Upgrade Lepton library to version 2019-06-02

lib/colvars/README

@@ -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

@@ -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

@@ -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

@@ -9,7 +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

@@ -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() {

lib/colvars/lepton/src/CompiledExpression.cpp

@@ -6,7 +6,7 @@
  * 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:                                                              *
  *                                                                            *
@@ -165,7 +165,7 @@ void CompiledExpression::setVariableLocations(map<string, double*>& variableLoca
 
 double CompiledExpression::evaluate() const {
 #ifdef LEPTON_USE_JIT
-    return ((double (*)()) jitCode)();
+    return jitCode();
 #else
     for (int i = 0; i < variablesToCopy.size(); i++)
         *variablesToCopy[i].first = *variablesToCopy[i].second;
@@ -188,24 +188,26 @@ double CompiledExpression::evaluate() const {
 
 #ifdef LEPTON_USE_JIT
 static double evaluateOperation(Operation* op, double* args) {
-    map<string, double>* dummyVariables = NULL;
+    static map<string, double> dummyVariables;
-    return op->evaluate(args, *dummyVariables);
+    return op->evaluate(args, dummyVariables);
 }
 
 void CompiledExpression::generateJitCode() {
-    X86Compiler c(&runtime);
+    CodeHolder code;
-    c.addFunc(kFuncConvHost, FuncBuilder0<double>());
+    code.init(runtime.getCodeInfo());
-    vector<X86XmmVar> workspaceVar(workspace.size());
+    X86Compiler c(&code);
+    c.addFunc(FuncSignature0<double>());
+    vector<X86Xmm> workspaceVar(workspace.size());
     for (int i = 0; i < (int) workspaceVar.size(); i++)
-        workspaceVar[i] = c.newXmmVar(kX86VarTypeXmmSd);
+        workspaceVar[i] = c.newXmmSd();
-    X86GpVar argsPointer(c);
+    X86Gp argsPointer = c.newIntPtr();
     c.mov(argsPointer, imm_ptr(&argValues[0]));
 
     // Load the arguments into variables.
 
     for (set<string>::const_iterator iter = variableNames.begin(); iter != variableNames.end(); ++iter) {
         map<string, int>::iterator index = variableIndices.find(*iter);
-        X86GpVar variablePointer(c);
+        X86Gp variablePointer = c.newIntPtr();
         c.mov(variablePointer, imm_ptr(&getVariableReference(index->first)));
         c.movsd(workspaceVar[index->second], x86::ptr(variablePointer, 0, 0));
     }
@@ -248,12 +250,12 @@ void CompiledExpression::generateJitCode() {
 
     // Load constants into variables.
 
-    vector<X86XmmVar> constantVar(constants.size());
+    vector<X86Xmm> constantVar(constants.size());
     if (constants.size() > 0) {
-        X86GpVar constantsPointer(c);
+        X86Gp constantsPointer = c.newIntPtr();
         c.mov(constantsPointer, imm_ptr(&constants[0]));
         for (int i = 0; i < (int) constants.size(); i++) {
-            constantVar[i] = c.newXmmVar(kX86VarTypeXmmSd);
+            constantVar[i] = c.newXmmSd();
             c.movsd(constantVar[i], x86::ptr(constantsPointer, 8*i, 0));
         }
     }
@@ -292,6 +294,9 @@ void CompiledExpression::generateJitCode() {
                 c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]);
                 c.divsd(workspaceVar[target[step]], workspaceVar[args[1]]);
                 break;
+            case Operation::POWER:
+                generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]], pow);
+                break;
             case Operation::NEGATE:
                 c.xorps(workspaceVar[target[step]], workspaceVar[target[step]]);
                 c.subsd(workspaceVar[target[step]], workspaceVar[args[0]]);
@@ -323,6 +328,9 @@ void CompiledExpression::generateJitCode() {
             case Operation::ATAN:
                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], atan);
                 break;
+            case Operation::ATAN2:
+                generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]], atan2);
+                break;
             case Operation::SINH:
                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], sinh);
                 break;
@@ -377,9 +385,9 @@ void CompiledExpression::generateJitCode() {
 
                 for (int i = 0; i < (int) args.size(); i++)
                     c.movsd(x86::ptr(argsPointer, 8*i, 0), workspaceVar[args[i]]);
-                X86GpVar fn(c, kVarTypeIntPtr);
+                X86Gp fn = c.newIntPtr();
                 c.mov(fn, imm_ptr((void*) evaluateOperation));
-                X86CallNode* call = c.call(fn, kFuncConvHost, FuncBuilder2<double, Operation*, double*>());
+                CCFuncCall* call = c.call(fn, FuncSignature2<double, Operation*, double*>());
                 call->setArg(0, imm_ptr(&op));
                 call->setArg(1, imm_ptr(&argValues[0]));
                 call->setRet(0, workspaceVar[target[step]]);
@@ -387,14 +395,24 @@ void CompiledExpression::generateJitCode() {
     }
     c.ret(workspaceVar[workspace.size()-1]);
     c.endFunc();
-    jitCode = c.make();
+    c.finalize();
+    runtime.add(&jitCode, &code);
 }
 
-void CompiledExpression::generateSingleArgCall(X86Compiler& c, X86XmmVar& dest, X86XmmVar& arg, double (*function)(double)) {
+void CompiledExpression::generateSingleArgCall(X86Compiler& c, X86Xmm& dest, X86Xmm& arg, double (*function)(double)) {
-    X86GpVar fn(c, kVarTypeIntPtr);
+    X86Gp fn = c.newIntPtr();
     c.mov(fn, imm_ptr((void*) function));
-    X86CallNode* call = c.call(fn, kFuncConvHost, FuncBuilder1<double, double>());
+    CCFuncCall* call = c.call(fn, FuncSignature1<double, double>());
     call->setArg(0, arg);
     call->setRet(0, dest);
 }
+
+void CompiledExpression::generateTwoArgCall(X86Compiler& c, X86Xmm& dest, X86Xmm& arg1, X86Xmm& arg2, double (*function)(double, double)) {
+    X86Gp fn = c.newIntPtr();
+    c.mov(fn, imm_ptr((void*) function));
+    CCFuncCall* call = c.call(fn, FuncSignature2<double, double, double>());
+    call->setArg(0, arg1);
+    call->setArg(1, arg2);
+    call->setRet(0, dest);
+}
 #endif

lib/colvars/lepton/src/ExpressionProgram.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2018 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -84,6 +84,11 @@ const Operation& ExpressionProgram::getOperation(int index) const {
     return *operations[index];
 }
 
+void ExpressionProgram::setOperation(int index, Operation* operation) {
+    delete operations[index];
+    operations[index] = operation;
+}
+
 int ExpressionProgram::getStackSize() const {
     return stackSize;
 }

lib/colvars/lepton/src/Operation.cpp

@@ -7,7 +7,7 @@
  * 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:                                                              *
  *                                                                            *
@@ -202,6 +202,16 @@ ExpressionTreeNode Operation::Atan::differentiate(const std::vector<ExpressionTr
                               childDerivs[0]);
 }
 
+ExpressionTreeNode Operation::Atan2::differentiate(const std::vector<ExpressionTreeNode>& children, const std::vector<ExpressionTreeNode>& childDerivs, const std::string& variable) const {
+    return ExpressionTreeNode(new Operation::Divide(),
+                              ExpressionTreeNode(new Operation::Subtract(),
+                                                 ExpressionTreeNode(new Operation::Multiply(), children[1], childDerivs[0]),
+                                                 ExpressionTreeNode(new Operation::Multiply(), children[0], childDerivs[1])),
+                              ExpressionTreeNode(new Operation::Add(),
+                                                 ExpressionTreeNode(new Operation::Square(), children[0]),
+                                                 ExpressionTreeNode(new Operation::Square(), children[1])));
+}
+
 ExpressionTreeNode Operation::Sinh::differentiate(const std::vector<ExpressionTreeNode>& children, const std::vector<ExpressionTreeNode>& childDerivs, const std::string& variable) const {
     return ExpressionTreeNode(new Operation::Multiply(),
                               ExpressionTreeNode(new Operation::Cosh(),

lib/colvars/lepton/src/ParsedExpression.cpp

@@ -271,6 +271,16 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio
                 return ExpressionTreeNode(new Operation::MultiplyConstant(-dynamic_cast<const Operation::MultiplyConstant*>(&node.getOperation())->getValue()), children[0].getChildren()[0]);
             break;
         }
+        case Operation::SQRT:
+        {
+            if (children[0].getOperation().getId() == Operation::SQUARE) // sqrt(square(x)) = abs(x)
+                return ExpressionTreeNode(new Operation::Abs(), children[0].getChildren()[0]);
+        }
+        case Operation::SQUARE:
+        {
+            if (children[0].getOperation().getId() == Operation::SQRT) // square(sqrt(x)) = x
+                return children[0].getChildren()[0];
+        }
         default:
         {
             // If operation ID is not one of the above,

lib/colvars/lepton/src/Parser.cpp

@@ -6,7 +6,7 @@
  * 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:                                                              *
  *                                                                            *
@@ -313,6 +313,7 @@ Operation* Parser::getFunctionOperation(const std::string& name, const map<strin
         opMap["asin"] = Operation::ASIN;
         opMap["acos"] = Operation::ACOS;
         opMap["atan"] = Operation::ATAN;
+        opMap["atan2"] = Operation::ATAN2;
         opMap["sinh"] = Operation::SINH;
         opMap["cosh"] = Operation::COSH;
         opMap["tanh"] = Operation::TANH;
@@ -368,6 +369,8 @@ Operation* Parser::getFunctionOperation(const std::string& name, const map<strin
             return new Operation::Acos();
         case Operation::ATAN:
             return new Operation::Atan();
+        case Operation::ATAN2:
+            return new Operation::Atan2();
         case Operation::SINH:
             return new Operation::Sinh();
         case Operation::COSH: