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Commit d547601c authored by peastman's avatar peastman
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Merge pull request #369 from peastman/rpmd 

Created RPMDIntegrator::getTotalEnergy()
parents e94afeaf efbcb899
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Showing with 39 additions and 71 deletions
plugins/rpmd/openmmapi/include/openmm/RPMDIntegrator.h
View file @ d547601c
......@@ -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) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -195,6 +195,11 @@ public:
* and energies. Group i will be included if (groups&(1<<i)) != 0. The default value includes all groups.
*/
State getState(int copy, int types, bool enforcePeriodicBox=false, int groups=0xFFFFFFFF);
/**
* Get the total energy of the ring polymer. This includes the potential and kinetic energies of all copies,
* plus the potential energy of the harmonic springs that link copies together.
*/
double getTotalEnergy();
/**
* Advance a simulation through time by taking a series of time steps.
*
......
plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp
View file @ d547601c
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2013 Stanford University and the Authors. *
* Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -34,6 +34,7 @@
#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/RpmdKernels.h"
#include "SimTKOpenMMRealType.h"
#include <cmath>
#include <ctime>
#include <string>
......@@ -195,3 +196,27 @@ void RPMDIntegrator::step(int steps) {
forcesAreValid = true;
}
}
double RPMDIntegrator::getTotalEnergy() {
const System& system = owner->getSystem();
int numParticles = system.getNumParticles();
double energy = 0.0;
const double hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
const double wn = numCopies*BOLTZ*temperature/hbar;
State prevState = getState(numCopies-1, State::Positions);
for (int i = 0; i < numCopies; i++) {
// Add the energy of this copy.
State state = getState(i, State::Positions | State::Energy);
energy += state.getKineticEnergy()+state.getPotentialEnergy();
// Add the energy from the springs connecting it to the previous copy.
for (int j = 0; j < numParticles; j++) {
Vec3 delta = state.getPositions()[j]-prevState.getPositions()[j];
energy += 0.5*wn*wn*system.getParticleMass(j)*delta.dot(delta);
}
prevState = state;
}
return energy;
}
plugins/rpmd/platforms/cuda/tests/TestCudaRpmd.cpp
View file @ d547601c
......@@ -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) 2011-2013 Stanford University and the Authors. *
* Portions copyright (c) 2011-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -466,30 +466,9 @@ void testWithoutThermostat() {
double initialEnergy;
int numSteps = 100;
const double hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
const double wn = numCopies*BOLTZ*temperature/hbar;
const double springConstant = mass*wn*wn;
for (int i = 0; i < numSteps; i++) {
integ.step(1);
// Sum the energies of all the copies.
double energy = 0.0;
for (int j = 0; j < numCopies; j++) {
State state = integ.getState(j, State::Positions | State::Energy);
positions[j] = state.getPositions();
energy += state.getPotentialEnergy()+state.getKineticEnergy();
}
// Add the energy from the springs connecting copies.
for (int j = 0; j < numCopies; j++) {
int previous = (j == 0 ? numCopies-1 : j-1);
for (int k = 0; k < numParticles; k++) {
Vec3 delta = positions[j][k]-positions[previous][k];
energy += 0.5*springConstant*delta.dot(delta);
}
}
double energy = integ.getTotalEnergy();
if (i == 0)
initialEnergy = energy;
else
......
plugins/rpmd/platforms/opencl/tests/TestOpenCLRpmd.cpp
View file @ d547601c
......@@ -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) 2011-2013 Stanford University and the Authors. *
* Portions copyright (c) 2011-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -467,30 +467,9 @@ void testWithoutThermostat() {
double initialEnergy;
int numSteps = 100;
const double hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
const double wn = numCopies*BOLTZ*temperature/hbar;
const double springConstant = mass*wn*wn;
for (int i = 0; i < numSteps; i++) {
integ.step(1);
// Sum the energies of all the copies.
double energy = 0.0;
for (int j = 0; j < numCopies; j++) {
State state = integ.getState(j, State::Positions | State::Energy);
positions[j] = state.getPositions();
energy += state.getPotentialEnergy()+state.getKineticEnergy();
}
// Add the energy from the springs connecting copies.
for (int j = 0; j < numCopies; j++) {
int previous = (j == 0 ? numCopies-1 : j-1);
for (int k = 0; k < numParticles; k++) {
Vec3 delta = positions[j][k]-positions[previous][k];
energy += 0.5*springConstant*delta.dot(delta);
}
}
double energy = integ.getTotalEnergy();
if (i == 0)
initialEnergy = energy;
else
......
plugins/rpmd/platforms/reference/tests/TestReferenceRpmd.cpp
View file @ d547601c
......@@ -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) 2011-2013 Stanford University and the Authors. *
* Portions copyright (c) 2011-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -350,30 +350,9 @@ void testWithoutThermostat() {
double initialEnergy;
int numSteps = 100;
const double hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
const double wn = numCopies*BOLTZ*temperature/hbar;
const double springConstant = mass*wn*wn;
for (int i = 0; i < numSteps; i++) {
integ.step(1);
// Sum the energies of all the copies.
double energy = 0.0;
for (int j = 0; j < numCopies; j++) {
State state = integ.getState(j, State::Positions | State::Energy);
positions[j] = state.getPositions();
energy += state.getPotentialEnergy()+state.getKineticEnergy();
}
// Add the energy from the springs connecting copies.
for (int j = 0; j < numCopies; j++) {
int previous = (j == 0 ? numCopies-1 : j-1);
for (int k = 0; k < numParticles; k++) {
Vec3 delta = positions[j][k]-positions[previous][k];
energy += 0.5*springConstant*delta.dot(delta);
}
}
double energy = integ.getTotalEnergy();
if (i == 0)
initialEnergy = energy;
else
......
wrappers/python/src/swig_doxygen/swigInputConfig.py
View file @ d547601c
......@@ -424,5 +424,6 @@ UNITS = {
("DrudeLangevinIntegrator", "getDrudeFriction") : ("1/unit.picosecond", ()),
("DrudeSCFIntegrator", "getMinimizationErrorTolerance") : ("unit.kilojoules_per_mole/unit.nanometer", ()),
("RPMDIntegrator", "getContractions") : (None, ()),
("RPMDIntegrator", "getTotalEnergy") : ("unit.kilojoules_per_mole", ()),
}
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