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Commit 51b7f9e2 authored by Robert McGibbon's avatar Robert McGibbon
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openmmapi/include/openmm/GBSAOBCForce.h
View file @ 51b7f9e2
......@@ -40,14 +40,14 @@ namespace OpenMM {
/**
* This class implements an implicit solvation force using the GBSA-OBC model.
*
*
* To use this class, create a GBSAOBCForce object, then call addParticle() once for each particle in the
* System to define its parameters. The number of particles for which you define GBSA parameters must
* be exactly equal to the number of particles in the System, or else an exception will be thrown when you
* try to create a Context. After a particle has been added, you can modify its force field parameters
* by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you
* call updateParametersInContext().
*
*
* When using this Force, the System should also include a NonbondedForce, and both objects must specify
* identical charges for all particles. Otherwise, the results will not be correct. Furthermore, if the
* nonbonded method is set to CutoffNonPeriodic or CutoffPeriodic, you should call setReactionFieldDielectric(1.0)
......@@ -98,16 +98,16 @@ public:
int addParticle(double charge, double radius, double scalingFactor);
/**
* Get the force field parameters for a particle.
*
* @param index the index of the particle for which to get parameters
* @param charge the charge of the particle, measured in units of the proton charge
* @param radius the GBSA radius of the particle, measured in nm
* @param scalingFactor the OBC scaling factor for the particle
*
* @param index the index of the particle for which to get parameters
* @param[out] charge the charge of the particle, measured in units of the proton charge
* @param[out] radius the GBSA radius of the particle, measured in nm
* @param[out] scalingFactor the OBC scaling factor for the particle
*/
void getParticleParameters(int index, double& charge, double& radius, double& scalingFactor) const;
/**
* Set the force field parameters for a particle.
*
*
* @param index the index of the particle for which to set parameters
* @param charge the charge of the particle, measured in units of the proton charge
* @param radius the GBSA radius of the particle, measured in nm
......@@ -177,7 +177,7 @@ public:
* 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
* 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
* by reinitializing the Context. Furthermore, this method cannot be used to add new particles, only to
......
openmmapi/include/openmm/GBVIForce.h
View file @ 51b7f9e2
......@@ -46,13 +46,13 @@ namespace OpenMM {
* be exactly equal to the number of particles in the System, or else an exception will be thrown when you
* try to create a Context. After a particle has been added, you can modify its force field parameters
* by calling setParticleParameters().
*
*
* @deprecated This class is not supported by most platforms, and will eventually be removed. You can implement the same force with CustomGBForce.
*/
class OPENMM_EXPORT GBVIForce : public Force {
public:
/**
/**
* This is an enumeration of the different methods that may be used for handling long range nonbonded forces.
*/
enum NonbondedMethod {
......@@ -70,9 +70,9 @@ public:
* each other particle. Interactions beyond the cutoff distance are ignored.
*/
CutoffPeriodic = 2,
};
};
/**
/**
* This is an enumeration of the different methods that may be used for scaling of the Born radii.
*/
enum BornRadiusScalingMethod {
......@@ -84,7 +84,7 @@ public:
* Use quintic spline scaling function
*/
QuinticSpline = 1
};
};
/*
* Create a GBVIForce.
......@@ -108,16 +108,16 @@ public:
int addParticle(double charge, double radius, double gamma);
/**
* Get the force field parameters for a particle.
*
* @param index the index of the particle for which to get parameters
* @param charge the charge of the particle, measured in units of the proton charge
* @param radius the GBSA radius of the particle, measured in nm
* @param gamma the gamma parameter
*
* @param index the index of the particle for which to get parameters
* @param[out] charge the charge of the particle, measured in units of the proton charge
* @param[out] radius the GBSA radius of the particle, measured in nm
* @param[out] gamma the gamma parameter
*/
void getParticleParameters(int index, double& charge, double& radius, double& gamma) const;
/**
* Set the force field parameters for a particle.
*
*
* @param index the index of the particle for which to set parameters
* @param charge the charge of the particle, measured in units of the proton charge
* @param radius the GB/VI radius of the particle, measured in nm
......@@ -125,36 +125,36 @@ public:
*/
void setParticleParameters(int index, double charge, double radius, double gamma);
/**
* Add a bond
* Add a bond
*
* @param particle1 the index of the first particle
* @param particle1 the index of the first particle
* @param particle2 the index of the second particle
* @param distance the distance between the two particles, measured in nm
* @return the index of the bond that was added
*/
int addBond(int particle1, int particle2, double distance);
/**
/**
* Get the parameters defining a bond
*
* @param index the index of the bond for which to get parameters
* @param particle1 the index of the first particle involved in the bond
* @param particle2 the index of the second particle involved in the bond
* @param distance the distance between the two particles, measured in nm
*
* @param index the index of the bond for which to get parameters
* @param[out] particle1 the index of the first particle involved in the bond
* @param[out] particle2 the index of the second particle involved in the bond
* @param[out] distance the distance between the two particles, measured in nm
*/
void getBondParameters(int index, int& particle1, int& particle2, double& distance) const;
/**
* Set 1-2 bonds
*
*
* @param index index of the bond for which to set parameters
* @param particle1 index of first atom in bond
* @param particle2 index of second atom in bond
* @param bondLength bond length, measured in nm
*/
void setBondParameters( int index, int particle1, int particle2, double bondLength);
/**
/**
* Get number of bonds
*
*
* @return number of bonds
*/
int getNumBonds() const;
......@@ -183,49 +183,49 @@ public:
void setSoluteDielectric(double dielectric) {
soluteDielectric = dielectric;
}
/**
/**
* Get the method used for handling long range nonbonded interactions.
*/
NonbondedMethod getNonbondedMethod() const;
/**
/**
* Set the method used for handling long range nonbonded interactions.
*/
void setNonbondedMethod(NonbondedMethod method);
/**
/**
* Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* is NoCutoff, this value will have no effect.
*
* @return the cutoff distance, measured in nm
*/
double getCutoffDistance() const;
/**
/**
* Set the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* is NoCutoff, this value will have no effect.
*
* @param distance the cutoff distance, measured in nm
*/
void setCutoffDistance(double distance);
/**
/**
* Get Born radius scaling method
*/
BornRadiusScalingMethod getBornRadiusScalingMethod() const;
/**
/**
* Set Born radius scaling method
*/
void setBornRadiusScalingMethod( BornRadiusScalingMethod method);
/**
/**
* Get the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)
*/
double getQuinticLowerLimitFactor() const;
/**
/**
* Set the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)
*/
void setQuinticLowerLimitFactor(double quinticLowerLimitFactor );
/**
/**
* Get the upper limit used in the quintic spline scaling method, measured in nm (~5.0)
*/
double getQuinticUpperBornRadiusLimit() const;
/**
/**
* Set the upper limit used in the quintic spline scaling method, measured in nm (~5.0)
*/
void setQuinticUpperBornRadiusLimit(double quinticUpperBornRadiusLimit);
......
openmmapi/include/openmm/HarmonicAngleForce.h
View file @ 51b7f9e2
......@@ -72,18 +72,18 @@ public:
int addAngle(int particle1, int particle2, int particle3, double angle, double k);
/**
* Get the force field parameters for an angle term.
*
* @param index the index of the angle for which to get parameters
* @param particle1 the index of the first particle forming the angle
* @param particle2 the index of the second particle forming the angle
* @param particle3 the index of the third particle forming the angle
* @param angle the equilibrium angle, measured in radians
* @param k the harmonic force constant for the angle, measured in kJ/mol/radian^2
*
* @param index the index of the angle for which to get parameters
* @param[out] particle1 the index of the first particle forming the angle
* @param[out] particle2 the index of the second particle forming the angle
* @param[out] particle3 the index of the third particle forming the angle
* @param[out] angle the equilibrium angle, measured in radians
* @param[out] k the harmonic force constant for the angle, measured in kJ/mol/radian^2
*/
void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, double& angle, double& k) const;
/**
* Set the force field parameters for an angle term.
*
*
* @param index the index of the angle for which to set parameters
* @param particle1 the index of the first particle forming the angle
* @param particle2 the index of the second particle forming the angle
......@@ -97,7 +97,7 @@ public:
* 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 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.
*/
......
openmmapi/include/openmm/HarmonicBondForce.h
View file @ 51b7f9e2
......@@ -71,17 +71,17 @@ public:
int addBond(int particle1, int particle2, double length, double k);
/**
* Get the force field parameters for a bond term.
*
* @param index the index of the bond for which to get parameters
* @param particle1 the index of the first particle connected by the bond
* @param particle2 the index of the second particle connected by the bond
* @param length the equilibrium length of the bond, measured in nm
* @param k the harmonic force constant for the bond, measured in kJ/mol/nm^2
*
* @param index the index of the bond for which to get parameters
* @param[out] particle1 the index of the first particle connected by the bond
* @param[out] particle2 the index of the second particle connected by the bond
* @param[out] length the equilibrium length of the bond, measured in nm
* @param[out] k the harmonic force constant for the bond, measured in kJ/mol/nm^2
*/
void getBondParameters(int index, int& particle1, int& particle2, double& length, double& k) const;
/**
* Set the force field parameters for a bond term.
*
*
* @param index the index of the bond for which to set parameters
* @param particle1 the index of the first particle connected by the bond
* @param particle2 the index of the second particle connected by the bond
......@@ -94,7 +94,7 @@ public:
* 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 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.
*/
......
openmmapi/include/openmm/Integrator.h
View file @ 51b7f9e2
......@@ -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) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -61,30 +61,22 @@ public:
*
* @return the step size, measured in ps
*/
double getStepSize() const {
return stepSize;
}
virtual double getStepSize() const;
/**
* Set the size of each time step, in picoseconds. If this integrator uses variable time steps,
* the effect of calling this method is undefined, and it may simply be ignored.
*
* @param size the step size, measured in ps
*/
void setStepSize(double size) {
stepSize = size;
}
virtual void setStepSize(double size);
/**
* Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
*/
double getConstraintTolerance() const {
return constraintTol;
}
virtual double getConstraintTolerance() const;
/**
* Set the distance tolerance within which constraints are maintained, as a fraction of the constrained distance.
*/
void setConstraintTolerance(double tol) {
constraintTol = tol;
}
virtual void setConstraintTolerance(double tol);
/**
* Advance a simulation through time by taking a series of time steps.
*
......@@ -94,6 +86,7 @@ public:
protected:
friend class Context;
friend class ContextImpl;
friend class CompoundIntegrator;
ContextImpl* context;
Context* owner;
/**
......
openmmapi/include/openmm/NonbondedForce.h
View file @ 51b7f9e2
......@@ -65,13 +65,13 @@ namespace OpenMM {
* This class provides a convenience method for this case called createExceptionsFromBonds(). You pass to it
* a list of bonds and the scale factors to use for 1-4 interactions. It identifies all pairs of particles which
* are separated by 1, 2, or 3 bonds, then automatically creates exceptions for them.
*
*
* When using a cutoff, by default Lennard-Jones interactions are sharply truncated at the cutoff distance.
* Optionally you can instead use a switching function to make the interaction smoothly go to zero over a finite
* distance range. To enable this, call setUseSwitchingFunction(). You must also call setSwitchingDistance()
* to specify the distance at which the interaction should begin to decrease. The switching distance must be
* less than the cutoff distance.
*
*
* Another optional feature of this class (enabled by default) is to add a contribution to the energy which approximates
* the effect of all Lennard-Jones interactions beyond the cutoff in a periodic system. When running a simulation
* at constant pressure, this can improve the quality of the result. Call setUseDispersionCorrection() to set whether
......@@ -182,7 +182,7 @@ public:
* which is acceptable. This value is used to select the reciprocal space cutoff and separation
* parameter so that the average error level will be less than the tolerance. There is not a
* rigorous guarantee that all forces on all atoms will be less than the tolerance, however.
*
*
* For PME calculations, if setPMEParameters() is used to set alpha to something other than 0,
* this value is ignored.
*/
......@@ -192,7 +192,7 @@ public:
* which is acceptable. This value is used to select the reciprocal space cutoff and separation
* parameter so that the average error level will be less than the tolerance. There is not a
* rigorous guarantee that all forces on all atoms will be less than the tolerance, however.
*
*
* For PME calculations, if setPMEParameters() is used to set alpha to something other than 0,
* this value is ignored.
*/
......@@ -200,17 +200,17 @@ public:
/**
* Get the parameters to use for PME calculations. If alpha is 0 (the default), these parameters are
* ignored and instead their values are chosen based on the Ewald error tolerance.
*
* @param alpha the separation parameter
* @param nx the number of grid points along the X axis
* @param ny the number of grid points along the Y axis
* @param nz the number of grid points along the Z axis
*
* @param[out] alpha the separation parameter
* @param[out] nx the number of grid points along the X axis
* @param[out] ny the number of grid points along the Y axis
* @param[out] nz the number of grid points along the Z axis
*/
void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
/**
* Set the parameters to use for PME calculations. If alpha is 0 (the default), these parameters are
* ignored and instead their values are chosen based on the Ewald error tolerance.
*
*
* @param alpha the separation parameter
* @param nx the number of grid points along the X axis
* @param ny the number of grid points along the Y axis
......@@ -222,12 +222,12 @@ public:
* on the allowed grid sizes, the values that are actually used may be slightly different from those
* specified with setPMEParameters(), or the standard values calculated based on the Ewald error tolerance.
* See the manual for details.
*
* @param context the Context for which to get the parameters
* @param alpha the separation parameter
* @param nx the number of grid points along the X axis
* @param ny the number of grid points along the Y axis
* @param nz the number of grid points along the Z axis
*
* @param context the Context for which to get the parameters
* @param[out] alpha the separation parameter
* @param[out] nx the number of grid points along the X axis
* @param[out] ny the number of grid points along the Y axis
* @param[out] nz the number of grid points along the Z axis
*/
void getPMEParametersInContext(const Context& context, double& alpha, int& nx, int& ny, int& nz) const;
/**
......@@ -246,10 +246,10 @@ public:
/**
* Get the nonbonded force parameters for a particle.
*
* @param index the index of the particle for which to get parameters
* @param charge the charge of the particle, measured in units of the proton charge
* @param sigma the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
* @param epsilon the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
* @param index the index of the particle for which to get parameters
* @param[out] charge the charge of the particle, measured in units of the proton charge
* @param[out] sigma the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
* @param[out] epsilon the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
*/
void getParticleParameters(int index, double& charge, double& sigma, double& epsilon) const;
/**
......@@ -282,20 +282,20 @@ public:
int addException(int particle1, int particle2, double chargeProd, double sigma, double epsilon, bool replace = false);
/**
* Get the force field parameters for an interaction that should be calculated differently from others.
*
* @param index the index of the interaction for which to get parameters
* @param particle1 the index of the first particle involved in the interaction
* @param particle2 the index of the second particle involved in the interaction
* @param chargeProd the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared
* @param sigma the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
* @param epsilon the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
*
* @param index the index of the interaction for which to get parameters
* @param[out] particle1 the index of the first particle involved in the interaction
* @param[out] particle2 the index of the second particle involved in the interaction
* @param[out] chargeProd the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared
* @param[out] sigma the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
* @param[out] epsilon the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
*/
void getExceptionParameters(int index, int& particle1, int& particle2, double& chargeProd, double& sigma, double& epsilon) const;
/**
* Set the force field parameters for an interaction that should be calculated differently from others.
* If chargeProd and epsilon are both equal to 0, this will cause the interaction to be completely omitted from
* force and energy calculations.
*
*
* @param index the index of the interaction for which to get parameters
* @param particle1 the index of the first particle involved in the interaction
* @param particle2 the index of the second particle involved in the interaction
......@@ -347,7 +347,7 @@ public:
* time step integrators to evaluate direct and reciprocal space interactions at different intervals: setForceGroup()
* specifies the group for direct space, and setReciprocalSpaceForceGroup() specifies the group for reciprocal space.
* If this is -1 (the default value), the same force group is used for reciprocal space as for direct space.
*
*
* @param group the group index. Legal values are between 0 and 31 (inclusive), or -1 to use the same force group
* that is specified for direct space.
*/
......@@ -357,7 +357,7 @@ public:
* 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
* 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
* changed by reinitializing the Context. Furthermore, only the chargeProd, sigma, and epsilon values of an exception
......
openmmapi/include/openmm/PeriodicTorsionForce.h
View file @ 51b7f9e2
......@@ -74,20 +74,20 @@ public:
int addTorsion(int particle1, int particle2, int particle3, int particle4, int periodicity, double phase, double k);
/**
* Get the force field parameters for a periodic torsion term.
*
* @param index the index of the torsion for which to get parameters
* @param particle1 the index of the first particle forming the torsion
* @param particle2 the index of the second particle forming the torsion
* @param particle3 the index of the third particle forming the torsion
* @param particle4 the index of the fourth particle forming the torsion
* @param periodicity the periodicity of the torsion
* @param phase the phase offset of the torsion, measured in radians
* @param k the force constant for the torsion
*
* @param index the index of the torsion for which to get parameters
* @param[out] particle1 the index of the first particle forming the torsion
* @param[out] particle2 the index of the second particle forming the torsion
* @param[out] particle3 the index of the third particle forming the torsion
* @param[out] particle4 the index of the fourth particle forming the torsion
* @param[out] periodicity the periodicity of the torsion
* @param[out] phase the phase offset of the torsion, measured in radians
* @param[out] k the force constant for the torsion
*/
void getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& periodicity, double& phase, double& k) const;
/**
* Set the force field parameters for a periodic torsion term.
*
*
* @param index the index of the torsion for which to set parameters
* @param particle1 the index of the first particle forming the torsion
* @param particle2 the index of the second particle forming the torsion
......@@ -103,7 +103,7 @@ public:
* 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 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.
*/
......
openmmapi/include/openmm/RBTorsionForce.h
View file @ 51b7f9e2
......@@ -77,23 +77,23 @@ public:
int addTorsion(int particle1, int particle2, int particle3, int particle4, double c0, double c1, double c2, double c3, double c4, double c5);
/**
* Get the force field parameters for a Ryckaert-Bellemans torsion term.
*
* @param index the index of the torsion for which to get parameters
* @param particle1 the index of the first particle forming the torsion
* @param particle2 the index of the second particle forming the torsion
* @param particle3 the index of the third particle forming the torsion
* @param particle4 the index of the fourth particle forming the torsion
* @param c0 the coefficient of the constant term, measured in kJ/mol
* @param c1 the coefficient of the 1st order term, measured in kJ/mol
* @param c2 the coefficient of the 2nd order term, measured in kJ/mol
* @param c3 the coefficient of the 3rd order term, measured in kJ/mol
* @param c4 the coefficient of the 4th order term, measured in kJ/mol
* @param c5 the coefficient of the 5th order term, measured in kJ/mol
*
* @param index the index of the torsion for which to get parameters
* @param[out] particle1 the index of the first particle forming the torsion
* @param[out] particle2 the index of the second particle forming the torsion
* @param[out] particle3 the index of the third particle forming the torsion
* @param[out] particle4 the index of the fourth particle forming the torsion
* @param[out] c0 the coefficient of the constant term, measured in kJ/mol
* @param[out] c1 the coefficient of the 1st order term, measured in kJ/mol
* @param[out] c2 the coefficient of the 2nd order term, measured in kJ/mol
* @param[out] c3 the coefficient of the 3rd order term, measured in kJ/mol
* @param[out] c4 the coefficient of the 4th order term, measured in kJ/mol
* @param[out] c5 the coefficient of the 5th order term, measured in kJ/mol
*/
void getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, double& c0, double& c1, double& c2, double& c3, double& c4, double& c5) const;
/**
* Set the force field parameters for a Ryckaert-Bellemans torsion term.
*
*
* @param index the index of the torsion for which to set parameters
* @param particle1 the index of the first particle forming the torsion
* @param particle2 the index of the second particle forming the torsion
......@@ -112,7 +112,7 @@ public:
* 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 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.
*/
......
openmmapi/include/openmm/State.h
View file @ 51b7f9e2
......@@ -43,7 +43,7 @@ namespace OpenMM {
/**
* A State object records a snapshot of the current state of a simulation at a point in time.
* You create it by calling getState() on a Context.
*
*
* When a State is created, you specify what information should be stored in it. This saves
* time and memory by only copying in the information that you actually want. This is especially
* important for forces and energies, since they may need to be calculated. If you query a
......@@ -81,7 +81,7 @@ public:
const std::vector<Vec3>& getForces() const;
/**
* Get the total kinetic energy of the system. If this State does not contain energies, this will throw an exception.
*
*
* Note that this may be different from simply mv<sup>2</sup>/2 summed over all particles. For example, a leapfrog
* integrator will store velocities offset by half a step, so they must be adjusted before computing the kinetic energy.
* This routine returns the kinetic energy at the current time, computed in a way that is appropriate for whatever
......@@ -95,9 +95,9 @@ public:
/**
* Get the vectors defining the axes of the periodic box (measured in nm).
*
* @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
* @param[out] a the vector defining the first edge of the periodic box
* @param[out] b the vector defining the second edge of the periodic box
* @param[out] c the vector defining the third edge of the periodic box
*/
void getPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const;
/**
......
openmmapi/include/openmm/System.h
View file @ 51b7f9e2
......@@ -44,19 +44,19 @@ class OPENMM_EXPORT VirtualSite;
/**
* This class represents a molecular system. The definition of a System involves
* four elements:
*
*
* <ol>
* <li>The set of particles in the system</li>
* <li>The forces acting on them</li>
* <li>Pairs of particles whose separation should be constrained to a fixed value</li>
* <li>For periodic systems, the dimensions of the periodic box</li>
* </ol>
*
*
* The particles and constraints are defined directly by the System object, while
* forces are defined by objects that extend the Force class. After creating a
* System, call addParticle() once for each particle, addConstraint() for each constraint,
* and addForce() for each Force.
*
*
* In addition, particles may be designated as "virtual sites". These are particles
* whose positions are computed automatically based on the positions of other particles.
* To define a virtual site, call setVirtualSite(), passing in a VirtualSite object
......@@ -94,7 +94,7 @@ public:
* the particle and not modify its position or velocity. This is most often
* used for virtual sites, but can also be used as a way to prevent a particle
* from moving.
*
*
* @param index the index of the particle for which to get the mass
*/
double getParticleMass(int index) const;
......@@ -103,7 +103,7 @@ public:
* the particle and not modify its position or velocity. This is most often
* used for virtual sites, but can also be used as a way to prevent a particle
* from moving.
*
*
* @param index the index of the particle for which to set the mass
* @param mass the mass of the particle
*/
......@@ -120,7 +120,7 @@ public:
void setVirtualSite(int index, VirtualSite* virtualSite);
/**
* Get whether a particle is a VirtualSite.
*
*
* @param index the index of the particle to check
*/
bool isVirtualSite(int index) const {
......@@ -129,7 +129,7 @@ public:
/**
* Get VirtualSite object for a particle. If the particle is not a virtual
* site, this throws an exception.
*
*
* @param index the index of the particle to get
*/
const VirtualSite& getVirtualSite(int index) const;
......@@ -151,17 +151,17 @@ public:
int addConstraint(int particle1, int particle2, double distance);
/**
* Get the parameters defining a distance constraint.
*
*
* @param index the index of the constraint for which to get parameters
* @param particle1 the index of the first particle involved in the constraint
* @param particle2 the index of the second particle involved in the constraint
* @param distance the required distance between the two particles, measured in nm
* @param[out] particle1 the index of the first particle involved in the constraint
* @param[out] particle2 the index of the second particle involved in the constraint
* @param[out] distance the required distance between the two particles, measured in nm
*/
void getConstraintParameters(int index, int& particle1, int& particle2, double& distance) const;
/**
* Set the parameters defining a distance constraint. Particles whose mass is 0 cannot participate
* in constraints.
*
*
* @param index the index of the constraint for which to set parameters
* @param particle1 the index of the first particle involved in the constraint
* @param particle2 the index of the second particle involved in the constraint
......@@ -170,7 +170,7 @@ public:
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);
......@@ -194,7 +194,7 @@ public:
}
/**
* Get a const reference to one of the Forces in this System.
*
*
* @param index the index of the Force to get
*/
const Force& getForce(int index) const;
......@@ -216,9 +216,9 @@ 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.
*
* @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
* @param[out] a the vector defining the first edge of the periodic box
* @param[out] b the vector defining the second edge of the periodic box
* @param[out] c the vector defining the third edge of the periodic box
*/
void getDefaultPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const;
/**
......
openmmapi/src/CompoundIntegrator.cpp 0 → 100644
View file @ 51b7f9e2
/* -------------------------------------------------------------------------- *
* 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) 2015 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 "openmm/CompoundIntegrator.h"
#include "openmm/Context.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/kernels.h"
#include <string>
using namespace OpenMM;
using namespace std;
CompoundIntegrator::CompoundIntegrator() : currentIntegrator(0) {
}
CompoundIntegrator::~CompoundIntegrator() {
for (int i = 0; i < integrators.size(); i++)
delete integrators[i];
}
int CompoundIntegrator::getNumIntegrators() const {
return integrators.size();
}
int CompoundIntegrator::addIntegrator(Integrator* integrator) {
if (owner != NULL)
throw OpenMMException("addIntegrator() cannot be called after a CustomIntegrator is already bound to a context");
integrators.push_back(integrator);
return integrators.size()-1;
}
Integrator& CompoundIntegrator::getIntegrator(int index) {
ASSERT_VALID_INDEX(index, integrators);
return *integrators[index];
}
const Integrator& CompoundIntegrator::getIntegrator(int index) const {
ASSERT_VALID_INDEX(index, integrators);
return *integrators[index];
}
int CompoundIntegrator::getCurrentIntegrator() const {
return currentIntegrator;
}
void CompoundIntegrator::setCurrentIntegrator(int index) {
if (index < 0 || index >= integrators.size())
throw OpenMMException("Illegal index for setCurrentIntegrator()");
currentIntegrator = index;
}
double CompoundIntegrator::getStepSize() const {
return integrators[currentIntegrator]->getStepSize();
}
void CompoundIntegrator::setStepSize(double size) {
integrators[currentIntegrator]->setStepSize(size);
}
double CompoundIntegrator::getConstraintTolerance() const {
return integrators[currentIntegrator]->getConstraintTolerance();
}
void CompoundIntegrator::setConstraintTolerance(double tol) {
integrators[currentIntegrator]->setConstraintTolerance(tol);
}
void CompoundIntegrator::step(int steps) {
integrators[currentIntegrator]->step(steps);
}
void CompoundIntegrator::initialize(ContextImpl& context) {
if (integrators.size() == 0)
throw OpenMMException("CompoundIntegrator must contain at least one Integrator");
for (int i = 0; i < integrators.size(); i++)
integrators[i]->initialize(context);
}
void CompoundIntegrator::cleanup() {
for (int i = 0; i < integrators.size(); i++)
integrators[i]->cleanup();
}
vector<string> CompoundIntegrator::getKernelNames() {
vector<string> kernels;
for (int i = 0; i < integrators.size(); i++) {
vector<string> integratorKernels = integrators[i]->getKernelNames();
kernels.insert(kernels.end(), integratorKernels.begin(), integratorKernels.end());
}
return kernels;
}
double CompoundIntegrator::computeKineticEnergy() {
return integrators[currentIntegrator]->computeKineticEnergy();
}
openmmapi/src/Context.cpp
View file @ 51b7f9e2
......@@ -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) 2008-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -114,21 +114,15 @@ State Context::getState(int types, bool enforcePeriodicBox, int groups) const {
center *= 1.0/molecules[i].size();
// Find the displacement to move it into the first periodic box.
int xcell = (int) floor(center[0]/periodicBoxSize[0][0]);
int ycell = (int) floor(center[1]/periodicBoxSize[1][1]);
int zcell = (int) floor(center[2]/periodicBoxSize[2][2]);
double dx = xcell*periodicBoxSize[0][0];
double dy = ycell*periodicBoxSize[1][1];
double dz = zcell*periodicBoxSize[2][2];
Vec3 diff;
diff -= periodicBoxSize[0]*static_cast<int>(center[0]/periodicBoxSize[0][0]);
diff -= periodicBoxSize[1]*static_cast<int>(center[1]/periodicBoxSize[1][1]);
diff -= periodicBoxSize[2]*static_cast<int>(center[2]/periodicBoxSize[2][2]);
// Translate all the particles in the molecule.
for (int j = 0; j < (int) molecules[i].size(); j++) {
Vec3& pos = positions[molecules[i][j]];
pos[0] -= dx;
pos[1] -= dy;
pos[2] -= dz;
pos -= diff;
}
}
}
......@@ -207,6 +201,10 @@ void Context::setVelocitiesToTemperature(double temperature, int randomSeed) {
impl->applyVelocityConstraints(1e-5);
}
const map<string, double>& Context::getParameters() const {
return impl->getParameters();
}
double Context::getParameter(const string& name) const {
return impl->getParameter(name);
}
......
openmmapi/src/CustomNonbondedForce.cpp
View file @ 51b7f9e2
......@@ -263,9 +263,9 @@ void CustomNonbondedForce::setFunctionParameters(int index, const std::string& n
int CustomNonbondedForce::addInteractionGroup(const std::set<int>& set1, const std::set<int>& set2) {
for (set<int>::iterator it = set1.begin(); it != set1.end(); ++it)
ASSERT_VALID_INDEX(*it, particles);
ASSERT(*it >= 0);
for (set<int>::iterator it = set2.begin(); it != set2.end(); ++it)
ASSERT_VALID_INDEX(*it, particles);
ASSERT(*it >= 0);
interactionGroups.push_back(InteractionGroupInfo(set1, set2));
return interactionGroups.size()-1;
}
......
openmmapi/src/CustomNonbondedForceImpl.cpp
View file @ 51b7f9e2
......@@ -111,6 +111,26 @@ void CustomNonbondedForceImpl::initialize(ContextImpl& context) {
if (cutoff > 0.5*boxVectors[0][0] || cutoff > 0.5*boxVectors[1][1] || cutoff > 0.5*boxVectors[2][2])
throw OpenMMException("CustomNonbondedForce: The cutoff distance cannot be greater than half the periodic box size.");
}
// Check that all interaction groups only specify particles that have been defined.
for (int group = 0; group < owner.getNumInteractionGroups(); group++) {
set<int> set1, set2;
owner.getInteractionGroupParameters(group, set1, set2);
for (set<int>::iterator it = set1.begin(); it != set1.end(); ++it)
if ((*it < 0) || (*it >= owner.getNumParticles())) {
stringstream msg;
msg << "CustomNonbondedForce: Interaction group " << group << " set1 contains a particle index (" << *it << ") "
<< "not present in system (" << owner.getNumParticles() << " particles).";
throw OpenMMException(msg.str());
}
for (set<int>::iterator it = set2.begin(); it != set2.end(); ++it)
if ((*it < 0) || (*it >= owner.getNumParticles())) {
stringstream msg;
msg << "CustomNonbondedForce: Interaction group " << group << " set2 contains a particle index (" << *it << ") "
<< "not present in system (" << owner.getNumParticles() << " particles).";
throw OpenMMException(msg.str());
}
}
kernel.getAs<CalcCustomNonbondedForceKernel>().initialize(context.getSystem(), owner);
}
......
openmmapi/src/Integrator.cpp
View file @ 51b7f9e2
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2015 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -47,3 +47,19 @@ Integrator::~Integrator() {
context->integratorDeleted();
}
}
double Integrator::getStepSize() const {
return stepSize;
}
void Integrator::setStepSize(double size) {
stepSize = size;
}
double Integrator::getConstraintTolerance() const {
return constraintTol;
}
void Integrator::setConstraintTolerance(double tol) {
constraintTol = tol;
}
platforms/cpu/tests/TestCpuCompoundIntegrator.cpp 0 → 100644
View file @ 51b7f9e2
/* -------------------------------------------------------------------------- *
* 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) 2015 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 "CpuTests.h"
#include "TestCompoundIntegrator.h"
void runPlatformTests() {
}
platforms/cuda/include/CudaIntegrationUtilities.h
View file @ 51b7f9e2
......@@ -62,6 +62,14 @@ public:
CudaArray& getStepSize() {
return *stepSize;
}
/**
* Set the size to use for the next step.
*/
void setNextStepSize(double size);
/**
* Get the size that was used for the last step.
*/
double getLastStepSize();
/**
* Apply constraints to the atom positions.
*
......@@ -154,6 +162,7 @@ private:
CudaArray* vsiteLocalCoordsParams;
int randomPos;
int lastSeed, numVsites;
double2 lastStepSize;
struct ShakeCluster;
struct ConstraintOrderer;
};
......
platforms/cuda/include/CudaKernels.h
View file @ 51b7f9e2
......@@ -592,7 +592,7 @@ class CudaCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
public:
CudaCalcNonbondedForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcNonbondedForceKernel(name, platform),
cu(cu), hasInitializedFFT(false), sigmaEpsilon(NULL), exceptionParams(NULL), cosSinSums(NULL), directPmeGrid(NULL), reciprocalPmeGrid(NULL),
pmeBsplineModuliX(NULL), pmeBsplineModuliY(NULL), pmeBsplineModuliZ(NULL), pmeAtomRange(NULL), pmeAtomGridIndex(NULL), sort(NULL), fft(NULL), pmeio(NULL) {
pmeBsplineModuliX(NULL), pmeBsplineModuliY(NULL), pmeBsplineModuliZ(NULL), pmeAtomRange(NULL), pmeAtomGridIndex(NULL), pmeEnergyBuffer(NULL), sort(NULL), fft(NULL), pmeio(NULL) {
}
~CudaCalcNonbondedForceKernel();
/**
......@@ -657,6 +657,7 @@ private:
CudaArray* pmeBsplineModuliZ;
CudaArray* pmeAtomRange;
CudaArray* pmeAtomGridIndex;
CudaArray* pmeEnergyBuffer;
CudaSort* sort;
Kernel cpuPme;
PmeIO* pmeio;
......@@ -1123,7 +1124,6 @@ public:
double computeKineticEnergy(ContextImpl& context, const VerletIntegrator& integrator);
private:
CudaContext& cu;
double prevStepSize;
CUfunction kernel1, kernel2;
};
......@@ -1354,7 +1354,7 @@ private:
void recordChangedParameters(ContextImpl& context);
bool evaluateCondition(int step);
CudaContext& cu;
double prevStepSize, energy;
double energy;
float energyFloat;
int numGlobalVariables;
bool hasInitializedKernels, deviceValuesAreCurrent, deviceGlobalsAreCurrent, modifiesParameters, keNeedsForce, hasAnyConstraints;
......
platforms/cuda/include/CudaPlatform.h
View file @ 51b7f9e2
......@@ -121,7 +121,7 @@ public:
ContextImpl* context;
std::vector<CudaContext*> contexts;
std::vector<double> contextEnergy;
bool removeCM, peerAccessSupported, useCpuPme;
bool hasInitializedContexts, removeCM, peerAccessSupported, useCpuPme;
int cmMotionFrequency;
int stepCount, computeForceCount;
double time;
......
platforms/cuda/src/CudaIntegrationUtilities.cpp
View file @ 51b7f9e2
......@@ -106,21 +106,21 @@ CudaIntegrationUtilities::CudaIntegrationUtilities(CudaContext& context, const S
vsiteOutOfPlaneAtoms(NULL), vsiteOutOfPlaneWeights(NULL), vsiteLocalCoordsAtoms(NULL), vsiteLocalCoordsParams(NULL) {
// Create workspace arrays.
lastStepSize = make_double2(0.0, 0.0);
if (context.getUseDoublePrecision() || context.getUseMixedPrecision()) {
posDelta = CudaArray::create<double4>(context, context.getPaddedNumAtoms(), "posDelta");
vector<double4> deltas(posDelta->getSize(), make_double4(0.0, 0.0, 0.0, 0.0));
posDelta->upload(deltas);
stepSize = CudaArray::create<double2>(context, 1, "stepSize");
vector<double2> step(1, make_double2(0.0, 0.0));
stepSize->upload(step);
stepSize->upload(&lastStepSize);
}
else {
posDelta = CudaArray::create<float4>(context, context.getPaddedNumAtoms(), "posDelta");
vector<float4> deltas(posDelta->getSize(), make_float4(0.0f, 0.0f, 0.0f, 0.0f));
posDelta->upload(deltas);
stepSize = CudaArray::create<float2>(context, 1, "stepSize");
vector<float2> step(1, make_float2(0.0f, 0.0f));
stepSize->upload(step);
float2 lastStepSizeFloat = make_float2(0.0f, 0.0f);
stepSize->upload(&lastStepSizeFloat);
}
// Record the set of constraints and how many constraints each atom is involved in.
......@@ -650,6 +650,29 @@ CudaIntegrationUtilities::~CudaIntegrationUtilities() {
delete vsiteLocalCoordsParams;
}
void CudaIntegrationUtilities::setNextStepSize(double size) {
if (size != lastStepSize.x || size != lastStepSize.y) {
lastStepSize = make_double2(size, size);
if (context.getUseDoublePrecision() || context.getUseMixedPrecision())
stepSize->upload(&lastStepSize);
else {
float2 lastStepSizeFloat = make_float2((float) size, (float) size);
stepSize->upload(&lastStepSizeFloat);
}
}
}
double CudaIntegrationUtilities::getLastStepSize() {
if (context.getUseDoublePrecision() || context.getUseMixedPrecision())
stepSize->download(&lastStepSize);
else {
float2 lastStepSizeFloat;
stepSize->download(&lastStepSizeFloat);
lastStepSize = make_double2(lastStepSizeFloat.x, lastStepSizeFloat.y);
}
return lastStepSize.y;
}
void CudaIntegrationUtilities::applyConstraints(double tol) {
applyConstraints(false, tol);
}
......
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