hillclimber 0.1.6__cp314-cp314t-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl

plumed/_lib/include/plumed/ves/Optimizer.h

@@ -0,0 +1,444 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2016-2021 The VES code team
+   (see the PEOPLE-VES file at the root of this folder for a list of names)
+
+   See http://www.ves-code.org for more information.
+
+   This file is part of VES code module.
+
+   The VES code module 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.
+
+   The VES code module 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 the VES code module.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_ves_Optimizer_h
+#define __PLUMED_ves_Optimizer_h
+
+#include "VesBias.h"
+
+#include "../core/ActionPilot.h"
+#include "../core/ActionWithValue.h"
+
+#include <vector>
+#include <string>
+#include <cmath>
+#include <memory>
+
+
+#define PLUMED_VES_OPTIMIZER_INIT(ao) Action(ao),Optimizer(ao)
+
+namespace PLMD {
+
+/**
+\ingroup INHERIT
+Abstract base class for implenting new optimization methods
+*/
+
+class OFile;
+
+namespace ves {
+
+class CoeffsVector;
+class VesBias;
+
+
+class Optimizer :
+  public ActionPilot,
+  public ActionWithValue {
+private:
+  const std::string description_;
+  const std::string type_;
+  //
+  std::vector<double> stepsizes_;
+  std::vector<double> current_stepsizes;
+  bool fixed_stepsize_;
+  //
+  unsigned int iter_counter;
+  //
+  bool use_hessian_;
+  bool diagonal_hessian_;
+  bool hessian_covariance_from_averages_;
+  //
+  bool monitor_instantaneous_gradient_;
+  //
+  bool use_mwalkers_mpi_;
+  bool mwalkers_mpi_single_files_;
+  //
+  std::vector<bool> dynamic_targetdists_;
+  unsigned int ustride_targetdist_;
+  //
+  unsigned int ustride_reweightfactor_;
+  //
+  std::string coeffssetid_prefix_;
+  //
+  unsigned int coeffs_wstride_;
+  std::vector<std::unique_ptr<OFile>> coeffsOFiles_;
+  std::string coeffs_output_fmt_;
+  //
+  unsigned int gradient_wstride_;
+  std::vector<std::unique_ptr<OFile>> gradientOFiles_;
+  std::string gradient_output_fmt_;
+  //
+  unsigned int hessian_wstride_;
+  std::vector<std::unique_ptr<OFile>> hessianOFiles_;
+  std::string hessian_output_fmt_;
+  //
+  unsigned int targetdist_averages_wstride_;
+  std::vector<std::unique_ptr<OFile>> targetdist_averagesOFiles_;
+  std::string targetdist_averages_output_fmt_;
+  //
+  unsigned int nbiases_;
+  std::vector<VesBias*> bias_pntrs_;
+  //
+  unsigned int ncoeffssets_;
+  std::vector<CoeffsVector*> coeffs_pntrs_;
+  std::vector<std::unique_ptr<CoeffsVector>> aux_coeffs_pntrs_;
+  std::vector<CoeffsVector*> gradient_pntrs_;
+  std::vector<std::unique_ptr<CoeffsVector>> aver_gradient_pntrs_;
+  std::vector<CoeffsMatrix*> hessian_pntrs_;
+  std::vector<std::unique_ptr<CoeffsVector>> coeffs_mask_pntrs_;
+  std::vector<CoeffsVector*> targetdist_averages_pntrs_;
+  //
+  bool identical_coeffs_shape_;
+  //
+  bool bias_output_active_;
+  unsigned int bias_output_stride_;
+  bool fes_output_active_;
+  unsigned int fes_output_stride_;
+  bool fesproj_output_active_;
+  unsigned int fesproj_output_stride_;
+  bool targetdist_output_active_;
+  unsigned int targetdist_output_stride_;
+  bool targetdist_proj_output_active_;
+  unsigned int targetdist_proj_output_stride_;
+  //
+  bool isFirstStep;
+  //
+private:
+  void updateOutputComponents();
+  void writeOutputFiles(const unsigned int coeffs_id = 0);
+  void readCoeffsFromFiles(const std::vector<std::string>&, const bool);
+  void setAllCoeffsSetIterationCounters();
+protected:
+  void turnOnHessian();
+  void turnOffHessian();
+  std::vector<CoeffsMatrix*> enableHessian(VesBias*, const bool diagonal_hessian=false);
+  // CoeffsMatrix* switchToDiagonalHessian(VesBias*);
+  // CoeffsMatrix* switchToFullHessian(VesBias*);
+  //
+  CoeffsVector& Coeffs(const unsigned int coeffs_id = 0) const;
+  CoeffsVector& AuxCoeffs(const unsigned int coeffs_id = 0) const;
+  CoeffsVector& Gradient(const unsigned int coeffs_id = 0) const;
+  CoeffsMatrix& Hessian(const unsigned int coeffs_id = 0) const;
+  CoeffsVector& CoeffsMask(const unsigned int coeffs_id = 0) const;
+  CoeffsVector& TargetDistAverages(const unsigned int coeffs_id = 0) const;
+  double StepSize(const unsigned int coeffs_id = 0) const;
+  virtual void coeffsUpdate(const unsigned int coeffs_id = 0) = 0;
+  void setCurrentStepSize(const double,const unsigned int i = 0);
+  void setCurrentStepSizes(const std::vector<double>&);
+  //
+  void turnOffCoeffsOutputFiles();
+  //
+  template<class T>
+  bool parseMultipleValues(const std::string&, std::vector<T>&);
+  template<class T>
+  bool parseMultipleValues(const std::string&, std::vector<T>&, const T&);
+  void parseFilenames(const std::string&, std::vector<std::string>&, const std::string&);
+  void parseFilenames(const std::string&, std::vector<std::string>&);
+  void addCoeffsSetIDsToFilenames(std::vector<std::string>&, std::string&);
+  void setupOFiles(std::vector<std::string>&, std::vector<std::unique_ptr<OFile>>&, const bool multi_sim_single_files=false);
+public:
+  static void registerKeywords(Keywords&);
+  static void useMultipleWalkersKeywords(Keywords&);
+  static void useHessianKeywords(Keywords&);
+  static void useFixedStepSizeKeywords(Keywords&);
+  static void useDynamicStepSizeKeywords(Keywords&);
+  static void useMaskKeywords(Keywords&);
+  static void useRestartKeywords(Keywords&);
+  static void useMonitorAverageGradientKeywords(Keywords&);
+  static void useDynamicTargetDistributionKeywords(Keywords&);
+  static void useReweightFactorKeywords(Keywords&);
+  //
+  explicit Optimizer(const ActionOptions&ao);
+  ~Optimizer();
+  std::string getType() const {
+    return type_;
+  }
+  std::string getDescription() const {
+    return description_;
+  }
+  //
+  unsigned int numberOfBiases() const {
+    return nbiases_;
+  }
+  unsigned int numberOfCoeffsSets() const {
+    return ncoeffssets_;
+  }
+  //
+  std::vector<double> getStepSizes() const;
+  std::vector<double> getCurrentStepSizes() const;
+  double getStepSize(const unsigned int coeffs_id = 0) const;
+  double getCurrentStepSize(const unsigned int coeffs_id = 0) const;
+  void setStepSizes(const std::vector<double>&);
+  void setStepSize(const double, const unsigned int coeffs_id = 0);
+  //
+  unsigned int getIterationCounter() const;
+  double getIterationCounterDbl() const;
+  std::string getIterationCounterStr(const int offset=0) const;
+  void setIterationCounter(const unsigned int);
+  void increaseIterationCounter();
+  //
+  void apply() override {};
+  void calculate() override {};
+  void update() override;
+  unsigned int getNumberOfDerivatives() override {
+    return 0;
+  }
+  //
+  bool fixedStepSize() const {
+    return fixed_stepsize_;
+  }
+  bool dynamicStepSize() const {
+    return !fixed_stepsize_;
+  }
+  //
+  bool useHessian() const {
+    return use_hessian_;
+  }
+  bool diagonalHessian() const {
+    return diagonal_hessian_;
+  }
+  //
+  bool useMultipleWalkers() const {
+    return use_mwalkers_mpi_;
+  }
+  //
+  std::vector<VesBias*> getBiasPntrs() const {
+    return bias_pntrs_;
+  }
+  std::vector<CoeffsVector*> getCoeffsPntrs() const {
+    return coeffs_pntrs_;
+  }
+  std::vector<CoeffsVector*> getAuxCoeffsPntrs() const {
+    return Tools::unique2raw(aux_coeffs_pntrs_);
+  }
+  std::vector<CoeffsVector*> getGradientPntrs()const {
+    return gradient_pntrs_;
+  }
+  std::vector<CoeffsMatrix*> getHessianPntrs() const {
+    return hessian_pntrs_;
+  }
+  std::vector<CoeffsVector*> getCoeffsMaskPntrs() const {
+    return Tools::unique2raw(coeffs_mask_pntrs_);
+  }
+  std::vector<CoeffsVector*> getTargetDistAveragesPntrs() const {
+    return targetdist_averages_pntrs_;
+  }
+  //
+  bool isBiasOutputActive() const {
+    return bias_output_active_;
+  }
+  unsigned int getBiasOutputStride() const {
+    return bias_output_stride_;
+  }
+  void setBiasOutputStride(unsigned int stride) {
+    bias_output_stride_=stride;
+  }
+  void writeBiasOutputFiles() const;
+  //
+  bool isFesOutputActive() const {
+    return fes_output_active_;
+  }
+  unsigned int getFesOutputStride() const {
+    return fes_output_stride_;
+  }
+  void setFesOutputStride(unsigned int stride) {
+    fes_output_stride_=stride;
+  }
+  void writeFesOutputFiles() const;
+  //
+  bool isFesProjOutputActive() const {
+    return fesproj_output_active_;
+  }
+  unsigned int getFesProjOutputStride() const {
+    return fesproj_output_stride_;
+  }
+  void setFesProjOutputStride(unsigned int stride) {
+    fesproj_output_stride_=stride;
+  }
+  void writeFesProjOutputFiles() const;
+  //
+  bool isTargetDistOutputActive() const {
+    return targetdist_output_active_;
+  }
+  unsigned int getTargetDistOutputStride() const {
+    return targetdist_output_stride_;
+  }
+  void setTargetDistOutputStride(unsigned int stride) {
+    targetdist_output_stride_=stride;
+  }
+  void writeTargetDistOutputFiles() const;
+  //
+  bool isTargetDistProjOutputActive() const {
+    return targetdist_proj_output_active_;
+  }
+  unsigned int getTargetDistProjOutputStride() const {
+    return targetdist_proj_output_stride_;
+  }
+  void setTargetDistProjOutputStride(unsigned int stride) {
+    targetdist_proj_output_stride_=stride;
+  }
+  void writeTargetDistProjOutputFiles() const;
+  //
+};
+
+inline
+double Optimizer::StepSize(const unsigned int coeffs_id) const {
+  return stepsizes_[coeffs_id];
+}
+
+inline
+CoeffsVector& Optimizer::Coeffs(const unsigned int coeffs_id) const {
+  return *coeffs_pntrs_[coeffs_id];
+}
+
+inline
+CoeffsVector& Optimizer::AuxCoeffs(const unsigned int coeffs_id) const {
+  return *aux_coeffs_pntrs_[coeffs_id];
+}
+
+inline
+CoeffsVector& Optimizer::Gradient(const unsigned int coeffs_id) const {
+  return *gradient_pntrs_[coeffs_id];
+}
+
+inline
+CoeffsMatrix& Optimizer::Hessian(const unsigned int coeffs_id) const {
+  plumed_massert(use_hessian_,"You cannot use the Hessian without asking for before");
+  return *hessian_pntrs_[coeffs_id];
+}
+
+inline
+CoeffsVector& Optimizer::CoeffsMask(const unsigned int coeffs_id) const {
+  return *coeffs_mask_pntrs_[coeffs_id];
+}
+
+inline
+std::vector<double> Optimizer::getStepSizes() const {
+  return stepsizes_;
+}
+
+inline
+std::vector<double> Optimizer::getCurrentStepSizes() const {
+  return current_stepsizes;
+}
+
+inline
+double Optimizer::getStepSize(const unsigned int coeffs_id) const {
+  return stepsizes_[coeffs_id];
+}
+
+inline
+double Optimizer::getCurrentStepSize(const unsigned int coeffs_id) const {
+  return current_stepsizes[coeffs_id];
+}
+
+inline
+void Optimizer::setStepSizes(const std::vector<double>& stepsizes_in) {
+  plumed_assert(stepsizes_in.size()==ncoeffssets_);
+  stepsizes_ = stepsizes_in;
+}
+
+inline
+void Optimizer::setStepSize(const double stepsize_in, const unsigned int coeffs_id) {
+  stepsizes_[coeffs_id] = stepsize_in;
+}
+
+inline
+void Optimizer::setCurrentStepSize(const double current_stepsize_in, const unsigned int coeffs_id) {
+  current_stepsizes[coeffs_id] = current_stepsize_in;
+}
+
+inline
+void Optimizer::setCurrentStepSizes(const std::vector<double>& current_stepsizes_in) {
+  plumed_assert(current_stepsizes_in.size()==ncoeffssets_);
+  current_stepsizes = current_stepsizes_in;
+}
+
+inline
+unsigned int Optimizer::getIterationCounter() const {
+  return iter_counter;
+}
+
+inline
+double Optimizer::getIterationCounterDbl() const {
+  return static_cast<double>(iter_counter);
+}
+
+inline
+void Optimizer::increaseIterationCounter() {
+  iter_counter++;
+}
+
+inline
+void Optimizer::setIterationCounter(const unsigned int iter_counter_in) {
+  iter_counter = iter_counter_in;
+}
+
+
+template<class T>
+bool Optimizer::parseMultipleValues(const std::string& keyword, std::vector<T>& values) {
+  plumed_assert(ncoeffssets_>0);
+  plumed_assert(values.size()==0);
+  bool identical_values=false;
+  //
+  parseVector(keyword,values);
+  if(values.size()==1 && ncoeffssets_>1) {
+    values.resize(ncoeffssets_,values[0]);
+    identical_values=true;
+  }
+  if(values.size()>0 && values.size()!=ncoeffssets_) {
+    std::string s1;
+    Tools::convert(ncoeffssets_,s1);
+    plumed_merror("Error in " + keyword + " keyword: either give 1 common value for all coefficient sets or " + s1 + " separate value for each set");
+  }
+  return identical_values;
+}
+
+template<class T>
+bool Optimizer::parseMultipleValues(const std::string& keyword, std::vector<T>& values, const T& default_value) {
+  bool identical_values = parseMultipleValues(keyword,values);
+  if(values.size()==0) {
+    values.resize(ncoeffssets_,default_value);
+    identical_values=true;
+  }
+  return identical_values;
+}
+
+inline
+void Optimizer::parseFilenames(const std::string& keyword, std::vector<std::string>& fnames, const std::string& default_fname) {
+  if(parseMultipleValues<std::string>(keyword,fnames,default_fname)) {
+    addCoeffsSetIDsToFilenames(fnames,coeffssetid_prefix_);
+  }
+}
+
+inline
+void Optimizer::parseFilenames(const std::string& keyword, std::vector<std::string>& fnames) {
+  if(parseMultipleValues<std::string>(keyword,fnames)) {
+    addCoeffsSetIDsToFilenames(fnames,coeffssetid_prefix_);
+  }
+}
+
+
+}
+}
+
+#endif

plumed/_lib/include/plumed/ves/TargetDistModifer.h

@@ -0,0 +1,53 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2016-2021 The VES code team
+   (see the PEOPLE-VES file at the root of this folder for a list of names)
+
+   See http://www.ves-code.org for more information.
+
+   This file is part of VES code module.
+
+   The VES code module 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.
+
+   The VES code module 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 the VES code module.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_ves_TargetDistModifer_h
+#define __PLUMED_ves_TargetDistModifer_h
+
+#include <vector>
+#include <cmath>
+
+namespace PLMD {
+namespace ves {
+
+class TargetDistModifer {
+public:
+  virtual double getModifedTargetDistValue(const double targetdist_value, const std::vector<double>& cv_values) const = 0;
+  virtual ~TargetDistModifer() {}
+};
+
+class WellTemperedModifer:public TargetDistModifer {
+private:
+  double invbiasf_;
+public:
+  explicit WellTemperedModifer(double biasfactor):invbiasf_(1.0/biasfactor) {}
+  double getModifedTargetDistValue(const double targetdist_value, const std::vector<double>& cv_values) const override {
+    return std::pow(targetdist_value,invbiasf_);
+  }
+};
+
+
+
+
+}
+}
+
+#endif