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Commit 61d5cc0f authored by Peter's avatar Peter
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Merge branch 'master' into applecl

parents e2999354 afae4bc8
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openmmapi/include/openmm/GBSAOBCForce.h
View file @ 61d5cc0f
......@@ -138,6 +138,18 @@ public:
void setSoluteDielectric(double dielectric) {
soluteDielectric = dielectric;
}
/**
* Get the energy scale for the surface energy term, measured in kJ/mol/nm^2.
*/
double getSurfaceAreaEnergy() const {
return surfaceAreaEnergy;
}
/**
* Set the energy scale for the surface energy term, measured in kJ/mol/nm^2.
*/
void setSurfaceAreaEnergy(double energy) {
surfaceAreaEnergy = energy;
}
/**
* Get the method used for handling long range nonbonded interactions.
*/
......@@ -164,7 +176,7 @@ public:
* Update the particle parameters in a Context to match those stored in this Force object. This method
* provides an efficient method to update certain parameters in an existing Context without needing to
* reinitialize it. Simply call setParticleParameters() to modify this object's parameters, then call
* updateParametersInState() to copy them over to the Context.
* updateParametersInContext() to copy them over to the Context.
*
* The only information this method updates is the values of per-particle parameters. All other aspects
* of the Force (the nonbonded method, the cutoff distance, etc.) are unaffected and can only be changed
......@@ -172,12 +184,21 @@ public:
* change the parameters of existing ones.
*/
void updateParametersInContext(Context& context);
/**
* 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 nonbondedMethod == GBSAOBCForce::CutoffPeriodic;
}
protected:
ForceImpl* createImpl() const;
private:
class ParticleInfo;
NonbondedMethod nonbondedMethod;
double cutoffDistance, solventDielectric, soluteDielectric;
double cutoffDistance, solventDielectric, soluteDielectric, surfaceAreaEnergy;
std::vector<ParticleInfo> particles;
};
......
openmmapi/include/openmm/GBVIForce.h
View file @ 61d5cc0f
......@@ -157,7 +157,7 @@ public:
*
* @return number of bonds
*/
int getNumBonds( void ) const;
int getNumBonds() const;
/**
* Get the dielectric constant for the solvent.
......@@ -208,7 +208,7 @@ public:
/**
* Get Born radius scaling method
*/
BornRadiusScalingMethod getBornRadiusScalingMethod( void ) const;
BornRadiusScalingMethod getBornRadiusScalingMethod() const;
/**
* Set Born radius scaling method
*/
......@@ -216,7 +216,7 @@ public:
/**
* Get the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)
*/
double getQuinticLowerLimitFactor( void ) const;
double getQuinticLowerLimitFactor() const;
/**
* Set the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)
*/
......@@ -224,11 +224,20 @@ public:
/**
* Get the upper limit used in the quintic spline scaling method, measured in nm (~5.0)
*/
double getQuinticUpperBornRadiusLimit( void ) const;
double getQuinticUpperBornRadiusLimit() const;
/**
* Set the upper limit used in the quintic spline scaling method, measured in nm (~5.0)
*/
void setQuinticUpperBornRadiusLimit(double quinticUpperBornRadiusLimit);
/**
* 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 nonbondedMethod == GBVIForce::CutoffPeriodic;
}
protected:
ForceImpl* createImpl() const;
private:
......
openmmapi/include/openmm/HarmonicAngleForce.h
View file @ 61d5cc0f
......@@ -95,13 +95,22 @@ public:
/**
* Update the per-angle parameters in a Context to match those stored in this Force object. This method provides
* an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
* Simply call setAngleParameters() to modify this object's parameters, then call updateParametersInState()
* Simply call setAngleParameters() to modify this object's parameters, then call updateParametersInContext()
* to copy them over to the Context.
*
* The only information this method updates is the values of per-angle parameters. The set of particles involved
* in a angle cannot be changed, nor can new angles be added.
*/
void updateParametersInContext(Context& context);
/**
* 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;
}
protected:
ForceImpl* createImpl() const;
private:
......
openmmapi/include/openmm/HarmonicBondForce.h
View file @ 61d5cc0f
......@@ -92,13 +92,22 @@ public:
/**
* Update the per-bond parameters in a Context to match those stored in this Force object. This method provides
* an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
* Simply call setBondParameters() to modify this object's parameters, then call updateParametersInState()
* Simply call setBondParameters() to modify this object's parameters, then call updateParametersInContext()
* to copy them over to the Context.
*
* The only information this method updates is the values of per-bond parameters. The set of particles involved
* in a bond cannot be changed, nor can new bonds be added.
*/
void updateParametersInContext(Context& context);
/**
* 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;
}
protected:
ForceImpl* createImpl() const;
private:
......
openmmapi/include/openmm/LangevinIntegrator.h
View file @ 61d5cc0f
......@@ -49,7 +49,7 @@ public:
*
* @param temperature the temperature of the heat bath (in Kelvin)
* @param frictionCoeff the friction coefficient which couples the system to the heat bath (in inverse picoseconds)
* @param stepSize the step size with which to integrator the system (in picoseconds)
* @param stepSize the step size with which to integrate the system (in picoseconds)
*/
LangevinIntegrator(double temperature, double frictionCoeff, double stepSize);
/**
......@@ -99,6 +99,10 @@ public:
* the other hand, no guarantees are made about the behavior of simulations that use the same seed.
* In particular, Platforms are permitted to use non-deterministic algorithms which produce different
* results on successive runs, even if those runs were initialized identically.
*
* If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
* is created from this Force. This is done to ensure that each Context receives unique random seeds
* without you needing to set them explicitly.
*/
void setRandomNumberSeed(int seed) {
randomNumberSeed = seed;
......
openmmapi/include/openmm/MonteCarloAnisotropicBarostat.h
View file @ 61d5cc0f
......@@ -167,10 +167,23 @@ public:
* the other hand, no guarantees are made about the behavior of simulations that use the same seed.
* In particular, Platforms are permitted to use non-deterministic algorithms which produce different
* results on successive runs, even if those runs were initialized identically.
*
* If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
* is created from this Force. This is done to ensure that each Context receives unique random seeds
* without you needing to set them explicitly.
*/
void setRandomNumberSeed(int seed) {
randomNumberSeed = seed;
}
/**
* 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 true;
}
protected:
ForceImpl* createImpl() const;
private:
......
openmmapi/include/openmm/MonteCarloBarostat.h
View file @ 61d5cc0f
......@@ -123,10 +123,23 @@ public:
* the other hand, no guarantees are made about the behavior of simulations that use the same seed.
* In particular, Platforms are permitted to use non-deterministic algorithms which produce different
* results on successive runs, even if those runs were initialized identically.
*
* If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
* is created from this Force. This is done to ensure that each Context receives unique random seeds
* without you needing to set them explicitly.
*/
void setRandomNumberSeed(int seed) {
randomNumberSeed = seed;
}
/**
* 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 true;
}
protected:
ForceImpl* createImpl() const;
private:
......
openmmapi/include/openmm/MonteCarloMembraneBarostat.h 0 → 100644
View file @ 61d5cc0f
#ifndef OPENMM_MONTECARLOMEMBRANEBAROSTAT_H_
#define OPENMM_MONTECARLOMEMBRANEBAROSTAT_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) 2010-2014 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. *
* -------------------------------------------------------------------------- */
#include "Force.h"
#include <string>
#include "internal/windowsExport.h"
namespace OpenMM {
/**
* This is a Monte Carlo barostat designed specifically for membrane simulations. It assumes the
* membrane lies in the XY plane. The Monte Carlo acceptance criterion includes a term to model
* isotropic pressure, which depends on the volume of the periodic box, and a second term to model
* surface tension, which depends on the cross sectional area of the box in the XY plane. Note
* that pressure and surface tension are defined with opposite senses: a larger pressure tends to
* make the box smaller, but a larger surface tension tends to make the box larger.
*
* There are options for configuring exactly how the various box dimensions are allowed to change:
*
* <ul>
* <li>The X and Y axes may be treated isotropically, in which case they always scale by the same
* amount and remain in proportion to each other; or they may be treated anisotropically, in which
* case they can vary independently of each other.</li>
* <li>The Z axis can be allowed to vary independently of the other axes; or held fixed; or constrained
* to vary in inverse proportion to the other two axes, so that the total box volume remains fixed.</li>
* </ul>
*
* This class assumes the simulation is also being run at constant temperature, and requires you
* to specify the system temperature (since it affects the acceptance probability for Monte Carlo
* moves). It does not actually perform temperature regulation, however. You must use another
* mechanism along with it to maintain the temperature, such as LangevinIntegrator or AndersenThermostat.
*/
class OPENMM_EXPORT MonteCarloMembraneBarostat : public Force {
public:
/**
* This is an enumeration of the different behaviors for the X and Y axes.
*/
enum XYMode {
/**
* The X and Y axes are always scaled by the same amount, so the ratio of their lengths remains constant.
*/
XYIsotropic = 0,
/**
* The X and Y axes are allowed to vary independently of each other.
*/
XYAnisotropic = 1
};
/**
* This is an enumeration of the different behaviors for Z axis.
*/
enum ZMode {
/**
* The Z axis is allowed to vary freely, independent of the other two axes.
*/
ZFree = 0,
/**
* The Z axis is held fixed and does not change.
*/
ZFixed = 1,
/**
* The Z axis is always scaled in inverse proportion to the other two axes so the box volume remains
* fixed. Note that in this mode pressure has no effect on the system, only surface tension.
*/
ConstantVolume = 2
};
/**
* This is the name of the parameter which stores the current pressure acting on
* the system (in bar).
*/
static const std::string& Pressure() {
static const std::string key = "MembraneMonteCarloPressure";
return key;
}
/**
* This is the name of the parameter which stores the current surface tension acting on
* the system (in bar*nm).
*/
static const std::string& SurfaceTension() {
static const std::string key = "MembraneMonteCarloSurfaceTension";
return key;
}
/**
* Create a MonteCarloMembraneBarostat.
*
* @param defaultPressure the default pressure acting on the system (in bar)
* @param defaultSurfaceTension the default surface tension acting on the system (in bar*nm)
* @param temperature the temperature at which the system is being maintained (in Kelvin)
* @param xymode the mode specifying the behavior of the X and Y axes
* @param zmode the mode specifying the behavior of the Z axis
* @param frequency the frequency at which Monte Carlo volume changes should be attempted (in time steps)
*/
MonteCarloMembraneBarostat(double defaultPressure, double defaultSurfaceTension, double temperature, XYMode xymode, ZMode zmode, int frequency = 25);
/**
* Get the default pressure acting on the system (in bar).
*
* @return the default pressure acting on the system, measured in bar.
*/
double getDefaultPressure() const {
return defaultPressure;
}
/**
* Set the default pressure acting on the system. This will affect any new Contexts you create,
* but not ones that already exist.
*
* @param pressure the default pressure acting on the system, measured in bar.
*/
void setDefaultPressure(double pressure) {
defaultPressure = pressure;
}
/**
* Get the default surface tension acting on the system (in bar*nm).
*
* @return the default surface tension acting on the system, measured in bar*nm.
*/
double getDefaultSurfaceTension() const {
return defaultSurfaceTension;
}
/**
* Set the default surface tension acting on the system. This will affect any new Contexts you create,
* but not ones that already exist.
*
* @param surfaceTension the default surface tension acting on the system, measured in bar.
*/
void setDefaultSurfaceTension(double surfaceTension) {
defaultSurfaceTension = surfaceTension;
}
/**
* Get the frequency (in time steps) at which Monte Carlo volume changes should be attempted. If this is set to
* 0, the barostat is disabled.
*/
int getFrequency() const {
return frequency;
}
/**
* Set the frequency (in time steps) at which Monte Carlo volume changes should be attempted. If this is set to
* 0, the barostat is disabled.
*/
void setFrequency(int freq) {
frequency = freq;
}
/**
* Get the temperature at which the system is being maintained, measured in Kelvin.
*/
double getTemperature() const {
return temperature;
}
/**
* Set the temperature at which the system is being maintained.
*
* @param temp the system temperature, measured in Kelvin.
*/
void setTemperature(double temp) {
temperature = temp;
}
/**
* Get the mode specifying the behavior of the X and Y axes.
*/
XYMode getXYMode() const {
return xymode;
}
/**
* Set the mode specifying the behavior of the X and Y axes.
*/
void setXYMode(XYMode mode) {
xymode = mode;
}
/**
* Get the mode specifying the behavior of the Z axis.
*/
ZMode getZMode() const {
return zmode;
}
/**
* Set the mode specifying the behavior of the Z axis.
*/
void setZMode(ZMode mode) {
zmode = mode;
}
/**
* Get the random number seed. See setRandomNumberSeed() for details.
*/
int getRandomNumberSeed() const {
return randomNumberSeed;
}
/**
* Set the random number seed. It is guaranteed that if two simulations are run
* with different random number seeds, the sequence of Monte Carlo steps will be different. On
* the other hand, no guarantees are made about the behavior of simulations that use the same seed.
* In particular, Platforms are permitted to use non-deterministic algorithms which produce different
* results on successive runs, even if those runs were initialized identically.
*
* If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
* is created from this Force. This is done to ensure that each Context receives unique random seeds
* without you needing to set them explicitly.
*/
void setRandomNumberSeed(int seed) {
randomNumberSeed = seed;
}
/**
* 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 true;
}
protected:
ForceImpl* createImpl() const;
private:
double defaultPressure, defaultSurfaceTension, temperature;
XYMode xymode;
ZMode zmode;
int frequency, randomNumberSeed;
};
} // namespace OpenMM
#endif /*OPENMM_MONTECARLOMEMBRANEBAROSTAT_H_*/
openmmapi/include/openmm/NonbondedForce.h
View file @ 61d5cc0f
......@@ -343,7 +343,7 @@ public:
* Update the particle and exception parameters in a Context to match those stored in this Force object. This method
* provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
* Simply call setParticleParameters() and setExceptionParameters() to modify this object's parameters, then call
* updateParametersInState() to copy them over to the Context.
* updateParametersInContext() to copy them over to the Context.
*
* This method has several limitations. The only information it updates is the parameters of particles and exceptions.
* All other aspects of the Force (the nonbonded method, the cutoff distance, etc.) are unaffected and can only be
......@@ -352,6 +352,17 @@ public:
* to add new particles or exceptions, only to change the parameters of existing ones.
*/
void updateParametersInContext(Context& context);
/**
* 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 nonbondedMethod == NonbondedForce::CutoffPeriodic ||
nonbondedMethod == NonbondedForce::Ewald ||
nonbondedMethod == NonbondedForce::PME;
}
protected:
ForceImpl* createImpl() const;
private:
......
openmmapi/include/openmm/PeriodicTorsionForce.h
View file @ 61d5cc0f
......@@ -101,13 +101,22 @@ public:
/**
* Update the per-torsion parameters in a Context to match those stored in this Force object. This method provides
* an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
* Simply call setTorsionParameters() to modify this object's parameters, then call updateParametersInState()
* Simply call setTorsionParameters() to modify this object's parameters, then call updateParametersInContext()
* to copy them over to the Context.
*
* The only information this method updates is the values of per-torsion parameters. The set of particles involved
* in a torsion cannot be changed, nor can new torsions be added.
*/
void updateParametersInContext(Context& context);
/**
* 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;
}
protected:
ForceImpl* createImpl() const;
private:
......
openmmapi/include/openmm/RBTorsionForce.h
View file @ 61d5cc0f
......@@ -110,13 +110,22 @@ public:
/**
* Update the per-torsion parameters in a Context to match those stored in this Force object. This method provides
* an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
* Simply call setTorsionParameters() to modify this object's parameters, then call updateParametersInState()
* Simply call setTorsionParameters() to modify this object's parameters, then call updateParametersInContext()
* to copy them over to the Context.
*
* The only information this method updates is the values of per-torsion parameters. The set of particles involved
* in a torsion cannot be changed, nor can new torsions be added.
*/
void updateParametersInContext(Context& context);
/**
* 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;
}
protected:
ForceImpl* createImpl() const;
private:
......
openmmapi/include/openmm/State.h
View file @ 61d5cc0f
......@@ -108,6 +108,10 @@ public:
* Get a map containing the values of all parameters. If this State does not contain parameters, this will throw an exception.
*/
const std::map<std::string, double>& getParameters() const;
/**
* Get which data types are stored in this State. The return value is a sum of DataType flags.
*/
int getDataTypes() const;
private:
State(double time);
void setPositions(const std::vector<Vec3>& pos);
......
openmmapi/include/openmm/System.h
View file @ 61d5cc0f
......@@ -168,6 +168,12 @@ public:
* @param distance the required distance between the two particles, measured in nm
*/
void setConstraintParameters(int index, int particle1, int particle2, double distance);
/**
* Remove a constraint from the System.
*
* @param index the index of the constraint to remove
*/
void removeConstraint(int index);
/**
* Add a Force to the System. The Force should have been created on the heap with the
* "new" operator. The System takes over ownership of it, and deletes the Force when the
......@@ -198,14 +204,18 @@ public:
* @param index the index of the Force to get
*/
Force& getForce(int index);
/**
* Remove a Force from the System. The memory associated with the removed Force
* object is deleted.
*
* @param index the index of the Force to remove
*/
void removeForce(int index);
/**
* Get the default values of the vectors defining the axes of the periodic box (measured in nm). Any newly
* created Context will have its box vectors set to these. They will affect
* any Force added to the System that uses periodic boundary conditions.
*
* Currently, only rectangular boxes are supported. This means that a, b, and c must be aligned with the
* x, y, and z axes respectively. Future releases may support arbitrary triclinic boxes.
*
* @param a on exit, this contains the vector defining the first edge of the periodic box
* @param b on exit, this contains the vector defining the second edge of the periodic box
* @param c on exit, this contains the vector defining the third edge of the periodic box
......@@ -216,14 +226,24 @@ public:
* created Context will have its box vectors set to these. They will affect
* any Force added to the System that uses periodic boundary conditions.
*
* Currently, only rectangular boxes are supported. This means that a, b, and c must be aligned with the
* x, y, and z axes respectively. Future releases may support arbitrary triclinic boxes.
* Triclinic boxes are supported, but the vectors must satisfy certain requirements. In particular,
* a must point in the x direction, b must point "mostly" in the y direction, and c must point "mostly"
* in the z direction. See the documentation for details.
*
* @param a the vector defining the first edge of the periodic box
* @param b the vector defining the second edge of the periodic box
* @param c the vector defining the third edge of the periodic box
*/
void setDefaultPeriodicBoxVectors(const Vec3& a, const Vec3& b, const Vec3& c);
/**
* Returns whether or not any forces in this System use periodic boundaries.
*
* If a force in this System does not implement usesPeriodicBoundaryConditions
* a OpenMM::OpenMMException is thrown
*
* @return true if at least one force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions();
private:
class ConstraintInfo;
Vec3 periodicBoxVectors[3];
......
openmmapi/include/openmm/VariableLangevinIntegrator.h
View file @ 61d5cc0f
......@@ -121,6 +121,10 @@ public:
* the other hand, no guarantees are made about the behavior of simulations that use the same seed.
* In particular, Platforms are permitted to use non-deterministic algorithms which produce different
* results on successive runs, even if those runs were initialized identically.
*
* If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
* is created from this Force. This is done to ensure that each Context receives unique random seeds
* without you needing to set them explicitly.
*/
void setRandomNumberSeed(int seed) {
randomNumberSeed = seed;
......
openmmapi/include/openmm/VerletIntegrator.h
View file @ 61d5cc0f
......@@ -47,7 +47,7 @@ public:
/**
* Create a VerletIntegrator.
*
* @param stepSize the step size with which to integrator the system (in picoseconds)
* @param stepSize the step size with which to integrate the system (in picoseconds)
*/
explicit VerletIntegrator(double stepSize);
/**
......
openmmapi/include/openmm/internal/CMAPTorsionForceImpl.h
View file @ 61d5cc0f
......@@ -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: *
* *
......@@ -60,6 +60,7 @@ public:
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
std::vector<std::string> getKernelNames();
void updateParametersInContext(ContextImpl& context);
/**
* Given the energy values for a map, compute the spline coefficients at each point of the map.
*/
......
openmmapi/include/openmm/internal/ContextImpl.h
View file @ 61d5cc0f
......@@ -142,9 +142,6 @@ public:
* Get the vectors defining the axes of the periodic box (measured in nm). They will affect
* any Force that uses periodic boundary conditions.
*
* Currently, only rectangular boxes are supported. This means that a, b, and c must be aligned with the
* x, y, and z axes respectively. Future releases may support arbitrary triclinic boxes.
*
* @param a the vector defining the first edge of the periodic box
* @param b the vector defining the second edge of the periodic box
* @param c the vector defining the third edge of the periodic box
......@@ -154,8 +151,9 @@ public:
* Set the vectors defining the axes of the periodic box (measured in nm). They will affect
* any Force that uses periodic boundary conditions.
*
* Currently, only rectangular boxes are supported. This means that a, b, and c must be aligned with the
* x, y, and z axes respectively. Future releases may support arbitrary triclinic boxes.
* Triclinic boxes are supported, but the vectors must satisfy certain requirements. In particular,
* a must point in the x direction, b must point "mostly" in the y direction, and c must point "mostly"
* in the z direction. See the documentation for details.
*
* @param a the vector defining the first edge of the periodic box
* @param b the vector defining the second edge of the periodic box
......
openmmapi/include/openmm/internal/MonteCarloMembraneBarostatImpl.h 0 → 100644
View file @ 61d5cc0f
#ifndef OPENMM_MONTECARLOMEMBRANEBAROSTATIMPL_H_
#define OPENMM_MONTECARLOMEMBRANEBAROSTATIMPL_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) 2010-2014 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. *
* -------------------------------------------------------------------------- */
#include "ForceImpl.h"
#include "openmm/MonteCarloMembraneBarostat.h"
#include "openmm/Kernel.h"
#include "sfmt/SFMT.h"
#include <string>
namespace OpenMM {
/**
* This is the internal implementation of MonteCarloMembraneBarostat.
*/
class MonteCarloMembraneBarostatImpl : public ForceImpl {
public:
MonteCarloMembraneBarostatImpl(const MonteCarloMembraneBarostat& owner);
void initialize(ContextImpl& context);
const MonteCarloMembraneBarostat& getOwner() const {
return owner;
}
void updateContextState(ContextImpl& context);
double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
// This force doesn't apply forces to particles.
return 0.0;
}
std::map<std::string, double> getDefaultParameters();
std::vector<std::string> getKernelNames();
private:
const MonteCarloMembraneBarostat& owner;
int step, numAttempted[3], numAccepted[3];
double volumeScale[3];
OpenMM_SFMT::SFMT random;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_MONTECARLOMEMBRANEBAROSTATIMPL_H_*/
openmmapi/include/openmm/internal/vectorize8.h
View file @ 61d5cc0f
......@@ -191,6 +191,18 @@ static inline fvec8 sqrt(const fvec8& v) {
return fvec8(_mm256_sqrt_ps(v.val));
}
static inline fvec8 rsqrt(const fvec8& v) {
// Initial estimate of rsqrt().
fvec8 y(_mm256_rsqrt_ps(v.val));
// Perform an iteration of Newton refinement.
fvec8 x2 = v*0.5f;
y *= fvec8(1.5f)-x2*y*y;
return y;
}
static inline float dot8(const fvec8& v1, const fvec8& v2) {
fvec8 result = _mm256_dp_ps(v1, v2, 0xF1);
return _mm_cvtss_f32(result.lowerVec())+_mm_cvtss_f32(result.upperVec());
......
openmmapi/include/openmm/internal/vectorize_neon.h
View file @ 61d5cc0f
......@@ -251,11 +251,15 @@ static inline fvec4 abs(const fvec4& v) {
return vabsq_f32(v);
}
static inline fvec4 sqrt(const fvec4& v) {
static inline fvec4 rsqrt(const fvec4& v) {
float32x4_t recipSqrt = vrsqrteq_f32(v);
recipSqrt = vmulq_f32(recipSqrt, vrsqrtsq_f32(vmulq_f32(recipSqrt, v), recipSqrt));
recipSqrt = vmulq_f32(recipSqrt, vrsqrtsq_f32(vmulq_f32(recipSqrt, v), recipSqrt));
return vmulq_f32(v, recipSqrt);
return recipSqrt;
}
static inline fvec4 sqrt(const fvec4& v) {
return rsqrt(v)*v;
}
static inline float dot3(const fvec4& v1, const fvec4& v2) {
......
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