diff --git a/CHANGES/Unreleased.txt b/CHANGES/Unreleased.txt
index 6737c1bec938ab8e6dff39aaa4adde1407b446e9..86b7bb8201a2557c7cc01eb1bb973e26e5e41825 100644
--- a/CHANGES/Unreleased.txt
+++ b/CHANGES/Unreleased.txt
@@ -32,6 +32,7 @@ Changes from version 2.2 which are relevant for users:
- \ref ROWSUMS
- \ref COLUMNSUMS
- \ref UPDATE_IF
+ - \ref PCA
- New features in MD patches (require repatch):
- Patch for amber 14 now passes charges with appropriate units (fixes \issue{165}). Notice that
the patch is still backward compatible with older PLUMED version, but the charges will only be passed
diff --git a/CHANGES/v2.2.txt b/CHANGES/v2.2.txt
index 5543cf015edaa947f39c2e899c9ab5545c1ecc6a..5c1b836c5f5cbd45e76e27e35955c8f651dfee57 100644
--- a/CHANGES/v2.2.txt
+++ b/CHANGES/v2.2.txt
@@ -105,7 +105,7 @@ For developers:
- ./configure is automatically relaunched when changing ./configure or Makefile.conf. This makes it more robust
to switch between branches.
-Unreleased changes (will be included in 2.2.2)
+Version 2.2.2 (coming soon)
----------------------------------------------
For users:
@@ -119,7 +119,8 @@ For users:
- Fixed a bug in the normalization of kernel functions (relevant for \ref HISTOGRAM).
- Fixed a regression introduced in v2.2 that was making \ref METAD with non-MPI multiple walkers crash
if reading frequently. See \issue{190}
-- Updated patch for gromacs 5.1
+- Updated patch for gromacs 5.x. Patches for gromacs 5.0 and 5.1 have been fixed so as to allow
+ patching in runtime mode.
- Possibility to control manual generation (including pdf) from ./configure. Pdf manual is now off
by default. Notice that on travis CI it is still generated.
diff --git a/regtest/analysis/rt-pca-2/Makefile b/regtest/analysis/rt-pca-2/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/analysis/rt-pca-2/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/analysis/rt-pca-2/colvar.in b/regtest/analysis/rt-pca-2/colvar.in
new file mode 100644
index 0000000000000000000000000000000000000000..3c1a6d4ff8bbca15ba5cc7bc12587585b89d3cbb
--- /dev/null
+++ b/regtest/analysis/rt-pca-2/colvar.in
@@ -0,0 +1,1001 @@
+#! FIELDS time cv1 cv2
+0 0.775540714036 0.114424044242
+1 0.875241253264 1.26867389701
+2 1.5823516279 0.605481219611
+3 -1.96997844317 -3.19169418421
+4 1.46732571381 0.768488126284
+5 0.666346341751 -0.470501561902
+6 0.860037532851 -0.407265735903
+7 0.356107752262 0.578949081633
+8 1.29856933615 0.877672309318
+9 -1.91795493292 -1.06303227781
+10 0.503769991835 -1.60084848817
+11 0.654256109546 0.897859999363
+12 1.02289470749 0.298766057397
+13 0.513653990173 -0.828578832591
+14 0.728689851987 0.386875652092
+15 0.897535288431 -0.102913855511
+16 3.05937675092 2.06078844086
+17 -0.250090711503 0.97082781137
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+22 -0.584719212221 -1.27184824226
+23 3.41759109718 0.796329037698
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+26 1.0466239386 0.986404889943
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diff --git a/regtest/analysis/rt-pca-2/config b/regtest/analysis/rt-pca-2/config
new file mode 100644
index 0000000000000000000000000000000000000000..58f0b8893460c32a1c9a774c2f8e59d2d9761a08
--- /dev/null
+++ b/regtest/analysis/rt-pca-2/config
@@ -0,0 +1,3 @@
+type=driver
+arg="--plumed plumed.dat --ixyz diala_traj_nm.xyz"
+extra_files="../../trajectories/diala_traj_nm.xyz"
diff --git a/regtest/analysis/rt-pca-2/pca-comp.pdb.reference b/regtest/analysis/rt-pca-2/pca-comp.pdb.reference
new file mode 100644
index 0000000000000000000000000000000000000000..4a7972a92b559a3d72825fe6b206e96622e2a667
--- /dev/null
+++ b/regtest/analysis/rt-pca-2/pca-comp.pdb.reference
@@ -0,0 +1,12 @@
+REMARK TYPE=EUCLIDEAN
+REMARK ARG=c1,c2
+REMARK c1=0.9663 c2=0.4730
+END
+REMARK TYPE=DIRECTION
+REMARK ARG=c1,c2
+REMARK c1=0.7142 c2=0.6999
+END
+REMARK TYPE=DIRECTION
+REMARK ARG=c1,c2
+REMARK c1=0.6999 c2=-0.7142
+END
diff --git a/regtest/analysis/rt-pca-2/plumed.dat b/regtest/analysis/rt-pca-2/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..aa6a39f97daf852438292389b69aa52ef43389da
--- /dev/null
+++ b/regtest/analysis/rt-pca-2/plumed.dat
@@ -0,0 +1,4 @@
+c1: READ FILE=colvar.in VALUES=cv1
+c2: READ FILE=colvar.in VALUES=cv2
+
+PCA METRIC=EUCLIDEAN ARG=c1,c2 USE_ALL_DATA NLOW_DIM=2 OFILE=pca-comp.pdb FMT=%8.4f
diff --git a/regtest/analysis/rt-pca/Makefile b/regtest/analysis/rt-pca/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/analysis/rt-pca/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/analysis/rt-pca/config b/regtest/analysis/rt-pca/config
new file mode 100644
index 0000000000000000000000000000000000000000..58f0b8893460c32a1c9a774c2f8e59d2d9761a08
--- /dev/null
+++ b/regtest/analysis/rt-pca/config
@@ -0,0 +1,3 @@
+type=driver
+arg="--plumed plumed.dat --ixyz diala_traj_nm.xyz"
+extra_files="../../trajectories/diala_traj_nm.xyz"
diff --git a/regtest/analysis/rt-pca/pca-comp.pdb.reference b/regtest/analysis/rt-pca/pca-comp.pdb.reference
new file mode 100644
index 0000000000000000000000000000000000000000..fc22670a085813745bf312a3803ddbea39367c40
--- /dev/null
+++ b/regtest/analysis/rt-pca/pca-comp.pdb.reference
@@ -0,0 +1,72 @@
+REMARK TYPE=OPTIMAL
+ATOM 1 X RES 0 -3.002 -0.303 1.042 0.05 0.05
+ATOM 2 X RES 1 -3.375 -0.131 1.046 0.05 0.05
+ATOM 3 X RES 2 -3.376 -0.402 1.084 0.05 0.05
+ATOM 4 X RES 3 -3.326 -0.239 1.294 0.05 0.05
+ATOM 5 X RES 4 -1.625 -0.479 0.681 0.05 0.05
+ATOM 6 X RES 5 -1.001 -0.681 1.355 0.05 0.05
+ATOM 7 X RES 6 -1.117 -0.412 -0.407 0.05 0.05
+ATOM 8 X RES 7 -1.688 -0.225 -0.895 0.05 0.05
+ATOM 9 X RES 8 0.167 -0.648 -0.993 0.05 0.05
+ATOM 10 X RES 9 0.264 -1.677 -1.119 0.05 0.05
+ATOM 11 X RES 10 0.199 -0.014 -2.349 0.05 0.05
+ATOM 12 X RES 11 0.278 0.101 -2.643 0.05 0.05
+ATOM 13 X RES 12 0.168 0.098 -2.737 0.05 0.05
+ATOM 14 X RES 13 0.174 0.229 -2.704 0.05 0.05
+ATOM 15 X RES 14 1.392 -0.272 -0.203 0.05 0.05
+ATOM 16 X RES 15 2.259 -0.716 -0.363 0.05 0.05
+ATOM 17 X RES 16 1.500 0.569 0.661 0.05 0.05
+ATOM 18 X RES 17 0.762 0.889 0.785 0.05 0.05
+ATOM 19 X RES 18 2.611 0.994 1.452 0.05 0.05
+ATOM 20 X RES 19 2.964 1.128 1.574 0.05 0.05
+ATOM 21 X RES 20 2.843 1.185 1.726 0.05 0.05
+ATOM 22 X RES 21 2.928 1.006 1.713 0.05 0.05
+END
+REMARK TYPE=DIRECTION
+ATOM 1 X RES 0 0.354 0.171 0.229 1.00 1.00
+ATOM 2 X RES 1 0.585 0.567 0.558 1.00 1.00
+ATOM 3 X RES 2 0.205 0.793 0.037 1.00 1.00
+ATOM 4 X RES 3 0.320 0.180 0.111 1.00 1.00
+ATOM 5 X RES 4 0.255 -1.235 0.169 1.00 1.00
+ATOM 6 X RES 5 0.252 -4.529 0.304 1.00 1.00
+ATOM 7 X RES 6 0.252 1.215 -0.073 1.00 1.00
+ATOM 8 X RES 7 0.435 3.800 -0.249 1.00 1.00
+ATOM 9 X RES 8 0.107 0.313 -0.066 1.00 1.00
+ATOM 10 X RES 9 0.093 0.161 1.087 1.00 1.00
+ATOM 11 X RES 10 -0.089 -1.113 -0.746 1.00 1.00
+ATOM 12 X RES 11 0.480 -3.066 -1.776 1.00 1.00
+ATOM 13 X RES 12 -2.025 -1.152 -0.684 1.00 1.00
+ATOM 14 X RES 13 1.185 -0.261 -0.272 1.00 1.00
+ATOM 15 X RES 14 0.099 1.372 -0.666 1.00 1.00
+ATOM 16 X RES 15 0.492 3.830 -2.307 1.00 1.00
+ATOM 17 X RES 16 -0.394 -0.438 0.775 1.00 1.00
+ATOM 18 X RES 17 -0.608 -2.369 1.984 1.00 1.00
+ATOM 19 X RES 18 -0.479 0.302 0.455 1.00 1.00
+ATOM 20 X RES 19 -0.662 0.700 0.477 1.00 1.00
+ATOM 21 X RES 20 -0.547 0.209 0.491 1.00 1.00
+ATOM 22 X RES 21 -0.309 0.548 0.162 1.00 1.00
+END
+REMARK TYPE=DIRECTION
+ATOM 1 X RES 0 0.040 -0.180 0.140 1.00 1.00
+ATOM 2 X RES 1 0.469 -1.519 2.216 1.00 1.00
+ATOM 3 X RES 2 0.337 2.166 0.164 1.00 1.00
+ATOM 4 X RES 3 -0.723 -1.344 -1.892 1.00 1.00
+ATOM 5 X RES 4 0.011 -0.017 0.057 1.00 1.00
+ATOM 6 X RES 5 0.044 0.234 -0.008 1.00 1.00
+ATOM 7 X RES 6 -0.006 -0.149 0.077 1.00 1.00
+ATOM 8 X RES 7 -0.009 -0.335 0.106 1.00 1.00
+ATOM 9 X RES 8 -0.007 -0.045 0.002 1.00 1.00
+ATOM 10 X RES 9 0.008 -0.058 -0.089 1.00 1.00
+ATOM 11 X RES 10 -0.099 0.067 0.048 1.00 1.00
+ATOM 12 X RES 11 2.890 -0.426 -0.116 1.00 1.00
+ATOM 13 X RES 12 -2.066 -1.963 -0.898 1.00 1.00
+ATOM 14 X RES 13 -1.117 2.728 1.157 1.00 1.00
+ATOM 15 X RES 14 0.018 -0.063 0.016 1.00 1.00
+ATOM 16 X RES 15 0.077 -0.275 0.135 1.00 1.00
+ATOM 17 X RES 16 -0.013 0.160 -0.129 1.00 1.00
+ATOM 18 X RES 17 -0.037 0.355 -0.233 1.00 1.00
+ATOM 19 X RES 18 0.046 0.169 -0.200 1.00 1.00
+ATOM 20 X RES 19 2.278 -3.179 -1.474 1.00 1.00
+ATOM 21 X RES 20 0.240 3.803 -2.326 1.00 1.00
+ATOM 22 X RES 21 -2.383 -0.130 3.246 1.00 1.00
+END
diff --git a/regtest/analysis/rt-pca/plumed.dat b/regtest/analysis/rt-pca/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..3bb806c3ad6fc770728daf3c1325763aefb4a55f
--- /dev/null
+++ b/regtest/analysis/rt-pca/plumed.dat
@@ -0,0 +1 @@
+PCA METRIC=OPTIMAL ATOMS=1-22 STRIDE=1 USE_ALL_DATA NLOW_DIM=2 OFILE=pca-comp.pdb
diff --git a/src/analysis/PCA.cpp b/src/analysis/PCA.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..624d2609164fa2ef6e80ad580350bdb349554d5f
--- /dev/null
+++ b/src/analysis/PCA.cpp
@@ -0,0 +1,237 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ 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 "tools/Matrix.h"
+#include "reference/Direction.h"
+#include "reference/MetricRegister.h"
+#include "reference/ReferenceConfiguration.h"
+#include "reference/ReferenceValuePack.h"
+#include "core/ActionRegister.h"
+
+//+PLUMEDOC ANALYSIS PCA
+/*
+Perform principal component analysis (PCA) using either the positions of the atoms a large number of collective variables as input.
+
+Principal component analysis is a statistical technique that uses an orthogonal transformation to convert a set of observations of
+poorly correlated variables into a set of linearly uncorrelated variables. You can read more about the specifics of this technique
+here: https://en.wikipedia.org/wiki/Principal_component_analysis
+
+When used in context with molecular dynamics simulations a set of frames taken from the trajectory, \f$\{X_i\}\f$, or the values of
+a number of collective variables which are calculated from the trajectory frames are used as input. In this second instance your
+input to the PCA analysis algorithm is thus a set of high-dimensional vectors of collective variables. However, if
+collective variables are calculated from the positions of the atoms or if the positions are used directly the assumption is that
+this input trajectory is a set of poorly correlated (high-dimensional) vectors. After principal component analysis has been
+performed the output is a set of orthogonal vectors that describe the directions in which the largest motions have been seen.
+In other words, principal component analysis provides a method for lowering the dimensionality of the data contained in a trajectory.
+These output directions are some linear combination of the \f$x\f$, \f$y\f$ and \f$z\f$ positions if the positions were used as input
+or some linear combination of the input collective variables if a high-dimensional vector of collective variables was used as input.
+
+As explained on the Wikipedia page you must calculate the average and covariance for each of the input coordinates. In other words, you must
+calculate the average structure and the amount the system fluctuates around this average structure. The problem in doing so when the
+\f$x\f$, \f$y\f$ and \f$z\f$ coordinates of a molecule are used as input is that the majority of the changes in the positions of the
+atoms comes from the translational and rotational degrees of freedom of the molecule. The first six principal components will thus, most likely,
+be uninteresting. Consequently, to remedy this problem PLUMED provides the functionality to perform an RMSD alignment of the all the structures
+to be analysed to the first frame in the trajectory. This can be used to effectively remove translational and/or rotational motions from
+consideration. The resulting principal components thus describe vibrational motions of the molecule.
+
+If you wish to calculate the projection of a trajectory on a set of principal components calculated from this PCA action then the output can be
+used as input for the \ref PCAVARS action.
+
+\par Examples
+
+The following input instructs PLUMED to perform a principal component analysis in which the covariance matrix is calculated from changes in the positions
+of the first 22 atoms. The TYPE=OPTIMAL instruction ensures that translational and rotational degrees of freedom are removed from consideration.
+The first two principal components will be output to a file called pca-comp.pdb. Trajectory frames will be collected on every step and the PCA calculation
+will be performed at the end of the simulation.
+
+\verbatim
+PCA METRIC=OPTIMAL ATOMS=1-22 STRIDE=1 USE_ALL_DATA NLOW_DIM=2 OFILE=pca-comp.pdb
+\endverbatim
+
+The following input instructs PLUMED to perform a principal component analysis in which the covariance matrix is calculated from chnages in the six distances
+seen in the previous lines. Notice that here the TYPE=EUCLIDEAN keyword is used to indicate that no alighment has to be done when calculating the various
+elements of the covariance matrix from the input vectors. In this calculation the first two principal components will be output to a file called pca-comp.pdb.
+Trajectory frames will be collected every five steps and the PCA calculation is performed every 1000 steps. Consequently, if you run a 2000 step simulation the
+PCA analysis will be performed twice. The REWEIGHT_BIAS keyword in this input tells PLUMED that rather that ascribing a weight of one to each of the frames
+when calculating averages and covariances a reweighting should be performed based and each frames' weight in these calculations should be determined based on
+the current value of the instantaneous bias (see \ref reweighting).
+
+\verbatim
+d1: DISTANCE ATOMS=1,2
+d2: DISTANCE ATOMS=1,3
+d3: DISTANCE ATOMS=1,4
+d4: DISTNACE ATOMS=2,3
+d5: DISTANCE ATOMS=2,4
+d6: DISTANCE ATOMS=3,4
+
+PCA ARG=d1,d2,d3,d4,d5,d6 METRIC=EUCLIDEAN STRIDE=5 RUN=1000 NLOW_DIM=2 REWEIGHT_BIAS OFILE=pca-comp.pdb
+\endverbatim
+
+*/
+//+ENDPLUMEDOC
+
+namespace PLMD {
+namespace analysis {
+
+class PCA : public Analysis {
+private:
+ unsigned ndim;
+/// The position of the reference configuration (the one we align to)
+ ReferenceConfiguration* myref;
+/// The eigenvectors for the atomic displacements
+ Matrix<Vector> atom_eigv;
+/// The eigenvectors for the displacements in argument space
+ Matrix<double> arg_eigv;
+ std::string ofilename;
+public:
+ static void registerKeywords( Keywords& keys );
+ explicit PCA(const ActionOptions&ao);
+ ~PCA();
+ void performAnalysis();
+ void performTask( const unsigned& , const unsigned& , MultiValue& ) const { plumed_error(); }
+};
+
+PLUMED_REGISTER_ACTION(PCA,"PCA")
+
+void PCA::registerKeywords( Keywords& keys ){
+ Analysis::registerKeywords( keys );
+ keys.add("compulsory","NLOW_DIM","number of PCA coordinates required");
+ keys.add("compulsory","OFILE","the file on which to output the eigenvectors");
+}
+
+PCA::PCA(const ActionOptions&ao):
+PLUMED_ANALYSIS_INIT(ao)
+{
+ // Setup reference configuration
+ log.printf(" performing PCA analysis using %s metric \n", getMetricName().c_str() );
+ myref = metricRegister().create<ReferenceConfiguration>( getMetricName() );
+ std::vector<std::string> argnames( getNumberOfArguments() );
+ for(unsigned i=0;i<argnames.size();++i){
+ if( getArguments()[i]->isPeriodic() ) error("cannot run PCA with periodic variables");
+ argnames[i] = getArguments()[i]->getName();
+ }
+ myref->setNamesAndAtomNumbers( getAbsoluteIndexes(), argnames );
+
+ parse("NLOW_DIM",ndim);
+ if( getNumberOfAtoms()>0 ) atom_eigv.resize( ndim, getNumberOfAtoms() );
+ if( getNumberOfArguments()>0 ) arg_eigv.resize( ndim, getNumberOfArguments() );
+
+ // Read stuff for output file
+ parseOutputFile("OFILE",ofilename);
+ checkRead();
+}
+
+PCA::~PCA(){
+ delete myref;
+}
+
+void PCA::performAnalysis(){
+ // Align everything to the first frame
+ MultiValue myval( 1, getNumberOfArguments() + 3*getNumberOfAtoms() + 9 );
+ ReferenceValuePack mypack( getNumberOfArguments(), getNumberOfAtoms(), myval );
+ for(unsigned i=0;i<getNumberOfAtoms();++i) mypack.setAtomIndex( i, i );
+ // Setup some PCA storage
+ data[0]->setupPCAStorage ( mypack );
+
+ // Create some arrays to store the average position
+ std::vector<double> sarg( getNumberOfArguments(), 0 );
+ std::vector<Vector> spos( getNumberOfAtoms() );
+ for(unsigned i=0;i<getNumberOfAtoms();++i) spos[i].zero();
+
+ // Calculate the average displacement from the first frame
+ for(unsigned i=1;i<getNumberOfDataPoints();++i){
+ double d = data[0]->calc( data[i]->getReferencePositions(), getPbc(), getArguments(), data[i]->getReferenceArguments(), mypack, true );
+ // Accumulate average displacement of arguments (Here PBC could do fucked up things - really needs Berry Phase ) GAT
+ for(unsigned j=0;j<getNumberOfArguments();++j) sarg[j] += 0.5*getWeight(i)*mypack.getArgumentDerivative(j);
+ // Accumulate average displacement of position
+ for(unsigned j=0;j<getNumberOfAtoms();++j) spos[j] += getWeight(i)*mypack.getAtomsDisplacementVector()[j];
+ }
+ // Now normalise the displacements to get the average and add these to the first frame
+ double inorm = 1.0 / getNormalization();
+ for(unsigned j=0;j<getNumberOfArguments();++j) sarg[j] = inorm*sarg[j] + data[0]->getReferenceArguments()[j];
+ for(unsigned j=0;j<getNumberOfAtoms();++j) spos[j] = inorm*spos[j] + data[0]->getReferencePositions()[j];
+ // And set the reference configuration
+ std::vector<double> empty( getNumberOfArguments(), 1.0 ); myref->setReferenceConfig( spos, sarg, empty );
+
+ // Now accumulate the covariance
+ unsigned narg=getNumberOfArguments();
+ Matrix<double> covar( getNumberOfArguments()+3*getNumberOfAtoms(), getNumberOfArguments()+3*getNumberOfAtoms() ); covar=0;
+ for(unsigned i=0;i<getNumberOfDataPoints();++i){
+ // double d = data[i]->calc( spos, getPbc(), getArguments(), sarg, mypack, true );
+ double d = data[0]->calc( data[i]->getReferencePositions(), getPbc(), getArguments(), data[i]->getReferenceArguments(), mypack, true );
+ for(unsigned jarg=0;jarg<getNumberOfArguments();++jarg){
+ // Need sorting for PBC with GAT
+ double jarg_d = 0.5*mypack.getArgumentDerivative(jarg) + data[0]->getReferenceArguments()[jarg] - sarg[jarg];
+ for(unsigned karg=0;karg<getNumberOfArguments();++karg){
+ // Need sorting for PBC with GAT
+ double karg_d = 0.5*mypack.getArgumentDerivative(karg) + data[0]->getReferenceArguments()[karg] - sarg[karg];
+ covar( jarg, karg ) += 0.25*getWeight(i)*jarg_d*karg_d; // mypack.getArgumentDerivative(jarg)*mypack.getArgumentDerivative(karg);
+ }
+ }
+ for(unsigned jat=0;jat<getNumberOfAtoms();++jat){
+ for(unsigned jc=0;jc<3;++jc){
+ double jdisplace = mypack.getAtomsDisplacementVector()[jat][jc] + data[0]->getReferencePositions()[jat][jc] - spos[jat][jc];
+ for(unsigned kat=0;kat<getNumberOfAtoms();++kat){
+ for(unsigned kc=0;kc<3;++kc){
+ double kdisplace = mypack.getAtomsDisplacementVector()[kat][kc] + data[0]->getReferencePositions()[kat][kc] - spos[kat][kc];
+ covar( narg+3*jat + jc, narg+3*kat + kc ) += getWeight(i)*jdisplace*kdisplace;
+ }
+ }
+ }
+ }
+ }
+ // Normalise
+ for(unsigned i=0;i<covar.nrows();++i){
+ for(unsigned j=0;j<covar.ncols();++j) covar(i,j) *= inorm;
+ }
+
+ // Diagonalise the covariance
+ std::vector<double> eigval( getNumberOfArguments()+3*getNumberOfAtoms() );
+ Matrix<double> eigvec( getNumberOfArguments()+3*getNumberOfAtoms(), getNumberOfArguments()+3*getNumberOfAtoms() );
+ diagMat( covar, eigval, eigvec );
+
+ // Open an output file
+ OFile ofile; ofile.link(*this); ofile.setBackupString("analysis");
+ ofile.open( ofilename );
+ // Output the reference configuration
+ myref->print( ofile, getOutputFormat(), atoms.getUnits().getLength()/0.1 );
+
+ // Store and print the eigenvectors
+ std::vector<Vector> tmp_atoms( getNumberOfAtoms() );
+ std::vector<double> tmp_args( getNumberOfArguments() );
+ Direction* tref = metricRegister().create<Direction>( "DIRECTION" );
+ tref->setNamesAndAtomNumbers( getAbsoluteIndexes(), argument_names );
+ for(unsigned dim=0;dim<ndim;++dim){
+ unsigned idim = covar.ncols() - 1 - dim;
+ for(unsigned i=0;i<getNumberOfArguments();++i) tmp_args[i]=arg_eigv(dim,i)=eigvec(idim,i);
+ for(unsigned i=0;i<getNumberOfAtoms();++i){
+ for(unsigned k=0;k<3;++k) tmp_atoms[i][k]=atom_eigv(dim,i)[k]=eigvec(idim,narg+3*i+k);
+ }
+ tref->setDirection( tmp_atoms, tmp_args );
+ tref->print( ofile, getOutputFormat(), atoms.getUnits().getLength()/0.1 );
+ }
+ // Close the output file
+ delete tref; ofile.close();
+}
+
+}
+}
diff --git a/src/bias/External.cpp b/src/bias/External.cpp
index 0a8193466426b2588940e6d34a6e52cdde3b73a2..b01c47fc642d7aeadcdfdd6f07dd19fa1c5e6a28 100644
--- a/src/bias/External.cpp
+++ b/src/bias/External.cpp
@@ -41,7 +41,7 @@ The following is an input for a calculation with an external potential that is
defined in the file bias.dat and that acts on the distance between atoms 3 and 5.
\verbatim
DISTANCE ATOMS=3,5 LABEL=d1
-EXTERNAL ARG=d1 FILENAME=bias.dat LABEL=external
+EXTERNAL ARG=d1 FILE=bias.dat LABEL=external
\endverbatim
(See also \ref DISTANCE \ref PRINT).
@@ -64,7 +64,7 @@ potential acting on two torsional angles:
\verbatim
TORSION ATOMS=4,5,6,7 LABEL=t1
TORSION ATOMS=6,7,8,9 LABEL=t2
-EXTERNAL ARG=t1,t2 FILENAME=bias.dat LABEL=ext
+EXTERNAL ARG=t1,t2 FILE=bias.dat LABEL=ext
\endverbatim
The header in the file bias.dat for this calculation would read:
diff --git a/src/mapping/Path.cpp b/src/mapping/Path.cpp
index 56fac268c68cf4a48367fcdf000cd42375b2e665..00b1596c692d3a2af7949793dc98b081e47a8349 100644
--- a/src/mapping/Path.cpp
+++ b/src/mapping/Path.cpp
@@ -66,12 +66,14 @@ PLUMED_REGISTER_ACTION(Path,"PATH")
void Path::registerKeywords( Keywords& keys ){
PathBase::registerKeywords( keys ); keys.remove("PROPERTY");
keys.addFlag("NOSPATH",false,"do not calculate the spath position");
+ keys.remove("LOWMEM");
}
Path::Path(const ActionOptions& ao):
Action(ao),
PathBase(ao)
{
+ setLowMemOption( true );
bool nos; parseFlag("NOSPATH",nos);
std::string empty;