hillclimber 0.1.5a8__cp314-cp314-macosx_15_0_x86_64.whl

plumed/_lib/include/plumed/matrixtools/OuterProduct.h

@@ -0,0 +1,238 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   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_matrixtools_OuterProduct_h
+#define __PLUMED_matrixtools_OuterProduct_h
+
+#include "../core/ActionWithMatrix.h"
+#include "../core/ParallelTaskManager.h"
+
+namespace PLMD {
+namespace matrixtools {
+
+template <class T>
+class OuterProductInput {
+public:
+  T funcinput;
+  RequiredMatrixElements outmat;
+};
+
+template <class T>
+class OuterProductBase : public ActionWithMatrix {
+public:
+  using input_type = OuterProductInput<T>;
+  using PTM = ParallelTaskManager<OuterProductBase<T>>;
+private:
+  bool isproduct;
+  PTM taskmanager;
+public:
+  static void registerKeywords( Keywords& keys );
+  explicit OuterProductBase(const ActionOptions&);
+  unsigned getNumberOfDerivatives() override;
+  void prepare() override ;
+  int checkTaskIsActive( const unsigned& itask ) const override ;
+  void calculate() override ;
+  void applyNonZeroRankForces( std::vector<double>& outforces ) override ;
+  static void performTask( std::size_t task_index,
+                           const OuterProductInput<T>& actiondata,
+                           ParallelActionsInput& input,
+                           ParallelActionsOutput& output );
+  static int getNumberOfValuesPerTask( std::size_t task_index,
+                                       const OuterProductInput<T>& actiondata );
+  static void getForceIndices( std::size_t task_index,
+                               std::size_t colno,
+                               std::size_t ntotal_force,
+                               const OuterProductInput<T>& actiondata,
+                               const ParallelActionsInput& input,
+                               ForceIndexHolder force_indices );
+};
+
+template <class T>
+void OuterProductBase<T>::registerKeywords( Keywords& keys ) {
+  ActionWithMatrix::registerKeywords(keys);
+  T::registerKeywords( keys );
+  PTM::registerKeywords( keys );
+  keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log");
+}
+
+template <class T>
+OuterProductBase<T>::OuterProductBase(const ActionOptions&ao):
+  Action(ao),
+  ActionWithMatrix(ao),
+  isproduct(false),
+  taskmanager(this) {
+  unsigned nargs=getNumberOfArguments();
+  if( getNumberOfMasks()>0 ) {
+    nargs = nargs - getNumberOfMasks();
+  }
+  if( nargs%2!=0 ) {
+    error("should be an even number of arguments to this action, they should all be vectors");
+  }
+  std::size_t nvals = nargs / 2;
+  for(unsigned i=0; i<nvals; ++i) {
+    if( getPntrToArgument(i)->getRank()!=1 || getPntrToArgument(i)->hasDerivatives() ) {
+      error("first argument to this action should be a vector");
+    }
+    if( getPntrToArgument(0)->getShape()[0]!=getPntrToArgument(i)->getShape()[0] ) {
+      error("mismatch between sizes of input vectors");
+    }
+    if( getPntrToArgument(nvals+i)->getRank()!=1 || getPntrToArgument(nvals+i)->hasDerivatives() ) {
+      error("first argument to this action should be a vector");
+    }
+    if( getPntrToArgument(nvals)->getShape()[0]!=getPntrToArgument(nvals+i)->getShape()[0] ) {
+      error("mismatch between sizes of input vectors");
+    }
+  }
+  if( getNumberOfMasks()==1 ) {
+    if( getPntrToArgument(nargs)->getRank()!=2 || getPntrToArgument(nargs)->hasDerivatives() ) {
+      error("mask argument should be a matrix");
+    }
+    for(unsigned i=0; i<nvals; ++i) {
+      if( getPntrToArgument(nargs)->getShape()[0]!=getPntrToArgument(i)->getShape()[0] ) {
+        error("mask argument has wrong size");
+      }
+      if( getPntrToArgument(nargs)->getShape()[1]!=getPntrToArgument(nvals+i)->getShape()[0] ) {
+        error("mask argument has wrong size");
+      }
+    }
+  }
+
+  std::vector<std::size_t> shape(2);
+  shape[0]=getPntrToArgument(0)->getShape()[0];
+  shape[1]=getPntrToArgument(nvals)->getShape()[0];
+
+  std::string func;
+  if( keywords.exists("FUNC") ) {
+    parse("FUNC",func);
+    isproduct=(func=="x*y");
+  }
+  OuterProductInput<T> actiondata;
+  actiondata.funcinput.setup( shape, func, this );
+
+  if( getNumberOfComponents()==0 ) {
+    addValue( shape );
+    setNotPeriodic();
+  }
+  if( getPntrToArgument(0)->isDerivativeZeroWhenValueIsZero() || getPntrToArgument(nvals)->isDerivativeZeroWhenValueIsZero() ) {
+    for(unsigned i=0; i<getNumberOfComponents(); ++i) {
+      getPntrToComponent(i)->setDerivativeIsZeroWhenValueIsZero();
+    }
+  }
+  taskmanager.setActionInput( actiondata );
+}
+
+template <class T>
+unsigned OuterProductBase<T>::getNumberOfDerivatives() {
+  unsigned nc = getNumberOfComponents();
+  return nc*(getPntrToArgument(0)->getNumberOfStoredValues() + getPntrToArgument(nc)->getNumberOfStoredValues());
+}
+
+template <class T>
+void OuterProductBase<T>::prepare() {
+  ActionWithVector::prepare();
+  Value* myval=getPntrToComponent(0);
+  if( myval->getShape()[0]==getPntrToArgument(0)->getShape()[0] && myval->getShape()[1]==getPntrToArgument(getNumberOfComponents())->getShape()[0] ) {
+    return;
+  }
+  std::vector<std::size_t> shape(2);
+  shape[0] = getPntrToArgument(0)->getShape()[0];
+  shape[1] = getPntrToArgument(getNumberOfComponents())->getShape()[0];
+  for(unsigned i=0; i<getNumberOfComponents(); ++i) {
+    getPntrToComponent(i)->setShape( shape );
+  }
+}
+
+template <class T>
+int OuterProductBase<T>::checkTaskIsActive( const unsigned& itask ) const {
+  if( getNumberOfMasks()>0 || !isproduct ) {
+    return ActionWithVector::checkTaskIsActive( itask );
+  }
+  if( fabs( getPntrToArgument(0)->get(itask))>epsilon ) {
+    return 1;
+  }
+  return -1;
+}
+
+template <class T>
+void OuterProductBase<T>::calculate() {
+  updateBookeepingArrays( taskmanager.getActionInput().outmat );
+  taskmanager.setupParallelTaskManager( 2*getNumberOfComponents(), getNumberOfComponents()*getPntrToComponent(0)->getShape()[1] );
+  taskmanager.setWorkspaceSize( 2*getNumberOfComponents() );
+  taskmanager.runAllTasks();
+}
+
+template <class T>
+void OuterProductBase<T>::performTask( std::size_t task_index,
+                                       const OuterProductInput<T>& actiondata,
+                                       ParallelActionsInput& input,
+                                       ParallelActionsOutput& output ) {
+  auto args = output.buffer.subview(0, 2*input.ncomponents);
+  for(unsigned i=0; i<input.ncomponents; ++i) {
+    args[i] = input.inputdata[input.argstarts[i] + task_index];
+  }
+  unsigned fstart = task_index*(1+actiondata.outmat.ncols);
+  unsigned nelements = actiondata.outmat[fstart];
+  for(unsigned i=0; i<nelements; ++i) {
+    std::size_t argpos = actiondata.outmat[fstart+1+i];
+    for(unsigned j=0; j<input.ncomponents; ++j) {
+      args[input.ncomponents+j] = input.inputdata[input.argstarts[input.ncomponents+j] + argpos];
+    }
+    MatrixElementOutput matout( input.ncomponents,
+                                2*input.ncomponents,
+                                output.values.data()+i*input.ncomponents,
+                                output.derivatives.data() + 2*i*input.ncomponents*input.ncomponents );
+    T::calculate( input.noderiv, actiondata.funcinput, {args.data(),args.size()}, matout );
+  }
+}
+
+template <class T>
+void OuterProductBase<T>::applyNonZeroRankForces( std::vector<double>& outforces ) {
+  taskmanager.applyForces( outforces );
+}
+
+template <class T>
+int OuterProductBase<T>::getNumberOfValuesPerTask( std::size_t task_index,
+    const OuterProductInput<T>& actiondata ) {
+  unsigned fstart = task_index*(1+actiondata.outmat.ncols);
+  return actiondata.outmat[fstart];
+}
+
+template <class T>
+void OuterProductBase<T>::getForceIndices( std::size_t task_index,
+    std::size_t colno,
+    std::size_t ntotal_force,
+    const OuterProductInput<T>& actiondata,
+    const ParallelActionsInput& input,
+    ForceIndexHolder force_indices ) {
+  unsigned fstart = task_index*(1+actiondata.outmat.ncols);
+  for(unsigned j=0; j<input.ncomponents; ++j) {
+    for(unsigned k=0; k<input.ncomponents; ++k) {
+      force_indices.indices[j][k] = input.argstarts[k] + task_index;
+      force_indices.indices[j][input.ncomponents+k] = input.argstarts[input.ncomponents+k] + actiondata.outmat[fstart+1+colno];
+    }
+    force_indices.threadsafe_derivatives_end[j] = input.ncomponents;
+    force_indices.tot_indices[j] = 2*input.ncomponents;
+  }
+}
+
+}
+}
+#endif

plumed/_lib/include/plumed/maze/Core.h

@@ -0,0 +1,65 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.
+
+See http://www.maze-code.github.io for more information.
+
+This file is part of maze.
+
+maze 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.
+
+maze 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 maze. If not, see <https://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_maze_Core_h
+#define __PLUMED_maze_Core_h
+
+/**
+ * @file Core.h
+ *
+ * @author J. Rydzewski (jr@fizyka.umk.pl)
+ *
+ * @brief Header with needed includes from std and PLMD.
+ */
+
+namespace PLMD {
+namespace maze {
+/* Nothing to do */
+} // namespace maze
+} // namespace PLMD
+
+// std
+#include <cmath>
+#include <cstdlib>
+#include <cstdio>
+#include <ctime>
+#include <utility>
+#include <string>
+#include <random>
+#include <iostream>
+#include <iomanip>
+#include <sstream>
+#include <vector>
+#include <limits>
+#include <numeric>
+#include <algorithm>
+#include <functional>
+#include <memory>
+
+// PLMD
+#include "../tools/Vector.h"
+#include "../tools/Tools.h"
+
+// maze
+#include "Random_MT.h"
+#include "Tools.h"
+
+#endif // __PLUMED_maze_Core_h

plumed/_lib/include/plumed/maze/Loss.h

@@ -0,0 +1,86 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.
+
+See http://www.maze-code.github.io for more information.
+
+This file is part of maze.
+
+maze 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.
+
+maze 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 maze. If not, see <https://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_maze_Loss_h
+#define __PLUMED_maze_Loss_h
+
+/**
+ * @file Loss.h
+ *
+ * @author J. Rydzewski (jr@fizyka.umk.pl)
+ */
+
+#include "../colvar/Colvar.h"
+#include "../core/ActionRegister.h"
+#include "Core.h"
+
+namespace PLMD {
+namespace maze {
+
+/**
+ * @class Loss Loss.h "maze/Loss.h"
+ *
+ * @brief Loss function describes a score between a ligand-protein conformation.
+ *
+ * Loss function must be defined for an optimizer as it minimizes a loss
+ * of a ligand-protein conformation in order to simulate the ligand-protein
+ * dissociation process.
+ */
+class Loss: public colvar::Colvar {
+public:
+  /**
+   * PLMD constructor.
+   *
+   * @param[in] ao PLMD::ActionOptions&.
+   */
+  explicit Loss(const ActionOptions& ao);
+
+  /**
+   * Destructor.
+   */
+  ~Loss() { /* Nothing to do. */ }
+
+  /**
+   * Register PLMD keywords.
+   *
+   * @param[in] keys Keywords.
+   */
+  static void registerKeywords(Keywords& keys);
+
+  /**
+   * Calculate a loss of a single pair of ligand-protein atoms.
+   *
+   * @param[in] distance Distance between atoms in the pair.
+   */
+  double pairing(double distance);
+
+  // Required by the Colvar class.
+  void calculate() override { /* Nothing to do. */ }
+
+protected:
+  //! Parameters of the loss function.
+  std::vector<double> params_;
+};
+
+} // namespace maze
+} // namespace PLMD
+
+#endif // __PLUMED_maze_Loss_h

plumed/_lib/include/plumed/maze/Member.h

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+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.
+
+See http://www.maze-code.github.io for more information.
+
+This file is part of maze.
+
+maze 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.
+
+maze 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 maze. If not, see <https://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_maze_Member_h
+#define __PLUMED_maze_Member_h
+
+/**
+ * @file Member.h
+ *
+ * @author J. Rydzewski (jr@fizyka.umk.pl)
+ */
+
+#include "Core.h"
+
+namespace PLMD {
+namespace maze {
+
+/**
+ * @class Member Member.h "maze/Member.h"
+ *
+ * @brief Defines the encoding for a ligand conformation.
+ *
+ * The Member class is required by some optimizers. Ligand conformations are
+ * encoded by a Cartesian translation relative to a ligand conformation from
+ * the MD simulation. Each translation has a loss (score) which tells how
+ * preferred is the encoding w.r.t. a chosen loss function.
+ */
+struct Member {
+public:
+  Member()
+    : score(-1),
+      translation({0, 0, 0}) { /* Nothing to do. */ }
+
+  //! Value of the loss function.
+  double score;
+
+  //! Encoding of a ligand conformation, i.e., its translation.
+  Vector translation;
+};
+
+inline bool compare(Member& m, Member& n) {
+  return m.score > n.score;
+}
+
+} // namespace maze
+} // namespace PLMD
+
+#endif // __PLUMED_maze_Member_h