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Commit 11d2d8ae authored by peastman's avatar peastman
Browse files

Merge pull request #1143 from peastman/variables 

Added error checking for illegal variable names
parents 5e1a87fb 213fbc03
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Showing with 390 additions and 23 deletions
openmmapi/include/openmm/internal/CustomCentroidBondForceImpl.h
View file @ 11d2d8ae
......@@ -41,6 +41,7 @@
#include "lepton/ParsedExpression.h"
#include <utility>
#include <map>
#include <set>
#include <string>
namespace OpenMM {
......@@ -93,7 +94,7 @@ private:
class FunctionPlaceholder;
static Lepton::ExpressionTreeNode replaceFunctions(const Lepton::ExpressionTreeNode& node, std::map<std::string, int> atoms,
std::map<std::string, std::vector<int> >& distances, std::map<std::string, std::vector<int> >& angles,
std::map<std::string, std::vector<int> >& dihedrals);
std::map<std::string, std::vector<int> >& dihedrals, std::set<std::string>& variables);
void addBondsBetweenGroups(int group1, int group2, std::vector<std::pair<int, int> >& bonds) const;
const CustomCentroidBondForce& owner;
Kernel kernel;
......
openmmapi/include/openmm/internal/CustomCompoundBondForceImpl.h
View file @ 11d2d8ae
......@@ -40,6 +40,7 @@
#include "lepton/ParsedExpression.h"
#include <utility>
#include <map>
#include <set>
#include <string>
namespace OpenMM {
......@@ -83,7 +84,7 @@ private:
class FunctionPlaceholder;
static Lepton::ExpressionTreeNode replaceFunctions(const Lepton::ExpressionTreeNode& node, std::map<std::string, int> atoms,
std::map<std::string, std::vector<int> >& distances, std::map<std::string, std::vector<int> >& angles,
std::map<std::string, std::vector<int> >& dihedrals);
std::map<std::string, std::vector<int> >& dihedrals, std::set<std::string>& variables);
const CustomCompoundBondForce& owner;
Kernel kernel;
};
......
openmmapi/include/openmm/internal/CustomHbondForceImpl.h
View file @ 11d2d8ae
......@@ -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) 2008-2010 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -40,6 +40,7 @@
#include "lepton/ParsedExpression.h"
#include <utility>
#include <map>
#include <set>
#include <string>
namespace OpenMM {
......@@ -84,7 +85,7 @@ private:
class FunctionPlaceholder;
static Lepton::ExpressionTreeNode replaceFunctions(const Lepton::ExpressionTreeNode& node, std::map<std::string, int> atoms,
std::map<std::string, std::vector<int> >& distances, std::map<std::string, std::vector<int> >& angles,
std::map<std::string, std::vector<int> >& dihedrals);
std::map<std::string, std::vector<int> >& dihedrals, std::set<std::string>& variables);
const CustomHbondForce& owner;
Kernel kernel;
};
......
openmmapi/include/openmm/internal/CustomManyParticleForceImpl.h
View file @ 11d2d8ae
......@@ -40,6 +40,7 @@
#include "lepton/ParsedExpression.h"
#include <utility>
#include <map>
#include <set>
#include <string>
namespace OpenMM {
......@@ -98,7 +99,7 @@ private:
class FunctionPlaceholder;
static Lepton::ExpressionTreeNode replaceFunctions(const Lepton::ExpressionTreeNode& node, std::map<std::string, int> atoms,
std::map<std::string, std::vector<int> >& distances, std::map<std::string, std::vector<int> >& angles,
std::map<std::string, std::vector<int> >& dihedrals);
std::map<std::string, std::vector<int> >& dihedrals, std::set<std::string>& variables);
static void generatePermutations(std::vector<int>& values, int numFixed, std::vector<std::vector<int> >& result);
const CustomManyParticleForce& owner;
Kernel kernel;
......
openmmapi/src/CustomCentroidBondForceImpl.cpp
View file @ 11d2d8ae
......@@ -150,24 +150,37 @@ ParsedExpression CustomCentroidBondForceImpl::prepareExpression(const CustomCent
functions["dihedral"] = &dihedral;
ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction(), functions);
map<string, int> groups;
set<string> variables;
for (int i = 0; i < force.getNumGroupsPerBond(); i++) {
stringstream name;
stringstream name, x, y, z;
name << 'g' << (i+1);
x << 'x' << (i+1);
y << 'y' << (i+1);
z << 'z' << (i+1);
groups[name.str()] = i;
variables.insert(x.str());
variables.insert(y.str());
variables.insert(z.str());
}
return ParsedExpression(replaceFunctions(expression.getRootNode(), groups, distances, angles, dihedrals)).optimize();
for (int i = 0; i < force.getNumGlobalParameters(); i++)
variables.insert(force.getGlobalParameterName(i));
for (int i = 0; i < force.getNumPerBondParameters(); i++)
variables.insert(force.getPerBondParameterName(i));
return ParsedExpression(replaceFunctions(expression.getRootNode(), groups, distances, angles, dihedrals, variables)).optimize();
}
ExpressionTreeNode CustomCentroidBondForceImpl::replaceFunctions(const ExpressionTreeNode& node, map<string, int> groups,
map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals, set<string>& variables) {
const Operation& op = node.getOperation();
if (op.getId() == Operation::VARIABLE && variables.find(op.getName()) == variables.end())
throw OpenMMException("CustomCentroidBondForce: Unknown variable '"+op.getName()+"'");
if (op.getId() != Operation::CUSTOM || (op.getName() != "distance" && op.getName() != "angle" && op.getName() != "dihedral"))
{
// This is not an angle or dihedral, so process its children.
vector<ExpressionTreeNode> children;
for (int i = 0; i < (int) node.getChildren().size(); i++)
children.push_back(replaceFunctions(node.getChildren()[i], groups, distances, angles, dihedrals));
children.push_back(replaceFunctions(node.getChildren()[i], groups, distances, angles, dihedrals, variables));
return ExpressionTreeNode(op.clone(), children);
}
const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);
......
openmmapi/src/CustomCompoundBondForceImpl.cpp
View file @ 11d2d8ae
......@@ -136,24 +136,37 @@ ParsedExpression CustomCompoundBondForceImpl::prepareExpression(const CustomComp
functions["dihedral"] = &dihedral;
ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction(), functions);
map<string, int> atoms;
set<string> variables;
for (int i = 0; i < force.getNumParticlesPerBond(); i++) {
stringstream name;
stringstream name, x, y, z;
name << 'p' << (i+1);
x << 'x' << (i+1);
y << 'y' << (i+1);
z << 'z' << (i+1);
atoms[name.str()] = i;
variables.insert(x.str());
variables.insert(y.str());
variables.insert(z.str());
}
return ParsedExpression(replaceFunctions(expression.getRootNode(), atoms, distances, angles, dihedrals)).optimize();
for (int i = 0; i < force.getNumGlobalParameters(); i++)
variables.insert(force.getGlobalParameterName(i));
for (int i = 0; i < force.getNumPerBondParameters(); i++)
variables.insert(force.getPerBondParameterName(i));
return ParsedExpression(replaceFunctions(expression.getRootNode(), atoms, distances, angles, dihedrals, variables)).optimize();
}
ExpressionTreeNode CustomCompoundBondForceImpl::replaceFunctions(const ExpressionTreeNode& node, map<string, int> atoms,
map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals, set<string>& variables) {
const Operation& op = node.getOperation();
if (op.getId() == Operation::VARIABLE && variables.find(op.getName()) == variables.end())
throw OpenMMException("CustomCompoundBondForce: Unknown variable '"+op.getName()+"'");
if (op.getId() != Operation::CUSTOM || (op.getName() != "distance" && op.getName() != "angle" && op.getName() != "dihedral"))
{
// This is not an angle or dihedral, so process its children.
vector<ExpressionTreeNode> children;
for (int i = 0; i < (int) node.getChildren().size(); i++)
children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals));
children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals, variables));
return ExpressionTreeNode(op.clone(), children);
}
const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);
......
openmmapi/src/CustomHbondForceImpl.cpp
View file @ 11d2d8ae
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -215,19 +215,28 @@ ParsedExpression CustomHbondForceImpl::prepareExpression(const CustomHbondForce&
atoms["d1"] = 3;
atoms["d2"] = 4;
atoms["d3"] = 5;
return ParsedExpression(replaceFunctions(expression.getRootNode(), atoms, distances, angles, dihedrals)).optimize();
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();
}
ExpressionTreeNode CustomHbondForceImpl::replaceFunctions(const ExpressionTreeNode& node, map<string, int> atoms,
map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals, set<string>& variables) {
const Operation& op = node.getOperation();
if (op.getId() == Operation::VARIABLE && variables.find(op.getName()) == variables.end())
throw OpenMMException("CustomHBondForce: Unknown variable '"+op.getName()+"'");
if (op.getId() != Operation::CUSTOM || op.getNumArguments() < 2)
{
// This is not an angle or dihedral, so process its children.
vector<ExpressionTreeNode> children;
for (int i = 0; i < (int) node.getChildren().size(); i++)
children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals));
children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals, variables));
return ExpressionTreeNode(op.clone(), children);
}
const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);
......
openmmapi/src/CustomManyParticleForceImpl.cpp
View file @ 11d2d8ae
......@@ -165,24 +165,40 @@ ParsedExpression CustomManyParticleForceImpl::prepareExpression(const CustomMany
functions["dihedral"] = &dihedral;
ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction(), functions);
map<string, int> atoms;
set<string> variables;
for (int i = 0; i < force.getNumParticlesPerSet(); i++) {
stringstream name;
stringstream name, x, y, z;
name << 'p' << (i+1);
x << 'x' << (i+1);
y << 'y' << (i+1);
z << 'z' << (i+1);
atoms[name.str()] = i;
variables.insert(x.str());
variables.insert(y.str());
variables.insert(z.str());
for (int j = 0; j < force.getNumPerParticleParameters(); j++) {
stringstream param;
param << force.getPerParticleParameterName(j) << (i+1);
variables.insert(param.str());
}
}
return ParsedExpression(replaceFunctions(expression.getRootNode(), atoms, distances, angles, dihedrals)).optimize();
for (int i = 0; i < force.getNumGlobalParameters(); i++)
variables.insert(force.getGlobalParameterName(i));
return ParsedExpression(replaceFunctions(expression.getRootNode(), atoms, distances, angles, dihedrals, variables)).optimize();
}
ExpressionTreeNode CustomManyParticleForceImpl::replaceFunctions(const ExpressionTreeNode& node, map<string, int> atoms,
map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals, set<string>& variables) {
const Operation& op = node.getOperation();
if (op.getId() == Operation::VARIABLE && variables.find(op.getName()) == variables.end())
throw OpenMMException("CustomManyParticleForce: Unknown variable '"+op.getName()+"'");
if (op.getId() != Operation::CUSTOM || (op.getName() != "distance" && op.getName() != "angle" && op.getName() != "dihedral"))
{
// This is not an angle or dihedral, so process its children.
vector<ExpressionTreeNode> children;
for (int i = 0; i < (int) node.getChildren().size(); i++)
children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals));
children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals, variables));
return ExpressionTreeNode(op.clone(), children);
}
const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);
......
platforms/cpu/src/CpuKernels.cpp
View file @ 11d2d8ae
......@@ -47,6 +47,7 @@
#include "RealVec.h"
#include "lepton/CompiledExpression.h"
#include "lepton/CustomFunction.h"
#include "lepton/Operation.h"
#include "lepton/Parser.h"
#include "lepton/ParsedExpression.h"
......@@ -83,6 +84,17 @@ static ReferenceConstraints& extractConstraints(ContextImpl& context) {
return *(ReferenceConstraints*) data->constraints;
}
/**
* Make sure an expression doesn't use any undefined variables.
*/
static void validateVariables(const Lepton::ExpressionTreeNode& node, const set<string>& variables) {
const Lepton::Operation& op = node.getOperation();
if (op.getId() == Lepton::Operation::VARIABLE && variables.find(op.getName()) == variables.end())
throw OpenMMException("Unknown variable in expression: "+op.getName());
for (int i = 0; i < (int) node.getChildren().size(); i++)
validateVariables(node.getChildren()[i], variables);
}
/**
* Compute the kinetic energy of the system, possibly shifting the velocities in time to account
* for a leapfrog integrator.
......@@ -737,6 +749,14 @@ void CpuCalcCustomNonbondedForceKernel::initialize(const System& system, const C
globalParameterNames.push_back(force.getGlobalParameterName(i));
globalParamValues[force.getGlobalParameterName(i)] = force.getGlobalParameterDefaultValue(i);
}
set<string> variables;
variables.insert("r");
for (int i = 0; i < numParameters; i++) {
variables.insert(parameterNames[i]+"1");
variables.insert(parameterNames[i]+"2");
}
variables.insert(globalParameterNames.begin(), globalParameterNames.end());
validateVariables(expression.getRootNode(), variables);
// Delete the custom functions.
......@@ -950,6 +970,18 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
vector<vector<Lepton::CompiledExpression> > valueGradientExpressions(force.getNumComputedValues());
vector<Lepton::CompiledExpression> valueExpressions;
vector<Lepton::CompiledExpression> energyExpressions;
set<string> particleVariables, pairVariables;
pairVariables.insert("r");
particleVariables.insert("x");
particleVariables.insert("y");
particleVariables.insert("z");
for (int i = 0; i < numPerParticleParameters; i++) {
particleVariables.insert(particleParameterNames[i]);
pairVariables.insert(particleParameterNames[i]+"1");
pairVariables.insert(particleParameterNames[i]+"2");
}
particleVariables.insert(globalParameterNames.begin(), globalParameterNames.end());
pairVariables.insert(globalParameterNames.begin(), globalParameterNames.end());
for (int i = 0; i < force.getNumComputedValues(); i++) {
string name, expression;
CustomGBForce::ComputationType type;
......@@ -958,15 +990,21 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
valueExpressions.push_back(ex.createCompiledExpression());
valueTypes.push_back(type);
valueNames.push_back(name);
if (i == 0)
if (i == 0) {
valueDerivExpressions[i].push_back(ex.differentiate("r").createCompiledExpression());
validateVariables(ex.getRootNode(), pairVariables);
}
else {
valueGradientExpressions[i].push_back(ex.differentiate("x").createCompiledExpression());
valueGradientExpressions[i].push_back(ex.differentiate("y").createCompiledExpression());
valueGradientExpressions[i].push_back(ex.differentiate("z").createCompiledExpression());
for (int j = 0; j < i; j++)
valueDerivExpressions[i].push_back(ex.differentiate(valueNames[j]).createCompiledExpression());
validateVariables(ex.getRootNode(), particleVariables);
}
particleVariables.insert(name);
pairVariables.insert(name+"1");
pairVariables.insert(name+"2");
}
// Parse the expressions for energy terms.
......@@ -988,10 +1026,12 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
energyGradientExpressions[i].push_back(ex.differentiate("x").createCompiledExpression());
energyGradientExpressions[i].push_back(ex.differentiate("y").createCompiledExpression());
energyGradientExpressions[i].push_back(ex.differentiate("z").createCompiledExpression());
validateVariables(ex.getRootNode(), particleVariables);
}
else {
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"1").createCompiledExpression());
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"2").createCompiledExpression());
validateVariables(ex.getRootNode(), pairVariables);
}
}
}
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 11d2d8ae
......@@ -77,6 +77,7 @@
#include "openmm/OpenMMException.h"
#include "SimTKOpenMMUtilities.h"
#include "lepton/CustomFunction.h"
#include "lepton/Operation.h"
#include "lepton/Parser.h"
#include "lepton/ParsedExpression.h"
#include <cmath>
......@@ -146,6 +147,17 @@ static ReferenceConstraints& extractConstraints(ContextImpl& context) {
return *(ReferenceConstraints*) data->constraints;
}
/**
* Make sure an expression doesn't use any undefined variables.
*/
static void validateVariables(const Lepton::ExpressionTreeNode& node, const set<string>& variables) {
const Lepton::Operation& op = node.getOperation();
if (op.getId() == Lepton::Operation::VARIABLE && variables.find(op.getName()) == variables.end())
throw OpenMMException("Unknown variable in expression: "+op.getName());
for (int i = 0; i < (int) node.getChildren().size(); i++)
validateVariables(node.getChildren()[i], variables);
}
/**
* Compute the kinetic energy of the system, possibly shifting the velocities in time to account
* for a leapfrog integrator.
......@@ -422,6 +434,11 @@ void ReferenceCalcCustomBondForceKernel::initialize(const System& system, const
parameterNames.push_back(force.getPerBondParameterName(i));
for (int i = 0; i < force.getNumGlobalParameters(); i++)
globalParameterNames.push_back(force.getGlobalParameterName(i));
set<string> variables;
variables.insert("r");
variables.insert(parameterNames.begin(), parameterNames.end());
variables.insert(globalParameterNames.begin(), globalParameterNames.end());
validateVariables(expression.getRootNode(), variables);
}
double ReferenceCalcCustomBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -536,6 +553,11 @@ void ReferenceCalcCustomAngleForceKernel::initialize(const System& system, const
parameterNames.push_back(force.getPerAngleParameterName(i));
for (int i = 0; i < force.getNumGlobalParameters(); i++)
globalParameterNames.push_back(force.getGlobalParameterName(i));
set<string> variables;
variables.insert("theta");
variables.insert(parameterNames.begin(), parameterNames.end());
variables.insert(globalParameterNames.begin(), globalParameterNames.end());
validateVariables(expression.getRootNode(), variables);
}
double ReferenceCalcCustomAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -780,6 +802,11 @@ void ReferenceCalcCustomTorsionForceKernel::initialize(const System& system, con
parameterNames.push_back(force.getPerTorsionParameterName(i));
for (int i = 0; i < force.getNumGlobalParameters(); i++)
globalParameterNames.push_back(force.getGlobalParameterName(i));
set<string> variables;
variables.insert("theta");
variables.insert(parameterNames.begin(), parameterNames.end());
variables.insert(globalParameterNames.begin(), globalParameterNames.end());
validateVariables(expression.getRootNode(), variables);
}
double ReferenceCalcCustomTorsionForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......@@ -1038,6 +1065,14 @@ void ReferenceCalcCustomNonbondedForceKernel::initialize(const System& system, c
globalParameterNames.push_back(force.getGlobalParameterName(i));
globalParamValues[force.getGlobalParameterName(i)] = force.getGlobalParameterDefaultValue(i);
}
set<string> variables;
variables.insert("r");
for (int i = 0; i < numParameters; i++) {
variables.insert(parameterNames[i]+"1");
variables.insert(parameterNames[i]+"2");
}
variables.insert(globalParameterNames.begin(), globalParameterNames.end());
validateVariables(expression.getRootNode(), variables);
// Delete the custom functions.
......@@ -1314,6 +1349,18 @@ void ReferenceCalcCustomGBForceKernel::initialize(const System& system, const Cu
valueDerivExpressions.resize(force.getNumComputedValues());
valueGradientExpressions.resize(force.getNumComputedValues());
set<string> particleVariables, pairVariables;
pairVariables.insert("r");
particleVariables.insert("x");
particleVariables.insert("y");
particleVariables.insert("z");
for (int i = 0; i < numPerParticleParameters; i++) {
particleVariables.insert(particleParameterNames[i]);
pairVariables.insert(particleParameterNames[i]+"1");
pairVariables.insert(particleParameterNames[i]+"2");
}
particleVariables.insert(globalParameterNames.begin(), globalParameterNames.end());
pairVariables.insert(globalParameterNames.begin(), globalParameterNames.end());
for (int i = 0; i < force.getNumComputedValues(); i++) {
string name, expression;
CustomGBForce::ComputationType type;
......@@ -1322,15 +1369,21 @@ void ReferenceCalcCustomGBForceKernel::initialize(const System& system, const Cu
valueExpressions.push_back(ex.createProgram());
valueTypes.push_back(type);
valueNames.push_back(name);
if (i == 0)
if (i == 0) {
valueDerivExpressions[i].push_back(ex.differentiate("r").optimize().createProgram());
validateVariables(ex.getRootNode(), pairVariables);
}
else {
valueGradientExpressions[i].push_back(ex.differentiate("x").optimize().createProgram());
valueGradientExpressions[i].push_back(ex.differentiate("y").optimize().createProgram());
valueGradientExpressions[i].push_back(ex.differentiate("z").optimize().createProgram());
for (int j = 0; j < i; j++)
valueDerivExpressions[i].push_back(ex.differentiate(valueNames[j]).optimize().createProgram());
validateVariables(ex.getRootNode(), particleVariables);
}
particleVariables.insert(name);
pairVariables.insert(name+"1");
pairVariables.insert(name+"2");
}
// Parse the expressions for energy terms.
......@@ -1352,10 +1405,12 @@ void ReferenceCalcCustomGBForceKernel::initialize(const System& system, const Cu
energyGradientExpressions[i].push_back(ex.differentiate("x").optimize().createProgram());
energyGradientExpressions[i].push_back(ex.differentiate("y").optimize().createProgram());
energyGradientExpressions[i].push_back(ex.differentiate("z").optimize().createProgram());
validateVariables(ex.getRootNode(), particleVariables);
}
else {
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"1").optimize().createProgram());
energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"2").optimize().createProgram());
validateVariables(ex.getRootNode(), pairVariables);
}
}
}
......@@ -1475,6 +1530,13 @@ void ReferenceCalcCustomExternalForceKernel::initialize(const System& system, co
parameterNames.push_back(force.getPerParticleParameterName(i));
for (int i = 0; i < force.getNumGlobalParameters(); i++)
globalParameterNames.push_back(force.getGlobalParameterName(i));
set<string> variables;
variables.insert("x");
variables.insert("y");
variables.insert("z");
variables.insert(parameterNames.begin(), parameterNames.end());
variables.insert(globalParameterNames.begin(), globalParameterNames.end());
validateVariables(expression.getRootNode(), variables);
}
double ReferenceCalcCustomExternalForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
......
tests/TestCustomAngleForce.h
View file @ 11d2d8ae
......@@ -126,12 +126,33 @@ void testAngles() {
}
}
void testIllegalVariable() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
CustomAngleForce* force = new CustomAngleForce("theta+none");
vector<double> params;
force->addAngle(0, 1, 2, params);
system.addForce(force);
VerletIntegrator integrator(0.001);
bool threwException = false;
try {
Context(system, integrator, platform);
}
catch (const exception& e) {
threwException = true;
}
ASSERT(threwException);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
try {
initializeTests(argc, argv);
testAngles();
testIllegalVariable();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestCustomBondForce.h
View file @ 11d2d8ae
......@@ -130,6 +130,25 @@ void testManyParameters() {
ASSERT_EQUAL_TOL(f*2.5, state.getPotentialEnergy(), TOL);
}
void testIllegalVariable() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
CustomBondForce* force = new CustomBondForce("r+none");
vector<double> params;
force->addBond(0, 1, params);
system.addForce(force);
VerletIntegrator integrator(0.001);
bool threwException = false;
try {
Context(system, integrator, platform);
}
catch (const exception& e) {
threwException = true;
}
ASSERT(threwException);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -137,6 +156,7 @@ int main(int argc, char* argv[]) {
initializeTests(argc, argv);
testBonds();
testManyParameters();
testIllegalVariable();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestCustomCentroidBondForce.h
View file @ 11d2d8ae
......@@ -252,6 +252,32 @@ void testCustomWeights() {
ASSERT_EQUAL_VEC(Vec3(0, -2*9*(1.0/3.0), 0), state.getForces()[3], TOL);
}
void testIllegalVariable() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "1+none");
vector<int> particles;
particles.push_back(0);
force->addGroup(particles);
force->addGroup(particles);
vector<int> groups;
groups.push_back(0);
groups.push_back(1);
vector<double> params;
force->addBond(groups, params);
system.addForce(force);
VerletIntegrator integrator(0.001);
bool threwException = false;
try {
Context(system, integrator, platform);
}
catch (const exception& e) {
threwException = true;
}
ASSERT(threwException);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -260,6 +286,7 @@ int main(int argc, char* argv[]) {
testHarmonicBond();
testComplexFunction();
testCustomWeights();
testIllegalVariable();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestCustomCompoundBondForce.h
View file @ 11d2d8ae
......@@ -309,6 +309,28 @@ void testMultipleBonds() {
ASSERT_EQUAL_VEC(Vec3(0.776, 0.0, -0.084), forces[3], 1e-3);
}
void testIllegalVariable() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
CustomCompoundBondForce* force = new CustomCompoundBondForce(2, "1+none");
vector<int> particles;
particles.push_back(0);
particles.push_back(1);
vector<double> params;
force->addBond(particles, params);
system.addForce(force);
VerletIntegrator integrator(0.001);
bool threwException = false;
try {
Context(system, integrator, platform);
}
catch (const exception& e) {
threwException = true;
}
ASSERT(threwException);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -319,6 +341,7 @@ int main(int argc, char* argv[]) {
testContinuous2DFunction();
testContinuous3DFunction();
testMultipleBonds();
testIllegalVariable();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestCustomExternalForce.h
View file @ 11d2d8ae
......@@ -165,7 +165,24 @@ void testPeriodic() {
ASSERT_EQUAL_TOL(delta.dot(delta), state.getPotentialEnergy(), TOL);
integrator.step(1);
}
}
void testIllegalVariable() {
System system;
system.addParticle(1.0);
CustomExternalForce* force = new CustomExternalForce("x+none");
vector<double> params;
force->addParticle(0, params);
system.addForce(force);
VerletIntegrator integrator(0.001);
bool threwException = false;
try {
Context(system, integrator, platform);
}
catch (const exception& e) {
threwException = true;
}
ASSERT(threwException);
}
void runPlatformTests();
......@@ -176,6 +193,7 @@ int main(int argc, char* argv[]) {
testForce();
testManyParameters();
testPeriodic();
testIllegalVariable();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestCustomGBForce.h
View file @ 11d2d8ae
......@@ -470,6 +470,25 @@ void testExclusions() {
}
}
void testIllegalVariable() {
System system;
system.addParticle(1.0);
CustomGBForce* force = new CustomGBForce();
force->addComputedValue("a", "r+none", CustomGBForce::ParticlePair);
vector<double> params;
force->addParticle(params);
system.addForce(force);
VerletIntegrator integrator(0.001);
bool threwException = false;
try {
Context(system, integrator, platform);
}
catch (const exception& e) {
threwException = true;
}
ASSERT(threwException);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -483,6 +502,7 @@ int main(int argc, char* argv[]) {
testMultipleChainRules();
testPositionDependence();
testExclusions();
testIllegalVariable();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestCustomHbondForce.h
View file @ 11d2d8ae
......@@ -225,6 +225,26 @@ void testCustomFunctions() {
ASSERT_EQUAL_TOL(0.1*2+0.1*2, state.getPotentialEnergy(), TOL);
}
void testIllegalVariable() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
CustomHbondForce* force = new CustomHbondForce("1+none");
vector<double> params;
force->addDonor(0, -1, -1, params);
force->addAcceptor(1, -1, -1, params);
system.addForce(force);
VerletIntegrator integrator(0.001);
bool threwException = false;
try {
Context(system, integrator, platform);
}
catch (const exception& e) {
threwException = true;
}
ASSERT(threwException);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -234,6 +254,7 @@ int main(int argc, char* argv[]) {
testExclusions();
testCutoff();
testCustomFunctions();
testIllegalVariable();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestCustomManyParticleForce.h
View file @ 11d2d8ae
......@@ -707,6 +707,24 @@ void testCentralParticleModeLargeSystem() {
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
}
void testIllegalVariable() {
System system;
system.addParticle(1.0);
CustomManyParticleForce* force = new CustomManyParticleForce(2, "x1+y2+none");
vector<double> params;
force->addParticle(params);
system.addForce(force);
VerletIntegrator integrator(0.001);
bool threwException = false;
try {
Context(system, integrator, platform);
}
catch (const exception& e) {
threwException = true;
}
ASSERT(threwException);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -725,6 +743,7 @@ int main(int argc, char* argv[]) {
testCentralParticleModeNoCutoff();
testCentralParticleModeCutoff();
testCentralParticleModeLargeSystem();
testIllegalVariable();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestCustomNonbondedForce.h
View file @ 11d2d8ae
......@@ -993,6 +993,24 @@ void testMultipleCutoffs() {
}
}
void testIllegalVariable() {
System system;
system.addParticle(1.0);
CustomNonbondedForce* force = new CustomNonbondedForce("r+none");
vector<double> params;
force->addParticle(params);
system.addForce(force);
VerletIntegrator integrator(0.001);
bool threwException = false;
try {
Context(system, integrator, platform);
}
catch (const exception& e) {
threwException = true;
}
ASSERT(threwException);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -1017,6 +1035,7 @@ int main(int argc, char* argv[]) {
testLargeInteractionGroup();
testInteractionGroupLongRangeCorrection();
testMultipleCutoffs();
testIllegalVariable();
runPlatformTests();
}
catch(const exception& e) {
......
tests/TestCustomTorsionForce.h
View file @ 11d2d8ae
......@@ -166,6 +166,27 @@ void testRange() {
ASSERT(maxAngle <= M_PI);
}
void testIllegalVariable() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
CustomTorsionForce* force = new CustomTorsionForce("theta+none");
vector<double> params;
force->addTorsion(0, 1, 2, 3, params);
system.addForce(force);
VerletIntegrator integrator(0.001);
bool threwException = false;
try {
Context(system, integrator, platform);
}
catch (const exception& e) {
threwException = true;
}
ASSERT(threwException);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -173,6 +194,7 @@ int main(int argc, char* argv[]) {
initializeTests(argc, argv);
testTorsions();
testRange();
testIllegalVariable();
runPlatformTests();
}
catch(const exception& e) {
......
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