Upgrade Lepton library to version 2019-06-02 (e04a18fc) · Commits · 郑智淋 / lammps

lib/colvars/README

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		@@ -50,6 +50,9 @@ settings in Makefile.common should work.
		Note: some Colvars functions use the Lepton mathematical expression parser,
		which is here included (no additional steps required). For more details, see:
		https://simtk.org/projects/lepton
		Starting from 2019-06-02, Lepton requires C++11. Please see:
		https://colvars.github.io/README-c++11.html
		https://lammps.sandia.gov/doc/Build_settings.html#cxx11


		## Documentation

lib/colvars/lepton/include/lepton/CompiledExpression.h

+6 −5

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		@@ -9,7 +9,7 @@
		* Biological Structures at Stanford, funded under the NIH Roadmap for *
		* Medical Research, grant U54 GM072970. See https://simtk.org. *
		* *
		* Portions copyright (c) 2013-2016 Stanford University and the Authors. *
		* Portions copyright (c) 2013-2019 Stanford University and the Authors. *
		* Authors: Peter Eastman *
		* Contributors: *
		* *
		@@ -99,10 +99,11 @@ private:
		mutable std::vector<double> workspace;
		mutable std::vector<double> argValues;
		std::map<std::string, double> dummyVariables;
		void* jitCode;
		double (*jitCode)();
		#ifdef LEPTON_USE_JIT
		void generateJitCode();
		void generateSingleArgCall(asmjit::X86Compiler& c, asmjit::X86XmmVar& dest, asmjit::X86XmmVar& arg, double (*function)(double));
		void generateSingleArgCall(asmjit::X86Compiler& c, asmjit::X86Xmm& dest, asmjit::X86Xmm& arg, double (*function)(double));
		void generateTwoArgCall(asmjit::X86Compiler& c, asmjit::X86Xmm& dest, asmjit::X86Xmm& arg1, asmjit::X86Xmm& arg2, double (*function)(double, double));
		std::vector<double> constants;
		asmjit::JitRuntime runtime;
		#endif

lib/colvars/lepton/include/lepton/CustomFunction.h

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		@@ -72,6 +72,38 @@ public:
		virtual CustomFunction* clone() const = 0;
		};

		/**
		* This class is an implementation of CustomFunction that does no computation. It just returns
		* 0 for the value and derivatives. This is useful when using the parser to analyze expressions
		* rather than to evaluate them. You can just create PlaceholderFunctions to represent any custom
		* functions that may appear in expressions.
		*/

		class LEPTON_EXPORT PlaceholderFunction : public CustomFunction {
		public:
		/**
		* Create a Placeholder function.
		*
		* @param numArgs the number of arguments the function expects
		*/
		PlaceholderFunction(int numArgs) : numArgs(numArgs) {
		}
		int getNumArguments() const {
		return numArgs;
		}
		double evaluate(const double* arguments) const {
		return 0.0;
		}
		double evaluateDerivative(const double* arguments, const int* derivOrder) const {
		return 0.0;
		}
		CustomFunction* clone() const {
		return new PlaceholderFunction(numArgs);
		};
		private:
		int numArgs;
		};

		} // namespace Lepton

		#endif /LEPTON_CUSTOM_FUNCTION_H_/

lib/colvars/lepton/include/lepton/ExpressionProgram.h

+9 −1

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		@@ -9,7 +9,7 @@
		* Biological Structures at Stanford, funded under the NIH Roadmap for *
		* Medical Research, grant U54 GM072970. See https://simtk.org. *
		* *
		* Portions copyright (c) 2009 Stanford University and the Authors. *
		* Portions copyright (c) 2009-2018 Stanford University and the Authors. *
		* Authors: Peter Eastman *
		* Contributors: *
		* *
		@@ -65,6 +65,14 @@ public:
		* Get an Operation in this program.
		*/
		const Operation& getOperation(int index) const;
		/**
		* Change an Operation in this program.
		*
		* The Operation must have been allocated on the heap with the "new" operator.
		* The ExpressionProgram assumes ownership of it and will delete it when it
		* is no longer needed.
		*/
		void setOperation(int index, Operation* operation);
		/**
		* Get the size of the stack needed to execute this program. This is the largest number of elements present
		* on the stack at any point during evaluation.

lib/colvars/lepton/include/lepton/Operation.h

+31 −3

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		@@ -9,7 +9,7 @@
		* Biological Structures at Stanford, funded under the NIH Roadmap for *
		* Medical Research, grant U54 GM072970. See https://simtk.org. *
		* *
		* Portions copyright (c) 2009-2015 Stanford University and the Authors. *
		* Portions copyright (c) 2009-2019 Stanford University and the Authors. *
		* Authors: Peter Eastman *
		* Contributors: *
		* *
		@@ -63,7 +63,7 @@ public:
		* can be used when processing or analyzing parsed expressions.
		*/
		enum Id {CONSTANT, VARIABLE, CUSTOM, ADD, SUBTRACT, MULTIPLY, DIVIDE, POWER, NEGATE, SQRT, EXP, LOG,
		SIN, COS, SEC, CSC, TAN, COT, ASIN, ACOS, ATAN, SINH, COSH, TANH, ERF, ERFC, STEP, DELTA, SQUARE, CUBE, RECIPROCAL,
		SIN, COS, SEC, CSC, TAN, COT, ASIN, ACOS, ATAN, ATAN2, SINH, COSH, TANH, ERF, ERFC, STEP, DELTA, SQUARE, CUBE, RECIPROCAL,
		ADD_CONSTANT, MULTIPLY_CONSTANT, POWER_CONSTANT, MIN, MAX, ABS, FLOOR, CEIL, SELECT};
		/**
		* Get the name of this Operation.
		@@ -137,6 +137,7 @@ public:
		class Asin;
		class Acos;
		class Atan;
		class Atan2;
		class Sinh;
		class Cosh;
		class Tanh;
		@@ -226,6 +227,11 @@ class LEPTON_EXPORT Operation::Custom : public Operation {
		public:
		Custom(const std::string& name, CustomFunction* function) : name(name), function(function), isDerivative(false), derivOrder(function->getNumArguments(), 0) {
		}
		Custom(const std::string& name, CustomFunction* function, const std::vector<int>& derivOrder) : name(name), function(function), isDerivative(false), derivOrder(derivOrder) {
		for (int order : derivOrder)
		if (order != 0)
		isDerivative = true;
		}
		Custom(const Custom& base, int derivIndex) : name(base.name), function(base.function->clone()), isDerivative(true), derivOrder(base.derivOrder) {
		derivOrder[derivIndex]++;
		}
		@@ -684,6 +690,28 @@ public:
		ExpressionTreeNode differentiate(const std::vector<ExpressionTreeNode>& children, const std::vector<ExpressionTreeNode>& childDerivs, const std::string& variable) const;
		};

		class LEPTON_EXPORT Operation::Atan2 : public Operation {
		public:
		Atan2() {
		}
		std::string getName() const {
		return "atan2";
		}
		Id getId() const {
		return ATAN2;
		}
		int getNumArguments() const {
		return 2;
		}
		Operation* clone() const {
		return new Atan2();
		}
		double evaluate(double* args, const std::map<std::string, double>& variables) const {
		return std::atan2(args[0], args[1]);
		}
		ExpressionTreeNode differentiate(const std::vector<ExpressionTreeNode>& children, const std::vector<ExpressionTreeNode>& childDerivs, const std::string& variable) const;
		};

		class LEPTON_EXPORT Operation::Sinh : public Operation {
		public:
		Sinh() {

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