpp
+++ b/src/colvar/Coordination.cpp
@@ -62,19 +62,19 @@ so that they actually count as "zero".
\par Examples
The following example instructs plumed to calculate the total coordination number of the atoms in group 1-10 with the atoms in group 20-100. For atoms 1-10 coordination numbers are calculated that count the number of atoms from the second group that are within 0.3 nm of the central atom. A neighbour list is used to make this calculation faster, this neighbour list is updated every 100 steps.
-\verbatim
+\plumedfile
COORDINATION GROUPA=1-10 GROUPB=20-100 R_0=0.3 NLIST NL_CUTOFF=0.5 NL_STRIDE=100
-\endverbatim
+\endplumedfile
The following is a dummy example which should compute the value 0 because the self interaction
of atom 1 is skipped. Notice that in plumed 2.0 "self interactions" were not skipped, and the
same calculation should return 1.
-\verbatim
+\plumedfile
c: COORDINATION GROUPA=1 GROUPB=1 R_0=0.3
PRINT ARG=c STRIDE=10
-\endverbatim
+\endplumedfile
-\verbatim
+\plumedfile
c1: COORDINATION GROUPA=1-10 GROUPB=1-10 R_0=0.3
x: COORDINATION GROUPA=1-10 R_0=0.3
c2: COMBINE ARG=x COEFFICIENTS=2
@@ -82,8 +82,7 @@ c2: COMBINE ARG=x COEFFICIENTS=2
# since it runs on half of the pairs. Notice that to get the same result you
# should double it
PRINT ARG=c1,c2 STRIDE=10
-\endverbatim
-See also \ref PRINT and \ref COMBINE
+\endplumedfile
diff --git a/src/colvar/DHEnergy.cpp b/src/colvar/DHEnergy.cpp
index 23ed21d58..d13aeecdc 100644
--- a/src/colvar/DHEnergy.cpp
+++ b/src/colvar/DHEnergy.cpp
@@ -56,12 +56,11 @@ Notice that if there are common atoms between GROUPA and GROUPB their interactio
\par Examples
-\verbatim
+\plumedfile
# this is printing the electrostatic interaction between two groups of atoms
dh: DHENERGY GROUPA=1-10 GROUPB=11-20 EPSILON=80.0 I=0.1 TEMP=300.0
PRINT ARG=dh
-\endverbatim
-(see also \ref PRINT)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/DRMSD.cpp b/src/colvar/DRMSD.cpp
index 5a3152ad4..49efb882a 100644
--- a/src/colvar/DRMSD.cpp
+++ b/src/colvar/DRMSD.cpp
@@ -65,15 +65,15 @@ the positions of the atoms in the reference file and their instantaneous
position. Only pairs of atoms whose distance in the reference structure is within
0.1 and 0.8 nm are considered.
-\verbatim
+\plumedfile
DRMSD REFERENCE=file.pdb LOWER_CUTOFF=0.1 UPPER_CUTOFF=0.8
-\endverbatim
+\endplumedfile
The following tells plumed to calculate a DRMSD value for a pair of molecules.
-\verbatim
+\plumedfile
DRMSD REFERENCE=file.pdb LOWER_CUTOFF=0.1 UPPER_CUTOFF=0.8 TYPE=INTER-DRMSD
-\endverbatim
+\endplumedfile
In the input reference file (file.pdb) the atoms in each of the two molecules are separated by a TER
command as shown below.
diff --git a/src/colvar/Dimer.cpp b/src/colvar/Dimer.cpp
index 827c84365..baead008e 100644
--- a/src/colvar/Dimer.cpp
+++ b/src/colvar/Dimer.cpp
@@ -85,43 +85,43 @@ the temperature of the system.
This line tells Plumed to compute the Dimer interaction energy for every dimer in the system.
-\verbatim
+\plumedfile
dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002
-\endverbatim
+\endplumedfile
If the simulation doesn't use virtual sites for the dimers centers of mass,
Plumed has to know in order to determine correctly the total number of dimers from
the total number of atoms:
-\verbatim
+\plumedfile
dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002 NOVSITES
-\endverbatim
+\endplumedfile
The NOVSITES flag is not required if one provides the atom serial of each Dimer. This is
defined as the atom serial of the first bead of the dimer and is thus a number between 1 and N.
Along with the ATOMS list also the number N of lines describing the first beads has to be given.
For example, the Dimer interaction energy of dimers 1,5,7 is:
-\verbatim
+\plumedfile
dim: DIMER TEMP=300 Q=0.5 NATOMS=N ATOMS=1,5,7 DSIGMA=0.002
-\endverbatim
+\endplumedfile
In a Replica Exchange simulation the keyword DSIGMA can be used in two ways:
if a plumed.n.dat file is provided for each replica, then DSIGMA is passed as a single value,
like in the previous examples, and each replica will read its own DSIGMA value. If
a unique plumed.dat is given, DSIGMA has to be a list containing a value for each replica.
For 4 replicas:
-\verbatim
+\plumedfile
dim: DIMER TEMP=300 Q=0.5 NATOMS=N ATOMS=1,5,7 DSIGMA=0.002,0.002,0.004,0.01
-\endverbatim
+\endplumedfile
\par Usage of the CV
The dimer interaction is not coded in the driver program and has to be inserted
in the hamiltonian of the system as a linear RESTRAINT (see \ref RESTRAINT):
-\verbatim
+\plumedfile
dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002
RESTRAINT ARG=dim AT=0 KAPPA=0 SLOPE=1 LABEL=dimforces
-\endverbatim
+\endplumedfile
In a replica exchange, Metadynamics (see \ref METAD) can be used on the Dimer CV to reduce
the number of replicas. Just keep in mind that METAD SIGMA values should be tuned
diff --git a/src/colvar/Dipole.cpp b/src/colvar/Dipole.cpp
index 09a4a6580..3cffa3553 100644
--- a/src/colvar/Dipole.cpp
+++ b/src/colvar/Dipole.cpp
@@ -37,11 +37,10 @@ Calculate the dipole moment for a group of atoms.
\par Examples
The following tells plumed to calculate the dipole of the group of atoms containing
the atoms from 1-10 and print it every 5 steps
-\verbatim
+\plumedfile
d: DIPOLE GROUP=1-10
PRINT FILE=output STRIDE=5 ARG=5
-\endverbatim
-(see also \ref PRINT)
+\endplumedfile
\attention
If the total charge Q of the group in non zero, then a charge Q/N will be subtracted to every atom,
diff --git a/src/colvar/Distance.cpp b/src/colvar/Distance.cpp
index c3a981771..279961b76 100644
--- a/src/colvar/Distance.cpp
+++ b/src/colvar/Distance.cpp
@@ -49,46 +49,44 @@ better to use SCALED_COMPONENTS.
The following input tells plumed to print the distance between atoms 3 and 5,
the distance between atoms 2 and 4 and the x component of the distance between atoms 2 and 4.
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=3,5
d2: DISTANCE ATOMS=2,4
d2c: DISTANCE ATOMS=2,4 COMPONENTS
PRINT ARG=d1,d2,d2c.x
-\endverbatim
-(See also \ref PRINT).
+\endplumedfile
The following input computes the end-to-end distance for a polymer
of 100 atoms and keeps it at a value around 5.
-\verbatim
+\plumedfile
WHOLEMOLECULES ENTITY0=1-100
e2e: DISTANCE ATOMS=1,100 NOPBC
RESTRAINT ARG=e2e KAPPA=1 AT=5
-\endverbatim
-(See also \ref WHOLEMOLECULES and \ref RESTRAINT).
+\endplumedfile
Notice that NOPBC is used
to be sure that if the end-to-end distance is larger than half the simulation
box the distance is compute properly. Also notice that, since many MD
codes break molecules across cell boundary, it might be necessary to
use the \ref WHOLEMOLECULES keyword (also notice that it should be
-_before_ distance). The list of atoms provided to WHOLEMOLECULES
+_before_ distance). The list of atoms provided to \ref WHOLEMOLECULES
here contains all the atoms between 1 and 100. Strictly speaking, this
is not necessary. If you know for sure that atoms with difference in
the index say equal to 10 are _not_ going to be farther than half cell
you can e.g. use
-\verbatim
+\plumedfile
WHOLEMOLECULES ENTITY0=1,10,20,30,40,50,60,70,80,90,100
e2e: DISTANCE ATOMS=1,100 NOPBC
RESTRAINT ARG=e2e KAPPA=1 AT=5
-\endverbatim
-Just be sure that the ordered list provide to WHOLEMOLECULES has the following
+\endplumedfile
+Just be sure that the ordered list provide to \ref WHOLEMOLECULES has the following
properties:
- Consecutive atoms should be closer than half-cell throughout the entire simulation.
- Atoms required later for the distance (e.g. 1 and 100) should be included in the list
The following example shows how to take into account periodicity e.g.
in z-component of a distance
-\verbatim
+\plumedfile
# this is a center of mass of a large group
c: COM ATOMS=1-100
# this is the distance between atom 101 and the group
@@ -99,8 +97,7 @@ d: DISTANCE ATOMS=c,101 COMPONENTS
dz: COMBINE ARG=d.z PERIODIC=-10,10
# metadynamics on dd
METAD ARG=dz SIGMA=0.1 HEIGHT=0.1 PACE=200
-\endverbatim
-(see also \ref COM, \ref COMBINE, and \ref METAD)
+\endplumedfile
Using SCALED_COMPONENTS this problem should not arise because they are always periodic
with domain (-0.5,+0.5).
diff --git a/src/colvar/ERMSD.cpp b/src/colvar/ERMSD.cpp
index 3602df086..fb5ff6cad 100644
--- a/src/colvar/ERMSD.cpp
+++ b/src/colvar/ERMSD.cpp
@@ -84,9 +84,9 @@ for a multi molecular system.
Calculate the eRMSD from reference structure reference.pdb using the default cutoff (2.4). The list of residues involved in the calculation has to be specified. In this example, the eRMSD is calculated
considering residues 1,2,3,4,5,6.
-\verbatim
+\plumedfile
eRMSD1: ERMSD REFERENCE=reference.pdb ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/Energy.cpp b/src/colvar/Energy.cpp
index 6f79eb883..4b3f80736 100644
--- a/src/colvar/Energy.cpp
+++ b/src/colvar/Energy.cpp
@@ -48,11 +48,10 @@ using GROMACS with lambda replica exchange of with plumed-hrex branch.
\par Examples
The following input instructs plumed to print the energy of the system
-\verbatim
+\plumedfile
ene: ENERGY
PRINT ARG=ene
-\endverbatim
-(See also \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/Fake.cpp b/src/colvar/Fake.cpp
index 70bd7f278..20d70aed9 100644
--- a/src/colvar/Fake.cpp
+++ b/src/colvar/Fake.cpp
@@ -39,10 +39,9 @@ and just support input and period definition
\par Examples
-\verbatim
+\plumedfile
FAKE ATOMS=1 PERIODIC=-3.14,3.14 LABEL=d2
-\endverbatim
-(See also \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/FretEfficiency.cpp b/src/colvar/FretEfficiency.cpp
index 02600e105..e6f149452 100644
--- a/src/colvar/FretEfficiency.cpp
+++ b/src/colvar/FretEfficiency.cpp
@@ -51,22 +51,20 @@ boundary conditions. This behavior can be changed with the NOPBC flag.
The following input tells plumed to print the FRET efficiencies
calculated as a function of the distance between atoms 3 and 5 and
the distance between atoms 2 and 4.
-\verbatim
+\plumedfile
fe1: FRET ATOMS=3,5 R0=5.5
fe2: FRET ATOMS=2,4 R0=5.5
PRINT ARG=fe1,fe2
-\endverbatim
-(See also \ref PRINT).
+\endplumedfile
The following input computes the FRET efficiency calculated on the
terminal atoms of a polymer
of 100 atoms and keeps it at a value around 0.5.
-\verbatim
+\plumedfile
WHOLEMOLECULES ENTITY0=1-100
fe: FRET ATOMS=1,100 R0=5.5 NOPBC
RESTRAINT ARG=fe KAPPA=100 AT=0.5
-\endverbatim
-(See also \ref WHOLEMOLECULES and \ref RESTRAINT).
+\endplumedfile
Notice that NOPBC is used
to be sure that if the distance is larger than half the simulation
diff --git a/src/colvar/Gyration.cpp b/src/colvar/Gyration.cpp
index 791f6a3ed..3764ad404 100644
--- a/src/colvar/Gyration.cpp
+++ b/src/colvar/Gyration.cpp
@@ -75,11 +75,10 @@ periodic image.
The following input tells plumed to print the radius of gyration of the
chain containing atoms 10 to 20.
-\verbatim
+\plumedfile
GYRATION TYPE=RADIUS ATOMS=10-20 LABEL=rg
PRINT ARG=rg STRIDE=1 FILE=colvar
-\endverbatim
-(See also \ref PRINT)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/Implicit.cpp b/src/colvar/Implicit.cpp
index ad53f243c..b43b3ad60 100644
--- a/src/colvar/Implicit.cpp
+++ b/src/colvar/Implicit.cpp
@@ -58,7 +58,7 @@ where \f$\Delta G^\mathrm{free}_i\f$ is the solvation free energy of the isolate
The output from this collective variable, the free energy of solvation, can be used with the \ref BIASVALUE keyword to provide implicit solvation to a system. All parameters are designed to be used with a modified CHARMM36 force field. It takes only non-hydrogen atoms as input, these can be conveniently specified using the \ref GROUP action with the NDX_GROUP parameter. To speed up the calculation, IMPLICIT internally uses a neighbourlist with a cutoff dependent on the type of atom (maximum of 1.95 nm). This cutoff can be extended further by using the NL_BUFFER keyword.
\par Examples
-\verbatim
+\plumedfile
MOLINFO MOLTYPE=protein STRUCTURE=peptide.pdb
WHOLEMOLECULES ENTITY0=1-111
@@ -72,8 +72,7 @@ solv: IMPLICIT ATOMS=protein-h NL_STRIDE=10 NL_BUFFER=0.2
bias: BIASVALUE ARG=solv
PRINT ARG=solv FILE=SOLV
-\endverbatim
-(see also \ref PRINT, \ref GROUP, \ref MOLINFO, \ref WHOLEMOLECULES)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/Jcoupling.cpp b/src/colvar/Jcoupling.cpp
index d192b8bbd..8d8975f91 100644
--- a/src/colvar/Jcoupling.cpp
+++ b/src/colvar/Jcoupling.cpp
@@ -62,7 +62,7 @@ In the following example we calculate the Ha-N J-coupling from a set of atoms in
dihedral \f$\psi\f$ angles in the peptide backbone. We also add the experimental datapoints and compute
the correlation and other measures and finally print the results.
-\verbatim
+\plumedfile
MOLINFO MOLTYPE=protein STRUCTURE=peptide.pdb
WHOLEMOLECULES ENTITY0=1-111
@@ -81,11 +81,7 @@ JCOUPLING ...
jhanst: STATS ARG=(jhan\.j_.*) PARARG=(jhan\.exp_.*)
PRINT ARG=jhanst.*,jhan.* FILE=COLVAR STRIDE=100
-
-ENDPLUMED
-
-\endverbatim
-(See also \ref PRINT, \ref STATS)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/MultiRMSD.cpp b/src/colvar/MultiRMSD.cpp
index 7656c232b..4cf4ff08b 100644
--- a/src/colvar/MultiRMSD.cpp
+++ b/src/colvar/MultiRMSD.cpp
@@ -99,17 +99,17 @@ The following tells plumed to calculate the RMSD distance between
the positions of the atoms in the reference file and their instantaneous
position. The Kearseley algorithm for each of the domains.
-\verbatim
+\plumedfile
MULTI-RMSD REFERENCE=file.pdb TYPE=MULTI-OPTIMAL
-\endverbatim
+\endplumedfile
The following tells plumed to calculate the RMSD distance btween the positions of
the atoms in the domains of reference the reference structure and their instantaneous
positions. Here distances are calculated using the \ref DRMSD measure.
-\verbatim
+\plumedfile
MULTI-RMSD REFERENCE=file.pdb TYPE=MULTI-DRMSD
-\endverbatim
+\endplumedfile
in this case it is possible to use the following DRMSD options in the pdb file using the REMARK syntax:
\verbatim
diff --git a/src/colvar/NOE.cpp b/src/colvar/NOE.cpp
index 82d2b4372..b46bd6597 100644
--- a/src/colvar/NOE.cpp
+++ b/src/colvar/NOE.cpp
@@ -52,7 +52,7 @@ In the following examples three noes are defined, the first is calculated based
of atom 1-2 and 3-2; the second is defined by the distance 5-7 and the third by the distances
4-15,4-16,8-15,8-16.
-\verbatim
+\plumedfile
NOE ...
GROUPA1=1,3 GROUPB1=2,2
GROUPA2=5 GROUPB2=7
@@ -61,8 +61,7 @@ LABEL=noes
... NOE
PRINT ARG=noes.* FILE=colvar
-\endverbatim
-(See also \ref PRINT)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/PCARMSD.cpp b/src/colvar/PCARMSD.cpp
index f5d1cf6f2..02861e109 100644
--- a/src/colvar/PCARMSD.cpp
+++ b/src/colvar/PCARMSD.cpp
@@ -57,9 +57,9 @@ Note that beta and occupancy values in the pdb are neglected and all the weights
\par Examples
-\verbatim
+\plumedfile
PCARMSD AVERAGE=file.pdb EIGENVECTORS=eigenvectors.pdb
-\endverbatim
+\endplumedfile
The input is taken so to be compatible with the output you get from g_covar utility of gromacs (suitably adapted to have a pdb input format).
diff --git a/src/colvar/PRE.cpp b/src/colvar/PRE.cpp
index 906826b1f..82c94eee2 100644
--- a/src/colvar/PRE.cpp
+++ b/src/colvar/PRE.cpp
@@ -47,7 +47,7 @@ In the following example five PRE intensities are calculated using the distance
oxigen of the spin label and the backbone hydrogens. Omega is the NMR frequency, RTWO the
R2 for the hydrogens, INEPT of 8 ms for the experiment and a TAUC of 1.21 ns
-\verbatim
+\plumedfile
PRE ...
LABEL=HN_pre
INEPT=8
@@ -63,7 +63,7 @@ GROUPA5=451 RTWO5=0.0086341843
PRINT ARG=HN_pre.* FILE=PRE.dat STRIDE=1
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/PathMSD.cpp b/src/colvar/PathMSD.cpp
index cdfd96ee1..17567f2d4 100644
--- a/src/colvar/PathMSD.cpp
+++ b/src/colvar/PathMSD.cpp
@@ -42,10 +42,10 @@ in input ("sss" component) and the distance from them ("zzz" component).
Here below is a case where you have defined three frames and you want to
calculate the progress along the path and the distance from it in p1
-\verbatim
+\plumedfile
p1: PATHMSD REFERENCE=file.pdb LAMBDA=500.0 NEIGH_STRIDE=4 NEIGH_SIZE=8
PRINT ARG=p1.sss,p1.zzz STRIDE=1 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
note that NEIGH_STRIDE=4 NEIGH_SIZE=8 control the neighborlist parameter (optional but
recommended for performance) and states that the neighbor list will be calculated every 4
diff --git a/src/colvar/Position.cpp b/src/colvar/Position.cpp
index a381e039e..b66ae5e6c 100644
--- a/src/colvar/Position.cpp
+++ b/src/colvar/Position.cpp
@@ -54,14 +54,12 @@ This can be done e.g. using \ref FIT_TO_TEMPLATE.
\par Examples
-\verbatim
+\plumedfile
# align to a template
FIT_TO_TEMPLATE REFERENCE=ref.pdb
p: POSITION ATOM=3
PRINT ARG=p.x,p.y,p.z
-\endverbatim
-(see also \ref FIT_TO_TEMPLATE)
-
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/PropertyMap.cpp b/src/colvar/PropertyMap.cpp
index a8a21fef2..eb1c27f02 100644
--- a/src/colvar/PropertyMap.cpp
+++ b/src/colvar/PropertyMap.cpp
@@ -46,10 +46,10 @@ where the parameters \f$X_i\f$ and \f$Y_i\f$ are provided in the input pdb (al
\f$D_i(x)\f$ is the MSD after optimal alignment calculated on the pdb frames you input (see Kearsley).
\par Examples
-\verbatim
+\plumedfile
p3: PROPERTYMAP REFERENCE=../../trajectories/path_msd/allv.pdb PROPERTY=X,Y LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=4
PRINT ARG=p3.X,p3.Y,p3.zzz STRIDE=1 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
note that NEIGH_STRIDE=4 NEIGH_SIZE=8 control the neighborlist parameter (optional but
recommended for performance) and states that the neighbor list will be calculated every 4
diff --git a/src/colvar/Puckering.cpp b/src/colvar/Puckering.cpp
index b90bdfbc4..66edb54c5 100644
--- a/src/colvar/Puckering.cpp
+++ b/src/colvar/Puckering.cpp
@@ -60,11 +60,11 @@ namespace colvar {
\par Examples
This input tells plumed to print the puckering phase angle of the 3rd nucleotide of a RNA molecule on file COLVAR.
- \verbatim
+ \plumedfile
MOLINFO STRUCTURE=rna.pdb MOLTYPE=rna
PUCKERING ATOMS=@sugar-3 LABEL=puck
PRINT ARG=puck.phs FILE=COLVAR
- \endverbatim
+ \endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/RDC.cpp b/src/colvar/RDC.cpp
index 18db38014..43dc4c1ee 100644
--- a/src/colvar/RDC.cpp
+++ b/src/colvar/RDC.cpp
@@ -94,7 +94,7 @@ respect to a set of experimental data is calculated and restrained. In addition,
and only for analysis purposes, the same RDCs are calculated using a Single Value
Decomposition algorithm.
-\verbatim
+\plumedfile
RDC ...
GYROM=-72.5388
SCALE=1.0
@@ -124,8 +124,7 @@ LABEL=svd
PRINT ARG=nh.corr,rdce.bias FILE=colvar
PRINT ARG=svd.* FILE=svd
-\endverbatim
-(See also \ref PRINT, \ref RESTRAINT)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/RMSD.cpp b/src/colvar/RMSD.cpp
index 8801dfeed..ffdcefeeb 100644
--- a/src/colvar/RMSD.cpp
+++ b/src/colvar/RMSD.cpp
@@ -133,9 +133,9 @@ The following tells plumed to calculate the RMSD distance between
the positions of the atoms in the reference file and their instantaneous
position. The Kearseley algorithm is used so this is done optimally.
-\verbatim
+\plumedfile
RMSD REFERENCE=file.pdb TYPE=OPTIMAL
-\endverbatim
+\endplumedfile
...
diff --git a/src/colvar/Template.cpp b/src/colvar/Template.cpp
index 85cb95d27..6fb3c5845 100644
--- a/src/colvar/Template.cpp
+++ b/src/colvar/Template.cpp
@@ -40,11 +40,11 @@ This file provides a template for if you want to introduce a new CV.
<!---You should put an example of how to use your CV here--->
-\verbatim
+\plumedfile
# This should be a sample input.
t: TEMPLATE ATOMS=1,2
PRINT ARG=t STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
<!---You should reference here the other actions used in this example--->
(see also \ref PRINT)
diff --git a/src/colvar/Torsion.cpp b/src/colvar/Torsion.cpp
index 274d0565a..4b697b069 100644
--- a/src/colvar/Torsion.cpp
+++ b/src/colvar/Torsion.cpp
@@ -43,23 +43,23 @@ orthogonal to an axis.
This input tells plumed to print the torsional angle between atoms 1, 2, 3 and 4
on file COLVAR.
-\verbatim
+\plumedfile
t: TORSION ATOMS=1,2,3,4
# this is an alternative, equivalent, definition:
# t: TORSION VECTOR1=2,1 AXIS=2,3 VECTOR2=3,4
PRINT ARG=t FILE=COLVAR
-\endverbatim
+\endplumedfile
If you are working with a protein you can specify the special named torsion angles \f$\phi\f$, \f$\psi\f$, \f$\omega\f$ and \f$\chi_1\f$
by using TORSION in combination with the \ref MOLINFO command. This can be done by using the following
syntax.
-\verbatim
+\plumedfile
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
t1: TORSION ATOMS=@phi-3
t2: TORSION ATOMS=@psi-4
PRINT ARG=t1,t2 FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.
Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the 4th residue of the protein.
diff --git a/src/colvar/Volume.cpp b/src/colvar/Volume.cpp
index 993dc802a..837f6ce75 100644
--- a/src/colvar/Volume.cpp
+++ b/src/colvar/Volume.cpp
@@ -36,11 +36,10 @@ Calculate the volume of the simulation box.
\par Examples
The following input tells plumed to print the volume of the system
-\verbatim
+\plumedfile
vol: VOLUME
PRINT ARG=vol
-\endverbatim
-(See also \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/Fccubic.cpp b/src/crystallization/Fccubic.cpp
index fc1793ab3..47154f4c6 100644
--- a/src/crystallization/Fccubic.cpp
+++ b/src/crystallization/Fccubic.cpp
@@ -63,10 +63,10 @@ so on. Notice also that you can rotate the reference frame if you are using a n
The following input calculates the FCCUBIC parameter for the 64 atoms in the system
and then calculates and prints the average value for this quantity.
-\verbatim
+\plumedfile
FCCUBIC SPECIES=1-64 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN LABEL=d
PRINT ARG=d.* FILE=colv
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/Gradient.cpp b/src/crystallization/Gradient.cpp
index 173d9e5ad..e3af25856 100644
--- a/src/crystallization/Gradient.cpp
+++ b/src/crystallization/Gradient.cpp
@@ -39,22 +39,22 @@ The input below calculates the gradient of the density of atoms in the manner
described in \cite fede-grad in order to detect whether or not atoms are distributed
uniformly along the x-axis of the simulation cell.
-\verbatim
+\plumedfile
d1: DENSITY SPECIES=1-50
s1: GRADIENT ORIGIN=1 DATA=d1 DIR=x NBINS=4 SIGMA=1.0
PRINT ARG=s1 FILE=colvar
-\endverbatim
+\endplumedfile
The input below calculates the coordination numbers of the 50 atoms in the simulation cell.
The gradient of this quantity is then evaluated in the manner described using the equation above
to detect whether the average values of the coordination number are uniformly distributed along the
x-axis of the simulation cell.
-\verbatim
+\plumedfile
d2: COORDINATIONNUMBER SPECIES=1-50 SWITCH={RATIONAL R_0=2.0} MORE_THAN={EXP R_0=4.0}
s2: GRADIENT ORIGIN=1 DATA=d2 DIR=x NBINS=4 SIGMA=1.0
PRINT ARG=s2 FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/InterMolecularTorsions.cpp b/src/crystallization/InterMolecularTorsions.cpp
index 3839e094d..58294492f 100644
--- a/src/crystallization/InterMolecularTorsions.cpp
+++ b/src/crystallization/InterMolecularTorsions.cpp
@@ -64,12 +64,12 @@ between the two molecules. As such the torsional angles between molecules that
histogram while the torsional angles between molecules that are far apart does not contribute to the histogram. The histogram is
averaged over the whole trajectory and output once all the trajectory frames have been read.
-\verbatim
+\plumedfile
m1: MOLECULES MOL1=1,2 MOL2=3,4 MOL3=5,6 MOL4=7,8
tt_p: INTERMOLECULARTORSIONS MOLS=m1 SWITCH={RATIONAL R_0=0.25 D_0=2.0 D_MAX=3.0}
htt_p: HISTOGRAM DATA=tt_p GRID_MIN=-pi GRID_MAX=pi BANDWIDTH=0.1 GRID_BIN=200 STRIDE=1
DUMPGRID GRID=htt_p FILE=myhist.out
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/MoleculeOrientation.cpp b/src/crystallization/MoleculeOrientation.cpp
index 5bade7022..6001f6f09 100644
--- a/src/crystallization/MoleculeOrientation.cpp
+++ b/src/crystallization/MoleculeOrientation.cpp
@@ -39,10 +39,10 @@ The following input tells plumed to calculate the distances between two of the a
This is done for the same set of atoms four different molecules and the average separation is then
calculated.
-\verbatim
+\plumedfile
MOLECULES MOL1=1,2 MOL2=3,4 MOL3=5,6 MOL4=7,8 MEAN LABEL=mm
PRINT ARG=mm.mean FILE=colvar
-\endverbatim
+\endplumedfile
*/
diff --git a/src/crystallization/Q3.cpp b/src/crystallization/Q3.cpp
index 6c3aeedc2..038115a92 100644
--- a/src/crystallization/Q3.cpp
+++ b/src/crystallization/Q3.cpp
@@ -60,28 +60,28 @@ the \f$q_{3}\f$ vectors on adjacent atoms. More information on these variables
The following command calculates the average Q3 parameter for the 64 atoms in a box of Lennard Jones and prints this
quantity to a file called colvar:
-\verbatim
+\plumedfile
Q3 SPECIES=1-64 D_0=1.3 R_0=0.2 MEAN LABEL=q3
PRINT ARG=q3.mean FILE=colvar
-\endverbatim
+\endplumedfile
The following command calculates the histogram of Q3 parameters for the 64 atoms in a box of Lennard Jones and prints these
quantities to a file called colvar:
-\verbatim
+\plumedfile
Q3 SPECIES=1-64 D_0=1.3 R_0=0.2 HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=q3
PRINT ARG=q3.* FILE=colvar
-\endverbatim
+\endplumedfile
The following command could be used to measure the Q3 paramters that describe the arrangement of chlorine ions around the
sodium atoms in NaCl. The imagined system here is composed of 64 NaCl formula units and the atoms are arranged in the input
with the 64 Na\f$^+\f$ ions followed by the 64 Cl\f$-\f$ ions. Once again the average Q3 paramter is calculated and output to a
file called colvar
-\verbatim
+\plumedfile
Q3 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN LABEL=q3
PRINT ARG=q3.mean FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
@@ -136,30 +136,30 @@ adjacent atoms is correlated.
The following command calculates the average value of the LOCAL_Q3 parameter for the 64 Lennard Jones atoms in the system under study and prints this
quantity to a file called colvar.
-\verbatim
+\plumedfile
Q3 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q3
LOCAL_Q3 ARG=q3 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LABEL=lq3
PRINT ARG=lq3.mean FILE=colvar
-\endverbatim
+\endplumedfile
The following input calculates the distribution of LOCAL_Q3 parameters at any given time and outputs this information to a file.
-\verbatim
+\plumedfile
Q3 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q3
LOCAL_Q3 ARG=q3 SWITCH={RATIONAL D_0=1.3 R_0=0.2} HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=lq3
PRINT ARG=lq3.* FILE=colvar
-\endverbatim
+\endplumedfile
The following calculates the LOCAL_Q3 parameters for atoms 1-5 only. For each of these atoms comparisons of the geometry of the coordination sphere
are done with those of all the other atoms in the system. The final quantity is the average and is outputted to a file
-\verbatim
+\plumedfile
Q3 SPECIESA=1-5 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q3a
Q3 SPECIESA=6-64 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q3b
LOCAL_Q3 ARG=q3a,q3b SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LOWMEM LABEL=w3
PRINT ARG=w3.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/Q4.cpp b/src/crystallization/Q4.cpp
index fa76b0d10..a4f7d327b 100644
--- a/src/crystallization/Q4.cpp
+++ b/src/crystallization/Q4.cpp
@@ -60,28 +60,28 @@ the \f$q_{4}\f$ vectors on adjacent atoms. More information on these variables
The following command calculates the average Q4 parameter for the 64 atoms in a box of Lennard Jones and prints this
quantity to a file called colvar:
-\verbatim
+\plumedfile
Q4 SPECIES=1-64 D_0=1.3 R_0=0.2 MEAN LABEL=q4
PRINT ARG=q4.mean FILE=colvar
-\endverbatim
+\endplumedfile
The following command calculates the histogram of Q4 parameters for the 64 atoms in a box of Lennard Jones and prints these
quantities to a file called colvar:
-\verbatim
+\plumedfile
Q4 SPECIES=1-64 D_0=1.3 R_0=0.2 HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=q4
PRINT ARG=q4.* FILE=colvar
-\endverbatim
+\endplumedfile
The following command could be used to measure the Q4 paramters that describe the arrangement of chlorine ions around the
sodium atoms in NaCl. The imagined system here is composed of 64 NaCl formula units and the atoms are arranged in the input
with the 64 Na\f$^+\f$ ions followed by the 64 Cl\f$-\f$ ions. Once again the average Q4 paramter is calculated and output to a
file called colvar
-\verbatim
+\plumedfile
Q4 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN LABEL=q4
PRINT ARG=q4.mean FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
@@ -136,30 +136,30 @@ adjacent atoms is correlated.
The following command calculates the average value of the LOCAL_Q4 parameter for the 64 Lennard Jones atoms in the system under study and prints this
quantity to a file called colvar.
-\verbatim
+\plumedfile
Q4 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q4
LOCAL_Q4 ARG=q4 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LABEL=lq4
PRINT ARG=lq4.mean FILE=colvar
-\endverbatim
+\endplumedfile
The following input calculates the distribution of LOCAL_Q4 parameters at any given time and outputs this information to a file.
-\verbatim
+\plumedfile
Q4 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q4
LOCAL_Q4 ARG=q4 SWITCH={RATIONAL D_0=1.3 R_0=0.2} HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=lq4
PRINT ARG=lq4.* FILE=colvar
-\endverbatim
+\endplumedfile
The following calculates the LOCAL_Q4 parameters for atoms 1-5 only. For each of these atoms comparisons of the geometry of the coordination sphere
are done with those of all the other atoms in the system. The final quantity is the average and is outputted to a file
-\verbatim
+\plumedfile
Q4 SPECIESA=1-5 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q4a
Q4 SPECIESA=6-64 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q4b
LOCAL_Q4 ARG=q4a,q4b SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LOWMEM LABEL=w4
PRINT ARG=w4.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/Q6.cpp b/src/crystallization/Q6.cpp
index 447b0e1cb..a848174ab 100644
--- a/src/crystallization/Q6.cpp
+++ b/src/crystallization/Q6.cpp
@@ -60,28 +60,28 @@ the \f$q_{6}\f$ vectors on adjacent atoms. More information on these variables
The following command calculates the average Q6 parameter for the 64 atoms in a box of Lennard Jones and prints this
quantity to a file called colvar:
-\verbatim
+\plumedfile
Q6 SPECIES=1-64 D_0=1.3 R_0=0.2 MEAN LABEL=q6
PRINT ARG=q6.mean FILE=colvar
-\endverbatim
+\endplumedfile
The following command calculates the histogram of Q6 parameters for the 64 atoms in a box of Lennard Jones and prints these
quantities to a file called colvar:
-\verbatim
+\plumedfile
Q6 SPECIES=1-64 D_0=1.3 R_0=0.2 HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=q6
PRINT ARG=q6.* FILE=colvar
-\endverbatim
+\endplumedfile
The following command could be used to measure the Q6 paramters that describe the arrangement of chlorine ions around the
sodium atoms in NaCl. The imagined system here is composed of 64 NaCl formula units and the atoms are arranged in the input
with the 64 Na\f$^+\f$ ions followed by the 64 Cl\f$-\f$ ions. Once again the average Q6 paramter is calculated and output to a
file called colvar
-\verbatim
+\plumedfile
Q6 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN LABEL=q6
PRINT ARG=q6.mean FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
@@ -136,30 +136,30 @@ adjacent atoms is correlated.
The following command calculates the average value of the LOCAL_Q6 parameter for the 64 Lennard Jones atoms in the system under study and prints this
quantity to a file called colvar.
-\verbatim
+\plumedfile
Q6 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q6
LOCAL_Q6 ARG=q6 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LABEL=lq6
PRINT ARG=lq6.mean FILE=colvar
-\endverbatim
+\endplumedfile
The following input calculates the distribution of LOCAL_Q6 parameters at any given time and outputs this information to a file.
-\verbatim
+\plumedfile
Q6 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q6
LOCAL_Q6 ARG=q6 SWITCH={RATIONAL D_0=1.3 R_0=0.2} HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=lq6
PRINT ARG=lq6.* FILE=colvar
-\endverbatim
+\endplumedfile
The following calculates the LOCAL_Q6 parameters for atoms 1-5 only. For each of these atoms comparisons of the geometry of the coordination sphere
are done with those of all the other atoms in the system. The final quantity is the average and is outputted to a file
-\verbatim
+\plumedfile
Q6 SPECIESA=1-5 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q6a
Q6 SPECIESA=6-64 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q6b
LOCAL_Q6 ARG=q4a,q4b SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LOWMEM LABEL=w4
PRINT ARG=w6.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/SMAC.cpp b/src/crystallization/SMAC.cpp
index ce83df738..3d7085a97 100644
--- a/src/crystallization/SMAC.cpp
+++ b/src/crystallization/SMAC.cpp
@@ -65,7 +65,7 @@ the indices of three atoms for each of the MOL keywords below we are telling PLU
numbers to determine the orientation of the molecule that will ultimately be used when calculating the \f$\theta_{ij}\f$
terms in the formula above. The atom with the third index meanwhile is used when we calculate \f$r_{ij}\f$.
-\verbatim
+\plumedfile
MOLECULES ...
MOL1=9,10,9
MOL2=89,90,89
@@ -86,13 +86,13 @@ SMAC ...
... SMAC
PRINT ARG=s2.* FILE=colvar
-\endverbatim
+\endplumedfile
This second example works in a way that is very similar to the previous command. Now, however,
the orientation of the molecules is determined by finding the plane that contains the positions
of three atoms.
-\verbatim
+\plumedfile
PLANES ...
MOL1=9,10,11
MOL2=89,90,91
@@ -114,7 +114,7 @@ SMAC ...
... SMAC
PRINT ARG=s2.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/SimpleCubic.cpp b/src/crystallization/SimpleCubic.cpp
index 4d50cc7d5..2c15767c2 100644
--- a/src/crystallization/SimpleCubic.cpp
+++ b/src/crystallization/SimpleCubic.cpp
@@ -55,15 +55,15 @@ so on. Notice also that you can rotate the reference frame if you are using a n
The following input tells plumed to calculate the simple cubic parameter for the atoms 1-100 with themselves.
The mean value is then calculated.
-\verbatim
+\plumedfile
SIMPLECUBIC SPECIES=1-100 R_0=1.0 MEAN
-\endverbatim
+\endplumedfile
The following input tells plumed to look at the ways atoms 1-100 are within 3.0 are arranged about atoms
from 101-110. The number of simple cubic parameters that are greater than 0.8 is then output
-\verbatim
+\plumedfile
SIMPLECUBIC SPECIESA=101-110 SPECIESB=1-100 R_0=3.0 MORE_THAN={RATIONAL R_0=0.8 NN=6 MM=12 D_0=0}
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/Tetrahedral.cpp b/src/crystallization/Tetrahedral.cpp
index 616cf766b..87c6e33ae 100644
--- a/src/crystallization/Tetrahedral.cpp
+++ b/src/crystallization/Tetrahedral.cpp
@@ -54,20 +54,20 @@ when atom \f$j\f$ is in the first coordination sphere of atom \f$i\f$ and is zer
The following command calculates the average value of the tetrahedrality parameter for a set of 64 atoms all of the same type
and outputs this quantity to a file called colvar.
-\verbatim
+\plumedfile
tt: TETRAHEDRAL SPECIES=1-64 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN
PRINT ARG=tt.mean FILE=colvar
-\endverbatim
+\endplumedfile
The following command calculates the number of tetrahedrality parameters that are greater than 0.8 in a set of 10 atoms.
In this calculation it is assumed that there are two atom types A and B and that the first coordination sphere of the
10 atoms of type A contains atoms of type B. The formula above is thus calculated for ten different A atoms and within
it the sum over \f$j\f$ runs over 40 atoms of type B that could be in the first coordination sphere.
-\verbatim
+\plumedfile
tt: TETRAHEDRAL SPECIESA=1-10 SPECIESB=11-40 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MORE_THAN={RATIONAL R_0=0.8}
PRINT ARG=tt.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/eds/EDS.cpp b/src/eds/EDS.cpp
index e5e575abe..e7e0e4331 100644
--- a/src/eds/EDS.cpp
+++ b/src/eds/EDS.cpp
@@ -63,7 +63,7 @@ It is not possible to set the target value of the observable to zero with the de
The following input for a harmonic oscillator of two beads will adaptively find a linear bias to change the mean and variance to the target values. The PRINT line shows how to access the value of the coupling constants.
-\verbatim
+\plumedfile
dist: DISTANCE ATOMS=1,2
# this is the squared of the distance
dist2: COMBINE ARG=dist POWERS=2 PERIODIC=NO
@@ -71,19 +71,19 @@ dist2: COMBINE ARG=dist POWERS=2 PERIODIC=NO
#bias mean and variance
eds: EDS ARG=dist,dist2 CENTER=2.0,1.0 PERIOD=50000 TEMP=1.0
PRINT ARG=dist,dist2,eds.dist_coupling,eds.dist2_coupling,eds.bias,eds.force2 FILE=colvars.dat STRIDE=100
-\endverbatim
+\endplumedfile
Rather than trying to find the coupling constants adaptively, can ramp up to a constant value.
-\verbatim
+\plumedfile
#ramp couplings from 0,0 to -1,1 over 50000 steps
eds: EDS ARG=dist,dist2 CENTER=2.0,1.0 FIXED=-1,1 RAMP PERIOD=50000 TEMP=1.0
#same as above, except starting at -0.5,0.5 rather than default of 0,0
eds: EDS ARG=dist,dist2 CENTER=2.0,1.0 FIXED=-1,1 INIT=-0.5,0.5 RAMP PERIOD=50000 TEMP=1.0
-\endverbatim
+\endplumedfile
A restart file can be added to dump information needed to restart/continue simulation using these parameters every STRIDE.
-\verbatim
+\plumedfile
#add the option to write to a restart file
eds: EDS ARG=dist,dist2 CENTER=2.0,1.0 PERIOD=50000 TEMP=1.0 OUT_RESTART=restart.dat
@@ -98,7 +98,7 @@ eds: EDS ARG=dist,dist2 CENTER=2.0,1.0 PERIOD=50000 TEMP=1.0 IN_RESTART=restart.
#add the option to read in a previous restart file and continue the bias, but use the mean from the previous run as the starting point
eds: EDS ARG=dist,dist2 CENTER=2.0,1.0 PERIOD=50000 TEMP=1.0 IN_RESTART=restart.dat MEAN
-\endverbatim
+\endplumedfile
*/
diff --git a/src/function/Combine.cpp b/src/function/Combine.cpp
index e76ed7b8b..62f66e35d 100644
--- a/src/function/Combine.cpp
+++ b/src/function/Combine.cpp
@@ -52,23 +52,23 @@ is periodic.
The following input tells plumed to print the distance between atoms 3 and 5
its square (as computed from the x,y,z components) and the distance
again as computed from the square root of the square.
-\verbatim
+\plumedfile
DISTANCE LABEL=dist ATOMS=3,5 COMPONENTS
COMBINE LABEL=distance2 ARG=dist.x,dist.y,dist.z POWERS=2,2,2 PERIODIC=NO
COMBINE LABEL=distance ARG=distance2 POWERS=0.5 PERIODIC=NO
PRINT ARG=distance,distance2
-\endverbatim
+\endplumedfile
(See also \ref PRINT and \ref DISTANCE).
The following input tells plumed to add a restraint on the
cube of a dihedral angle. Notice that since the angle has a
periodic domain
-pi,pi its cube has a domain -pi**3,pi**3.
-\verbatim
+\plumedfile
t: TORSION ATOMS=1,3,5,7
c: COMBINE ARG=t POWERS=3 PERIODIC=-31.0062766802998,31.0062766802998
RESTRAINT ARG=c KAPPA=10 AT=0
-\endverbatim
+\endplumedfile
diff --git a/src/function/Ensemble.cpp b/src/function/Ensemble.cpp
index 9976c2501..bc1e05fb2 100644
--- a/src/function/Ensemble.cpp
+++ b/src/function/Ensemble.cpp
@@ -38,12 +38,11 @@ Each collective variable is averaged separately and stored in a component labell
\par Examples
The following input tells plumed to calculate the distance between atoms 3 and 5
and the average it over the available replicas.
-\verbatim
+\plumedfile
dist: DISTANCE ATOMS=3,5
ens: ENSEMBLE ARG=dist
PRINT ARG=dist,ens.dist
-\endverbatim
-(See also \ref PRINT and \ref DISTANCE).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/function/FuncPathMSD.cpp b/src/function/FuncPathMSD.cpp
index f4d481d73..25a87e718 100644
--- a/src/function/FuncPathMSD.cpp
+++ b/src/function/FuncPathMSD.cpp
@@ -49,17 +49,17 @@ It is a function of MSD that are obtained by the joint use of MSD variable and S
Here below is a case where you have defined three frames and you want to
calculate the progress alng the path and the distance from it in p1
-\verbatim
+\plumedfile
t1: RMSD REFERENCE=frame_1.dat TYPE=OPTIMAL SQUARED
t2: RMSD REFERENCE=frame_21.dat TYPE=OPTIMAL SQUARED
t3: RMSD REFERENCE=frame_42.dat TYPE=OPTIMAL SQUARED
p1: FUNCPATHMSD ARG=t1,t2,t3 LAMBDA=500.0
PRINT ARG=t1,t2,t3,p1.s,p1.z STRIDE=1 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
In this second example is shown how to define a PATH in the \ref CONTACTMAP space:
-\verbatim
+\plumedfile
CONTACTMAP ...
ATOMS1=1,2 REFERENCE1=0.1
ATOMS2=3,4 REFERENCE2=0.5
@@ -92,7 +92,7 @@ CMDIST
p1: FUNCPATHMSD ARG=c1,c2,c3 LAMBDA=500.0
PRINT ARG=c1,c2,c3,p1.s,p1.z STRIDE=1 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/function/LocalEnsemble.cpp b/src/function/LocalEnsemble.cpp
index 6e3bd96f6..429a5a143 100644
--- a/src/function/LocalEnsemble.cpp
+++ b/src/function/LocalEnsemble.cpp
@@ -40,7 +40,7 @@ The following input tells plumed to calculate the chemical shifts for four
different proteins in the same simulation box then average them, calcualated
the sum of the squared deviation with respect to the experiemntal values and
applies a linear restraint.
-\verbatim
+\plumedfile
MOLINFO STRUCTURE=data/template.pdb
chaina: GROUP ATOMS=1-1640
@@ -68,7 +68,7 @@ sthn: STATS ARG=(enshn\.csa\.hn_.*) PARARG=(csa\.exphn_.*) SQDEVSUM
stnh: STATS ARG=(ensnh\.csa\.nh_.*) PARARG=(csa\.expnh_.*) SQDEVSUM
res: RESTRAINT ARG=stca.*,stcb.*,stco.*,sthn.*,stnh.* AT=0.,0.,0.,0.,0. KAPPA=0.,0.,0.,0.,0 SLOPE=16.,16.,12.,24.,0.5
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/function/Matheval.cpp b/src/function/Matheval.cpp
index 59e6e9bf0..d21907e68 100644
--- a/src/function/Matheval.cpp
+++ b/src/function/Matheval.cpp
@@ -54,14 +54,14 @@ PLUMED has been linked to it
The following input tells plumed to perform a metadynamics
using as a CV the difference between two distances.
-\verbatim
+\plumedfile
dAB: DISTANCE ARG=10,12
dAC: DISTANCE ARG=10,15
diff: MATHEVAL ARG=dAB,dAC FUNC=y-x PERIODIC=NO
# notice: the previous line could be replaced with the following
# diff: COMBINE ARG=dAB,dAC COEFFICIENTS=-1,1
METAD ARG=diff WIDTH=0.1 HEIGHT=0.5 BIASFACTOR=10 PACE=100
-\endverbatim
+\endplumedfile
(see also \ref DISTANCE, \ref COMBINE, and \ref METAD).
Notice that forces applied to diff will be correctly propagated
to atoms 10, 12, and 15.
@@ -75,7 +75,7 @@ The following input tells plumed to print the angle between vectors
identified by atoms 1,2 and atoms 2,3
its square (as computed from the x,y,z components) and the distance
again as computed from the square root of the square.
-\verbatim
+\plumedfile
DISTANCE LABEL=d1 ATOMS=1,2 COMPONENTS
DISTANCE LABEL=d2 ATOMS=2,3 COMPONENTS
MATHEVAL ...
@@ -86,7 +86,7 @@ MATHEVAL ...
PERIODIC=NO
... MATHEVAL
PRINT ARG=theta
-\endverbatim
+\endplumedfile
(See also \ref PRINT and \ref DISTANCE).
Notice that the matheval library implements a large number of functions (trigonometric, exp, log, etc).
@@ -96,13 +96,13 @@ a straightforward implementation of if clauses.
For example, imagine that you want to implement a restraint that only acts when a
distance is larger than 0.5. You can do it with
-\verbatim
+\plumedfile
d: DISTANCE ATOMS=10,15
m: MATHEVAL ARG=d FUNC=0.5*step(0.5-x)+x*step(x-0.5) PERIODIC=NO
# check the function you are applying:
PRINT ARG=d,n FILE=checkme
RESTRAINT ARG=d AT=0.5 KAPPA=10.0
-\endverbatim
+\endplumedfile
(see also \ref DISTANCE, \ref PRINT, and \ref RESTRAINT)
The meaning of the function `0.5*step(0.5-x)+x*step(x-0.5)` is:
@@ -133,7 +133,7 @@ MATHEVAL can be used in combination with \ref DISTANCE to implement variants of
DISTANCE keyword that were present in PLUMED 1.3 and that allowed to compute
the distance of a point from a line defined by two other points, or the progression
along that line.
-\verbatim
+\plumedfile
# take center of atoms 1 to 10 as reference point 1
p1: CENTER ATOMS=1-10
# take center of atoms 11 to 20 as reference point 2
@@ -156,7 +156,7 @@ fromaxis: MATHEVAL ARG=d13,d23,d12,onaxis VAR=x,y,z,o FUNC=(0.5*(y^2+x^2)-o^2-0.
PRINT ARG=onaxis,fromaxis
-\endverbatim
+\endplumedfile
Notice that these equations have been used to combine \ref RMSD
from different snapshots of a protein so as to define
diff --git a/src/function/Piecewise.cpp b/src/function/Piecewise.cpp
index e0f4bbd52..ebd886de0 100644
--- a/src/function/Piecewise.cpp
+++ b/src/function/Piecewise.cpp
@@ -55,15 +55,14 @@ in a vector of values. Each value will be named as the name of the original
argument with suffix _pfunc.
\par Examples
-\verbatim
+\plumedfile
dist1: DISTANCE ATOMS=1,10
dist2: DISTANCE ATOMS=2,11
pw: PIECEWISE POINT0=1,10 POINT1=1,PI POINT2=3,10 ARG=dist1
ppww: PIECEWISE POINT0=1,10 POINT1=1,PI POINT2=3,10 ARG=dist1,dist2
PRINT ARG=pw,ppww.dist1_pfunc,ppww.dist2_pfunc
-\endverbatim
-(See also \ref PRINT and \ref DISTANCE).
+\endplumedfile
*/
diff --git a/src/function/Sort.cpp b/src/function/Sort.cpp
index f1e9b2a71..fc8e4ca23 100644
--- a/src/function/Sort.cpp
+++ b/src/function/Sort.cpp
@@ -43,15 +43,14 @@ labelled <em>label</em>.1, the second lowest will be labelled <em>label</em>.2 a
\par Examples
The following input tells plumed to print the distance of the closest and of
the farthest atoms to atom 1, chosen among atoms from 2 to 5
-\verbatim
+\plumedfile
d12: DISTANCE ATOMS=1,2
d13: DISTANCE ATOMS=1,3
d14: DISTANCE ATOMS=1,4
d15: DISTANCE ATOMS=1,5
sort: SORT ARG=d12,d13,d14,d15
PRINT ARG=sort.1,sort.4
-\endverbatim
-(See also \ref PRINT and \ref DISTANCE).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/function/Stats.cpp b/src/function/Stats.cpp
index 429442e6d..438d8f98b 100644
--- a/src/function/Stats.cpp
+++ b/src/function/Stats.cpp
@@ -41,13 +41,13 @@ from other actions using PARARG (for example using experimental values from coll
The following input tells plumed to print the distance between three couple of atoms
and compare them with three reference distances.
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=10,50
d2: DISTANCE ATOMS=1,100
d3: DISTANCE ATOMS=45,75
st: STATS ARG=d1,d2,d3 PARAMETERS=1.5,4.0,2.0
PRINT ARG=d1,d2,d3,st.*
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/function/Target.cpp b/src/function/Target.cpp
index 5ce912495..1724cf3ff 100644
--- a/src/function/Target.cpp
+++ b/src/function/Target.cpp
@@ -75,12 +75,12 @@ specified in the input.
The following input calculates the distance between a reference configuration and the instaneous position of the system in the trajectory.
The position of the reference configuration is specified by providing the values of the distance between atoms 1 and 2 and atoms 3 and 4.
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=1,2
d2: DISTANCE ATOMS=3,4
t1: TARGET REFERENCE=myref.pdb TYPE=EUCLIDEAN
PRINT ARG=t1 FILE=colvar
-\endverbatim
+\endplumedfile
The contents of the file containing the reference structure (myref.pdb) is shown below. As you can see you must provide information on the
labels of the CVs that are being used to define the position of the reference configuration in this file together with the values that these
diff --git a/src/generic/Debug.cpp b/src/generic/Debug.cpp
index 742b3b854..36654b0d9 100644
--- a/src/generic/Debug.cpp
+++ b/src/generic/Debug.cpp
@@ -37,12 +37,12 @@ Can be used while debugging or optimizing plumed.
\par Examples
-\verbatim
+\plumedfile
# print detailed (action-by-action) timers at the end of simulation
DEBUG DETAILED_TIMERS
# dump every two steps which are the atoms required from the MD code
DEBUG logRequestedAtoms STRIDE=2
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/DumpAtoms.cpp b/src/generic/DumpAtoms.cpp
index d6ee37748..c144b5f07 100644
--- a/src/generic/DumpAtoms.cpp
+++ b/src/generic/DumpAtoms.cpp
@@ -70,15 +70,14 @@ Notice that gro/xtc/trr files can only contain coordinates in nm.
The following input instructs plumed to print out the positions of atoms
1-10 together with the position of the center of mass of atoms 11-20 every
10 steps to a file called file.xyz.
-\verbatim
+\plumedfile
COM ATOMS=11-20 LABEL=c1
DUMPATOMS STRIDE=10 FILE=file.xyz ATOMS=1-10,c1
-\endverbatim
-(see also \ref COM)
+\endplumedfile
The following input is very similar but dumps a .gro (gromacs) file,
which also contains atom and residue names.
-\verbatim
+\plumedfile
# this is required to have proper atom names:
MOLINFO STRUCTURE=reference.pdb
# if omitted, atoms will have "X" name...
@@ -87,8 +86,7 @@ COM ATOMS=11-20 LABEL=c1
DUMPATOMS STRIDE=10 FILE=file.gro ATOMS=1-10,c1
# notice that last atom is a virtual one and will not have
# a correct name in the resulting gro file
-\endverbatim
-(see also \ref COM and \ref MOLINFO)
+\endplumedfile
*/
diff --git a/src/generic/DumpDerivatives.cpp b/src/generic/DumpDerivatives.cpp
index c74343aca..38c686d7b 100644
--- a/src/generic/DumpDerivatives.cpp
+++ b/src/generic/DumpDerivatives.cpp
@@ -42,11 +42,11 @@ can be done by outputting the derivatives calculated analytically and numericall
\par Examples
The following input instructs plumed to write a file called deriv that contains both the
analytical and numerical derivatives of the distance between atoms 1 and 2.
-\verbatim
+\plumedfile
DISTANCE ATOM=1,2 LABEL=distance
DISTANCE ATOM=1,2 LABEL=distanceN NUMERICAL_DERIVATIVES
DUMPDERIVATIVES ARG=distance,distanceN STRIDE=1 FILE=deriv
-\endverbatim
+\endplumedfile
(See also \ref DISTANCE)
diff --git a/src/generic/DumpForces.cpp b/src/generic/DumpForces.cpp
index f5e204d65..a376de281 100644
--- a/src/generic/DumpForces.cpp
+++ b/src/generic/DumpForces.cpp
@@ -43,12 +43,10 @@ by specifying more than one argument. You can control the buffering of output us
\par Examples
The following input instructs plumed to write a file called forces that contains
the force acting on the distance between atoms 1 and 2.
-\verbatim
+\plumedfile
DISTANCE ATOM=1,2 LABEL=distance
DUMPFORCES ARG=distance STRIDE=1 FILE=forces
-\endverbatim
-
-(See also \ref DISTANCE)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/DumpMassCharge.cpp b/src/generic/DumpMassCharge.cpp
index 4153bc838..25224f3b3 100644
--- a/src/generic/DumpMassCharge.cpp
+++ b/src/generic/DumpMassCharge.cpp
@@ -49,14 +49,13 @@ masses for all atoms are written.
You can add the DUMPMASSCHARGE action at the end of the plumed.dat
file that you use during an MD simulations:
-\verbatim
+\plumedfile
c1: COM ATOMS=1-10
c2: COM ATOMS=11-20
PRINT ARG=c1,c2 FILE=colvar STRIDE=100
DUMPMASSCHARGE FILE=mcfile
-\endverbatim
-(see also \ref COM and \ref PRINT)
+\endplumedfile
In this way, you will be able to use the same masses while processing
a trajectory from the \ref driver . To do so, you need to
@@ -67,11 +66,11 @@ plumed driver --mc mcfile --plumed plumed.dat --ixyz traj.xyz
With the following input you can dump only the charges for a specific
group.
-\verbatim
+\plumedfile
solute_ions: GROUP ATOMS=1-121,200-2012
DUMPATOMS FILE=traj.gro ATOMS=solute_ions STRIDE=100
DUMPMASSCHARGE FILE=mcfile ATOMS=solute_ions
-\endverbatim
+\endplumedfile
Notice however that if you want to process the charges
with the driver (e.g. reading traj.gro) you have to fix atom
numbers first, e.g. with the script
diff --git a/src/generic/DumpProjections.cpp b/src/generic/DumpProjections.cpp
index 3f0d40429..c3a0ca750 100644
--- a/src/generic/DumpProjections.cpp
+++ b/src/generic/DumpProjections.cpp
@@ -39,12 +39,12 @@ Dump the derivatives with respect to the input parameters for one or more object
Compute the distance between two groups and write on a file the
derivatives of this distance with respect to all the atoms of the two groups
-\verbatim
+\plumedfile
x1: CENTER ATOMS=1-10
x2: CENTER ATOMS=11-20
d: DISTANCE ATOMS=x1,x2
DUMPPROJECTIONS ARG=d FILE=proj STRIDE=20
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/EffectiveEnergyDrift.cpp b/src/generic/EffectiveEnergyDrift.cpp
index 1c3961390..a9ca15e6c 100644
--- a/src/generic/EffectiveEnergyDrift.cpp
+++ b/src/generic/EffectiveEnergyDrift.cpp
@@ -55,18 +55,18 @@ Print the effective energy drift described in Ref \cite Ferrarotti2015
This is to monitor the effective energy drift for a metadynamics
simulation on the Debye-Huckel energy. Since this variable is very expensive,
it could be conveniently computed every second step.
-\verbatim
+\plumedfile
dh: DHENERGY GROUPA=1-10 GROUPB=11-20 EPSILON=80.0 I=0.1 TEMP=300.0
METAD ARG=dh HEIGHT=0.5 SIGMA=0.1 PACE=500 STRIDE=2
EFFECTIVE_ENERGY_DRIFT PRINT_STRIDE=100 FILE=eff
-\endverbatim
+\endplumedfile
This is to monitor if a restraint is too stiff
-\verbatim
+\plumedfile
d: DISTANCE ATOMS=10,20
RESTRAINT ARG=d KAPPA=100000 AT=0.6
EFFECTIVE_ENERGY_DRIFT PRINT_STRIDE=100 FILE=eff
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/FitToTemplate.cpp b/src/generic/FitToTemplate.cpp
index 37e38333f..6fa379e1f 100644
--- a/src/generic/FitToTemplate.cpp
+++ b/src/generic/FitToTemplate.cpp
@@ -78,13 +78,12 @@ this action is performed at every MD step.
\par Examples
Align the atomic position to a template then print them
-\verbatim
+\plumedfile
# to see the effect, one could dump the atoms before alignment
DUMPATOMS FILE=dump-before.xyz ATOMS=1-20
FIT_TO_TEMPLATE STRIDE=1 REFERENCE=ref.pdb TYPE=SIMPLE
DUMPATOMS FILE=dump-after.xyz ATOMS=1-20
-\endverbatim
-(see also \ref DUMPATOMS)
+\endplumedfile
diff --git a/src/generic/Flush.cpp b/src/generic/Flush.cpp
index 78c00f87d..71e9a06d3 100644
--- a/src/generic/Flush.cpp
+++ b/src/generic/Flush.cpp
@@ -41,7 +41,7 @@ plumed input file, it will flush all the open files.
\par Examples
A command like this in the input will instruct plumed to flush all the output files every 100 steps
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=1,10
PRINT ARG=d1 STRIDE=5 FILE=colvar1
@@ -50,7 +50,7 @@ FLUSH STRIDE=100
d2: DISTANCE ATOMS=2,11
# also this print is flushed every 100 steps:
PRINT ARG=d2 STRIDE=10 FILE=colvar2
-\endverbatim
+\endplumedfile
(see also \ref DISTANCE and \ref PRINT).
*/
//+ENDPLUMEDOC
diff --git a/src/generic/Group.cpp b/src/generic/Group.cpp
index 80393a9ce..0f04cf75f 100644
--- a/src/generic/Group.cpp
+++ b/src/generic/Group.cpp
@@ -65,7 +65,7 @@ the \ref INCLUDE command so as to store long group definitions in a separate fil
This command create a group of atoms containing atoms 1,4,7,11 and 14 (labeled 'o'), and another containing
atoms 2,3,5,6,8,9,12,13 (labeled 'h'):
-\verbatim
+\plumedfile
o: GROUP ATOMS=1,4,7,11,14
h: GROUP ATOMS=2,3,5,6,8,9,12,13
# compute the coordination among the two groups
@@ -75,45 +75,41 @@ c: COORDINATION GROUPA=o GROUPB=h R_0=0.3
# print the coordination on file 'colvar'
PRINT ARG=c FILE=colvar
-\endverbatim
-(see also \ref COORDINATION and \ref PRINT)
+\endplumedfile
Groups can be conveniently stored in a separate file.
E.g. one could create a file named 'groups.dat' which reads
-\verbatim
+\plumedfile
o: GROUP ATOMS=1,4,7,11,14
h: GROUP ATOMS=2,3,5,6,8,9,12,13
-\endverbatim
+\endplumedfile
and then include it in the main 'plumed.dat' file
-\verbatim
+\plumedfile
INCLUDE FILE=groups.dat
# compute the coordination among the two groups
c: COORDINATION GROUPA=o GROUPB=h R_0=0.3
# print the coordination on file 'colvar'
PRINT ARG=c FILE=colvar
-\endverbatim
-(see also \ref INCLUDE, \ref COORDINATION, and \ref PRINT).
+\endplumedfile
The groups.dat file could be very long and include lists of thousand atoms without cluttering the main plumed.dat file.
A GROMACS index file can also be imported
-\verbatim
+\plumedfile
# import group named 'protein' from file index.ndx
pro: GROUP NDX_FILE=index.ndx NDX_GROUP=protein
# dump all the atoms of the protein on a trajectory file
DUMPATOMS ATOMS=pro FILE=traj.gro
-\endverbatim
-(see also \ref DUMPATOMS)
+\endplumedfile
A list can be edited with REMOVE
-\verbatim
+\plumedfile
# take one atom every three
ox: GROUP ATOMS=1-90:3
# take the remaining atoms
hy: GROUP ATOMS=1-90 REMOVE=ox
DUMPATOMS ATOMS=ox FILE=ox.gro
DUMPATOMS ATOMS=hy FILE=hy.gro
-\endverbatim
-(see also \ref DUMPATOMS)
+\endplumedfile
*/
diff --git a/src/generic/Include.cpp b/src/generic/Include.cpp
index 664c84ba6..30539f0bb 100644
--- a/src/generic/Include.cpp
+++ b/src/generic/Include.cpp
@@ -38,25 +38,25 @@ Useful to split very large plumed.dat files.
\par Examples
This input
-\verbatim
+\plumedfile
c1: COM ATOMS=1-100
c2: COM ATOMS=101-202
d: DISTANCE ARG=c1,c2
PRINT ARG=d
-\endverbatim
+\endplumedfile
can be replaced with
-\verbatim
+\plumedfile
INCLUDE FILE=pippo.dat
d: DISTANCE ARG=c1,c2
PRINT ARG=d
-\endverbatim
+\endplumedfile
where the content of file pippo.dat is
-\verbatim
+\plumedfile
c1: COM ATOMS=1-100
c2: COM ATOMS=101-202
-\endverbatim
+\endplumedfile
(see also \ref COM, \ref DISTANCE, and \ref PRINT).
diff --git a/src/generic/Print.cpp b/src/generic/Print.cpp
index 2a87d1f7b..74245cf99 100644
--- a/src/generic/Print.cpp
+++ b/src/generic/Print.cpp
@@ -40,13 +40,12 @@ to different files. You can control the buffering of output using the \subpage
The following input instructs plumed to print the distance between atoms 3 and 5 on a file
called COLVAR every 10 steps, and the distance and total energy on a file called COLVAR_ALL
every 1000 steps.
-\verbatim
+\plumedfile
DISTANCE ATOMS=2,5 LABEL=distance
ENERGY LABEL=energy
PRINT ARG=distance STRIDE=10 FILE=COLVAR
PRINT ARG=distance,energy STRIDE=1000 FILE=COLVAR_ALL
-\endverbatim
-(See also \ref DISTANCE and \ref ENERGY).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/RandomExchanges.cpp b/src/generic/RandomExchanges.cpp
index be36873bc..60d207120 100644
--- a/src/generic/RandomExchanges.cpp
+++ b/src/generic/RandomExchanges.cpp
@@ -44,25 +44,25 @@ metadynamics simulation using a different angle in each replica.
Exchanges will be randomly tried between replicas 0-1, 0-2 and 1-2
Here is plumed.0.dat
-\verbatim
+\plumedfile
RANDOM_EXCHANGES
t: TORSION ATOMS=1,2,3,4
METAD ARG=t HEIGHT=0.1 PACE=100 SIGMA=0.3
-\endverbatim
+\endplumedfile
Here is plumed.1.dat
-\verbatim
+\plumedfile
RANDOM_EXCHANGES
t: TORSION ATOMS=2,3,4,5
METAD ARG=t HEIGHT=0.1 PACE=100 SIGMA=0.3
-\endverbatim
+\endplumedfile
Here is plumed.2.dat
-\verbatim
+\plumedfile
RANDOM_EXCHANGES
t: TORSION ATOMS=3,4,5,6
METAD ARG=t HEIGHT=0.1 PACE=100 SIGMA=0.3
-\endverbatim
+\endplumedfile
\warning Multi replica simulations are presently only working with gromacs.
diff --git a/src/generic/Read.cpp b/src/generic/Read.cpp
index 88c279630..63b8f8fc8 100644
--- a/src/generic/Read.cpp
+++ b/src/generic/Read.cpp
@@ -52,11 +52,11 @@ This input reads in data from a file called input_colvar.data that was generated
in a calculation that involved PLUMED. The first command reads in the data from the
column headed phi1 while the second reads in the data from the column headed phi2.
-\verbatim
+\plumedfile
rphi1: READ FILE=input_colvar.data VALUES=phi1
rphi2: READ FILE=input_colvar.data VALUES=phi2
PRINT ARG=rphi1,rphi2 STRIDE=500 FILE=output_colvar.data
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/ResetCell.cpp b/src/generic/ResetCell.cpp
index fd14c1fe1..5268d52de 100644
--- a/src/generic/ResetCell.cpp
+++ b/src/generic/ResetCell.cpp
@@ -71,14 +71,13 @@ this action is performed at every MD step.
\par Examples
Reset cell to be triangular after a rototranslational fit
-\verbatim
+\plumedfile
DUMPATOMS FILE=dump-original.xyz ATOMS=1-20
FIT_TO_TEMPLATE STRIDE=1 REFERENCE=ref.pdb TYPE=OPTIMAL
DUMPATOMS FILE=dump-fit.xyz ATOMS=1-20
RESET_CELL TYPE=TRIANGULAR
DUMPATOMS FILE=dump-reset.xyz ATOMS=1-20
-\endverbatim
-(see also \ref DUMPATOMS)
+\endplumedfile
*/
diff --git a/src/generic/Time.cpp b/src/generic/Time.cpp
index 3512cb53d..9a821f0b6 100644
--- a/src/generic/Time.cpp
+++ b/src/generic/Time.cpp
@@ -35,11 +35,10 @@ retrieve the time of the simulation to be used elsewere
\par Examples
-\verbatim
+\plumedfile
TIME LABEL=t1
PRINT ARG=t1
-\endverbatim
-(See also \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/UpdateIf.cpp b/src/generic/UpdateIf.cpp
index 2d067fcf3..696e66c20 100644
--- a/src/generic/UpdateIf.cpp
+++ b/src/generic/UpdateIf.cpp
@@ -62,7 +62,7 @@ can lead to unexpected results.
\par Examples
The following input instructs plumed dump all the snapshots where an atom is in touch with
the solute.
-\verbatim
+\plumedfile
solute: GROUP ATOMS=1-124
coord: COORDINATION GROUPA=solute GROUPB=500 R_0=0.5
@@ -72,8 +72,7 @@ coord: COORDINATION GROUPA=solute GROUPB=500 R_0=0.5
UPDATE_IF ARG=coord MORE_THAN=0.5
DUMPATOMS ATOMS=solute,500 FILE=output.xyz
UPDATE_IF ARG=coord END
-\endverbatim
-(See also \ref GROUP, \ref COORDINATION, and \ref DUMPATOMS)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/WholeMolecules.cpp b/src/generic/WholeMolecules.cpp
index 12e9c8281..e43c0aa07 100644
--- a/src/generic/WholeMolecules.cpp
+++ b/src/generic/WholeMolecules.cpp
@@ -74,30 +74,27 @@ to skip some atoms, provided consecute chosen atoms are close enough.
This command instructs plumed to reconstruct the molecule containing atoms 1-20
at every step of the calculation and dump them on a file.
-\verbatim
+\plumedfile
# to see the effect, one could dump the atoms as they were before molecule reconstruction:
# DUMPATOMS FILE=dump-broken.xyz ATOMS=1-20
WHOLEMOLECULES ENTITY0=1-20
DUMPATOMS FILE=dump.xyz ATOMS=1-20
-\endverbatim
-(see also \ref DUMPATOMS)
+\endplumedfile
This command instructs plumed to reconstruct two molecules containing atoms 1-20 and 30-40
-\verbatim
+\plumedfile
WHOLEMOLECULES ENTITY0=1-20 ENTITY1=30-40
DUMPATOMS FILE=dump.xyz ATOMS=1-20,30-40
-\endverbatim
-(see also \ref DUMPATOMS)
+\endplumedfile
This command instructs plumed to reconstruct the chain of backbone atoms in a
protein
-\verbatim
+\plumedfile
MOLINFO STRUCTURE=helix.pdb
WHOLEMOLECULES RESIDUES=all MOLTYPE=protein
-\endverbatim
-(See also \ref MOLINFO)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/WrapAround.cpp b/src/generic/WrapAround.cpp
index 946a060fd..6320ee4bb 100644
--- a/src/generic/WrapAround.cpp
+++ b/src/generic/WrapAround.cpp
@@ -69,20 +69,19 @@ consider the possibility of using the STRIDE keyword here (with great care).
This command instructs plumed to move all the ions to their periodic image that is as close as possible to
the rna group.
-\verbatim
+\plumedfile
rna: GROUP ATOMS=1-100
ions: GROUP ATOMS=101-110
# first make the rna molecule whole
WHOLEMOLECULES ENTITY0=rna
WRAPAROUND ATOMS=ions AROUND=rna
DUMPATOMS FILE=dump.xyz ATOMS=rna,ions
-\endverbatim
-(see also \ref WHOLEMOLECULES, \ref GROUP and \ref DUMPATOMS)
+\endplumedfile
In case you want to do it during a simulation and you only care about wrapping the ions in
the `dump.xyz` file, you can use the following:
-\verbatim
+\plumedfile
# add some restraint that do not require molecules to be whole:
a: TORSION ATOMS=1,2,10,11
RESTRAINT ARG=a AT=0.0 KAPPA=5
@@ -98,15 +97,14 @@ ions: GROUP ATOMS=101-110
WHOLEMOLECULES ENTITY0=rna STRIDE=100
WRAPAROUND ATOMS=ions AROUND=rna STRIDE=100
DUMPATOMS FILE=dump.xyz ATOMS=rna,ions STRIDE=100
-\endverbatim
-(see also \ref TORSION, \ref GROUP, \ref WHOLEMOLECULES and \ref DUMPATOMS)
+\endplumedfile
Notice that if the biased variable requires a molecule to be whole, you might have to put
just the \ref WHOLEMOLECULES command before computing that variable and leave the default STRIDE=1.
This command instructs plumed to center all atoms around the center of mass of a solute molecule.
-\verbatim
+\plumedfile
solute: GROUP ATOMS=1-100
all: GROUP ATOMS=1-1000
# center of the solute:
@@ -116,8 +114,7 @@ com: COM ATOMS=solute
# notice that we wrap around a single atom. this should be fast
WRAPAROUND ATOMS=all AROUND=com
DUMPATOMS FILE=dump.xyz ATOMS=all
-\endverbatim
-(see also \ref GROUP \ref COM \ref DUMPATOMS)
+\endplumedfile
Notice that whereas \ref WHOLEMOLECULES is designed to make molecules whole,
\ref WRAPAROUND can easily break molecules. In the last example,
@@ -136,7 +133,7 @@ in the following examples all the water oxygens will be brought
close to the solute, and all the hydrogens will be kept close
to their related oxygen.
-\verbatim
+\plumedfile
solute: GROUP ATOMS=1-100
water: GROUP ATOMS=101-1000
com: COM ATOMS=solute
@@ -145,8 +142,7 @@ WRAPAROUND ATOMS=solute AROUND=com
# notice that we wrap around a single atom. this should be fast
WRAPAROUND ATOMS=water AROUND=com GROUPBY=3
DUMPATOMS FILE=dump.xyz ATOMS=solute,water
-\endverbatim
-(see also \ref GROUP \ref COM \ref DUMPATOMS)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/gridtools/ConvertToFES.cpp b/src/gridtools/ConvertToFES.cpp
index 4e3bbdf17..661aa2bde 100644
--- a/src/gridtools/ConvertToFES.cpp
+++ b/src/gridtools/ConvertToFES.cpp
@@ -46,12 +46,12 @@ and the HISTOGRAM action. All the data within this trajectory is used in the co
HISTOGRAM. Finally, once all the data has been read in, the histogram is converted to a free energy
using the formula above and the free energy is output to a file called fes.dat
-\verbatim
+\plumedfile
x: DISTANCE ATOMS=1,2
hA1: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1
ff: CONVERT_TO_FES GRID=hA1 TEMP=300
DUMPGRID GRID=ff FILE=fes.dat
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/gridtools/DumpCube.cpp b/src/gridtools/DumpCube.cpp
index 0fbc47f56..f1df7406e 100644
--- a/src/gridtools/DumpCube.cpp
+++ b/src/gridtools/DumpCube.cpp
@@ -46,14 +46,14 @@ between atoms 1 and 2, the distance between atom 1 and 3 and the angle between t
all the kernels have been added the resulting histogram is output to a file called histoA1.cube. This file has the
Gaussian cube file format. The histogram can thus be visualized using tools such as VMD.
-\verbatim
+\plumedfile
x1: DISTANCE ATOMS=1,2
x2: DISTANCE ATOMS=1,3
x3: ANGLE ATOMS=1,2,3
hA1: HISTOGRAM ARG=x1,x2,x3 GRID_MIN=0.0,0.0,0.0 GRID_MAX=3.0,3.0,3.0 GRID_BIN=10,10,10 BANDWIDTH=1.0,1.0,1.0
DUMPCUBE GRID=hA1 FILE=histoA1.cube
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/gridtools/DumpGrid.cpp b/src/gridtools/DumpGrid.cpp
index 608742a8b..e3524d563 100644
--- a/src/gridtools/DumpGrid.cpp
+++ b/src/gridtools/DumpGrid.cpp
@@ -67,7 +67,7 @@ for y. This block is then followed by a blank line again and this pattern conti
The following input monitors two torsional angles during a simulation
and outputs a continuos histogram as a function of them at the end of the simulation.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
@@ -80,11 +80,11 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hh FILE=histo
-\endverbatim
+\endplumedfile
The following input monitors two torsional angles during a simulation
and outputs a discrete histogram as a function of them at the end of the simulation.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
@@ -98,11 +98,11 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hh FILE=histo
-\endverbatim
+\endplumedfile
The following input monitors two torsional angles during a simulation
and outputs the histogram accumulated thus far every 100000 steps.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
@@ -115,14 +115,14 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hh FILE=histo STRIDE=100000
-\endverbatim
+\endplumedfile
The following input monitors two torsional angles during a simulation
and outputs a separate histogram for each 100000 steps worth of trajectory.
Notice how the CLEAR keyword is used here and how it is not used in the
previous example.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
@@ -136,7 +136,7 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hh FILE=histo STRIDE=100000
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/gridtools/FindContour.cpp b/src/gridtools/FindContour.cpp
index a58e4f650..1bae86d43 100644
--- a/src/gridtools/FindContour.cpp
+++ b/src/gridtools/FindContour.cpp
@@ -67,7 +67,7 @@ solidness at each point in the simulation cell. The Willard-Chandler dividing s
at which the value of this phase field is equal to 0.5. This set of points is output to file called mycontour.dat. A new contour
is found on every single step for each frame that is read in.
-\verbatim
+\plumedfile
UNITS NATURAL
FCCUBIC ...
SPECIES=1-96000 SWITCH={CUBIC D_0=1.2 D_MAX=1.5}
@@ -84,7 +84,7 @@ MULTICOLVARDENS ...
... MULTICOLVARDENS
FIND_CONTOUR GRID=dens CONTOUR=0.5 FILE=mycontour.dat
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/gridtools/FindSphericalContour.cpp b/src/gridtools/FindSphericalContour.cpp
index a2ee2aa86..7d36e818c 100644
--- a/src/gridtools/FindSphericalContour.cpp
+++ b/src/gridtools/FindSphericalContour.cpp
@@ -81,7 +81,7 @@ by exploiting the functionality within \ref CENTER_OF_MULTICOLVAR. We can then
cluster and the values of the coordination numbers of these atoms. The final line in the input then finds the a set of points on the dividing surface that separates
teh droplet from the surrounding gas. The value of the phase field on this isocontour is equal to 0.75.
-\verbatim
+\plumedfile
# Calculate coordination numbers
c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}
# Select coordination numbers that are more than 2.0
@@ -98,7 +98,7 @@ cent: CENTER_OF_MULTICOLVAR DATA=trans1
dens: MULTICOLVARDENS DATA=trans1 ORIGIN=cent DIR=xyz NBINS=30,30,30 BANDWIDTH=2.0,2.0,2.0
# Find the isocontour around the nucleus
FIND_SPHERICAL_CONTOUR GRID=dens CONTOUR=0.85 INNER_RADIUS=10.0 OUTER_RADIUS=40.0 FILE=mysurface.xyz UNITS=A PRECISION=4 NPOINTS=100
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/gridtools/FourierTransform.cpp b/src/gridtools/FourierTransform.cpp
index 5a53b390d..87a078336 100644
--- a/src/gridtools/FourierTransform.cpp
+++ b/src/gridtools/FourierTransform.cpp
@@ -57,9 +57,9 @@ The default values of these parameters are: \f$a=1\f$ and \f$b=1\f$.
\par Examples
The following example tells Plumed to compute the complex 2D 'backward' Discrete Fourier Transform by taking the data saved on a grid called 'density', and normalizing the output by \f$ \frac{1}{\sqrt{N_x\, N_y}}\f$, where \f$N_x\f$ and \f$N_y\f$ are the number of data on the grid (it can be the case that \f$N_x \neq N_y\f$):
-\verbatim
+\plumedfile
FOURIER_TRANSFORM STRIDE=1 GRID=density FT_TYPE=complex FOURIER_PARAMETERS=0,-1 FILE=fourier.dat
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/gridtools/InterpolateGrid.cpp b/src/gridtools/InterpolateGrid.cpp
index e8f97c0d4..7fbc1d65d 100644
--- a/src/gridtools/InterpolateGrid.cpp
+++ b/src/gridtools/InterpolateGrid.cpp
@@ -38,12 +38,12 @@ distance between atoms 1 and 2 using kernel density estimation. During the calc
are evaluated at 100 points on a uniform grid between 0.0 and 3.0. Prior to outputting this function at the end of the
simulation this function is interpolated onto a finer grid of 200 points between 0.0 and 3.0.
-\verbatim
+\plumedfile
x: DISTANCE ATOMS=1,2
hA1: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1
ii: INTERPOLATE_GRID GRID=hA1 GRID_BIN=200
DUMPGRID GRID=ii FILE=histo.dat
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/maketools/plumedcheck b/src/maketools/plumedcheck
index 120808dec..5886ec086 100755
--- a/src/maketools/plumedcheck
+++ b/src/maketools/plumedcheck
@@ -354,6 +354,12 @@ BEGINFILE{
if(in_plumed_doc && (in_plumed_doc in provide_examples) && match($0,"^ *\\\\verbatim *$")){
provide_verbatim[in_plumed_doc]=1
}
+# check if, besides the \par Examples text, there is a plumedfile command
+# now it is considered equivalent to a verbatim
+# later on we might make plumedfile compulsory instead of verbatim
+ if(in_plumed_doc && (in_plumed_doc in provide_examples) && match($0,"^ *\\\\plumedfile *$")){
+ provide_verbatim[in_plumed_doc]=1
+ }
#print match($0,"^ *\\\\verbatim *$"),"X" $0 "X"
# take note of actions or cltools that provide examples
diff --git a/src/manyrestraints/LWalls.cpp b/src/manyrestraints/LWalls.cpp
index 7c0ad569e..c98405d04 100644
--- a/src/manyrestraints/LWalls.cpp
+++ b/src/manyrestraints/LWalls.cpp
@@ -45,10 +45,10 @@ The following set of commands can be used to stop any of the 800 atoms in group
in the z direction from atom 34137. This is done by adding a lower wall on the z-distance between all the atoms in
group A and the position of 34137.
-\verbatim
+\plumedfile
l: ZDISTANCES GROUPA=1-800 GROUPB=34137 NOPBC
LWALLS DATA=l AT=2.46465 KAPPA=150.0 EXP=2 EPS=1 OFFSET=0 LABEL=lwall
-\endverbatim
+\endplumedfile
*/
diff --git a/src/manyrestraints/UWalls.cpp b/src/manyrestraints/UWalls.cpp
index f4c75f0d8..2c0f75367 100644
--- a/src/manyrestraints/UWalls.cpp
+++ b/src/manyrestraints/UWalls.cpp
@@ -48,11 +48,11 @@ and the center of mass of the cluster. These distances are then passed to the U
a \ref UPPER_WALLS restraint on each of them and thereby prevents each of them from moving very far from the centre
of mass of the cluster.
-\verbatim
+\plumedfile
COM ATOMS=1-20 LABEL=c1
DISTANCES GROUPA=c1 GROUPB=1-20 LABEL=d1
UWALLS DATA=d1 AT=2.5 KAPPA=0.2 LABEL=sr
-\endverbatim
+\endplumedfile
*/
diff --git a/src/mapping/PCAVars.cpp b/src/mapping/PCAVars.cpp
index d029720ed..20ae00301 100644
--- a/src/mapping/PCAVars.cpp
+++ b/src/mapping/PCAVars.cpp
@@ -76,10 +76,10 @@ frame are removed from these displacements. The matrix \f$A\f$ and the referenc
configuration \f$R^{ref}\f$ are specified in the pdb input file reference.pdb and the
value of all projections (and the residual) are output to a file called colvar2.
-\verbatim
+\plumedfile
PCAVARS REFERENCE=reference.pdb TYPE=OPTIMAL LABEL=pca2
PRINT ARG=pca2.* FILE=colvar2
-\endverbatim
+\endplumedfile
The reference configurations can be specified using a pdb file. The first configuration that you provide is the reference configuration,
which is refered to in the above as \f$X^{ref}\f$ subsequent configurations give the directions of row vectors that are contained in
diff --git a/src/mapping/Path.cpp b/src/mapping/Path.cpp
index 37db777d2..4808fad15 100644
--- a/src/mapping/Path.cpp
+++ b/src/mapping/Path.cpp
@@ -73,21 +73,21 @@ In the example below the path is defined using RMSD distance from frames.
The reference frames in the path are defined in the pdb file. In this frame
each configuration in the path is separated by a line containing just the word END.
-\verbatim
+\plumedfile
p1: PATH REFERENCE=file.pdb TYPE=OPTIMAL LAMBDA=500.0
PRINT ARG=p1.sss,p1.zzz STRIDE=1 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
In the example below the path is defined using the values of two torsional angles (t1 and t2).
In addition, the \f$s\f$ and \f$z\f$ are calculated using the geometric expressions described
above rather than the alegebraic expressions that are used by default.
-\verbatim
+\plumedfile
t1: TORSION ATOMS=5,7,9,15
t2: TORSION ATOMS=7,9,15,17
pp: PATH TYPE=EUCLIDEAN REFERENCE=epath.pdb GPATH NOSPATH NOZPATH
PRINT ARG=pp.* FILE=colvar
-\endverbatim
+\endplumedfile
Notice that the LAMBDA parameter is not required here as we are not calculating \f$s\f$ and \f$s\f$
using the algebraic formulae defined earlier. The positions of the frames in the path are defined
@@ -109,19 +109,19 @@ The following input instructs PLUMED to calculate the values of the path collect
path are defined in the file all.pdb and all distances are measured using the OPTIMAL metric that is discussed in the manual
page on \ref RMSD.
-\verbatim
+\plumedfile
p2: PATH REFERENCE=all.pdb LAMBDA=69087
PRINT ARG=p2.spath,p2.zpath STRIDE=1 FILE=colvar
-\endverbatim
+\endplumedfile
If you wish to use collective variable values in the definition of your path you would use an input file with something like this:
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=1,2
d2: DISTANCE ATOMS=3,4a
p2: PATH REFERENCE=mypath.pdb LAMBDA=2 TYPE=EUCLIDEAN
PRINT ARG=p2.spath,p2.zpath STRIDE=1 FILE=colvar
-\endverbatim
+\endplumedfile
The corresponding pdb file containing the definitions of the frames in the path would then look like this:
diff --git a/src/mapping/PropertyMap.cpp b/src/mapping/PropertyMap.cpp
index 9da32b47b..91c96f4dd 100644
--- a/src/mapping/PropertyMap.cpp
+++ b/src/mapping/PropertyMap.cpp
@@ -47,10 +47,10 @@ that these properties take at a set of reference configurations and using the fo
between the reference configurations and the instantaneous configurations are calculated using the OPTIMAL metric that is
discussed at length in the manual pages on \ref RMSD.
-\verbatim
+\plumedfile
p2: GPROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087
PRINT ARG=p2.X,p2.Y,p2.zpath STRIDE=1 FILE=colvar
-\endverbatim
+\endplumedfile
The additional input file for this calculation, which contains the reference frames and the values of X and Y at these reference
points has the following format.
diff --git a/src/multicolvar/AlphaBeta.cpp b/src/multicolvar/AlphaBeta.cpp
index 01379c583..aea79fc2e 100644
--- a/src/multicolvar/AlphaBeta.cpp
+++ b/src/multicolvar/AlphaBeta.cpp
@@ -49,7 +49,7 @@ The \f$\phi_i^{\textrm{Ref}}\f$ values are the user-specified reference values f
The following provides an example of the input for an alpha beta similarity.
-\verbatim
+\plumedfile
ALPHABETA ...
ATOMS1=168,170,172,188 REFERENCE1=3.14
ATOMS2=170,172,188,190 REFERENCE2=3.14
@@ -57,11 +57,11 @@ ATOMS3=188,190,192,230 REFERENCE3=3.14
LABEL=ab
... ALPHABETA
PRINT ARG=ab FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
Because all the reference values are the same we can calculate the same quantity using
-\verbatim
+\plumedfile
ALPHABETA ...
ATOMS1=168,170,172,188 REFERENCE=3.14
ATOMS2=170,172,188,190
@@ -69,13 +69,13 @@ ATOMS3=188,190,192,230
LABEL=ab
... ALPHABETA
PRINT ARG=ab FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
Writing out the atoms involved in all the torsions in this way can be rather tedious. Thankfully if you are working with protein you
can avoid this by using the \ref MOLINFO command. PLUMED uses the pdb file that you provide to this command to learn
about the topology of the protein molecule. This means that you can specify torsion angles using the following syntax:
-\verbatim
+\plumedfile
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
ALPHABETA ...
ATOMS1=@phi-3 REFERENCE=3.14
@@ -84,7 +84,7 @@ ATOMS3=@phi-4
LABEL=ab
... ALPHABETA
PRINT ARG=ab FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.
Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the 4th residue of the protein.
diff --git a/src/multicolvar/Angles.cpp b/src/multicolvar/Angles.cpp
index a42233cbd..cdc062579 100644
--- a/src/multicolvar/Angles.cpp
+++ b/src/multicolvar/Angles.cpp
@@ -58,28 +58,28 @@ an atom / molecule \cite lj-recon.
The following example instructs plumed to find the average of two angles and to
print it to a file
-\verbatim
+\plumedfile
ANGLES ATOMS1=1,2,3 ATOMS2=4,5,6 MEAN LABEL=a1
PRINT ARG=a1.mean FILE=colvar
-\endverbatim
+\endplumedfile
The following example tells plumed to calculate all angles involving
at least one atom from GROUPA and two atoms from GROUPB in which the distances
are less than 1.0. The number of angles between \f$\frac{\pi}{4}\f$ and
\f$\frac{3\pi}{4}\f$ is then output
-\verbatim
+\plumedfile
ANGLES GROUPA=1-10 GROUPB=11-100 BETWEEN={GAUSSIAN LOWER=0.25pi UPPER=0.75pi} SWITCH={GAUSSIAN R_0=1.0} LABEL=a1
PRINT ARG=a1.between FILE=colvar
-\endverbatim
+\endplumedfile
This final example instructs plumed to calculate all the angles in the first coordination
spheres of the atoms. A discretized-normalized histogram of the distribution is then output
-\verbatim
+\plumedfile
ANGLES GROUP=1-38 HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=pi NBINS=20} SWITCH={GAUSSIAN R_0=1.0} LABEL=a1
PRINT ARG=a1.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/Bridge.cpp b/src/multicolvar/Bridge.cpp
index 42198ffa1..53e76158b 100644
--- a/src/multicolvar/Bridge.cpp
+++ b/src/multicolvar/Bridge.cpp
@@ -51,10 +51,10 @@ The following example instructs plumed to calculate the number of water molecule
that are bridging betweeen atoms 1-10 and atoms 11-20 and to print the value
to a file
-\verbatim
+\plumedfile
BRIDGE BRIDGING_ATOMS=100-200 GROUPA=1-10 GROUPB=11-20 LABEL=w1
PRINT ARG=a1.mean FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/CenterOfMultiColvar.cpp b/src/multicolvar/CenterOfMultiColvar.cpp
index f8b5be660..0708bd402 100644
--- a/src/multicolvar/CenterOfMultiColvar.cpp
+++ b/src/multicolvar/CenterOfMultiColvar.cpp
@@ -55,10 +55,10 @@ As you want to calculate the position of the droplets you thus recognise that th
numbers should have a high weight in the weighted average you are using to calculate the position of the droplet.
You can thus calculate the position of the droplet using an input like the one shown below:
-\verbatim
+\plumedfile
c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5}
cc: CENTER_OF_MULTICOLVAR DATA=c1
-\endverbatim
+\endplumedfile
The first line here calclates the coordination numbers of all the atoms in the system. The virtual atom then uses the values
of the coordination numbers calculated by the action labelled c1 when it calculates the Berry Phase average described above.
@@ -66,11 +66,11 @@ of the coordination numbers calculated by the action labelled c1 when it calcula
The above input is fine we can, however, refine this somewhat by making use of a multicolvar transform action as shown below:
-\verbatim
+\plumedfile
c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5}
cf: MTRANSFORM_MORE DATA=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM
cc: CENTER_OF_MULTICOLVAR DATA=cf
-\endverbatim
+\endplumedfile
This input once again calculates the coordination numbers of all the atoms in the system. The middle line then transforms these
coordinations numbers to numbers between 0 and 1. Essentially any atom with a coordination number larger than 2.0 is given a weight
diff --git a/src/multicolvar/CoordinationNumbers.cpp b/src/multicolvar/CoordinationNumbers.cpp
index a3823b488..38c26d348 100644
--- a/src/multicolvar/CoordinationNumbers.cpp
+++ b/src/multicolvar/CoordinationNumbers.cpp
@@ -48,16 +48,16 @@ s = \frac{ 1 - \left(\frac{r-d_0}{r_0}\right)^n } { 1 - \left(\frac{r-d_0}{r_0}\
The following input tells plumed to calculate the coordination numbers of atoms 1-100 with themselves.
The minimum coordination number is then calculated.
-\verbatim
+\plumedfile
COORDINATIONNUMBER SPECIES=1-100 R_0=1.0 MIN={BETA=0.1}
-\endverbatim
+\endplumedfile
The following input tells plumed to calculate how many atoms from 1-100 are within 3.0 of each of the atoms
from 101-110. In the first 101 is the central atom, in the second 102 is the central atom and so on. The
number of coordination numbers more than 6 is then computed.
-\verbatim
+\plumedfile
COORDINATIONNUMBER SPECIESA=101-110 SPECIESB=1-100 R_0=3.0 MORE_THAN={RATIONAL R_0=6.0 NN=6 MM=12 D_0=0}
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/Density.cpp b/src/multicolvar/Density.cpp
index 0351140a3..598e16b30 100644
--- a/src/multicolvar/Density.cpp
+++ b/src/multicolvar/Density.cpp
@@ -40,11 +40,11 @@ the number of atoms in half the box.
The following example calculates the number of atoms in one half of the simulation box.
-\verbatim
+\plumedfile
DENSITY SPECIES=1-100 LABEL=d
AROUND ARG=d XLOWER=0.0 XUPPER=0.5 LABEL=d1
PRINT ARG=d1.* FILE=colvar1 FMT=%8.4f
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/DihedralCorrelation.cpp b/src/multicolvar/DihedralCorrelation.cpp
index e75bde668..a1f5ea872 100644
--- a/src/multicolvar/DihedralCorrelation.cpp
+++ b/src/multicolvar/DihedralCorrelation.cpp
@@ -48,14 +48,14 @@ where the \f$\phi_i\f$ and \f$\psi\f$ values and the instantaneous values for th
The following provides an example input for the dihcor action
-\verbatim
+\plumedfile
DIHCOR ...
ATOMS1=1,2,3,4,5,6,7,8
ATOMS2=5,6,7,8,9,10,11,12
LABEL=dih
... DIHCOR
PRINT ARG=dih FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
In the above input we are calculating the correation between the torsion angle involving atoms 1, 2, 3 and 4 and the torsion angle
involving atoms 5, 6, 7 and 8. This is then added to the correlation betwene the torsion angle involving atoms 5, 6, 7 and 8 and the
@@ -65,7 +65,7 @@ Writing out the atoms involved in all the torsions in this way can be rather ted
can avoid this by using the \ref MOLINFO command. PLUMED uses the pdb file that you provide to this command to learn
about the topology of the protein molecule. This means that you can specify torsion angles using the following syntax:
-\verbatim
+\plumedfile
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
DIHCOR ...
ATOMS1=@phi-3,@psi-3
@@ -73,7 +73,7 @@ ATOMS2=@psi-3,@phi-4
ATOMS4=@phi-4,@psi-4
... DIHCOR
PRINT ARG=dih FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.
Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the 4th residue of the protein.
diff --git a/src/multicolvar/DistanceFromContour.cpp b/src/multicolvar/DistanceFromContour.cpp
index 214930392..6f99e214a 100644
--- a/src/multicolvar/DistanceFromContour.cpp
+++ b/src/multicolvar/DistanceFromContour.cpp
@@ -58,10 +58,10 @@ In this example atoms 2-100 are assumed to be concentraed along some part of the
an interface between a liquid/solid and the vapour. The quantity dc measures the distance between the
surface at which the density of 2-100 atoms is equal to 0.2 and the position of the test particle atom 1.
-\verbatim
+\plumedfile
dens: DENSITY SPECIES=2-100
dc: DISTANCE_FROM_CONTOUR DATA=dens ATOM=1 BANDWIDTH=0.5,0.5,0.5 DIR=z CONTOUR=0.2
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/Distances.cpp b/src/multicolvar/Distances.cpp
index d5cb8fde0..579668b88 100644
--- a/src/multicolvar/Distances.cpp
+++ b/src/multicolvar/Distances.cpp
@@ -42,36 +42,36 @@ distances such as the minimum, the number less than a certain quantity and so on
The following input tells plumed to calculate the distances between atoms 3 and 5 and between atoms 1 and 2 and to
print the minimum for these two distances.
-\verbatim
+\plumedfile
DISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
The following input tells plumed to calculate the distances between atoms 3 and 5 and between atoms 1 and 2
and then to calculate the number of these distances that are less than 0.1 nm. The number of distances
less than 0.1nm is then printed to a file.
-\verbatim
+\plumedfile
DISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
PRINT ARG=d1.lt0.1
-\endverbatim
+\endplumedfile
(See also \ref PRINT \ref switchingfunction).
The following input tells plumed to calculate all the distances between atoms 1, 2 and 3 (i.e. the distances between atoms
1 and 2, atoms 1 and 3 and atoms 2 and 3). The average of these distances is then calculated.
-\verbatim
+\plumedfile
DISTANCES GROUP=1-3 MEAN LABEL=d1
PRINT ARG=d1.mean
-\endverbatim
+\endplumedfile
(See also \ref PRINT)
The following input tells plumed to calculate all the distances between the atoms in GROUPA and the atoms in GROUPB.
In other words the distances between atoms 1 and 2 and the distance between atoms 1 and 3. The number of distances
more than 0.1 is then printed to a file.
-\verbatim
+\plumedfile
DISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
PRINT ARG=d1.gt0.1
-\endverbatim
+\endplumedfile
(See also \ref PRINT \ref switchingfunction)
@@ -79,10 +79,10 @@ PRINT ARG=d1.gt0.1
To calculate and print the minimum distance between two groups of atoms you use the following commands
-\verbatim
+\plumedfile
d1: DISTANCES GROUPA=1-10 GROUPB=11-20 MIN={BETA=500.}
PRINT ARG=d1.min FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
(see \ref DISTANCES and \ref PRINT)
In order to ensure differentiability the minimum is calculated using the following function:
@@ -102,7 +102,7 @@ allow you to calculate multiple functions of a distribution of simple collective
can calculate the number of distances less than 1.0, the minimum distance, the number of distances more than
2.0 and the number of distances between 1.0 and 2.0 by using the following command:
-\verbatim
+\plumedfile
DISTANCES ...
GROUPA=1-10 GROUPB=11-20
LESS_THAN={RATIONAL R_0=1.0}
@@ -111,7 +111,7 @@ DISTANCES ...
MIN={BETA=500.}
... DISTANCES
PRINT ARG=d1.lessthan,d1.morethan,d1.between,d1.min FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
(see \ref DISTANCES and \ref PRINT)
A calculation performed this way is fast because the expensive part of the calculation - the calculation of all the distances - is only
diff --git a/src/multicolvar/DumpMultiColvar.cpp b/src/multicolvar/DumpMultiColvar.cpp
index 27029a436..fb08af5b4 100644
--- a/src/multicolvar/DumpMultiColvar.cpp
+++ b/src/multicolvar/DumpMultiColvar.cpp
@@ -49,13 +49,13 @@ In this examples we calculate the distances between the atoms of the first and
group and we write them in the file MULTICOLVAR.xyz. For each couple it writes the
coordinates of their geometric center and their distance.
-\verbatim
+\plumedfile
pos: GROUP ATOMS=220,221,235,236,247,248,438,439,450,451,534,535
neg: GROUP ATOMS=65,68,138,182,185,267,270,291,313,316,489,583,621,711
DISTANCES GROUPA=pos GROUPB=neg LABEL=slt
DUMPMULTICOLVAR DATA=slt FILE=MULTICOLVAR.xyz
-\endverbatim
+\endplumedfile
(see also \ref DISTANCES)
diff --git a/src/multicolvar/FilterBetween.cpp b/src/multicolvar/FilterBetween.cpp
index d6a418711..17ad0be9e 100644
--- a/src/multicolvar/FilterBetween.cpp
+++ b/src/multicolvar/FilterBetween.cpp
@@ -59,22 +59,22 @@ In other words, you are calculating the mean for the transformed colvar.
The following input gives an example of how a MTRANSFORM_BETWEEN action can be used to duplicate
functionality that is elsehwere in PLUMED.
-\verbatim
+\plumedfile
DISTANCES ...
GROUPA=1-10 GROUPB=11-20
LABEL=d1
... DISTANCES
MTRANSFORM_BETWEEN DATA=d1 LOWER=1.0 UPPER=2.0 SMEAR=0.5
-\endverbatim
+\endplumedfile
In this case you can achieve the same result by using:
-\verbatim
+\plumedfile
DISTANCES ...
GROUPA=1-10 GROUPB=11-20
BETWEEN={GAUSSIAN LOWER=1.0 UPPER=2.0}
... DISTANCES
-\endverbatim
+\endplumedfile
(see \ref DISTANCES)
The advantage of MTRANSFORM_BETWEEN comes, however, if you want to use transformed colvars as input
@@ -112,10 +112,10 @@ One is thus calculating the mean for those colvars that are within the range of
The example shown below calculates the mean for those distances that are between 0 and 3 nm in length
-\verbatim
+\plumedfile
DISTANCES GROUPA=1 GROUPB=2-50 MEAN LABEL=d1
MFILTER_BETWEEN DATA=d1 LOWER=0 UPPER=3.0 SMEAR=0.0001 MEAN LABEL=d4
-\endverbatim
+\endplumedfile
More complicated things can be done by using the label of a filter as input to a new multicolvar as shown
in the example below. Here the coordination numbers of all atoms are computed. The atoms with a coordination
@@ -123,11 +123,11 @@ number between 4 and 6 are then identified using the filter. This reduced list
to a second coordination number calculation. This second coordination number thus measures the number of atoms
4-6 coordinated atoms each of the 4-6 coordination atoms is bound to.
-\verbatim
+\plumedfile
c1: COORDINATIONNUMBER SPECIES=1-150 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}
cf: MFILTER_BETWEEN DATA=c1 LOWER=4 UPPER=6 SMEAR=0.5 LOWMEM
c2: COORDINATIONNUMBER SPECIES=cf SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0} MORE_THAN={RATIONAL D_0=2.0 R_0=0.1}
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/FilterLessThan.cpp b/src/multicolvar/FilterLessThan.cpp
index 6363bcbb4..e65d5fcd1 100644
--- a/src/multicolvar/FilterLessThan.cpp
+++ b/src/multicolvar/FilterLessThan.cpp
@@ -51,22 +51,22 @@ In other words, you are calculating the mean for the transformed colvar.
The following input gives an example of how a MTRANSFORM_LESS action can be used to duplicate
functionality that is elsehwere in PLUMED.
-\verbatim
+\plumedfile
DISTANCES ...
GROUPA=1-10 GROUPB=11-20
LABEL=d1
... DISTANCES
MTRANSFORM_LESS DATA=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.00001}
-\endverbatim
+\endplumedfile
In this case you can achieve the same result by using:
-\verbatim
+\plumedfile
DISTANCES ...
GROUPA=1-10 GROUPB=11-20
LESS_THAN={GAUSSIAN D_0=1.5 R_0=0.00001}
... DISTANCES
-\endverbatim
+\endplumedfile
(see \ref DISTANCES)
The advantage of MTRANSFORM_LESS comes, however, if you want to use transformed colvars as input
@@ -99,10 +99,10 @@ One is thus calculating the mean for those colvars that are less than the target
The example shown below calculates the mean for those distances that less than 1.5 nm in length
-\verbatim
+\plumedfile
DISTANCES GROUPA=1 GROUPB=2-50 MEAN LABEL=d1
MFILTER_LESS DATA=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.00001} MEAN LABEL=d4
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/FilterMoreThan.cpp b/src/multicolvar/FilterMoreThan.cpp
index 961c33d01..50c1dc59b 100644
--- a/src/multicolvar/FilterMoreThan.cpp
+++ b/src/multicolvar/FilterMoreThan.cpp
@@ -51,22 +51,22 @@ In other words, you are calculating the mean for the transformed colvar.
The following input gives an example of how a MTRANSFORM_MORE action can be used to duplicate
functionality that is elsehwere in PLUMED.
-\verbatim
+\plumedfile
DISTANCES ...
GROUPA=1-10 GROUPB=11-20
LABEL=d1
... DISTANCES
MTRANSFORM_MORE DATA=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.00001}
-\endverbatim
+\endplumedfile
In this case you can achieve the same result by using:
-\verbatim
+\plumedfile
DISTANCES ...
GROUPA=1-10 GROUPB=11-20
MORE_THAN={GAUSSIAN D_0=1.5 R_0=0.00001}
... DISTANCES
-\endverbatim
+\endplumedfile
(see \ref DISTANCES)
The advantage of MTRANSFORM_MORE comes, however, if you want to use transformed colvars as input
@@ -104,10 +104,10 @@ One is thus calculating the mean for those colvars that are greater than the tar
The example shown below calculates the mean for those distances that greater than 1.5 nm in length
-\verbatim
+\plumedfile
DISTANCES GROUPA=1 GROUPB=2-50 MEAN LABEL=d1
MFILTER_MORE DATA=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.00001} MEAN LABEL=d4
-\endverbatim
+\endplumedfile
More complicated things can be done by using the label of a filter as input to a new multicolvar as shown
in the example below. Here the coordination numbers of all atoms are computed. The atoms with a coordination
@@ -115,11 +115,11 @@ number greater than 2 are then identified using the filter. This reduced list o
to a second coordination number calculation. This second coordination number thus measures the number of
two-coordinated atoms that each of the two-coordinated atoms is bound to.
-\verbatim
+\plumedfile
1: COORDINATIONNUMBER SPECIES=1-150 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}
cf: MFILTER_MORE DATA=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM
c2: COORDINATIONNUMBER SPECIES=cf SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0} MORE_THAN={RATIONAL D_0=2.0 R_0=0.1}
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/InPlaneDistances.cpp b/src/multicolvar/InPlaneDistances.cpp
index d041fa1e0..ef9f4a55f 100644
--- a/src/multicolvar/InPlaneDistances.cpp
+++ b/src/multicolvar/InPlaneDistances.cpp
@@ -53,10 +53,10 @@ Keywords such as MORE_THAN and LESS_THAN can then be used to calculate the numbe
The following input can be used to calculate the number of atoms that have indices greater than 3 and less than 101 that
are within a cylinder with a radius of 0.3 nm that has its long axis aligned with the vector connecting atoms 1 and 2.
-\verbatim
+\plumedfile
d1: INPLANEDISTANCES VECTORSTART=1 VECTOREND=2 GROUP=3-100 LESS_THAN={RATIONAL D_0=0.2 R_0=0.1}
PRINT ARG=d1.lessthan FILE=colvar
-\endverbatim
+\endplumedfile
*/
diff --git a/src/multicolvar/LocalAverage.cpp b/src/multicolvar/LocalAverage.cpp
index fdc3e09c4..c8bae1d56 100644
--- a/src/multicolvar/LocalAverage.cpp
+++ b/src/multicolvar/LocalAverage.cpp
@@ -59,21 +59,21 @@ and so on. You can also probe the value of these averaged variables in regions
This example input calculates the coordination numbers for all the atoms in the system. These coordination numbers are then averaged over
spherical regions. The number of averaged coordination numbers that are greater than 4 is then output to a file.
-\verbatim
+\plumedfile
COORDINATIONNUMBER SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=d1
LOCAL_AVERAGE ARG=d1 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MORE_THAN={RATIONAL R_0=4} LABEL=la
PRINT ARG=la.* FILE=colvar
-\endverbatim
+\endplumedfile
This example input calculates the \f$q_4\f$ (see \ref Q4) vectors for each of the atoms in the system. These vectors are then averaged
component by component over a spherical region. The average value for this quantity is then outputeed to a file. This calculates the
quantities that were used in the paper by Lechner and Dellago \cite dellago-q6
-\verbatim
+\plumedfile
Q4 SPECIES=1-64 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=q4
LOCAL_AVERAGE ARG=q4 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LABEL=la
PRINT ARG=la.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/MultiColvarDensity.cpp b/src/multicolvar/MultiColvarDensity.cpp
index 7ea3dc009..8e63b6e51 100644
--- a/src/multicolvar/MultiColvarDensity.cpp
+++ b/src/multicolvar/MultiColvarDensity.cpp
@@ -58,11 +58,11 @@ The following example shows perhaps the simplest way in which this action can be
input computes the density of atoms at each point on the grid and ouptuts this quantity to a file. In
other words this input instructs plumed to calculate \f$\rho(\mathbf{r}) = \sum_i K(\mathbf{r} - \mathbf{r}_i )\f$
-\verbatim
+\plumedfile
dens: DENSITY SPECIES=1-100
grid: MULTICOLVARDENS DATA=dens ORIGIN=1 DIR=xyz NBINS=100,100,100 BANDWIDTH=0.05,0.05,0.05 STRIDE=1
DUMPGRID GRID=grid STRIDE=500 FILE=density
-\endverbatim
+\endplumedfile
In the above example density is added to the grid on every step. The PRINT_GRID instruction thus tells PLUMED to
output the average density at each point on the grid every 500 steps of simulation. Notice that the that grid output
@@ -72,11 +72,11 @@ of data separately you must use the CLEAR flag.
This second example computes an order parameter (in this case \ref FCCUBIC) and constructs a phase field model
for this order parameter using the equation above.
-\verbatim
+\plumedfile
fcc: FCCUBIC SPECIES=1-5184 SWITCH={CUBIC D_0=1.2 D_MAX=1.5} ALPHA=27
dens: MULTICOLVARDENS DATA=fcc ORIGIN=1 DIR=xyz NBINS=14,14,28 BANDWIDTH=1.0,1.0,1.0 STRIDE=1 CLEAR=1
DUMPCUBE GRID=dens STRIDE=1 FILE=dens.cube
-\endverbatim
+\endplumedfile
In this example the phase field model is computed and output to a file on every step of the simulation. Furthermore,
because the CLEAR=1 keyword is set on the MULTICOLVARDENS line each Gaussian cube file output is a phase field
diff --git a/src/multicolvar/NumberOfLinks.cpp b/src/multicolvar/NumberOfLinks.cpp
index b8257c5e4..c8850755b 100644
--- a/src/multicolvar/NumberOfLinks.cpp
+++ b/src/multicolvar/NumberOfLinks.cpp
@@ -43,22 +43,22 @@ similar orientations. The vectors on individual atoms could be Steinhardt param
The following calculates how many bonds there are in a system containing 64 atoms and outputs
this quantity to a file.
-\verbatim
+\plumedfile
DENSITY SPECIES=1-64 LABEL=d1
NLINKS ARG=d1 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=dd
PRINT ARG=dd FILE=colvar
-\endverbatim
+\endplumedfile
The following calculates how many pairs of neighbouring atoms in a system containg 64 atoms have
similar dispositions for the atoms in their coordination sphere. This calculation uses the
dot product of the Q6 vectors on adjacent atoms to measure whether or not two atoms have the same
``orientation"
-\verbatim
+\plumedfile
Q6 SPECIES=1-64 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=q6
NLINKS ARG=q6 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=dd
PRINT ARG=dd FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/Torsions.cpp b/src/multicolvar/Torsions.cpp
index 59d02cbfd..4e3fcfbb2 100644
--- a/src/multicolvar/Torsions.cpp
+++ b/src/multicolvar/Torsions.cpp
@@ -40,7 +40,7 @@ Calculate whether or not a set of torsional angles are within a particular range
The following provides an example of the input for the torsions command
-\verbatim
+\plumedfile
TORSIONS ...
ATOMS1=168,170,172,188
ATOMS2=170,172,188,190
@@ -48,13 +48,13 @@ ATOMS3=188,190,192,230
LABEL=ab
... TORSIONS
PRINT ARG=ab.* FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
Writing out the atoms involved in all the torsions in this way can be rather tedious. Thankfully if you are working with protein you
can avoid this by using the \ref MOLINFO command. PLUMED uses the pdb file that you provide to this command to learn
about the topology of the protein molecule. This means that you can specify torsion angles using the following syntax:
-\verbatim
+\plumedfile
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
TORSIONS ...
ATOMS1=@phi-3
@@ -63,7 +63,7 @@ ATOMS3=@phi-4
LABEL=ab
... TORSIONS
PRINT ARG=ab FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.
Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the 4th residue of the protein.
diff --git a/src/multicolvar/VolumeAround.cpp b/src/multicolvar/VolumeAround.cpp
index bab79d8e0..d44f36d4b 100644
--- a/src/multicolvar/VolumeAround.cpp
+++ b/src/multicolvar/VolumeAround.cpp
@@ -55,11 +55,11 @@ When AROUND is used with the \ref DENSITY action the number of atoms in the spec
The following commands tell plumed to calculate the average coordination number for the atoms
that have x (in fractional coordinates) within 2.0 nm of the com of mass c1. The final value will be labeled s.mean.
-\verbatim
+\plumedfile
COM ATOMS=1-100 LABEL=c1
COORDINATIONNUMBER SPECIES=1-100 R_0=1.0 LABEL=c
AROUND DATA=c ORIGIN=c1 XLOWER=-2.0 XUPPER=2.0 SIGMA=0.1 MEAN LABEL=s
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/VolumeCavity.cpp b/src/multicolvar/VolumeCavity.cpp
index af14a2be0..70d8254f3 100644
--- a/src/multicolvar/VolumeCavity.cpp
+++ b/src/multicolvar/VolumeCavity.cpp
@@ -86,19 +86,19 @@ described above and the resulting projections determine the \f$u'\f$, \f$v'\f$ a
The following commands tell plumed to calculate the number of atoms in an ion chanel in a protein.
The extent of the chanel is calculated from the positions of atoms 1, 4, 5 and 11. The final value will be labeled cav.
-\verbatim
+\plumedfile
d1: DENSITY SPECIES=20-500
CAVITY DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 LABEL=cav
-\endverbatim
+\endplumedfile
The following command tells plumed to calculate the coordination numbers (with other water molecules) for the water
molecules in the protein channel described above. The average coordination number and the number of coordination
numbers more than 4 is then calculated. The values of these two quantities are given the labels cav.mean and cav.morethan
-\verbatim
+\plumedfile
d1: COORDINATIONNUMBER SPECIES=20-500
CAVITY DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 MEAN MORE_THAN={RATIONAL R_0=4} LABEL=cav
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/VolumeInCylinder.cpp b/src/multicolvar/VolumeInCylinder.cpp
index eb6bc611e..3e8acfb22 100644
--- a/src/multicolvar/VolumeInCylinder.cpp
+++ b/src/multicolvar/VolumeInCylinder.cpp
@@ -59,11 +59,11 @@ When INCYLINDER is used with the \ref DENSITY action the number of atoms in the
The input below can be use to calculate the average coordination numbers for those atoms that are within a cylindrical tube
of radius 1.5 nm that is centered on the position of atom 101 and that has its long axis parallel to the z-axis.
-\verbatim
+\plumedfile
c1: COORDINATIONNUMBER SPECIES=1-100 SWITCH={RATIONAL R_0=0.1}
d2: INCYLINDER ATOM=101 DATA=d1 DIRECTION=Z RADIUS={TANH R_0=1.5} SIGMA=0.1 LOWER=-0.1 UPPER=0.1 MEAN
PRINT ARG=d2.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/VolumeInSphere.cpp b/src/multicolvar/VolumeInSphere.cpp
index 632af88df..937e067dd 100644
--- a/src/multicolvar/VolumeInSphere.cpp
+++ b/src/multicolvar/VolumeInSphere.cpp
@@ -58,11 +58,11 @@ When INCYLINDER is used with the \ref DENSITY action the number of atoms in the
The input below can be use to calculate the average coordination numbers for those atoms that are within a sphere
of radius 1.5 nm that is centered on the position of atom 101.
-\verbatim
+\plumedfile
c1: COORDINATIONNUMBER SPECIES=1-100 SWITCH={RATIONAL R_0=0.1}
d2: INSPHERE ATOM=101 DATA=d1 RADIUS={TANH R_0=1.5} SIGMA=0.1 LOWER=-0.1 UPPER=0.1 MEAN
PRINT ARG=d2.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/VolumeTetrapore.cpp b/src/multicolvar/VolumeTetrapore.cpp
index 98fe915c3..c7dcd66d0 100644
--- a/src/multicolvar/VolumeTetrapore.cpp
+++ b/src/multicolvar/VolumeTetrapore.cpp
@@ -94,19 +94,19 @@ This is in fact the only point of difference between these two actions.
The following commands tell plumed to calculate the number of atom inside a tetrahedral cavity. The extent of the tetrahedral
cavity is calculated from the positions of atoms 1, 4, 5, and 11, The final value will be labeled cav.
-\verbatim
+\plumedfile
d1: DENSITY SPECIES=20-500
TETRAHEDRALPORE DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 LABEL=cav
-\endverbatim
+\endplumedfile
The following command tells plumed to calculate the coordination numbers (with other water molecules) for the water
molecules in the tetrahedral cavity described above. The average coordination number and the number of coordination
numbers more than 4 is then calculated. The values of these two quantities are given the labels cav.mean and cav.morethan
-\verbatim
+\plumedfile
d1: COORDINATIONNUMBER SPECIES=20-500
CAVITY DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 MEAN MORE_THAN={RATIONAL R_0=4} LABEL=cav
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/XAngle.cpp b/src/multicolvar/XAngle.cpp
index fbc2ab1d7..dd90c187f 100644
--- a/src/multicolvar/XAngle.cpp
+++ b/src/multicolvar/XAngle.cpp
@@ -41,10 +41,10 @@ Calculate the angles between the vector connecting two atoms and the x axis.
The following input tells plumed to calculate the angles between the x-axis and the vector connecting atom 3 to atom 5 and between the x-axis
and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
-\verbatim
+\plumedfile
XANLGES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
@@ -57,10 +57,10 @@ Calculate the angles between the vector connecting two atoms and the y axis.
The following input tells plumed to calculate the angles between the y-axis and the vector connecting atom 3 to atom 5 and between the y-axis
and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
-\verbatim
+\plumedfile
YANLGES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
@@ -73,10 +73,10 @@ Calculate the angles between the vector connecting two atoms and the z axis.
The following input tells plumed to calculate the angles between the z-axis and the vector connecting atom 3 to atom 5 and between the z-axis
and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
-\verbatim
+\plumedfile
ZANLGES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/XDistances.cpp b/src/multicolvar/XDistances.cpp
index 009b04de5..fe29a8b65 100644
--- a/src/multicolvar/XDistances.cpp
+++ b/src/multicolvar/XDistances.cpp
@@ -42,38 +42,38 @@ values such as the minimum, the number less than a certain quantity and so on.
The following input tells plumed to calculate the x-component of the vector connecting atom 3 to atom 5 and
the x-component of the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
printed
-\verbatim
+\plumedfile
XDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
The following input tells plumed to calculate the x-component of the vector connecting atom 3 to atom 5 and
the x-component of the vector connecting atom 1 to atom 2. The number of values that are
less than 0.1nm is then printed to a file.
-\verbatim
+\plumedfile
XDISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
PRINT ARG=d1.lt0.1
-\endverbatim
+\endplumedfile
(See also \ref PRINT \ref switchingfunction).
The following input tells plumed to calculate the x-components of all the distinct vectors that can be created
between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3).
The average of these quantities is then calculated.
-\verbatim
+\plumedfile
XDISTANCES GROUP=1-3 AVERAGE LABEL=d1
PRINT ARG=d1.average
-\endverbatim
+\endplumedfile
(See also \ref PRINT)
The following input tells plumed to calculate all the vectors connecting the the atoms in GROUPA to the atoms in GROUPB.
In other words the vector between atoms 1 and 2 and the vector between atoms 1 and 3. The number of values
more than 0.1 is then printed to a file.
-\verbatim
+\plumedfile
XDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
PRINT ARG=d1.gt0.1
-\endverbatim
+\endplumedfile
(See also \ref PRINT \ref switchingfunction)
*/
//+ENDPLUMEDOC
@@ -89,38 +89,38 @@ values such as the minimum, the number less than a certain quantity and so on.
The following input tells plumed to calculate the y-component of the vector connecting atom 3 to atom 5 and
the y-component of the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
printed
-\verbatim
+\plumedfile
YDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
The following input tells plumed to calculate the y-component of the vector connecting atom 3 to atom 5 and
the y-component of the vector connecting atom 1 to atom 2. The number of values that are
less than 0.1nm is then printed to a file.
-\verbatim
+\plumedfile
YDISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
PRINT ARG=d1.lt0.1
-\endverbatim
+\endplumedfile
(See also \ref PRINT \ref switchingfunction).
The following input tells plumed to calculate the y-components of all the distinct vectors that can be created
between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3).
The average of these quantities is then calculated.
-\verbatim
+\plumedfile
YDISTANCES GROUP=1-3 AVERAGE LABEL=d1
PRINT ARG=d1.average
-\endverbatim
+\endplumedfile
(See also \ref PRINT)
The following input tells plumed to calculate all the vectors connecting the the atoms in GROUPA to the atoms in GROUPB.
In other words the vector between atoms 1 and 2 and the vector between atoms 1 and 3. The number of values
more than 0.1 is then printed to a file.
-\verbatim
+\plumedfile
YDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
PRINT ARG=d1.gt0.1
-\endverbatim
+\endplumedfile
(See also \ref PRINT \ref switchingfunction)
*/
@@ -137,38 +137,38 @@ values such as the minimum, the number less than a certain quantity and so on.
The following input tells plumed to calculate the z-component of the vector connecting atom 3 to atom 5 and
the z-component of the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
printed
-\verbatim
+\plumedfile
ZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
The following input tells plumed to calculate the z-component of the vector connecting atom 3 to atom 5 and
the z-component of the vector connecting atom 1 to atom 2. The number of values that are
less than 0.1nm is then printed to a file.
-\verbatim
+\plumedfile
ZDISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
PRINT ARG=d1.lt0.1
-\endverbatim
+\endplumedfile
(See also \ref PRINT \ref switchingfunction).
The following input tells plumed to calculate the z-components of all the distinct vectors that can be created
between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3).
The average of these quantities is then calculated.
-\verbatim
+\plumedfile
ZDISTANCES GROUP=1-3 AVERAGE LABEL=d1
PRINT ARG=d1.average
-\endverbatim
+\endplumedfile
(See also \ref PRINT)
The following input tells plumed to calculate all the vectors connecting the the atoms in GROUPA to the atoms in GROUPB.
In other words the vector between atoms 1 and 2 and the vector between atoms 1 and 3. The number of values
more than 0.1 is then printed to a file.
-\verbatim
+\plumedfile
ZDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
PRINT ARG=d1.gt0.1
-\endverbatim
+\endplumedfile
(See also \ref PRINT \ref switchingfunction)
*/
diff --git a/src/multicolvar/XYDistances.cpp b/src/multicolvar/XYDistances.cpp
index 767c64a86..c0c8d4aa5 100644
--- a/src/multicolvar/XYDistances.cpp
+++ b/src/multicolvar/XYDistances.cpp
@@ -43,10 +43,10 @@ The following input tells plumed to calculate the projection of the length of th
to atom 5 projected in the xy-plane and the projection of the length of the vector
the vector connecting atom 1 to atom 2 in the xy-plane. The minimum of these two quantities is then
printed
-\verbatim
+\plumedfile
XYDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
@@ -64,10 +64,10 @@ The following input tells plumed to calculate the projection of the length of th
to atom 5 projected in the xz-plane and the projection of the length of the vector
the vector connecting atom 1 to atom 2 in the xz-plane. The minimum of these two quantities is then
printed
-\verbatim
+\plumedfile
XZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
@@ -85,10 +85,10 @@ The following input tells plumed to calculate the projection of the length of th
to atom 5 in the yz-plane and the projection of the length of the vector
the vector connecting atom 1 to atom 2 in the yz-plane. The minimum of these two quantities is then
printed
-\verbatim
+\plumedfile
YZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
diff --git a/src/multicolvar/XYTorsion.cpp b/src/multicolvar/XYTorsion.cpp
index fd512799a..4e0804a50 100644
--- a/src/multicolvar/XYTorsion.cpp
+++ b/src/multicolvar/XYTorsion.cpp
@@ -41,10 +41,10 @@ Calculate the torsional angle around the x axis from the positive y direction.
The following input tells plumed to calculate the angle around the x direction between the positive y-axis and the vector connecting atom 3 to atom 5 and
the angle around the x direction between the positive y axis and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
-\verbatim
+\plumedfile
XYTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
@@ -57,10 +57,10 @@ Calculate the torsional angle around the x axis from the positive z direction.
The following input tells plumed to calculate the angle around the x direction between the positive z-axis and the vector connecting atom 3 to atom 5 and
the angle around the x direction between the positive z direction and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
-\verbatim
+\plumedfile
XZTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
@@ -73,10 +73,10 @@ Calculate the torsional angle around the y axis from the positive x direction.
The following input tells plumed to calculate the angle around the y direction between the positive x-direction and the vector connecting atom 3 to atom 5 and
the angle around the y direction between the positive x axis and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
-\verbatim
+\plumedfile
YXTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
@@ -89,10 +89,10 @@ Calculate the torsional angle around the y axis from the positive z direction.
The following input tells plumed to calculate the angle around the y direction between the positive z-direction and the vector connecting atom 3 to atom 5 and
the angle around the y direction between the positive z direction and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
-\verbatim
+\plumedfile
YZTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
@@ -105,10 +105,10 @@ Calculate the torsional angle around the z axis from the positive x direction.
The following input tells plumed to calculate the angle around the z direction between the positive x-direction and the vector connecting atom 3 to atom 5 and
the angle around the z direction between the positive x-direction and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
-\verbatim
+\plumedfile
ZXTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
@@ -121,10 +121,10 @@ Calculate the torsional angle around the z axis from the positive y direction.
The following input tells plumed to calculate the angle around the z direction between the positive y-axis and the vector connecting atom 3 to atom 5 and
the angle around the z direction between the positive y axis and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
-\verbatim
+\plumedfile
ZYTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
diff --git a/src/secondarystructure/AlphaRMSD.cpp b/src/secondarystructure/AlphaRMSD.cpp
index 6c9b49083..ecf10eacb 100644
--- a/src/secondarystructure/AlphaRMSD.cpp
+++ b/src/secondarystructure/AlphaRMSD.cpp
@@ -68,11 +68,10 @@ anthing other than TYPE=DRMSD. For more details as to how to do this see \ref W
The following input calculates the number of six residue segments of
protein that are in an alpha helical configuration.
-\verbatim
+\plumedfile
MOLINFO STRUCTURE=helix.pdb
ALPHARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=a
-\endverbatim
-(see also \ref MOLINFO)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/secondarystructure/AntibetaRMSD.cpp b/src/secondarystructure/AntibetaRMSD.cpp
index 6e60d5445..637e4c0b3 100644
--- a/src/secondarystructure/AntibetaRMSD.cpp
+++ b/src/secondarystructure/AntibetaRMSD.cpp
@@ -70,11 +70,10 @@ anthing other than TYPE=DRMSD. For more details as to how to do this see \ref W
The following input calculates the number of six residue segments of
protein that are in an antiparallel beta sheet configuration.
-\verbatim
+\plumedfile
MOLINFO STRUCTURE=helix.pdb
ANTIBETARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=a
-\endverbatim
-(see also \ref MOLINFO)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/secondarystructure/ParabetaRMSD.cpp b/src/secondarystructure/ParabetaRMSD.cpp
index fe8740864..1a67ec8af 100644
--- a/src/secondarystructure/ParabetaRMSD.cpp
+++ b/src/secondarystructure/ParabetaRMSD.cpp
@@ -70,11 +70,10 @@ anthing other than TYPE=DRMSD. For more details as to how to do this see \ref W
The following input calculates the number of six residue segments of
protein that are in an parallel beta sheet configuration.
-\verbatim
+\plumedfile
MOLINFO STRUCTURE=helix.pdb
PARABETARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=a
-\endverbatim
-(see also \ref MOLINFO)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/setup/Load.cpp b/src/setup/Load.cpp
index 93f9d39b8..4002ed0f0 100644
--- a/src/setup/Load.cpp
+++ b/src/setup/Load.cpp
@@ -43,9 +43,9 @@ If you have a shared object named extensions.so and want to
use the functionalities implemented in it within PLUMED you can
load it with the following syntax
-\verbatim
+\plumedfile
LOAD FILE=extensions.so
-\endverbatim
+\endplumedfile
As a more practical example, imagine that you want to make a
small change to one collective variable that is already implemented
@@ -61,7 +61,7 @@ with different names. Then you can compile it into a shared object using
This will generate a file `Distance2.so` (or `Distance2.dylib` on a mac)
that can be loaded.
Now you can use your new implementation with the following input
-\verbatim
+\plumedfile
# load the new library
LOAD FILE=Distance2.so
# compute standard distance
@@ -70,11 +70,11 @@ d: DISTANCE ATOMS=1,10
d2: DISTANCE2 ATOMS=1,10
# print them on a file
PRINT ARG=d,d2 FILE=compare-them
-\endverbatim
+\endplumedfile
You can even skip the initial step and directly feed PLUMED
with the `Distance2.cpp` file: it will be compiled on the fly.
-\verbatim
+\plumedfile
# load the new definition
# this is a cpp file so it will be compiled
LOAD FILE=Distance2.cpp
@@ -84,7 +84,7 @@ d: DISTANCE ATOMS=1,10
d2: DISTANCE2 ATOMS=1,10
# print them on a file
PRINT ARG=d,d2 FILE=compare-them
-\endverbatim
+\endplumedfile
This will allow to make quick tests while developing your own
variables. Of course, after your implementation is ready you might
diff --git a/src/setup/MolInfo.cpp b/src/setup/MolInfo.cpp
index 03a0012f9..24f2cb689 100644
--- a/src/setup/MolInfo.cpp
+++ b/src/setup/MolInfo.cpp
@@ -111,23 +111,21 @@ interpret terminal residue 1.
In the following example the MOLINFO command is used to provide the information on which atoms
are in the backbone of a protein to the ALPHARMSD CV.
-\verbatim
+\plumedfile
MOLINFO STRUCTURE=reference.pdb
ALPHARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=a
-\endverbatim
-(see also \ref ALPHARMSD)
+\endplumedfile
The following example prints the distance corresponding to the hydrogen bonds
in a GC Watson-Crick pair.
-\verbatim
+\plumedfile
MOLINFO STRUCTURE=reference.pdb
hb1: DISTANCE ATOMS=@N2-1,@O2-14
hb2: DISTANCE ATOMS=@N1-1,@N3-14
hb3: DISTANCE ATOMS=@O6-1,@N4-14
PRINT ARG=hb1,hb2,hb3
-\endverbatim
-(see also \ref DISTANCE).
+\endplumedfile
*/
diff --git a/src/setup/Restart.cpp b/src/setup/Restart.cpp
index ffa4f46b1..4cfb03ef0 100644
--- a/src/setup/Restart.cpp
+++ b/src/setup/Restart.cpp
@@ -51,31 +51,28 @@ and \ref PBMETAD and on some analysis action.
\par Examples
Using the following input:
-\verbatim
+\plumedfile
d: DISTANCE ATOMS=1,2
PRINT ARG=d FILE=out
-\endverbatim
-(See also \ref DISTANCE and \ref PRINT).
+\endplumedfile
a new 'out' file will be created. If an old one is on the way, it will be automatically backed up.
On the other hand, using the following input:
-\verbatim
+\plumedfile
RESTART
d: DISTANCE ATOMS=1,2
PRINT ARG=d FILE=out
-\endverbatim
+\endplumedfile
the file 'out' will be appended.
-(See also \ref DISTANCE and \ref PRINT).
In the following case, file out1 will be backed up and file out2 will be concatenated
-\verbatim
+\plumedfile
RESTART
d1: DISTANCE ATOMS=1,2
d2: DISTANCE ATOMS=1,2
PRINT ARG=d1 FILE=out1 RESTART=NO
PRINT ARG=d2 FILE=out2
-\endverbatim
-(See also \ref DISTANCE and \ref PRINT).
+\endplumedfile
diff --git a/src/setup/Units.cpp b/src/setup/Units.cpp
index 1b4225d24..617e8c0a6 100644
--- a/src/setup/Units.cpp
+++ b/src/setup/Units.cpp
@@ -44,16 +44,15 @@ the units. For example, trajectories written in .gro format (with \ref DUMPATOMS
are going to be always in nm.
\par Examples
-\verbatim
+\plumedfile
# this is using nm - kj/mol - fs
UNITS LENGTH=nm TIME=fs
-\endverbatim
+\endplumedfile
If a number, x, is found, the new unit is equal to x (default units)
-\verbatim
+\plumedfile
# this is using nm - kj/mol - fs
UNITS LENGTH=nm TIME=0.001
-\endverbatim
-
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/vatom/COM.cpp b/src/vatom/COM.cpp
index 8eb60b64d..d0cfd0b1f 100644
--- a/src/vatom/COM.cpp
+++ b/src/vatom/COM.cpp
@@ -54,13 +54,12 @@ periodic image.
The following input instructs plumed to print the distance between the
center of mass for atoms 1,2,3,4,5,6,7 and that for atoms 15,20:
-\verbatim
+\plumedfile
c1: COM ATOMS=1-7
c2: COM ATOMS=15,20
d1: DISTANCE ATOMS=c1,c2
PRINT ARG=d1
-\endverbatim
-(See also \ref DISTANCE and \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/vatom/Center.cpp b/src/vatom/Center.cpp
index 7e4cdd440..64eea7d74 100644
--- a/src/vatom/Center.cpp
+++ b/src/vatom/Center.cpp
@@ -54,7 +54,7 @@ periodic image.
\par Examples
-\verbatim
+\plumedfile
# a point which is on the line connecting atoms 1 and 10, so that its distance
# from 10 is twice its distance from 1:
c1: CENTER ATOMS=1,1,10
@@ -67,8 +67,7 @@ c2: CENTER ATOMS=2,3,4,5 MASS
d1: DISTANCE ATOMS=c1,c2
PRINT ARG=d1
-\endverbatim
-(See also \ref DISTANCE, \ref COM and \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/vatom/FixedAtom.cpp b/src/vatom/FixedAtom.cpp
index ccf7eb52c..3baf40379 100644
--- a/src/vatom/FixedAtom.cpp
+++ b/src/vatom/FixedAtom.cpp
@@ -51,24 +51,22 @@ then it is safe to add further fixed atoms without breaking translational invari
The following input instructs plumed to compute the angle between
distance of atoms 15 and 20 and the z axis and keeping it close to zero.
-\verbatim
+\plumedfile
a: FIXEDATOM AT=0,0,0
b: FIXEDATOM AT=0,0,1
an: ANGLE ATOMS=a,b,15,20
RESTRAINT ARG=an AT=0.0 KAPPA=100.0
-\endverbatim
-(See also \ref ANGLE and \ref RESTRAINT).
+\endplumedfile
The following input instructs plumed to align a protein on a template
and then compute the distance of one of its atom from the point
(10,20,30).
-\verbatim
+\plumedfile
FIT_TO_TEMPLATE STRIDE=1 REFERENCE=ref.pdb TYPE=SIMPLE
a: FIXEDATOM AT=10,20,30
d: DISTANCE ARG=a,20
PRINT ARG=d FILE=colvar
-\endverbatim
-(See also \ref FIT_TO_TEMPLATE and \ref DISTANCE).
+\endplumedfile
*/
diff --git a/src/vatom/Ghost.cpp b/src/vatom/Ghost.cpp
index b2c783717..7c57cee4f 100644
--- a/src/vatom/Ghost.cpp
+++ b/src/vatom/Ghost.cpp
@@ -39,13 +39,12 @@ an atom list through the the label for the GHOST action that creates it.
\par Examples
The following input instructs plumed to print the distance between the
ghost atom and the center of mass for atoms 15,20:
-\verbatim
+\plumedfile
c1: GHOST ATOMS=1,5,10 COORDINATES=10.0,10.0,10.0
c2: COM ATOMS=15,20
d1: DISTANCE ATOMS=c1,c2
PRINT ARG=d1
-\endverbatim
-(See also \ref DISTANCE and \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/user-doc/Analysis.txt b/user-doc/Analysis.txt
index a5a0e5572..ef3a00589 100644
--- a/user-doc/Analysis.txt
+++ b/user-doc/Analysis.txt
@@ -45,11 +45,11 @@ As an example the following set of commands instructs PLUMED to calculate the di
atoms 1 and 2 for every 5th frame in the trajectory and to accumulate a histogram from this data
which will be output every 100 steps (i.e. when 20 distances have been added to the histogram).
-\verbatim
+\plumedfile
x: DISTANCE ATOMS=1,2
h: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1 STRIDE=5
DUMPGRID GRID=h FILE=histo STRIDE=100
-\endverbatim
+\endplumedfile
It is important to note when using commands such as the above the first frame in the trajectory is assumed
to be the initial configuration that was input to the MD code. It is thus ignored. Furthermore, if you are
@@ -57,11 +57,11 @@ running with driver and you would like to analyse the whole trajectory (without
and then print the result you simply call \ref DUMPGRID (or any of the commands above) without a STRIDE
keyword as shown in the example below.
-\verbatim
+\plumedfile
x: DISTANCE ATOMS=1,2
h: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1 STRIDE=5
DUMPGRID GRID=h FILE=histo
-\endverbatim
+\endplumedfile
Please note that even with this calculation the first frame in the trajectory is ignored when computing the
histogram.
diff --git a/user-doc/Colvar.txt b/user-doc/Colvar.txt
index 7c6557796..e3e20d2a1 100644
--- a/user-doc/Colvar.txt
+++ b/user-doc/Colvar.txt
@@ -92,9 +92,9 @@ Oftentimes the simplest way to specify the atoms involved is to use multiple ins
i.e. ATOMS1, ATOMS2, ATOMS3,... Separate instances of the quantity specified by NAME are then calculated for
each of the sets of atoms. For example if the command issued contains the following:
-\verbatim
+\plumedfile
DISTANCES ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6
-\endverbatim
+\endplumedfile
The distances between atoms 1 and 2, atoms 3 and 4, and atoms 5 and 6 are calculated. Obviously, generating
this sort of input is rather tedious so short cuts are also available many of the collective variables.
@@ -163,11 +163,11 @@ prevent the cluster subliming. Alternatively, you may wish to insist that a par
coordination number greater than 2. You can add these sorts of restraints by employing the following biases, which all act
on the set of collective variable values calculated by a multicolvar. So for example the following set of commands:
-\verbatim
+\plumedfile
COM ATOMS=1-20 LABEL=c1
DISTANCES GROUPA=c1 GROUPB=1-20 LABEL=d1
UWALLS DATA=d1 AT=2.5 KAPPA=0.2 LABEL=sr
-\endverbatim
+\endplumedfile
creates the aforementioned set of restraints on the distances between the 20 atoms in a cluster and the center of mass of the cluster.
diff --git a/user-doc/Files.txt b/user-doc/Files.txt
index f360af5d2..2ed8f21ee 100644
--- a/user-doc/Files.txt
+++ b/user-doc/Files.txt
@@ -34,11 +34,10 @@ since your disk might fill up quickly with this setting.
When running with multiple replicas (e.g., with GROMACS, -multi option) PLUMED adds the replica index as a suffix to
all the files. The following command
will thus print files named COLVAR.0, COLVAR.1, etc for the different replicas.
-\verbatim
+\plumedfile
d: DISTANCE ATOMS=1,2
PRINT ARG=d FILE=COLVAR
-\endverbatim
-(see also \ref DISTANCE and \ref PRINT).
+\endplumedfile
When reading a file, PLUMED will try to add the suffix. If the file is not found, it will fall back to
the name without suffix. The most important case is the reading of the plumed input file.
@@ -51,12 +50,11 @@ extension. Before PLUMED 2.2, the only recognized suffix was ".gz". Since 2.2, a
less or equal to five letters is recognized.
This means that using in a multireplica context an input such as
-\verbatim
+\plumedfile
d: DISTANCE ATOMS=1,2
PRINT ARG=d FILE=COLVAR.gz
METAD ARG=d FILE=test.HILLS SIGMA=0.1 HEIGHT=0.1
-\endverbatim
-(see \ref DISTANCE, \ref PRINT, and \ref METAD)
+\endplumedfile
PLUMED will write files named COLVAR.0.gz, COLVAR.1.gz, test.0.HILLS, test.1.HILLS, etc
etc. This is useful since the preserved extension makes it easy
to process the files later.
diff --git a/user-doc/Functions.txt b/user-doc/Functions.txt
index 8bf37c42d..53de40f36 100644
--- a/user-doc/Functions.txt
+++ b/user-doc/Functions.txt
@@ -23,7 +23,7 @@ is the smallest value and `B` is the largest value. In case the answer is that t
values at the discontinuity are not always the same, then you cannot construct a variable that
can be biased with PLUMED. Consider the following examples:
-\verbatim
+\plumedfile
t: TORSION ATOMS=1,2,3,4
# When atoms are moved, t could jump suddenly from -pi to +pi
@@ -39,7 +39,7 @@ d: DISTANCE ATOMS=1,10 COMPONENTS
# make a new variable equal to d.z but with the correct periodicity
dz: COMBINE ARG=d.z PERIODIC=-10,10
# here we assumed the system is in a orthorhombic box with z side = 20
-\endverbatim
+\endplumedfile
@FUNCTION@
diff --git a/user-doc/Group.txt b/user-doc/Group.txt
index 6365d9f7d..6edc0225b 100644
--- a/user-doc/Group.txt
+++ b/user-doc/Group.txt
@@ -56,12 +56,12 @@ See http://en.wikipedia.org/wiki/Ramachandran_plot
The following example shows how to use \ref MOLINFO with \ref TORSION to calculate the torsion angles phi and psi for the first and fourth residue
of the protein:
-\verbatim
+\plumedfile
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
t1: TORSION ATOMS=@phi-3
t2: TORSION ATOMS=@psi-4
PRINT ARG=t1,t2 FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
\subsection pbc Broken Molecules and PBC
@@ -76,11 +76,11 @@ using the ALIGN_ATOMS keyword. In PLUMED 2 the same effect can be achieved usin
The following input computes the end-to-end distance for a polymer of 100 atoms and keeps it at a value around 5.
-\verbatim
+\plumedfile
WHOLEMOLECULES ENTITY0=1-100
e2e: DISTANCE ATOMS=1,100 NOPBC
RESTRAINT ARG=e2e KAPPA=1 AT=5
-\endverbatim
+\endplumedfile
Notice that NOPBC is used to be sure in \ref DISTANCE that if the end-to-end distance is larger than half the simulation box the distance
is compute properly. Also notice that, since many MD codes break molecules across cell boundary, it might be necessary to use the
@@ -90,12 +90,12 @@ Notice that most expressions are invariant with respect to a change in the order
but some of them depend on that order. E.g., with \ref WHOLEMOLECULES it could be useful to
specify atom lists in a reversed order.
-\verbatim
+\plumedfile
# to see the effect, one could dump the atoms as they were before molecule reconstruction:
# DUMPATOMS FILE=dump-broken.xyz ATOMS=1-20
WHOLEMOLECULES STRIDE=1 ENTITY0=1-20
DUMPATOMS FILE=dump.xyz ATOMS=1-20
-\endverbatim
+\endplumedfile
Notice that there are other ways to manipulate the coordinates stored within PLUMED:
- Using the \subpage FIT_TO_TEMPLATE they can be aligned to a template structure.
@@ -116,10 +116,10 @@ To specify to a colvar that you want to use the position of a virtual atom to ca
in your system you simply use the label for your virtual atom in place of the usual numerical index. Virtual
atoms and normal atoms can be mixed together in the input to colvars as shown below:
-\verbatim
+\plumedfile
COM ATOMS=1,10 LABEL=com1
DISTANCE ATOMS=11,com1
-\endverbatim
+\endplumedfile
If you don't want to calculate CVs from the virtual atom. That is to say you just want to monitor the position of a virtual atom
(or any set of atoms) over the course of your trajectory you can do this using \ref DUMPATOMS.
diff --git a/user-doc/Misc.txt b/user-doc/Misc.txt
index 284a2a6e9..4fceb133d 100644
--- a/user-doc/Misc.txt
+++ b/user-doc/Misc.txt
@@ -19,12 +19,12 @@ particular simulation you might find it useful to put comments in your input fil
comments can be added using a # sign. On any given line everything after the # sign is ignored so
erm... yes add lines of comments or trailing comments to your hearts content as shown below (using Shakespeare is optional):
-\verbatim
+\plumedfile
# This is the distance between two atoms:
DISTANCE ATOM=1,2 LABEL=d1
UPPER_WALLS ARG=d1 AT=3.0 KAPPA=3.0 LABEL=Snout # In this same interlude it doth befall.
# That I, one Snout by name, present a wall.
-\endverbatim
+\endplumedfile
(see \ref DISTANCE and \ref UPPER_WALLS)
An alternative to including comments in this way is to use line starting ENDPLUMED. Everything in the PLUMED input after this
@@ -37,14 +37,14 @@ We at PLUMED are aware of this fact and thus have provided a way of doing line c
easier - aren't we kind? Well no not really, we have to use this code too. Anyway, you can do continuations by using the "..." syntax
as this makes this:
-\verbatim
+\plumedfile
DISTANCES ATOMS1=1,300 ATOMS2=1,400 ATOMS3=1,500 LABEL=dist
-\endverbatim
+\endplumedfile
(see \ref DISTANCES)
equivalent to this:
-\verbatim
+\plumedfile
DISTANCES ...
LABEL=dist
# we can also insert comments here
@@ -54,11 +54,11 @@ DISTANCES ...
#empty lines are also allowed
... DISTANCES
-\endverbatim
+\endplumedfile
Notice that the closing `...` is followed by the word `DISTANCES`. This is optional, but might be
useful to find more easily which is the matching start of the statement. The following is equally correct
-\verbatim
+\plumedfile
DISTANCES ...
LABEL=dist
# we can also insert comments here
@@ -68,12 +68,12 @@ DISTANCES ...
#empty lines are also allowed
...
-\endverbatim
+\endplumedfile
Notice that PLUMED makes a check that the word following the closing `...` is actually identical to
the first word in the line with the first `...`. If not, it will throw an error.
Also notice that you might put more than one word in the first line. E.g.
-\verbatim
+\plumedfile
DISTANCES LABEL=dist ...
# we can also insert comments here
ATOMS1=1,300
@@ -81,9 +81,9 @@ DISTANCES LABEL=dist ...
ATOMS2=1,400 ATOMS3=1,500
#empty lines are also allowed
...
-\endverbatim
+\endplumedfile
or, equivalently,
-\verbatim
+\plumedfile
dist: DISTANCES ...
# we can also insert comments here
ATOMS1=1,300
@@ -91,7 +91,7 @@ dist: DISTANCES ...
ATOMS2=1,400 ATOMS3=1,500
#empty lines are also allowed
...
-\endverbatim
+\endplumedfile
\page VimSyntax Using VIM syntax file
@@ -171,11 +171,11 @@ Add to your `.vimrc` file the following commands
:set modelines=5
\endverbatim
Then, at the beginning of your PLUMED input file, put the following comment:
-\verbatim
+\plumedfile
# vim:ft=plumed
d: DISTANCE ATOMS=1,2
RESTRAINT ARG=d AT=0.0 KAPPA=1.0
-\endverbatim
+\endplumedfile
Now, every time you open this file, you will see it highlighted.
\par Syntax highlighting
@@ -220,27 +220,27 @@ Folded lines can be expanded with `zo` and folded with `zc`. Look at VIM documen
learn more.
In case you want to use this feature, we suggest you to put both label
and action type on the first line of multi-line statements. E.g.
-\verbatim
+\plumedfile
m: METAD ...
ARG=d
HEIGHT=1.0
SIGMA=0.5
PACE=100
...
-\endverbatim
+\endplumedfile
will be folded to
\verbatim
+-- 6 lines: m: METAD ...------------------------------------------------------
\endverbatim
and
-\verbatim
+\plumedfile
METAD LABEL=m ...
ARG=d
HEIGHT=1.0
SIGMA=0.5
PACE=100
...
-\endverbatim
+\endplumedfile
will be folded to
\verbatim
+-- 6 lines: METAD LABEL=m ...-------------------------------------------------
@@ -293,9 +293,9 @@ Try to do the following. Enable plumed syntax:
:set ft=plumed
\endverbatim
Then add the following line
-\verbatim
+\plumedfile
DISTANCE
-\endverbatim
+\endplumedfile
Now, in normal mode, go with the cursor on the `DISTANCE` line and type
\verbatim
:PHelp
@@ -365,38 +365,37 @@ vimrc file.
If, for some reason, you want to spread your PLUMED input over a number of files you can use \subpage INCLUDE as shown below:
-\verbatim
+\plumedfile
INCLUDE FILE=filename
-\endverbatim
+\endplumedfile
So, for example, a single "plumed.dat" file:
-\verbatim
+\plumedfile
DISTANCE ATOMS=0,1 LABEL=dist
RESTRAINT ARG=dist
-\endverbatim
-(see \ref DISTANCE and \ref RESTRAINT)
+\endplumedfile
could be split up into two files as shown below:
-\verbatim
+\plumedfile
DISTANCE ATOMS=0,1 LABEL=dist
INCLUDE FILE=toBeIncluded.dat
-\endverbatim
+\endplumedfile
plus a "toBeIncluded.dat" file
-\verbatim
+\plumedfile
RESTRAINT ARG=dist
-\endverbatim
+\endplumedfile
However, when you do this it is important to recognise that \ref INCLUDE is a real directive that is only resolved
after all the \ref comments have been stripped and the \ref ContinuationLines have been unrolled. This means it
is not possible to do things like:
-\verbatim
+\plumedfile
# this is wrong:
DISTANCE INCLUDE FILE=options.dat
RESTRAINT ARG=dist
-\endverbatim
+\endplumedfile
\page load Loading shared libraries
@@ -405,9 +404,9 @@ PLUMED libraries. Alternatively, if you want to keep your code independent from
so you can release it independely - we won't be offended), then you can create your own dynamic library. To use this
in conjuction with PLUMED you can then load it at runtime by using the \subpage LOAD keyword as shown below:
-\verbatim
+\plumedfile
LOAD FILE=library.so
-\endverbatim
+\endplumedfile
N.B. If your system uses a different suffix for dynamic libraries (e.g. macs use .dylib) then PLUMED will try to
automatically adjust the suffix accordingly.
diff --git a/user-doc/Performances.txt b/user-doc/Performances.txt
index 57bc2c66a..00fc973ac 100644
--- a/user-doc/Performances.txt
+++ b/user-doc/Performances.txt
@@ -105,12 +105,12 @@ a factor equal to STRIDE.
This technique can allow your simulation to run faster if you need
the apply a bias potential on some very expensive collective variable.
Consider the following input:
-\verbatim
+\plumedfile
c1: COM ATOMS=1-1000
c2: COM ATOMS=1001-2000
d: DISTANCE ATOMS=c1,c2
METAD ARG=d HEIGHT=1 SIGMA=0.1 BIASFACTOR=5 PACE=500
-\endverbatim
+\endplumedfile
This performs a \ref METAD simulation biasing the distance between two
centers of mass. Since computing these centers requires a lot of atoms
to be imported from the MD engine, it could slow down significantly the
@@ -118,12 +118,12 @@ simulation. Notice that whereas the bias is changed every PACE=500 steps,
it is applied every STRIDE step, where STRIDE=1 by default.
The following input could lead to a significantly faster simulation at the price
of a negligible systematic error
-\verbatim
+\plumedfile
c1: COM ATOMS=1-1000
c2: COM ATOMS=1001-2000
d: DISTANCE ATOMS=c1,c2
METAD ARG=d HEIGHT=1 SIGMA=0.1 BIASFACTOR=5 PACE=500 STRIDE=2
-\endverbatim
+\endplumedfile
Similarly, the STRIDE keyword can be used with other biases (e.g. \ref RESTRAINT).
The technique is discussed in details here \cite Ferrarotti2015.
@@ -133,9 +133,9 @@ See also \subpage EFFECTIVE_ENERGY_DRIFT.
Whenever you have a multicolvar action such as:
-\verbatim
+\plumedfile
COORDINATIONNUMBER SPECIES=1-100 SWITCH={RATIONAL R_0=1. D_MAX=3.0} MORE_THAN={RATIONAL R_0=6.0 NN=6 MM=12 D_0=0}
-\endverbatim
+\endplumedfile
You will get a collosal speedup by specifying the D_MAX keyword in all switching functions that act on distances.
D_MAX tells PLUMED that the switching function is strictly zero if the distance is greater than this value. As a result
diff --git a/user-doc/Regex.txt b/user-doc/Regex.txt
index b24524a0f..93561f632 100644
--- a/user-doc/Regex.txt
+++ b/user-doc/Regex.txt
@@ -14,14 +14,14 @@ Regular expressions are enclosed in round braces and must not contain spaces (th
names have no spaces indeed, so why use them?).
As an example then command
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=1,2 COMPONENTS
PRINT ARG=(d1\.[xy]) STRIDE=100 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
will cause both the d1.x and d1.y components of the DISTANCE action to be printed out in the order that they are created by plumed.
The "." character must be escaped in order to interpret it as a literal ".". An unescaped dot is a wildcard which is matched by any character,
So as an example
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=1,2 COMPONENTS
dxy: DISTANCE ATOMS=1,3
@@ -30,26 +30,26 @@ PRINT ARG=(d1.[xy]) STRIDE=100 FILE=colvar FMT=%8.4f
# while this will match d1.x,d1.y only
PRINT ARG=(d1\.[xy]) STRIDE=100 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
You can include more than one regular expression by using comma separated regular expressions
-\verbatim
+\plumedfile
t1: TORSION ATOMS=5,7,9,15
t2: TORSION ATOMS=7,9,15,17
d1: DISTANCE ATOMS=7,17 COMPONENTS
PRINT ARG=(d1\.[xy]),(t[0-9]) STRIDE=100 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
(this selects t1,t2,d1.x and d2.x) Be aware that if you have overlapping selection they will be duplicated so it
a better alternative is to use the "or" operator "|".
-\verbatim
+\plumedfile
t1: TORSION ATOMS=5,7,9,15
t2: TORSION ATOMS=7,9,15,17
d1: DISTANCE ATOMS=7,17 COMPONENTS
PRINT ARG=(d1\.[xy]|t[0-9]) STRIDE=100 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
this selects the same set of arguments as the previous example.
diff --git a/user-doc/Syntax.txt b/user-doc/Syntax.txt
index 47c73c1f2..277d339e9 100644
--- a/user-doc/Syntax.txt
+++ b/user-doc/Syntax.txt
@@ -25,18 +25,16 @@ is enclosed in curly braces (e.g. ATOMS={1 2 3 4}). Please note that you can sp
The most important of these keywords is the label keyword as it is only by using these labels that we can pass data
from one action to another. As an example if you do:
-\verbatim
+\plumedfile
DISTANCE ATOMS=1,2
-\endverbatim
-(see \ref DISTANCE)
+\endplumedfile
Then PLUMED will do nothing other than read in your input file. In contrast if you do:
-\verbatim
+\plumedfile
DISTANCE ATOMS=1,2 LABEL=d1
PRINT ARG=d1 FILE=colvar STRIDE=10
-\endverbatim
-(see \ref PRINT)
+\endplumedfile
then PLUMED will print out the value of the distance between atoms 1 and 2 every 10 steps to the file colvar as you have told
PLUMED to take the value calculated by the action d1 and to print it. You can use any character string to label your actions
@@ -46,10 +44,10 @@ code-generated groups of atoms and to give labels to any Actions for which the u
Notice that if a word followed by a column is added at the beginning of the line (e.g. pippo:), PLUMED automatically
removes it and adds an equivalent label (LABEL=pippo).
Thus, a completely equivalent result can be obtained with the following shortcut:
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=1,2
PRINT ARG=d1 FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
Also notice that all the actions can be labeled, and that many actions besides normal collective variables can define
one or more value, which can be then referred using the corresponding label.
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