diff --git a/regtest/analysis/rt-read-dissims2/Makefile b/regtest/analysis/rt-read-dissims2/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/analysis/rt-read-dissims2/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/analysis/rt-read-dissims2/config b/regtest/analysis/rt-read-dissims2/config
new file mode 100644
index 0000000000000000000000000000000000000000..4804b7f2a86c1dcb06f52d08f8dff331e318192f
--- /dev/null
+++ b/regtest/analysis/rt-read-dissims2/config
@@ -0,0 +1,4 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+extra_files="../../trajectories/trajectory.xyz"
diff --git a/regtest/analysis/rt-read-dissims2/configs-stride.pdb.reference b/regtest/analysis/rt-read-dissims2/configs-stride.pdb.reference
new file mode 100644
index 0000000000000000000000000000000000000000..21925e4d814064ba08fc05134b9572f4a6da0d39
--- /dev/null
+++ b/regtest/analysis/rt-read-dissims2/configs-stride.pdb.reference
@@ -0,0 +1,115 @@
+DESCRIPTION: analysis data from calculation done at time 0.200000
+REMARK WEIGHT=1.0000 TYPE=OPTIMAL
+ATOM 1 X RES 0 -4.506 -11.060 -17.545 0.05 0.05
+ATOM 2 X RES 1 4.963 -11.182 -9.194 0.05 0.05
+ATOM 3 X RES 2 4.162 -2.540 -17.207 0.05 0.05
+ATOM 4 X RES 3 -3.809 -2.069 -9.681 0.05 0.05
+ATOM 5 X RES 4 -4.180 -10.584 -1.418 0.05 0.05
+ATOM 6 X RES 5 4.447 -10.620 7.264 0.05 0.05
+ATOM 7 X RES 6 4.385 -2.599 -0.952 0.05 0.05
+ATOM 8 X RES 7 -4.264 -2.879 7.660 0.05 0.05
+ATOM 9 X RES 8 -5.027 -10.867 15.899 0.05 0.05
+ATOM 10 X RES 9 3.620 -10.890 24.529 0.05 0.05
+ATOM 11 X RES 10 4.490 -2.292 15.828 0.05 0.05
+ATOM 12 X RES 11 -4.496 -2.174 24.340 0.05 0.05
+ATOM 13 X RES 12 -3.720 5.418 -17.405 0.05 0.05
+ATOM 14 X RES 13 3.623 5.966 -9.542 0.05 0.05
+ATOM 15 X RES 14 4.401 14.249 -18.015 0.05 0.05
+ATOM 16 X RES 15 -3.820 14.172 -9.591 0.05 0.05
+ATOM 17 X RES 16 -4.504 5.758 -0.036 0.05 0.05
+ATOM 18 X RES 17 3.305 5.096 7.190 0.05 0.05
+ATOM 19 X RES 18 4.331 14.345 0.009 0.05 0.05
+ATOM 20 X RES 19 -3.402 14.752 7.866 0.05 0.05
+END
+DESCRIPTION: analysis data from calculation done at time 0.200000
+REMARK WEIGHT=1.0000 TYPE=OPTIMAL
+ATOM 1 X RES 0 -4.670 -11.130 -17.511 0.05 0.05
+ATOM 2 X RES 1 5.583 -11.209 -9.235 0.05 0.05
+ATOM 3 X RES 2 4.301 -2.482 -16.840 0.05 0.05
+ATOM 4 X RES 3 -3.760 -1.929 -9.998 0.05 0.05
+ATOM 5 X RES 4 -4.201 -10.212 -1.856 0.05 0.05
+ATOM 6 X RES 5 4.506 -10.293 7.185 0.05 0.05
+ATOM 7 X RES 6 4.647 -2.750 -1.114 0.05 0.05
+ATOM 8 X RES 7 -4.477 -3.337 7.694 0.05 0.05
+ATOM 9 X RES 8 -5.755 -10.773 16.018 0.05 0.05
+ATOM 10 X RES 9 3.124 -11.030 24.688 0.05 0.05
+ATOM 11 X RES 10 4.814 -2.000 15.677 0.05 0.05
+ATOM 12 X RES 11 -4.491 -1.806 24.342 0.05 0.05
+ATOM 13 X RES 12 -3.379 5.315 -17.527 0.05 0.05
+ATOM 14 X RES 13 3.257 6.072 -9.818 0.05 0.05
+ATOM 15 X RES 14 4.689 14.018 -18.419 0.05 0.05
+ATOM 16 X RES 15 -3.518 14.143 -9.834 0.05 0.05
+ATOM 17 X RES 16 -4.862 5.640 0.653 0.05 0.05
+ATOM 18 X RES 17 2.779 4.548 6.887 0.05 0.05
+ATOM 19 X RES 18 4.460 14.224 0.649 0.05 0.05
+ATOM 20 X RES 19 -3.049 14.991 8.360 0.05 0.05
+END
+DESCRIPTION: analysis data from calculation done at time 0.200000
+REMARK WEIGHT=1.0000 TYPE=OPTIMAL
+ATOM 1 X RES 0 -4.797 -10.892 -17.524 0.05 0.05
+ATOM 2 X RES 1 6.238 -10.978 -9.016 0.05 0.05
+ATOM 3 X RES 2 4.510 -2.450 -16.757 0.05 0.05
+ATOM 4 X RES 3 -4.186 -2.197 -10.094 0.05 0.05
+ATOM 5 X RES 4 -4.154 -9.504 -2.049 0.05 0.05
+ATOM 6 X RES 5 4.557 -9.886 7.278 0.05 0.05
+ATOM 7 X RES 6 4.879 -2.888 -1.227 0.05 0.05
+ATOM 8 X RES 7 -4.895 -3.556 7.522 0.05 0.05
+ATOM 9 X RES 8 -6.393 -11.011 16.310 0.05 0.05
+ATOM 10 X RES 9 2.498 -11.182 24.664 0.05 0.05
+ATOM 11 X RES 10 5.288 -1.860 15.693 0.05 0.05
+ATOM 12 X RES 11 -3.861 -1.562 24.588 0.05 0.05
+ATOM 13 X RES 12 -3.013 5.578 -18.094 0.05 0.05
+ATOM 14 X RES 13 3.214 6.210 -9.768 0.05 0.05
+ATOM 15 X RES 14 5.034 13.706 -18.661 0.05 0.05
+ATOM 16 X RES 15 -3.380 14.173 -10.000 0.05 0.05
+ATOM 17 X RES 16 -5.496 5.677 0.663 0.05 0.05
+ATOM 18 X RES 17 2.962 4.118 6.770 0.05 0.05
+ATOM 19 X RES 18 4.381 13.795 0.873 0.05 0.05
+ATOM 20 X RES 19 -3.386 14.709 8.831 0.05 0.05
+END
+DESCRIPTION: analysis data from calculation done at time 0.200000
+REMARK WEIGHT=1.0000 TYPE=OPTIMAL
+ATOM 1 X RES 0 -4.972 -10.651 -17.468 0.05 0.05
+ATOM 2 X RES 1 6.834 -10.601 -8.619 0.05 0.05
+ATOM 3 X RES 2 4.839 -2.454 -16.913 0.05 0.05
+ATOM 4 X RES 3 -4.685 -2.410 -10.241 0.05 0.05
+ATOM 5 X RES 4 -4.184 -8.718 -1.928 0.05 0.05
+ATOM 6 X RES 5 4.622 -9.418 7.529 0.05 0.05
+ATOM 7 X RES 6 5.110 -2.972 -1.473 0.05 0.05
+ATOM 8 X RES 7 -5.319 -3.420 7.484 0.05 0.05
+ATOM 9 X RES 8 -7.099 -11.271 16.457 0.05 0.05
+ATOM 10 X RES 9 1.795 -11.424 24.536 0.05 0.05
+ATOM 11 X RES 10 6.011 -2.234 15.660 0.05 0.05
+ATOM 12 X RES 11 -3.246 -1.671 24.754 0.05 0.05
+ATOM 13 X RES 12 -2.534 5.845 -18.557 0.05 0.05
+ATOM 14 X RES 13 3.368 6.364 -9.489 0.05 0.05
+ATOM 15 X RES 14 5.174 13.639 -18.574 0.05 0.05
+ATOM 16 X RES 15 -3.367 14.132 -10.036 0.05 0.05
+ATOM 17 X RES 16 -6.083 5.704 0.149 0.05 0.05
+ATOM 18 X RES 17 3.390 3.801 6.837 0.05 0.05
+ATOM 19 X RES 18 4.216 13.533 0.747 0.05 0.05
+ATOM 20 X RES 19 -3.871 14.225 9.145 0.05 0.05
+END
+DESCRIPTION: analysis data from calculation done at time 0.200000
+REMARK WEIGHT=1.0000 TYPE=OPTIMAL
+ATOM 1 X RES 0 -5.103 -10.424 -17.164 0.05 0.05
+ATOM 2 X RES 1 7.050 -10.389 -8.531 0.05 0.05
+ATOM 3 X RES 2 5.143 -2.344 -17.090 0.05 0.05
+ATOM 4 X RES 3 -5.107 -2.193 -10.548 0.05 0.05
+ATOM 5 X RES 4 -4.327 -8.390 -1.659 0.05 0.05
+ATOM 6 X RES 5 4.658 -8.831 7.681 0.05 0.05
+ATOM 7 X RES 6 5.148 -2.700 -1.836 0.05 0.05
+ATOM 8 X RES 7 -5.562 -2.969 7.578 0.05 0.05
+ATOM 9 X RES 8 -7.494 -11.552 16.355 0.05 0.05
+ATOM 10 X RES 9 1.117 -11.563 24.384 0.05 0.05
+ATOM 11 X RES 10 6.514 -2.686 15.870 0.05 0.05
+ATOM 12 X RES 11 -2.790 -2.003 24.821 0.05 0.05
+ATOM 13 X RES 12 -1.938 5.998 -18.490 0.05 0.05
+ATOM 14 X RES 13 3.749 6.279 -9.026 0.05 0.05
+ATOM 15 X RES 14 5.216 13.612 -18.212 0.05 0.05
+ATOM 16 X RES 15 -3.250 14.142 -9.905 0.05 0.05
+ATOM 17 X RES 16 -6.457 5.381 -0.665 0.05 0.05
+ATOM 18 X RES 17 3.858 3.517 6.807 0.05 0.05
+ATOM 19 X RES 18 3.999 13.370 0.561 0.05 0.05
+ATOM 20 X RES 19 -4.422 13.745 9.068 0.05 0.05
+END
diff --git a/regtest/analysis/rt-read-dissims2/mymatrix.dat b/regtest/analysis/rt-read-dissims2/mymatrix.dat
new file mode 100644
index 0000000000000000000000000000000000000000..e26db230a9ca85f11de378f39b9b6e989b87498d
--- /dev/null
+++ b/regtest/analysis/rt-read-dissims2/mymatrix.dat
@@ -0,0 +1,5 @@
+ 0.0000 1.0000 1.0000 4.0000 9.0000
+ 1.0000 0.0000 1.0000 4.0000 9.0000
+ 1.0000 1.0000 0.0000 1.0000 4.0000
+ 4.0000 4.0000 1.0000 0.0000 1.0000
+ 9.0000 9.0000 4.0000 1.0000 0.0000
diff --git a/regtest/analysis/rt-read-dissims2/mymatrix_stride.dat.reference b/regtest/analysis/rt-read-dissims2/mymatrix_stride.dat.reference
new file mode 100644
index 0000000000000000000000000000000000000000..6871b4a6dd78d38831fb479a2a6cec68a0166eb8
--- /dev/null
+++ b/regtest/analysis/rt-read-dissims2/mymatrix_stride.dat.reference
@@ -0,0 +1,5 @@
+ 0.0000 1.0000 1.0000 4.0000 9.0000
+ 1.0000 0.0000 1.0000 4.0000 9.0000
+ 1.0000 1.0000 0.0000 1.0000 4.0000
+ 4.0000 4.0000 1.0000 0.0000 1.0000
+ 9.0000 9.0000 4.0000 1.0000 0.0000
diff --git a/regtest/analysis/rt-read-dissims2/plumed.dat b/regtest/analysis/rt-read-dissims2/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..313bb905b96ec1038f252569c07f7570ec9cee88
--- /dev/null
+++ b/regtest/analysis/rt-read-dissims2/plumed.dat
@@ -0,0 +1,8 @@
+c1: READ_ANALYSIS_FRAMES ATOMS=1-20 STRIDE=1
+
+r1: READ_DISSIMILARITY_MATRIX TRAJ=c1 FILE=mymatrix.dat
+PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=r1 FILE=mymatrix_out.dat FMT=%8.4f
+
+l1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=r1 NLANDMARKS=5
+PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=l1 FILE=mymatrix_stride.dat FMT=%8.4f
+OUTPUT_ANALYSIS_DATA_TO_PDB USE_OUTPUT_DATA_FROM=l1 FILE=configs-stride.pdb FMT=%8.4f
diff --git a/src/analysis/AnalysisBase.cpp b/src/analysis/AnalysisBase.cpp
index 8e3a3413793ddea9d64e5622f59c24ec5e34627b..deda1e0ca0b9180473a1801e1a82401d26a607ac 100644
--- a/src/analysis/AnalysisBase.cpp
+++ b/src/analysis/AnalysisBase.cpp
@@ -20,6 +20,7 @@
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "AnalysisBase.h"
+#include "ReadAnalysisFrames.h"
#include "core/PlumedMain.h"
#include "core/ActionSet.h"
@@ -50,6 +51,8 @@ mydata(NULL)
!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 );
+ ReadAnalysisFrames* checkt = dynamic_cast<ReadAnalysisFrames*>( mydata );
+ if( checkt ) error("READ_ANALYSIS_FRAMES should only be used in association with READ_DISSSIMILARITY_MATRIX");
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;
diff --git a/src/analysis/AnalysisWithDataCollection.cpp b/src/analysis/AnalysisWithDataCollection.cpp
index efb2ae8face9ebdbfb725ffa4c0ca3f69503d6f6..71afb441dc52e6791b57d990457579bcf6a772c5 100644
--- a/src/analysis/AnalysisWithDataCollection.cpp
+++ b/src/analysis/AnalysisWithDataCollection.cpp
@@ -20,6 +20,7 @@
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "AnalysisWithDataCollection.h"
+#include "ReadAnalysisFrames.h"
#include "reference/ReferenceConfiguration.h"
#include "reference/ReferenceArguments.h"
#include "reference/ReferenceAtoms.h"
@@ -71,6 +72,8 @@ old_norm(0.0)
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");
+ ReadAnalysisFrames* checkt = dynamic_cast<ReadAnalysisFrames*>( checkd );
+ if( checkt ) error("READ_ANALYSIS_FRAMES should only be used in association with READ_DISSSIMILARITY_MATRIX");
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;
@@ -86,7 +89,8 @@ old_norm(0.0)
if( keywords.exists("METRIC") ){
std::string metrictmp; parse("METRIC",metrictmp);
if( metrictmp.length()==0 ){
- metricname="EUCLIDEAN";
+ if( keywords.exists("ARG") ) metricname="EUCLIDEAN";
+ else metricname="OPTIMAL";
} else {
std::vector<std::string> metricwords = Tools::getWords( metrictmp );
metricname=metricwords[0]; metricwords.erase(metricwords.begin());
@@ -126,7 +130,10 @@ old_norm(0.0)
}
// Read in the information about how often to run the analysis (storage is read in in ActionPilot.cpp)
- if( keywords.exists("USE_ALL_DATA") ) parseFlag("USE_ALL_DATA",use_all_data);
+ if( keywords.exists("USE_ALL_DATA") ){
+ if( !keywords.exists("RUN") ) use_all_data=true;
+ else parseFlag("USE_ALL_DATA",use_all_data);
+ }
if(!use_all_data){
if( keywords.exists("RUN") ) parse("RUN",freq);
// Setup everything given the ammount of data that we will have in each analysis
@@ -268,7 +275,6 @@ ReferenceConfiguration* AnalysisWithDataCollection::getInputReferenceConfigurati
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 ;
diff --git a/src/analysis/ReadAnalysisFrames.cpp b/src/analysis/ReadAnalysisFrames.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..e6afb86f0163846ac9951de2bc73c80fe58c2ed5
--- /dev/null
+++ b/src/analysis/ReadAnalysisFrames.cpp
@@ -0,0 +1,57 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ 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 "ReadAnalysisFrames.h"
+#include "core/PlumedMain.h"
+#include "core/ActionSet.h"
+#include "core/ActionRegister.h"
+
+//+PLUMEDOC ANALYSIS READ_ANALYSIS_FRAMES
+/*
+This allows you to convert a trajectory and a dissimilarity matrix into a dissimilarity object
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+namespace PLMD {
+namespace analysis {
+
+PLUMED_REGISTER_ACTION(ReadAnalysisFrames,"READ_ANALYSIS_FRAMES")
+
+void ReadAnalysisFrames::registerKeywords( Keywords& keys ){
+ AnalysisWithDataCollection::registerKeywords( keys );
+ keys.reset_style("USE_ALL_DATA","hidden"); keys.remove("RUN"); keys.remove("REWEIGHT_BIAS"); keys.remove("REWEIGHT_TEMP");
+ keys.remove("TEMP"); keys.remove("WRITE_CHECKPOINT"); keys.remove("NOMEMORY"); keys.remove("RESTART");
+ keys.remove("UPDATE_FROM"); keys.remove("UPDATE_UNTIL"); keys.remove("USE_OUTPUT_DATA_FROM");
+ keys.remove("ARG"); keys.remove("SERIAL"); keys.remove("REUSE_INPUT_DATA_FROM");
+}
+
+ReadAnalysisFrames::ReadAnalysisFrames( const ActionOptions& ao ):
+Action(ao),
+AnalysisWithDataCollection(ao)
+{
+ if( plumed.getActionSet().size()!=0 ) error("read analysis frames command must be at top of input file");
+}
+
+}
+}
diff --git a/src/analysis/ReadAnalysisFrames.h b/src/analysis/ReadAnalysisFrames.h
new file mode 100644
index 0000000000000000000000000000000000000000..11f43740cb1b1a3cff9739442e653e32c7252b8e
--- /dev/null
+++ b/src/analysis/ReadAnalysisFrames.h
@@ -0,0 +1,42 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ 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_ReadAnalysisFrames_h
+#define __PLUMED_analysis_ReadAnalysisFrames_h
+
+#include "AnalysisWithDataCollection.h"
+
+namespace PLMD {
+namespace analysis {
+
+class ReadAnalysisFrames : public AnalysisWithDataCollection {
+public:
+ static void registerKeywords( Keywords& keys );
+ ReadAnalysisFrames( const ActionOptions& ao );
+/// Select landmark configurations
+ void performAnalysis(){}
+/// This does nothing - it just ensures the final class is not abstract
+ void performTask( const unsigned& , const unsigned& , MultiValue& ) const { plumed_error(); }
+};
+
+}
+}
+#endif
diff --git a/src/analysis/ReadDissimilarityMatrix.cpp b/src/analysis/ReadDissimilarityMatrix.cpp
index 7dec6c1ddd1171dcadd447d32f52569fd9c6a0e2..41905756f697d465c9b5886cd9019128a9dcc839 100644
--- a/src/analysis/ReadDissimilarityMatrix.cpp
+++ b/src/analysis/ReadDissimilarityMatrix.cpp
@@ -20,6 +20,7 @@
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "AnalysisBase.h"
+#include "ReadAnalysisFrames.h"
#include "core/PlumedMain.h"
#include "core/ActionSet.h"
#include "core/ActionRegister.h"
@@ -46,7 +47,7 @@ private:
public:
static void registerKeywords( Keywords& keys );
ReadDissimilarityMatrix( const ActionOptions& ao );
- unsigned getNumberOfDataPoints() const { return nnodes; }
+ unsigned getNumberOfDataPoints() const ;
/// This gives an error as if we read in the matrix we dont have the coordinates
ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata );
ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idata );
@@ -71,6 +72,7 @@ PLUMED_REGISTER_ACTION(ReadDissimilarityMatrix,"READ_DISSIMILARITY_MATRIX")
void ReadDissimilarityMatrix::registerKeywords( Keywords& keys ){
AnalysisBase::registerKeywords( keys ); keys.remove("USE_OUTPUT_DATA_FROM");
keys.add("compulsory","FILE","an input file containing the matrix of dissimilarities");
+ keys.add("optional","TRAJ","the label for a READ_ANALYSIS_FRAMES action that stores the trajectory");
keys.add("optional","WFILE","input file containing weights of points");
}
@@ -79,11 +81,20 @@ Action(ao),
AnalysisBase(ao),
nnodes(1)
{
- if( plumed.getActionSet().size()!=0 ) error("read dissimilarity matrix command must be at top of input file");
+ std::string mytraj; parse("TRAJ",mytraj);
+ if( mytraj.length()>0 ){
+ ReadAnalysisFrames* mtraj = plumed.getActionSet().selectWithLabel<ReadAnalysisFrames*>( mytraj );
+ if( !mtraj ) error(mytraj + " is not the label of a READ_ANALYSIS_FRAMES object");
+ mydata = dynamic_cast<AnalysisBase*>( mtraj );
+ }
+
+ if( mytraj.length()>0 && plumed.getActionSet().size()!=1 ) error("should only be this action and the READ_ANALYSIS_FRAMES command in the input file");
+ if( mytraj.length()==0 && plumed.getActionSet().size()!=0 ) error("read dissimilarity matrix command must be at top of input file");
parse("FILE",fname);
log.printf(" reading dissimilarity matrix from file %s \n",fname.c_str() );
parse("WFILE",wfile);
+
if( wfile.length()>0 ) log.printf(" reading weights of nodes from file named %s \n",wfile.c_str() );
else log.printf(" setting weights of all nodes equal to one\n");
@@ -92,7 +103,7 @@ nnodes(1)
use_all_data=true; freq=1; setStride(1);
}
-void ReadDissimilarityMatrix::update(){ plumed.stop(); }
+void ReadDissimilarityMatrix::update(){ if(!mydata) plumed.stop(); }
void ReadDissimilarityMatrix::performAnalysis(){
IFile mfile; mfile.open(fname);
@@ -107,6 +118,7 @@ void ReadDissimilarityMatrix::performAnalysis(){
for(unsigned j=0;j<nnodes;++j) Tools::convert( words[j], dissimilarities(i,j) );
}
mfile.close();
+ if( mydata && nnodes!=getNumberOfDataPoints() ) error("mismatch between number of data points in trajectory and the dimensions of the dissimilarity matrix");
weights.resize( nnodes );
if( wfile.length()>0 ){
@@ -120,21 +132,29 @@ void ReadDissimilarityMatrix::performAnalysis(){
}
}
+unsigned ReadDissimilarityMatrix::getNumberOfDataPoints() const {
+ if( mydata ) return AnalysisBase::getNumberOfDataPoints();
+ return nnodes;
+}
+
double ReadDissimilarityMatrix::getDissimilarity( const unsigned& iframe, const unsigned& jframe ){
return dissimilarities( iframe, jframe );
}
ReferenceConfiguration* ReadDissimilarityMatrix::getReferenceConfiguration( const unsigned& idata ){
+ if( mydata ) return AnalysisBase::getReferenceConfiguration( idata );
plumed_merror("cannot get reference configurations from read in dissimilarity matrix");
return NULL;
}
ReferenceConfiguration* ReadDissimilarityMatrix::getInputReferenceConfiguration( const unsigned& idata ){
+ if( mydata ) return AnalysisBase::getInputReferenceConfiguration( idata );
plumed_merror("cannot get reference configurations from read in dissimilarity matrix");
return NULL;
}
void ReadDissimilarityMatrix::getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const {
+ if( mydata ){ AnalysisBase::getDataPoint( idata, point, weight ); return; }
plumed_merror("cannot get data points from read in dissmimilarity matrix");
}
diff --git a/user-doc/Analysis.txt b/user-doc/Analysis.txt
index b00dadfaea938600232f220c13312ed80233da4a..0491904070a9dc790b2463f763be726f4775107b 100644
--- a/user-doc/Analysis.txt
+++ b/user-doc/Analysis.txt
@@ -122,7 +122,9 @@ external file
<tr> <td width=5%> \subpage READ_DISSIMILARITY_MATRIX </td> <td> Read a matrix of dissimilarities between a trajectory of atomic configurations from a file. </td> </tr>
</table>
-N.B. You can only use the \ref READ_DISSIMILARITY_MATRIX command when you are doing post-processing.
+N.B. You can only use the \ref READ_DISSIMILARITY_MATRIX command when you are doing post-processing. If you have a
+trajectory that contains the configurations you read in the configurations from the trajectory using
+\ref READ_ANALYSIS_FRAMES
\ref landmarks Landmark Selection