hillclimber 0.1.6__cp314-cp314t-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl

plumed/_lib/include/plumed/tools/Matrix.h

@@ -0,0 +1,721 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2011-2023 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_tools_Matrix_h
+#define __PLUMED_tools_Matrix_h
+#include <vector>
+#include <string>
+#include <set>
+#include <cmath>
+#include "Exception.h"
+#include "MatrixSquareBracketsAccess.h"
+#include "Tools.h"
+#include "Log.h"
+#include "../lapack/lapack.h"
+
+namespace PLMD {
+
+/// Calculate the dot product between two vectors
+template <typename T> T dotProduct( const std::vector<T>& A, const std::vector<T>& B ) {
+  plumed_assert( A.size()==B.size() );
+  T val;
+  for(unsigned i=0; i<A.size(); ++i) {
+    val+=A[i]*B[i];
+  }
+  return val;
+}
+
+/// Calculate the dot product between a vector and itself
+template <typename T> T norm( const std::vector<T>& A ) {
+  T val;
+  for(unsigned i=0; i<A.size(); ++i) {
+    val+=A[i]*A[i];
+  }
+  return val;
+}
+
+/// This class stores a full matrix and allows one to do some simple matrix operations
+template <typename T>
+class Matrix:
+  public MatrixSquareBracketsAccess<Matrix<T>,T> {
+  /// Multiply matrix by scalar
+  template <typename U> friend Matrix<U> operator*(U&, const Matrix<U>& );
+  /// Matrix matrix multiply
+  template <typename U> friend void mult( const Matrix<U>&, const Matrix<U>&, Matrix<U>& );
+  /// Matrix times a std::vector
+  template <typename U> friend void mult( const Matrix<U>&, const std::vector<U>&, std::vector<U>& );
+  /// std::vector times a Matrix
+  template <typename U> friend void mult( const std::vector<U>&, const Matrix<U>&, std::vector<U>& );
+  /// Matrix transpose
+  template <typename U> friend void transpose( const Matrix<U>&, Matrix<U>& );
+  /// Output the entire matrix on a single line
+  template <typename U> friend Log& operator<<(Log&, const Matrix<U>& );
+  /// Output the Matrix in matrix form
+  template <typename U> friend void matrixOut( Log&, const Matrix<U>& );
+  /// Diagonalize a symmetric matrix - returns zero if diagonalization worked
+  template <typename U> friend int diagMat( const Matrix<U>&, std::vector<U>&, Matrix<U>& );
+  /// Calculate the Moore-Penrose Pseudoinverse of a matrix
+  template <typename U> friend int pseudoInvert( const Matrix<U>&, Matrix<U>& );
+  /// Calculate the logarithm of the determinant of a symmetric matrix - returns zero if succesfull
+  template <typename U> friend int logdet( const Matrix<U>&, U& );
+  /// Invert a matrix (works for both symmetric and asymmetric matrices) - returns zero if sucesfull
+  template <typename U> friend int Invert( const Matrix<U>&, Matrix<U>& );
+  /// Do a cholesky decomposition of a matrix
+  template <typename U> friend void cholesky( const Matrix<U>&, Matrix<U>& );
+  /// Solve a system of equations using the cholesky decomposition
+  template <typename U> friend void chol_elsolve( const Matrix<U>&, const std::vector<U>&, std::vector<U>& );
+private:
+  /// Number of elements in matrix (nrows*ncols)
+  unsigned sz;
+  /// Number of rows in matrix
+  unsigned rw;
+  /// Number of columns in matrix
+  unsigned cl;
+  /// The data in the matrix
+  std::vector<T> data;
+  template <typename Y>
+  struct  openAccVectorHelper {
+    using pointer = Y*;
+    size_t sz=0;
+    pointer data=nullptr;
+    void toACCDevice() const {
+#pragma acc enter data copyin(this[0:1],sz,data[0:sz])
+    }
+    void removeFromACCDevice() const {
+#pragma acc exit data delete(data[0:sz],sz,this[0:1])
+    }
+    void update(std::vector<Y>&x) {
+      data = x.data();
+      sz = x.size();
+    }
+  };
+  openAccVectorHelper<T> helper{};
+
+public:
+  explicit Matrix(const unsigned nr=0, const unsigned nc=0 )  : sz(nr*nc), rw(nr), cl(nc), data(nr*nc) {
+    helper.update(data);
+  }
+  void toACCDevice() const {
+#pragma acc enter data copyin(this[0:1])
+    helper.toACCDevice();
+  }
+  void removeFromACCDevice() const {
+    helper.removeFromACCDevice();
+    // and delete
+#pragma acc exit data delete( this[0:1])
+  }
+  Matrix(const Matrix<T>& t) : sz(t.sz), rw(t.rw), cl(t.cl), data(t.data) {
+    helper.update(data);
+  }
+  /// Resize the matrix
+  void resize( const unsigned nr, const unsigned nc ) {
+    rw=nr;
+    cl=nc;
+    sz=nr*nc;
+    data.resize(sz);
+    helper.update(data);
+  }
+  /// Return the number of rows
+  inline unsigned nrows() const {
+    return rw;
+  }
+  /// Return the number of columns
+  inline unsigned ncols() const {
+    return cl;
+  }
+  /// Return the contents of the matrix as a vector of length rw*cl
+  inline std::vector<T>& getVector() {
+    return data;
+  }
+  /// Set the matrix from a vector input
+  inline void setFromVector( const std::vector<T>& vecin ) {
+    plumed_assert( vecin.size()==sz );
+    for(unsigned i=0; i<sz; ++i) {
+      data[i]=vecin[i];
+    }
+  }
+  /// Return element i,j of the matrix
+  inline const T& operator () (const unsigned& i, const unsigned& j) const {
+    return helper.data[j+i*cl];
+    // return data[j+i*cl];
+  }
+  /// Return a referenre to element i,j of the matrix
+  inline T& operator () (const unsigned& i, const unsigned& j)      {
+    return helper.data[j+i*cl];
+    // return data[j+i*cl];
+  }
+  /// Set all elements of the matrix equal to the value of v
+  Matrix<T>& operator=(const T& v) {
+    for(unsigned i=0; i<sz; ++i) {
+      data[i]=v;
+    }
+    return *this;
+  }
+  /// Set the Matrix equal to another Matrix
+  Matrix<T>& operator=(const Matrix<T>& m) {
+    sz=m.sz;
+    rw=m.rw;
+    cl=m.cl;
+    data=m.data;
+    helper.update(data);
+    return *this;
+  }
+  /// Set the Matrix equal to the value of a standard vector - used for readin
+  Matrix<T>& operator=(const std::vector<T>& v) {
+    plumed_dbg_assert( v.size()==sz );
+    for(unsigned i=0; i<sz; ++i) {
+      data[i]=v[i];
+    }
+    return *this;
+  }
+  /// Add v to all elements of the Matrix
+  Matrix<T> operator+=(const T& v) {
+    for(unsigned i=0; i<sz; ++i) {
+      data[i]+=v;
+    }
+    return *this;
+  }
+  /// Multiply all elements by v
+  Matrix<T> operator*=(const T& v) {
+    for(unsigned i=0; i<sz; ++i) {
+      data[i]*=v;
+    }
+    return *this;
+  }
+  /// Matrix addition
+  Matrix<T>& operator+=(const Matrix<T>& m) {
+    plumed_dbg_assert( m.rw==rw && m.cl==cl );
+    data+=m.data;
+    return *this;
+  }
+  /// Subtract v from all elements of the Matrix
+  Matrix<T> operator-=(const T& v) {
+    for(unsigned i=0; i<sz; ++i) {
+      data-=v;
+    }
+    return *this;
+  }
+  /// Matrix subtraction
+  Matrix<T>& operator-=(const Matrix<T>& m) {
+    plumed_dbg_assert( m.rw==rw && m.cl==cl );
+    data-=m.data;
+    return *this;
+  }
+  /// Test if the matrix is symmetric or not
+  unsigned isSymmetric() const {
+    if (rw!=cl) {
+      return 0;
+    }
+    unsigned sym=1;
+    for(unsigned i=1; i<rw; ++i)
+      for(unsigned j=0; j<i; ++j)
+        if( std::fabs(data[i+j*cl]-data[j+i*cl])>1.e-10 ) {
+          sym=0;
+          break;
+        }
+    return sym;
+  }
+};
+
+/// Multiply matrix by scalar
+template <typename T> Matrix<T> operator*(T& v, const Matrix<T>& m ) {
+  Matrix<T> new_m(m);
+  new_m*=v;
+  return new_m;
+}
+
+template <typename T> void mult( const Matrix<T>& A, const Matrix<T>& B, Matrix<T>& C ) {
+  plumed_assert(A.cl==B.rw);
+  if( A.rw !=C.rw  || B.cl !=C.cl ) {
+    C.resize( A.rw, B.cl );
+  }
+  C=static_cast<T>( 0 );
+  for(unsigned i=0; i<A.rw; ++i)
+    for(unsigned j=0; j<B.cl; ++j)
+      for (unsigned k=0; k<A.cl; ++k) {
+        C(i,j)+=A(i,k)*B(k,j);
+      }
+}
+
+template <typename T> void mult( const Matrix<T>& A, const std::vector<T>& B, std::vector<T>& C) {
+  plumed_assert( A.cl==B.size() );
+  if( C.size()!=A.rw  ) {
+    C.resize(A.rw);
+  }
+  for(unsigned i=0; i<A.rw; ++i) {
+    C[i]= static_cast<T>( 0 );
+  }
+  for(unsigned i=0; i<A.rw; ++i)
+    for(unsigned k=0; k<A.cl; ++k) {
+      C[i]+=A(i,k)*B[k] ;
+    }
+}
+
+template <typename T> void mult( const std::vector<T>& A, const Matrix<T>& B, std::vector<T>& C) {
+  plumed_assert( B.rw==A.size() );
+  if( C.size()!=B.cl ) {
+    C.resize( B.cl );
+  }
+  for(unsigned i=0; i<B.cl; ++i) {
+    C[i]=static_cast<T>( 0 );
+  }
+  for(unsigned i=0; i<B.cl; ++i)
+    for(unsigned k=0; k<B.rw; ++k) {
+      C[i]+=A[k]*B(k,i);
+    }
+}
+
+template <typename T> void transpose( const Matrix<T>& A, Matrix<T>& AT ) {
+  if( A.rw!=AT.cl || A.cl!=AT.rw ) {
+    AT.resize( A.cl, A.rw );
+  }
+  for(unsigned i=0; i<A.cl; ++i)
+    for(unsigned j=0; j<A.rw; ++j) {
+      AT(i,j)=A(j,i);
+    }
+}
+
+template <typename T> Log& operator<<(Log& ostr, const Matrix<T>& mat) {
+  for(unsigned i=0; i<mat.sz; ++i) {
+    ostr<<mat.data[i]<<" ";
+  }
+  return ostr;
+}
+
+template <typename T> void matrixOut( Log& ostr, const Matrix<T>& mat) {
+  for(unsigned i=0; i<mat.rw; ++i) {
+    for(unsigned j=0; j<mat.cl; ++j) {
+      ostr<<mat(i,j)<<" ";
+    }
+    ostr<<"\n";
+  }
+  return;
+}
+
+template <typename T> int diagMat( const Matrix<T>& A, std::vector<T>& eigenvals, Matrix<T>& eigenvecs ) {
+
+  // Check matrix is square and symmetric
+  plumed_assert( A.rw==A.cl );
+  plumed_assert( A.isSymmetric()==1 );
+  std::vector<T> da(A.sz);
+  unsigned k=0;
+  std::vector<T> evals(A.cl);
+  // Transfer the matrix to the local array
+  for (unsigned i=0; i<A.cl; ++i)
+    for (unsigned j=0; j<A.rw; ++j) {
+      da[k++]=static_cast<T>( A(j,i) );
+    }
+
+  int n=A.cl;
+  int lwork=-1;
+  int liwork=-1;
+  int m;
+  int info=0;
+  int one=1;
+  std::vector<T> work(A.cl);
+  std::vector<int> iwork(A.cl);
+  T vl, vu, abstol=0.0;
+  std::vector<int> isup(2*A.cl);
+  std::vector<T> evecs(A.sz);
+  if constexpr (std::is_same_v<T,double>) {
+    plumed_lapack_dsyevr("V", "I", "U", &n, da.data(), &n, &vl, &vu, &one, &n,
+                         &abstol, &m, evals.data(), evecs.data(), &n,
+                         isup.data(), work.data(), &lwork, iwork.data(), &liwork, &info);
+  } else if constexpr (std::is_same_v<T,float>) {
+    plumed_lapack_ssyevr("V", "I", "U", &n, da.data(), &n, &vl, &vu, &one, &n,
+                         &abstol, &m, evals.data(), evecs.data(), &n,
+                         isup.data(), work.data(), &lwork, iwork.data(), &liwork, &info);
+  } else {
+    static_assert(std::is_same_v<T,double> || std::is_same_v<T,float>, "diagMat is only compatible with float and double");
+  }
+  if (info!=0) {
+    return info;
+  }
+
+  // Retrieve correct sizes for work and iwork then reallocate
+  liwork=iwork[0];
+  iwork.resize(liwork);
+  lwork=static_cast<int>( work[0] );
+  work.resize(lwork);
+
+  if constexpr (std::is_same_v<T,double>) {
+    plumed_lapack_dsyevr("V", "I", "U", &n, da.data(), &n, &vl, &vu, &one, &n,
+                         &abstol, &m, evals.data(), evecs.data(), &n,
+                         isup.data(), work.data(), &lwork, iwork.data(), &liwork, &info);
+  } else if constexpr (std::is_same_v<T,float>) {
+    plumed_lapack_ssyevr("V", "I", "U", &n, da.data(), &n, &vl, &vu, &one, &n,
+                         &abstol, &m, evals.data(), evecs.data(), &n,
+                         isup.data(), work.data(), &lwork, iwork.data(), &liwork, &info);
+  } else {
+    static_assert(std::is_same_v<T,double> || std::is_same_v<T,float>, "diagMat is only compatible with float and double");
+  }
+  if (info!=0) {
+    return info;
+  }
+
+  if( eigenvals.size()!=A.cl ) {
+    eigenvals.resize( A.cl );
+  }
+  if( eigenvecs.rw!=A.rw || eigenvecs.cl!=A.cl ) {
+    eigenvecs.resize( A.rw, A.cl );
+  }
+  k=0;
+  for(unsigned i=0; i<A.cl; ++i) {
+    eigenvals[i]=evals[i];
+    // N.B. For ease of producing projectors we store the eigenvectors
+    // ROW-WISE in the eigenvectors matrix.  The first index is the
+    // eigenvector number and the second the component
+    for(unsigned j=0; j<A.rw; ++j) {
+      eigenvecs(i,j)=evecs[k++];
+    }
+  }
+
+  // This changes eigenvectors so that the first non-null element
+  // of each of them is positive
+  // We can do it because the phase is arbitrary, and helps making
+  // the result reproducible
+  for(int i=0; i<n; ++i) {
+    int j;
+    for(j=0; j<n; j++)
+      if(eigenvecs(i,j)*eigenvecs(i,j)>1e-14) {
+        break;
+      }
+    if(j<n)
+      if(eigenvecs(i,j)<0.0)
+        for(j=0; j<n; j++) {
+          eigenvecs(i,j)*=-1;
+        }
+  }
+  return 0;
+}
+
+template <typename T> int pseudoInvert( const Matrix<T>& A, Matrix<T>& pseudoinverse ) {
+  std::vector<T> da(A.sz);
+  unsigned k=0;
+  // Transfer the matrix to the local array
+  for (unsigned i=0; i<A.cl; ++i)
+    for (unsigned j=0; j<A.rw; ++j) {
+      da[k++]=static_cast<T>( A(j,i) );
+    }
+
+  int nsv;
+  int info=0;
+  int nrows=A.rw, ncols=A.cl;
+  if(A.rw>A.cl) {
+    nsv=A.cl;
+  } else {
+    nsv=A.rw;
+  }
+
+  // Create some containers for stuff from single value decomposition
+  std::vector<T> S(nsv);
+  std::vector<T> U(nrows*nrows);
+  std::vector<T> VT(ncols*ncols);
+  std::vector<int> iwork(8*nsv);
+
+  // This optimizes the size of the work array used in lapack singular value decomposition
+  int lwork=-1;
+  std::vector<T> work(1);
+  if constexpr (std::is_same_v<T,double> ) {
+    plumed_lapack_dgesdd( "A", &nrows, &ncols, da.data(), &nrows, S.data(),
+                          U.data(), &nrows, VT.data(), &ncols, work.data(),
+                          &lwork, iwork.data(), &info );
+  } else if constexpr (std::is_same_v<T,float>) {
+    plumed_lapack_sgesdd( "A", &nrows, &ncols, da.data(), &nrows, S.data(),
+                          U.data(), &nrows, VT.data(), &ncols, work.data(),
+                          &lwork, iwork.data(), &info );
+  } else {
+    static_assert(std::is_same_v<T,double> || std::is_same_v<T,float>, "pseudoInvert works only for float and double");
+  }
+  if(info!=0) {
+    return info;
+  }
+
+  // Retrieve correct sizes for work and rellocate
+  lwork=(int) work[0];
+  work.resize(lwork);
+
+  // This does the singular value decomposition
+  if constexpr (std::is_same_v<T,double> ) {
+    plumed_lapack_dgesdd( "A", &nrows, &ncols, da.data(), &nrows, S.data(),
+                          U.data(), &nrows, VT.data(), &ncols, work.data(),
+                          &lwork, iwork.data(), &info );
+  } else if constexpr (std::is_same_v<T,float>) {
+    plumed_lapack_sgesdd( "A", &nrows, &ncols, da.data(), &nrows, S.data(),
+                          U.data(), &nrows, VT.data(), &ncols, work.data(),
+                          &lwork, iwork.data(), &info );
+  } else {
+    static_assert(std::is_same_v<T,double> || std::is_same_v<T,float>, "pseudoInvert works only for float and double");
+  }
+  if(info!=0) {
+    return info;
+  }
+
+  // Compute the tolerance on the singular values ( machine epsilon * number of singular values * maximum singular value )
+  T tol;
+  tol=S[0];
+  for(int i=1; i<nsv; ++i) {
+    if( S[i]>tol ) {
+      tol=S[i];
+    }
+  }
+  tol*=nsv*epsilon;
+
+  // Get the inverses of the singlular values
+  Matrix<T> Si( ncols, nrows );
+  Si=0.0;
+  for(int i=0; i<nsv; ++i) {
+    if( S[i]>tol ) {
+      Si(i,i)=1./S[i];
+    } else {
+      Si(i,i)=0.0;
+    }
+  }
+
+  // Now extract matrices for pseudoinverse
+  Matrix<T> V( ncols, ncols ), UT( nrows, nrows ), tmp( ncols, nrows );
+  k=0;
+  for(int i=0; i<nrows; ++i) {
+    for(int j=0; j<nrows; ++j) {
+      UT(i,j)=U[k++];
+    }
+  }
+  k=0;
+  for(int i=0; i<ncols; ++i) {
+    for(int j=0; j<ncols; ++j) {
+      V(i,j)=VT[k++];
+    }
+  }
+
+  // And do matrix algebra to construct the pseudoinverse
+  if( pseudoinverse.rw!=static_cast<unsigned>(ncols)
+      || pseudoinverse.cl!=static_cast<unsigned>(nrows) ) {
+    pseudoinverse.resize( ncols, nrows );
+  }
+  mult( V, Si, tmp );
+  mult( tmp, UT, pseudoinverse );
+
+  return 0;
+}
+
+template <typename T> int Invert( const Matrix<T>& A, Matrix<T>& inverse ) {
+
+  if( A.isSymmetric()==1 ) {
+    // GAT -- I only ever use symmetric matrices so I can invert them like this.
+    // I choose to do this as I have had problems with the more general way of doing this that
+    // is implemented below.
+    std::vector<T> eval(A.rw);
+    Matrix<T> evec(A.rw,A.cl), tevec(A.rw,A.cl);
+    int err;
+    err=diagMat( A, eval, evec );
+    if(err!=0) {
+      return err;
+    }
+    for (unsigned i=0; i<A.rw; ++i)
+      for (unsigned j=0; j<A.cl; ++j) {
+        tevec(i,j)=evec(j,i)/eval[j];
+      }
+    mult(tevec,evec,inverse);
+  } else {
+    std::vector<T> da(A.sz);
+    std::vector<int> ipiv(A.cl);
+    unsigned k=0;
+    int n=A.rw;
+    int info=0;
+    for(unsigned i=0; i<A.cl; ++i)
+      for(unsigned j=0; j<A.rw; ++j) {
+        da[k++]=static_cast<T>( A(j,i) );
+      }
+    if constexpr (std::is_same_v<T,double> ) {
+      plumed_lapack_dgetrf(&n,&n,da.data(),&n,ipiv.data(),&info);
+    } else if constexpr (std::is_same_v<T,float>) {
+      plumed_lapack_sgetrf(&n,&n,da.data(),&n,ipiv.data(),&info);
+    } else {
+      static_assert(std::is_same_v<T,double> || std::is_same_v<T,float>, "Invert works only for float and double");
+    }
+    if(info!=0) {
+      return info;
+    }
+
+    int lwork=-1;
+    std::vector<T> work(A.cl);
+    if constexpr (std::is_same_v<T,double> ) {
+      plumed_lapack_dgetri(&n,da.data(),&n,ipiv.data(),work.data(),&lwork,&info);
+    } else if constexpr (std::is_same_v<T,float>) {
+      plumed_lapack_sgetri(&n,da.data(),&n,ipiv.data(),work.data(),&lwork,&info);
+    } else {
+      static_assert(std::is_same_v<T,double> || std::is_same_v<T,float>, "Invert works only for float and double");
+    }
+    if(info!=0) {
+      return info;
+    }
+
+    lwork=static_cast<int>( work[0] );
+    work.resize(lwork);
+    if constexpr (std::is_same_v<T,double> ) {
+      plumed_lapack_dgetri(&n,da.data(),&n,ipiv.data(),work.data(),&lwork,&info);
+    } else if constexpr (std::is_same_v<T,float>) {
+      plumed_lapack_sgetri(&n,da.data(),&n,ipiv.data(),work.data(),&lwork,&info);
+    } else {
+      static_assert(std::is_same_v<T,double> || std::is_same_v<T,float>, "Invert works only for float and double");
+    }
+    if(info!=0) {
+      return info;
+    }
+
+    if( inverse.cl!=A.cl || inverse.rw!=A.rw ) {
+      inverse.resize(A.rw,A.cl);
+    }
+    k=0;
+    for(unsigned i=0; i<A.rw; ++i)
+      for(unsigned j=0; j<A.cl; ++j) {
+        inverse(j,i)=da[k++];
+      }
+  }
+
+  return 0;
+}
+
+template <typename T> void cholesky( const Matrix<T>& A, Matrix<T>& B ) {
+
+  plumed_assert( A.rw==A.cl && A.isSymmetric() );
+  Matrix<T> L(A.rw,A.cl);
+  L=0.;
+  std::vector<T> D(A.rw,0.);
+  for(unsigned i=0; i<A.rw; ++i) {
+    L(i,i)=static_cast<T>( 1 );
+    for (unsigned j=0; j<i; ++j) {
+      L(i,j)=A(i,j);
+      for (unsigned k=0; k<j; ++k) {
+        L(i,j)-=L(i,k)*L(j,k)*D[k];
+      }
+      if (D[j]!=0.) {
+        L(i,j)/=D[j];
+      } else {
+        L(i,j)=static_cast<T>( 0 );
+      }
+    }
+    D[i]=A(i,i);
+    for (unsigned k=0; k<i; ++k) {
+      D[i]-=L(i,k)*L(i,k)*D[k];
+    }
+  }
+
+  for(unsigned i=0; i<A.rw; ++i) {
+    D[i]=(D[i]>0.?std::sqrt(D[i]):0.);
+  }
+  if( B.rw!=A.rw || B.cl!=A.cl ) {
+    B.resize( A.rw, A.cl);
+  }
+  B=0.;
+  for(unsigned i=0; i<A.rw; ++i)
+    for(unsigned j=0; j<=i; ++j) {
+      B(i,j)+=L(i,j)*D[j];
+    }
+}
+
+template <typename T> void chol_elsolve( const Matrix<T>& M, const std::vector<T>& b, std::vector<T>& y ) {
+
+  plumed_assert( M.rw==M.cl && M(0,1)==0.0 && b.size()==M.rw );
+  if( y.size()!=M.rw ) {
+    y.resize( M.rw );
+  }
+  for(unsigned i=0; i<M.rw; ++i) {
+    y[i]=b[i];
+    for(unsigned j=0; j<i; ++j) {
+      y[i]-=M(i,j)*y[j];
+    }
+    y[i]*=1.0/M(i,i);
+  }
+}
+
+template <typename T> int logdet( const Matrix<T>& M, T& ldet ) {
+  // Check matrix is square and symmetric
+  plumed_assert( M.rw==M.cl || M.isSymmetric() );
+
+  std::vector<T> da(M.sz);
+  unsigned k=0;
+  std::vector<T> evals(M.cl);
+  // Transfer the matrix to the local array
+  for (unsigned i=0; i<M.rw; ++i)
+    for (unsigned j=0; j<M.cl; ++j) {
+      da[k++]=static_cast<T>( M(j,i) );
+    }
+
+  int n=M.cl;
+  int lwork=-1;
+  int liwork=-1;
+  int info=0;
+  int m;
+  int one=1;
+  std::vector<T> work(M.rw);
+  std::vector<int> iwork(M.rw);
+  T vl, vu, abstol=0.0;
+  std::vector<int> isup(2*M.rw);
+  std::vector<T> evecs(M.sz);
+  if constexpr (std::is_same_v<T,double> ) {
+    plumed_lapack_dsyevr("N", "I", "U", &n, da.data(), &n, &vl, &vu, &one, &n,
+                         &abstol, &m, evals.data(), evecs.data(), &n,
+                         isup.data(), work.data(), &lwork, iwork.data(), &liwork, &info);
+  } else if constexpr (std::is_same_v<T,float>) {
+    plumed_lapack_ssyevr("N", "I", "U", &n, da.data(), &n, &vl, &vu, &one, &n,
+                         &abstol, &m, evals.data(), evecs.data(), &n,
+                         isup.data(), work.data(), &lwork, iwork.data(), &liwork, &info);
+  } else {
+    static_assert(std::is_same_v<T,double> || std::is_same_v<T,float>, "logdet works only for float and double");
+  }
+  if (info!=0) {
+    return info;
+  }
+
+  // Retrieve correct sizes for work and iwork then reallocate
+  lwork=static_cast<int>( work[0] );
+  work.resize(lwork);
+  liwork=iwork[0];
+  iwork.resize(liwork);
+  if constexpr (std::is_same_v<T,double> ) {
+    plumed_lapack_dsyevr("N", "I", "U", &n, da.data(), &n, &vl, &vu, &one, &n,
+                         &abstol, &m, evals.data(), evecs.data(), &n,
+                         isup.data(), work.data(), &lwork, iwork.data(), &liwork, &info);
+  } else if constexpr (std::is_same_v<T,float>) {
+    plumed_lapack_ssyevr("N", "I", "U", &n, da.data(), &n, &vl, &vu, &one, &n,
+                         &abstol, &m, evals.data(), evecs.data(), &n,
+                         isup.data(), work.data(), &lwork, iwork.data(), &liwork, &info);
+  } else {
+    static_assert(std::is_same_v<T,double> || std::is_same_v<T,float>, "logdet works only for float and double");
+  }
+  if (info!=0) {
+    return info;
+  }
+
+  // Transfer the eigenvalues and eigenvectors to the output
+  ldet=0;
+  for(unsigned i=0; i<M.cl; i++) {
+    ldet+=log(evals[i]);
+  }
+
+  return 0;
+}
+
+
+
+}
+#endif