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Commit 5a06df78 authored by tic20's avatar tic20
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Merge https://github.com/openmm/openmm

parents 8dd60914 a9223eea
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Showing with 3567 additions and 118 deletions
libraries/lepton/include/lepton/ParsedExpression.h
View file @ 5a06df78
......@@ -116,6 +116,7 @@ private:
static ExpressionTreeNode precalculateConstantSubexpressions(const ExpressionTreeNode& node);
static ExpressionTreeNode substituteSimplerExpression(const ExpressionTreeNode& node);
static ExpressionTreeNode differentiate(const ExpressionTreeNode& node, const std::string& variable);
static bool isConstant(const ExpressionTreeNode& node);
static double getConstantValue(const ExpressionTreeNode& node);
static ExpressionTreeNode renameNodeVariables(const ExpressionTreeNode& node, const std::map<std::string, std::string>& replacements);
ExpressionTreeNode rootNode;
......
libraries/lepton/src/ParsedExpression.cpp
View file @ 5a06df78
......@@ -121,19 +121,33 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio
vector<ExpressionTreeNode> children(node.getChildren().size());
for (int i = 0; i < (int) children.size(); i++)
children[i] = substituteSimplerExpression(node.getChildren()[i]);
// Collect some info on constant expressions in children
bool first_const = children.size() > 0 && isConstant(children[0]); // is first child constant?
bool second_const = children.size() > 1 && isConstant(children[1]); ; // is second child constant?
double first, second; // if yes, value of first and second child
if (first_const)
first = getConstantValue(children[0]);
if (second_const)
second = getConstantValue(children[1]);
switch (node.getOperation().getId()) {
case Operation::ADD:
{
double first = getConstantValue(children[0]);
double second = getConstantValue(children[1]);
if (first == 0.0) // Add 0
if (first_const) {
if (first == 0.0) { // Add 0
return children[1];
if (second == 0.0) // Add 0
return children[0];
if (first == first) // Add a constant
} else { // Add a constant
return ExpressionTreeNode(new Operation::AddConstant(first), children[1]);
if (second == second) // Add a constant
}
}
if (second_const) {
if (second == 0.0) { // Add 0
return children[0];
} else { // Add a constant
return ExpressionTreeNode(new Operation::AddConstant(second), children[0]);
}
}
if (children[1].getOperation().getId() == Operation::NEGATE) // a+(-b) = a-b
return ExpressionTreeNode(new Operation::Subtract(), children[0], children[1].getChildren()[0]);
if (children[0].getOperation().getId() == Operation::NEGATE) // (-a)+b = b-a
......@@ -144,34 +158,35 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio
{
if (children[0] == children[1])
return ExpressionTreeNode(new Operation::Constant(0.0)); // Subtracting anything from itself is 0
double first = getConstantValue(children[0]);
if (first_const) {
if (first == 0.0) // Subtract from 0
return ExpressionTreeNode(new Operation::Negate(), children[1]);
double second = getConstantValue(children[1]);
if (second == 0.0) // Subtract 0
}
if (second_const) {
if (second == 0.0) { // Subtract 0
return children[0];
if (second == second) // Subtract a constant
} else { // Subtract a constant
return ExpressionTreeNode(new Operation::AddConstant(-second), children[0]);
}
}
if (children[1].getOperation().getId() == Operation::NEGATE) // a-(-b) = a+b
return ExpressionTreeNode(new Operation::Add(), children[0], children[1].getChildren()[0]);
break;
}
case Operation::MULTIPLY:
{
double first = getConstantValue(children[0]);
double second = getConstantValue(children[1]);
if (first == 0.0 || second == 0.0) // Multiply by 0
if ((first_const && first == 0.0) || (second_const && second == 0.0)) // Multiply by 0
return ExpressionTreeNode(new Operation::Constant(0.0));
if (first == 1.0) // Multiply by 1
if (first_const && first == 1.0) // Multiply by 1
return children[1];
if (second == 1.0) // Multiply by 1
if (second_const && second == 1.0) // Multiply by 1
return children[0];
if (children[0].getOperation().getId() == Operation::CONSTANT) { // Multiply by a constant
if (first_const) { // Multiply by a constant
if (children[1].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Combine two multiplies into a single one
return ExpressionTreeNode(new Operation::MultiplyConstant(first*dynamic_cast<const Operation::MultiplyConstant*>(&children[1].getOperation())->getValue()), children[1].getChildren()[0]);
return ExpressionTreeNode(new Operation::MultiplyConstant(first), children[1]);
}
if (children[1].getOperation().getId() == Operation::CONSTANT) { // Multiply by a constant
if (second_const) { // Multiply by a constant
if (children[0].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Combine two multiplies into a single one
return ExpressionTreeNode(new Operation::MultiplyConstant(second*dynamic_cast<const Operation::MultiplyConstant*>(&children[0].getOperation())->getValue()), children[0].getChildren()[0]);
return ExpressionTreeNode(new Operation::MultiplyConstant(second), children[0]);
......@@ -202,18 +217,16 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio
{
if (children[0] == children[1])
return ExpressionTreeNode(new Operation::Constant(1.0)); // Dividing anything from itself is 0
double numerator = getConstantValue(children[0]);
if (numerator == 0.0) // 0 divided by something
if (first_const && first == 0.0) // 0 divided by something
return ExpressionTreeNode(new Operation::Constant(0.0));
if (numerator == 1.0) // 1 divided by something
if (first_const && first == 1.0) // 1 divided by something
return ExpressionTreeNode(new Operation::Reciprocal(), children[1]);
double denominator = getConstantValue(children[1]);
if (denominator == 1.0) // Divide by 1
if (second_const && second == 1.0) // Divide by 1
return children[0];
if (children[1].getOperation().getId() == Operation::CONSTANT) {
if (second_const) {
if (children[0].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Combine a multiply and a divide into one multiply
return ExpressionTreeNode(new Operation::MultiplyConstant(dynamic_cast<const Operation::MultiplyConstant*>(&children[0].getOperation())->getValue()/denominator), children[0].getChildren()[0]);
return ExpressionTreeNode(new Operation::MultiplyConstant(1.0/denominator), children[0]); // Replace a divide with a multiply
return ExpressionTreeNode(new Operation::MultiplyConstant(dynamic_cast<const Operation::MultiplyConstant*>(&children[0].getOperation())->getValue()/second), children[0].getChildren()[0]);
return ExpressionTreeNode(new Operation::MultiplyConstant(1.0/second), children[0]); // Replace a divide with a multiply
}
if (children[0].getOperation().getId() == Operation::NEGATE && children[1].getOperation().getId() == Operation::NEGATE) // The two negations cancel
return ExpressionTreeNode(new Operation::Divide(), children[0].getChildren()[0], children[1].getChildren()[0]);
......@@ -229,34 +242,34 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio
}
case Operation::POWER:
{
double base = getConstantValue(children[0]);
if (base == 0.0) // 0 to any power is 0
if (first_const && first == 0.0) // 0 to any power is 0
return ExpressionTreeNode(new Operation::Constant(0.0));
if (base == 1.0) // 1 to any power is 1
if (first_const && first == 1.0) // 1 to any power is 1
return ExpressionTreeNode(new Operation::Constant(1.0));
double exponent = getConstantValue(children[1]);
if (exponent == 0.0) // x^0 = 1
if (second_const) { // Constant exponent
if (second == 0.0) // x^0 = 1
return ExpressionTreeNode(new Operation::Constant(1.0));
if (exponent == 1.0) // x^1 = x
if (second == 1.0) // x^1 = x
return children[0];
if (exponent == -1.0) // x^-1 = recip(x)
if (second == -1.0) // x^-1 = recip(x)
return ExpressionTreeNode(new Operation::Reciprocal(), children[0]);
if (exponent == 2.0) // x^2 = square(x)
if (second == 2.0) // x^2 = square(x)
return ExpressionTreeNode(new Operation::Square(), children[0]);
if (exponent == 3.0) // x^3 = cube(x)
if (second == 3.0) // x^3 = cube(x)
return ExpressionTreeNode(new Operation::Cube(), children[0]);
if (exponent == 0.5) // x^0.5 = sqrt(x)
if (second == 0.5) // x^0.5 = sqrt(x)
return ExpressionTreeNode(new Operation::Sqrt(), children[0]);
if (exponent == exponent) // Constant power
return ExpressionTreeNode(new Operation::PowerConstant(exponent), children[0]);
// Constant power
return ExpressionTreeNode(new Operation::PowerConstant(second), children[0]);
}
break;
}
case Operation::NEGATE:
{
if (children[0].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Combine a multiply and a negate into a single multiply
return ExpressionTreeNode(new Operation::MultiplyConstant(-dynamic_cast<const Operation::MultiplyConstant*>(&children[0].getOperation())->getValue()), children[0].getChildren()[0]);
if (children[0].getOperation().getId() == Operation::CONSTANT) // Negate a constant
return ExpressionTreeNode(new Operation::Constant(-getConstantValue(children[0])));
if (first_const) // Negate a constant
return ExpressionTreeNode(new Operation::Constant(-first));
if (children[0].getOperation().getId() == Operation::NEGATE) // The two negations cancel
return children[0].getChildren()[0];
break;
......@@ -265,7 +278,7 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio
{
if (children[0].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Combine two multiplies into a single one
return ExpressionTreeNode(new Operation::MultiplyConstant(dynamic_cast<const Operation::MultiplyConstant*>(&node.getOperation())->getValue()*dynamic_cast<const Operation::MultiplyConstant*>(&children[0].getOperation())->getValue()), children[0].getChildren()[0]);
if (children[0].getOperation().getId() == Operation::CONSTANT) // Multiply two constants
if (first_const) // Multiply two constants
return ExpressionTreeNode(new Operation::Constant(dynamic_cast<const Operation::MultiplyConstant*>(&node.getOperation())->getValue()*getConstantValue(children[0])));
if (children[0].getOperation().getId() == Operation::NEGATE) // Combine a multiply and a negate into a single multiply
return ExpressionTreeNode(new Operation::MultiplyConstant(-dynamic_cast<const Operation::MultiplyConstant*>(&node.getOperation())->getValue()), children[0].getChildren()[0]);
......@@ -303,10 +316,15 @@ ExpressionTreeNode ParsedExpression::differentiate(const ExpressionTreeNode& nod
return node.getOperation().differentiate(node.getChildren(),childDerivs, variable);
}
bool ParsedExpression::isConstant(const ExpressionTreeNode& node) {
return (node.getOperation().getId() == Operation::CONSTANT);
}
double ParsedExpression::getConstantValue(const ExpressionTreeNode& node) {
if (node.getOperation().getId() == Operation::CONSTANT)
if (node.getOperation().getId() != Operation::CONSTANT) {
throw Exception("getConstantValue called on a non-constant ExpressionNode");
}
return dynamic_cast<const Operation::Constant&>(node.getOperation()).getValue();
return numeric_limits<double>::quiet_NaN();
}
ExpressionProgram ParsedExpression::createProgram() const {
......
olla/include/openmm/kernels.h
View file @ 5a06df78
......@@ -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) 2008-2019 Stanford University and the Authors. *
* Portions copyright (c) 2008-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -33,7 +33,7 @@
* -------------------------------------------------------------------------- */
#include "openmm/AndersenThermostat.h"
#include "openmm/BAOABLangevinIntegrator.h"
#include "openmm/LangevinMiddleIntegrator.h"
#include "openmm/BrownianIntegrator.h"
#include "openmm/CMAPTorsionForce.h"
#include "openmm/CMMotionRemover.h"
......@@ -64,6 +64,8 @@
#include "openmm/VariableLangevinIntegrator.h"
#include "openmm/VariableVerletIntegrator.h"
#include "openmm/VerletIntegrator.h"
#include "openmm/NoseHooverIntegrator.h"
#include "openmm/NoseHooverChain.h"
#include <iosfwd>
#include <set>
#include <string>
......@@ -1058,6 +1060,41 @@ public:
virtual double computeKineticEnergy(ContextImpl& context, const VerletIntegrator& integrator) = 0;
};
/**
* This kernel is invoked by NoseHooverIntegrator to take one time step.
*/
class IntegrateVelocityVerletStepKernel : public KernelImpl {
public:
static std::string Name() {
return "IntegrateVelocityVerletStep";
}
IntegrateVelocityVerletStepKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param integrator the NoseHooverIntegrator this kernel will be used for
*/
virtual void initialize(const System& system, const NoseHooverIntegrator& integrator) = 0;
/**
* Execute the kernel.
*
* @param context the context in which to execute this kernel
* @param integrator the NoseHooverIntegrator this kernel is being used for
* @param forcesAreValid a reference to the parent integrator's boolean for keeping
* track of the validity of the current forces.
*/
virtual void execute(ContextImpl& context, const NoseHooverIntegrator& integrator, bool &forcesAreValid) = 0;
/**
* Compute the kinetic energy.
*
* @param context the context in which to execute this kernel
* @param integrator the NoseHooverIntegrator this kernel is being used for
*/
virtual double computeKineticEnergy(ContextImpl& context, const NoseHooverIntegrator& integrator) = 0;
};
/**
* This kernel is invoked by LangevinIntegrator to take one time step.
*/
......@@ -1092,40 +1129,36 @@ public:
};
/**
* This kernel is invoked by BAOABLangevinIntegrator to take one time step.
* This kernel is invoked by LangevinMiddleIntegrator to take one time step.
*/
class IntegrateBAOABStepKernel : public KernelImpl {
class IntegrateLangevinMiddleStepKernel : public KernelImpl {
public:
static std::string Name() {
return "IntegrateBAOABStep";
return "IntegrateLangevinMiddleStep";
}
IntegrateBAOABStepKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
IntegrateLangevinMiddleStepKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param integrator the BAOABLangevinIntegrator this kernel will be used for
* @param integrator the LangevinMiddleIntegrator this kernel will be used for
*/
virtual void initialize(const System& system, const BAOABLangevinIntegrator& integrator) = 0;
virtual void initialize(const System& system, const LangevinMiddleIntegrator& integrator) = 0;
/**
* Execute the kernel.
*
* @param context the context in which to execute this kernel
* @param integrator the BAOABLangevinIntegrator this kernel is being used for
* @param forcesAreValid if the context has been modified since the last time step, this will be
* false to show that cached forces are invalid and must be recalculated.
* On exit, this should specify whether the cached forces are valid at the
* end of the step.
* @param integrator the LangevinMiddleIntegrator this kernel is being used for
*/
virtual void execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator, bool& forcesAreValid) = 0;
virtual void execute(ContextImpl& context, const LangevinMiddleIntegrator& integrator) = 0;
/**
* Compute the kinetic energy.
*
* @param context the context in which to execute this kernel
* @param integrator the BAOABLangevinIntegrator this kernel is being used for
* @param integrator the LangevinMiddleIntegrator this kernel is being used for
*/
virtual double computeKineticEnergy(ContextImpl& context, const BAOABLangevinIntegrator& integrator) = 0;
virtual double computeKineticEnergy(ContextImpl& context, const LangevinMiddleIntegrator& integrator) = 0;
};
/**
......@@ -1327,6 +1360,58 @@ public:
virtual void execute(ContextImpl& context) = 0;
};
/**
* This kernel is invoked by NoseHooverChainThermostat at the beginning and end of each time step
* to update the Nose-Hoover chain.
*/
class NoseHooverChainKernel : public KernelImpl {
public:
static std::string Name() {
return "NoseHooverChain";
}
NoseHooverChainKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*/
virtual void initialize() = 0;
/**
* Execute the kernel that propagates the Nose Hoover chain and determines the velocity scale factor.
*
* @param context the context in which to execute this kernel
* @param noseHooverChain the object describing the chain to be propagated.
* @param kineticEnergy the {center of mass, relative} kineticEnergies of the particles being thermostated by this chain.
* @param timeStep the time step used by the integrator.
* @return the velocity scale factor to apply to the particles associated with this heat bath.
*/
virtual std::pair<double, double> propagateChain(ContextImpl& context, const NoseHooverChain &noseHooverChain, std::pair<double, double> kineticEnergy, double timeStep) = 0;
/**
* Execute the kernal that computes the total (kinetic + potential) heat bath energy.
*
* @param context the context in which to execute this kernel
* @param noseHooverChain the chain whose energy is to be determined.
* @return the total heat bath energy.
*/
virtual double computeHeatBathEnergy(ContextImpl& context, const NoseHooverChain &noseHooverChain) = 0;
/**
* Execute the kernel that computes the kinetic energy for a subset of atoms,
* or the relative kinetic energy of Drude particles with respect to their parent atoms
*
* @param context the context in which to execute this kernel
* @param noseHooverChain the chain whose energy is to be determined.
* @param downloadValue whether the computed value should be downloaded and returned.
*/
virtual std::pair<double, double> computeMaskedKineticEnergy(ContextImpl& context, const NoseHooverChain &noseHooverChain, bool downloadValue) = 0;
/**
* Execute the kernel that scales the velocities of particles associated with a nose hoover chain
*
* @param context the context in which to execute this kernel
* @param noseHooverChain the chain whose energy is to be determined.
* @param scaleFactor the multiplicative factor by which {absolute, relative} velocities are scaled.
*/
virtual void scaleVelocities(ContextImpl& context, const NoseHooverChain &noseHooverChain, std::pair<double, double> scaleFactor) = 0;
};
/**
* This kernel is invoked by MonteCarloBarostat to adjust the periodic box volume
*/
......
openmmapi/include/OpenMM.h
View file @ 5a06df78
......@@ -33,7 +33,6 @@
* -------------------------------------------------------------------------- */
#include "openmm/AndersenThermostat.h"
#include "openmm/BAOABLangevinIntegrator.h"
#include "openmm/BrownianIntegrator.h"
#include "openmm/CMAPTorsionForce.h"
#include "openmm/CMMotionRemover.h"
......@@ -57,6 +56,7 @@
#include "openmm/HarmonicBondForce.h"
#include "openmm/Integrator.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/LangevinMiddleIntegrator.h"
#include "openmm/LocalEnergyMinimizer.h"
#include "openmm/MonteCarloAnisotropicBarostat.h"
#include "openmm/MonteCarloBarostat.h"
......@@ -75,6 +75,8 @@
#include "openmm/VariableVerletIntegrator.h"
#include "openmm/Vec3.h"
#include "openmm/VerletIntegrator.h"
#include "openmm/NoseHooverIntegrator.h"
#include "openmm/NoseHooverChain.h"
#include "openmm/VirtualSite.h"
#include "openmm/Platform.h"
#include "openmm/serialization/XmlSerializer.h"
......
openmmapi/include/openmm/CustomIntegrator.h
View file @ 5a06df78
......@@ -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) 2011-2019 Stanford University and the Authors. *
* Portions copyright (c) 2011-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -50,8 +50,8 @@ namespace OpenMM {
* with the particle positions and momenta.
*
* To create an integration algorithm, you first define a set of variables the
* integrator will compute. Variables come in two types: <i>global</i> variables
* have a single value, while <i>per-DOF</i> variables have a value for every
* integrator will compute. Variables come in two types: global variables
* have a single value, while per-DOF variables have a value for every
* degree of freedom (x, y, or z coordinate of a particle). You can define as
* many variables as you want of each type. The value of any variable can be
* computed by the integration algorithm, or set directly by calling a method on
......@@ -112,14 +112,14 @@ namespace OpenMM {
* evaluated, a different value will be used. When used in a per-DOF
* expression, a different value will be used for every degree of freedom.
* Note, however, that if this variable appears multiple times in a single
* expression, the <i>same</i> value is used everywhere it appears in that
* expression, the same value is used everywhere it appears in that
* expression.</li>
* <li>gaussian: (either global or per-DOF, read-only) This is a Gaussian
* distributed random number with mean 0 and variance 1. Every time an expression
* is evaluated, a different value will be used. When used in a per-DOF
* expression, a different value will be used for every degree of freedom.
* Note, however, that if this variable appears multiple times in a single
* expression, the <i>same</i> value is used everywhere it appears in that
* expression, the same value is used everywhere it appears in that
* expression.</li>
* <li>A global variable is created for every adjustable parameter defined
* in the integrator's Context.</li>
......@@ -218,6 +218,43 @@ namespace OpenMM {
* integrator.addComputePerDof("angularMomentum", "m*cross(x, v)");
* </pre></tt>
*
* Here are two more examples that may be useful as starting points for writing
* your own integrators. The first one implements the algorithm used by the
* standard VerletIntegrator class. This is a leapfrog algorithm, in contrast
* to the velocity Verlet algorithm shown above, so it only requires applying
* constraints once in each time step.
*
* <tt><pre>
* CustomIntegrator integrator(dt);
* integrator.addPerDofVariable("x0", 0);
* integrator.addUpdateContextState();
* integrator.addComputePerDof("x0", "x");
* integrator.addComputePerDof("v", "v+dt*f/m");
* integrator.addComputePerDof("x", "x+dt*v");
* integrator.addConstrainPositions();
* integrator.addComputePerDof("v", "(x-x0)/dt");
* </pre></tt>
*
* The second one implements the algorithm used by the standard
* LangevinMiddleIntegrator class. kB is Boltzmann's constant.
*
* <tt><pre>
* CustomIntegrator integrator(dt);
* integrator.addGlobalVariable("a", exp(-friction*dt));
* integrator.addGlobalVariable("b", sqrt(1-exp(-2*friction*dt)));
* integrator.addGlobalVariable("kT", kB*temperature);
* integrator.addPerDofVariable("x1", 0);
* integrator.addUpdateContextState();
* integrator.addComputePerDof("v", "v + dt*f/m");
* integrator.addConstrainVelocities();
* integrator.addComputePerDof("x", "x + 0.5*dt*v");
* integrator.addComputePerDof("v", "a*v + b*sqrt(kT/m)*gaussian");
* integrator.addComputePerDof("x", "x + 0.5*dt*v");
* integrator.addComputePerDof("x1", "x");
* integrator.addConstrainPositions();
* integrator.addComputePerDof("v", "v + (x-x1)/dt");
* </pre></tt>
*
* Another feature of CustomIntegrator is that it can use derivatives of the
* potential energy with respect to context parameters. These derivatives are
* typically computed by custom forces, and are only computed if a Force object
......@@ -230,7 +267,7 @@ namespace OpenMM {
*
* An Integrator has one other job in addition to evolving the equations of motion:
* it defines how to compute the kinetic energy of the system. Depending on the
* integration method used, simply summing mv<sup>2</sup>/2 over all degrees of
* integration method used, simply summing (mv^2)/2 over all degrees of
* freedom may not give the correct answer. For example, in a leapfrog integrator
* the velocities are "delayed" by half a time step, so the above formula would
* give the kinetic energy half a time step ago, not at the current time.
......@@ -250,7 +287,7 @@ namespace OpenMM {
* The kinetic energy expression may depend on the following pre-defined variables:
* x, v, f, m, dt. It also may depend on user-defined global and per-DOF variables,
* and on the values of adjustable parameters defined in the integrator's Context.
* It may <i>not</i> depend on any other variable, such as the potential energy,
* It may not depend on any other variable, such as the potential energy,
* the force from a single force group, or a random number.
*
* Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
......
openmmapi/include/openmm/BAOABLangevinIntegrator.h → openmmapi/include/openmm/LangevinMiddleIntegrator.h
View file @ 5a06df78
#ifndef OPENMM_BAOABLANGEVININTEGRATOR_H_
#define OPENMM_BAOABLANGEVININTEGRATOR_H_
#ifndef OPENMM_LANGEVINMIDDLEINTEGRATOR_H_
#define OPENMM_LANGEVINMIDDLEINTEGRATOR_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
......@@ -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) 2008-2019 Stanford University and the Authors. *
* Portions copyright (c) 2008-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -40,21 +40,21 @@ namespace OpenMM {
/**
* This is an Integrator which simulates a System using Langevin dynamics, with
* the BAOAB discretization of Leimkuhler and Matthews (http://dx.doi.org/10.1093/amrx/abs010).
* the LFMiddle discretization (http://dx.doi.org/10.1021/acs.jpca.9b02771).
* This method tend to produce more accurate configurational sampling than other
* discretizations, such as the one used in LangevinIntegrator.
*/
class OPENMM_EXPORT BAOABLangevinIntegrator : public Integrator {
class OPENMM_EXPORT LangevinMiddleIntegrator : public Integrator {
public:
/**
* Create a BAOABLangevinIntegrator.
* Create a LangevinMiddleIntegrator.
*
* @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 integrate the system (in picoseconds)
*/
BAOABLangevinIntegrator(double temperature, double frictionCoeff, double stepSize);
LangevinMiddleIntegrator(double temperature, double frictionCoeff, double stepSize);
/**
* Get the temperature of the heat bath (in Kelvin).
*
......@@ -128,10 +128,6 @@ protected:
* cleanup. It will also get called again if the application calls reinitialize() on the Context.
*/
void cleanup();
/**
* When the user modifies the state, we need to mark that the forces need to be recalculated.
*/
void stateChanged(State::DataType changed);
/**
* Get the names of all Kernels used by this Integrator.
*/
......@@ -147,10 +143,9 @@ protected:
private:
double temperature, friction;
int randomNumberSeed;
bool forcesAreValid;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_BAOABLANGEVININTEGRATOR_H_*/
#endif /*OPENMM_LANGEVINMIDDLEINTEGRATOR_H_*/
openmmapi/include/openmm/NonbondedForce.h
View file @ 5a06df78
......@@ -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) 2008-2018 Stanford University and the Authors. *
* Portions copyright (c) 2008-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -568,6 +568,32 @@ public:
nonbondedMethod == NonbondedForce::PME ||
nonbondedMethod == NonbondedForce::LJPME;
}
/**
* Get whether periodic boundary conditions should be applied to exceptions. Usually this is not
* appropriate, because exceptions are normally used to represent bonded interactions (1-2, 1-3, and
* 1-4 pairs), but there are situations when it does make sense. For example, you may want to simulate
* an infinite chain where one end of a molecule is bonded to the opposite end of the next periodic
* copy.
*
* Regardless of this value, periodic boundary conditions are only applied to exceptions if they also
* are applied to other interactions. If the nonbonded method is NoCutoff or CutoffNonPeriodic, this
* value is ignored. Also note that cutoffs are never applied to exceptions, again because they are
* normally used to represent bonded interactions.
*/
bool getExceptionsUsePeriodicBoundaryConditions() const;
/**
* Set whether periodic boundary conditions should be applied to exceptions. Usually this is not
* appropriate, because exceptions are normally used to represent bonded interactions (1-2, 1-3, and
* 1-4 pairs), but there are situations when it does make sense. For example, you may want to simulate
* an infinite chain where one end of a molecule is bonded to the opposite end of the next periodic
* copy.
*
* Regardless of this value, periodic boundary conditions are only applied to exceptions if they also
* get applied to other interactions. If the nonbonded method is NoCutoff or CutoffNonPeriodic, this
* value is ignored. Also note that cutoffs are never applied to exceptions, again because they are
* normally used to represent bonded interactions.
*/
void setExceptionsUsePeriodicBoundaryConditions(bool periodic);
protected:
ForceImpl* createImpl() const;
private:
......@@ -578,7 +604,7 @@ private:
class ExceptionOffsetInfo;
NonbondedMethod nonbondedMethod;
double cutoffDistance, switchingDistance, rfDielectric, ewaldErrorTol, alpha, dalpha;
bool useSwitchingFunction, useDispersionCorrection;
bool useSwitchingFunction, useDispersionCorrection, exceptionsUsePeriodic;
int recipForceGroup, nx, ny, nz, dnx, dny, dnz;
void addExclusionsToSet(const std::vector<std::set<int> >& bonded12, std::set<int>& exclusions, int baseParticle, int fromParticle, int currentLevel) const;
int getGlobalParameterIndex(const std::string& parameter) const;
......
openmmapi/include/openmm/NoseHooverChain.h 0 → 100644
View file @ 5a06df78
#ifndef OPENMM_NOSEHOOVERCHAIN_H_
#define OPENMM_NOSEHOOVERCHAIN_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) 2019 Stanford University and the Authors. *
* Authors: Andreas Krämer and Andrew C. Simmonett *
* 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/Force.h"
#include <string>
#include <vector>
#include "openmm/OpenMMException.h"
#include "internal/windowsExport.h"
namespace OpenMM {
/**
* This class defines a chain of Nose-Hoover particles to be used as a heat bath to
* scale the velocities of a collection of particles subject to thermostating. The
* heat bath is propagated using the multi time step approach detailed in
*
* G. J. Martyna, M. E. Tuckerman, D. J. Tobias and M. L. Klein, Mol. Phys. 87, 1117 (1996).
*
* where the total number of timesteps used to propagate the chain in each step is
* the number of MTS steps multiplied by the number of terms in the Yoshida-Suzuki decomposition.
*
* Two types of NHC may be created. The first is a simple thermostat that couples with a given subset
* of the atoms within a system, controling their absolute motion. The second is more elaborate and
* can thermostat tethered pairs of atoms and in this case two thermostats are created: one that controls
* the absolute center of mass velocity of each pair and another that controls their motion relative to
* one another.
*/
class OPENMM_EXPORT NoseHooverChain {
public:
/**
* Create a NoseHooverChain.
*
* @param temperature the temperature of the heat bath for absolute motion (in Kelvin)
* @param collisionFrequency the collision frequency for absolute motion (in 1/ps)
* @param relativeTemperature the temperature of the heat bath for relative motion(in Kelvin).
* This is only used if the list of thermostated pairs is not empty.
* @param relativeCollisionFrequency the collision frequency for relative motion(in 1/ps).
* This is only used if the list of thermostated pairs is not empty.
* @param numDOFs the number of degrees of freedom in the particles that
* interact with this chain
* @param chainLength the length of (number of particles in) this heat bath
* @param numMTS the number of multi time steps used to propagate this chain
* @param numYoshidaSuzuki the number of Yoshida Suzuki steps used to propagate this chain (1, 3, or 5).
* @param chainID the chain id used to distinguish this Nose-Hoover chain from others that may
* be used to control a different set of particles, e.g. for Drude oscillators
* @param thermostatedAtoms the list of atoms to be handled by this thermostat
* @param thermostatedPairs the list of connected pairs to be thermostated; their absolute center of mass motion will
* be thermostated independently from their motion relative to one another.
*/
NoseHooverChain(double temperature, double relativeTemperature, double collisionFrequency,
double relativeCollisionFrequency, int numDOFs, int chainLength,
int numMTS, int numYoshidaSuzuki, int chainID,
const std::vector<int>& thermostatedAtoms, const std::vector< std::pair< int, int > > &thermostatedPairs);
/**
* Get the temperature of the heat bath for treating absolute particle motion (in Kelvin).
*
* @return the temperature of the heat bath, measured in Kelvin.
*/
double getTemperature() const {
return temp;
}
/**
* Set the temperature of the heat bath for treating absolute particle motion.
* This will affect any new Contexts you create, but not ones that already exist.
*
* @param temperature the temperature of the heat bath (in Kelvin)
*/
void setTemperature(double temperature) {
temp = temperature;
}
/**
* Get the temperature of the heat bath for treating relative particle motion (in Kelvin).
*
* @return the temperature of the heat bath, measured in Kelvin.
*/
double getRelativeTemperature() const {
return relativeTemp;
}
/**
* Set the temperature of the heat bath for treating relative motion if this thermostat has
* been set up to treat connected pairs of atoms. This will affect any new Contexts you create,
* but not ones that already exist.
*
* @param temperature the temperature of the heat bath for relative motion (in Kelvin)
*/
void setRelativeTemperature(double temperature) {
relativeTemp = temperature;
}
/**
* Get the collision frequency for treating absolute particle motion (in 1/ps).
*
* @return the collision frequency, measured in 1/ps.
*/
double getCollisionFrequency() const {
return freq;
}
/**
* Set the collision frequency for treating absolute particle motion.
* This will affect any new Contexts you create, but not those that already exist.
*
* @param frequency the collision frequency (in 1/ps)
*/
void setCollisionFrequency(double frequency) {
freq = frequency;
}
/**
* Get the collision frequency for treating relative particle motion (in 1/ps).
*
* @return the collision frequency, measured in 1/ps.
*/
double getRelativeCollisionFrequency() const {
return relativeFreq;
}
/**
* Set the collision frequency for treating relative particle motion if this thermostat has
* been set up to handle connected pairs of atoms. This will affect any new Contexts you create,
* but not those that already exist.
*
* @param frequency the collision frequency (in 1/ps)
*/
void setRelativeCollisionFrequency(double frequency) {
relativeFreq = frequency;
}
/**
* Get the number of degrees of freedom in the particles controled by this heat bath.
*
* @return the number of degrees of freedom.
*/
int getNumDegreesOfFreedom() const {
return numDOFs;
}
/**
* Set the number of degrees of freedom in the particles controled by this heat bath.
* This will affect any new Contexts you create, but not those that already exist.
*
* @param numDOF the number of degrees of freedom.
*/
void setNumDegreesOfFreedom(int numDOF) {
numDOFs = numDOF;
}
/**
* Get the chain length of this heat bath.
*
* @return the chain length.
*/
int getChainLength() const {
return chainLength;
}
/**
* Get the number of steps used in the multi time step propagation.
*
* @returns the number of multi time steps.
*/
int getNumMultiTimeSteps() const {
return numMTS;
}
/**
* Get the number of steps used in the Yoshida-Suzuki decomposition for
* multi time step propagation.
*
* @returns the number of multi time steps in the Yoshida-Suzuki decomposition.
*/
int getNumYoshidaSuzukiTimeSteps() const {
return numYS;
}
/**
* Get the chain id used to identify this chain
*
* @returns the chain id
*/
int getChainID() const {
return chainID;
}
/**
* Get the atom ids of all atoms that are thermostated
*
* @returns ids of all atoms that are being handled by this thermostat
*/
const std::vector<int>& getThermostatedAtoms() const {
return thermostatedAtoms;
}
/**
* Set list of atoms that are handled by this thermostat
*
* @param atomIDs
*/
void setThermostatedAtoms(const std::vector<int>& atomIDs){
thermostatedAtoms = atomIDs;
}
/**
* Get the list of any connected pairs to be handled by this thermostat.
* If this is a regular thermostat, returns an empty vector.
*
* @returns list of connected pairs.
*/
const std::vector< std::pair< int, int > >& getThermostatedPairs() const {
return thermostatedPairs;
}
/**
* In case this thermostat handles the kinetic energy of Drude particles
* set the atom IDs of all parent atoms.
*
* @param pairIDs the list of connected pairs to thermostat.
*/
void setThermostatedPairs(const std::vector< std::pair< int, int > >& pairIDs){
thermostatedPairs = pairIDs;
}
/**
* Get the weights used in the Yoshida Suzuki multi time step decomposition (dimensionless)
*
* @returns the weights for the Yoshida-Suzuki integration
*/
std::vector<double> getYoshidaSuzukiWeights() const;
/**
* 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;
}
private:
double temp, freq, relativeTemp, relativeFreq;
int numDOFs, chainLength, numMTS, numYS;
// The suffix used to distinguish NH chains, e.g. for Drude particles vs. regular particles.
int chainID;
std::vector<int> thermostatedAtoms;
std::vector<std::pair<int, int> > thermostatedPairs;
};
} // namespace OpenMM
#endif /*OPENMM_NOSEHOOVERCHAIN_H_*/
openmmapi/include/openmm/NoseHooverIntegrator.h 0 → 100644
View file @ 5a06df78
#ifndef OPENMM_NOSEHOOVERINTEGRATOR_H_
#define OPENMM_NOSEHOOVERINTEGRATOR_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) 2019 Stanford University and the Authors. *
* Authors: Andreas Krämer and Andrew C. Simmonett *
* 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 "Integrator.h"
#include "openmm/State.h"
#include "openmm/Kernel.h"
#include "NoseHooverChain.h"
#include "internal/windowsExport.h"
#include <tuple>
namespace OpenMM {
class System;
/**
* This is an Integrator which simulates a System using one or more Nose Hoover chain
* thermostats, using the velocity Verlet propagation algorithm.
*/
class OPENMM_EXPORT NoseHooverIntegrator : public Integrator {
public:
/**
* Create a NoseHooverIntegrator. This version creates a bare velocity Verlet integrator
* with no thermostats; any thermostats should be added by calling addThermostat.
*
* @param stepSize the step size with which to integrate the system (in picoseconds)
*/
explicit NoseHooverIntegrator(double stepSize);
/**
* Create a NoseHooverIntegrator.
*
* @param temperature the target temperature for the system (in Kelvin).
* @param collisionFrequency the frequency of the interaction with the heat bath (in inverse picoseconds).
* @param stepSize the step size with which to integrate the system (in picoseconds)
* @param chainLength the number of beads in the Nose-Hoover chain.
* @param numMTS the number of step in the multiple time step chain propagation algorithm.
* @param numYoshidaSuzuki the number of terms in the Yoshida-Suzuki multi time step decomposition
* used in the chain propagation algorithm (must be 1, 3, or 5).
*/
explicit NoseHooverIntegrator(double temperature, double collisionFrequency, double stepSize,
int chainLength = 3, int numMTS = 3, int numYoshidaSuzuki = 3);
virtual ~NoseHooverIntegrator();
/**
* Advance a simulation through time by taking a series of time steps.
*
* @param steps the number of time steps to take
*/
void step(int steps);
/**
* Add a simple Nose-Hoover Chain thermostat to control the temperature of the full system
*
* @param temperature the target temperature for the system.
* @param collisionFrequency the frequency of the interaction with the heat bath (in 1/ps).
* @param chainLength the number of beads in the Nose-Hoover chain
* @param numMTS the number of step in the multiple time step chain propagation algorithm.
* @param numYoshidaSuzuki the number of terms in the Yoshida-Suzuki multi time step decomposition
* used in the chain propagation algorithm (must be 1, 3, or 5).
*/
int addThermostat(double temperature, double collisionFrequency,
int chainLength, int numMTS, int numYoshidaSuzuki);
/**
* Add a Nose-Hoover Chain thermostat to control the temperature of a collection of atoms and/or pairs of
* connected atoms within the full system. A list of atoms defining the atoms to be thermostated is
* provided and the thermostat will only control members of that list. Additionally a list of pairs of
* connected atoms may be provided; in this case both the center of mass absolute motion of each pair is
* controlled as well as their motion relative to each other, which is independently thermostated.
* If both the list of thermostated particles and thermostated pairs are empty all particles will be thermostated.
*
* @param thermostatedParticles list of particle ids to be thermostated.
* @param thermostatedPairs a list of pairs of connected atoms whose absolute center of mass motion
* and motion relative to one another will be independently thermostated.
* @param temperature the target temperature for each pair's absolute of center of mass motion.
* @param collisionFrequency the frequency of the interaction with the heat bath for the
* pairs' center of mass motion (in 1/ps).
* @param relativeTemperature the target temperature for each pair's relative motion.
* @param relativeCollisionFrequency the frequency of the interaction with the heat bath for the
* pairs' relative motion (in 1/ps).
* @param chainLength the number of beads in the Nose-Hoover chain.
* @param numMTS the number of step in the multiple time step chain propagation algorithm.
* @param numYoshidaSuzuki the number of terms in the Yoshida-Suzuki multi time step decomposition
* used in the chain propagation algorithm (must be 1, 3, or 5).
*/
int addSubsystemThermostat(const std::vector<int>& thermostatedParticles,
const std::vector< std::pair< int, int> >& thermostatedPairs,
double temperature, double collisionFrequency, double relativeTemperature,
double relativeCollisionFrequency,
int chainLength = 3, int numMTS = 3, int numYoshidaSuzuki = 3);
/**
* Get the temperature of the i-th chain for controling absolute particle motion (in Kelvin).
*
* @param chainID the index of the Nose-Hoover chain thermostat (default=0).
*
* @return the temperature.
*/
double getTemperature(int chainID=0) const;
/**
* set the (absolute motion) temperature of the i-th chain.
*
* @param temperature the temperature for the Nose-Hoover chain thermostat (in Kelvin).
* @param chainID The id of the Nose-Hoover chain thermostat for which the temperature is set (default=0).
*/
void setTemperature(double temperature, int chainID=0);
/**
* Get the temperature of the i-th chain for controling pairs' relative particle motion (in Kelvin).
*
* @param chainID the index of the Nose-Hoover chain thermostat (default=0).
*
* @return the temperature.
*/
double getRelativeTemperature(int chainID=0) const;
/**
* set the (relative pair motion) temperature of the i-th chain.
*
* @param temperature the temperature for the Nose-Hoover chain thermostat (in Kelvin).
* @param chainID The id of the Nose-Hoover chain thermostat for which the temperature is set (default=0).
*/
void setRelativeTemperature(double temperature, int chainID=0);
/**
* Get the collision frequency for absolute motion of the i-th chain (in 1/picosecond).
*
* @param chainID the index of the Nose-Hoover chain thermostat (default=0).
*
* @return the collision frequency.
*/
double getCollisionFrequency(int chainID=0) const;
/**
* Set the collision frequency for absolute motion of the i-th chain.
*
* @param frequency the collision frequency in picosecond.
* @param chainID the index of the Nose-Hoover chain thermostat (default=0).
*/
void setCollisionFrequency(double frequency, int chainID=0);
/**
* Get the collision frequency for pairs' relative motion of the i-th chain (in 1/picosecond).
*
* @param chainID the index of the Nose-Hoover chain thermostat (default=0).
*
* @return the collision frequency.
*/
double getRelativeCollisionFrequency(int chainID=0) const;
/**
* Set the collision frequency for pairs' relative motion of the i-th chain.
*
* @param frequency the collision frequency in picosecond.
* @param chainID the index of the Nose-Hoover chain thermostat (default=0).
*/
void setRelativeCollisionFrequency(double frequency, int chainID=0);
/**
* Compute the total (potential + kinetic) heat bath energy for all heat baths
* associated with this integrator, at the current time.
*/
double computeHeatBathEnergy();
/**
* Get the number of Nose-Hoover chains registered with this integrator.
*/
int getNumThermostats() const {
return noseHooverChains.size();
}
/**
* Get the NoseHooverChain thermostat
*
* @param chainID the index of the Nose-Hoover chain thermostat (default=0).
*/
const NoseHooverChain& getThermostat(int chainID=0) const ;
/**
* This will be called by the Context when the user modifies aspects of the context state, such
* as positions, velocities, or parameters. This gives the Integrator a chance to discard cached
* information. This is <i>only</i> called when the user modifies information using methods of the Context
* object. It is <i>not</i> called when a ForceImpl object modifies state information in its updateContextState()
* method (unless the ForceImpl calls a Context method to perform the modification).
*
* @param changed this specifies what aspect of the Context was changed
*/
virtual void stateChanged(State::DataType changed) {
if (State::Positions == changed) forcesAreValid = false;
}
/**
* Return false, if this integrator was set up with the 'default constructor' that thermostats the whole system,
* true otherwise. Required for serialization.
*/
bool hasSubsystemThermostats() const {
return hasSubsystemThermostats_;
}
/**
* Gets the maximum distance (in nm) that a connected pair may stray from each other. If zero, there are no
* constraints on the intra-pair separation.
*/
double getMaximumPairDistance() const { return maxPairDistance_; }
/**
* Sets the maximum distance (in nm) that a connected pair may stray from each other, implemented using a hard
* wall. If set to zero, the hard wall constraint is omited and the pairs are free to be separated by any distance.
*/
void setMaximumPairDistance(double distance) { maxPairDistance_ = distance; }
/**
* Get a list of all individual atoms (i.e. not involved in a connected Drude-like pair) in the system.
*/
const std::vector<int> & getAllThermostatedIndividualParticles() const { return allAtoms; }
/**
* Get a list of all connected Drude-like pairs, and their target relative temperature, in the system.
*/
const std::vector<std::tuple<int, int, double> > & getAllThermostatedPairs() const { return allPairs; }
protected:
/**
* Advance any Nose-Hoover chains associated with this integrator and determine
* scale factor for the velocities.
*
* @param kineticEnergy the {absolute, relative} kinetic energies of the system that the chain is thermostating
* @param chainID id of the Nose-Hoover-Chain
* @return the scale factor to be applied to the velocities of the particles thermostated by the chain.
*/
std::pair<double, double> propagateChain(std::pair<double, double> kineticEnergy, int chainID=0);
/**
* This will be called by the Context when it is created. It informs the Integrator
* of what context it will be integrating, and gives it a chance to do any necessary initialization.
* It will also get called again if the application calls reinitialize() on the Context.
*/
void initialize(ContextImpl& context);
/**
* Goes through the list of thermostats, sets the number of DOFs, and checks for errors in the thermostats.
*/
void initializeThermostats(const System& system);
/**
* This will be called by the Context when it is destroyed to let the Integrator do any necessary
* cleanup. It will also get called again if the application calls reinitialize() on the Context.
*/
void cleanup();
/**
* Get the names of all Kernels used by this Integrator.
*/
std::vector<std::string> getKernelNames();
/**
* Compute the kinetic energy of the system at the current time.
*/
virtual double computeKineticEnergy();
std::vector<NoseHooverChain> noseHooverChains;
std::vector<int> allAtoms;
std::vector<std::tuple<int, int, double> > allPairs;
bool forcesAreValid;
Kernel vvKernel, nhcKernel;
bool hasSubsystemThermostats_;
double maxPairDistance_;
};
} // namespace OpenMM
#endif /*OPENMM_NOSEHOOVERINTEGRATOR_H_*/
openmmapi/src/ContextImpl.cpp
View file @ 5a06df78
......@@ -481,6 +481,10 @@ void ContextImpl::loadCheckpoint(istream& stream) {
}
updateStateDataKernel.getAs<UpdateStateDataKernel>().loadCheckpoint(*this, stream);
hasSetPositions = true;
integrator.stateChanged(State::Positions);
integrator.stateChanged(State::Velocities);
integrator.stateChanged(State::Parameters);
integrator.stateChanged(State::Energy);
}
void ContextImpl::systemChanged() {
......
openmmapi/src/BAOABLangevinIntegrator.cpp → openmmapi/src/LangevinMiddleIntegrator.cpp
View file @ 5a06df78
......@@ -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) 2008-2019 Stanford University and the Authors. *
* Portions copyright (c) 2008-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -29,7 +29,7 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/BAOABLangevinIntegrator.h"
#include "openmm/LangevinMiddleIntegrator.h"
#include "openmm/Context.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
......@@ -40,51 +40,47 @@ using namespace OpenMM;
using std::string;
using std::vector;
BAOABLangevinIntegrator::BAOABLangevinIntegrator(double temperature, double frictionCoeff, double stepSize) {
LangevinMiddleIntegrator::LangevinMiddleIntegrator(double temperature, double frictionCoeff, double stepSize) {
setTemperature(temperature);
setFriction(frictionCoeff);
setStepSize(stepSize);
setConstraintTolerance(1e-5);
setRandomNumberSeed(0);
forcesAreValid = false;
}
void BAOABLangevinIntegrator::initialize(ContextImpl& contextRef) {
void LangevinMiddleIntegrator::initialize(ContextImpl& contextRef) {
if (owner != NULL && &contextRef.getOwner() != owner)
throw OpenMMException("This Integrator is already bound to a context");
context = &contextRef;
owner = &contextRef.getOwner();
kernel = context->getPlatform().createKernel(IntegrateBAOABStepKernel::Name(), contextRef);
kernel.getAs<IntegrateBAOABStepKernel>().initialize(contextRef.getSystem(), *this);
kernel = context->getPlatform().createKernel(IntegrateLangevinMiddleStepKernel::Name(), contextRef);
kernel.getAs<IntegrateLangevinMiddleStepKernel>().initialize(contextRef.getSystem(), *this);
}
void BAOABLangevinIntegrator::cleanup() {
void LangevinMiddleIntegrator::cleanup() {
kernel = Kernel();
}
void BAOABLangevinIntegrator::stateChanged(State::DataType changed) {
forcesAreValid = false;
}
vector<string> BAOABLangevinIntegrator::getKernelNames() {
vector<string> LangevinMiddleIntegrator::getKernelNames() {
std::vector<std::string> names;
names.push_back(IntegrateBAOABStepKernel::Name());
names.push_back(IntegrateLangevinMiddleStepKernel::Name());
return names;
}
double BAOABLangevinIntegrator::computeKineticEnergy() {
return kernel.getAs<IntegrateBAOABStepKernel>().computeKineticEnergy(*context, *this);
double LangevinMiddleIntegrator::computeKineticEnergy() {
return kernel.getAs<IntegrateLangevinMiddleStepKernel>().computeKineticEnergy(*context, *this);
}
bool BAOABLangevinIntegrator::kineticEnergyRequiresForce() const {
bool LangevinMiddleIntegrator::kineticEnergyRequiresForce() const {
return false;
}
void BAOABLangevinIntegrator::step(int steps) {
void LangevinMiddleIntegrator::step(int steps) {
if (context == NULL)
throw OpenMMException("This Integrator is not bound to a context!");
for (int i = 0; i < steps; ++i) {
context->updateContextState();
kernel.getAs<IntegrateBAOABStepKernel>().execute(*context, *this, forcesAreValid);
context->calcForcesAndEnergy(true, false);
kernel.getAs<IntegrateLangevinMiddleStepKernel>().execute(*context, *this);
}
}
openmmapi/src/NonbondedForce.cpp
View file @ 5a06df78
......@@ -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) 2008-2018 Stanford University and the Authors. *
* Portions copyright (c) 2008-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -48,7 +48,7 @@ using std::stringstream;
using std::vector;
NonbondedForce::NonbondedForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), switchingDistance(-1.0), rfDielectric(78.3),
ewaldErrorTol(5e-4), alpha(0.0), dalpha(0.0), useSwitchingFunction(false), useDispersionCorrection(true), recipForceGroup(-1),
ewaldErrorTol(5e-4), alpha(0.0), dalpha(0.0), useSwitchingFunction(false), useDispersionCorrection(true), exceptionsUsePeriodic(false), recipForceGroup(-1),
nx(0), ny(0), nz(0), dnx(0), dny(0), dnz(0) {
}
......@@ -347,3 +347,11 @@ void NonbondedForce::setReciprocalSpaceForceGroup(int group) {
void NonbondedForce::updateParametersInContext(Context& context) {
dynamic_cast<NonbondedForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
bool NonbondedForce::getExceptionsUsePeriodicBoundaryConditions() const {
return exceptionsUsePeriodic;
}
void NonbondedForce::setExceptionsUsePeriodicBoundaryConditions(bool periodic) {
exceptionsUsePeriodic = periodic;
}
openmmapi/src/NoseHooverChain.cpp 0 → 100644
View file @ 5a06df78
/* -------------------------------------------------------------------------- *
* 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) 2019 Stanford University and the Authors. *
* Authors: Andreas Krämer and Andrew C. Simmonett *
* 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/NoseHooverChain.h"
#include "openmm/OpenMMException.h"
using namespace OpenMM;
NoseHooverChain::NoseHooverChain(double temperature, double relativeTemperature, double collisionFrequency,
double relativeCollisionFrequency,
int numDOFs_, int chainLength_, int numMTS_,
int numYoshidaSuzuki, int chainID_,
const std::vector<int>& thermostatedAtoms, const std::vector<std::pair<int, int> > &thermostatedPairs):
temp(temperature), relativeTemp(relativeTemperature), freq(collisionFrequency),
relativeFreq(relativeCollisionFrequency), numDOFs(numDOFs_),
chainLength(chainLength_), numMTS(numMTS_), numYS(numYoshidaSuzuki),
chainID(chainID_), thermostatedAtoms(thermostatedAtoms), thermostatedPairs(thermostatedPairs)
{}
std::vector<double> NoseHooverChain::getYoshidaSuzukiWeights() const {
switch (numYS) {
case 1:
return {1};
case 3:
return {0.828981543588751, -0.657963087177502, 0.828981543588751};
case 5:
return {0.2967324292201065, 0.2967324292201065, -0.186929716880426, 0.2967324292201065,
0.2967324292201065};
default:
throw OpenMMException("The number of Yoshida-Suzuki weights must be 1,3, or 5.");
}
}
openmmapi/src/NoseHooverIntegrator.cpp 0 → 100644
View file @ 5a06df78
/* -------------------------------------------------------------------------- *
* 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) 2019 Stanford University and the Authors. *
* Authors: Andreas Krämer and Andrew C. Simmonett *
* 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/NoseHooverIntegrator.h"
#include "openmm/Context.h"
#include "openmm/Force.h"
#include "openmm/System.h"
#include "openmm/NoseHooverChain.h"
#include "openmm/OpenMMException.h"
#include "openmm/CMMotionRemover.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/kernels.h"
#include <iostream>
#include <string>
#include <algorithm>
using namespace OpenMM;
using std::string;
using std::vector;
NoseHooverIntegrator::NoseHooverIntegrator(double stepSize):
forcesAreValid(false),
hasSubsystemThermostats_(true)
{
setStepSize(stepSize);
setConstraintTolerance(1e-5);
setMaximumPairDistance(0.0);
}
NoseHooverIntegrator::NoseHooverIntegrator(double temperature, double collisionFrequency, double stepSize,
int chainLength, int numMTS, int numYoshidaSuzuki) :
forcesAreValid(false),
hasSubsystemThermostats_(false) {
setStepSize(stepSize);
setConstraintTolerance(1e-5);
setMaximumPairDistance(0.0);
addThermostat(temperature, collisionFrequency, chainLength, numMTS, numYoshidaSuzuki);
}
NoseHooverIntegrator::~NoseHooverIntegrator() {}
std::pair<double, double> NoseHooverIntegrator::propagateChain(std::pair<double, double> kineticEnergy, int chainID) {
return nhcKernel.getAs<NoseHooverChainKernel>().propagateChain(*context, noseHooverChains.at(chainID), kineticEnergy, getStepSize());
}
int NoseHooverIntegrator::addThermostat(double temperature, double collisionFrequency,
int chainLength, int numMTS, int numYoshidaSuzuki) {
hasSubsystemThermostats_ = false;
return addSubsystemThermostat(std::vector<int>(), std::vector<std::pair<int, int>>(), temperature,
collisionFrequency, temperature, collisionFrequency, chainLength, numMTS, numYoshidaSuzuki);
}
int NoseHooverIntegrator::addSubsystemThermostat(const std::vector<int>& thermostatedParticles,
const std::vector< std::pair< int, int> > &thermostatedPairs,
double temperature, double collisionFrequency,
double relativeTemperature, double relativeCollisionFrequency,
int chainLength, int numMTS, int numYoshidaSuzuki) {
int chainID = noseHooverChains.size();
// check if one thermostat already applies to all atoms or pairs
if ( (chainID > 0) && (noseHooverChains[0].getThermostatedAtoms().size()*noseHooverChains[0].getThermostatedPairs().size() == 0) ) {
throw OpenMMException(
"Cannot add thermostat, since one of the thermostats already in the integrator applies to all particles. "
"To manually add thermostats, use the constructor that takes only the "
"step size as an input argument."
);
}
int nDOF = 0; // is set in initializeThermostats()
noseHooverChains.emplace_back(temperature, relativeTemperature,
collisionFrequency, relativeCollisionFrequency,
nDOF, chainLength, numMTS,
numYoshidaSuzuki, chainID,
thermostatedParticles, thermostatedPairs);
return chainID;
}
const NoseHooverChain& NoseHooverIntegrator::getThermostat(int chainID) const {
ASSERT_VALID_INDEX(chainID, noseHooverChains);
return noseHooverChains[chainID];
}
void NoseHooverIntegrator::initializeThermostats(const System &system) {
allAtoms.clear();
allPairs.clear();
std::set<int> allAtomsSet;
for (int atom = 0; atom < system.getNumParticles(); ++atom) allAtomsSet.insert(atom);
for (auto &thermostat : noseHooverChains) {
const auto &thermostatedParticles = thermostat.getThermostatedAtoms();
const auto &thermostatedPairs = thermostat.getThermostatedPairs();
for( auto& pair : thermostatedPairs ) {
allAtomsSet.erase(pair.first);
allAtomsSet.erase(pair.second);
allPairs.emplace_back(pair.first, pair.second, thermostat.getRelativeTemperature());
}
// figure out the number of DOFs
int nDOF = 3*(thermostatedParticles.size() + thermostatedPairs.size());
for (int constraintNum = 0; constraintNum < system.getNumConstraints(); constraintNum++) {
int particle1, particle2;
double distance;
system.getConstraintParameters(constraintNum, particle1, particle2, distance);
bool particle1_in_thermostatedParticles = ((std::find(thermostatedParticles.begin(),
thermostatedParticles.end(), particle1)
!= thermostatedParticles.end())) ||
(std::find_if(thermostatedPairs.begin(),
thermostatedPairs.end(),
[&particle1](const std::pair<int, int>& pair){
return pair.first == particle1 || pair.second == particle1;})
!= thermostatedPairs.end());
bool particle2_in_thermostatedParticles = ((std::find(thermostatedParticles.begin(),
thermostatedParticles.end(), particle2)
!= thermostatedParticles.end())) ||
(std::find_if(thermostatedPairs.begin(),
thermostatedPairs.end(),
[&particle2](const std::pair<int, int>& pair){
return pair.first == particle2 || pair.second == particle2;})
!= thermostatedPairs.end());
if ((system.getParticleMass(particle1) > 0) && (system.getParticleMass(particle2) > 0)){
if ((particle1_in_thermostatedParticles && !particle2_in_thermostatedParticles) ||
(!particle1_in_thermostatedParticles && particle2_in_thermostatedParticles)){
throw OpenMMException("Cannot add only one of particles " + std::to_string(particle1) + " and " + std::to_string(particle2)
+ " to NoseHooverChain, because they are connected by a constraint.");
}
if (particle1_in_thermostatedParticles && particle2_in_thermostatedParticles){
nDOF -= 1;
}
}
}
// remove 3 degrees of freedom from thermostats that act on absolute motions
int numForces = system.getNumForces();
if (thermostatedPairs.size() == 0){
for (int forceNum = 0; forceNum < numForces; ++forceNum) {
if (dynamic_cast<const CMMotionRemover*>(&system.getForce(forceNum))) nDOF -= 3;
}
}
// set number of DoFs for chain
thermostat.setNumDegreesOfFreedom(nDOF);
}
for (int chain1 = 0; chain1 < noseHooverChains.size(); ++chain1){
const auto& nhc = noseHooverChains[chain1];
// make sure that thermostats do not overlap
for (int chain2 = 0; chain2 < chain1; ++chain2){
const auto& other_nhc = noseHooverChains[chain2];
for (auto &particle: nhc.getThermostatedAtoms()){
bool isParticleInOtherChain = (std::find(other_nhc.getThermostatedAtoms().begin(),
other_nhc.getThermostatedAtoms().end(),
particle) != other_nhc.getThermostatedAtoms().end()) ||
(std::find_if(other_nhc.getThermostatedPairs().begin(),
other_nhc.getThermostatedPairs().end(),
[&particle](const std::pair<int, int>& pair){ return pair.first == particle || pair.second == particle;})
!= other_nhc.getThermostatedPairs().end());
if (isParticleInOtherChain){
throw OpenMMException("Found particle " + std::to_string(particle) + "in a different NoseHooverChain, "
"but particles can only be thermostated by one thermostat.");
}
}
for (auto &pair: nhc.getThermostatedPairs()){
bool isParticleInOtherChain = (std::find(other_nhc.getThermostatedAtoms().begin(),
other_nhc.getThermostatedAtoms().end(),
pair.first) != other_nhc.getThermostatedAtoms().end()) ||
(std::find(other_nhc.getThermostatedAtoms().begin(),
other_nhc.getThermostatedAtoms().end(),
pair.second) != other_nhc.getThermostatedAtoms().end()) ||
(std::find_if(other_nhc.getThermostatedPairs().begin(),
other_nhc.getThermostatedPairs().end(),
[&pair](const std::pair<int, int>& other_pair){
return pair.first == other_pair.first || pair.first == other_pair.second ||
pair.second == other_pair.first || pair.second == other_pair.second;})
!= other_nhc.getThermostatedPairs().end());
if (isParticleInOtherChain){
throw OpenMMException("Found pair " + std::to_string(pair.first) + "," +
std::to_string(pair.second) + " in a different NoseHooverChain, "
"but particles can only be thermostated by one thermostat.");
}
}
}
// make sure that massless particles are not thermostated
for(auto particle: nhc.getThermostatedAtoms()){
double mass = system.getParticleMass(particle);
if (mass == 0.0) {
throw OpenMMException("Found a particle with no mass (" + std::to_string(particle) + ") in a thermostat. Massless particles cannot be thermostated.");
}
}
}
for(const auto& atom : allAtomsSet) allAtoms.push_back(atom);
}
double NoseHooverIntegrator::getTemperature(int chainID) const {
ASSERT_VALID_INDEX(chainID, noseHooverChains);
return noseHooverChains[chainID].getTemperature();
}
void NoseHooverIntegrator::setTemperature(double temperature, int chainID){
ASSERT_VALID_INDEX(chainID, noseHooverChains);
noseHooverChains[chainID].setTemperature(temperature);
}
double NoseHooverIntegrator::getRelativeTemperature(int chainID) const {
ASSERT_VALID_INDEX(chainID, noseHooverChains);
return noseHooverChains[chainID].getRelativeTemperature();
}
void NoseHooverIntegrator::setRelativeTemperature(double temperature, int chainID){
ASSERT_VALID_INDEX(chainID, noseHooverChains);
noseHooverChains[chainID].setRelativeTemperature(temperature);
}
double NoseHooverIntegrator::getCollisionFrequency(int chainID) const {
ASSERT_VALID_INDEX(chainID, noseHooverChains);
return noseHooverChains[chainID].getCollisionFrequency();
}
void NoseHooverIntegrator::setCollisionFrequency(double frequency, int chainID){
ASSERT_VALID_INDEX(chainID, noseHooverChains);
noseHooverChains[chainID].setCollisionFrequency(frequency);
}
double NoseHooverIntegrator::getRelativeCollisionFrequency(int chainID) const {
ASSERT_VALID_INDEX(chainID, noseHooverChains);
return noseHooverChains[chainID].getRelativeCollisionFrequency();
}
void NoseHooverIntegrator::setRelativeCollisionFrequency(double frequency, int chainID){
ASSERT_VALID_INDEX(chainID, noseHooverChains);
noseHooverChains[chainID].setRelativeCollisionFrequency(frequency);
}
double NoseHooverIntegrator::computeKineticEnergy() {
double kE = 0.0;
if(noseHooverChains.size() > 0) {
for (const auto &nhc: noseHooverChains){
kE += nhcKernel.getAs<NoseHooverChainKernel>().computeMaskedKineticEnergy(*context, nhc, true).first;
}
} else {
kE = vvKernel.getAs<IntegrateVelocityVerletStepKernel>().computeKineticEnergy(*context, *this);
}
return kE;
}
double NoseHooverIntegrator::computeHeatBathEnergy() {
double energy = 0;
for(auto &nhc : noseHooverChains) {
if (context && (nhc.getNumDegreesOfFreedom() > 0)) {
energy += nhcKernel.getAs<NoseHooverChainKernel>().computeHeatBathEnergy(*context, nhc);
}
}
return energy;
}
void NoseHooverIntegrator::initialize(ContextImpl& contextRef) {
if (owner != NULL && &contextRef.getOwner() != owner)
throw OpenMMException("This Integrator is already bound to a context");
context = &contextRef;
const System& system = context->getSystem();
owner = &contextRef.getOwner();
vvKernel = context->getPlatform().createKernel(IntegrateVelocityVerletStepKernel::Name(), contextRef);
vvKernel.getAs<IntegrateVelocityVerletStepKernel>().initialize(contextRef.getSystem(), *this);
nhcKernel = context->getPlatform().createKernel(NoseHooverChainKernel::Name(), contextRef);
nhcKernel.getAs<NoseHooverChainKernel>().initialize();
forcesAreValid = false;
// check for drude particles and build the Nose-Hoover Chains
for (auto& thermostat: noseHooverChains){
// if there are no thermostated particles or pairs in the lists this is a regular thermostat for the whole (non-Drude) system
if ( (thermostat.getThermostatedAtoms().size() == 0) && (thermostat.getThermostatedPairs().size() == 0) ){
std::vector<int> thermostatedParticles;
for(int particle = 0; particle < system.getNumParticles(); ++particle) {
double mass = system.getParticleMass(particle);
if ( (mass > 0) && (mass < 0.8) ){
std::cout << "Warning: Found particles with mass between 0.0 and 0.8 dalton. Did you mean to make a DrudeNoseHooverIntegrator instead? "
"The thermostat you are about to use will not treat these particles as Drude particles!" << std::endl;
}
if(system.getParticleMass(particle) > 0) {
thermostatedParticles.push_back(particle);
}
}
thermostat.setThermostatedAtoms(thermostatedParticles);
}
}
initializeThermostats(system);
}
void NoseHooverIntegrator::cleanup() {
vvKernel = Kernel();
nhcKernel = Kernel();
}
vector<string> NoseHooverIntegrator::getKernelNames() {
std::vector<std::string> names;
names.push_back(NoseHooverChainKernel::Name());
names.push_back(IntegrateVelocityVerletStepKernel::Name());
return names;
}
void NoseHooverIntegrator::step(int steps) {
if (context == NULL)
throw OpenMMException("This Integrator is not bound to a context!");
std::pair<double, double> scale, kineticEnergy;
for (int i = 0; i < steps; ++i) {
context->updateContextState();
for(auto &nhc : noseHooverChains) {
kineticEnergy = nhcKernel.getAs<NoseHooverChainKernel>().computeMaskedKineticEnergy(*context, nhc, false);
scale = nhcKernel.getAs<NoseHooverChainKernel>().propagateChain(*context, nhc, kineticEnergy, getStepSize());
nhcKernel.getAs<NoseHooverChainKernel>().scaleVelocities(*context, nhc, scale);
}
vvKernel.getAs<IntegrateVelocityVerletStepKernel>().execute(*context, *this, forcesAreValid);
for(auto &nhc : noseHooverChains) {
kineticEnergy = nhcKernel.getAs<NoseHooverChainKernel>().computeMaskedKineticEnergy(*context, nhc, false);
scale = nhcKernel.getAs<NoseHooverChainKernel>().propagateChain(*context, nhc, kineticEnergy, getStepSize());
nhcKernel.getAs<NoseHooverChainKernel>().scaleVelocities(*context, nhc, scale);
}
}
}
platforms/common/CMakeLists.txt 0 → 100644
View file @ 5a06df78
# Encode the kernel sources into a C++ class.
SET(KERNEL_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/src")
SET(KERNEL_SOURCE_CLASS CommonKernelSources)
SET(KERNELS_CPP ${CMAKE_CURRENT_BINARY_DIR}/src/${KERNEL_SOURCE_CLASS}.cpp)
SET(KERNELS_H ${CMAKE_CURRENT_BINARY_DIR}/src/${KERNEL_SOURCE_CLASS}.h)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_BINARY_DIR}/src)
FILE(GLOB COMMON_KERNELS ${KERNEL_SOURCE_DIR}/kernels/*.cc)
ADD_CUSTOM_COMMAND(OUTPUT ${KERNELS_CPP} ${KERNELS_H}
COMMAND ${CMAKE_COMMAND}
ARGS -D KERNEL_SOURCE_DIR=${KERNEL_SOURCE_DIR} -D KERNELS_CPP=${KERNELS_CPP} -D KERNELS_H=${KERNELS_H} -D KERNEL_SOURCE_CLASS=${KERNEL_SOURCE_CLASS} -D KERNEL_FILE_EXTENSION=cc -P ${CMAKE_SOURCE_DIR}/cmake_modules/EncodeKernelFiles.cmake
DEPENDS ${COMMON_KERNELS}
)
SET_SOURCE_FILES_PROPERTIES(${KERNELS_CPP} ${KERNELS_H} PROPERTIES GENERATED TRUE)
ADD_CUSTOM_TARGET(CommonKernels DEPENDS ${KERNELS_CPP} ${KERNELS_H})
# Install headers
FILE(GLOB CORE_HEADERS include/openmm/common/*.h)
INSTALL_FILES(/include/openmm/common FILES ${CORE_HEADERS})
platforms/common/include/openmm/common/ArrayInterface.h 0 → 100644
View file @ 5a06df78
#ifndef OPENMM_ARRAYINTERFACE_H_
#define OPENMM_ARRAYINTERFACE_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) 2019 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
#include "openmm/OpenMMException.h"
#include "openmm/common/windowsExportCommon.h"
#include <vector>
namespace OpenMM {
class ComputeContext;
/**
* This abstract class defines the interface for arrays stored on a computing device.
*/
class OPENMM_EXPORT_COMMON ArrayInterface {
public:
virtual ~ArrayInterface() {
}
/**
* Initialize this array.
*
* @param context the context for which to create the array
* @param size the number of elements in the array
* @param elementSize the size of each element in bytes
* @param name the name of the array
*/
virtual void initialize(ComputeContext& context, int size, int elementSize, const std::string& name) = 0;
/**
* Initialize this object. The template argument is the data type of each array element.
*
* @param context the context for which to create the array
* @param size the number of elements in the array
* @param name the name of the array
*/
template <class T>
void initialize(ComputeContext& context, int size, const std::string& name) {
initialize(context, size, sizeof(T), name);
}
/**
* Recreate the internal storage to have a different size.
*/
virtual void resize(int size) = 0;
/**
* Get whether this array has been initialized.
*/
virtual bool isInitialized() const = 0;
/**
* Get the number of elements in the array.
*/
virtual int getSize() const = 0;
/**
* Get the size of each element in bytes.
*/
virtual int getElementSize() const = 0;
/**
* Get the name of the array.
*/
virtual const std::string& getName() const = 0;
/**
* Get the context this array belongs to.
*/
virtual ComputeContext& getContext() = 0;
/**
* Copy the values in a vector to the device memory.
*
* @param data the data in host memory to copy
* @param convert if true, automatic conversions between single and double
* precision will be performed as necessary
*/
template <class T>
void upload(const std::vector<T>& data, bool convert=false) {
if (convert && data.size() == getSize() && sizeof(T) != getElementSize()) {
if (sizeof(T) == 2*getElementSize()) {
// Convert values from double to single precision.
const double* d = reinterpret_cast<const double*>(&data[0]);
std::vector<float> v(getElementSize()*getSize()/sizeof(float));
for (int i = 0; i < v.size(); i++)
v[i] = (float) d[i];
upload(&v[0], true);
return;
}
if (2*sizeof(T) == getElementSize()) {
// Convert values from single to double precision.
const float* d = reinterpret_cast<const float*>(&data[0]);
std::vector<double> v(getElementSize()*getSize()/sizeof(double));
for (int i = 0; i < v.size(); i++)
v[i] = (double) d[i];
upload(&v[0], true);
return;
}
}
if (sizeof(T) != getElementSize() || data.size() != getSize())
throw OpenMMException("Error uploading array "+getName()+": The specified vector does not match the size of the array");
upload(&data[0], true);
}
/**
* Copy the values in the array to a vector.
*/
template <class T>
void download(std::vector<T>& data) const {
if (sizeof(T) != getElementSize())
throw OpenMMException("Error downloading array "+getName()+": The specified vector has the wrong element size");
if (data.size() != getSize())
data.resize(getSize());
download(&data[0], true);
}
/**
* Copy the values from host memory to the array.
*
* @param data the data to copy
* @param blocking if true, this call will block until the transfer is complete. Subclasses often
* have restrictions on non-blocking copies, such as that the source data must be
* in page-locked memory.
*/
virtual void upload(const void* data, bool blocking=true) = 0;
/**
* Copy the values in the array to host memory.
*
* @param data the destination to copy the value to
* @param blocking if true, this call will block until the transfer is complete. Subclasses often
* have restrictions on non-blocking copies, such as that the destination must be
* in page-locked memory.
*/
virtual void download(void* data, bool blocking=true) const = 0;
/**
* Copy the values in this array to a second array.
*
* @param dest the destination array to copy to
*/
virtual void copyTo(ArrayInterface& dest) const = 0;
};
} // namespace OpenMM
#endif /*OPENMM_ARRAYINTERFACE_H_*/
platforms/common/include/openmm/common/BondedUtilities.h 0 → 100644
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#ifndef OPENMM_BONDEDUTILITIES_H_
#define OPENMM_BONDEDUTILITIES_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) 2011-2019 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
#include "openmm/common/ArrayInterface.h"
#include <string>
#include <vector>
namespace OpenMM {
/**
* This abstract class defines an interface for computing bonded interactions. Call
* getBondedUtilities() on a ComputeContext to get the BondedUtilities object for that
* context.
*
* This class provides a generic mechanism for evaluating bonded interactions. You write only
* the source code needed to compute one interaction, and this object takes care of creating
* and executing a complete kernel that loops over bonds, evaluates each one, and accumulates
* the resulting forces and energies. This offers two advantages. First, it simplifies the
* task of writing a new Force. Second, it allows multiple forces to be evaluated by a single
* kernel, which reduces overhead and improves performance.
*
* A "bonded interaction" means an interaction that affects a small, fixed set of particles.
* The interaction energy may depend on the positions of only those particles, and the list of
* particles forming a "bond" may not change with time. Examples of bonded interactions
* include HarmonicBondForce, HarmonicAngleForce, and PeriodicTorsionForce.
*
* To create a bonded interaction, call addInteraction(). You pass to it a block of source
* code for evaluating the interaction. The inputs and outputs for that source code are as
* follows:
*
* <ol>
* <li>The index of the bond being evaluated will have been stored in the unsigned int variable "index".</li>
* <li>The indices of the atoms forming that bond will have been stored in the unsigned int variables "atom1",
* "atom2", ....</li>
* <li>The positions of those atoms will have been stored in the real4 variables "pos1", "pos2", ....</li>
* <li>A real variable called "energy" will exist. Your code should add the potential energy of the
* bond to that variable.</li>
* <li>Your code should define real3 variables called "force1", "force2", ... that contain the force to
* apply to each atom.</li>
* </ol>
*
* As a simple example, the following source code would be used to implement a pairwise interaction of
* the form E=r^2:
*
* <tt><pre>
* real4 delta = pos2-pos1;
* energy += delta.x*delta.x + delta.y*delta.y + delta.z*delta.z;
* real3 force1 = 2.0f*delta;
* real3 force2 = -2.0f*delta;
* </pre></tt>
*
* Interactions will often depend on parameters or other data. Call addArgument() to provide the data
* to this class. It will be passed to the interaction kernel as an argument, and you can refer to it
* from your interaction code.
*/
class OPENMM_EXPORT_COMMON BondedUtilities {
public:
virtual ~BondedUtilities() {
}
/**
* Add a bonded interaction.
*
* @param atoms this should have one entry for each bond, and that entry should contain the list
* of atoms involved in the bond. Every entry must have the same number of atoms.
* @param source the code to evaluate the interaction
* @param group the force group in which the interaction should be calculated
*/
virtual void addInteraction(const std::vector<std::vector<int> >& atoms, const std::string& source, int group) = 0;
/**
* Add an argument that should be passed to the interaction kernel.
*
* @param data the array containing the data to pass
* @param type the data type contained in the memory (e.g. "float4")
* @return the name that will be used for the argument. Any code you pass to addInteraction() should
* refer to it by this name.
*/
virtual std::string addArgument(ArrayInterface& data, const std::string& type) = 0;
/**
* Register that the interaction kernel will be computing the derivative of the potential energy
* with respect to a parameter.
*
* @param param the name of the parameter
* @return the variable that will be used to accumulate the derivative. Any code you pass to addInteraction() should
* add its contributions to this variable.
*/
virtual std::string addEnergyParameterDerivative(const std::string& param) = 0;
/**
* Add some code that should be included in the program, before the start of the kernel.
* This can be used, for example, to define functions that will be called by the kernel.
*
* @param source the code to include
*/
virtual void addPrefixCode(const std::string& source) = 0;
};
} // namespace OpenMM
#endif /*OPENMM_BONDEDUTILITIES_H_*/
platforms/common/include/openmm/common/CommonKernels.h 0 → 100644
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platforms/common/include/openmm/common/ComputeArray.h 0 → 100644
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#ifndef OPENMM_COMPUTEARRAY_H_
#define OPENMM_COMPUTEARRAY_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) 2019 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
#include "openmm/common/ArrayInterface.h"
namespace OpenMM {
/**
* This is an implementation of ArrayInterface that acts as a wrapper around a platform-specific
* array implementation (typically CudaArray or OpenCLArray). This class can be used in code that
* is not platform-specific, and an appropriate implementation array is created automatically
* based on the ComputeContext.
*/
class OPENMM_EXPORT_COMMON ComputeArray : public ArrayInterface {
public:
/**
* Create an uninitialized ComputeArray object. It cannot be used until initialize() is called on it.
*/
ComputeArray();
/**
* Release all resources allocated by this object.
*/
~ComputeArray();
/**
* Get the internal array this object is wrapping.
*/
ArrayInterface& getArray();
/**
* Initialize this array.
*
* @param context the context for which to create the array
* @param size the number of elements in the array
* @param elementSize the size of each element in bytes
* @param name the name of the array
*/
void initialize(ComputeContext& context, int size, int elementSize, const std::string& name);
/**
* Initialize this object. The template argument is the data type of each array element.
*
* @param context the context for which to create the array
* @param size the number of elements in the array
* @param name the name of the array
*/
template <class T>
void initialize(ComputeContext& context, int size, const std::string& name) {
initialize(context, size, sizeof(T), name);
}
/**
* Recreate the internal storage to have a different size.
*/
void resize(int size);
/**
* Get whether this array has been initialized.
*/
bool isInitialized() const;
/**
* Get the number of elements in the array.
*/
int getSize() const;
/**
* Get the size of each element in bytes.
*/
int getElementSize() const;
/**
* Get the name of the array.
*/
const std::string& getName() const;
/**
* Get the context this array belongs to.
*/
ComputeContext& getContext();
/**
* Copy the values in a vector to the Buffer.
*/
template <class T>
void upload(const std::vector<T>& data, bool convert=false) {
ArrayInterface::upload(data, convert);
}
/**
* Copy the values in the Buffer to a vector.
*/
template <class T>
void download(std::vector<T>& data) const {
ArrayInterface::download(data);
}
/**
* Copy the values from host memory to the array.
*
* @param data the data to copy
* @param blocking if true, this call will block until the transfer is complete. Subclasses often
* have restrictions on non-blocking copies, such as that the source data must be
* in page-locked memory.
*/
void upload(const void* data, bool blocking=true);
/**
* Copy the values in the array to host memory.
*
* @param data the destination to copy the value to
* @param blocking if true, this call will block until the transfer is complete. Subclasses often
* have restrictions on non-blocking copies, such as that the destination must be
* in page-locked memory.
*/
void download(void* data, bool blocking=true) const;
/**
* Copy the values in this array to a second array.
*
* @param dest the destination array to copy to
*/
void copyTo(ArrayInterface& dest) const;
private:
ArrayInterface* impl;
};
} // namespace OpenMM
#endif /*OPENMM_COMPUTEARRAY_H_*/
platforms/common/include/openmm/common/ComputeContext.h 0 → 100644
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