hillclimber 0.1.5__cp313-cp313-musllinux_1_2_aarch64.whl

plumed/_lib/include/plumed/gridtools/SumOfKernels.h

@@ -0,0 +1,219 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2015-2023 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.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_gridtools_SumOfKernels_h
+#define __PLUMED_gridtools_SumOfKernels_h
+
+#include "../function/FunctionSetup.h"
+#include "../tools/SwitchingFunction.h"
+#include "../tools/HistogramBead.h"
+#include "../tools/Matrix.h"
+
+namespace PLMD {
+namespace gridtools {
+
+template <class K>
+class RegularKernel;
+
+class DiagonalKernelParams {
+public:
+  std::vector<double> at;
+  std::vector<double> sigma;
+  double height;
+  static bool bandwidthIsConstant( std::size_t ndim, const std::vector<Value*>& args );
+  static bool bandwidthsAllSame( std::size_t ndim, const std::vector<Value*>& args );
+  static bool setKernelAndCheckHeight( DiagonalKernelParams& kp, std::size_t ndim, const std::vector<double>& args );
+  static std::size_t getNumberOfParameters( const DiagonalKernelParams& kp );
+  static void getSigmaProjections( const DiagonalKernelParams& kp, std::vector<double>& support );
+  static double evaluateR2( const RegularKernel<DiagonalKernelParams>& p, const DiagonalKernelParams& kp, View<const double> x, View<double> paramderivs );
+};
+
+class NonDiagonalKernelParams {
+public:
+  std::vector<double> at;
+  Matrix<double> sigma, metric;
+  double height;
+  static bool bandwidthIsConstant( std::size_t ndim, const std::vector<Value*>& args );
+  static bool bandwidthsAllSame( std::size_t ndim, const std::vector<Value*>& args );
+  static bool setKernelAndCheckHeight( NonDiagonalKernelParams& kp, std::size_t ndim, const std::vector<double>& args );
+  static std::size_t getNumberOfParameters( const NonDiagonalKernelParams& kp );
+  static void getSigmaProjections( const NonDiagonalKernelParams& kp, std::vector<double>& support );
+  static double evaluateR2( const RegularKernel<NonDiagonalKernelParams>& p, const NonDiagonalKernelParams& kp, View<const double> x, View<double> paramderivs );
+};
+
+class DiscreteKernel {
+public:
+  static void registerKeywords( Keywords& keys ) {}
+  static void read( DiscreteKernel& p, ActionWithArguments* action, const std::vector<Value*>& args ) {}
+  static void setArgumentDomain( const unsigned& i, DiscreteKernel& params, const double& spacing, const bool isp, const std::string& min1, const std::string& max1 ) {}
+  static void getSupport( DiscreteKernel& params, const DiagonalKernelParams& kp, double dp2cutoff, std::vector<double>& support ) {}
+  static double calc( const DiscreteKernel& params, const DiagonalKernelParams& kp, View<const double> x, View<double> der, View<double> paramderivs );
+};
+
+class HistogramBeadKernel {
+public:
+  std::vector<HistogramBead> beads;
+  std::vector<double> gridspacing;
+  static void registerKeywords( Keywords& keys );
+  static void read( HistogramBeadKernel& p, ActionWithArguments* action, const std::vector<Value*>& args );
+  static void setArgumentDomain( const unsigned& i, HistogramBeadKernel& params, const double& spacing, const bool isp, const std::string& min1, const std::string& max1 );
+  static void getSupport( HistogramBeadKernel& params, const DiagonalKernelParams& kp, double dp2cutoff, std::vector<double>& support );
+  static double calc( const HistogramBeadKernel& params, const DiagonalKernelParams& kp, View<const double> x, View<double> der, View<double> paramderivs );
+};
+
+template <class K>
+class RegularKernel {
+public:
+  bool canusevol;
+  SwitchingFunction switchingFunction;
+  std::vector<bool> periodic;
+  std::vector<double> max_minus_min, inv_max_minus_min;
+  static void registerKeywords( Keywords& keys );
+  static void read( RegularKernel& p, ActionWithArguments* action, const std::vector<Value*>& args );
+  static void setArgumentDomain( const unsigned& i, RegularKernel& params, const double& spacing, const bool isp, const std::string& min1, const std::string& max1 );
+  static double difference( const RegularKernel& params, unsigned i, const double& val1, const double& val2 );
+  static void getSupport( const RegularKernel& params, const K& kp, double dp2cutoff, std::vector<double>& support );
+  static double calc( const RegularKernel& params, const K& kp, View<const double> x, View<double> der, View<double> paramderivs );
+};
+
+template <class K>
+void RegularKernel<K>::registerKeywords( Keywords& keys ) {
+  keys.add("compulsory","KERNEL","GAUSSIAN","the kernel function you are using.");
+}
+
+template <class K>
+void RegularKernel<K>::read( RegularKernel& p, ActionWithArguments* action, const std::vector<Value*>& args ) {
+  std::string kerneltype;
+  action->parse("KERNEL",kerneltype);
+  std::string errors;
+  for(auto & c: kerneltype) {
+    c = std::toupper(c);
+  }
+  p.canusevol = (kerneltype=="GAUSSIAN");
+  p.switchingFunction.set( kerneltype + " R_0=1.0 NOSTRETCH", errors );
+  if( errors.length()!=0 ) {
+    action->error("problem reading switching function description " + errors);
+  }
+  p.periodic.resize( args.size() );
+  p.max_minus_min.resize( args.size() );
+  p.inv_max_minus_min.resize( args.size() );
+}
+
+template <class K>
+void RegularKernel<K>::setArgumentDomain( const unsigned& i, RegularKernel& params, const double& spacing, const bool isp, const std::string& min1, const std::string& max1 ) {
+  params.periodic[i] = isp;
+  if( params.periodic[i] ) {
+    double min, max;
+    Tools::convert( min1, min );
+    Tools::convert( max1, max );
+    params.max_minus_min[i]=max-min;
+    params.inv_max_minus_min[i]=1.0/params.max_minus_min[i];
+  }
+}
+
+template <class K>
+double RegularKernel<K>::difference( const RegularKernel<K>& params, unsigned i, const double& val1, const double& val2 ) {
+  if( !params.periodic[i] ) {
+    return val1 - val2;
+  }
+  return params.max_minus_min[i]*Tools::pbc( params.inv_max_minus_min[i]*( val1 - val2 ) );
+}
+
+template <class K>
+void RegularKernel<K>::getSupport( const RegularKernel<K>& params, const K& kp, double dp2cutoff, std::vector<double>& support ) {
+  K::getSigmaProjections( kp, support );
+  for(unsigned i=0; i<support.size(); ++i) {
+    support[i] = sqrt(2.0*dp2cutoff)*support[i];
+  }
+}
+
+template <class K>
+double RegularKernel<K>::calc( const RegularKernel<K>& params, const K& kp, View<const double> x, View<double> der, View<double> paramderivs ) {
+  double r2 = K::evaluateR2( params, kp, x, paramderivs );
+  double dval, val = kp.height*params.switchingFunction.calculateSqr( r2, dval );
+  dval *= kp.height;
+  for(unsigned i=0; i<der.size(); ++i) {
+    der[i] += dval*paramderivs[i];
+    paramderivs[i] = -dval*paramderivs[i];
+  }
+  paramderivs[2*kp.at.size()] = val / kp.height;
+  return val;
+}
+
+class VonMissesKernelParams {
+public:
+  std::vector<double> at;
+  double concentration;
+  double norm;
+  double height;
+  static bool bandwidthIsConstant( std::size_t ndim, const std::vector<Value*>& args );
+  static bool bandwidthsAllSame( std::size_t ndim, const std::vector<Value*>& args );
+  static bool setKernelAndCheckHeight( VonMissesKernelParams& kp, std::size_t ndim, const std::vector<double>& argval );
+  static std::size_t getNumberOfParameters( const VonMissesKernelParams& kp );
+};
+
+class UniversalVonMisses {
+public:
+  std::string kerneltype;
+  SwitchingFunction switchingFunction;
+  static void registerKeywords( Keywords& keys ) {}
+  static void read( UniversalVonMisses& p, ActionWithArguments* action, const std::vector<Value*>& args ) {}
+  static void setArgumentDomain( const unsigned& i, UniversalVonMisses& params, const double& spacing, const bool isp, const std::string& min1, const std::string& max1 ) {}
+  static double calc( const UniversalVonMisses& params, const VonMissesKernelParams& kp, View<const double> x, View<double> der, View<double> paramderivs );
+};
+
+template <class K, class P>
+class SumOfKernels {
+public:
+  P params;
+  std::vector<K> kernelParams;
+/// This is used to setup the input gridobject's bounds with the grid data from values
+  static void registerKeywords( Keywords& keys );
+  static void read( SumOfKernels<K,P>& func, ActionWithArguments* action, const std::vector<Value*>& args, function::FunctionOptions& options );
+  static void calc( View<const std::size_t> klist, const SumOfKernels<K,P>& func, View<const double> args, View<double> values, View<double> der, View<double> paramderivs );
+};
+
+template <class K, class P>
+void SumOfKernels<K,P>::registerKeywords( Keywords& keys ) {
+  P::registerKeywords( keys );
+}
+
+template <class K, class P>
+void SumOfKernels<K,P>::read( SumOfKernels<K,P>& func, ActionWithArguments* action, const std::vector<Value*>& args, function::FunctionOptions& options ) {
+// Read the universal parameters for the kernel
+  P::read( func.params, action, args );
+}
+
+template <class K, class P>
+void SumOfKernels<K,P>::calc( View<const std::size_t> klist, const SumOfKernels<K,P>& func, View<const double> args, View<double> values, View<double> der, View<double> paramderivs ) {
+  values[0] = 0;
+  for(unsigned i=0; i<der.size(); ++i) {
+    der[i] = 0;
+  }
+  std::size_t nparams = K::getNumberOfParameters( func.kernelParams[0] );
+  for(unsigned i=0; i<klist.size(); ++i) {
+    values[0] += P::calc( func.params, func.kernelParams[klist[i]], args, der, View<double>( paramderivs.data() + i*nparams, nparams ) );
+  }
+}
+
+}
+}
+#endif

plumed/_lib/include/plumed/isdb/MetainferenceBase.h

@@ -0,0 +1,398 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2017-2023 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed.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_isdb_MetainferenceBase_h
+#define __PLUMED_isdb_MetainferenceBase_h
+
+#include "../core/ActionWithValue.h"
+#include "../core/ActionAtomistic.h"
+#include "../core/ActionWithArguments.h"
+#include "../tools/Communicator.h"
+#include "../core/PlumedMain.h"
+#include "../tools/Random.h"
+#include "../tools/OpenMP.h"
+
+#define PLUMED_METAINF_INIT(ao) Action(ao),MetainferenceBase(ao)
+
+namespace PLMD {
+namespace isdb {
+
+/**
+\ingroup INHERIT
+This is the abstract base class to use for implementing new ISDB Metainference actions, within it there is
+information as to how to go about implementing a new Metainference action.
+*/
+
+class MetainferenceBase :
+  public ActionAtomistic,
+  public ActionWithArguments,
+  public ActionWithValue {
+private:
+  std::vector<double> forces;
+  std::vector<double> forcesToApply;
+
+  // activate metainference
+  bool doscore_;
+  unsigned write_stride_;
+  // number of experimental data
+  unsigned narg;
+  // experimental data
+  std::vector<double> parameters;
+  // metainference derivatives
+  std::vector<double> metader_;
+  // vector of back-calculated experimental data
+  std::vector<double> calc_data_;
+
+  // noise type
+  unsigned noise_type_;
+  enum { GAUSS, MGAUSS, OUTLIERS, MOUTLIERS, GENERIC };
+  unsigned gen_likelihood_;
+  enum { LIKE_GAUSS, LIKE_LOGN };
+  bool   doscale_;
+  unsigned scale_prior_;
+  enum { SC_GAUSS, SC_FLAT };
+  double scale_;
+  double scale_mu_;
+  double scale_min_;
+  double scale_max_;
+  double Dscale_;
+  // scale is data scaling factor
+  // noise type
+  unsigned offset_prior_;
+  bool   dooffset_;
+  double offset_;
+  double offset_mu_;
+  double offset_min_;
+  double offset_max_;
+  double Doffset_;
+  // scale and offset regression
+  bool doregres_zero_;
+  int  nregres_zero_;
+  // sigma is data uncertainty
+  std::vector<double> sigma_;
+  std::vector<double> sigma_min_;
+  std::vector<double> sigma_max_;
+  std::vector<double> Dsigma_;
+  // sigma_mean is uncertainty in the mean estimate
+  std::vector<double> sigma_mean2_;
+  // this is the estimator of the mean value per replica for generic metainference
+  std::vector<double> ftilde_;
+  double Dftilde_;
+
+  // temperature in kbt
+  double   kbt_;
+
+  // Monte Carlo stuff
+  std::vector<Random> random;
+  unsigned MCsteps_;
+  long long unsigned MCaccept_;
+  long long unsigned MCacceptScale_;
+  long long unsigned MCacceptFT_;
+  long long unsigned MCtrial_;
+  unsigned MCchunksize_;
+
+  // output
+  Value*   valueScore;
+  Value*   valueScale;
+  Value*   valueOffset;
+  Value*   valueAccept;
+  Value*   valueAcceptScale;
+  Value*   valueAcceptFT;
+  std::vector<Value*> valueSigma;
+  std::vector<Value*> valueSigmaMean;
+  std::vector<Value*> valueFtilde;
+
+  // restart
+  std::string status_file_name_;
+  OFile    sfile_;
+  std::string fmt_;
+
+  // others
+  bool     firstTime;
+  std::vector<bool> firstTimeW;
+  bool     master;
+  bool     do_reweight_;
+  unsigned do_optsigmamean_;
+  unsigned nrep_;
+  unsigned replica_;
+
+  // selector
+  unsigned nsel_;
+  std::string selector_;
+  unsigned iselect;
+
+  // optimize sigma mean
+  std::vector< std::vector < std::vector <double> > > sigma_mean2_last_;
+  unsigned optsigmamean_stride_;
+  // optimize sigma max
+  unsigned N_optimized_step_;
+  unsigned optimized_step_;
+  bool sigmamax_opt_done_;
+  std::vector<double> sigma_max_est_;
+
+  // average weights
+  double decay_w_;
+  std::vector< std::vector <double> >  average_weights_;
+
+  double getEnergyMIGEN(const std::vector<double> &mean, const std::vector<double> &ftilde, const std::vector<double> &sigma,
+                        const double scale, const double offset);
+  double getEnergySP(const std::vector<double> &mean, const std::vector<double> &sigma,
+                     const double scale, const double offset);
+  double getEnergySPE(const std::vector<double> &mean, const std::vector<double> &sigma,
+                      const double scale, const double offset);
+  double getEnergyGJ(const std::vector<double> &mean, const std::vector<double> &sigma,
+                     const double scale, const double offset);
+  double getEnergyGJE(const std::vector<double> &mean, const std::vector<double> &sigma,
+                      const double scale, const double offset);
+  void setMetaDer(const unsigned index, const double der);
+  void getEnergyForceSP(const std::vector<double> &mean, const std::vector<double> &dmean_x, const std::vector<double> &dmean_b);
+  void getEnergyForceSPE(const std::vector<double> &mean, const std::vector<double> &dmean_x, const std::vector<double> &dmean_b);
+  void getEnergyForceGJ(const std::vector<double> &mean, const std::vector<double> &dmean_x, const std::vector<double> &dmean_b);
+  void getEnergyForceGJE(const std::vector<double> &mean, const std::vector<double> &dmean_x, const std::vector<double> &dmean_b);
+  void getEnergyForceMIGEN(const std::vector<double> &mean, const std::vector<double> &dmean_x, const std::vector<double> &dmean_b);
+  double getCalcData(const unsigned index);
+  void get_weights(double &weight, double &norm, double &neff);
+  void replica_averaging(const double weight, const double norm, std::vector<double> &mean, std::vector<double> &dmean_b);
+  void get_sigma_mean(const double weight, const double norm, const double neff, const std::vector<double> &mean);
+  void do_regression_zero(const std::vector<double> &mean);
+  void moveTilde(const std::vector<double> &mean_, double &old_energy);
+  void moveScaleOffset(const std::vector<double> &mean_, double &old_energy);
+  void moveSigmas(const std::vector<double> &mean_, double &old_energy, const unsigned i, const std::vector<unsigned> &indices, bool &breaknow);
+  double doMonteCarlo(const std::vector<double> &mean);
+
+public:
+  static void registerKeywords( Keywords& keys );
+  explicit MetainferenceBase(const ActionOptions&);
+  ~MetainferenceBase();
+  void Initialise(const unsigned input);
+  void Selector();
+  unsigned getNarg();
+  void setNarg(const unsigned input);
+  void setParameters(const std::vector<double>& input);
+  void setParameter(const double input);
+  void setCalcData(const unsigned index, const double datum);
+  void setCalcData(const std::vector<double>& data);
+  bool getDoScore();
+  unsigned getWstride();
+  double getScore();
+  void setScore(const double score);
+  void setDerivatives();
+  double getMetaDer(const unsigned index);
+  void writeStatus();
+  void turnOnDerivatives() override;
+  unsigned getNumberOfDerivatives() override;
+  void lockRequests() override;
+  void unlockRequests() override;
+  void calculateNumericalDerivatives( ActionWithValue* a ) override;
+  void apply() override;
+  void setArgDerivatives(Value *v, const double &d);
+  void setAtomsDerivatives(Value*v, const unsigned i, const Vector&d);
+  void setBoxDerivatives(Value*v, const Tensor&d);
+};
+
+inline
+void MetainferenceBase::setNarg(const unsigned input) {
+  narg = input;
+}
+
+inline
+bool MetainferenceBase::getDoScore() {
+  return doscore_;
+}
+
+inline
+unsigned MetainferenceBase::getWstride() {
+  return write_stride_;
+}
+
+inline
+unsigned MetainferenceBase::getNarg() {
+  return narg;
+}
+
+inline
+void MetainferenceBase::setMetaDer(const unsigned index, const double der) {
+  metader_[index] = der;
+}
+
+inline
+double MetainferenceBase::getMetaDer(const unsigned index) {
+  return metader_[index];
+}
+
+inline
+double MetainferenceBase::getCalcData(const unsigned index) {
+  return calc_data_[index];
+}
+
+inline
+void MetainferenceBase::setCalcData(const unsigned index, const double datum) {
+  calc_data_[index] = datum;
+}
+
+inline
+void MetainferenceBase::setCalcData(const std::vector<double>& data) {
+  for(unsigned i=0; i<data.size(); i++) {
+    calc_data_[i] = data[i];
+  }
+}
+
+inline
+void MetainferenceBase::setParameters(const std::vector<double>& input) {
+  for(unsigned i=0; i<input.size(); i++) {
+    parameters.push_back(input[i]);
+  }
+}
+
+inline
+void MetainferenceBase::setParameter(const double input) {
+  parameters.push_back(input);
+}
+
+inline
+void MetainferenceBase::setScore(const double score) {
+  valueScore->set(score);
+}
+
+inline
+void MetainferenceBase::setDerivatives() {
+  // Get appropriate number of derivatives
+  // Derivatives are first for arguments and then for atoms
+  unsigned nder;
+  if( getNumberOfAtoms()>0 ) {
+    nder = 3*getNumberOfAtoms() + 9 + getNumberOfArguments();
+  } else {
+    nder = getNumberOfArguments();
+  }
+
+  // Resize all derivative arrays
+  forces.resize( nder );
+  forcesToApply.resize( nder );
+  for(unsigned i=0; i<getNumberOfComponents(); ++i) {
+    getPntrToComponent(i)->resizeDerivatives(nder);
+  }
+}
+
+inline
+void MetainferenceBase::turnOnDerivatives() {
+  ActionWithValue::turnOnDerivatives();
+}
+
+inline
+unsigned MetainferenceBase::getNumberOfDerivatives() {
+  if( getNumberOfAtoms()>0 ) {
+    return 3*getNumberOfAtoms() + 9 + getNumberOfArguments();
+  }
+  return getNumberOfArguments();
+}
+
+inline
+void MetainferenceBase::lockRequests() {
+  ActionAtomistic::lockRequests();
+  ActionWithArguments::lockRequests();
+}
+
+inline
+void MetainferenceBase::unlockRequests() {
+  ActionAtomistic::unlockRequests();
+  ActionWithArguments::unlockRequests();
+}
+
+inline
+void MetainferenceBase::calculateNumericalDerivatives( ActionWithValue* a=NULL ) {
+  if( getNumberOfArguments()>0 ) {
+    ActionWithArguments::calculateNumericalDerivatives( a );
+  }
+  if( getNumberOfAtoms()>0 ) {
+    Matrix<double> save_derivatives( getNumberOfComponents(), getNumberOfArguments() );
+    for(unsigned j=0; j<getNumberOfComponents(); ++j) {
+      for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+        if(getPntrToComponent(j)->hasDerivatives()) {
+          save_derivatives(j,i)=getPntrToComponent(j)->getDerivative(i);
+        }
+      }
+    }
+    calculateAtomicNumericalDerivatives( a, getNumberOfArguments() );
+    for(unsigned j=0; j<getNumberOfComponents(); ++j) {
+      for(unsigned i=0; i<getNumberOfArguments(); ++i) {
+        if(getPntrToComponent(j)->hasDerivatives()) {
+          getPntrToComponent(j)->addDerivative( i, save_derivatives(j,i) );
+        }
+      }
+    }
+  }
+}
+
+inline
+void MetainferenceBase::apply() {
+  bool wasforced=false;
+  forcesToApply.assign(forcesToApply.size(),0.0);
+  for(unsigned i=0; i<getNumberOfComponents(); ++i) {
+    if( getPntrToComponent(i)->applyForce( forces ) ) {
+      wasforced=true;
+      for(unsigned ii=0; ii<forces.size(); ++ii) {
+        forcesToApply[ii]+=forces[ii];
+      }
+    }
+  }
+  if( wasforced ) {
+    unsigned ind=0;
+    addForcesOnArguments( 0, forcesToApply, ind );
+    if( getNumberOfAtoms()>0 ) {
+      setForcesOnAtoms( forcesToApply, ind );
+    }
+  }
+}
+
+inline
+void MetainferenceBase::setArgDerivatives(Value *v, const double &d) {
+  v->addDerivative(0,d);
+}
+
+inline
+void MetainferenceBase::setAtomsDerivatives(Value*v, const unsigned i, const Vector&d) {
+  const unsigned noa=getNumberOfArguments();
+  v->addDerivative(noa+3*i+0,d[0]);
+  v->addDerivative(noa+3*i+1,d[1]);
+  v->addDerivative(noa+3*i+2,d[2]);
+}
+
+inline
+void MetainferenceBase::setBoxDerivatives(Value* v,const Tensor&d) {
+  const unsigned noa=getNumberOfArguments();
+  const unsigned nat=getNumberOfAtoms();
+  v->addDerivative(noa+3*nat+0,d(0,0));
+  v->addDerivative(noa+3*nat+1,d(0,1));
+  v->addDerivative(noa+3*nat+2,d(0,2));
+  v->addDerivative(noa+3*nat+3,d(1,0));
+  v->addDerivative(noa+3*nat+4,d(1,1));
+  v->addDerivative(noa+3*nat+5,d(1,2));
+  v->addDerivative(noa+3*nat+6,d(2,0));
+  v->addDerivative(noa+3*nat+7,d(2,1));
+  v->addDerivative(noa+3*nat+8,d(2,2));
+}
+
+
+}
+}
+
+#endif
+