Skip to content

GitLab

Commit 923ccea5 authored by peastman's avatar peastman
Browse files

Merge pull request #765 from swails/stochastic-forces 

Make it so that random forces and integrators generate unique seeds each time a Context is made
parents 9972e293 df99352d
Show whitespace changes
Inline Side-by-side
Showing with 41 additions and 11 deletions
openmmapi/src/VariableLangevinIntegrator.cpp
View file @ 923ccea5
......@@ -33,7 +33,6 @@
#include "openmm/Context.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/OSRngSeed.h"
#include "openmm/kernels.h"
#include <limits>
#include <string>
......@@ -48,7 +47,7 @@ VariableLangevinIntegrator::VariableLangevinIntegrator(double temperature, doubl
setFriction(frictionCoeff);
setErrorTolerance(errorTol);
setConstraintTolerance(1e-5);
setRandomNumberSeed(osrngseed());
setRandomNumberSeed(0);
setStepSize(0.0);
}
......
platforms/cpu/src/CpuRandom.cpp
View file @ 923ccea5
......@@ -23,6 +23,7 @@
*/
#include "CpuRandom.h"
#include "openmm/internal/OSRngSeed.h"
#include "openmm/OpenMMException.h"
#include <cmath>
......@@ -49,9 +50,13 @@ void CpuRandom::initialize(int seed, int numThreads) {
nextGaussian.resize(numThreads);
nextGaussianIsValid.resize(numThreads, false);
// Use a quick and dirty RNG to pick seeds for the real random number generator.
/* Use a quick and dirty RNG to pick seeds for the real random number generator.
* A random seed of 0 means pick a unique seed
*/
unsigned int r = (unsigned int) seed;
if (r == 0)
r = (unsigned int) osrngseed();
for (int i = 0; i < numThreads; i++) {
r = (1664525*r + 1013904223) & 0xFFFFFFFF;
threadRandom[i] = new OpenMM_SFMT::SFMT();
......
platforms/cuda/src/CudaIntegrationUtilities.cpp
View file @ 923ccea5
......@@ -27,6 +27,7 @@
#include "CudaIntegrationUtilities.h"
#include "CudaArray.h"
#include "CudaKernelSources.h"
#include "openmm/internal/OSRngSeed.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/VirtualSite.h"
#include "quern.h"
......@@ -858,6 +859,7 @@ void CudaIntegrationUtilities::initRandomNumberGenerator(unsigned int randomNumb
vector<int4> seed(randomSeed->getSize());
unsigned int r = randomNumberSeed;
if (r == 0) r = (unsigned int) osrngseed();
for (int i = 0; i < randomSeed->getSize(); i++) {
seed[i].x = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
seed[i].y = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
......
platforms/cuda/src/CudaKernels.cpp
View file @ 923ccea5
......@@ -36,6 +36,7 @@
#include "openmm/internal/CustomManyParticleForceImpl.h"
#include "openmm/internal/CustomNonbondedForceImpl.h"
#include "openmm/internal/NonbondedForceImpl.h"
#include "openmm/internal/OSRngSeed.h"
#include "CudaBondedUtilities.h"
#include "CudaExpressionUtilities.h"
#include "CudaIntegrationUtilities.h"
......@@ -5967,7 +5968,11 @@ void CudaIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context,
uniformRandoms = CudaArray::create<float4>(cu, maxUniformRandoms, "uniformRandoms");
randomSeed = CudaArray::create<int4>(cu, cu.getNumThreadBlocks()*CudaContext::ThreadBlockSize, "randomSeed");
vector<int4> seed(randomSeed->getSize());
unsigned int r = integrator.getRandomNumberSeed()+1;
int rseed = integrator.getRandomNumberSeed();
// A random seed of 0 means use a unique one
if (rseed == 0)
rseed = osrngseed();
unsigned int r = (unsigned int) (rseed+1);
for (int i = 0; i < randomSeed->getSize(); i++) {
seed[i].x = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
seed[i].y = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
......
platforms/opencl/src/OpenCLIntegrationUtilities.cpp
View file @ 923ccea5
......@@ -27,6 +27,7 @@
#include "OpenCLIntegrationUtilities.h"
#include "OpenCLArray.h"
#include "OpenCLKernelSources.h"
#include "openmm/internal/OSRngSeed.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/VirtualSite.h"
#include "quern.h"
......@@ -1003,6 +1004,8 @@ void OpenCLIntegrationUtilities::initRandomNumberGenerator(unsigned int randomNu
vector<mm_int4> seed(randomSeed->getSize());
unsigned int r = randomNumberSeed;
// A seed of 0 means use a unique one
if (r == 0) r = (unsigned int) osrngseed();
for (int i = 0; i < randomSeed->getSize(); i++) {
seed[i].x = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
seed[i].y = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 923ccea5
......@@ -36,6 +36,7 @@
#include "openmm/internal/CustomManyParticleForceImpl.h"
#include "openmm/internal/CustomNonbondedForceImpl.h"
#include "openmm/internal/NonbondedForceImpl.h"
#include "openmm/internal/OSRngSeed.h"
#include "OpenCLBondedUtilities.h"
#include "OpenCLExpressionUtilities.h"
#include "OpenCLIntegrationUtilities.h"
......@@ -6200,7 +6201,11 @@ void OpenCLIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
uniformRandoms = OpenCLArray::create<mm_float4>(cl, maxUniformRandoms, "uniformRandoms");
randomSeed = OpenCLArray::create<mm_int4>(cl, cl.getNumThreadBlocks()*OpenCLContext::ThreadBlockSize, "randomSeed");
vector<mm_int4> seed(randomSeed->getSize());
unsigned int r = integrator.getRandomNumberSeed()+1;
int rseed = integrator.getRandomNumberSeed();
// A random seed of 0 means use a unique one
if (rseed == 0)
rseed = osrngseed();
unsigned int r = (unsigned int) (rseed+1);
for (int i = 0; i < randomSeed->getSize(); i++) {
seed[i].x = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
seed[i].y = r = (1664525*r + 1013904223) & 0xFFFFFFFF;
......
platforms/reference/src/SimTKUtilities/SimTKOpenMMUtilities.cpp
View file @ 923ccea5
......@@ -24,6 +24,7 @@
// class of shared, static utility methods
#include "openmm/internal/OSRngSeed.h"
#include "SimTKOpenMMUtilities.h"
#include "SimTKOpenMMLog.h"
#include "sfmt/SFMT.h"
......@@ -361,6 +362,10 @@ void SimTKOpenMMUtilities::setRandomNumberSeed( uint32_t seed ) {
// ---------------------------------------------------------------------------------------
// If the seed is 0, use a unique seed
if (seed == 0)
_randomNumberSeed = (uint32_t) osrngseed();
else
_randomNumberSeed = seed;
_randomInitialized = false;
}
......
plugins/drude/openmmapi/include/openmm/DrudeLangevinIntegrator.h
View file @ 923ccea5
......@@ -142,6 +142,10 @@ public:
* the other hand, no guarantees are made about the behavior of simulations that use the same seed.
* In particular, Platforms are permitted to use non-deterministic algorithms which produce different
* results on successive runs, even if those runs were initialized identically.
*
* If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
* is created from this Force. This is done to ensure that each Context receives unique random seeds
* without you needing to set them explicitly.
*/
void setRandomNumberSeed(int seed) {
randomNumberSeed = seed;
......
plugins/drude/openmmapi/src/DrudeLangevinIntegrator.cpp
View file @ 923ccea5
......@@ -33,7 +33,6 @@
#include "openmm/Context.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/OSRngSeed.h"
#include "openmm/DrudeKernels.h"
#include <ctime>
#include <string>
......@@ -49,7 +48,7 @@ DrudeLangevinIntegrator::DrudeLangevinIntegrator(double temperature, double fric
setDrudeFriction(drudeFrictionCoeff);
setStepSize(stepSize);
setConstraintTolerance(1e-5);
setRandomNumberSeed(osrngseed());
setRandomNumberSeed(0);
}
void DrudeLangevinIntegrator::initialize(ContextImpl& contextRef) {
......
plugins/rpmd/openmmapi/include/openmm/RPMDIntegrator.h
View file @ 923ccea5
......@@ -155,6 +155,10 @@ public:
* the other hand, no guarantees are made about the behavior of simulations that use the same seed.
* In particular, Platforms are permitted to use non-deterministic algorithms which produce different
* results on successive runs, even if those runs were initialized identically.
*
* If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
* is created from this Force. This is done to ensure that each Context receives unique random seeds
* without you needing to set them explicitly.
*/
void setRandomNumberSeed(int seed) {
randomNumberSeed = seed;
......
plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp
View file @ 923ccea5
......@@ -33,7 +33,6 @@
#include "openmm/Context.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/OSRngSeed.h"
#include "openmm/RpmdKernels.h"
#include "SimTKOpenMMRealType.h"
#include <cmath>
......@@ -48,7 +47,7 @@ RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictio
setFriction(frictionCoeff);
setStepSize(stepSize);
setConstraintTolerance(1e-5);
setRandomNumberSeed(osrngseed());
setRandomNumberSeed(0);
}
RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize) :
......@@ -57,7 +56,7 @@ RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictio
setFriction(frictionCoeff);
setStepSize(stepSize);
setConstraintTolerance(1e-5);
setRandomNumberSeed(osrngseed());
setRandomNumberSeed(0);
}
void RPMDIntegrator::initialize(ContextImpl& contextRef) {
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment