hillclimber 0.1.5a8__cp314-cp314-macosx_15_0_x86_64.whl

plumed/_lib/include/plumed/ves/GridProjWeights.h

@@ -0,0 +1,61 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   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_GridProjWeights_h
+#define __PLUMED_ves_GridProjWeights_h
+
+#include "../tools/Grid.h"
+
+
+namespace PLMD {
+namespace ves {
+
+
+class MarginalWeight:public WeightBase {
+public:
+  explicit MarginalWeight() {}
+  double projectInnerLoop(double &input, double &v) {
+    return  input+v;
+  }
+  double projectOuterLoop(double &v) {
+    return v;
+  }
+};
+
+class FesWeight:public WeightBase {
+public:
+  double beta,invbeta;
+  explicit FesWeight(double v) {
+    beta=v;
+    invbeta=1./beta;
+  }
+  double projectInnerLoop(double &input, double &v) {
+    return  input+exp(-beta*v);
+  }
+  double projectOuterLoop(double &v) {
+    return -invbeta*std::log(v);
+  }
+};
+
+}
+}
+
+#endif

plumed/_lib/include/plumed/ves/LinearBasisSetExpansion.h

@@ -0,0 +1,303 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   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_LinearBasisSetExpansion_h
+#define __PLUMED_ves_LinearBasisSetExpansion_h
+
+#include <vector>
+#include <string>
+#include <memory>
+
+
+namespace PLMD {
+
+class Action;
+class Keywords;
+class Value;
+class Communicator;
+class Grid;
+class OFile;
+
+
+namespace ves {
+
+class CoeffsVector;
+class BasisFunctions;
+class TargetDistribution;
+class VesBias;
+
+
+class LinearBasisSetExpansion {
+  LinearBasisSetExpansion& operator=(const LinearBasisSetExpansion&) = delete;
+private:
+  std::string label_;
+  //
+  Action* action_pntr_;
+  VesBias* vesbias_pntr_;
+  Communicator& mycomm_;
+  bool serial_;
+  //
+  double beta_;
+  double kbt_;
+  //
+  std::vector<Value*> args_pntrs_;
+  unsigned int nargs_;
+  //
+  std::vector<BasisFunctions*> basisf_pntrs_;
+  std::vector<unsigned int> nbasisf_;
+  //
+  CoeffsVector* bias_coeffs_pntr_;
+  size_t ncoeffs_;
+  std::unique_ptr<CoeffsVector> targetdist_averages_pntr_;
+  //
+  std::vector<std::string> grid_min_;
+  std::vector<std::string> grid_max_;
+  std::vector<unsigned int> grid_bins_;
+  //
+  std::string targetdist_grid_label_;
+  //
+  long long int step_of_last_biasgrid_update;
+  long long int step_of_last_biaswithoutcutoffgrid_update;
+  long long int step_of_last_fesgrid_update;
+  //
+  std::unique_ptr<Grid> bias_grid_pntr_;
+  std::unique_ptr<Grid> bias_withoutcutoff_grid_pntr_;
+  std::unique_ptr<Grid> fes_grid_pntr_;
+  Grid* log_targetdist_grid_pntr_;
+  Grid* targetdist_grid_pntr_;
+  //
+  TargetDistribution* targetdist_pntr_;
+  //
+  std::string grid_fmt_;
+public:
+  static void registerKeywords( Keywords& keys );
+  // Constructor
+  explicit LinearBasisSetExpansion(
+    const std::string&,
+    const double,
+    Communicator&,
+    const std::vector<Value*>&,
+    std::vector<BasisFunctions*>&,
+    CoeffsVector* bias_coeffs_pntr_in=NULL);
+  //
+private:
+  // copy constructor is disabled (private and unimplemented)
+  explicit LinearBasisSetExpansion(const LinearBasisSetExpansion&);
+public:
+  ~LinearBasisSetExpansion();
+  //
+  std::vector<Value*> getPntrsToArguments() const {
+    return args_pntrs_;
+  }
+  std::vector<BasisFunctions*> getPntrsToBasisFunctions() const {
+    return basisf_pntrs_;
+  }
+  CoeffsVector* getPntrToBiasCoeffs() const {
+    return bias_coeffs_pntr_;
+  }
+  Grid* getPntrToBiasGrid() const {
+    return bias_grid_pntr_.get();
+  };
+  //
+  unsigned int getNumberOfArguments() const {
+    return nargs_;
+  };
+  std::vector<unsigned int> getNumberOfBasisFunctions() const {
+    return nbasisf_;
+  };
+  size_t getNumberOfCoeffs() const {
+    return ncoeffs_;
+  };
+  //
+  CoeffsVector& BiasCoeffs() const {
+    return *bias_coeffs_pntr_;
+  };
+  CoeffsVector& TargetDistAverages() const {
+    return *targetdist_averages_pntr_;
+  };
+  void setGridFMT(const std::string& fmt) {
+    grid_fmt_=fmt;
+  };
+  //
+  void setSerial() {
+    serial_=true;
+  }
+  void setParallel() {
+    serial_=false;
+  }
+  //
+  void linkVesBias(VesBias*);
+  void linkAction(Action*);
+  // calculate bias and derivatives
+  static double getBiasAndForces(const std::vector<double>&, bool&, std::vector<double>&, std::vector<double>&, std::vector<BasisFunctions*>&, CoeffsVector*, Communicator* comm_in=NULL);
+  double getBiasAndForces(const std::vector<double>&, bool&, std::vector<double>&, std::vector<double>&);
+  double getBiasAndForces(const std::vector<double>&, bool&, std::vector<double>&);
+  double getBias(const std::vector<double>&, bool&, const bool parallel=true);
+  //
+  static void getBasisSetValues(const std::vector<double>&, std::vector<double>&, std::vector<BasisFunctions*>&, CoeffsVector*, Communicator* comm_in=NULL);
+  void getBasisSetValues(const std::vector<double>&, std::vector<double>&, const bool parallel=true);
+  //
+  static double getBasisSetValue(const std::vector<double>&, const size_t, std::vector<BasisFunctions*>&, CoeffsVector*);
+  double getBasisSetValue(const std::vector<double>&, const size_t);
+  double getBasisSetConstant();
+  // Bias grid and output stuff
+  void setupBiasGrid(const bool usederiv=false);
+  void updateBiasGrid();
+  void resetStepOfLastBiasGridUpdate() {
+    step_of_last_biasgrid_update = -1000;
+  }
+  void setStepOfLastBiasGridUpdate(long long int step) {
+    step_of_last_biasgrid_update = step;
+  }
+  long long int getStepOfLastBiasGridUpdate() const {
+    return step_of_last_biasgrid_update;
+  }
+  void writeBiasGridToFile(OFile&, const bool append=false) const;
+  //
+  void updateBiasWithoutCutoffGrid();
+  void resetStepOfLastBiasWithoutCutoffGridUpdate() {
+    step_of_last_biaswithoutcutoffgrid_update = -1000;
+  }
+  void setStepOfLastBiasWithoutCutoffGridUpdate(long long int step) {
+    step_of_last_biaswithoutcutoffgrid_update = step;
+  }
+  long long int getStepOfLastBiasWithoutCutoffGridUpdate() const {
+    return step_of_last_biaswithoutcutoffgrid_update;
+  }
+  void writeBiasWithoutCutoffGridToFile(OFile&, const bool append=false) const;
+  //
+  void setBiasMinimumToZero();
+  void setBiasMaximumToZero();
+  //
+  void setupFesGrid();
+  void updateFesGrid();
+  void resetStepOfLastFesGridUpdate() {
+    step_of_last_fesgrid_update = -1000;
+  }
+  void setStepOfLastFesGridUpdate(long long int step) {
+    step_of_last_fesgrid_update = step;
+  }
+  long long int getStepOfLastFesGridUpdate() const {
+    return step_of_last_fesgrid_update;
+  }
+  void writeFesGridToFile(OFile&, const bool append=false) const;
+  //
+  void setupFesProjGrid();
+  void writeFesProjGridToFile(const std::vector<std::string>&, OFile&, const bool append=false) const;
+  //
+  void writeTargetDistGridToFile(OFile&, const bool append=false) const;
+  void writeLogTargetDistGridToFile(OFile&, const bool append=false) const;
+  void writeTargetDistProjGridToFile(const std::vector<std::string>&, OFile&, const bool append=false) const;
+  void writeTargetDistributionToFile(const std::string&) const;
+  //
+  std::vector<unsigned int> getGridBins() const {
+    return grid_bins_;
+  }
+  void setGridBins(const std::vector<unsigned int>&);
+  void setGridBins(const unsigned int);
+  //
+  double getBeta() const {
+    return beta_;
+  }
+  double getKbT() const {
+    return kbt_;
+  }
+  double beta() const {
+    return beta_;
+  }
+  double kBT() const {
+    return kbt_;
+  }
+  //
+  void setupUniformTargetDistribution();
+  void setupTargetDistribution(TargetDistribution*);
+  void updateTargetDistribution();
+  //
+  void readInRestartTargetDistribution(const std::string&);
+  void restartTargetDistribution();
+  //
+  bool biasCutoffActive() const;
+  //
+  double calculateReweightFactor() const;
+  //
+private:
+  //
+  std::unique_ptr<Grid> setupGeneralGrid(const std::string&, const bool usederiv=false);
+  //
+  void calculateTargetDistAveragesFromGrid(const Grid*);
+  //
+  bool isStaticTargetDistFileOutputActive() const;
+};
+
+
+inline
+double LinearBasisSetExpansion::getBiasAndForces(const std::vector<double>& args_values, bool& all_inside, std::vector<double>& forces, std::vector<double>& coeffsderivs_values) {
+  return getBiasAndForces(args_values,all_inside,forces,coeffsderivs_values,basisf_pntrs_, bias_coeffs_pntr_, &mycomm_);
+}
+
+
+inline
+double LinearBasisSetExpansion::getBiasAndForces(const std::vector<double>& args_values, bool& all_inside, std::vector<double>& forces) {
+  std::vector<double> coeffsderivs_values_dummy(ncoeffs_);
+  return getBiasAndForces(args_values,all_inside,forces,coeffsderivs_values_dummy,basisf_pntrs_, bias_coeffs_pntr_, &mycomm_);
+}
+
+
+inline
+double LinearBasisSetExpansion::getBias(const std::vector<double>& args_values, bool& all_inside, const bool parallel) {
+  std::vector<double> forces_dummy(nargs_);
+  std::vector<double> coeffsderivs_values_dummy(ncoeffs_);
+  if(parallel) {
+    return getBiasAndForces(args_values,all_inside,forces_dummy,coeffsderivs_values_dummy,basisf_pntrs_, bias_coeffs_pntr_, &mycomm_);
+  } else {
+    return getBiasAndForces(args_values,all_inside,forces_dummy,coeffsderivs_values_dummy,basisf_pntrs_, bias_coeffs_pntr_, NULL);
+  }
+}
+
+
+inline
+void LinearBasisSetExpansion::getBasisSetValues(const std::vector<double>& args_values, std::vector<double>& basisset_values, const bool parallel) {
+  if(parallel) {
+    getBasisSetValues(args_values,basisset_values,basisf_pntrs_, bias_coeffs_pntr_, &mycomm_);
+  } else {
+    getBasisSetValues(args_values,basisset_values,basisf_pntrs_, bias_coeffs_pntr_, NULL);
+  }
+}
+
+
+inline
+double LinearBasisSetExpansion::getBasisSetValue(const std::vector<double>& args_values, const size_t basisset_index) {
+  return getBasisSetValue(args_values,basisset_index,basisf_pntrs_, bias_coeffs_pntr_);
+}
+
+
+inline
+double LinearBasisSetExpansion::getBasisSetConstant() {
+  std::vector<double> args_dummy(nargs_,0.0);
+  return getBasisSetValue(args_dummy,0,basisf_pntrs_, bias_coeffs_pntr_);
+}
+
+
+}
+
+}
+
+#endif