Test PR for pycv

plugins/pycv/.gitignore

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+Make.inc
+*.o
+*.so
+env

plugins/pycv/ActionWithPython.cpp

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+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+Copyright (c) 2019 of Toni Giorgino
+
+The pycv 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 pycv 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 plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+
+#include "ActionWithPython.h"
+
+#include "core/ActionWithValue.h"
+
+#include <pybind11/embed.h> // everything needed for embedding
+#include <pybind11/numpy.h>
+
+#include <iostream>
+
+
+namespace py = pybind11;
+
+
+namespace PLMD {
+namespace pycv {
+
+
+// We can only have one interpreter globally. This is less than ideal
+// because CVs can interfere with each other. The whole purpose of
+// this superclass is to make a singleton. Putting it in the
+// constructor makes it so that the interpreter is only initialized if
+// one of the PYCV actions are used.
+// https://pybind11.readthedocs.io/en/stable/reference.html#_CPPv422initialize_interpreterb
+
+unsigned PlumedScopedPythonInterpreter::use_count=0;
+std::unique_ptr<py::scoped_interpreter> PlumedScopedPythonInterpreter::interpreterGuard =
+  nullptr;
+std::mutex PlumedScopedPythonInterpreter::interpreterMutex{};
+
+PlumedScopedPythonInterpreter::PlumedScopedPythonInterpreter(::PLMD::Log&outlog)
+  :log(outlog) {
+  std::lock_guard<std::mutex> lk(interpreterMutex);
+  if(use_count==0 && Py_IsInitialized()) {
+    //this addresses the "calling pycv within a python interpreter problem"
+    ++use_count;
+  }
+
+  if(use_count==0) {
+    std::cerr<< "------ initialized Python interpreter\n";
+    log<< "------ initialized Python interpreter\n";
+    interpreterGuard = std::make_unique<py::scoped_interpreter>();
+  } else {
+    std::cerr << "------ Python interpreter already initializated\n";
+    log << "------ Python interpreter already initializated\n";
+  }
+  ++use_count;
+}
+
+PlumedScopedPythonInterpreter::~PlumedScopedPythonInterpreter() {
+  // Finalization is tricky, because it should happen AFTER the
+  // destruction of ALL the python declared variables
+  std::lock_guard<std::mutex> lk(interpreterMutex);
+  --use_count;
+  if(use_count==0) {
+    interpreterGuard.reset(nullptr);
+    std::cerr << "------ Python interpreter finalized\n";
+    log << "------ Python interpreter finalized\n";
+  }
+}
+
+ActionWithPython::ActionWithPython (const ActionOptions&ao)
+  :Action(ao),guard(log) {}
+
+void ActionWithPython::pyParseFlag(const char* key, const ::pybind11::dict &initDict, bool& returnValue) {
+  parseFlag(key, returnValue);
+  if(initDict.contains(key)) {
+    bool defaultRet;
+    keywords.getLogicalDefault(key,defaultRet);
+    if (returnValue!=defaultRet) {
+      error(std::string("you specified the same keyword ").append(key)+ " both in python and in the settings file");
+    }
+    returnValue = initDict[key].cast<bool>();
+  }
+}
+/******************************************************************************/
+//Value/components init
+void initializeValue(::PLMD::ActionWithValue& action,pybind11::dict &settingsDict) {
+  action.log << "  will have a single component";
+  bool withDerivatives=false;
+  if(settingsDict.contains("derivative")) {
+    withDerivatives=settingsDict["derivative"].cast<bool>();
+  }
+  if(withDerivatives) {
+    action.addValueWithDerivatives();
+    action.log << " WITH derivatives\n";
+  } else {
+    action.addValue();
+    action.log << " WITHOUT derivatives\n";
+  }
+}
+
+void initializeComponent(::PLMD::ActionWithValue& action,const std::string&name,py::dict &settingsDict) {
+  bool withDerivatives=false;
+  if(settingsDict.contains("derivative")) {
+    withDerivatives=settingsDict["derivative"].cast<bool>();
+  }
+
+  if(withDerivatives) {
+    action.addComponentWithDerivatives(name);
+    action.log << " WITH derivatives\n";
+  } else {
+    action.addComponent(name);
+    action.log << " WITHOUT derivatives\n";
+  }
+}
+
+void valueSettings(py::dict &settings, Value* valPtr) {
+  if(settings.contains("period")) {
+    if (settings["period"].is_none()) {
+      valPtr->setNotPeriodic();
+    } else {
+      py::tuple t = settings["period"];
+      if(t.size()!=2) {
+        plumed_merror("period must have exactly 2 components");
+      }
+      //the ballad py::str(t[0]).cast<std::string>() is to not care about the type of input of the user
+      std::string min=py::str(t[0]).cast<std::string>();
+      std::string max=py::str(t[1]).cast<std::string>();
+      valPtr->setDomain(min, max);
+    }
+  }
+}
+
+} // namespace pycv
+} // namespace PLMD

plugins/pycv/ActionWithPython.h

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+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+Copyright (c) 2019 of Toni Giorgino
+
+The pycv 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 pycv 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 plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_pycv_ActionWithPython_h //{
+#define __PLUMED_pycv_ActionWithPython_h
+
+#include <mutex>
+#include <string>
+
+#include "core/Action.h"
+
+#include <pybind11/embed.h> // everything needed for embedding
+
+namespace PLMD {
+class Value;
+namespace pycv {
+
+using pycvComm_t = double;
+static constexpr auto PYTHONCV_CITATION = "Giorgino, (2019). PYCV: a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python. Journal of Open Source Software, 4(42), 1773. doi:10.21105/joss.01773";
+static constexpr auto BIASING_DISABLED = "PYCV: Gradient was expected as a second return value but is missing. Biasing won't work\n";
+static constexpr std::string_view PYCV_COMPONENTPREFIX="py";
+
+///This class act both as a guard for the interpreter and a a case container for the python module and functions
+class PlumedScopedPythonInterpreter final {
+public:
+  PlumedScopedPythonInterpreter(::PLMD::Log&);
+  ~PlumedScopedPythonInterpreter();
+private:
+  ::PLMD::Log& log;
+  static unsigned use_count;
+  static std::unique_ptr<::pybind11::scoped_interpreter> interpreterGuard;
+  static std::mutex interpreterMutex;
+};
+
+class ActionWithPython: public virtual ::PLMD::Action {
+  //the guard MUST be set up before the python objects
+  // (so that it can be destroyed after them)
+  PlumedScopedPythonInterpreter guard;
+public:
+  explicit ActionWithPython (const ActionOptions&);
+  ///redefinition of parse to avoid confict between plumed.dat and python options
+  template<typename T>
+  void pyParse(const char* key, const ::pybind11::dict &initDict, T& returnValue);
+///redefinition of parseFlag to avoid confict between plumed.dat and python options
+  void pyParseFlag(const char* key, const ::pybind11::dict &initDict, bool& returnValue);
+};
+
+template<typename T>
+void ActionWithPython::pyParse(
+  const char* key, const ::pybind11::dict &initDict, T& returnValue) {
+  T initVal(returnValue);
+  parse(key,returnValue);
+  //this is not robust, but with no access to Action::line we cannot use Tools::findKeyword
+  if(initDict.contains(key)) {
+    if (returnValue != initVal) {
+      error(std::string("you specified the same keyword ").append(key)+ " both in python and in the settings file");
+    }
+    returnValue = initDict[key].cast<T>();
+  }
+}
+
+void initializeValue(::PLMD::ActionWithValue&, pybind11::dict &);
+void initializeComponent(::PLMD::ActionWithValue&,const std::string&,pybind11::dict &);
+void valueSettings( pybind11::dict &r, Value* valPtr);
+
+} // namespace pycv
+} // namespace PLMD
+#endif //__PLUMED_pycv_ActionWithPython_h //}

plugins/pycv/COPYRIGHT

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+Copyright (c) 2019 of Toni Giorgino
+
+The pycv 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 pycv 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 plumed.  If not, see <http://www.gnu.org/licenses/>.

plugins/pycv/Makefile

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+include Make.inc
+
+#Dependency tracking based on https://make.mad-scientist.net/papers/advanced-auto-dependency-generation/#tldr
+#this assumes gcc
+DEPDIR := .deps
+DEPFLAGS = -MT $@ -MMD -MP -MF $(DEPDIR)/$*.d
+
+OBJS = ActionWithPython.o PythonCVInterface.o PythonFunction.o PlumedPythonEmbeddedModule.o
+
+ADDCPPFLAGS=$(shell python3-config --cflags --embed) $(shell python -m pybind11 --includes) $(PLUMED_INCLUDE)
+ADDCLDFLAGS=$(shell python3-config --ldflags --embed) 
+
+ifeq ($(SOEXT),dylib)
+  SONAME_OPTION:=-Wl,-install_name
+else
+  SONAME_OPTION:=-Wl,-soname
+endif
+
+all: PythonCVInterface.$(SOEXT)
+
+
+%.o: %.cpp $(DEPDIR)/%.d | $(DEPDIR)
+	@echo Compiling object $@
+	@$(CXX) -c $(DEPFLAGS) $(CPPFLAGS) $(ADDCPPFLAGS) $(CXXFLAGS) $< -o $@
+
+$(DEPDIR): ; @mkdir -p $@
+
+DEPFILES := $(OBJS:%.o=$(DEPDIR)/%.d)
+$(DEPFILES):
+include $(wildcard $(DEPFILES))
+
+PythonCVInterface.$(SOEXT): $(OBJS)
+	@echo Compiling linking $@
+	@$(LDSHARED) $(ADDCLDFLAGS) $(SONAME_OPTION),"$(notdir $@)" $(DYNAMIC_LIBS) $(PLUMED_KERNEL) -o $@ $^
+
+clean:
+	rm -f $(OBJS) PythonCVInterface.$(SOEXT)