Ejemplo n.º 1
0
ParsedExpression CustomHbondForceImpl::prepareExpression(const CustomHbondForce& force, const map<string, CustomFunction*>& customFunctions, map<string, vector<int> >& distances,
        map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
    CustomHbondForceImpl::FunctionPlaceholder custom(1);
    CustomHbondForceImpl::FunctionPlaceholder distance(2);
    CustomHbondForceImpl::FunctionPlaceholder angle(3);
    CustomHbondForceImpl::FunctionPlaceholder dihedral(4);
    map<string, CustomFunction*> functions = customFunctions;
    functions["distance"] = &distance;
    functions["angle"] = &angle;
    functions["dihedral"] = &dihedral;
    ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction(), functions);
    map<string, int> atoms;
    atoms["a1"] = 0;
    atoms["a2"] = 1;
    atoms["a3"] = 2;
    atoms["d1"] = 3;
    atoms["d2"] = 4;
    atoms["d3"] = 5;
    set<string> variables;
    for (int i = 0; i < force.getNumPerDonorParameters(); i++)
        variables.insert(force.getPerDonorParameterName(i));
    for (int i = 0; i < force.getNumPerAcceptorParameters(); i++)
        variables.insert(force.getPerAcceptorParameterName(i));
    for (int i = 0; i < force.getNumGlobalParameters(); i++)
        variables.insert(force.getGlobalParameterName(i));
    return ParsedExpression(replaceFunctions(expression.getRootNode(), atoms, distances, angles, dihedrals, variables)).optimize();
}
Ejemplo n.º 2
0
CompiledExpression::CompiledExpression(const ParsedExpression& expression) : jitCode(NULL) {
    ParsedExpression expr = expression.optimize(); // Just in case it wasn't already optimized.
    vector<pair<ExpressionTreeNode, int> > temps;
    compileExpression(expr.getRootNode(), temps);
    int maxArguments = 1;
    for (int i = 0; i < (int) operation.size(); i++)
        if (operation[i]->getNumArguments() > maxArguments)
            maxArguments = operation[i]->getNumArguments();
    argValues.resize(maxArguments);
#ifdef LEPTON_USE_JIT
    generateJitCode();
#endif
}
Ejemplo n.º 3
0
void VectorExpression::analyzeExpression(const ParsedExpression& expression) {
    parsed = expression.optimize();
    program = parsed.createProgram();
    stack.resize(program.getStackSize()+1);
    for (int i = 0; i < program.getNumOperations(); i++) {
        const Operation& op = program.getOperation(i);
        if (op.getId() == Operation::VARIABLE)
            operations.push_back(new Variable(op.getName()));
        else if (op.getId() == Operation::CONSTANT)
            operations.push_back(new Constant(dynamic_cast<const Operation::Constant&>(op).getValue()));
        else if (op.getName() == "dot")
            operations.push_back(new Dot());
        else if (op.getName() == "cross")
            operations.push_back(new Cross());
        else if (op.getName() == "_x")
            operations.push_back(new Component(0));
        else if (op.getName() == "_y")
            operations.push_back(new Component(1));
        else if (op.getName() == "_z")
            operations.push_back(new Component(2));
        else if (op.getName() == "vector")
            operations.push_back(new Vector());
        else if (op.getNumArguments() == 1)
            operations.push_back(new OpWrapper1(op));
        else if (op.getNumArguments() == 2)
            operations.push_back(new OpWrapper2(op));
        else if (op.getNumArguments() == 3)
            operations.push_back(new OpWrapper3(op));
        else
            throw OpenMMException("Unsupported operator in vector expression: "+op.getName());
    }
}
ExpressionProgram::ExpressionProgram(const ParsedExpression& expression) : maxArgs(0), stackSize(0) {
    buildProgram(expression.getRootNode());
    int currentStackSize = 0;
    for (int i = 0; i < (int) operations.size(); i++) {
        int args = operations[i]->getNumArguments();
        if (args > maxArgs)
            maxArgs = args;
        currentStackSize += 1-args;
        if (currentStackSize > stackSize)
            stackSize = currentStackSize;
    }
}
Ejemplo n.º 5
0
void verifyEvaluation(const string& expression, double expectedValue) {
    map<string, CustomFunction*> customFunctions;
    ParsedExpression parsed = Parser::parse(expression, customFunctions);
    double value = parsed.evaluate();
    ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);

    // Try optimizing it and make sure the result is still correct.

    value = parsed.optimize().evaluate();
    ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);

    // Create an ExpressionProgram and see if that also gives the same result.

    ExpressionProgram program = parsed.createProgram();
    value = program.evaluate();
    ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);

    // Create a CompiledExpression and see if that also gives the same result.

    CompiledExpression compiled = parsed.createCompiledExpression();
    value = compiled.evaluate();
    ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);
}
Ejemplo n.º 6
0
void verifySameValue(const ParsedExpression& exp1, const ParsedExpression& exp2, double x, double y) {
    map<string, double> variables;
    variables["x"] = x;
    variables["y"] = y;
    double val1 = exp1.evaluate(variables);
    double val2 = exp2.evaluate(variables);
    assertNumbersEqual(val1, val2);
    
    // Now create CompiledExpressions from them and see if those also match.

    CompiledExpression compiled1 = exp1.createCompiledExpression();
    CompiledExpression compiled2 = exp2.createCompiledExpression();
    if (compiled1.getVariables().find("x") != compiled1.getVariables().end())
        compiled1.getVariableReference("x") = x;
    if (compiled1.getVariables().find("y") != compiled1.getVariables().end())
        compiled1.getVariableReference("y") = y;
    if (compiled2.getVariables().find("x") != compiled2.getVariables().end())
        compiled2.getVariableReference("x") = x;
    if (compiled2.getVariables().find("y") != compiled2.getVariables().end())
        compiled2.getVariableReference("y") = y;
    assertNumbersEqual(val1, compiled1.evaluate());
    assertNumbersEqual(val2, compiled2.evaluate());
}
Ejemplo n.º 7
0
void verifyEvaluation(const string& expression, double x, double y, double expectedValue) {
    map<string, double> variables;
    variables["x"] = x;
    variables["y"] = y;
    ParsedExpression parsed = Parser::parse(expression);
    double value = parsed.evaluate(variables);
    ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);

    // Try optimizing it and make sure the result is still correct.

    value = parsed.optimize().evaluate(variables);
    ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);

    // Try optimizing with predefined values for the variables.

    value = parsed.optimize(variables).evaluate();
    ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);

    // Create an ExpressionProgram and see if that also gives the same result.

    ExpressionProgram program = parsed.createProgram();
    value = program.evaluate(variables);
    ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);

    // Create a CompiledExpression and see if that also gives the same result.

    CompiledExpression compiled = parsed.createCompiledExpression();
    if (compiled.getVariables().find("x") != compiled.getVariables().end())
        compiled.getVariableReference("x") = x;
    if (compiled.getVariables().find("y") != compiled.getVariables().end())
        compiled.getVariableReference("y") = y;
    value = compiled.evaluate();
    ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);

    // Make sure that variable renaming works.

    variables.clear();
    variables["w"] = x;
    variables["y"] = y;
    map<string, string> replacements;
    replacements["x"] = "w";
    value = parsed.renameVariables(replacements).evaluate(variables);
    ASSERT_EQUAL_TOL(expectedValue, value, 1e-10);
}
Ejemplo n.º 8
0
CompiledExpression::CompiledExpression(const ParsedExpression& expression) {
    ParsedExpression expr = expression.optimize(); // Just in case it wasn't already optimized.
    vector<pair<ExpressionTreeNode, int> > temps;
    compileExpression(expr.getRootNode(), temps);
}