diff --git a/developer-doc/AddingAnAnalysis.txt b/developer-doc/AddingAnAnalysis.txt
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+++ b/developer-doc/AddingAnAnalysis.txt
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+// This document is formatted for Doxygen
+/**
+
+\page AddingAnAnalysis Implementing analysis methods in PLUMED
+
+Information on implementing methods that perform analysis on stored trajectory information eg dimensionality reduction
+
+Implementing methods for analysing trajectory data is more complex than implementing collective variables.
+Consequently it is difficult to write a step by step guide like those we have written on implementing \ref AddingAColvar "colvars" or
+\ref AddingAFunction "functions". Hence, this document tries to explain the things that we have considered and the way these
+have been incorporated into the PLMD::analysis::AnalysisBase and PLMD::analysis::AnalysisWithDataCollection abstract base classes.
+Hopefully this will provide some insight into our rationale in writing these parts of the code and will help you to understand how
+any new analysis method can be implemented in the PLUMED code in a way that exploits those features that are already there.
+
+\section overview An overview of analysis methods in PLUMED
+
+There are two distinct ways in which one may wish to perform some form of analysis on a molecular dynamics trajectory. In the first method some quantity
+is calculated for each of the atoms in the trajectory in each of the frames and this is then averaged over the whole trajectory. Velocity
+autocorrelation functions or mean squared displacements are examples of forms of analysis of this type. The methods implemented in PLMD::analysis are
+not of this type. These methods are designed to collect set of snapshots of the trajectory and to perform some analysis of these snapshots.
+These trajectory snapshots might be the values of a particular set of collective variables for each of the frames, they might be the
+instantaneous positions of the atoms in each frame or they might be some combination of the above. The assumption then when running one of these
+analysis methods is that a representation (or snapshot) will be collected intermittently from the trajectory and then once a sufficiently large
+ collection of these snapshots are collected they will be analysed.
+
+\section antraj Analysis on the fly
+
+It is important to remember that PLUMED is primarily a code for performing biased molecular dynamics. The code's original purpose was
+to be a plugin that could be easily added to a number of different molecular dynamics engines that allowed additional forces to be
+incorporated when integrating the equations of motion. The command line tools that allows one to analyse trajectories during post
+processing were added later as an afterthought. This consideration is particularly important when considering analysis algorithms
+in this code because most analysis codes that are used in the community read in the trajectory and to do all their calculations
+during post processing. The analysis functions that have been implemented in PLUMED can be used to post-process trajectories - you
+simply make use of the command line tool driver - however, they can also be used to analyse trajectories on the fly. We believe this
+is useful for a number of reasons:
+
+- Computers are becoming more powerful so it is possible to run simulations for much longer. At the same time, however, hard drives
+space is at a premium and it is thus difficult to store these large trajectories for post-processing. If trajectories can be analysed
+on the fly this presents less of a problem.
+- A number of free energy methods (e.g. Gaussian mixture umbrella sampling, adaptive umbrella sampling and reconnaissance metadynamics)
+work by performing a sophistacated analysis of the trajectory and then using the result from this analysis to design a bias for the
+dynamics.
+- Analysis methods implemented in PLUMED can take advantage of the many different collective variables that we have implemented in
+this code and are thus extremely flexible implementations of these techniques.
+- Analysis methods implemented in PLUMED make use of the PLUMED input syntax, which hopefully allows users already familiar with
+PLUMED to get to grips with using these tools more rapidly.
+
+\section genphil General Phillosopy
+
+The aim in the PLMD::analysis and PLMD::dimred modules is to write code that is very flexible and that allows the user a great deal of
+flexibility in the input. For example we would like to be able to write the code so that a user can collect data from the trajectory and
+then at analysis time they can:
+
+- Select a subset of landmark points from the stored data
+- Generate projections of these landmark points using sketch-map
+- Project the remaining non-landmark points using the sketch-map projection generated and construct a histogram as a function of the sketch-map coordinates.
+
+Furthermore, we would like to be able to do all the above with a minimum of syntax for the user and with a minimum amount of code to maintain.
+This is why the analysis class is structured in the way it is. The general idea is that one PLMD::analysis::AnalysisWithDataCollection object
+collects the trajectory data as the simulation progresses (for the example above this would be an object of type PLMD::analysis::EuclideanDissimilarityMatrix).
+Then when it is time to analyse a chain of analysis objects are run on the data collected by the PLMD::analysis::AnalysisWithDataCollection.
+There are thus two types of analysis actions:
+
+- Those that inherit from PLMD::analysis::AnalysisWithDataCollection - these can collect data from a trajectory
+- Those that inherit from PLMD::analysis::AnalysisBase - these cannot collect data from a trajectory. They get their input from another PLMD::analysis::AnalysisBase Action
+
+If you look at the code most of the routines in the PLMD::analysis and PLMD::dimred modules do not inherit from PLMD::analysis::AnalysisWithDataCollection.
+In fact the only ones where this is an option that users really see in the manual are PLMD::analysis::Histogram and PLMD::analysis::EuclideanDissimilarityMatrix
+(many of the other analysis actions that inherit from PLMD::analysis::AnalysisWithDataCollection only do so because this allows us to write straightforward
+regression tests for this part of the code). The remaining analysis actions inherit from PLMD::analysis::AnalysisBase because in general they require some
+dissimilarity information in order to function and because this information is calculated within PLMD::analysis::EuclideanDissimilarityMatrix.
+Consequently, if you are writing a new analysis class it should probably not inherit from PLMD::analysis::AnalysisWithDataCollection.
+
+\section storing Storing trajectory data for analysis
+
+As discussed in the previous section the methods in PLMD::analysis all work by storing a snapshot of the trajectory every \f$N\f$ steps
+and by then running an analysis method every \f$M\f$ steps, where \f$M\f$ is some substantial multiple of \f$N\f$. This intermittent
+storing of trajectory frames and occasional analysis of the trajectory is all looked after within the PLMD::analysis::AnalysisWithDataCollection
+abstract base class. Users can then set of a chain of analysis actions on the stored data by using actions that inherit from
+PLMD::analysis::AnalysisBase. Any class inheriting from PLMD::analysis::AnalysisBase must have a method within it named performAnalysis(),
+which will actually perform the analysis on the stored trajectory frames. When implementing a new analysis method the majority of your
+development time will probably be spent implementing some part of this performAnalysis method.
+
+\section reweight Reweighting trajectories
+
+As discussed in previous sections PLUMED is primarily a code for doing biased molecular dynamics simulations. This bias is used to force rare events
+to occur in the short time scales that are accessible within a molecular dynamics simulation. Oftentimes when analysing a trajectory we would like
+to remove the contribution of the bias and to reweight the simulation so as to get the underlying free energy surface. When performing any analysis of
+the trajectory one may similarly wish to remove the effect of the bias and to consider what weight each sampled point would have had if it had been sampled
+in accordance with the underlying canonical probability distribution function. This process of reweighting points - of ascribing a weight to each snapshot
+that discounts the effect of the simulation bias - is again looked after within PLMD::analysis::AnalysisWithDataCollection. If you wish to take these
+weights into account in your analysis method you should use the method PLMD::analysis::AnalysisBase::getWeight to access them. Obviously, if you have
+no simulation bias on the system then each point will have a weight of one and this will be the weight returned by PLMD::analysis::AnalysisBase::getWeight.
+
+\section output Outputting data files
+
+The fact that PLMD::analysis::AnalysisWithDataCollection can be used to run trajectory analysis in either post processing or on the fly during a trajectory means
+that this class must also look after a number of things. For example one might wish to perform multiple analyses of the trajectory
+during a simulation. Obviously, you do not want to overwrite the output file from your first analysis when you perform the second
+analysis of the trajectory. In addition, you do not want to overwrite files from earlier runs if you choose to rerun your analysis
+in a directory where you had already run an earlier calculation. For these reasons whenever you wish to read in the name of an output file
+you should use the following code to make sure that any old files are backed up on restart:
+
+\verbatim
+if( !getRestart() ){ OFile ofile; ofile.link(*this); ofile.setBackupString("analysis"); ofile.backupAllFiles(fname); }
+\endverbatim
+
+where fname is the name of your output file. On top of this when you open an output file in your analysis method you should use the following
+set of commands:
+
+\verbatim
+OFile gfile; gfile.link(*this);
+gfile.setBackupString("analysis");
+gfile.open( ofilename.c_str() );
+\endverbatim
+
+The second line ensures that files are named analysis.0.ofilename, analysis.1.ofilename and so on. Having said that it is probably best
+to not write routines to output data in analysis classes and to simply ensure that you can pass any output data from your method to the
+PLMD::analysis::OutputColvarFile and PLMD::analysis::OutputPDBFile methods. If you have done everything properly these classes should be
+able to interact with your new class through methods that are in PLMD::analysis::AnalysisBase.
+
+\section metrics Calculating dissimilarity matrices
+
+One of the most basic ways in which you can analyse a collection of trajectory snapshots is to calculate the matrix of dissimilarities between each of the pairs
+of trajectories frames. In plumed this is done in by the class PLMD::analysis::EuclideanDissimilarityMatrix. Notice as well that this class makes full use
+of the PLMD::reference module that is discussed in \ref AddingAMetric and so this class alone allows you to calculate the dissimilairity between any pair of
+trajectory frames in a wide variety of different ways. In addition, you can use PLMD::analysis::ReadDissimilarityMatrix to get the dissimilarities from an
+input file. There should thus be little need to implement new objects for calculating dissimilarity matrices -- if you really feel you need something other than
+what is already there or that is not implementable by \ref AddingAMetric then you are doing a calculation that is very unusual.
+
+\section landmarks Landmark selection algorithms
+
+Many analyses methods scale poorly with the number of trajectory frames that you wish to analyse. This happens in part because you need to compute the matrix
+of pairwise disimiarities (a square matrix in which the number of columns is equal to the number of trajectory frames) but also because you then have to
+do some algebra involving this matrix. To alleviate these problems a common strategy is to perform the analysis on a set of so-called landmark frames and to
+then project the non-landmark snapshots from the trajectory using some out-of-sample extension of your analysis algorithm. Classes that inherit from
+PLMD::analysis::LandmarkSelectionBase are implementations of the various landmark selection algorithms that are commonly employed. If your favourite landmark
+selection algorithm is not there you may choose to implement a new landmark selection algorithm by writing a new PLMD::Action that inherits from this class.
+Within this new class you need to only define a registerKeywords function, a constructor and a method that actually selects the landmarks that will be a function
+that must be called selectLandmarks. Once you are satisfied that you want frame \f$k\f$ in your landmark set then you can select this using
+PLMD::analysis::LandmarkSelectionBase::selectFrame. Please note that you can get the number of landmarks to select by calling:
+
+\verbatim
+getNumberOfDataPoints()
+\endverbatim
+
+If you would like to get the total number of frames from which you can get your subset of landmarks you should call:
+
+\verbatim
+mydata->getNumberOfDataPoints()
+\endverbatim
+
+Lastly, if you are using a method, which like PLMD::analysis::FarthestPointSampling uses the distances between your input points in some way, you should
+add something akin to:
+
+\verbatim
+if( !dissimilaritiesWereSet() ) error("dissimilarities have not been calcualted in input action");
+\endverbatim
+
+in your constructor as this will ensure that users are told what they are doing wrong if they do not specify how to calculate distances between points in the
+input. To then get the dissimilirity between input point \f$i\f$ and input point \f$j\f$ use:
+
+\verbatim
+mydata->getDissimilarity( landmarks[i], k );
+\endverbatim
+
+Calling PLMD::analysis::AnalysisBase::getDissimilarity will give you the distance between a pair of landmarks, which is not what you need.
+
+\section dimred Dimensionality reduction
+
+The aim when writing any large code such as PLUMED is to minise the number of lines of code as fewer lines of code means fewer bugs on average.
+Hence, as explained in other sections of this developer manual, all the object oriented programming, inheritance and polymorphism. Given this
+consider how we would go about implementing a library of dimensionality reduction algorithms. In LLE, ISOMAP, sketch-map or MDS the aim is to
+generate a low-dimensional projection of some set of high-dimensional data points. For all these methods we can use the same code to to store
+the high and low dimensional points and to output this data to a file. In fact the only things that differ in these various different methods are
+the ways in which the dissimilarities between the high-dimensional points are calculated and the manner in which the low-dimensional projections
+are generated. We have already discussed how PLUMED calculates matrices of dissimilarities between points using PLMD::analysis::EuclideanDissimilarityMatrix
+and how one can think about introduce new methods of calculating dissimilarities. Priting to files meanwhile can be looked after by PLMD::analysis::OutputColvarFile
+and PLMD::analysis::OutputPDBFile. Furthermore, if dimensionality reduction classes are written properly it is even possible to pass the projections
+generated by them to PLMD::analysis::Histogram and to output histograms and free energy surfaces as a function of the low-dimensional coordinates.
+As such in PLMD::dimred::DimensionalityReductionBase and its daughter classes we are thus solely concerned with calculating projections of data points.
+The dissimilarities between the input high dimensional frames will always be calculated by some method akin to PLMD::analysis::EuclideanDissimilarityMatrix.
+PLMD::dimred::DimensionalityReductionBase inherits from PLMD::analysis::AnalysisBase and expects another PLMD::analysis::AnalysisBase object as input.
+Furthermore, with the exception of PLMD::dimred::ClassicalMultiDimensionalScaling the input PLMD::AnalysisBase must be an
+PLMD::dimred::DimensionalityReductionBase as initial guesses must be suggested when using an interative optimization algorithm such as PLMD::dimred::SMACOF.
+
+Much of the work of dimensionality reduction done in the base PLMD::dimred::DimensionalityReductionBase class. When implementing any new
+dimensionality reduction algorithm your focus will be on writing a PLMD::dimred::calculateProjections routines. This function will take as
+input the matrix of pairwise dissimilarities between points (be they landmark points or otherwise) and is expected to return a matrix
+containing the projections of the high-dimensional data points. Depending on the stress function you minimise to find projections you
+may also have to implement PLMD::dimred::DimensionalityReductionBase::setTargetDistance and PLMD::dimred::DimensionalityReductionBase::calculateStress
+functions. This is necessary with PLMD::dimred::SketchMapBase for example because sketch-map uses transformed versions of the dissimilarities
+and distances in its stress function. These two routines are used within PLMD::dimred::ProjectNonLandmarkPoints which will product optimal projections of
+points that were not selected as landmarks.
+
+\section cluster Clustering trajectory data
+
+There are currently no clustering methods implemented in the PLMD::analysis module. This section is thus here to explain how I (Gareth Tribello) imagined one
+might go about implementing these methods. Again there are many commonalities between methods such as kmeans, Gaussian mixture models and so on, which should
+be thought about when constructing an abstract base class. Furthermore, this abstract base class should (like PLMD::analysis::DimensionalityReductionBase)
+inherit from PLMD::analysis::AnalysisBase and be implemented in a way that allows one to exploit the use of landmark selection algorithms that inherit from
+PLMD::analysis::LandmarkSelectionBase and the measure actions such as PLMD::analysis::EuclideanDissimilarityMatrix. It should also be able to work with the
+weights you get by reweiting the trajectories with the bias and so on. I don't think that you should have this inheriting from
+PLMD::analysis::AnalysisWithDataCollection as I believe you want the clustering to work with projections of data generated by dimensionality reduction algorithms.
+Obviously, if you are thinking of adding methods to cluster trajectory frames within PLUMED please feel free to get in touch with me (gareth.tribello\@gmail.com).
+I will be more than happy to discuss these ideas with you.
+
+*/
diff --git a/developer-doc/Doxyfile b/developer-doc/Doxyfile
index dcf741eb8b07197109ddb9ba8cd8268bf2abe79a..136576e65c3071242c35e15458ac1857b64bb124 100644
--- a/developer-doc/Doxyfile
+++ b/developer-doc/Doxyfile
@@ -742,7 +742,8 @@ INPUT = ./Intro.txt \
./AddingAColvar.txt \
./AddingAFunction.txt \
./AddingACLTool.txt \
- ./AddingAMultColvar.txt
+ ./AddingAMultColvar.txt \
+ ./AddingAnAnalysis.txt
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
diff --git a/regtest/analysis/rt-mds/Makefile b/regtest/analysis/rt-mds/Makefile
deleted file mode 100644
index 3703b27cea227aa053fb6d1d73f861e4384dbcee..0000000000000000000000000000000000000000
--- a/regtest/analysis/rt-mds/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-include ../../scripts/test.make
diff --git a/regtest/analysis/rt-mds/analysis.0.embed.reference b/regtest/analysis/rt-mds/analysis.0.embed.reference
deleted file mode 100644
index 2e7d4808e54541161da11dea5fa411b231f08a1e..0000000000000000000000000000000000000000
--- a/regtest/analysis/rt-mds/analysis.0.embed.reference
+++ /dev/null
@@ -1,401 +0,0 @@
-DESCRIPTION: results from classical mds analysis performed at time 5.0000
-REMARK WEIGHT=0.0054 CLASSICAL_MDS.1=0.0873 CLASSICAL_MDS.2=0.0013
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7551 c1.moment-3=1.3322
-END
-REMARK WEIGHT=0.0285 CLASSICAL_MDS.1=0.0535 CLASSICAL_MDS.2=0.0044
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7434 c1.moment-3=1.3003
-END
-REMARK WEIGHT=0.0359 CLASSICAL_MDS.1=0.0150 CLASSICAL_MDS.2=0.0044
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7333 c1.moment-3=1.2632
-END
-REMARK WEIGHT=0.0136 CLASSICAL_MDS.1=-0.0136 CLASSICAL_MDS.2=0.0019
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7283 c1.moment-3=1.2349
-END
-REMARK WEIGHT=0.0047 CLASSICAL_MDS.1=-0.0308 CLASSICAL_MDS.2=-0.0012
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7268 c1.moment-3=1.2175
-END
-REMARK WEIGHT=0.0042 CLASSICAL_MDS.1=-0.0355 CLASSICAL_MDS.2=-0.0018
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7262 c1.moment-3=1.2128
-END
-REMARK WEIGHT=0.0289 CLASSICAL_MDS.1=-0.0090 CLASSICAL_MDS.2=-0.0015
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7327 c1.moment-3=1.2385
-END
-REMARK WEIGHT=0.0481 CLASSICAL_MDS.1=0.0145 CLASSICAL_MDS.2=0.0004
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7371 c1.moment-3=1.2616
-END
-REMARK WEIGHT=0.0430 CLASSICAL_MDS.1=0.0191 CLASSICAL_MDS.2=0.0022
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7366 c1.moment-3=1.2666
-END
-REMARK WEIGHT=0.1867 CLASSICAL_MDS.1=0.0278 CLASSICAL_MDS.2=0.0015
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7394 c1.moment-3=1.2748
-END
-REMARK WEIGHT=0.0735 CLASSICAL_MDS.1=0.0091 CLASSICAL_MDS.2=-0.0004
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7365 c1.moment-3=1.2562
-END
-REMARK WEIGHT=0.0012 CLASSICAL_MDS.1=-0.0359 CLASSICAL_MDS.2=-0.0012
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7255 c1.moment-3=1.2126
-END
-REMARK WEIGHT=0.0006 CLASSICAL_MDS.1=-0.0540 CLASSICAL_MDS.2=0.0004
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7193 c1.moment-3=1.1955
-END
-REMARK WEIGHT=0.0082 CLASSICAL_MDS.1=-0.0322 CLASSICAL_MDS.2=-0.0034
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7286 c1.moment-3=1.2156
-END
-REMARK WEIGHT=0.0036 CLASSICAL_MDS.1=-0.0205 CLASSICAL_MDS.2=-0.0150
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7429 c1.moment-3=1.2239
-END
-REMARK WEIGHT=0.0005 CLASSICAL_MDS.1=-0.0282 CLASSICAL_MDS.2=-0.0289
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7542 c1.moment-3=1.2128
-END
-REMARK WEIGHT=0.0002 CLASSICAL_MDS.1=-0.0530 CLASSICAL_MDS.2=-0.0358
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7544 c1.moment-3=1.1871
-END
-REMARK WEIGHT=0.0002 CLASSICAL_MDS.1=-0.0769 CLASSICAL_MDS.2=-0.0312
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7438 c1.moment-3=1.1652
-END
-REMARK WEIGHT=0.0001 CLASSICAL_MDS.1=-0.0893 CLASSICAL_MDS.2=-0.0259
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7355 c1.moment-3=1.1546
-END
-REMARK WEIGHT=0.0000 CLASSICAL_MDS.1=-0.0697 CLASSICAL_MDS.2=-0.0246
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7393 c1.moment-3=1.1739
-END
-REMARK WEIGHT=0.0001 CLASSICAL_MDS.1=-0.0301 CLASSICAL_MDS.2=-0.0196
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7448 c1.moment-3=1.2133
-END
-REMARK WEIGHT=0.0019 CLASSICAL_MDS.1=0.0093 CLASSICAL_MDS.2=-0.0072
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7430 c1.moment-3=1.2547
-END
-REMARK WEIGHT=0.0160 CLASSICAL_MDS.1=0.0274 CLASSICAL_MDS.2=0.0009
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7400 c1.moment-3=1.2742
-END
-REMARK WEIGHT=0.0740 CLASSICAL_MDS.1=0.0301 CLASSICAL_MDS.2=0.0016
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7400 c1.moment-3=1.2770
-END
-REMARK WEIGHT=0.0150 CLASSICAL_MDS.1=0.0265 CLASSICAL_MDS.2=-0.0033
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7438 c1.moment-3=1.2723
-END
-REMARK WEIGHT=0.0029 CLASSICAL_MDS.1=0.0433 CLASSICAL_MDS.2=-0.0053
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7501 c1.moment-3=1.2879
-END
-REMARK WEIGHT=0.0061 CLASSICAL_MDS.1=0.0514 CLASSICAL_MDS.2=-0.0019
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7489 c1.moment-3=1.2967
-END
-REMARK WEIGHT=0.0328 CLASSICAL_MDS.1=0.0222 CLASSICAL_MDS.2=0.0031
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7365 c1.moment-3=1.2698
-END
-REMARK WEIGHT=0.0299 CLASSICAL_MDS.1=-0.0129 CLASSICAL_MDS.2=0.0061
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7245 c1.moment-3=1.2366
-END
-REMARK WEIGHT=0.0072 CLASSICAL_MDS.1=-0.0322 CLASSICAL_MDS.2=0.0084
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7172 c1.moment-3=1.2186
-END
-REMARK WEIGHT=0.0039 CLASSICAL_MDS.1=-0.0355 CLASSICAL_MDS.2=0.0080
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7168 c1.moment-3=1.2153
-END
-REMARK WEIGHT=0.0045 CLASSICAL_MDS.1=-0.0337 CLASSICAL_MDS.2=0.0067
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7185 c1.moment-3=1.2168
-END
-REMARK WEIGHT=0.0059 CLASSICAL_MDS.1=-0.0308 CLASSICAL_MDS.2=0.0047
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7211 c1.moment-3=1.2191
-END
-REMARK WEIGHT=0.0125 CLASSICAL_MDS.1=-0.0253 CLASSICAL_MDS.2=0.0016
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7255 c1.moment-3=1.2235
-END
-REMARK WEIGHT=0.0144 CLASSICAL_MDS.1=-0.0132 CLASSICAL_MDS.2=-0.0021
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7323 c1.moment-3=1.2343
-END
-REMARK WEIGHT=0.0307 CLASSICAL_MDS.1=0.0040 CLASSICAL_MDS.2=-0.0031
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7377 c1.moment-3=1.2506
-END
-REMARK WEIGHT=0.0437 CLASSICAL_MDS.1=0.0107 CLASSICAL_MDS.2=0.0011
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7354 c1.moment-3=1.2582
-END
-REMARK WEIGHT=0.1212 CLASSICAL_MDS.1=0.0299 CLASSICAL_MDS.2=0.0060
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7357 c1.moment-3=1.2780
-END
-REMARK WEIGHT=0.8415 CLASSICAL_MDS.1=0.0540 CLASSICAL_MDS.2=0.0070
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7410 c1.moment-3=1.3015
-END
-REMARK WEIGHT=0.6449 CLASSICAL_MDS.1=0.0650 CLASSICAL_MDS.2=0.0039
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7468 c1.moment-3=1.3114
-END
-REMARK WEIGHT=0.0450 CLASSICAL_MDS.1=0.0415 CLASSICAL_MDS.2=0.0025
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7421 c1.moment-3=1.2882
-END
-REMARK WEIGHT=0.0093 CLASSICAL_MDS.1=0.0074 CLASSICAL_MDS.2=0.0033
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7325 c1.moment-3=1.2555
-END
-REMARK WEIGHT=0.0134 CLASSICAL_MDS.1=-0.0185 CLASSICAL_MDS.2=0.0059
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7232 c1.moment-3=1.2312
-END
-REMARK WEIGHT=0.0068 CLASSICAL_MDS.1=-0.0413 CLASSICAL_MDS.2=0.0073
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7158 c1.moment-3=1.2096
-END
-REMARK WEIGHT=0.0035 CLASSICAL_MDS.1=-0.0548 CLASSICAL_MDS.2=0.0074
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7123 c1.moment-3=1.1966
-END
-REMARK WEIGHT=0.0043 CLASSICAL_MDS.1=-0.0385 CLASSICAL_MDS.2=0.0041
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7197 c1.moment-3=1.2114
-END
-REMARK WEIGHT=0.0021 CLASSICAL_MDS.1=-0.0383 CLASSICAL_MDS.2=-0.0006
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7243 c1.moment-3=1.2104
-END
-REMARK WEIGHT=0.0007 CLASSICAL_MDS.1=-0.0584 CLASSICAL_MDS.2=-0.0008
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7192 c1.moment-3=1.1910
-END
-REMARK WEIGHT=0.0034 CLASSICAL_MDS.1=-0.0584 CLASSICAL_MDS.2=0.0023
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7162 c1.moment-3=1.1918
-END
-REMARK WEIGHT=0.0039 CLASSICAL_MDS.1=-0.0553 CLASSICAL_MDS.2=0.0090
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7105 c1.moment-3=1.1965
-END
-REMARK WEIGHT=0.0004 CLASSICAL_MDS.1=-0.0772 CLASSICAL_MDS.2=0.0146
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6995 c1.moment-3=1.1768
-END
-REMARK WEIGHT=0.0006 CLASSICAL_MDS.1=-0.0757 CLASSICAL_MDS.2=0.0157
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6988 c1.moment-3=1.1785
-END
-REMARK WEIGHT=0.0031 CLASSICAL_MDS.1=-0.0644 CLASSICAL_MDS.2=0.0144
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7030 c1.moment-3=1.1891
-END
-REMARK WEIGHT=0.0033 CLASSICAL_MDS.1=-0.0816 CLASSICAL_MDS.2=0.0141
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6988 c1.moment-3=1.1724
-END
-REMARK WEIGHT=0.0016 CLASSICAL_MDS.1=-0.1045 CLASSICAL_MDS.2=0.0148
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6922 c1.moment-3=1.1504
-END
-REMARK WEIGHT=0.0022 CLASSICAL_MDS.1=-0.0867 CLASSICAL_MDS.2=0.0111
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7004 c1.moment-3=1.1667
-END
-REMARK WEIGHT=0.0035 CLASSICAL_MDS.1=-0.0365 CLASSICAL_MDS.2=0.0014
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7228 c1.moment-3=1.2126
-END
-REMARK WEIGHT=0.0011 CLASSICAL_MDS.1=0.0113 CLASSICAL_MDS.2=-0.0067
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7431 c1.moment-3=1.2567
-END
-REMARK WEIGHT=0.0038 CLASSICAL_MDS.1=0.0272 CLASSICAL_MDS.2=-0.0074
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7479 c1.moment-3=1.2718
-END
-REMARK WEIGHT=0.0211 CLASSICAL_MDS.1=0.0381 CLASSICAL_MDS.2=-0.0012
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7448 c1.moment-3=1.2840
-END
-REMARK WEIGHT=0.0278 CLASSICAL_MDS.1=0.0548 CLASSICAL_MDS.2=0.0021
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7459 c1.moment-3=1.3010
-END
-REMARK WEIGHT=0.0246 CLASSICAL_MDS.1=0.0470 CLASSICAL_MDS.2=0.0012
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7447 c1.moment-3=1.2933
-END
-REMARK WEIGHT=0.0024 CLASSICAL_MDS.1=0.0227 CLASSICAL_MDS.2=-0.0019
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7414 c1.moment-3=1.2690
-END
-REMARK WEIGHT=0.0146 CLASSICAL_MDS.1=0.0132 CLASSICAL_MDS.2=-0.0022
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7392 c1.moment-3=1.2597
-END
-REMARK WEIGHT=0.0126 CLASSICAL_MDS.1=0.0040 CLASSICAL_MDS.2=0.0004
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7343 c1.moment-3=1.2515
-END
-REMARK WEIGHT=0.0031 CLASSICAL_MDS.1=-0.0045 CLASSICAL_MDS.2=0.0008
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7317 c1.moment-3=1.2434
-END
-REMARK WEIGHT=0.0019 CLASSICAL_MDS.1=-0.0145 CLASSICAL_MDS.2=0.0006
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7293 c1.moment-3=1.2337
-END
-REMARK WEIGHT=0.0042 CLASSICAL_MDS.1=-0.0116 CLASSICAL_MDS.2=0.0025
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7282 c1.moment-3=1.2370
-END
-REMARK WEIGHT=0.0093 CLASSICAL_MDS.1=-0.0031 CLASSICAL_MDS.2=0.0044
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7286 c1.moment-3=1.2457
-END
-REMARK WEIGHT=0.0099 CLASSICAL_MDS.1=-0.0148 CLASSICAL_MDS.2=0.0086
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7216 c1.moment-3=1.2355
-END
-REMARK WEIGHT=0.0052 CLASSICAL_MDS.1=-0.0318 CLASSICAL_MDS.2=0.0109
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7149 c1.moment-3=1.2196
-END
-REMARK WEIGHT=0.0030 CLASSICAL_MDS.1=-0.0166 CLASSICAL_MDS.2=0.0078
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7218 c1.moment-3=1.2336
-END
-REMARK WEIGHT=0.0136 CLASSICAL_MDS.1=0.0154 CLASSICAL_MDS.2=0.0036
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7342 c1.moment-3=1.2633
-END
-REMARK WEIGHT=0.0938 CLASSICAL_MDS.1=0.0451 CLASSICAL_MDS.2=0.0018
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7437 c1.moment-3=1.2915
-END
-REMARK WEIGHT=0.1720 CLASSICAL_MDS.1=0.0364 CLASSICAL_MDS.2=0.0021
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7411 c1.moment-3=1.2832
-END
-REMARK WEIGHT=0.0154 CLASSICAL_MDS.1=0.0125 CLASSICAL_MDS.2=0.0036
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7335 c1.moment-3=1.2606
-END
-REMARK WEIGHT=0.0938 CLASSICAL_MDS.1=0.0330 CLASSICAL_MDS.2=0.0045
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7379 c1.moment-3=1.2806
-END
-REMARK WEIGHT=1.0000 CLASSICAL_MDS.1=0.0605 CLASSICAL_MDS.2=0.0048
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7448 c1.moment-3=1.3072
-END
-REMARK WEIGHT=0.3337 CLASSICAL_MDS.1=0.0417 CLASSICAL_MDS.2=0.0041
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7406 c1.moment-3=1.2889
-END
-REMARK WEIGHT=0.0764 CLASSICAL_MDS.1=0.0115 CLASSICAL_MDS.2=0.0011
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7356 c1.moment-3=1.2590
-END
-REMARK WEIGHT=0.1257 CLASSICAL_MDS.1=0.0257 CLASSICAL_MDS.2=-0.0018
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7421 c1.moment-3=1.2719
-END
-REMARK WEIGHT=0.1215 CLASSICAL_MDS.1=0.0451 CLASSICAL_MDS.2=-0.0029
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7483 c1.moment-3=1.2904
-END
-REMARK WEIGHT=0.0290 CLASSICAL_MDS.1=0.0387 CLASSICAL_MDS.2=-0.0032
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7469 c1.moment-3=1.2841
-END
-REMARK WEIGHT=0.0162 CLASSICAL_MDS.1=0.0254 CLASSICAL_MDS.2=-0.0017
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7420 c1.moment-3=1.2716
-END
-REMARK WEIGHT=0.0639 CLASSICAL_MDS.1=0.0311 CLASSICAL_MDS.2=-0.0001
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7418 c1.moment-3=1.2775
-END
-REMARK WEIGHT=0.2186 CLASSICAL_MDS.1=0.0448 CLASSICAL_MDS.2=0.0006
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7448 c1.moment-3=1.2909
-END
-REMARK WEIGHT=0.3093 CLASSICAL_MDS.1=0.0499 CLASSICAL_MDS.2=0.0020
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7448 c1.moment-3=1.2962
-END
-REMARK WEIGHT=0.5713 CLASSICAL_MDS.1=0.0543 CLASSICAL_MDS.2=0.0037
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7443 c1.moment-3=1.3009
-END
-REMARK WEIGHT=0.2377 CLASSICAL_MDS.1=0.0486 CLASSICAL_MDS.2=0.0054
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7412 c1.moment-3=1.2959
-END
-REMARK WEIGHT=0.0425 CLASSICAL_MDS.1=0.0459 CLASSICAL_MDS.2=0.0051
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7407 c1.moment-3=1.2932
-END
-REMARK WEIGHT=0.1714 CLASSICAL_MDS.1=0.0715 CLASSICAL_MDS.2=-0.0001
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7524 c1.moment-3=1.3166
-END
-REMARK WEIGHT=0.0831 CLASSICAL_MDS.1=0.0764 CLASSICAL_MDS.2=-0.0063
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7596 c1.moment-3=1.3196
-END
-REMARK WEIGHT=0.0194 CLASSICAL_MDS.1=0.0603 CLASSICAL_MDS.2=-0.0119
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7609 c1.moment-3=1.3027
-END
-REMARK WEIGHT=0.0149 CLASSICAL_MDS.1=0.0378 CLASSICAL_MDS.2=-0.0153
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7583 c1.moment-3=1.2800
-END
-REMARK WEIGHT=0.0217 CLASSICAL_MDS.1=0.0214 CLASSICAL_MDS.2=-0.0124
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7512 c1.moment-3=1.2649
-END
-REMARK WEIGHT=0.0127 CLASSICAL_MDS.1=0.0063 CLASSICAL_MDS.2=-0.0091
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7441 c1.moment-3=1.2513
-END
-REMARK WEIGHT=0.0063 CLASSICAL_MDS.1=-0.0095 CLASSICAL_MDS.2=-0.0016
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7327 c1.moment-3=1.2380
-END
-REMARK WEIGHT=0.0067 CLASSICAL_MDS.1=-0.0259 CLASSICAL_MDS.2=0.0036
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7234 c1.moment-3=1.2235
-END
-REMARK WEIGHT=0.0085 CLASSICAL_MDS.1=-0.0234 CLASSICAL_MDS.2=0.0061
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7217 c1.moment-3=1.2265
-END
-REMARK WEIGHT=0.0069 CLASSICAL_MDS.1=0.0012 CLASSICAL_MDS.2=0.0060
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7282 c1.moment-3=1.2502
-END
diff --git a/regtest/analysis/rt-mds/analysis.0.list_embed.reference b/regtest/analysis/rt-mds/analysis.0.list_embed.reference
deleted file mode 100644
index a5fdcd999b09c16b758fa6803ca3388b314be2a8..0000000000000000000000000000000000000000
--- a/regtest/analysis/rt-mds/analysis.0.list_embed.reference
+++ /dev/null
@@ -1,101 +0,0 @@
-#! FIELDS @17.1 @17.2
- 0.0873 0.0013
- 0.0535 0.0044
- 0.0150 0.0044
- -0.0136 0.0019
- -0.0308 -0.0012
- -0.0355 -0.0018
- -0.0090 -0.0015
- 0.0145 0.0004
- 0.0191 0.0022
- 0.0278 0.0015
- 0.0091 -0.0004
- -0.0359 -0.0012
- -0.0540 0.0004
- -0.0322 -0.0034
- -0.0205 -0.0150
- -0.0282 -0.0289
- -0.0530 -0.0358
- -0.0769 -0.0312
- -0.0893 -0.0259
- -0.0697 -0.0246
- -0.0301 -0.0196
- 0.0093 -0.0072
- 0.0274 0.0009
- 0.0301 0.0016
- 0.0265 -0.0033
- 0.0433 -0.0053
- 0.0514 -0.0019
- 0.0222 0.0031
- -0.0129 0.0061
- -0.0322 0.0084
- -0.0355 0.0080
- -0.0337 0.0067
- -0.0308 0.0047
- -0.0253 0.0016
- -0.0132 -0.0021
- 0.0040 -0.0031
- 0.0107 0.0011
- 0.0299 0.0060
- 0.0540 0.0070
- 0.0650 0.0039
- 0.0415 0.0025
- 0.0074 0.0033
- -0.0185 0.0059
- -0.0413 0.0073
- -0.0548 0.0074
- -0.0385 0.0041
- -0.0383 -0.0006
- -0.0584 -0.0008
- -0.0584 0.0023
- -0.0553 0.0090
- -0.0772 0.0146
- -0.0757 0.0157
- -0.0644 0.0144
- -0.0816 0.0141
- -0.1045 0.0148
- -0.0867 0.0111
- -0.0365 0.0014
- 0.0113 -0.0067
- 0.0272 -0.0074
- 0.0381 -0.0012
- 0.0548 0.0021
- 0.0470 0.0012
- 0.0227 -0.0019
- 0.0132 -0.0022
- 0.0040 0.0004
- -0.0045 0.0008
- -0.0145 0.0006
- -0.0116 0.0025
- -0.0031 0.0044
- -0.0148 0.0086
- -0.0318 0.0109
- -0.0166 0.0078
- 0.0154 0.0036
- 0.0451 0.0018
- 0.0364 0.0021
- 0.0125 0.0036
- 0.0330 0.0045
- 0.0605 0.0048
- 0.0417 0.0041
- 0.0115 0.0011
- 0.0257 -0.0018
- 0.0451 -0.0029
- 0.0387 -0.0032
- 0.0254 -0.0017
- 0.0311 -0.0001
- 0.0448 0.0006
- 0.0499 0.0020
- 0.0543 0.0037
- 0.0486 0.0054
- 0.0459 0.0051
- 0.0715 -0.0001
- 0.0764 -0.0063
- 0.0603 -0.0119
- 0.0378 -0.0153
- 0.0214 -0.0124
- 0.0063 -0.0091
- -0.0095 -0.0016
- -0.0259 0.0036
- -0.0234 0.0061
- 0.0012 0.0060
diff --git a/regtest/analysis/rt-mds/config b/regtest/analysis/rt-mds/config
deleted file mode 100644
index 57d886c44c9b5b615e6e31bf117a02928408814b..0000000000000000000000000000000000000000
--- a/regtest/analysis/rt-mds/config
+++ /dev/null
@@ -1,2 +0,0 @@
-type=simplemd
-
diff --git a/regtest/analysis/rt-mds/embed.reference b/regtest/analysis/rt-mds/embed.reference
deleted file mode 100644
index b9a6a8a057f789ab3b966abd3e229839cdeca138..0000000000000000000000000000000000000000
--- a/regtest/analysis/rt-mds/embed.reference
+++ /dev/null
@@ -1,401 +0,0 @@
-DESCRIPTION: results from classical mds analysis performed at time 10.0000
-REMARK WEIGHT=0.0073 CLASSICAL_MDS.1=0.0594 CLASSICAL_MDS.2=0.0053
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7340 c1.moment-3=1.2672
-END
-REMARK WEIGHT=0.0102 CLASSICAL_MDS.1=0.0683 CLASSICAL_MDS.2=0.0034
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7371 c1.moment-3=1.2758
-END
-REMARK WEIGHT=0.0032 CLASSICAL_MDS.1=0.0705 CLASSICAL_MDS.2=0.0006
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7401 c1.moment-3=1.2777
-END
-REMARK WEIGHT=0.0085 CLASSICAL_MDS.1=0.0729 CLASSICAL_MDS.2=-0.0019
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7428 c1.moment-3=1.2796
-END
-REMARK WEIGHT=0.0190 CLASSICAL_MDS.1=0.0874 CLASSICAL_MDS.2=-0.0069
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7497 c1.moment-3=1.2934
-END
-REMARK WEIGHT=0.0162 CLASSICAL_MDS.1=0.0961 CLASSICAL_MDS.2=-0.0095
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7533 c1.moment-3=1.3018
-END
-REMARK WEIGHT=0.0202 CLASSICAL_MDS.1=0.0867 CLASSICAL_MDS.2=-0.0062
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7489 c1.moment-3=1.2928
-END
-REMARK WEIGHT=0.0262 CLASSICAL_MDS.1=0.0719 CLASSICAL_MDS.2=-0.0008
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7417 c1.moment-3=1.2788
-END
-REMARK WEIGHT=0.1019 CLASSICAL_MDS.1=0.0575 CLASSICAL_MDS.2=0.0031
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7360 c1.moment-3=1.2651
-END
-REMARK WEIGHT=0.0543 CLASSICAL_MDS.1=0.0552 CLASSICAL_MDS.2=0.0034
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7354 c1.moment-3=1.2628
-END
-REMARK WEIGHT=0.0187 CLASSICAL_MDS.1=0.0682 CLASSICAL_MDS.2=-0.0002
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7405 c1.moment-3=1.2753
-END
-REMARK WEIGHT=0.0250 CLASSICAL_MDS.1=0.0781 CLASSICAL_MDS.2=-0.0024
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7440 c1.moment-3=1.2847
-END
-REMARK WEIGHT=0.0086 CLASSICAL_MDS.1=0.0785 CLASSICAL_MDS.2=-0.0025
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7441 c1.moment-3=1.2852
-END
-REMARK WEIGHT=0.0031 CLASSICAL_MDS.1=0.0763 CLASSICAL_MDS.2=-0.0027
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7441 c1.moment-3=1.2829
-END
-REMARK WEIGHT=0.0113 CLASSICAL_MDS.1=0.0755 CLASSICAL_MDS.2=-0.0041
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7454 c1.moment-3=1.2820
-END
-REMARK WEIGHT=0.0598 CLASSICAL_MDS.1=0.0792 CLASSICAL_MDS.2=-0.0069
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7486 c1.moment-3=1.2853
-END
-REMARK WEIGHT=0.0825 CLASSICAL_MDS.1=0.0778 CLASSICAL_MDS.2=-0.0062
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7477 c1.moment-3=1.2840
-END
-REMARK WEIGHT=0.0659 CLASSICAL_MDS.1=0.0727 CLASSICAL_MDS.2=-0.0025
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7434 c1.moment-3=1.2795
-END
-REMARK WEIGHT=0.1233 CLASSICAL_MDS.1=0.0726 CLASSICAL_MDS.2=0.0014
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7396 c1.moment-3=1.2798
-END
-REMARK WEIGHT=0.2603 CLASSICAL_MDS.1=0.0756 CLASSICAL_MDS.2=0.0030
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7384 c1.moment-3=1.2830
-END
-REMARK WEIGHT=0.1474 CLASSICAL_MDS.1=0.0821 CLASSICAL_MDS.2=0.0017
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7405 c1.moment-3=1.2893
-END
-REMARK WEIGHT=0.0116 CLASSICAL_MDS.1=0.0816 CLASSICAL_MDS.2=0.0001
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7420 c1.moment-3=1.2886
-END
-REMARK WEIGHT=0.1441 CLASSICAL_MDS.1=0.0774 CLASSICAL_MDS.2=0.0008
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7407 c1.moment-3=1.2845
-END
-REMARK WEIGHT=0.2022 CLASSICAL_MDS.1=0.0766 CLASSICAL_MDS.2=0.0008
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7407 c1.moment-3=1.2837
-END
-REMARK WEIGHT=0.1476 CLASSICAL_MDS.1=0.0838 CLASSICAL_MDS.2=-0.0005
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7429 c1.moment-3=1.2906
-END
-REMARK WEIGHT=0.2285 CLASSICAL_MDS.1=0.0931 CLASSICAL_MDS.2=-0.0016
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7452 c1.moment-3=1.2997
-END
-REMARK WEIGHT=0.4499 CLASSICAL_MDS.1=0.0936 CLASSICAL_MDS.2=-0.0010
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7446 c1.moment-3=1.3004
-END
-REMARK WEIGHT=0.4344 CLASSICAL_MDS.1=0.0923 CLASSICAL_MDS.2=-0.0009
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7443 c1.moment-3=1.2990
-END
-REMARK WEIGHT=0.3822 CLASSICAL_MDS.1=0.0906 CLASSICAL_MDS.2=-0.0008
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7440 c1.moment-3=1.2974
-END
-REMARK WEIGHT=0.2334 CLASSICAL_MDS.1=0.0706 CLASSICAL_MDS.2=0.0025
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7382 c1.moment-3=1.2780
-END
-REMARK WEIGHT=0.1038 CLASSICAL_MDS.1=0.0664 CLASSICAL_MDS.2=0.0050
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7352 c1.moment-3=1.2741
-END
-REMARK WEIGHT=0.4459 CLASSICAL_MDS.1=0.0901 CLASSICAL_MDS.2=0.0019
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7412 c1.moment-3=1.2972
-END
-REMARK WEIGHT=0.7086 CLASSICAL_MDS.1=0.1059 CLASSICAL_MDS.2=-0.0015
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7467 c1.moment-3=1.3125
-END
-REMARK WEIGHT=0.1776 CLASSICAL_MDS.1=0.0917 CLASSICAL_MDS.2=0.0006
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7428 c1.moment-3=1.2986
-END
-REMARK WEIGHT=0.1777 CLASSICAL_MDS.1=0.0876 CLASSICAL_MDS.2=0.0021
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7407 c1.moment-3=1.2948
-END
-REMARK WEIGHT=0.1789 CLASSICAL_MDS.1=0.1008 CLASSICAL_MDS.2=-0.0001
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7446 c1.moment-3=1.3076
-END
-REMARK WEIGHT=0.2332 CLASSICAL_MDS.1=0.0955 CLASSICAL_MDS.2=-0.0014
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7452 c1.moment-3=1.3022
-END
-REMARK WEIGHT=0.1479 CLASSICAL_MDS.1=0.0858 CLASSICAL_MDS.2=-0.0018
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7444 c1.moment-3=1.2925
-END
-REMARK WEIGHT=0.2978 CLASSICAL_MDS.1=0.0894 CLASSICAL_MDS.2=-0.0005
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7436 c1.moment-3=1.2963
-END
-REMARK WEIGHT=0.7063 CLASSICAL_MDS.1=0.0922 CLASSICAL_MDS.2=0.0014
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7420 c1.moment-3=1.2992
-END
-REMARK WEIGHT=1.0000 CLASSICAL_MDS.1=0.0917 CLASSICAL_MDS.2=0.0010
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7423 c1.moment-3=1.2987
-END
-REMARK WEIGHT=0.2296 CLASSICAL_MDS.1=0.0925 CLASSICAL_MDS.2=-0.0043
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7477 c1.moment-3=1.2989
-END
-REMARK WEIGHT=0.0617 CLASSICAL_MDS.1=0.0967 CLASSICAL_MDS.2=-0.0102
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7541 c1.moment-3=1.3023
-END
-REMARK WEIGHT=0.3089 CLASSICAL_MDS.1=0.1073 CLASSICAL_MDS.2=-0.0096
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7548 c1.moment-3=1.3129
-END
-REMARK WEIGHT=0.2276 CLASSICAL_MDS.1=0.1065 CLASSICAL_MDS.2=-0.0047
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7499 c1.moment-3=1.3126
-END
-REMARK WEIGHT=0.0747 CLASSICAL_MDS.1=0.0935 CLASSICAL_MDS.2=-0.0003
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7439 c1.moment-3=1.3003
-END
-REMARK WEIGHT=0.0472 CLASSICAL_MDS.1=0.0668 CLASSICAL_MDS.2=0.0049
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7353 c1.moment-3=1.2745
-END
-REMARK WEIGHT=0.0408 CLASSICAL_MDS.1=0.0411 CLASSICAL_MDS.2=0.0087
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7284 c1.moment-3=1.2494
-END
-REMARK WEIGHT=0.0419 CLASSICAL_MDS.1=0.0264 CLASSICAL_MDS.2=0.0110
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7242 c1.moment-3=1.2352
-END
-REMARK WEIGHT=0.0119 CLASSICAL_MDS.1=0.0254 CLASSICAL_MDS.2=0.0125
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7226 c1.moment-3=1.2344
-END
-REMARK WEIGHT=0.0125 CLASSICAL_MDS.1=0.0503 CLASSICAL_MDS.2=0.0085
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7297 c1.moment-3=1.2586
-END
-REMARK WEIGHT=0.0217 CLASSICAL_MDS.1=0.0855 CLASSICAL_MDS.2=0.0007
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7419 c1.moment-3=1.2925
-END
-REMARK WEIGHT=0.0392 CLASSICAL_MDS.1=0.0975 CLASSICAL_MDS.2=-0.0028
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7469 c1.moment-3=1.3039
-END
-REMARK WEIGHT=0.2898 CLASSICAL_MDS.1=0.0983 CLASSICAL_MDS.2=-0.0035
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7477 c1.moment-3=1.3047
-END
-REMARK WEIGHT=0.4917 CLASSICAL_MDS.1=0.0997 CLASSICAL_MDS.2=-0.0044
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7487 c1.moment-3=1.3059
-END
-REMARK WEIGHT=0.0181 CLASSICAL_MDS.1=0.0877 CLASSICAL_MDS.2=-0.0021
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7449 c1.moment-3=1.2944
-END
-REMARK WEIGHT=0.0013 CLASSICAL_MDS.1=0.0501 CLASSICAL_MDS.2=0.0053
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7328 c1.moment-3=1.2580
-END
-REMARK WEIGHT=0.0036 CLASSICAL_MDS.1=0.0104 CLASSICAL_MDS.2=0.0140
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7192 c1.moment-3=1.2197
-END
-REMARK WEIGHT=0.0076 CLASSICAL_MDS.1=-0.0199 CLASSICAL_MDS.2=0.0221
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7074 c1.moment-3=1.1907
-END
-REMARK WEIGHT=0.0033 CLASSICAL_MDS.1=-0.0416 CLASSICAL_MDS.2=0.0277
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6990 c1.moment-3=1.1698
-END
-REMARK WEIGHT=0.0002 CLASSICAL_MDS.1=-0.0688 CLASSICAL_MDS.2=0.0338
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6895 c1.moment-3=1.1436
-END
-REMARK WEIGHT=0.0000 CLASSICAL_MDS.1=-0.0858 CLASSICAL_MDS.2=0.0354
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6858 c1.moment-3=1.1269
-END
-REMARK WEIGHT=0.0001 CLASSICAL_MDS.1=-0.0897 CLASSICAL_MDS.2=0.0313
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6894 c1.moment-3=1.1226
-END
-REMARK WEIGHT=0.0002 CLASSICAL_MDS.1=-0.0920 CLASSICAL_MDS.2=0.0254
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6950 c1.moment-3=1.1195
-END
-REMARK WEIGHT=0.0004 CLASSICAL_MDS.1=-0.1168 CLASSICAL_MDS.2=0.0227
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6945 c1.moment-3=1.0946
-END
-REMARK WEIGHT=0.0007 CLASSICAL_MDS.1=-0.1447 CLASSICAL_MDS.2=0.0227
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6910 c1.moment-3=1.0669
-END
-REMARK WEIGHT=0.0031 CLASSICAL_MDS.1=-0.1636 CLASSICAL_MDS.2=0.0221
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6892 c1.moment-3=1.0481
-END
-REMARK WEIGHT=0.0095 CLASSICAL_MDS.1=-0.1461 CLASSICAL_MDS.2=0.0182
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6953 c1.moment-3=1.0650
-END
-REMARK WEIGHT=0.0030 CLASSICAL_MDS.1=-0.1212 CLASSICAL_MDS.2=0.0139
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7027 c1.moment-3=1.0891
-END
-REMARK WEIGHT=0.0040 CLASSICAL_MDS.1=-0.0775 CLASSICAL_MDS.2=0.0056
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7164 c1.moment-3=1.1314
-END
-REMARK WEIGHT=0.0032 CLASSICAL_MDS.1=-0.0008 CLASSICAL_MDS.2=-0.0041
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7358 c1.moment-3=1.2063
-END
-REMARK WEIGHT=0.0057 CLASSICAL_MDS.1=0.0469 CLASSICAL_MDS.2=-0.0038
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7415 c1.moment-3=1.2537
-END
-REMARK WEIGHT=0.0638 CLASSICAL_MDS.1=0.0771 CLASSICAL_MDS.2=-0.0004
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7419 c1.moment-3=1.2840
-END
-REMARK WEIGHT=0.3314 CLASSICAL_MDS.1=0.0917 CLASSICAL_MDS.2=0.0005
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7428 c1.moment-3=1.2986
-END
-REMARK WEIGHT=0.1319 CLASSICAL_MDS.1=0.0656 CLASSICAL_MDS.2=0.0042
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7359 c1.moment-3=1.2732
-END
-REMARK WEIGHT=0.0139 CLASSICAL_MDS.1=-0.0034 CLASSICAL_MDS.2=0.0115
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7200 c1.moment-3=1.2057
-END
-REMARK WEIGHT=0.0053 CLASSICAL_MDS.1=-0.0901 CLASSICAL_MDS.2=0.0141
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7064 c1.moment-3=1.1200
-END
-REMARK WEIGHT=0.0040 CLASSICAL_MDS.1=-0.1784 CLASSICAL_MDS.2=0.0069
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7024 c1.moment-3=1.0315
-END
-REMARK WEIGHT=0.0020 CLASSICAL_MDS.1=-0.2253 CLASSICAL_MDS.2=-0.0077
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7109 c1.moment-3=0.9832
-END
-REMARK WEIGHT=0.0006 CLASSICAL_MDS.1=-0.2372 CLASSICAL_MDS.2=-0.0248
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7264 c1.moment-3=0.9692
-END
-REMARK WEIGHT=0.0001 CLASSICAL_MDS.1=-0.2415 CLASSICAL_MDS.2=-0.0448
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7456 c1.moment-3=0.9624
-END
-REMARK WEIGHT=0.0000 CLASSICAL_MDS.1=-0.2562 CLASSICAL_MDS.2=-0.0539
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7529 c1.moment-3=0.9466
-END
-REMARK WEIGHT=0.0000 CLASSICAL_MDS.1=-0.2901 CLASSICAL_MDS.2=-0.0433
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7381 c1.moment-3=0.9144
-END
-REMARK WEIGHT=0.0001 CLASSICAL_MDS.1=-0.3173 CLASSICAL_MDS.2=-0.0215
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7130 c1.moment-3=0.8902
-END
-REMARK WEIGHT=0.0001 CLASSICAL_MDS.1=-0.3117 CLASSICAL_MDS.2=0.0096
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6829 c1.moment-3=0.8996
-END
-REMARK WEIGHT=0.0001 CLASSICAL_MDS.1=-0.2787 CLASSICAL_MDS.2=0.0317
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6651 c1.moment-3=0.9352
-END
-REMARK WEIGHT=0.0001 CLASSICAL_MDS.1=-0.2319 CLASSICAL_MDS.2=0.0372
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6656 c1.moment-3=0.9823
-END
-REMARK WEIGHT=0.0001 CLASSICAL_MDS.1=-0.1897 CLASSICAL_MDS.2=0.0305
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6776 c1.moment-3=1.0233
-END
-REMARK WEIGHT=0.0005 CLASSICAL_MDS.1=-0.1592 CLASSICAL_MDS.2=0.0142
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.6975 c1.moment-3=1.0515
-END
-REMARK WEIGHT=0.0000 CLASSICAL_MDS.1=-0.1211 CLASSICAL_MDS.2=-0.0049
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7213 c1.moment-3=1.0868
-END
-REMARK WEIGHT=0.0000 CLASSICAL_MDS.1=-0.0960 CLASSICAL_MDS.2=-0.0150
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7345 c1.moment-3=1.1105
-END
-REMARK WEIGHT=0.0010 CLASSICAL_MDS.1=-0.0842 CLASSICAL_MDS.2=-0.0162
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7372 c1.moment-3=1.1221
-END
-REMARK WEIGHT=0.0005 CLASSICAL_MDS.1=-0.0813 CLASSICAL_MDS.2=-0.0187
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7401 c1.moment-3=1.1246
-END
-REMARK WEIGHT=0.0000 CLASSICAL_MDS.1=-0.0823 CLASSICAL_MDS.2=-0.0193
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7406 c1.moment-3=1.1235
-END
-REMARK WEIGHT=0.0000 CLASSICAL_MDS.1=-0.0773 CLASSICAL_MDS.2=-0.0179
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7398 c1.moment-3=1.1287
-END
-REMARK WEIGHT=0.0001 CLASSICAL_MDS.1=-0.0621 CLASSICAL_MDS.2=-0.0202
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7440 c1.moment-3=1.1435
-END
-REMARK WEIGHT=0.0000 CLASSICAL_MDS.1=-0.0449 CLASSICAL_MDS.2=-0.0215
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7475 c1.moment-3=1.1604
-END
-REMARK WEIGHT=0.0000 CLASSICAL_MDS.1=-0.0269 CLASSICAL_MDS.2=-0.0307
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7589 c1.moment-3=1.1770
-END
-REMARK WEIGHT=0.0001 CLASSICAL_MDS.1=-0.0075 CLASSICAL_MDS.2=-0.0368
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7673 c1.moment-3=1.1955
-END
-REMARK WEIGHT=0.0015 CLASSICAL_MDS.1=0.0266 CLASSICAL_MDS.2=-0.0342
-REMARK ARG=c1.moment-2,c1.moment-3
-REMARK c1.moment-2=0.7690 c1.moment-3=1.2297
-END
diff --git a/regtest/analysis/rt-mds/in b/regtest/analysis/rt-mds/in
deleted file mode 100644
index 030417936fdc6c7f1f4d0edff090893b1485f13d..0000000000000000000000000000000000000000
--- a/regtest/analysis/rt-mds/in
+++ /dev/null
@@ -1,11 +0,0 @@
-inputfile input.xyz
-outputfile output.xyz
-temperature 0.2
-tstep 0.005
-friction 1
-forcecutoff 2.5
-listcutoff 3.0
-ndim 2
-nstep 2000
-nconfig 1000 trajectory.xyz
-nstat 1000 energies.dat
diff --git a/regtest/analysis/rt-mds/input.xyz b/regtest/analysis/rt-mds/input.xyz
deleted file mode 100644
index 9e1e59174c1ce7a8d31fa8220d64ea05a9edbc14..0000000000000000000000000000000000000000
--- a/regtest/analysis/rt-mds/input.xyz
+++ /dev/null
@@ -1,9 +0,0 @@
-7
-100. 100. 100.
-Ar 7.3933470660 -2.6986483924 0.0000000000
-Ar 7.8226765198 -0.7390907295 0.0000000000
-Ar 7.1014969839 -1.6164766614 0.0000000000
-Ar 8.2357184242 -1.7097824975 0.0000000000
-Ar 6.7372520842 -0.5111536183 0.0000000000
-Ar 6.3777119489 -2.4640437401 0.0000000000
-Ar 5.9900631495 -1.3385375043 0.0000000000
diff --git a/regtest/analysis/rt-mds/list_embed.reference b/regtest/analysis/rt-mds/list_embed.reference
deleted file mode 100644
index 6f40ac6e8c9694f04ba5de8a9359facec1e04047..0000000000000000000000000000000000000000
--- a/regtest/analysis/rt-mds/list_embed.reference
+++ /dev/null
@@ -1,101 +0,0 @@
-#! FIELDS @17.1 @17.2
- 0.0594 0.0053
- 0.0683 0.0034
- 0.0705 0.0006
- 0.0729 -0.0019
- 0.0874 -0.0069
- 0.0961 -0.0095
- 0.0867 -0.0062
- 0.0719 -0.0008
- 0.0575 0.0031
- 0.0552 0.0034
- 0.0682 -0.0002
- 0.0781 -0.0024
- 0.0785 -0.0025
- 0.0763 -0.0027
- 0.0755 -0.0041
- 0.0792 -0.0069
- 0.0778 -0.0062
- 0.0727 -0.0025
- 0.0726 0.0014
- 0.0756 0.0030
- 0.0821 0.0017
- 0.0816 0.0001
- 0.0774 0.0008
- 0.0766 0.0008
- 0.0838 -0.0005
- 0.0931 -0.0016
- 0.0936 -0.0010
- 0.0923 -0.0009
- 0.0906 -0.0008
- 0.0706 0.0025
- 0.0664 0.0050
- 0.0901 0.0019
- 0.1059 -0.0015
- 0.0917 0.0006
- 0.0876 0.0021
- 0.1008 -0.0001
- 0.0955 -0.0014
- 0.0858 -0.0018
- 0.0894 -0.0005
- 0.0922 0.0014
- 0.0917 0.0010
- 0.0925 -0.0043
- 0.0967 -0.0102
- 0.1073 -0.0096
- 0.1065 -0.0047
- 0.0935 -0.0003
- 0.0668 0.0049
- 0.0411 0.0087
- 0.0264 0.0110
- 0.0254 0.0125
- 0.0503 0.0085
- 0.0855 0.0007
- 0.0975 -0.0028
- 0.0983 -0.0035
- 0.0997 -0.0044
- 0.0877 -0.0021
- 0.0501 0.0053
- 0.0104 0.0140
- -0.0199 0.0221
- -0.0416 0.0277
- -0.0688 0.0338
- -0.0858 0.0354
- -0.0897 0.0313
- -0.0920 0.0254
- -0.1168 0.0227
- -0.1447 0.0227
- -0.1636 0.0221
- -0.1461 0.0182
- -0.1212 0.0139
- -0.0775 0.0056
- -0.0008 -0.0041
- 0.0469 -0.0038
- 0.0771 -0.0004
- 0.0917 0.0005
- 0.0656 0.0042
- -0.0034 0.0115
- -0.0901 0.0141
- -0.1784 0.0069
- -0.2253 -0.0077
- -0.2372 -0.0248
- -0.2415 -0.0448
- -0.2562 -0.0539
- -0.2901 -0.0433
- -0.3173 -0.0215
- -0.3117 0.0096
- -0.2787 0.0317
- -0.2319 0.0372
- -0.1897 0.0305
- -0.1592 0.0142
- -0.1211 -0.0049
- -0.0960 -0.0150
- -0.0842 -0.0162
- -0.0813 -0.0187
- -0.0823 -0.0193
- -0.0773 -0.0179
- -0.0621 -0.0202
- -0.0449 -0.0215
- -0.0269 -0.0307
- -0.0075 -0.0368
- 0.0266 -0.0342
diff --git a/regtest/analysis/rt-mds/plumed.dat b/regtest/analysis/rt-mds/plumed.dat
deleted file mode 100755
index 2d8d22c09ce508dc3313b4ebcface5d989294bea..0000000000000000000000000000000000000000
--- a/regtest/analysis/rt-mds/plumed.dat
+++ /dev/null
@@ -1,28 +0,0 @@
-UNITS NATURAL
-COM ATOMS=1-7 LABEL=com
-DISTANCE ATOMS=1,com LABEL=d1
-UPPER_WALLS ARG=d1 AT=2.0 KAPPA=100.
-DISTANCE ATOMS=2,com LABEL=d2
-UPPER_WALLS ARG=d2 AT=2.0 KAPPA=100.
-DISTANCE ATOMS=3,com LABEL=d3
-UPPER_WALLS ARG=d3 AT=2.0 KAPPA=100.
-DISTANCE ATOMS=4,com LABEL=d4
-UPPER_WALLS ARG=d4 AT=2.0 KAPPA=100.
-DISTANCE ATOMS=5,com LABEL=d5
-UPPER_WALLS ARG=d5 AT=2.0 KAPPA=100.
-DISTANCE ATOMS=6,com LABEL=d6
-UPPER_WALLS ARG=d6 AT=2.0 KAPPA=100.
-DISTANCE ATOMS=7,com LABEL=d7
-UPPER_WALLS ARG=d7 AT=2.0 KAPPA=100.
-
-COORDINATIONNUMBER SPECIES=1-7 MOMENTS=2-3 SWITCH={RATIONAL R_0=1.5 NN=8 MM=16} LABEL=c1
-CLASSICAL_MDS ...
- ARG=c1.moment-2,c1.moment-3
- REWEIGHT_TEMP=0.1 TEMP=0.2
- STRIDE=10
- RUN=1000
- NLOW_DIM=2
- FMT=%8.4f
- OUTPUT_FILE=list_embed
- EMBEDDING_OFILE=embed
-... CLASSICAL_MDS
diff --git a/src/analysis/Analysis.cpp b/src/analysis/Analysis.cpp
deleted file mode 100644
index 86c8c1cb59ed620f05de0dd87df744bf794b174e..0000000000000000000000000000000000000000
--- a/src/analysis/Analysis.cpp
+++ /dev/null
@@ -1,427 +0,0 @@
-/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2015 The plumed team
- (see the PEOPLE file at the root of the distribution for a list of names)
-
- See http://www.plumed-code.org for more information.
-
- This file is part of plumed, version 2.
-
- plumed is free software: you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- plumed is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with plumed. If not, see <http://www.gnu.org/licenses/>.
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-
-#include "Analysis.h"
-#include "core/ActionSet.h"
-#include "core/ActionWithValue.h"
-#include "core/PlumedMain.h"
-#include "core/Atoms.h"
-#include "tools/IFile.h"
-#include "reference/ReferenceConfiguration.h"
-#include "reference/ReferenceArguments.h"
-#include "reference/ReferenceAtoms.h"
-#include "reference/MetricRegister.h"
-
-namespace PLMD {
-namespace analysis {
-
-//+PLUMEDOC INTERNAL reweighting
-/*
-Calculate free energies from a biassed/higher temperature trajectory.
-
-We can use our knowledge of the Boltzmann distribution in the cannonical ensemble to reweight the data
-contained in trajectories. Using this procedure we can take trajectory at temperature \f$T_1\f$ and use it to
-extract probabilities at a different temperature, \f$T_2\f$, using:
-
-\f[
-P(s',t) = \frac{ \sum_{t'}^t \delta( s(x) - s' ) \exp\left( +( \left[\frac{1}{T_1} - \frac{1}{T_2}\right] \frac{U(x,t')}{k_B} \right) }{ \sum_{t'}^t \exp\left( +\left[\frac{1}{T_1} - \frac{1}{T_2}\right] \frac{U(x,t')}{k_B} \right) }
-\f]
-
-where \f$U(x,t')\f$ is the potential energy of the system. Alternatively, if a static or pseudo-static bias \f$V(x,t')\f$ is acting on
-the system we can remove this bias and get the unbiased probability distribution using:
-
-\f[
-P(s',t) = \frac{ \sum_{t'}^t \delta( s(x) - s' ) \exp\left( +\frac{V(x,t')}{k_B T} \right) }{ \sum_t'^t \exp\left( +\frac{V(x,t')}{k_B T} \right) }
-\f]
-
-*/
-//+ENDPLUMEDOC
-
-void Analysis::registerKeywords( Keywords& keys ){
- Action::registerKeywords( keys );
- ActionPilot::registerKeywords( keys );
- ActionAtomistic::registerKeywords( keys );
- ActionWithArguments::registerKeywords( keys );
- keys.use("ARG"); keys.reset_style("ARG","optional");
- keys.add("atoms","ATOMS","the atoms whose positions we are tracking for the purpose of analysing the data");
- keys.add("compulsory","METRIC","EUCLIDEAN","how are we measuring the distances between configurations");
- keys.add("compulsory","STRIDE","1","the frequency with which data should be stored for analysis");
- keys.addFlag("USE_ALL_DATA",false,"use the data from the entire trajectory to perform the analysis");
- keys.add("compulsory","RUN","the frequency with which to run the analysis algorithm. This is not required if you specify USE_ALL_DATA");
- keys.add("optional","FMT","the format that should be used in analysis output files");
- keys.addFlag("REWEIGHT_BIAS",false,"reweight the data using all the biases acting on the dynamics. For more information see \\ref reweighting.");
- keys.add("optional","TEMP","the system temperature. This is required if you are reweighting or doing free energies.");
- keys.add("optional","REWEIGHT_TEMP","reweight data from a trajectory at one temperature and output the probability "
- "distribution at a second temperature. For more information see \\ref reweighting. "
- "This is not possible during postprocessing.");
- keys.addFlag("WRITE_CHECKPOINT",false,"write out a checkpoint so that the analysis can be restarted in a later run");
- keys.add("hidden","REUSE_DATA_FROM","eventually this will allow you to analyse the same set of data multiple times");
- keys.add("hidden","IGNORE_REWEIGHTING","this allows you to ignore any reweighting factors");
- keys.reserveFlag("NOMEMORY",false,"analyse each block of data separately");
- keys.use("RESTART");
- keys.use("UPDATE_FROM");
- keys.use("UPDATE_UNTIL");
- ActionWithVessel::registerKeywords( keys ); keys.remove("TOL");
-}
-
-Analysis::Analysis(const ActionOptions&ao):
-Action(ao),
-ActionPilot(ao),
-ActionAtomistic(ao),
-ActionWithArguments(ao),
-ActionWithVessel(ao),
-single_run(false),
-nomemory(true),
-write_chq(false),
-reusing_data(false),
-ignore_reweight(false),
-needeng(false),
-idata(0),
-firstAnalysisDone(false),
-old_norm(0.0),
-ofmt("%f"),
-current_args(getNumberOfArguments()),
-argument_names(getNumberOfArguments())
-{
- parse("FMT",ofmt); // Read the format for output files
- // Make a vector containing all the argument names
- for(unsigned i=0;i<getNumberOfArguments();++i) argument_names[i]=getPntrToArgument(i)->getName();
- // Read in the metric style
- parse("METRIC",metricname); std::vector<AtomNumber> atom_numbers;
- ReferenceConfiguration* checkref=metricRegister().create<ReferenceConfiguration>( metricname );
- // Check if we should read atoms
- ReferenceAtoms* hasatoms=dynamic_cast<ReferenceAtoms*>( checkref );
- if( hasatoms ){
- parseAtomList("ATOMS",atom_numbers); requestAtoms(atom_numbers);
- log.printf(" monitoring positions of atoms ");
- for(unsigned i=0;i<atom_numbers.size();++i) log.printf("%d ",atom_numbers[i].serial() );
- log.printf("\n");
- }
- // Check if we should read arguments
- ReferenceArguments* hasargs=dynamic_cast<ReferenceArguments*>( checkref );
- if( !hasargs && getNumberOfArguments()!=0 ) error("use of arguments with metric type " + metricname + " is invalid");
- if( hasatoms && hasargs ) error("currently dependencies break if you have both arguments and atoms");
- // And delte the fake reference we created
- delete checkref;
-
- std::string prev_analysis; parse("REUSE_DATA_FROM",prev_analysis);
- if( prev_analysis.length()>0 ){
- reusing_data=true;
- mydatastash=plumed.getActionSet().selectWithLabel<Analysis*>( prev_analysis );
- if( !mydatastash ) error("could not find analysis action named " + prev_analysis );
- parseFlag("IGNORE_REWEIGHTING",ignore_reweight);
- if( ignore_reweight ) log.printf(" reusing data stored by %s but ignoring all reweighting\n",prev_analysis.c_str() );
- else log.printf(" reusing data stored by %s\n",prev_analysis.c_str() );
- } else {
- if( keywords.exists("REWEIGHT_BIAS") ){
- bool dobias; parseFlag("REWEIGHT_BIAS",dobias);
- if( dobias ){
- std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
- if( all.empty() ) error("your input file is not telling plumed to calculate anything");
- std::vector<Value*> arg( getArguments() );
- log.printf(" reweigting using the following biases ");
- for(unsigned j=0;j<all.size();j++){
- std::string flab; flab=all[j]->getLabel() + ".bias";
- if( all[j]->exists(flab) ){
- biases.push_back( all[j]->copyOutput(flab) );
- arg.push_back( all[j]->copyOutput(flab) );
- log.printf(" %s",flab.c_str());
- }
- }
- log.printf("\n");
- if( biases.empty() ) error("you are asking to reweight bias but there does not appear to be a bias acting on your system");
- requestArguments( arg );
- }
- }
-
- rtemp=0;
- if( keywords.exists("REWEIGHT_TEMP") ) parse("REWEIGHT_TEMP",rtemp);
- if( rtemp!=0 ){
- needeng=true;
- log.printf(" reweighting simulation to probabilities at temperature %f\n",rtemp);
- rtemp*=plumed.getAtoms().getKBoltzmann();
- }
- simtemp=0.; parse("TEMP",simtemp);
- if(simtemp>0) simtemp*=plumed.getAtoms().getKBoltzmann();
- else simtemp=plumed.getAtoms().getKbT();
-
- if( rtemp>0 || !biases.empty() ){
- if(simtemp==0) error("The MD engine does not pass the temperature to plumed so you have to specify it using TEMP");
- }
-
- parseFlag("USE_ALL_DATA",single_run);
- if( !single_run ){
- parse("RUN",freq );
- log.printf(" running analysis every %u steps\n",freq);
- if( freq%getStride()!= 0 ) error("Frequncy of running is not a multiple of the stride");
- ndata=freq/getStride();
- data.resize( ndata );
- for(unsigned i=0;i<ndata;++i){
- data[i]=metricRegister().create<ReferenceConfiguration>( metricname );
- data[i]->setNamesAndAtomNumbers( atom_numbers, argument_names );
- }
- logweights.resize( ndata );
- } else {
- log.printf(" analyzing all data in trajectory\n");
- }
- if( keywords.exists("NOMEMORY") ){ nomemory=false; parseFlag("NOMEMORY",nomemory); }
- if(nomemory) log.printf(" doing a separate analysis for each block of data\n");
- parseFlag("WRITE_CHECKPOINT",write_chq);
- if( write_chq && single_run ){
- write_chq=false;
- warning("ignoring WRITE_CHECKPOINT flag because we are analyzing all data");
- }
-
- // We need no restart file if we are just collecting data and analyzing all of it
- std::string filename = getName() + "_" + getLabel() + ".chkpnt";
- if( write_chq ) rfile.link(*this);
- if( getRestart() ){
- if( single_run ) error("cannot restart histogram when using the USE_ALL_DATA option");
- if( !write_chq ) warning("restarting without writing a checkpoint file is somewhat strange");
- // Read in data from input file
- readDataFromFile( filename );
- // Setup the restart file (append mode)
- if( write_chq ) rfile.open( filename.c_str() ); // In append mode automatically because of restart
- // Run the analysis if we stoped in the middle of it last time
- log.printf(" restarting analysis with %u points read from restart file\n",idata);
- } else if( write_chq ){
- // Setup the restart file (delete any old one)
- rfile.open( filename.c_str() ); // In overwrite mode automatically because there is no restart
- }
- if( write_chq ){
- rfile.addConstantField("old_normalization");
- for(unsigned i=0;i<getNumberOfArguments();++i) rfile.setupPrintValue( getPntrToArgument(i) );
- }
- }
-}
-
-void Analysis::readDataFromFile( const std::string& filename ){
- FILE* fp=fopen(filename.c_str(),"r"); double tstep, oldtstep;
- if(fp!=NULL){
- bool do_read=true, first=true;
- while (do_read) {
- PDB mypdb;
- do_read=mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());
- if(do_read){
- data[idata]->set( mypdb );
- data[idata]->parse("TIME",tstep);
- if( !first && ((tstep-oldtstep) - getStride()*plumed.getAtoms().getTimeStep())>plumed.getAtoms().getTimeStep() ){
- error("frequency of data storage in " + filename + " is not equal to frequency of data storage plumed.dat file");
- }
- data[idata]->parse("LOG_WEIGHT",logweights[idata]);
- data[idata]->parse("OLD_NORM",old_norm);
- data[idata]->checkRead();
- idata++; first=false; oldtstep=tstep;
- } else{
- break;
- }
- }
- fclose(fp);
- }
- if(old_norm>0) firstAnalysisDone=true;
-}
-
-void Analysis::parseOutputFile( const std::string& key, std::string& filename ){
- parse(key,filename);
- if(filename=="dont output") return;
-
- if( !getRestart() ){
- OFile ofile; ofile.link(*this);
- ofile.setBackupString("analysis");
- ofile.backupAllFiles(filename);
- }
-}
-
-void Analysis::prepare(){
- if(needeng) plumed.getAtoms().setCollectEnergy(true);
-}
-
-void Analysis::calculate(){
-// do nothing
-}
-
-void Analysis::accumulate(){
- // Don't store the first step (also don't store if we are getting data from elsewhere)
- if( (!single_run && getStep()==0) || reusing_data ) return;
- // This is used when we have a full quota of data from the first run
- if( !single_run && idata==logweights.size() ) return;
-
- // Retrieve the bias
- double bias=0.0; for(unsigned i=0;i<biases.size();++i) bias+=biases[i]->get();
-
- double ww=0;
- if(needeng){
- double energy=plumed.getAtoms().getEnergy()+bias;
- // Reweighting because of temperature difference
- ww=-( (1.0/rtemp) - (1.0/simtemp) )*(energy+bias);
- }
- // Reweighting because of biases
- if( !biases.empty() ) ww += bias/ simtemp;
-
- // Get the arguments ready to transfer to reference configuration
- for(unsigned i=0;i<getNumberOfArguments();++i) current_args[i]=getArgument(i);
-
- if(single_run){
- data.push_back( metricRegister().create<ReferenceConfiguration>( metricname ) );
- plumed_dbg_assert( data.size()==idata+1 );
- data[idata]->setNamesAndAtomNumbers( getAbsoluteIndexes(), argument_names );
- data[idata]->setReferenceConfig( getPositions(), current_args, getMetric() );
- logweights.push_back(ww);
- } else {
- // Get the arguments and store them in a vector of vectors
- data[idata]->setReferenceConfig( getPositions(), current_args, getMetric() );
- logweights[idata] = ww;
- }
-
- // Write data to checkpoint file
- if( write_chq ){
- rfile.rewind();
- data[idata]->print( rfile, getTime(), logweights[idata], old_norm );
- rfile.flush();
- }
- // Increment data counter
- idata++;
-}
-
-Analysis::~Analysis(){
- for(unsigned i=0;i<data.size();++i ) delete data[i];
- if( write_chq ) rfile.close();
-}
-
-std::vector<double> Analysis::getMetric() const {
- // Add more exotic metrics in here -- FlexibleHill for instance
- std::vector<double> empty;
- if( metricname=="EUCLIDEAN" ){
- empty.resize( getNumberOfArguments(), 1.0 );
- }
- return empty;
-}
-
-double Analysis::getWeight( const unsigned& idata ) const {
- if( !reusing_data ){
- plumed_dbg_assert( idata<data.size() );
- return data[idata]->getWeight();
- } else {
- return mydatastash->getWeight(idata);
- }
-}
-
-void Analysis::finalizeWeights( const bool& ignore_weights ){
- // Check that we have the correct ammount of data
- if( !reusing_data && idata!=logweights.size() ) error("something has gone wrong. Am trying to run analysis but I don't have sufficient data");
-
- norm=0; // Reset normalization constant
- if( ignore_weights ){
- for(unsigned i=0;i<logweights.size();++i){
- data[i]->setWeight(1.0); norm+=1.0;
- }
- } else if( nomemory ){
- // Find the maximum weight
- double maxweight=logweights[0];
- for(unsigned i=1;i<getNumberOfDataPoints();++i){
- if(logweights[i]>maxweight) maxweight=logweights[i];
- }
- // Calculate normalization constant
- for(unsigned i=0;i<logweights.size();++i){
- norm+=exp( logweights[i]-maxweight );
- }
- // Calculate weights (no memory)
- for(unsigned i=0;i<logweights.size();++i){
- data[i]->setWeight( exp( logweights[i]-maxweight ) );
- }
- // Calculate normalized weights (with memory)
- } else {
- // Calculate normalization constant
- for(unsigned i=0;i<logweights.size();++i){
- norm+=exp( logweights[i] );
- }
- if( !firstAnalysisDone ) old_norm=1.0;
- // Calculate weights (with memory)
- for(unsigned i=0;i<logweights.size();++i){
- data[i]->setWeight( exp( logweights[i] ) / old_norm );
- }
- if( !firstAnalysisDone ) old_norm=0.0;
- }
-
-}
-
-void Analysis::getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const {
- plumed_dbg_assert( getNumberOfAtoms()==0 );
- if( !reusing_data ){
- plumed_dbg_assert( idata<logweights.size() && point.size()==getNumberOfArguments() );
- for(unsigned i=0;i<point.size();++i) point[i]=data[idata]->getReferenceArgument(i);
- weight=data[idata]->getWeight();
- } else {
- return mydatastash->getDataPoint( idata, point, weight );
- }
-}
-
-void Analysis::runAnalysis(){
-
- // Note : could add multiple walkers here - simply read in the data from all
- // other walkers here if we are writing the check points.
-
- // Calculate the final weights from the log weights
- if( !reusing_data ){
- finalizeWeights( ignore_reweight );
- } else {
- mydatastash->finalizeWeights( ignore_reweight );
- norm=mydatastash->retrieveNorm();
- }
- // And run the analysis
- performAnalysis(); idata=0;
- // Update total normalization constant
- old_norm+=norm; firstAnalysisDone=true;
-
-}
-
-double Analysis::getNormalization() const {
- if( nomemory || !firstAnalysisDone ) return norm;
- return ( 1. + norm/old_norm );
-}
-
-double Analysis::getTemp() const {
- return simtemp;
-}
-
-void Analysis::update(){
- accumulate();
- if( !single_run ){
- if( getStep()>0 && getStep()%freq==0 ) runAnalysis();
- else if( idata==logweights.size() ) error("something has gone wrong. Probably a wrong initial time on restart");
- }
-}
-
-bool Analysis::getPeriodicityInformation(const unsigned& i, std::string& dmin, std::string& dmax){
- bool isperiodic=getPntrToArgument(i)->isPeriodic();
- if(isperiodic) getPntrToArgument(i)->getDomain(dmin,dmax);
- return isperiodic;
-}
-
-void Analysis::runFinalJobs() {
- if( !single_run ) return;
- if( getNumberOfDataPoints()==0 ) error("no data is available for analysis");
- runAnalysis();
-}
-
-}
-}
diff --git a/src/analysis/Analysis.h b/src/analysis/Analysis.h
deleted file mode 100644
index 33a01f9726c1be0dd4253b4e9f7468c9c98563f7..0000000000000000000000000000000000000000
--- a/src/analysis/Analysis.h
+++ /dev/null
@@ -1,216 +0,0 @@
-/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2014 The plumed team
- (see the PEOPLE file at the root of the distribution for a list of names)
-
- See http://www.plumed-code.org for more information.
-
- This file is part of plumed, version 2.
-
- plumed is free software: you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- plumed is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with plumed. If not, see <http://www.gnu.org/licenses/>.
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_analysis_Analysis_h
-#define __PLUMED_analysis_Analysis_h
-
-#include "core/ActionPilot.h"
-#include "core/ActionAtomistic.h"
-#include "core/ActionWithArguments.h"
-#include "vesselbase/ActionWithVessel.h"
-
-#define PLUMED_ANALYSIS_INIT(ao) Action(ao),Analysis(ao)
-
-namespace PLMD {
-
-class ReferenceConfiguration;
-
-namespace analysis {
-
-/**
-\ingroup INHERIT
-This is the abstract base class to use for implementing new methods for analyzing the trajectory, within it there
-is information as to how to go about implementing a new analysis method.
-
-*/
-
-class Analysis :
- public ActionPilot,
- public ActionAtomistic,
- public ActionWithArguments,
- public vesselbase::ActionWithVessel
- {
-private:
-/// Are we running only once for the whole trajectory
- bool single_run;
-/// Are we treating each block of data separately
- bool nomemory;
-/// Are we writing a checkpoint file
- bool write_chq;
-/// Are we reusing data stored by another analysis action
- bool reusing_data;
-/// If we are reusing data are we ignoring the reweighting in that data
- bool ignore_reweight;
-/// The Analysis action that we are reusing data from
- Analysis* mydatastash;
-/// The frequency with which we are performing analysis
- unsigned freq;
-/// Number of data point we need to run analysis
- unsigned ndata;
-/// The temperature at which we are running the calculation
- double simtemp;
-/// The temperature at which we want the histogram
- double rtemp;
-/// Do we need the energy (are we reweighting at a different temperature)
- bool needeng;
-/// The biases we are using in reweighting and the args we store them separately
- std::vector<Value*> biases;
-/// The piece of data we are inserting
- unsigned idata;
-/// The weights of all the data points
- std::vector<double> logweights;
-/// Have we analyzed the data for the first time
- bool firstAnalysisDone;
-/// The value of the old normalization constant
- double norm, old_norm;
-/// The format to use in output files
- std::string ofmt;
-/// Tempory vector to store values of arguments
- std::vector<double> current_args;
-/// List of argument names
- std::vector<std::string> argument_names;
-/// The type of metric we are using to measure distances
- std::string metricname;
-/// The checkpoint file
- OFile rfile;
-/// Read in data from a file
- void readDataFromFile( const std::string& filename );
-/// This retrieves the value of norm from the analysis action.
-/// It is only used to transfer data from one analysis action to
-/// another. You should never need to use it. If you think you need it
-/// you probably need getNormalization()
- double retrieveNorm() const ;
-/// Get the metric if we are using malonobius distance and flexible hill
- std::vector<double> getMetric() const ;
-protected:
-/// This is used to read in output file names for analysis methods. When
-/// this method is used and the calculation is not restarted old analysis
-/// files are backed up.
- void parseOutputFile( const std::string& key, std::string& filename );
-/// The data we are going to analyze
- std::vector<ReferenceConfiguration*> data;
-/// Get the name of the metric we are using to measure distances
- std::string getMetricName() const ;
-/// Return the number of arguments (this overwrites the one in ActionWithArguments)
- unsigned getNumberOfArguments() const;
-/// Return the number of data points
- unsigned getNumberOfDataPoints() const;
-/// Return the weight of the ith point
- double getWeight( const unsigned& idata ) const ;
-/// Retrieve the ith point
- void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
-/// Returns true if argument i is periodic together with the domain
- bool getPeriodicityInformation(const unsigned& i, std::string& dmin, std::string& dmax);
-/// Return the normalization constant
- double getNormalization() const;
-/// Return the set temperature (N.B. k_B T is what is returned by this function)
- double getTemp () const;
-/// Are we analyzing each data block separately (if we are not this also returns the old normalization )
- bool usingMemory() const;
-/// Convert the stored log weights to proper weights
- void finalizeWeights( const bool& ignore_weights );
-/// Overwrite ActionWithArguments getArguments() so that we don't return
-/// the bias
- std::vector<Value*> getArguments();
-/// Return the format to use for numbers in output files
- std::string getOutputFormat() const ;
-public:
- static void registerKeywords( Keywords& keys );
- Analysis(const ActionOptions&);
- ~Analysis();
- void prepare();
- void calculate();
- void update();
- void accumulate();
- virtual void performAnalysis()=0;
- void apply(){}
- void runFinalJobs();
- void runAnalysis();
- void lockRequests();
- void unlockRequests();
- void calculateNumericalDerivatives( ActionWithValue* a=NULL ){ plumed_error(); }
- bool isPeriodic(){ plumed_error(); return false; }
- unsigned getNumberOfDerivatives(){ plumed_error(); return 0; }
-};
-
-inline
-std::string Analysis::getMetricName() const {
- return metricname;
-}
-
-inline
-void Analysis::lockRequests(){
- ActionAtomistic::lockRequests();
- ActionWithArguments::lockRequests();
-}
-
-inline
-void Analysis::unlockRequests(){
- ActionAtomistic::unlockRequests();
- ActionWithArguments::unlockRequests();
-}
-
-inline
-unsigned Analysis::getNumberOfDataPoints() const {
- if( !reusing_data ){
- plumed_dbg_assert( data.size()==logweights.size() );
- return data.size();
- } else {
- return mydatastash->getNumberOfDataPoints();
- }
-}
-
-inline
-bool Analysis::usingMemory() const {
- if( !reusing_data ){
- return !nomemory;
- } else {
- return mydatastash->usingMemory();
- }
-}
-
-inline
-unsigned Analysis::getNumberOfArguments() const {
- unsigned nargs=ActionWithArguments::getNumberOfArguments();
- return nargs - biases.size();
-}
-
-inline
-double Analysis::retrieveNorm() const {
- return norm;
-}
-
-inline
-std::vector<Value*> Analysis::getArguments(){
- std::vector<Value*> arg_vals( ActionWithArguments::getArguments() );
- for(unsigned i=0;i<biases.size();++i) arg_vals.erase(arg_vals.end()-1);
- return arg_vals;
-}
-
-inline
-std::string Analysis::getOutputFormat() const {
- return ofmt;
-}
-
-}
-}
-
-#endif
diff --git a/src/analysis/AnalysisBase.cpp b/src/analysis/AnalysisBase.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..26fb94e17540d6d70c2d41ec4858ffb8198f015a
--- /dev/null
+++ b/src/analysis/AnalysisBase.cpp
@@ -0,0 +1,79 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012-2015 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "AnalysisBase.h"
+#include "core/PlumedMain.h"
+#include "core/ActionSet.h"
+
+namespace PLMD {
+namespace analysis {
+
+void AnalysisBase::registerKeywords( Keywords& keys ){
+ Action::registerKeywords( keys );
+ ActionPilot::registerKeywords( keys );
+ ActionAtomistic::registerKeywords( keys );
+ ActionWithArguments::registerKeywords( keys );
+ ActionWithVessel::registerKeywords( keys ); keys.remove("TOL"); keys.remove("LOWMEM");
+ keys.add("atoms-2","USE_OUTPUT_DATA_FROM","use the ouput of the analysis performed by this object as input to your new analysis object");
+}
+
+AnalysisBase::AnalysisBase(const ActionOptions&ao):
+Action(ao),
+ActionPilot(ao),
+ActionAtomistic(ao),
+ActionWithArguments(ao),
+ActionWithVessel(ao),
+mydata(NULL)
+{
+ // We have an if statement here so that this doesn't break with READ_DISSIMILARITIES
+ std::string datastr; if( keywords.exists("USE_OUTPUT_DATA_FROM") ) parse("USE_OUTPUT_DATA_FROM",datastr);
+ if( keywords.exists("USE_OUTPUT_DATA_FROM") &&
+ datastr.length()==0 &&
+ !keywords.exists("REUSE_INPUT_DATA_FROM") ) error("input analysis action was not specified use USE_OUTPUT_DATA_FROM");
+ if( datastr.length()>0 ){
+ mydata=plumed.getActionSet().selectWithLabel<AnalysisBase*>( datastr );
+ log.printf(" performing analysis on output from %s \n",datastr.c_str() );
+ if( !mydata ) error("could not find analysis action named " + datastr );
+ freq=mydata->freq; use_all_data=mydata->use_all_data;
+ if( !use_all_data ) setStride( freq );
+ }
+}
+
+void AnalysisBase::update(){
+ // Do nothing if we are just analysing at the end of the calculation
+ if( use_all_data ) return ;
+ // Check that we are on step
+ plumed_dbg_assert( getStep()%freq==0 );
+ // And do the analysis
+ if( getStep()>0 ) performAnalysis();
+}
+
+void AnalysisBase::runFinalJobs(){
+ // Nothing to do if we are not analysing all the data in the trajectory
+ if( !use_all_data ) return;
+ // Erm ... user has done something weird
+ if( getNumberOfDataPoints()==0 ) error("no data is available for analysis");
+ // And do the analysis
+ if( use_all_data ) performAnalysis();
+}
+
+}
+}
diff --git a/src/analysis/AnalysisBase.h b/src/analysis/AnalysisBase.h
new file mode 100644
index 0000000000000000000000000000000000000000..cfa1a613a1d21ece74eaf3c2a38b91cfeae1c298
--- /dev/null
+++ b/src/analysis/AnalysisBase.h
@@ -0,0 +1,166 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012-2014 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_analysis_AnalysisBase_h
+#define __PLUMED_analysis_AnalysisBase_h
+
+#include "core/ActionPilot.h"
+#include "core/ActionAtomistic.h"
+#include "core/ActionWithArguments.h"
+#include "vesselbase/ActionWithVessel.h"
+
+namespace PLMD {
+
+class ReferenceConfiguration;
+
+namespace analysis {
+
+/**
+\ingroup INHERIT
+This is the abstract base class to use for implementing new methods for analyzing the trajectory. You can find
+\ref AddingAnAnalysis "information" on how to use it to implement new analysis methods here.
+
+*/
+
+class AnalysisBase :
+ public ActionPilot,
+ public ActionAtomistic,
+ public ActionWithArguments,
+ public vesselbase::ActionWithVessel
+ {
+friend class ReadDissimilarityMatrix;
+friend class AnalysisWithDataCollection;
+private:
+/// Just run the analysis a single time
+ bool use_all_data;
+/// The frequency with which we are performing analysis
+ unsigned freq;
+protected:
+/// The Analysis action that we are reusing data from
+ AnalysisBase* mydata;
+public:
+ static void registerKeywords( Keywords& keys );
+ AnalysisBase(const ActionOptions&);
+/// These are required because we inherit from both ActionAtomistic and ActionWithArguments
+ void lockRequests();
+ void unlockRequests();
+/// Return the number of data points
+ virtual unsigned getNumberOfDataPoints() const ;
+/// Return the index of the data point in the base class
+ virtual unsigned getDataPointIndexInBase( const unsigned& idata ) const ;
+/// Return the weight of the ith point
+ virtual double getWeight( const unsigned& idata ) const ;
+/// Are we using memory in this calculation this affects the weights of points
+ virtual bool usingMemory() const ;
+/// Return the normalisation constant for the calculation
+ virtual double getNormalization() const ;
+/// Ensures that dissimilarities were set somewhere
+ virtual bool dissimilaritiesWereSet() const ;
+/// Get the squared dissimilarity between two reference configurations
+ virtual double getDissimilarity( const unsigned& i, const unsigned& j );
+/// This returns the label of the object that contains the base data
+ virtual std::string getBaseDataLabel() const ;
+/// Get the ith data point
+ virtual void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
+/// Get a reference configuration
+ virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata );
+/// This actually performs the analysis
+ virtual void performAnalysis()=0;
+/// These overwrite things from inherited classes (this is a bit of a fudge)
+ bool isPeriodic(){ plumed_error(); return false; }
+ unsigned getNumberOfDerivatives(){ plumed_error(); return 0; }
+ void calculateNumericalDerivatives( ActionWithValue* a=NULL ){ plumed_error(); }
+/// Calculate and apply do nothing all analysis is done during update step
+ void calculate(){}
+ void apply(){}
+/// This will call the analysis to be performed
+ virtual void update();
+/// This calls the analysis to be performed in the final step of the calculation
+/// i.e. when use_all_data is true
+ virtual void runFinalJobs();
+};
+
+inline
+void AnalysisBase::lockRequests(){
+ ActionAtomistic::lockRequests();
+ ActionWithArguments::lockRequests();
+}
+
+inline
+void AnalysisBase::unlockRequests(){
+ ActionAtomistic::unlockRequests();
+ ActionWithArguments::unlockRequests();
+}
+
+inline
+unsigned AnalysisBase::getNumberOfDataPoints() const {
+ return mydata->getNumberOfDataPoints();
+}
+
+inline
+unsigned AnalysisBase::getDataPointIndexInBase( const unsigned& idata ) const {
+ return mydata->getDataPointIndexInBase( idata );
+}
+
+inline
+double AnalysisBase::getWeight( const unsigned& idata ) const {
+ return mydata->getWeight( idata );
+}
+
+inline
+bool AnalysisBase::usingMemory() const {
+ return mydata->usingMemory();
+}
+
+inline
+double AnalysisBase::getNormalization() const {
+ return mydata->getNormalization();
+}
+
+inline
+bool AnalysisBase::dissimilaritiesWereSet() const {
+ return mydata->dissimilaritiesWereSet();
+}
+
+inline
+double AnalysisBase::getDissimilarity( const unsigned& i, const unsigned& j ){
+ return mydata->getDissimilarity( i, j );
+}
+
+inline
+std::string AnalysisBase::getBaseDataLabel() const {
+ return mydata->getBaseDataLabel();
+}
+
+inline
+void AnalysisBase::getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const {
+ mydata->getDataPoint( idata, point, weight );
+}
+
+inline
+ReferenceConfiguration* AnalysisBase::getReferenceConfiguration( const unsigned& idata ){
+ return mydata->getReferenceConfiguration( idata );
+}
+
+}
+}
+
+#endif
diff --git a/src/analysis/AnalysisWithDataCollection.cpp b/src/analysis/AnalysisWithDataCollection.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..e19409dbdcc4219b0fcf8b8177bf4e001fb4ea83
--- /dev/null
+++ b/src/analysis/AnalysisWithDataCollection.cpp
@@ -0,0 +1,343 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012-2015 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "AnalysisWithDataCollection.h"
+#include "reference/ReferenceConfiguration.h"
+#include "reference/ReferenceArguments.h"
+#include "reference/ReferenceAtoms.h"
+#include "reference/MetricRegister.h"
+#include "core/PlumedMain.h"
+#include "core/ActionSet.h"
+#include "core/Atoms.h"
+#include "tools/IFile.h"
+
+namespace PLMD {
+namespace analysis {
+
+void AnalysisWithDataCollection::registerKeywords( Keywords& keys ){
+ AnalysisBase::registerKeywords( keys );
+ keys.use("ARG"); keys.reset_style("ARG","atoms-1");
+ keys.add("atoms-1","ATOMS","the atoms whose positions we are tracking for the purpose of analysing the data");
+ keys.add("hidden","METRIC","how are we measuring the distances between configurations. If you have only arguments this will by default be the euclidean metric. You must specify a metric if you are analysing atoms");
+ keys.add("atoms-1","STRIDE","the frequency with which data should be stored for analysis. By default data is collected on every step");
+ keys.add("atoms-1","RUN","the frequency with which to run the analysis algorithms.");
+ keys.addFlag("USE_ALL_DATA",false,"just analyse all the data in the trajectory. This option should be used in tandem with ATOMS/ARG + STRIDE");
+ keys.addFlag("REWEIGHT_BIAS",false,"reweight the data using all the biases acting on the dynamics. This option must be used in tandem with ATOMS/ARG + STRIDE. For more information see \\ref reweighting");
+ keys.add("optional","REWEIGHT_TEMP","reweight data from a trajectory at one temperature and output the probability distribution at a second temperature. This option must be used in tandem with ATOMS/ARG + STRIDE. For more information see \\ref reweighting");
+ keys.add("optional","TEMP","the system temperature. This is required if you are reweighting (REWEIGHT_BIAS/REWEIGHT_TEMP) or if you are calculating free energies. You are not required to specify the temperature if this is passed by the underlying MD code.");
+ keys.add("atoms-3","REUSE_INPUT_DATA_FROM","do a second form of analysis on the data stored by a previous analysis object");
+ keys.addFlag("WRITE_CHECKPOINT",false,"write out a checkpoint so that the analysis can be restarted in a later run. This option must be used in tandem with ATOMS/ARG + STRIDE.");
+ keys.addFlag("NOMEMORY",false,"do a block averaging i.e. analyse each block of data separately. This option must be used in tandem with ATOMS/ARG + STRIDE.");
+ keys.use("RESTART"); keys.use("UPDATE_FROM"); keys.use("UPDATE_UNTIL");
+}
+
+AnalysisWithDataCollection::AnalysisWithDataCollection( const ActionOptions& ao ):
+Action(ao),
+AnalysisBase(ao),
+nomemory(false),
+write_chq(false),
+rtemp(0),
+idata(0),
+firstAnalysisDone(false),
+old_norm(0.0)
+{
+ if( !mydata ){
+ // Check if we are using the input data from another action
+ std::string datastr; parse("REUSE_INPUT_DATA_FROM",datastr);
+ if( datastr.length()>0 ) {
+ AnalysisWithDataCollection* checkd = plumed.getActionSet().selectWithLabel<AnalysisWithDataCollection*>( datastr );
+ if( !checkd) error("cannot reuse input data from action with label " + datastr + " as this does not store data");
+ mydata=dynamic_cast<AnalysisBase*>( checkd );
+ log.printf(" performing analysis on input data stored in from %s \n",datastr.c_str() );
+ freq=mydata->freq; use_all_data=mydata->use_all_data;
+ if( !use_all_data ) setStride( freq );
+ // If we are not using input data from elsewhere or output data from another object then
+ // we must collect data from the trajectory
+ } else {
+ // Get information on numbers of atoms and argument names
+ std::vector<AtomNumber> atom_numbers; std::vector<std::string> argument_names( getNumberOfArguments() );
+ for(unsigned i=0;i<getNumberOfArguments();++i) argument_names[i]=getPntrToArgument(i)->getName();
+
+ // Read in information on the metric that is being used in this analysis object
+ parse("METRIC",metricname);
+ if( metricname.length()==0 ) metricname="EUCLIDEAN";
+ ReferenceConfiguration* checkref=metricRegister().create<ReferenceConfiguration>( metricname );
+ // Check if we should read atoms
+ ReferenceAtoms* hasatoms=dynamic_cast<ReferenceAtoms*>( checkref );
+ if( hasatoms ){
+ parseAtomList("ATOMS",atom_numbers); requestAtoms(atom_numbers);
+ if( atom_numbers.size()==0 ) error("no atom positions have been specified in input");
+ log.printf(" monitoring positions of atoms ");
+ for(unsigned i=0;i<atom_numbers.size();++i) log.printf("%d ",atom_numbers[i].serial() );
+ log.printf("\n");
+ }
+ // Check if we should read arguments
+ ReferenceArguments* hasargs=dynamic_cast<ReferenceArguments*>( checkref );
+ if( !hasargs && getNumberOfArguments()!=0 ) error("use of arguments with metric type " + metricname + " is invalid");
+ if( hasargs && getNumberOfArguments()==0 ) error("no arguments have been specified in input");
+ if( hasatoms && hasargs ) error("currently dependencies break if you have both arguments and atoms"); // Not sure if this is really a problem anymore
+ // And delte the fake reference we created
+ delete checkref;
+ log.printf(" storing data as %s type reference objects \n",metricname.c_str() );
+
+ // Read in the information about how often to run the analysis (storage is read in in ActionPilot.cpp)
+ parseFlag("USE_ALL_DATA",use_all_data);
+ if(!use_all_data){
+ parse("RUN",freq);
+ // Setup everything given the ammount of data that we will have in each analysis
+ if( freq%getStride()!= 0 ) error("Frequncy of running is not a multiple of the stride");
+ unsigned ndata=freq/getStride(); data.resize(ndata); logweights.resize( ndata );
+ for(unsigned i=0;i<ndata;++i){
+ data[i]=metricRegister().create<ReferenceConfiguration>( metricname );
+ data[i]->setNamesAndAtomNumbers( atom_numbers, argument_names );
+ }
+ log.printf(" running analysis every %u steps\n",freq);
+ // Check if we are doing block averaging
+ parseFlag("NOMEMORY",nomemory);
+ if(nomemory) log.printf(" doing block averaging and analysing each portion of trajectory separately\n");
+ } else {
+ log.printf(" analysing all data in trajectory\n");
+ }
+
+ // Read in stuff for reweighting of trajectories
+
+ // Reweighting for biases
+ bool dobias; parseFlag("REWEIGHT_BIAS",dobias);
+ if( dobias ){
+ std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
+ if( all.empty() ) error("your input file is not telling plumed to calculate anything");
+ std::vector<Value*> arg( getArguments() );
+ log.printf(" reweigting using the following biases ");
+ for(unsigned j=0;j<all.size();j++){
+ std::string flab; flab=all[j]->getLabel() + ".bias";
+ if( all[j]->exists(flab) ){
+ biases.push_back( all[j]->copyOutput(flab) );
+ arg.push_back( all[j]->copyOutput(flab) );
+ log.printf(" %s",flab.c_str());
+ }
+ }
+ log.printf("\n");
+ if( biases.empty() ) error("you are asking to reweight bias but there does not appear to be a bias acting on your system");
+ requestArguments( arg );
+ }
+
+ // Reweighting for temperatures
+ rtemp=0; parse("REWEIGHT_TEMP",rtemp);
+ if( rtemp!=0 ){
+ rtemp*=plumed.getAtoms().getKBoltzmann();
+ log.printf(" reweighting simulation to probabilities at temperature %f\n",rtemp);
+ }
+ // Now retrieve the temperature in the simulation
+ simtemp=0; parse("TEMP",simtemp);
+ if(simtemp>0) simtemp*=plumed.getAtoms().getKBoltzmann();
+ else simtemp=plumed.getAtoms().getKbT();
+ if(simtemp==0 && (rtemp!=0 || !biases.empty()) ) error("The MD engine does not pass the temperature to plumed so you have to specify it using TEMP");
+
+ // Check if a check point is required (this should be got rid of at some point when we have proper checkpointing) GAT
+ parseFlag("WRITE_CHECKPOINT",write_chq);
+ std::string filename = getName() + "_" + getLabel() + ".chkpnt";
+ if( write_chq ) rfile.link(*this);
+ if( getRestart() ){
+ if( !write_chq ) warning("restarting without writing a checkpoint file is somewhat strange");
+ // Read in data from input file
+ readCheckPointFile( filename );
+ // Setup the restart file (append mode)
+ if( write_chq ) rfile.open( filename.c_str() ); // In append mode automatically because of restart
+ // Run the analysis if we stoped in the middle of it last time
+ log.printf(" restarting analysis with %u points read from restart file\n",idata);
+ } else if( write_chq ){
+ // Setup the restart file (delete any old one)
+ rfile.open( filename.c_str() ); // In overwrite mode automatically because there is no restart
+ }
+ if( write_chq ){
+ rfile.addConstantField("old_normalization");
+ for(unsigned i=0;i<getNumberOfArguments();++i) rfile.setupPrintValue( getPntrToArgument(i) );
+ }
+ // This is the end of the stuff for the checkpoint file - hopefully get rid of all this in not too distant future GAT
+ }
+ }
+}
+
+AnalysisWithDataCollection::~AnalysisWithDataCollection(){
+ for(unsigned i=0;i<data.size();++i ) delete data[i];
+ if( write_chq ) rfile.close();
+}
+
+
+void AnalysisWithDataCollection::readCheckPointFile( const std::string& filename ){
+ FILE* fp=fopen(filename.c_str(),"r"); double tstep, oldtstep;
+ if(fp!=NULL){
+ bool do_read=true, first=true;
+ while (do_read) {
+ PDB mypdb;
+ do_read=mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());
+ if(do_read){
+ data[idata]->set( mypdb );
+ data[idata]->parse("TIME",tstep);
+ if( !first && ((tstep-oldtstep) - getStride()*plumed.getAtoms().getTimeStep())>plumed.getAtoms().getTimeStep() ){
+ error("frequency of data storage in " + filename + " is not equal to frequency of data storage plumed.dat file");
+ }
+ data[idata]->parse("LOG_WEIGHT",logweights[idata]);
+ data[idata]->parse("OLD_NORM",old_norm);
+ data[idata]->checkRead();
+ idata++; first=false; oldtstep=tstep;
+ } else{
+ break;
+ }
+ }
+ fclose(fp);
+ }
+ if(old_norm>0) firstAnalysisDone=true;
+}
+
+void AnalysisWithDataCollection::prepare(){
+ if(rtemp!=0) plumed.getAtoms().setCollectEnergy(true);
+}
+
+double AnalysisWithDataCollection::getWeight( const unsigned& idat ) const {
+ if( !mydata ){ plumed_dbg_assert( idat<data.size() ); return data[idat]->getWeight(); }
+ return AnalysisBase::getWeight( idat );
+}
+
+void AnalysisWithDataCollection::getDataPoint( const unsigned& idat, std::vector<double>& point, double& weight ) const {
+ if( !mydata ){
+ plumed_dbg_assert( idat<data.size() && point.size()==getNumberOfArguments() );
+ weight = data[idat]->getWeight();
+ for(unsigned i=0;i<point.size();++i) point[i]=data[idat]->getReferenceArgument(i);
+ } else {
+ AnalysisBase::getDataPoint( idat, point, weight );
+ }
+}
+
+ReferenceConfiguration* AnalysisWithDataCollection::getReferenceConfiguration( const unsigned& idat ){
+ if( !mydata ){ plumed_dbg_assert( idat<data.size() ); return data[idat]; }
+ return AnalysisBase::getReferenceConfiguration( idat );
+}
+
+void AnalysisWithDataCollection::update(){
+ if( mydata ){ AnalysisBase::update(); return; }
+
+ // Ignore first bit of data if we are not using all data - this is a weird choice - I am not sure I understand GAT (perhaps this should be changed)?
+ if( !use_all_data && getStep()==0 ) return ;
+
+ // This bit does the collection of data
+ if( idata<logweights.size() || use_all_data ){
+ // Retrieve the bias
+ double bias=0.0; for(unsigned i=0;i<biases.size();++i) bias+=biases[i]->get();
+
+ double ww=0;
+ if(rtemp!=0){
+ double energy=plumed.getAtoms().getEnergy()+bias;
+ // Reweighting because of temperature difference
+ ww=-( (1.0/rtemp) - (1.0/simtemp) )*(energy+bias);
+ }
+ // Reweighting because of biases
+ if( !biases.empty() ) ww += bias/simtemp;
+
+ // Get the arguments ready to transfer to reference configuration
+ std::vector<double> current_args( getNumberOfArguments() );
+ for(unsigned i=0;i<getNumberOfArguments();++i) current_args[i]=getArgument(i);
+ // Could add stuff for fancy metrics here eventually but for now unecessary
+ std::vector<double> mymetric( getNumberOfArguments(), 1.0 );
+
+ if(use_all_data){
+ data.push_back( metricRegister().create<ReferenceConfiguration>( metricname ) );
+ plumed_dbg_assert( data.size()==idata+1 );
+ std::vector<std::string> argument_names( getNumberOfArguments() );
+ for(unsigned i=0;i<getNumberOfArguments();++i) argument_names[i] = getPntrToArgument(i)->getName();
+ data[idata]->setNamesAndAtomNumbers( getAbsoluteIndexes(), argument_names );
+ data[idata]->setReferenceConfig( getPositions(), current_args, mymetric );
+ logweights.push_back(ww);
+ } else {
+ // Get the arguments and store them in a vector of vectors
+ data[idata]->setReferenceConfig( getPositions(), current_args, mymetric );
+ logweights[idata] = ww;
+ }
+
+ // Write data to checkpoint file
+ if( write_chq ){
+ rfile.rewind();
+ if( plumed.getAtoms().usingNaturalUnits() ) data[idata]->print( 1.0, rfile, getTime(), logweights[idata], old_norm );
+ else data[idata]->print( atoms.getUnits().getLength()/0.1, rfile, getTime(), logweights[idata], old_norm );
+ rfile.flush();
+ }
+ // Increment data counter
+ idata++;
+ }
+
+ // This makes sure analysis is done when it should be done
+ if( !use_all_data ){
+ if( getStep()>0 && getStep()%freq==0 ) runAnalysis();
+ else if( idata==logweights.size() ) error("something has gone wrong. Probably a wrong initial time on restart");
+ }
+}
+
+void AnalysisWithDataCollection::runFinalJobs(){
+ if( mydata ){ AnalysisBase::runFinalJobs(); return; }
+ if( use_all_data ) runAnalysis();
+}
+
+void AnalysisWithDataCollection::runAnalysis(){
+ // Note : could add multiple walkers here - simply read in the data from all
+ // other walkers here if we are writing the check points.
+
+ // Ensure weights are not finalized if we are using readDissimilarityMatrix
+ if( logweights.size()>0 ){
+ // Check for errors
+ if( getNumberOfDataPoints()==0 ) error("no data is available for analysis");
+ if( idata!=logweights.size() ) error("something has gone wrong. Am trying to run analysis but I don't have sufficient data");
+ norm=0; // Reset normalization constant
+ if( biases.empty() && rtemp==0 ){
+ for(unsigned i=0;i<logweights.size();++i){
+ data[i]->setWeight(1.0); norm+=1.0;
+ }
+ } else if( nomemory ){
+ // Find the maximum weight
+ double maxweight=logweights[0];
+ for(unsigned i=1;i<getNumberOfDataPoints();++i){
+ if(logweights[i]>maxweight) maxweight=logweights[i];
+ }
+ // Calculate normalization constant
+ for(unsigned i=0;i<logweights.size();++i){
+ norm+=exp( logweights[i]-maxweight );
+ }
+ // Calculate weights (no memory)
+ for(unsigned i=0;i<logweights.size();++i) data[i]->setWeight( exp( logweights[i]-maxweight ) );
+ // Calculate normalized weights (with memory)
+ } else {
+ // Calculate normalization constant
+ for(unsigned i=0;i<logweights.size();++i){
+ norm+=exp( logweights[i] );
+ }
+ if( !firstAnalysisDone ) old_norm=1.0;
+ // Calculate weights (with memory)
+ for(unsigned i=0;i<logweights.size();++i) data[i]->setWeight( exp( logweights[i] ) / old_norm );
+ if( !firstAnalysisDone ) old_norm=0.0;
+ }
+ }
+ // And run the analysis
+ performAnalysis(); idata=0;
+ // Update total normalization constant
+ old_norm+=norm; firstAnalysisDone=true;
+}
+
+}
+}
diff --git a/src/analysis/AnalysisWithDataCollection.h b/src/analysis/AnalysisWithDataCollection.h
new file mode 100644
index 0000000000000000000000000000000000000000..2d4dd9bc6b56ba3ea0339a3dea43c5e57f2dbe66
--- /dev/null
+++ b/src/analysis/AnalysisWithDataCollection.h
@@ -0,0 +1,148 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012-2014 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_analysis_AnalysisWithDataCollection_h
+#define __PLUMED_analysis_AnalysisWithDataCollection_h
+
+#include "AnalysisBase.h"
+
+namespace PLMD {
+
+class ReferenceConfiguration;
+
+namespace analysis {
+
+class AnalysisWithDataCollection : public AnalysisBase {
+private:
+/// Are we treating each block of data separately
+ bool nomemory;
+/// Are we writing a checkpoint file
+ bool write_chq;
+/// The temperature at which we are running the calculation
+ double simtemp;
+/// The temperature at which we want the histogram
+ double rtemp;
+/// The biases we are using in reweighting and the args we store them separately
+ std::vector<Value*> biases;
+/// The piece of data we are inserting
+ unsigned idata;
+/// The data we are going to analyze
+ std::vector<ReferenceConfiguration*> data;
+/// The weights of all the data points
+ std::vector<double> logweights;
+/// Have we analyzed the data for the first time
+ bool firstAnalysisDone;
+/// The value of the old normalization constant
+ double norm, old_norm;
+/// List of argument names
+ std::vector<std::string> argument_names;
+/// The type of metric we are using to measure distances
+ std::string metricname;
+/// The checkpoint file --- really I would like to get rid of this and have some universal mechanism and a single file GT
+ OFile rfile;
+/// Read the checkpoint file
+ void readCheckPointFile( const std::string& filename );
+/// Perform the analysis -- we have a funciton as it is called from both runFinalJobs() and upate()
+ void runAnalysis();
+protected:
+/// Return the temperature (used by Histogram)
+ double getTemp() const { return simtemp; }
+public:
+ static void registerKeywords( Keywords& keys );
+ AnalysisWithDataCollection(const ActionOptions&);
+ ~AnalysisWithDataCollection();
+/// Return the number of arguments (this overwrites the one in ActionWithArguments)
+ unsigned getNumberOfArguments() const;
+/// Return the number of data points
+ virtual unsigned getNumberOfDataPoints() const ;
+/// Return the index of the data point in the base class
+ virtual unsigned getDataPointIndexInBase( const unsigned& idata ) const ;
+/// Return the weight of the ith point
+ virtual double getWeight( const unsigned& idata ) const ;
+/// Are we using memory in this calculation this affects the weights
+ virtual bool usingMemory() const ;
+/// Return the normalisation constant for the calculation
+ virtual double getNormalization() const ;
+/// By default dissimilarities are not set - they are only set in dissimilarity objects
+ virtual bool dissimilaritiesWereSet() const ;
+/// This returns the label of the object that contains the base data
+ std::string getBaseDataLabel() const ;
+/// Get the ith data point
+ virtual void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
+/// Get a reference configuration
+ virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat );
+/// This ensures that the energy is stored if we are reweighting
+ void prepare();
+/// This stores the data and calls the analysis to be performed
+ void update();
+/// This does the analysis if it is to be done in the final step of the calculation
+ void runFinalJobs();
+};
+
+inline
+unsigned AnalysisWithDataCollection::getNumberOfDataPoints() const {
+ if( !mydata ) return data.size();
+ return AnalysisBase::getNumberOfDataPoints();
+}
+
+inline
+unsigned AnalysisWithDataCollection::getDataPointIndexInBase( const unsigned& idata ) const {
+ if( !mydata ) return idata;
+ return AnalysisBase::getDataPointIndexInBase( idata );
+}
+
+inline
+bool AnalysisWithDataCollection::usingMemory() const {
+ if( !mydata ) return !nomemory;
+ return AnalysisBase::usingMemory();
+}
+
+inline
+bool AnalysisWithDataCollection::dissimilaritiesWereSet() const {
+ if( !mydata ) return false;
+ return AnalysisBase::dissimilaritiesWereSet();
+}
+
+inline
+double AnalysisWithDataCollection::getNormalization() const {
+ if( !mydata ){
+ if( nomemory || !firstAnalysisDone ) return norm;
+ return ( 1. + norm/old_norm );
+ }
+ return AnalysisBase::getNormalization();
+}
+
+inline
+std::string AnalysisWithDataCollection::getBaseDataLabel() const {
+ if( !mydata ) return getLabel();
+ return AnalysisBase::getBaseDataLabel();
+}
+
+inline
+unsigned AnalysisWithDataCollection::getNumberOfArguments() const {
+ unsigned nargs=ActionWithArguments::getNumberOfArguments();
+ return nargs - biases.size();
+}
+
+}
+}
+
+#endif
diff --git a/src/analysis/AnalysisWithLandmarks.cpp b/src/analysis/AnalysisWithLandmarks.cpp
deleted file mode 100644
index 4a4548b884a11ec9317ba71c904d336be0426fbc..0000000000000000000000000000000000000000
--- a/src/analysis/AnalysisWithLandmarks.cpp
+++ /dev/null
@@ -1,79 +0,0 @@
-/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013,2014 The plumed team
- (see the PEOPLE file at the root of the distribution for a list of names)
-
- See http://www.plumed-code.org for more information.
-
- This file is part of plumed, version 2.
-
- plumed is free software: you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- plumed is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with plumed. If not, see <http://www.gnu.org/licenses/>.
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#include "AnalysisWithLandmarks.h"
-#include "LandmarkRegister.h"
-#include "LandmarkSelectionBase.h"
-
-//+PLUMEDOC INTERNAL landmarkselection
-/*
-This is currently a filler page.
-
-Just use LANDMARKS=ALL. More complex versions will appear in later versions.
-
-*/
-//+ENDPLUMEDOC
-
-namespace PLMD {
-namespace analysis {
-
-void AnalysisWithLandmarks::registerKeywords( Keywords& keys ){
- Analysis::registerKeywords( keys );
- keys.add("compulsory","LANDMARKS","ALL","only use a subset of the data that was collected. "
- "For more information on the landmark selection algorithms that are available in "
- "plumed see \\ref landmarkselection.");
-}
-
-AnalysisWithLandmarks::AnalysisWithLandmarks( const ActionOptions& ao):
-Action(ao),
-Analysis(ao),
-data_to_analyze(NULL)
-{
- std::string linput; parse("LANDMARKS",linput);
- std::vector<std::string> words=Tools::getWords(linput);
- landmarkSelector=landmarkRegister().create( LandmarkSelectionOptions(words,this) );
- log.printf(" %s\n", landmarkSelector->description().c_str() );
-}
-
-AnalysisWithLandmarks::~AnalysisWithLandmarks(){
- delete landmarkSelector;
-}
-
-void AnalysisWithLandmarks::setDataToAnalyze( MultiReferenceBase* mydata ){
- data_to_analyze=mydata;
-}
-
-unsigned AnalysisWithLandmarks::getNumberOfLandmarks() const {
- return landmarkSelector->getNumberOfLandmarks();
-}
-
-void AnalysisWithLandmarks::performAnalysis(){
- plumed_assert( data_to_analyze );
- landmarkSelector->selectLandmarks( data_to_analyze );
- analyzeLandmarks();
-}
-
-void AnalysisWithLandmarks::performTask( const unsigned& taskIndex, const unsigned& current, MultiValue& myvals ) const {
- plumed_merror("Should not be here");
-}
-
-}
-}
diff --git a/src/analysis/AnalysisWithLandmarks.h b/src/analysis/AnalysisWithLandmarks.h
deleted file mode 100644
index 86426fc7961c612b86af1e9c0bf6ad25cd96991b..0000000000000000000000000000000000000000
--- a/src/analysis/AnalysisWithLandmarks.h
+++ /dev/null
@@ -1,61 +0,0 @@
-/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2014 The plumed team
- (see the PEOPLE file at the root of the distribution for a list of names)
-
- See http://www.plumed-code.org for more information.
-
- This file is part of plumed, version 2.
-
- plumed is free software: you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- plumed is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with plumed. If not, see <http://www.gnu.org/licenses/>.
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_analysis_AnalysisWithLandmarks_h
-#define __PLUMED_analysis_AnalysisWithLandmarks_h
-
-#include "Analysis.h"
-
-namespace PLMD {
-
-class MultiReferenceBase;
-
-namespace analysis {
-
-class LandmarkSelectionBase;
-
-class AnalysisWithLandmarks : public Analysis {
-friend class LandmarkSelectionBase;
-friend class CopyAllFrames;
-private:
-/// This object selects landmarks from the data
- LandmarkSelectionBase* landmarkSelector;
-/// A pointer to the data we are analyzing
- MultiReferenceBase* data_to_analyze;
-protected:
-/// Set the data that needs to be analyzed
- void setDataToAnalyze( MultiReferenceBase* mydata );
-/// Return the number of landmarks we are selecting
- unsigned getNumberOfLandmarks() const ;
-public:
- static void registerKeywords( Keywords& keys );
- AnalysisWithLandmarks( const ActionOptions& );
- ~AnalysisWithLandmarks();
-/// Do the analysis
- void performAnalysis();
- virtual void analyzeLandmarks()=0;
-/// This does nothing
- void performTask( const unsigned& , const unsigned& , MultiValue& ) const ;
-};
-
-}
-}
-#endif
diff --git a/src/analysis/ClassicalMultiDimensionalScaling.cpp b/src/analysis/ClassicalMultiDimensionalScaling.cpp
deleted file mode 100644
index f64e5211d5a1f1a4c2be805f11ac494c526516bf..0000000000000000000000000000000000000000
--- a/src/analysis/ClassicalMultiDimensionalScaling.cpp
+++ /dev/null
@@ -1,248 +0,0 @@
-/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013,2014 The plumed team
- (see the PEOPLE file at the root of the distribution for a list of names)
-
- See http://www.plumed-code.org for more information.
-
- This file is part of plumed, version 2.
-
- plumed is free software: you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- plumed is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with plumed. If not, see <http://www.gnu.org/licenses/>.
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#include "AnalysisWithLandmarks.h"
-#include "ClassicalScaling.h"
-#include "reference/PointWiseMapping.h"
-#include "core/ActionRegister.h"
-
-namespace PLMD {
-namespace analysis {
-
-//+PLUMEDOC ANALYSIS CLASSICAL_MDS
-/*
-Create a low-dimensional projection of a trajectory using the classical multidimensional
-scaling algorithm.
-
-Multidimensional scaling (MDS) is similar to what is done when you make a map. You start with distances
-between London, Belfast, Paris and Dublin and then you try to arrange points on a piece of paper so that the (suitably scaled)
-distances between the points in your map representing each of those cities are related to the true distances between the cities.
-Stating this more mathematically MDS endeavors to find an <a href="http://en.wikipedia.org/wiki/Isometry">isometry</a>
-between points distributed in a high-dimensional space and a set of points distributed in a low-dimensional plane.
-In other words, if we have \f$M\f$ \f$D\f$-dimensional points, \f$\mathbf{X}\f$,
-and we can calculate dissimilarities between pairs them, \f$D_{ij}\f$, we can, with an MDS calculation, try to create \f$M\f$ projections,
-\f$\mathbf{x}\f$, of the high dimensionality points in a \f$d\f$-dimensional linear space by trying to arrange the projections so that the
-Euclidean distances between pairs of them, \f$d_{ij}\f$, resemble the dissimilarities between the high dimensional points. In short we minimize:
-
-\f[
-\chi^2 = \sum_{i \ne j} \left( D_{ij} - d_{ij} \right)^2
-\f]
-
-where \f$D_{ij}\f$ is the distance between point \f$X^{i}\f$ and point \f$X^{j}\f$ and \f$d_{ij}\f$ is the distance between the projection
-of \f$X^{i}\f$, \f$x^i\f$, and the projection of \f$X^{j}\f$, \f$x^j\f$. A tutorial on this approach can be used to analyse simulations
-can be found in the tutorial \ref belfast-3 and in the following <a href="https://www.youtube.com/watch?v=ofC2qz0_9_A&feature=youtu.be" > short video.</a>
-
-\par Examples
-
-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
-CLASSICAL_MDS ...
- ATOMS=1-256
- METRIC=OPTIMAL-FAST
- USE_ALL_DATA
- NLOW_DIM=2
- OUTPUT_FILE=rmsd-embed
-... CLASSICAL_MDS
-\endverbatim
-
-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.
-
-\section dim-sec Method of optimisation
-
-The stress function can be minimized using a standard optimization algorithm such as conjugate gradients or steepest descent.
-However, it is more common to do this minimization using a technique known as classical scaling. Classical scaling works by
-recognizing that each of the distances $D_{ij}$ in the above sum can be written as:
-
-\f[
-D_{ij}^2 = \sum_{\alpha} (X^i_\alpha - X^j_\alpha)^2 = \sum_\alpha (X^i_\alpha)^2 + (X^j_\alpha)^2 - 2X^i_\alpha X^j_\alpha
-\f]
-
-We can use this expression and matrix algebra to calculate multiple distances at once. For instance if we have three points,
-\f$\mathbf{X}\f$, we can write distances between them as:
-
-\f{eqnarray*}{
-D^2(\mathbf{X}) &=& \left[ \begin{array}{ccc}
-0 & d_{12}^2 & d_{13}^2 \\
-d_{12}^2 & 0 & d_{23}^2 \\
-d_{13}^2 & d_{23}^2 & 0
-\end{array}\right] \\
-&=&
-\sum_\alpha \left[ \begin{array}{ccc}
-(X^1_\alpha)^2 & (X^1_\alpha)^2 & (X^1_\alpha)^2 \\
-(X^2_\alpha)^2 & (X^2_\alpha)^2 & (X^2_\alpha)^2 \\
-(X^3_\alpha)^2 & (X^3_\alpha)^2 & (X^3_\alpha)^2 \\
-\end{array}\right]
- + \sum_\alpha \left[ \begin{array}{ccc}
-(X^1_\alpha)^2 & (X^2_\alpha)^2 & (X^3_\alpha)^2 \\
-(X^1_\alpha)^2 & (X^2_\alpha)^2 & (X^3_\alpha)^2 \\
-(X^1_\alpha)^2 & (X^2_\alpha)^2 & (X^3_\alpha)^2 \\
-\end{array}\right]
-- 2 \sum_\alpha \left[ \begin{array}{ccc}
-X^1_\alpha X^1_\alpha & X^1_\alpha X^2_\alpha & X^1_\alpha X^3_\alpha \\
-X^2_\alpha X^1_\alpha & X^2_\alpha X^2_\alpha & X^2_\alpha X^3_\alpha \\
-X^1_\alpha X^3_\alpha & X^3_\alpha X^2_\alpha & X^3_\alpha X^3_\alpha
-\end{array}\right] \nonumber \\
-&=& \mathbf{c 1^T} + \mathbf{1 c^T} - 2 \sum_\alpha \mathbf{x}_a \mathbf{x}^T_a = \mathbf{c 1^T} + \mathbf{1 c^T} - 2\mathbf{X X^T}
-\f}
-
-This last equation can be extended to situations when we have more than three points. In it \f$\mathbf{X}\f$ is a matrix that has
-one high-dimensional point on each of its rows and \f$\mathbf{X^T}\f$ is its transpose. \f$\mathbf{1}\f$ is an \f$M \times 1\f$ vector
-of ones and \f$\mathbf{c}\f$ is a vector with components given by:
-
-\f[
-c_i = \sum_\alpha (x_\alpha^i)^2
-\f]
-
-These quantities are the diagonal elements of \f$\mathbf{X X^T}\f$, which is a dot product or Gram Matrix that contains the
-dot product of the vector \f$X_i\f$ with the vector \f$X_j\f$ in element \f$i,j\f$.
-
-In classical scaling we introduce a centering matrix \f$\mathbf{J}\f$ that is given by:
-
-\f[
-\mathbf{J} = \mathbf{I} - \frac{1}{M} \mathbf{11^T}
-\f]
-
-where \f$\mathbf{I}\f$ is the identity. Multiplying the equations above from the front and back by this matrix and a factor of a \f$-\frac{1}{2}\f$ gives:
-
-\f{eqnarray*}{
- -\frac{1}{2} \mathbf{J} \mathbf{D}^2(\mathbf{X}) \mathbf{J} &=& -\frac{1}{2}\mathbf{J}( \mathbf{c 1^T} + \mathbf{1 c^T} - 2\mathbf{X X^T})\mathbf{J} \\
- &=& -\frac{1}{2}\mathbf{J c 1^T J} - \frac{1}{2} \mathbf{J 1 c^T J} + \frac{1}{2} \mathbf{J}(2\mathbf{X X^T})\mathbf{J} \\
- &=& \mathbf{ J X X^T J } = \mathbf{X X^T } \label{eqn:scaling}
-\f}
-
-The fist two terms in this expression disappear because \f$\mathbf{1^T J}=\mathbf{J 1} =\mathbf{0}\f$, where \f$\mathbf{0}\f$
-is a matrix containing all zeros. In the final step meanwhile we use the fact that the matrix of squared distances will not
-change when we translate all the points. We can thus assume that the mean value, \f$\mu\f$, for each of the components, \f$\alpha\f$:
-\f[
-\mu_\alpha = \frac{1}{M} \sum_{i=1}^N \mathbf{X}^i_\alpha
-\f]
-is equal to 0 so the columns of \f$\mathbf{X}\f$ add up to 0. This in turn means that each of the columns of
-\f$\mathbf{X X^T}\f$ adds up to zero, which is what allows us to write \f$\mathbf{ J X X^T J } = \mathbf{X X^T }\f$.
-
-The matrix of squared distances is symmetric and positive-definite we can thus use the spectral decomposition to decompose it as:
-
-\f[
-\Phi= \mathbf{V} \Lambda \mathbf{V}^T
-\f]
-
-Furthermore, because the matrix we are diagonalizing, \f$\mathbf{X X^T}\f$, is the product of a matrix and its transpose
-we can use this decomposition to write:
-
-\f[
-\mathbf{X} =\mathbf{V} \Lambda^\frac{1}{2}
-\f]
-
-Much as in PCA there are generally a small number of large eigenvalues in \f$\Lambda\f$ and many small eigenvalues.
-We can safely use only the large eigenvalues and their corresponding eigenvectors to express the relationship between
-the coordinates \f$\mathbf{X}\f$. This gives us our set of low-dimensional projections.
-
-This derivation makes a number of assumptions about the how the low dimensional points should best be arranged to minimise
-the stress. If you use an interative optimization algorithm such as SMACOF you may thus be able to find a better
-(lower-stress) projection of the points. For more details on the assumptions made
-see <a href="http://quest4rigor.com/tag/multidimensional-scaling/"> this website.</a>
-*/
-//+ENDPLUMEDOC
-
-class ClassicalMultiDimensionalScaling : public AnalysisWithLandmarks {
-private:
- unsigned nlow;
- std::string ofilename;
- std::string efilename;
- PointWiseMapping* myembedding;
-public:
- static void registerKeywords( Keywords& keys );
- ClassicalMultiDimensionalScaling( const ActionOptions& ao );
- ~ClassicalMultiDimensionalScaling();
- void analyzeLandmarks();
-};
-
-PLUMED_REGISTER_ACTION(ClassicalMultiDimensionalScaling,"CLASSICAL_MDS")
-
-void ClassicalMultiDimensionalScaling::registerKeywords( Keywords& keys ){
- AnalysisWithLandmarks::registerKeywords( keys );
- keys.add("compulsory","NLOW_DIM","number of low-dimensional coordinates required");
- keys.add("compulsory","OUTPUT_FILE","file on which to output the final embedding coordinates");
- keys.add("compulsory","EMBEDDING_OFILE","dont output","file on which to output the embedding in plumed input format");
-}
-
-ClassicalMultiDimensionalScaling::ClassicalMultiDimensionalScaling( const ActionOptions& ao ):
-Action(ao),
-AnalysisWithLandmarks(ao)
-{
- myembedding = new PointWiseMapping( getMetricName(), false );
- setDataToAnalyze( dynamic_cast<MultiReferenceBase*>(myembedding) );
-
- parse("NLOW_DIM",nlow);
- if( nlow<1 ) error("dimensionality of low dimensional space must be at least one");
- std::vector<std::string> propnames( nlow ); std::string num;
- for(unsigned i=0;i<propnames.size();++i){
- Tools::convert(i+1,num); std::string lab=getLabel();
- if(lab.find("@")!=std::string::npos) propnames[i]=getName() + "." + num;
- else propnames[i]=getLabel() + "." + num;
- }
- myembedding->setPropertyNames( propnames, false );
-
- parseOutputFile("EMBEDDING_OFILE",efilename);
- parseOutputFile("OUTPUT_FILE",ofilename);
-}
-
-ClassicalMultiDimensionalScaling::~ClassicalMultiDimensionalScaling(){
- delete myembedding;
-}
-
-void ClassicalMultiDimensionalScaling::analyzeLandmarks(){
- // Calculate all pairwise diatances
- myembedding->calculateAllDistances( getPbc(), getArguments(), comm, myembedding->modifyDmat(), true );
-
- // Run multidimensional scaling
- ClassicalScaling::run( myembedding );
-
- // Output the embedding as long lists of data
-// std::string gfname=saveResultsFromPreviousAnalyses( ofilename );
- OFile gfile; gfile.link(*this);
- gfile.setBackupString("analysis");
- gfile.fmtField(getOutputFormat()+" ");
- gfile.open( ofilename.c_str() );
-
- // Print embedding coordinates
- for(unsigned i=0;i<myembedding->getNumberOfReferenceFrames();++i){
- for(unsigned j=0;j<nlow;++j){
- std::string num; Tools::convert(j+1,num);
- gfile.printField( getLabel() + "." + num , myembedding->getProjectionCoordinate(i,j) );
- }
- gfile.printField();
- }
- gfile.close();
-
- // Output the embedding in plumed format
- if( efilename!="dont output"){
- OFile afile; afile.link(*this); afile.setBackupString("analysis");
- afile.open( efilename.c_str() );
- myembedding->print( "classical mds", getTime(), afile, getOutputFormat() );
- afile.close();
- }
-}
-
-}
-}
diff --git a/src/analysis/ClassicalScaling.cpp b/src/analysis/ClassicalScaling.cpp
deleted file mode 100644
index 051ffbd92012435ed371a95297ac6a09ed8f77a6..0000000000000000000000000000000000000000
--- a/src/analysis/ClassicalScaling.cpp
+++ /dev/null
@@ -1,56 +0,0 @@
-/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2014 The plumed team
- (see the PEOPLE file at the root of the distribution for a list of names)
-
- See http://www.plumed-code.org for more information.
-
- This file is part of plumed, version 2.
-
- plumed is free software: you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- plumed is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with plumed. If not, see <http://www.gnu.org/licenses/>.
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#include "ClassicalScaling.h"
-#include "reference/PointWiseMapping.h"
-
-namespace PLMD {
-namespace analysis {
-
-void ClassicalScaling::run( PointWiseMapping* mymap ){
- // Retrieve the distances from the dimensionality reduction object
- double half=(-0.5); Matrix<double> distances( half*mymap->modifyDmat() );
-
- // Apply centering transtion
- unsigned n=distances.nrows(); double sum;
- // First HM
- for(unsigned i=0;i<n;++i){
- sum=0; for(unsigned j=0;j<n;++j) sum+=distances(i,j);
- for(unsigned j=0;j<n;++j) distances(i,j) -= sum/n;
- }
- // Now (HM)H
- for(unsigned i=0;i<n;++i){
- sum=0; for(unsigned j=0;j<n;++j) sum+=distances(j,i);
- for(unsigned j=0;j<n;++j) distances(j,i) -= sum/n;
- }
-
- // Diagonalize matrix
- std::vector<double> eigval(n); Matrix<double> eigvec(n,n);
- diagMat( distances, eigval, eigvec );
-
- // Pass final projections to map object
- for(unsigned i=0;i<n;++i){
- for(unsigned j=0;j<mymap->getNumberOfProperties();++j) mymap->setProjectionCoordinate( i, j, sqrt(eigval[n-1-j])*eigvec(n-1-j,i) );
- }
-}
-
-}
-}
diff --git a/src/analysis/ClassicalScaling.h b/src/analysis/ClassicalScaling.h
deleted file mode 100644
index 90cd03561fc4a867be22f21773d48cab3f1f7e62..0000000000000000000000000000000000000000
--- a/src/analysis/ClassicalScaling.h
+++ /dev/null
@@ -1,40 +0,0 @@
-/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2014 The plumed team
- (see the PEOPLE file at the root of the distribution for a list of names)
-
- See http://www.plumed-code.org for more information.
-
- This file is part of plumed, version 2.
-
- plumed is free software: you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- plumed is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with plumed. If not, see <http://www.gnu.org/licenses/>.
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_analysis_ClassicalScaling_h
-#define __PLUMED_analysis_ClassicalScaling_h
-
-#include <vector>
-
-namespace PLMD {
-
-class PointWiseMapping;
-
-namespace analysis {
-
-class ClassicalScaling {
-public:
- static void run( PointWiseMapping* mymap );
-};
-
-}
-}
-#endif
diff --git a/src/analysis/Histogram.cpp b/src/analysis/Histogram.cpp
index 761d8a26a9dc12c2a22c5ce66cdc4ef6c3c49d0a..c0f8cc961994f0184429415c6ee69c97409242a0 100644
--- a/src/analysis/Histogram.cpp
+++ b/src/analysis/Histogram.cpp
@@ -19,7 +19,7 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#include "Analysis.h"
+#include "AnalysisWithDataCollection.h"
#include "core/PlumedMain.h"
#include "core/ActionRegister.h"
#include "tools/Grid.h"
@@ -111,11 +111,12 @@ HISTOGRAM ...
*/
//+ENDPLUMEDOC
-class Histogram : public Analysis {
+class Histogram : public AnalysisWithDataCollection {
private:
std::vector<std::string> gmin, gmax;
std::vector<double> point, bw;
std::vector<unsigned> gbin;
+ std::string fmt;
std::string gridfname;
std::string kerneltype;
bool fenergy;
@@ -130,8 +131,8 @@ public:
PLUMED_REGISTER_ACTION(Histogram,"HISTOGRAM")
void Histogram::registerKeywords( Keywords& keys ){
- Analysis::registerKeywords( keys ); keys.reset_style("METRIC","hidden");
- keys.remove("ATOMS"); keys.reset_style("ARG","compulsory");
+ AnalysisWithDataCollection::registerKeywords( keys );
+ keys.remove("ATOMS");
keys.add("compulsory","GRID_MIN","the lower bounds for the grid");
keys.add("compulsory","GRID_MAX","the upper bounds for the grid");
keys.add("optional","GRID_BIN","the number of bins for the grid");
@@ -141,16 +142,20 @@ void Histogram::registerKeywords( Keywords& keys ){
keys.add("optional","BANDWIDTH","the bandwdith for kernel density estimation");
keys.addFlag("FREE-ENERGY",false,"Set to TRUE if you want a FREE ENERGY instead of a probabilty density (you need to set TEMP).");
keys.addFlag("UNNORMALIZED",false,"Set to TRUE if you don't want histogram to be normalized or free energy to be shifted.");
+ keys.add("optional","FMT","the format that should be used in the output file");
keys.add("compulsory","GRID_WFILE","histogram","the file on which to write the grid");
- keys.use("NOMEMORY");
}
Histogram::Histogram(const ActionOptions&ao):
-PLUMED_ANALYSIS_INIT(ao),
+Action(ao),
+AnalysisWithDataCollection(ao),
point(getNumberOfArguments()),
+fmt("%f"),
fenergy(false),
unnormalized(false)
{
+ // Read output format
+ parse("FMT",fmt);
// Read stuff for Grid
parseVector("GRID_MIN",gmin);
if(gmin.size()!=getNumberOfArguments()) error("Wrong number of values for GRID_MIN: they should be equal to the number of arguments");
@@ -177,7 +182,8 @@ unnormalized(false)
unsigned n=((b-a)/gspacing[i])+1;
if(gbin[i]<n) gbin[i]=n;
}
- parseOutputFile("GRID_WFILE",gridfname);
+ parse("GRID_WFILE",gridfname);
+ if( !getRestart() ){ OFile ofile; ofile.link(*this); ofile.setBackupString("analysis"); ofile.backupAllFiles(gridfname); }
// Read the type of kernel we are using
parse("KERNEL",kerneltype);
@@ -223,8 +229,9 @@ void Histogram::performAnalysis(){
pmin.resize(getNumberOfArguments());
pmax.resize(getNumberOfArguments());
for(unsigned i=0;i<getNumberOfArguments();++i){
- pbc.push_back( getPeriodicityInformation(i,dmin,dmax) );
+ pbc.push_back( getPntrToArgument(i)->isPeriodic() );
if(pbc[i]){
+ getPntrToArgument(i)->getDomain(dmin,dmax);
Tools::convert(dmin,gmin[i]);
Tools::convert(dmax,gmax[i]);
Tools::convert(dmin,pmin[i]);
@@ -232,16 +239,22 @@ void Histogram::performAnalysis(){
}
}
- Grid* gg; IFile oldf; oldf.link(*this);
+ Grid* gg; IFile oldf; oldf.link(*this);
+
+ // Retrieve the arguments remembering to delete all biases
+ std::vector<Value*> arg_vals( ActionWithArguments::getArguments() );
+ unsigned nbias = arg_vals.size() - getNumberOfArguments();
+ for(unsigned i=0;i<nbias;++i) arg_vals.erase(arg_vals.end()-1);
+
if( usingMemory() && oldf.FileExist(gridfname) ){
oldf.open(gridfname);
- gg = Grid::create( "probs", getArguments(), oldf, gmin, gmax, gbin, false, false, false );
+ gg = Grid::create( "probs", arg_vals, oldf, gmin, gmax, gbin, false, false, false );
oldf.close();
} else {
- gg = new Grid( "probs", getArguments(), gmin, gmax, gbin,false,false);
+ gg = new Grid( "probs", arg_vals, gmin, gmax, gbin,false,false);
}
// Set output format for grid
- gg->setOutputFmt( getOutputFormat() );
+ gg->setOutputFmt( fmt );
// Now build the histogram
double weight; std::vector<double> point( getNumberOfArguments() );
diff --git a/src/analysis/LandmarkRegister.cpp b/src/analysis/LandmarkRegister.cpp
deleted file mode 100644
index 375315d7d038c7829df3741b98a07c6ab4ca6f04..0000000000000000000000000000000000000000
--- a/src/analysis/LandmarkRegister.cpp
+++ /dev/null
@@ -1,69 +0,0 @@
-/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2011-2014 The plumed team
- (see the PEOPLE file at the root of the distribution for a list of names)
-
- See http://www.plumed-code.org for more information.
-
- This file is part of plumed, version 2.
-
- plumed is free software: you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- plumed is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with plumed. If not, see <http://www.gnu.org/licenses/>.
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#include "LandmarkRegister.h"
-#include <iostream>
-
-namespace PLMD{
-namespace analysis{
-
-LandmarkRegister::~LandmarkRegister(){
- if(m.size()>0){
- std::string names="";
- for(std::map<std::string,creator_pointer>::iterator p=m.begin();p!=m.end();++p) names+=p->first+" ";
- std::cerr<<"WARNING: ReferenceConfiguration "+ names +" has not been properly unregistered. This might lead to memory leak!!\n";
- }
-}
-
-LandmarkRegister& landmarkRegister(){
- static LandmarkRegister ans;
- return ans;
-}
-
-void LandmarkRegister::remove(creator_pointer f){
- for(std::map<std::string,creator_pointer>::iterator p=m.begin();p!=m.end();++p){
- if((*p).second==f){
- m.erase(p); break;
- }
- }
-}
-
-void LandmarkRegister::add( std::string type, creator_pointer f ){
- plumed_massert(m.count(type)==0,"type has already been registered");
- m.insert(std::pair<std::string,creator_pointer>(type,f));
-}
-
-bool LandmarkRegister::check(std::string type){
- if( m.count(type)>0 ) return true;
- return false;
-}
-
-LandmarkSelectionBase* LandmarkRegister::create( const LandmarkSelectionOptions& lo ){
- LandmarkSelectionBase* lselect;
- if( check(lo.words[0]) ){
- lselect=m[lo.words[0]](lo);
- lselect->checkRead();
- } else lselect=NULL;
- return lselect;
-}
-
-}
-}
diff --git a/src/analysis/LandmarkRegister.h b/src/analysis/LandmarkRegister.h
deleted file mode 100644
index ef7b3cfb650350a3315279bfdcf41f398f54a1b3..0000000000000000000000000000000000000000
--- a/src/analysis/LandmarkRegister.h
+++ /dev/null
@@ -1,68 +0,0 @@
-/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013,2014 The plumed team
- (see the PEOPLE file at the root of the distribution for a list of names)
-
- See http://www.plumed-code.org for more information.
-
- This file is part of plumed, version 2.
-
- plumed is free software: you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- plumed is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with plumed. If not, see <http://www.gnu.org/licenses/>.
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_analysis_LandmarkRegister_h
-#define __PLUMED_analysis_LandmarkRegister_h
-
-#include <string>
-#include <cstring>
-#include <vector>
-#include <map>
-#include "LandmarkSelectionBase.h"
-
-namespace PLMD{
-
-class PDB;
-
-namespace analysis{
-
-class LandmarkRegister{
-private:
-/// Pointer to a function which, given the type for a ReferenceConfiguration, creates it
- typedef LandmarkSelectionBase*(*creator_pointer)(const LandmarkSelectionOptions&);
-/// The set of possible landmark selection algorithms we can work with
- std::map<std::string,creator_pointer> m;
-public:
-/// The destructor
- ~LandmarkRegister();
-/// Add a new landmark selection style to the register of landmark selectors
- void add( std::string type, creator_pointer );
-/// Remove a landmark selection style from the register of metrics
- void remove(creator_pointer f);
-/// Verify if a landmark selection style is present in the register
- bool check(std::string type);
-/// Create a landmark selection object
- LandmarkSelectionBase* create( const LandmarkSelectionOptions& lo );
-};
-
-LandmarkRegister& landmarkRegister();
-
-#define PLUMED_REGISTER_LANDMARKS(classname,type) \
- static class classname##RegisterMe{ \
- static LandmarkSelectionBase * create(const LandmarkSelectionOptions&lo){return new classname(lo);} \
- public: \
- classname##RegisterMe(){landmarkRegister().add(type,create);}; \
- ~classname##RegisterMe(){landmarkRegister().remove(create);}; \
- } classname##RegisterMeObject;
-
-}
-}
-#endif
diff --git a/src/analysis/LandmarkSelectionBase.cpp b/src/analysis/LandmarkSelectionBase.cpp
deleted file mode 100644
index 505d91dac04a163dfafe48f90b2307624b1f7a3c..0000000000000000000000000000000000000000
--- a/src/analysis/LandmarkSelectionBase.cpp
+++ /dev/null
@@ -1,116 +0,0 @@
-/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2015 The plumed team
- (see the PEOPLE file at the root of the distribution for a list of names)
-
- See http://www.plumed-code.org for more information.
-
- This file is part of plumed, version 2.
-
- plumed is free software: you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- plumed is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with plumed. If not, see <http://www.gnu.org/licenses/>.
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#include "LandmarkSelectionBase.h"
-#include "reference/MultiReferenceBase.h"
-
-namespace PLMD {
-namespace analysis {
-
-LandmarkSelectionOptions::LandmarkSelectionOptions( const std::vector<std::string>& input, AnalysisWithLandmarks* myanalysis ):
-words(input),
-action(myanalysis)
-{
-}
-
-LandmarkSelectionBase::LandmarkSelectionBase( const LandmarkSelectionOptions& lo ):
-style(lo.words[0]),
-input(lo.words),
-action(lo.action)
-{
- input.erase( input.begin() );
- if( style=="ALL" ){
- novoronoi=true;
- } else {
- parse("N",nlandmarks);
- parseFlag("NOVORONOI",novoronoi);
- }
- parseFlag("IGNORE_WEIGHTS",noweights);
-}
-
-LandmarkSelectionBase::~LandmarkSelectionBase(){
-}
-
-void LandmarkSelectionBase::parseFlag(const std::string& key, bool& t){
- Tools::parseFlag(input,key,t);
-}
-
-void LandmarkSelectionBase::checkRead() const {
- if(!input.empty()){
- std::string msg="cannot understand the following words from landmark selection input : ";
- for(unsigned i=0;i<input.size();++i) msg = msg + input[i] + ", ";
- plumed_merror(msg);
- }
-}
-
-std::string LandmarkSelectionBase::description(){
- std::ostringstream ostr;
- if( style=="ALL"){
- ostr<<"using all data";
- } else {
- ostr<<"selecting "<<nlandmarks<<" using "<<style<<" algorithm to analyze\n";
- ostr<<" "<<rest_of_description()<<"\n";
- if(noweights) ostr<<" ignoring all reweighting of data during landmark selection\n";
- if(novoronoi) ostr<<" voronoi weights will not be ascribed to points\n";
- }
- return ostr.str();
-}
-
-double LandmarkSelectionBase::getWeightOfFrame( const unsigned& iframe ){
- if(noweights) return 1.0;
- return action->getWeight(iframe);
-}
-double LandmarkSelectionBase::getDistanceBetweenFrames( const unsigned& iframe, const unsigned& jframe ){
- return distance( action->getPbc(), action->getArguments(), action->data[iframe], action->data[jframe], false );
-}
-
-void LandmarkSelectionBase::selectFrame( const unsigned& iframe, MultiReferenceBase* myframes){
- plumed_assert( myframes->getNumberOfReferenceFrames()<nlandmarks );
- myframes->copyFrame( action->data[iframe] );
-}
-
-void LandmarkSelectionBase::selectLandmarks( MultiReferenceBase* myframes ){
- // Select landmarks
- myframes->clearFrames(); select( myframes );
- plumed_assert( myframes->getNumberOfReferenceFrames()==nlandmarks );
-
- // Now calculate voronoi weights
- if( !novoronoi ){
- unsigned rank=action->comm.Get_rank();
- unsigned size=action->comm.Get_size();
- std::vector<double> weights( nlandmarks, 0.0 );
- for(unsigned i=rank;i<action->data.size();i+=size){
- unsigned closest=0;
- double mindist=distance( action->getPbc(), action->getArguments(), action->data[i], myframes->getFrame(0), false );
- for(unsigned j=1;j<nlandmarks;++j){
- double dist=distance( action->getPbc(), action->getArguments(), action->data[i], myframes->getFrame(j), false );
- if( dist<mindist ){ mindist=dist; closest=j; }
- }
- weights[closest] += getWeightOfFrame(i);
- }
- action->comm.Sum( &weights[0], weights.size() );
- myframes->setWeights( weights );
- }
-}
-
-}
-}
-
diff --git a/src/analysis/LandmarkSelectionBase.h b/src/analysis/LandmarkSelectionBase.h
deleted file mode 100644
index 123dd14cfe8d72eb9424b4fed2b869277b7262f5..0000000000000000000000000000000000000000
--- a/src/analysis/LandmarkSelectionBase.h
+++ /dev/null
@@ -1,110 +0,0 @@
-/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2013-2015 The plumed team
- (see the PEOPLE file at the root of the distribution for a list of names)
-
- See http://www.plumed-code.org for more information.
-
- This file is part of plumed, version 2.
-
- plumed is free software: you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- plumed is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with plumed. If not, see <http://www.gnu.org/licenses/>.
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_analysis_LandmarkSelectionBase_h
-#define __PLUMED_analysis_LandmarkSelectionBase_h
-
-#include "reference/ReferenceConfiguration.h"
-#include "AnalysisWithLandmarks.h"
-
-namespace PLMD {
-namespace analysis {
-
-class LandmarkSelectionOptions{
-friend class LandmarkRegister;
-friend class LandmarkSelectionBase;
-private:
- std::vector<std::string> words;
- AnalysisWithLandmarks* action;
-public:
- LandmarkSelectionOptions( const std::vector<std::string>& input, AnalysisWithLandmarks* myanalysis );
-};
-
-class LandmarkSelectionBase {
-friend class AnalysisWithLandmarks;
-friend class CopyAllFrames;
-private:
-/// Name of the method we are using for landmark selection
- std::string style;
-/// The number of landmarks we are selecting
- unsigned nlandmarks;
-/// The input to the landmark selection object
- std::vector<std::string> input;
-/// A pointer to the underlying action
- AnalysisWithLandmarks* action;
-/// How do we treat weights
- bool novoronoi, noweights;
-protected:
-/// Return the numbe of landmarks
- unsigned getNumberOfLandmarks() const ;
-/// Return the communicator
- Communicator& getCommunicator();
-/// Read a keywords from the input
- template <class T>
- void parse(const std::string& ,T& );
-/// Read a flag from the input
- void parseFlag(const std::string& key, bool& t);
-/// Get the number of frames in the underlying action
- unsigned getNumberOfFrames() const;
-/// Get the weight of the ith frame
- double getWeightOfFrame( const unsigned& );
-/// Calculate the distance between the ith and jth frames
- double getDistanceBetweenFrames( const unsigned& , const unsigned& );
-/// Transfer frame i in the underlying action to the object we are going to analyze
- void selectFrame( const unsigned& , MultiReferenceBase* );
-public:
- LandmarkSelectionBase( const LandmarkSelectionOptions& lo );
- virtual ~LandmarkSelectionBase();
-/// Check everything was read in
- void checkRead() const ;
-/// Return a description of the landmark selection protocol
- std::string description();
-/// Overwrite this to have a more descriptive output
- virtual std::string rest_of_description(){ return ""; };
-/// Actually do landmark selection
- void selectLandmarks( MultiReferenceBase* );
- virtual void select( MultiReferenceBase* )=0;
-};
-
-inline
-unsigned LandmarkSelectionBase::getNumberOfLandmarks() const {
- return nlandmarks;
-}
-
-inline
-Communicator& LandmarkSelectionBase::getCommunicator(){
- return action->comm;
-}
-
-inline
-unsigned LandmarkSelectionBase::getNumberOfFrames() const {
- return action->getNumberOfDataPoints();
-}
-
-template <class T>
-void LandmarkSelectionBase::parse( const std::string& key, T& t ){
- bool found=Tools::parse(input,key,t);
- if(!found) plumed_merror("landmark seleciton style " + style + " requires " + key + " keyword");
-}
-
-}
-}
-#endif
diff --git a/src/analysis/SelectAllFrames.cpp b/src/analysis/SelectAllFrames.cpp
deleted file mode 100644
index b0f7512643bcd3b4814b74b0912276340d9c49d7..0000000000000000000000000000000000000000
--- a/src/analysis/SelectAllFrames.cpp
+++ /dev/null
@@ -1,47 +0,0 @@
-/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- Copyright (c) 2012-2014 The plumed team
- (see the PEOPLE file at the root of the distribution for a list of names)
-
- See http://www.plumed-code.org for more information.
-
- This file is part of plumed, version 2.
-
- plumed is free software: you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- plumed is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with plumed. If not, see <http://www.gnu.org/licenses/>.
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#include "LandmarkSelectionBase.h"
-#include "LandmarkRegister.h"
-
-namespace PLMD {
-namespace analysis {
-
-class CopyAllFrames : public LandmarkSelectionBase {
-public:
- CopyAllFrames( const LandmarkSelectionOptions& lo );
- void select( MultiReferenceBase* );
-};
-
-PLUMED_REGISTER_LANDMARKS(CopyAllFrames,"ALL")
-
-CopyAllFrames::CopyAllFrames( const LandmarkSelectionOptions& lo ):
-LandmarkSelectionBase(lo)
-{
-}
-
-void CopyAllFrames::select( MultiReferenceBase* myframes ){
- nlandmarks = action->getNumberOfDataPoints();
- for(unsigned i=0;i<getNumberOfFrames();++i) selectFrame( i, myframes );
-}
-
-}
-}
diff --git a/src/core/ActionPilot.cpp b/src/core/ActionPilot.cpp
index 34b53adba45229e6a74c79ef628a9cbcd12a1089..ab3db6a3c292178d12ff13ca78a364c6a2a1df27 100644
--- a/src/core/ActionPilot.cpp
+++ b/src/core/ActionPilot.cpp
@@ -31,8 +31,14 @@ ActionPilot::ActionPilot(const ActionOptions&ao):
Action(ao),
stride(1)
{
- parse("STRIDE",stride);
- log.printf(" with stride %d\n",stride);
+ if( keywords.exists("STRIDE") ){
+ parse("STRIDE",stride);
+ log.printf(" with stride %d\n",stride);
+ }
+}
+
+void ActionPilot::setStride( const unsigned& s ){
+ stride=s;
}
bool ActionPilot::onStep()const{
diff --git a/src/core/ActionPilot.h b/src/core/ActionPilot.h
index 551c73d0b901504bf5a2c5233096406a60996e31..bc44b5da17bf405271ce62ef6ebeb11a2ea625d9 100644
--- a/src/core/ActionPilot.h
+++ b/src/core/ActionPilot.h
@@ -42,6 +42,7 @@ class ActionPilot:
int stride; // multiple time step
protected:
int getStride()const;
+ void setStride( const unsigned& s );
public:
ActionPilot(const ActionOptions&);
/// Create the keywords for actionPilot
diff --git a/src/reference/PointWiseMapping.cpp b/src/reference/PointWiseMapping.cpp
index 034f7fd772d5e26cd6d5118b2607293cb96e2bba..30b4ae1d3f4bede1a7448aacce33a80cbeb401c8 100644
--- a/src/reference/PointWiseMapping.cpp
+++ b/src/reference/PointWiseMapping.cpp
@@ -77,24 +77,24 @@ unsigned PointWiseMapping::getPropertyIndex( const std::string& name ) const {
return 0;
}
-void PointWiseMapping::print( const std::string& method, const double & time, OFile& afile, const std::string& fmt ){
- std::string descr2, descr="DESCRIPTION: results from %s analysis performed at time " + fmt +"\n";
- afile.printf(descr.c_str(), method.c_str(), time );
- if(fmt.find("-")!=std::string::npos){
- descr="REMARK WEIGHT=" + fmt + " %s=" + fmt + " "; descr2="%s=" + fmt;
- } else {
- // This ensures numbers are left justified (i.e. next to the equals sign
- std::size_t psign=fmt.find("%");
- plumed_assert( psign!=std::string::npos );
- descr="REMARK WEIGHT=%-" + fmt.substr(psign+1) + " %s=%-" + fmt.substr(psign+1) + " ";
- descr2="%s=%-" + fmt.substr(psign+1);
- }
- for(unsigned i=0;i<frames.size();++i){
- afile.printf(descr.c_str(), frames[i]->getWeight(), property[0].c_str(), low_dim[i][0] );
- for(unsigned j=1;j<property.size();++j) afile.printf(descr2.c_str(), property[j].c_str(), low_dim[i][j]);
- afile.printf("\n");
- frames[i]->print( afile, fmt );
- }
-}
+// void PointWiseMapping::print( const std::string& method, const double & time, OFile& afile, const std::string& fmt ){
+// std::string descr2, descr="DESCRIPTION: results from %s analysis performed at time " + fmt +"\n";
+// afile.printf(descr.c_str(), method.c_str(), time );
+// if(fmt.find("-")!=std::string::npos){
+// descr="REMARK WEIGHT=" + fmt + " %s=" + fmt + " "; descr2="%s=" + fmt;
+// } else {
+// // This ensures numbers are left justified (i.e. next to the equals sign
+// std::size_t psign=fmt.find("%");
+// plumed_assert( psign!=std::string::npos );
+// descr="REMARK WEIGHT=%-" + fmt.substr(psign+1) + " %s=%-" + fmt.substr(psign+1) + " ";
+// descr2="%s=%-" + fmt.substr(psign+1);
+// }
+// for(unsigned i=0;i<frames.size();++i){
+// afile.printf(descr.c_str(), frames[i]->getWeight(), property[0].c_str(), low_dim[i][0] );
+// for(unsigned j=1;j<property.size();++j) afile.printf(descr2.c_str(), property[j].c_str(), low_dim[i][j]);
+// afile.printf("\n");
+// frames[i]->print( afile, fmt );
+// }
+// }
}
diff --git a/src/reference/PointWiseMapping.h b/src/reference/PointWiseMapping.h
index b5358f5133cc70af63f38879635c67536e7ec14f..950d949e6b4e1124524a0c6c7c2b90a42a0360f2 100644
--- a/src/reference/PointWiseMapping.h
+++ b/src/reference/PointWiseMapping.h
@@ -71,7 +71,7 @@ public:
/// Get a pointer to the matrix of pairwise distances
Matrix<double>& modifyDmat();
/// Print out the low dimensional mapping
- void print( const std::string& method, const double & time, OFile& afile, const std::string& fmt );
+// void print( const std::string& method, const double & time, OFile& afile, const std::string& fmt );
/// Get the low dimensional embedding coordinate
double getProjectionCoordinate( const unsigned& iframe, const unsigned& jcoord ) const ;
/// Set the value of the projection coordinate
diff --git a/src/reference/ReferenceAtoms.cpp b/src/reference/ReferenceAtoms.cpp
index 1fecbaef9b4bf7f5d62db12952d69b3af550597a..c28dc682e8f07b6cdb25c1a9e18bdc50068761cf 100644
--- a/src/reference/ReferenceAtoms.cpp
+++ b/src/reference/ReferenceAtoms.cpp
@@ -50,11 +50,11 @@ void ReferenceAtoms::setAtomNumbers( const std::vector<AtomNumber>& numbers ){
}
}
-void ReferenceAtoms::printAtoms( OFile& ofile ) const {
+void ReferenceAtoms::printAtoms( const double& lunits, OFile& ofile ) const {
for(unsigned i=0;i<reference_atoms.size();++i){
ofile.printf("ATOM %4d X RES %4u %8.3f %8.3f %8.3f %6.2f %6.2f\n",
indices[i].serial(), i,
- reference_atoms[i][0], reference_atoms[i][1], reference_atoms[i][2],
+ lunits*reference_atoms[i][0], lunits*reference_atoms[i][1], lunits*reference_atoms[i][2],
align[i], displace[i] );
}
}
diff --git a/src/reference/ReferenceAtoms.h b/src/reference/ReferenceAtoms.h
index b8ce2d36ad2b6a4ad8a74f3790005013958a4a3d..5e7e0c12e79cef387520c281df99d9c228f678dc 100644
--- a/src/reference/ReferenceAtoms.h
+++ b/src/reference/ReferenceAtoms.h
@@ -97,7 +97,7 @@ public:
/// Set the positions of the reference atoms
virtual void setReferenceAtoms( const std::vector<Vector>& conf, const std::vector<double>& align_in, const std::vector<double>& displace_in )=0;
/// Print the atomic positions
- void printAtoms( OFile& ofile ) const ;
+ void printAtoms( const double& lunits, OFile& ofile ) const ;
/// Return all atom indexes
const std::vector<AtomNumber>& getAbsoluteIndexes();
/// This returns how many atoms there should be
diff --git a/src/reference/ReferenceConfiguration.cpp b/src/reference/ReferenceConfiguration.cpp
index dafbc0f4670643bc3cc546db619117eca34cbd3c..530013ef2039928db35a0e7fd58ba6c010f7db0b 100644
--- a/src/reference/ReferenceConfiguration.cpp
+++ b/src/reference/ReferenceConfiguration.cpp
@@ -156,16 +156,16 @@ double ReferenceConfiguration::calculate( const std::vector<Vector>& pos, const
// virialWasSet=ref->virialWasSet; virial=ref->virial;
// }
-void ReferenceConfiguration::print( OFile& ofile, const double& time, const double& weight, const double& old_norm ){
+void ReferenceConfiguration::print( const double& lunits, OFile& ofile, const double& time, const double& weight, const double& old_norm ){
ofile.printf("REMARK TIME=%f LOG_WEIGHT=%f OLD_NORM=%f\n",time, weight, old_norm );
- print( ofile, "%f" ); // HARD CODED FORMAT HERE AS THIS IS FOR CHECKPOINT FILE
+ print( lunits, ofile, "%f" ); // HARD CODED FORMAT HERE AS THIS IS FOR CHECKPOINT FILE
}
-void ReferenceConfiguration::print( OFile& ofile, const std::string& fmt ){
+void ReferenceConfiguration::print( const double& lunits, OFile& ofile, const std::string& fmt ){
ReferenceArguments* args=dynamic_cast<ReferenceArguments*>(this);
if(args) args->printArguments( ofile, fmt );
ReferenceAtoms* atoms=dynamic_cast<ReferenceAtoms*>(this);
- if(atoms) atoms->printAtoms( ofile );
+ if(atoms) atoms->printAtoms( lunits, ofile );
ofile.printf("END\n");
}
diff --git a/src/reference/ReferenceConfiguration.h b/src/reference/ReferenceConfiguration.h
index 37509736bc5dcdd5ff302100f9cd19cd89f7dbae..6864a19efa5537004b52050c1f8c9ce84e1f53e9 100644
--- a/src/reference/ReferenceConfiguration.h
+++ b/src/reference/ReferenceConfiguration.h
@@ -142,8 +142,8 @@ public:
/// Set the reference structure (perhaps should also pass the pbc and align and displace )
void setReferenceConfig( const std::vector<Vector>& pos, const std::vector<double>& arg, const std::vector<double>& metric );
/// Print a pdb file containing the reference configuration
- void print( OFile& ofile, const double& time, const double& weight, const double& old_norm );
- void print( OFile& ofile, const std::string& fmt );
+ void print( const double& lunits, OFile& ofile, const double& time, const double& weight, const double& old_norm );
+ void print( const double& lunits, OFile& ofile, const std::string& fmt );
/// Get one of the referene arguments
virtual double getReferenceArgument( const unsigned& i ) const { plumed_error(); return 0.0; }
/// These are overwritten in ReferenceArguments and ReferenceAtoms but are required here