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Commit dca54ec7 authored by Saurabh Belsare's avatar Saurabh Belsare
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Merged fork with latest original master

parents cace5edf 01f9e415
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openmmapi/include/openmm/PeriodicTorsionForce.h
View file @ dca54ec7
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -108,20 +108,24 @@ public:
* in a torsion cannot be changed, nor can new torsions be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
private:
class PeriodicTorsionInfo;
std::vector<PeriodicTorsionInfo> periodicTorsions;
bool usePeriodic;
};
/**
......
openmmapi/include/openmm/RBTorsionForce.h
View file @ dca54ec7
......@@ -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) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -117,20 +117,24 @@ public:
* in a torsion cannot be changed, nor can new torsions be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
private:
class RBTorsionInfo;
std::vector<RBTorsionInfo> rbTorsions;
bool usePeriodic;
};
/**
......
openmmapi/include/openmm/System.h
View file @ dca54ec7
......@@ -243,7 +243,7 @@ public:
*
* @return true if at least one force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions();
bool usesPeriodicBoundaryConditions() const;
private:
class ConstraintInfo;
Vec3 periodicBoxVectors[3];
......
openmmapi/include/openmm/TabulatedFunction.h
View file @ dca54ec7
......@@ -80,11 +80,11 @@ public:
/**
* Get the parameters for the tabulated function.
*
* @param values the tabulated values of the function f(x) at uniformly spaced values of x between min
* @param[out] values the tabulated values of the function f(x) at uniformly spaced values of x between min
* and max. A natural cubic spline is used to interpolate between the tabulated values.
* The function is assumed to be zero for x &lt; min or x &gt; max.
* @param min the value of x corresponding to the first element of values
* @param max the value of x corresponding to the last element of values
* @param[out] min the value of x corresponding to the first element of values
* @param[out] max the value of x corresponding to the last element of values
*/
void getFunctionParameters(std::vector<double>& values, double& min, double& max) const;
/**
......@@ -129,16 +129,16 @@ public:
/**
* Get the parameters for the tabulated function.
*
* @param values the tabulated values of the function f(x,y) at xsize uniformly spaced values of x between xmin
* @param[out] values the tabulated values of the function f(x,y) at xsize uniformly spaced values of x between xmin
* and xmax, and ysize values of y between ymin and ymax. A natural cubic spline is used to interpolate between the tabulated values.
* The function is assumed to be zero when x or y is outside its specified range. The values should be ordered so that
* values[i+xsize*j] = f(x_i,y_j), where x_i is the i'th uniformly spaced value of x. This must be of length xsize*ysize.
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param xmin the value of x corresponding to the first element of values
* @param xmax the value of x corresponding to the last element of values
* @param ymin the value of y corresponding to the first element of values
* @param ymax the value of y corresponding to the last element of values
* @param[out] xsize the number of table elements along the x direction
* @param[out] ysize the number of table elements along the y direction
* @param[out] xmin the value of x corresponding to the first element of values
* @param[out] xmax the value of x corresponding to the last element of values
* @param[out] ymin the value of y corresponding to the first element of values
* @param[out] ymax the value of y corresponding to the last element of values
*/
void getFunctionParameters(int& xsize, int& ysize, std::vector<double>& values, double& xmin, double& xmax, double& ymin, double& ymax) const;
/**
......@@ -194,21 +194,21 @@ public:
/**
* Get the parameters for the tabulated function.
*
* @param values the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin
* @param[out] values the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin
* and xmax, ysize values of y between ymin and ymax, and zsize values of z between zmin and zmax.
* A natural cubic spline is used to interpolate between the tabulated values. The function is
* assumed to be zero when x, y, or z is outside its specified range. The values should be ordered so
* that values[i+xsize*j+xsize*ysize*k] = f(x_i,y_j,z_k), where x_i is the i'th uniformly spaced value of x.
* This must be of length xsize*ysize*zsize.
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param ysize the number of table elements along the z direction
* @param xmin the value of x corresponding to the first element of values
* @param xmax the value of x corresponding to the last element of values
* @param ymin the value of y corresponding to the first element of values
* @param ymax the value of y corresponding to the last element of values
* @param zmin the value of z corresponding to the first element of values
* @param zmax the value of z corresponding to the last element of values
* @param[out] xsize the number of table elements along the x direction
* @param[out] ysize the number of table elements along the y direction
* @param[out] zsize the number of table elements along the z direction
* @param[out] xmin the value of x corresponding to the first element of values
* @param[out] xmax the value of x corresponding to the last element of values
* @param[out] ymin the value of y corresponding to the first element of values
* @param[out] ymax the value of y corresponding to the last element of values
* @param[out] zmin the value of z corresponding to the first element of values
* @param[out] zmax the value of z corresponding to the last element of values
*/
void getFunctionParameters(int& xsize, int& ysize, int& zsize, std::vector<double>& values, double& xmin, double& xmax, double& ymin, double& ymax, double& zmin, double& zmax) const;
/**
......@@ -222,7 +222,7 @@ public:
* This must be of length xsize*ysize*zsize.
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param ysize the number of table elements along the z direction
* @param zsize the number of table elements along the z direction
* @param xmin the value of x corresponding to the first element of values
* @param xmax the value of x corresponding to the last element of values
* @param ymin the value of y corresponding to the first element of values
......@@ -257,7 +257,7 @@ public:
/**
* Get the parameters for the tabulated function.
*
* @param values the tabulated values of the function f(x)
* @param[out] values the tabulated values of the function f(x)
*/
void getFunctionParameters(std::vector<double>& values) const;
/**
......@@ -293,9 +293,9 @@ public:
/**
* Get the parameters for the tabulated function.
*
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param values the tabulated values of the function f(x,y), ordered so that
* @param[out] xsize the number of table elements along the x direction
* @param[out] ysize the number of table elements along the y direction
* @param[out] values the tabulated values of the function f(x,y), ordered so that
* values[i+xsize*j] = f(i,j). This must be of length xsize*ysize.
*/
void getFunctionParameters(int& xsize, int& ysize, std::vector<double>& values) const;
......@@ -337,10 +337,10 @@ public:
/**
* Get the parameters for the tabulated function.
*
* @param xsize the number of table elements along the x direction
* @param ysize the number of table elements along the y direction
* @param zsize the number of table elements along the z direction
* @param values the tabulated values of the function f(x,y,z), ordered so that
* @param[out] xsize the number of table elements along the x direction
* @param[out] ysize the number of table elements along the y direction
* @param[out] zsize the number of table elements along the z direction
* @param[out] values the tabulated values of the function f(x,y,z), ordered so that
* values[i+xsize*j+xsize*ysize*k] = f(i,j,k). This must be of length xsize*ysize*zsize.
*/
void getFunctionParameters(int& xsize, int& ysize, int& zsize, std::vector<double>& values) const;
......
openmmapi/include/openmm/internal/OSRngSeed.h
View file @ dca54ec7
#ifndef OPENMM_OSRNGSEED_H_
#ifndef OPENMM_OSRNGSEED_H_
#define OPENMM_OSRNGSEED_H_
......
openmmapi/include/openmm/internal/timer.h 0 → 100644
View file @ dca54ec7
#ifndef OPENMM_TIMER_H_
#define OPENMM_TIMER_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This header provides a static function for querying the current system time in seconds.
* It is useful when profiling.
*/
#ifdef _MSC_VER
#include <Windows.h>
static double getCurrentTime() {
FILETIME ft;
GetSystemTimeAsFileTime(&ft); // 100-nanoseconds since 1-1-1601
ULARGE_INTEGER result;
result.LowPart = ft.dwLowDateTime;
result.HighPart = ft.dwHighDateTime;
return 1e-7*result.QuadPart;
}
#else
#include <sys/time.h>
static double getCurrentTime() {
struct timeval tod;
gettimeofday(&tod, 0);
return tod.tv_sec+1e-6*tod.tv_usec;
}
#endif
#endif /*OPENMM_TIMER_H_*/
openmmapi/src/CMAPTorsionForce.cpp
View file @ dca54ec7
......@@ -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) 2010-2015 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -37,7 +37,7 @@
using namespace OpenMM;
CMAPTorsionForce::CMAPTorsionForce() {
CMAPTorsionForce::CMAPTorsionForce() : usePeriodic(false) {
}
int CMAPTorsionForce::addMap(int size, const std::vector<double>& energy) {
......@@ -99,3 +99,11 @@ ForceImpl* CMAPTorsionForce::createImpl() const {
void CMAPTorsionForce::updateParametersInContext(Context& context) {
dynamic_cast<CMAPTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void CMAPTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool CMAPTorsionForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
openmmapi/src/ContextImpl.cpp
View file @ dca54ec7
......@@ -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) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -84,15 +84,20 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
// Validate the list of properties.
const vector<string>& platformProperties = platform->getPropertyNames();
map<string, string> validatedProperties;
for (map<string, string>::const_iterator iter = properties.begin(); iter != properties.end(); ++iter) {
string property = iter->first;
if (platform->deprecatedPropertyReplacements.find(property) != platform->deprecatedPropertyReplacements.end())
property = platform->deprecatedPropertyReplacements[property];
bool valid = false;
for (int i = 0; i < (int) platformProperties.size(); i++)
if (platformProperties[i] == iter->first) {
if (platformProperties[i] == property) {
valid = true;
break;
}
if (!valid)
throw OpenMMException("Illegal property name: "+iter->first);
validatedProperties[property] = iter->second;
}
// Find the list of kernels required.
......@@ -139,7 +144,7 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
for (int i = candidatePlatforms.size()-1; i >= 0; i--) {
try {
this->platform = platform = candidatePlatforms[i].second;
platform->contextCreated(*this, properties);
platform->contextCreated(*this, validatedProperties);
break;
}
catch (...) {
......@@ -449,4 +454,5 @@ void ContextImpl::loadCheckpoint(istream& stream) {
parameters[name] = value;
}
updateStateDataKernel.getAs<UpdateStateDataKernel>().loadCheckpoint(*this, stream);
hasSetPositions = true;
}
openmmapi/src/CustomAngleForce.cpp
View file @ dca54ec7
......@@ -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) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -44,7 +44,7 @@ using std::string;
using std::stringstream;
using std::vector;
CustomAngleForce::CustomAngleForce(const string& energy) : energyExpression(energy) {
CustomAngleForce::CustomAngleForce(const string& energy) : energyExpression(energy), usePeriodic(false) {
}
const string& CustomAngleForce::getEnergyFunction() const {
......@@ -123,3 +123,11 @@ ForceImpl* CustomAngleForce::createImpl() const {
void CustomAngleForce::updateParametersInContext(Context& context) {
dynamic_cast<CustomAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void CustomAngleForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool CustomAngleForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
openmmapi/src/CustomBondForce.cpp
View file @ dca54ec7
......@@ -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) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -44,7 +44,7 @@ using std::string;
using std::stringstream;
using std::vector;
CustomBondForce::CustomBondForce(const string& energy) : energyExpression(energy) {
CustomBondForce::CustomBondForce(const string& energy) : energyExpression(energy), usePeriodic(false) {
}
const string& CustomBondForce::getEnergyFunction() const {
......@@ -121,3 +121,11 @@ ForceImpl* CustomBondForce::createImpl() const {
void CustomBondForce::updateParametersInContext(Context& context) {
dynamic_cast<CustomBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void CustomBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool CustomBondForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
openmmapi/src/CustomCentroidBondForce.cpp
View file @ dca54ec7
......@@ -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) 2015 Stanford University and the Authors. *
* Portions copyright (c) 2015-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -48,7 +48,7 @@ using std::string;
using std::stringstream;
using std::vector;
CustomCentroidBondForce::CustomCentroidBondForce(int numGroups, const string& energy) : groupsPerBond(numGroups), energyExpression(energy) {
CustomCentroidBondForce::CustomCentroidBondForce(int numGroups, const string& energy) : groupsPerBond(numGroups), energyExpression(energy), usePeriodic(false) {
}
CustomCentroidBondForce::~CustomCentroidBondForce() {
......@@ -173,3 +173,11 @@ ForceImpl* CustomCentroidBondForce::createImpl() const {
void CustomCentroidBondForce::updateParametersInContext(Context& context) {
dynamic_cast<CustomCentroidBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void CustomCentroidBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool CustomCentroidBondForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
openmmapi/src/CustomCompoundBondForce.cpp
View file @ dca54ec7
......@@ -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) 2008-2014 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -48,7 +48,7 @@ using std::string;
using std::stringstream;
using std::vector;
CustomCompoundBondForce::CustomCompoundBondForce(int numParticles, const string& energy) : particlesPerBond(numParticles), energyExpression(energy) {
CustomCompoundBondForce::CustomCompoundBondForce(int numParticles, const string& energy) : particlesPerBond(numParticles), energyExpression(energy), usePeriodic(false) {
}
......@@ -176,3 +176,11 @@ ForceImpl* CustomCompoundBondForce::createImpl() const {
void CustomCompoundBondForce::updateParametersInContext(Context& context) {
dynamic_cast<CustomCompoundBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void CustomCompoundBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool CustomCompoundBondForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
openmmapi/src/CustomIntegrator.cpp
View file @ dca54ec7
......@@ -248,21 +248,21 @@ int CustomIntegrator::addUpdateContextState() {
int CustomIntegrator::beginIfBlock(const string& expression) {
if (owner != NULL)
throw OpenMMException("The integrator cannot be modified after it is bound to a context");
computations.push_back(ComputationInfo(BeginIfBlock, "", expression));
computations.push_back(ComputationInfo(IfBlockStart, "", expression));
return computations.size()-1;
}
int CustomIntegrator::beginWhileBlock(const string& expression) {
if (owner != NULL)
throw OpenMMException("The integrator cannot be modified after it is bound to a context");
computations.push_back(ComputationInfo(BeginWhileBlock, "", expression));
computations.push_back(ComputationInfo(WhileBlockStart, "", expression));
return computations.size()-1;
}
int CustomIntegrator::endBlock() {
if (owner != NULL)
throw OpenMMException("The integrator cannot be modified after it is bound to a context");
computations.push_back(ComputationInfo(EndBlock, "", ""));
computations.push_back(ComputationInfo(BlockEnd, "", ""));
return computations.size()-1;
}
......
openmmapi/src/CustomIntegratorUtilities.cpp
View file @ dca54ec7
......@@ -87,7 +87,7 @@ void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context,
for (int step = 0; step < numSteps; step++) {
string expression;
integrator.getComputationStep(step, stepType[step], stepVariable[step], expression);
if (stepType[step] == CustomIntegrator::BeginIfBlock || stepType[step] == CustomIntegrator::BeginWhileBlock) {
if (stepType[step] == CustomIntegrator::IfBlockStart || stepType[step] == CustomIntegrator::WhileBlockStart) {
// This step involves a condition.
string lhs, rhs;
......@@ -158,9 +158,9 @@ void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context,
vector<int> blockStart;
blockEnd.resize(numSteps, -1);
for (int step = 0; step < numSteps; step++) {
if (stepType[step] == CustomIntegrator::BeginIfBlock || stepType[step] == CustomIntegrator::BeginWhileBlock)
if (stepType[step] == CustomIntegrator::IfBlockStart || stepType[step] == CustomIntegrator::WhileBlockStart)
blockStart.push_back(step);
else if (stepType[step] == CustomIntegrator::EndBlock) {
else if (stepType[step] == CustomIntegrator::BlockEnd) {
if (blockStart.size() == 0) {
stringstream error("CustomIntegrator: Unexpected end of block at computation ");
error << step;
......@@ -207,7 +207,7 @@ void CustomIntegratorUtilities::enumeratePaths(int firstStep, vector<int> steps,
jumps[step] = -1;
step = nextStep;
}
else if (stepType[step] == CustomIntegrator::BeginIfBlock) {
else if (stepType[step] == CustomIntegrator::IfBlockStart) {
// Consider skipping the block.
enumeratePaths(blockEnd[step]+1, steps, jumps, blockEnd, stepType, needsForces, needsEnergy, invalidatesForces, forceGroup, computeBoth);
......@@ -216,7 +216,7 @@ void CustomIntegratorUtilities::enumeratePaths(int firstStep, vector<int> steps,
step++;
}
else if (stepType[step] == CustomIntegrator::BeginWhileBlock && jumps[step] != -2) {
else if (stepType[step] == CustomIntegrator::WhileBlockStart && jumps[step] != -2) {
// Consider skipping the block.
enumeratePaths(blockEnd[step]+1, steps, jumps, blockEnd, stepType, needsForces, needsEnergy, invalidatesForces, forceGroup, computeBoth);
......
openmmapi/src/CustomNonbondedForce.cpp
View file @ dca54ec7
......@@ -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) 2008-2014 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -195,6 +195,9 @@ void CustomNonbondedForce::setExclusionParticles(int index, int particle1, int p
void CustomNonbondedForce::createExclusionsFromBonds(const vector<pair<int, int> >& bonds, int bondCutoff) {
if (bondCutoff < 1)
return;
for (int i = 0; i < (int) bonds.size(); ++i)
if (bonds[i].first < 0 || bonds[i].second < 0 || bonds[i].first >= particles.size() || bonds[i].second >= particles.size())
throw OpenMMException("createExclusionsFromBonds: Illegal particle index in list of bonds");
vector<set<int> > exclusions(particles.size());
vector<set<int> > bonded12(exclusions.size());
for (int i = 0; i < (int) bonds.size(); ++i) {
......
openmmapi/src/CustomTorsionForce.cpp
View file @ dca54ec7
......@@ -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) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -44,7 +44,7 @@ using std::string;
using std::stringstream;
using std::vector;
CustomTorsionForce::CustomTorsionForce(const string& energy) : energyExpression(energy) {
CustomTorsionForce::CustomTorsionForce(const string& energy) : energyExpression(energy), usePeriodic(false) {
}
const string& CustomTorsionForce::getEnergyFunction() const {
......@@ -125,3 +125,11 @@ ForceImpl* CustomTorsionForce::createImpl() const {
void CustomTorsionForce::updateParametersInContext(Context& context) {
dynamic_cast<CustomTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void CustomTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool CustomTorsionForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
openmmapi/src/HarmonicAngleForce.cpp
View file @ dca54ec7
......@@ -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) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -37,7 +37,7 @@
using namespace OpenMM;
HarmonicAngleForce::HarmonicAngleForce() {
HarmonicAngleForce::HarmonicAngleForce() : usePeriodic(false) {
}
int HarmonicAngleForce::addAngle(int particle1, int particle2, int particle3, double angle, double k) {
......@@ -70,3 +70,11 @@ ForceImpl* HarmonicAngleForce::createImpl() const {
void HarmonicAngleForce::updateParametersInContext(Context& context) {
dynamic_cast<HarmonicAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void HarmonicAngleForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool HarmonicAngleForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
openmmapi/src/HarmonicBondForce.cpp
View file @ dca54ec7
......@@ -37,7 +37,7 @@
using namespace OpenMM;
HarmonicBondForce::HarmonicBondForce() {
HarmonicBondForce::HarmonicBondForce() : usePeriodic(false) {
}
int HarmonicBondForce::addBond(int particle1, int particle2, double length, double k) {
......@@ -68,3 +68,11 @@ ForceImpl* HarmonicBondForce::createImpl() const {
void HarmonicBondForce::updateParametersInContext(Context& context) {
dynamic_cast<HarmonicBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void HarmonicBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool HarmonicBondForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
openmmapi/src/LocalEnergyMinimizer.cpp
View file @ dca54ec7
......@@ -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) 2010-2012 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -36,6 +36,7 @@
#include <cmath>
#include <sstream>
#include <vector>
#include <algorithm>
using namespace OpenMM;
using namespace std;
......@@ -108,7 +109,8 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
if (x == NULL)
throw OpenMMException("LocalEnergyMinimizer: Failed to allocate memory");
double constraintTol = context.getIntegrator().getConstraintTolerance();
double k = tolerance/constraintTol;
double workingConstraintTol = std::max(1e-4, constraintTol);
double k = tolerance/workingConstraintTol;
// Initialize the minimizer.
......@@ -121,7 +123,7 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
// Make sure the initial configuration satisfies all constraints.
context.applyConstraints(constraintTol);
context.applyConstraints(workingConstraintTol);
// Record the initial positions and determine a normalization constant for scaling the tolerance.
......@@ -162,14 +164,14 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
if (error > maxError)
maxError = error;
}
if (maxError <= constraintTol)
if (maxError <= workingConstraintTol)
break; // All constraints are satisfied.
context.setPositions(initialPos);
if (maxError >= prevMaxError)
break; // Further tightening the springs doesn't seem to be helping, so just give up.
prevMaxError = maxError;
k *= 10;
if (maxError > 100*constraintTol) {
if (maxError > 100*workingConstraintTol) {
// We've gotten far enough from a valid state that we might have trouble getting
// back, so reset to the original positions.
......@@ -181,5 +183,11 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
}
}
lbfgs_free(x);
// If necessary, do a final constraint projection to make sure they are satisfied
// to the full precision requested by the user.
if (constraintTol < workingConstraintTol)
context.applyConstraints(workingConstraintTol);
}
openmmapi/src/MonteCarloAnisotropicBarostat.cpp
View file @ dca54ec7
......@@ -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) 2010 Stanford University and the Authors. *
* Portions copyright (c) 2010-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -34,8 +34,8 @@
using namespace OpenMM;
MonteCarloAnisotropicBarostat::MonteCarloAnisotropicBarostat(const Vec3& defaultPressure, double temperature, bool scaleX, bool scaleY, bool scaleZ, int frequency) :
defaultPressure(defaultPressure), temperature(temperature), scaleX(scaleX), scaleY(scaleY), scaleZ(scaleZ), frequency(frequency) {
MonteCarloAnisotropicBarostat::MonteCarloAnisotropicBarostat(const Vec3& defaultPressure, double defaultTemperature, bool scaleX, bool scaleY, bool scaleZ, int frequency) :
defaultPressure(defaultPressure), defaultTemperature(defaultTemperature), scaleX(scaleX), scaleY(scaleY), scaleZ(scaleZ), frequency(frequency) {
setRandomNumberSeed(0);
}
......
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