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Commit 1945dd6c authored by Andy Simmonett's avatar Andy Simmonett
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Merge branch 'master' of github.com:pandegroup/openmm into dpme

parents 203e5407 9963e51a
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Showing with 325 additions and 318 deletions
.travis.yml
View file @ 1945dd6c
......@@ -108,6 +108,11 @@ before_install:
brew install doxygen fftw;
sudo easy_install pytest;
fi
- if [[ "${TRAVIS_OS_NAME}" == "linux" ]]; then
CMAKE_URL="https://cmake.org/files/v3.7/cmake-3.7.2-Linux-x86_64.tar.gz";
mkdir $HOME/cmake && travis_retry wget --no-check-certificate --quiet -O - ${CMAKE_URL} | tar --strip-components=1 -xz -C $HOME/cmake;
export PATH=${HOME}/cmake/bin:${PATH};
fi
- if [[ "$OPENCL" == "true" ]]; then
wget http://s3.amazonaws.com/omnia-ci/AMD-APP-SDKInstaller-v3.0.130.135-GA-linux64.tar.bz2;
tar -xjf AMD-APP-SDK*.tar.bz2;
......
CMakeLists.txt
View file @ 1945dd6c
......@@ -21,10 +21,11 @@ IF( NOT PROJECT_NAME )
PROJECT (OpenMM)
ENDIF( NOT PROJECT_NAME )
CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
if("${CMAKE_VERSION}" VERSION_GREATER "3.0" OR "${CMAKE_VERSION}" VERSION_EQUAL "3.0")
CMAKE_POLICY(SET CMP0042 OLD)
endif()
CMAKE_MINIMUM_REQUIRED(VERSION 3.1)
CMAKE_POLICY(SET CMP0042 OLD)
CMAKE_POLICY(SET CMP0003 NEW)
CMAKE_POLICY(SET CMP0005 NEW)
CMAKE_POLICY(SET CMP0011 NEW)
#SET(CMAKE_VERBOSE_MAKEFILE 1)
......@@ -39,21 +40,6 @@ IF(NOT cmv EQUAL "2.4") # This whole file...
# We have custom cmake modules for FindOpenMM and running python tests
SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake_modules")
# Older cmake versions do not have cmake_policy command
# Cmake 2.4.5, the default cmake on red hat linux, has the
# cmake_policy command, but it does not work
# "if(POLICY ..." does not work with cmake 2.4.[56] on red hat
# (cmake 2.4.7 is OK)
if(COMMAND cmake_policy)
if(CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 5)
cmake_policy(SET CMP0003 NEW)
cmake_policy(SET CMP0005 NEW)
endif(CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 5)
if(CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 6 OR CMAKE_PATCH_VERSION GREATER 2)
cmake_policy(SET CMP0011 NEW)
endif(CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 6 OR CMAKE_PATCH_VERSION GREATER 2)
endif(COMMAND cmake_policy)
# Where to install
IF(WIN32)
IF(NOT OPENMM_INSTALL_PREFIX)
......@@ -69,6 +55,9 @@ IF(WIN32)
ADD_DEFINITIONS(-DWIN32)
ENDIF(WIN32)
# What type of libraries to build
SET(OPENMM_BUILD_SHARED_LIB ON CACHE BOOL "Whether to build shared OpenMM libraries")
SET(OPENMM_BUILD_STATIC_LIB OFF CACHE BOOL "Whether to build static OpenMM libraries")
# Include CPU-Features for Android
IF (ANDROID)
......@@ -114,6 +103,7 @@ ELSE( CMAKE_SIZEOF_VOID_P EQUAL 8 )
SET( LIB64 )
ENDIF( CMAKE_SIZEOF_VOID_P EQUAL 8 )
SET (CMAKE_CXX_STANDARD 11)
IF (APPLE AND (NOT PNACL))
# Build 64 bit binaries compatible with OS X 10.7
......@@ -283,7 +273,7 @@ IF (ANDROID OR PNACL)
ELSE (ANDROID OR PNACL)
SET_SOURCE_FILES_PROPERTIES(${CMAKE_SOURCE_DIR}/libraries/sfmt/src/SFMT.cpp PROPERTIES COMPILE_FLAGS "-DHAVE_SSE2=1")
ENDIF(ANDROID OR PNACL)
IF (NOT (ANDROID OR PNACL))
IF (NOT (ANDROID OR PNACL OR (WIN32 AND OPENMM_BUILD_STATIC_LIB)))
FILE(GLOB src_files ${CMAKE_CURRENT_SOURCE_DIR}/libraries/asmjit/*/*.cpp)
FILE(GLOB incl_files ${CMAKE_CURRENT_SOURCE_DIR}/libraries/asmjit/*.h)
SET(SOURCE_FILES ${SOURCE_FILES} ${src_files})
......@@ -302,8 +292,6 @@ ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
SET(OPENMM_BUILD_SHARED_LIB ON CACHE BOOL "Whether to build shared OpenMM libraries")
SET(EXTRA_LINK_FLAGS ${EXTRA_COMPILE_FLAGS})
IF (CMAKE_SYSTEM_NAME MATCHES "Linux")
IF (NOT ANDROID)
......@@ -319,7 +307,6 @@ IF(OPENMM_BUILD_SHARED_LIB)
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DPTHREAD_BUILDING_SHARED_LIBRARY")
ENDIF(OPENMM_BUILD_SHARED_LIB)
SET(OPENMM_BUILD_STATIC_LIB OFF CACHE BOOL "Whether to build static OpenMM libraries")
IF(OPENMM_BUILD_STATIC_LIB)
ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
SET(EXTRA_COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DLEPTON_USE_STATIC_LIBRARIES -DPTW32_STATIC_LIB")
......
appveyor.yml
View file @ 1945dd6c
os: Windows Server 2012 R2
os: Visual Studio 2015
platform: x64
configuration: Release
shallow_clone: true
install:
# Setup shell for VS2010, x64, release mode
- >
"%ProgramFiles%\Microsoft SDKs\Windows\v7.1\Bin\SetEnv.cmd" /x64 /release
# Setup shell for VS2015, x64
- call "c:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\vcvarsall.bat" amd64
# Set path to python, git-bash tools.
- "set PATH=C:\\Python34-x64;C:\\Python34-x64\\Scripts;%PATH%"
- "set PATH=C:\\Python35-x64;C:\\Python35-x64\\Scripts;%PATH%"
- "set PATH=C:\\Program Files (x86)\\Git\\bin;%PATH%"
- pip install pytest
......
docs-source/usersguide/library.rst
View file @ 1945dd6c
......@@ -404,7 +404,7 @@ version of Visual Studio.
Install CMake
=============
CMake is the build system used for OpenMM. You must install CMake version 2.8
CMake is the build system used for OpenMM. You must install CMake version 3.1
or higher before attempting to build OpenMM from source. You can get CMake from
http://www.cmake.org/. If you choose to build CMake from source on Linux, make
sure you have the curses library installed beforehand, so that you will be able
......@@ -509,7 +509,7 @@ Windows
On Windows, perform the following steps:
#. Click Start->All Programs->CMake 2.8->CMake
#. Click Start->All Programs->CMake 3.1->CMake
#. In the box labeled "Where is the source code:" browse to OpenMM src directory
(containing top CMakeLists.txt)
#. In the box labeled "Where to build the binaries" browse to your build_openmm
......
libraries/lbfgs/src/lbfgs.cpp
View file @ 1945dd6c
......@@ -408,210 +408,231 @@ int lbfgs(
pf = (lbfgsfloatval_t*)vecalloc(param.past * sizeof(lbfgsfloatval_t));
}
/* Evaluate the function value and its gradient. */
fx = cd.proc_evaluate(cd.instance, x, g, cd.n, 0);
if (0. != param.orthantwise_c) {
/* Compute the L1 norm of the variable and add it to the object value. */
xnorm = owlqn_x1norm(x, param.orthantwise_start, param.orthantwise_end);
fx += xnorm * param.orthantwise_c;
owlqn_pseudo_gradient(
pg, x, g, n,
param.orthantwise_c, param.orthantwise_start, param.orthantwise_end
);
}
/* Store the initial value of the objective function. */
if (pf != NULL) {
pf[0] = fx;
}
/*
Compute the direction;
we assume the initial hessian matrix H_0 as the identity matrix.
*/
if (param.orthantwise_c == 0.) {
vecncpy(d, g, n);
} else {
vecncpy(d, pg, n);
}
/*
Make sure that the initial variables are not a minimizer.
*/
vec2norm(&xnorm, x, n);
if (param.orthantwise_c == 0.) {
vec2norm(&gnorm, g, n);
} else {
vec2norm(&gnorm, pg, n);
}
if (xnorm < 1.0) xnorm = 1.0;
if (gnorm / xnorm <= param.epsilon) {
ret = LBFGS_ALREADY_MINIMIZED;
goto lbfgs_exit;
}
/* Compute the initial step:
step = 1.0 / sqrt(vecdot(d, d, n))
*/
vec2norminv(&step, d, n);
k = 1;
end = 0;
for (;;) {
/* Store the current position and gradient vectors. */
veccpy(xp, x, n);
veccpy(gp, g, n);
/* Search for an optimal step. */
if (param.orthantwise_c == 0.) {
ls = linesearch(n, x, &fx, g, d, &step, xp, gp, w, &cd, &param);
} else {
ls = linesearch(n, x, &fx, g, d, &step, xp, pg, w, &cd, &param);
try {
/* Evaluate the function value and its gradient. */
fx = cd.proc_evaluate(cd.instance, x, g, cd.n, 0);
if (0. != param.orthantwise_c) {
/* Compute the L1 norm of the variable and add it to the object value. */
xnorm = owlqn_x1norm(x, param.orthantwise_start, param.orthantwise_end);
fx += xnorm * param.orthantwise_c;
owlqn_pseudo_gradient(
pg, x, g, n,
param.orthantwise_c, param.orthantwise_start, param.orthantwise_end
);
}
if (ls < 0) {
/* Revert to the previous point. */
veccpy(x, xp, n);
veccpy(g, gp, n);
ret = ls;
goto lbfgs_exit;
/* Store the initial value of the objective function. */
if (pf != NULL) {
pf[0] = fx;
}
/* Compute x and g norms. */
vec2norm(&xnorm, x, n);
/*
Compute the direction;
we assume the initial hessian matrix H_0 as the identity matrix.
*/
if (param.orthantwise_c == 0.) {
vec2norm(&gnorm, g, n);
vecncpy(d, g, n);
} else {
vec2norm(&gnorm, pg, n);
}
/* Report the progress. */
if (cd.proc_progress) {
if (ret = cd.proc_progress(cd.instance, x, g, fx, xnorm, gnorm, step, cd.n, k, ls)) {
goto lbfgs_exit;
}
vecncpy(d, pg, n);
}
/*
Convergence test.
The criterion is given by the following formula:
|g(x)| / \max(1, |x|) < \epsilon
Make sure that the initial variables are not a minimizer.
*/
vec2norm(&xnorm, x, n);
if (param.orthantwise_c == 0.) {
vec2norm(&gnorm, g, n);
} else {
vec2norm(&gnorm, pg, n);
}
if (xnorm < 1.0) xnorm = 1.0;
if (gnorm / xnorm <= param.epsilon) {
/* Convergence. */
ret = LBFGS_SUCCESS;
break;
ret = LBFGS_ALREADY_MINIMIZED;
goto lbfgs_exit;
}
/*
Test for stopping criterion.
The criterion is given by the following formula:
(f(past_x) - f(x)) / f(x) < \delta
/* Compute the initial step:
step = 1.0 / sqrt(vecdot(d, d, n))
*/
if (pf != NULL) {
/* We don't test the stopping criterion while k < past. */
if (param.past <= k) {
/* Compute the relative improvement from the past. */
rate = (pf[k % param.past] - fx) / fx;
/* The stopping criterion. */
if (rate < param.delta) {
ret = LBFGS_STOP;
break;
vec2norminv(&step, d, n);
k = 1;
end = 0;
for (;;) {
/* Store the current position and gradient vectors. */
veccpy(xp, x, n);
veccpy(gp, g, n);
/* Search for an optimal step. */
if (param.orthantwise_c == 0.) {
ls = linesearch(n, x, &fx, g, d, &step, xp, gp, w, &cd, &param);
} else {
ls = linesearch(n, x, &fx, g, d, &step, xp, pg, w, &cd, &param);
owlqn_pseudo_gradient(
pg, x, g, n,
param.orthantwise_c, param.orthantwise_start, param.orthantwise_end
);
}
if (ls < 0) {
/* Revert to the previous point. */
veccpy(x, xp, n);
veccpy(g, gp, n);
ret = ls;
goto lbfgs_exit;
}
/* Compute x and g norms. */
vec2norm(&xnorm, x, n);
if (param.orthantwise_c == 0.) {
vec2norm(&gnorm, g, n);
} else {
vec2norm(&gnorm, pg, n);
}
/* Report the progress. */
if (cd.proc_progress) {
if (ret = cd.proc_progress(cd.instance, x, g, fx, xnorm, gnorm, step, cd.n, k, ls)) {
goto lbfgs_exit;
}
}
/* Store the current value of the objective function. */
pf[k % param.past] = fx;
}
/*
Convergence test.
The criterion is given by the following formula:
|g(x)| / \max(1, |x|) < \epsilon
*/
if (xnorm < 1.0) xnorm = 1.0;
if (gnorm / xnorm <= param.epsilon) {
/* Convergence. */
ret = LBFGS_SUCCESS;
break;
}
if (param.max_iterations != 0 && param.max_iterations < k+1) {
/* Maximum number of iterations. */
ret = LBFGSERR_MAXIMUMITERATION;
break;
}
/*
Test for stopping criterion.
The criterion is given by the following formula:
(f(past_x) - f(x)) / f(x) < \delta
*/
if (pf != NULL) {
/* We don't test the stopping criterion while k < past. */
if (param.past <= k) {
/* Compute the relative improvement from the past. */
rate = (pf[k % param.past] - fx) / fx;
/* The stopping criterion. */
if (rate < param.delta) {
ret = LBFGS_STOP;
break;
}
}
/*
Update vectors s and y:
s_{k+1} = x_{k+1} - x_{k} = \step * d_{k}.
y_{k+1} = g_{k+1} - g_{k}.
*/
it = &lm[end];
vecdiff(it->s, x, xp, n);
vecdiff(it->y, g, gp, n);
/* Store the current value of the objective function. */
pf[k % param.past] = fx;
}
/*
Compute scalars ys and yy:
ys = y^t \cdot s = 1 / \rho.
yy = y^t \cdot y.
Notice that yy is used for scaling the hessian matrix H_0 (Cholesky factor).
*/
vecdot(&ys, it->y, it->s, n);
vecdot(&yy, it->y, it->y, n);
it->ys = ys;
if (param.max_iterations != 0 && param.max_iterations < k+1) {
/* Maximum number of iterations. */
ret = LBFGSERR_MAXIMUMITERATION;
break;
}
/*
Recursive formula to compute dir = -(H \cdot g).
This is described in page 779 of:
Jorge Nocedal.
Updating Quasi-Newton Matrices with Limited Storage.
Mathematics of Computation, Vol. 35, No. 151,
pp. 773--782, 1980.
*/
bound = (m <= k) ? m : k;
++k;
end = (end + 1) % m;
/*
Update vectors s and y:
s_{k+1} = x_{k+1} - x_{k} = \step * d_{k}.
y_{k+1} = g_{k+1} - g_{k}.
*/
it = &lm[end];
vecdiff(it->s, x, xp, n);
vecdiff(it->y, g, gp, n);
/* Compute the steepest direction. */
if (param.orthantwise_c == 0.) {
/* Compute the negative of gradients. */
vecncpy(d, g, n);
} else {
vecncpy(d, pg, n);
}
/*
Compute scalars ys and yy:
ys = y^t \cdot s = 1 / \rho.
yy = y^t \cdot y.
Notice that yy is used for scaling the hessian matrix H_0 (Cholesky factor).
*/
vecdot(&ys, it->y, it->s, n);
vecdot(&yy, it->y, it->y, n);
it->ys = ys;
j = end;
for (i = 0;i < bound;++i) {
j = (j + m - 1) % m; /* if (--j == -1) j = m-1; */
it = &lm[j];
/* \alpha_{j} = \rho_{j} s^{t}_{j} \cdot q_{k+1}. */
vecdot(&it->alpha, it->s, d, n);
it->alpha /= it->ys;
/* q_{i} = q_{i+1} - \alpha_{i} y_{i}. */
vecadd(d, it->y, -it->alpha, n);
}
/*
Recursive formula to compute dir = -(H \cdot g).
This is described in page 779 of:
Jorge Nocedal.
Updating Quasi-Newton Matrices with Limited Storage.
Mathematics of Computation, Vol. 35, No. 151,
pp. 773--782, 1980.
*/
bound = (m <= k) ? m : k;
++k;
end = (end + 1) % m;
/* Compute the steepest direction. */
if (param.orthantwise_c == 0.) {
/* Compute the negative of gradients. */
vecncpy(d, g, n);
} else {
vecncpy(d, pg, n);
}
vecscale(d, ys / yy, n);
j = end;
for (i = 0;i < bound;++i) {
j = (j + m - 1) % m; /* if (--j == -1) j = m-1; */
it = &lm[j];
/* \alpha_{j} = \rho_{j} s^{t}_{j} \cdot q_{k+1}. */
vecdot(&it->alpha, it->s, d, n);
it->alpha /= it->ys;
/* q_{i} = q_{i+1} - \alpha_{i} y_{i}. */
vecadd(d, it->y, -it->alpha, n);
}
for (i = 0;i < bound;++i) {
it = &lm[j];
/* \beta_{j} = \rho_{j} y^t_{j} \cdot \gamma_{i}. */
vecdot(&beta, it->y, d, n);
beta /= it->ys;
/* \gamma_{i+1} = \gamma_{i} + (\alpha_{j} - \beta_{j}) s_{j}. */
vecadd(d, it->s, it->alpha - beta, n);
j = (j + 1) % m; /* if (++j == m) j = 0; */
}
vecscale(d, ys / yy, n);
/*
Constrain the search direction for orthant-wise updates.
*/
if (param.orthantwise_c != 0.) {
for (i = param.orthantwise_start;i < param.orthantwise_end;++i) {
if (d[i] * pg[i] >= 0) {
d[i] = 0;
for (i = 0;i < bound;++i) {
it = &lm[j];
/* \beta_{j} = \rho_{j} y^t_{j} \cdot \gamma_{i}. */
vecdot(&beta, it->y, d, n);
beta /= it->ys;
/* \gamma_{i+1} = \gamma_{i} + (\alpha_{j} - \beta_{j}) s_{j}. */
vecadd(d, it->s, it->alpha - beta, n);
j = (j + 1) % m; /* if (++j == m) j = 0; */
}
/*
Constrain the search direction for orthant-wise updates.
*/
if (param.orthantwise_c != 0.) {
for (i = param.orthantwise_start;i < param.orthantwise_end;++i) {
if (d[i] * pg[i] >= 0) {
d[i] = 0;
}
}
}
}
/*
Now the search direction d is ready. We try step = 1 first.
*/
step = 1.0;
/*
Now the search direction d is ready. We try step = 1 first.
*/
step = 1.0;
}
}
catch (...) {
vecfree(pf);
/* Free memory blocks used by this function. */
if (lm != NULL) {
for (i = 0;i < m;++i) {
vecfree(lm[i].s);
vecfree(lm[i].y);
}
vecfree(lm);
}
vecfree(pg);
vecfree(w);
vecfree(d);
vecfree(gp);
vecfree(g);
vecfree(xp);
throw;
}
lbfgs_exit:
......
openmmapi/include/openmm/internal/ThreadPool.h
View file @ 1945dd6c
......@@ -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) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -34,6 +34,7 @@
#define NOMINMAX
#include "windowsExport.h"
#include <functional>
#include <pthread.h>
#include <vector>
......@@ -69,6 +70,10 @@ public:
* Execute a Task in parallel on the worker threads.
*/
void execute(Task& task);
/**
* Execute a function in parallel on the worker threads.
*/
void execute(std::function<void (ThreadPool&, int)> task);
/**
* This is called by the worker threads to block until all threads have reached the same point
* and the master thread instructs them to continue by calling resumeThreads().
......@@ -90,6 +95,8 @@ private:
std::vector<ThreadData*> threadData;
pthread_cond_t startCondition, endCondition;
pthread_mutex_t lock;
Task* currentTask;
std::function<void (ThreadPool& pool, int)> currentFunction;
};
/**
......
openmmapi/src/LocalEnergyMinimizer.cpp
View file @ 1945dd6c
......@@ -105,83 +105,89 @@ static lbfgsfloatval_t evaluate(void *instance, const lbfgsfloatval_t *x, lbfgsf
void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxIterations) {
const System& system = context.getSystem();
int numParticles = system.getNumParticles();
lbfgsfloatval_t *x = lbfgs_malloc(numParticles*3);
if (x == NULL)
throw OpenMMException("LocalEnergyMinimizer: Failed to allocate memory");
double constraintTol = context.getIntegrator().getConstraintTolerance();
double workingConstraintTol = std::max(1e-4, constraintTol);
double k = tolerance/workingConstraintTol;
lbfgsfloatval_t *x = lbfgs_malloc(numParticles*3);
if (x == NULL)
throw OpenMMException("LocalEnergyMinimizer: Failed to allocate memory");
try {
// Initialize the minimizer.
// Initialize the minimizer.
lbfgs_parameter_t param;
lbfgs_parameter_init(&param);
if (!context.getPlatform().supportsDoublePrecision())
param.xtol = 1e-7;
param.max_iterations = maxIterations;
param.linesearch = LBFGS_LINESEARCH_BACKTRACKING_STRONG_WOLFE;
lbfgs_parameter_t param;
lbfgs_parameter_init(&param);
if (!context.getPlatform().supportsDoublePrecision())
param.xtol = 1e-7;
param.max_iterations = maxIterations;
param.linesearch = LBFGS_LINESEARCH_BACKTRACKING_STRONG_WOLFE;
// Make sure the initial configuration satisfies all constraints.
// Make sure the initial configuration satisfies all constraints.
context.applyConstraints(workingConstraintTol);
context.applyConstraints(workingConstraintTol);
// Record the initial positions and determine a normalization constant for scaling the tolerance.
// Record the initial positions and determine a normalization constant for scaling the tolerance.
vector<Vec3> initialPos = context.getState(State::Positions).getPositions();
double norm = 0.0;
for (int i = 0; i < numParticles; i++) {
x[3*i] = initialPos[i][0];
x[3*i+1] = initialPos[i][1];
x[3*i+2] = initialPos[i][2];
norm += initialPos[i].dot(initialPos[i]);
}
norm /= numParticles;
norm = (norm < 1 ? 1 : sqrt(norm));
param.epsilon = tolerance/norm;
// Repeatedly minimize, steadily increasing the strength of the springs until all constraints are satisfied.
double prevMaxError = 1e10;
while (true) {
// Perform the minimization.
lbfgsfloatval_t fx;
MinimizerData data(context, k);
lbfgs(numParticles*3, x, &fx, evaluate, NULL, &data, &param);
// Check whether all constraints are satisfied.
vector<Vec3> positions = context.getState(State::Positions).getPositions();
int numConstraints = system.getNumConstraints();
double maxError = 0.0;
for (int i = 0; i < numConstraints; i++) {
int particle1, particle2;
double distance;
system.getConstraintParameters(i, particle1, particle2, distance);
Vec3 delta = positions[particle2]-positions[particle1];
double r = sqrt(delta.dot(delta));
double error = fabs(r-distance);
if (error > maxError)
maxError = error;
vector<Vec3> initialPos = context.getState(State::Positions).getPositions();
double norm = 0.0;
for (int i = 0; i < numParticles; i++) {
x[3*i] = initialPos[i][0];
x[3*i+1] = initialPos[i][1];
x[3*i+2] = initialPos[i][2];
norm += initialPos[i].dot(initialPos[i]);
}
if (maxError <= workingConstraintTol)
break; // All constraints are satisfied.
context.setPositions(initialPos);
if (maxError >= prevMaxError)
break; // Further tightening the springs doesn't seem to be helping, so just give up.
prevMaxError = maxError;
k *= 10;
if (maxError > 100*workingConstraintTol) {
// We've gotten far enough from a valid state that we might have trouble getting
// back, so reset to the original positions.
for (int i = 0; i < numParticles; i++) {
x[3*i] = initialPos[i][0];
x[3*i+1] = initialPos[i][1];
x[3*i+2] = initialPos[i][2];
norm /= numParticles;
norm = (norm < 1 ? 1 : sqrt(norm));
param.epsilon = tolerance/norm;
// Repeatedly minimize, steadily increasing the strength of the springs until all constraints are satisfied.
double prevMaxError = 1e10;
while (true) {
// Perform the minimization.
lbfgsfloatval_t fx;
MinimizerData data(context, k);
lbfgs(numParticles*3, x, &fx, evaluate, NULL, &data, &param);
// Check whether all constraints are satisfied.
vector<Vec3> positions = context.getState(State::Positions).getPositions();
int numConstraints = system.getNumConstraints();
double maxError = 0.0;
for (int i = 0; i < numConstraints; i++) {
int particle1, particle2;
double distance;
system.getConstraintParameters(i, particle1, particle2, distance);
Vec3 delta = positions[particle2]-positions[particle1];
double r = sqrt(delta.dot(delta));
double error = fabs(r-distance);
if (error > maxError)
maxError = error;
}
if (maxError <= workingConstraintTol)
break; // All constraints are satisfied.
context.setPositions(initialPos);
if (maxError >= prevMaxError)
break; // Further tightening the springs doesn't seem to be helping, so just give up.
prevMaxError = maxError;
k *= 10;
if (maxError > 100*workingConstraintTol) {
// We've gotten far enough from a valid state that we might have trouble getting
// back, so reset to the original positions.
for (int i = 0; i < numParticles; i++) {
x[3*i] = initialPos[i][0];
x[3*i+1] = initialPos[i][1];
x[3*i+2] = initialPos[i][2];
}
}
}
}
catch (...) {
lbfgs_free(x);
throw;
}
lbfgs_free(x);
// If necessary, do a final constraint projection to make sure they are satisfied
......
openmmapi/src/ThreadPool.cpp
View file @ 1945dd6c
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013-2014 Stanford University and the Authors. *
* Portions copyright (c) 2013-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -40,10 +40,17 @@ class ThreadPool::ThreadData {
public:
ThreadData(ThreadPool& owner, int index) : owner(owner), index(index), isDeleted(false) {
}
void executeTask() {
if (owner.currentTask != NULL)
owner.currentTask->execute(owner, index);
else
owner.currentFunction(owner, index);
}
ThreadPool& owner;
int index;
bool isDeleted;
Task* currentTask;
function<void (ThreadPool& pool, int)> currentFunction;
};
static void* threadBody(void* args) {
......@@ -54,13 +61,13 @@ static void* threadBody(void* args) {
data.owner.syncThreads();
if (data.isDeleted)
break;
data.currentTask->execute(data.owner, data.index);
data.executeTask();
}
delete &data;
return 0;
}
ThreadPool::ThreadPool(int numThreads) {
ThreadPool::ThreadPool(int numThreads) : currentTask(NULL) {
if (numThreads <= 0)
numThreads = getNumProcessors();
this->numThreads = numThreads;
......@@ -99,8 +106,13 @@ int ThreadPool::getNumThreads() const {
}
void ThreadPool::execute(Task& task) {
for (int i = 0; i < (int) threadData.size(); i++)
threadData[i]->currentTask = &task;
currentTask = &task;
resumeThreads();
}
void ThreadPool::execute(function<void (ThreadPool&, int)> task) {
currentTask = NULL;
currentFunction = task;
resumeThreads();
}
......
platforms/cpu/include/CpuBondForce.h
View file @ 1945dd6c
......@@ -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) 2014 Stanford University and the Authors. *
* Portions copyright (c) 2014-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -46,7 +46,6 @@ namespace OpenMM {
*/
class OPENMM_EXPORT_CPU CpuBondForce {
public:
class ComputeForceTask;
CpuBondForce();
/**
* Analyze the set of bonds and decide which to compute with each thread.
......
platforms/cpu/include/CpuCustomGBForce.h
View file @ 1945dd6c
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
/* Portions copyright (c) 2009-2017 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -39,7 +39,6 @@ namespace OpenMM {
class CpuCustomGBForce {
private:
class ComputeForceTask;
class ThreadData;
bool cutoff;
......
platforms/cpu/include/CpuCustomManyParticleForce.h
View file @ 1945dd6c
/* Portions copyright (c) 2009-2014 Stanford University and Simbios.
/* Portions copyright (c) 2009-2017 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -48,7 +48,6 @@ private:
class DistanceTermInfo;
class AngleTermInfo;
class DihedralTermInfo;
class ComputeForceTask;
class ThreadData;
int numParticles, numParticlesPerSet, numPerParticleParameters, numTypes;
bool useCutoff, usePeriodic, triclinic, centralParticleMode;
......
platforms/cpu/include/CpuCustomNonbondedForce.h
View file @ 1945dd6c
/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
/* Portions copyright (c) 2009-2017 Stanford University and Simbios.
* Contributors: Peter Eastman
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -122,7 +122,6 @@ class CpuCustomNonbondedForce {
RealOpenMM* fixedParameters, const std::map<std::string, double>& globalParameters,
std::vector<AlignedArray<float> >& threadForce, bool includeForce, bool includeEnergy, double& totalEnergy, double* energyParamDerivs);
private:
class ComputeForceTask;
class ThreadData;
bool cutoff;
......
platforms/cpu/include/CpuGBSAOBCForce.h
View file @ 1945dd6c
/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
/* Portions copyright (c) 2006-2017 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -36,7 +36,6 @@ namespace OpenMM {
class CpuGBSAOBCForce {
public:
class ComputeTask;
CpuGBSAOBCForce();
/**
......
platforms/cpu/include/CpuGayBerneForce.h
View file @ 1945dd6c
......@@ -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) 2016 Stanford University and the Authors. *
* Portions copyright (c) 2016-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -45,7 +45,6 @@ namespace OpenMM {
class CpuGayBerneForce {
public:
struct Matrix;
class ComputeTask;
/**
* Constructor.
......
platforms/cpu/include/CpuKernels.h
View file @ 1945dd6c
......@@ -54,8 +54,6 @@ namespace OpenMM {
*/
class CpuCalcForcesAndEnergyKernel : public CalcForcesAndEnergyKernel {
public:
class InitForceTask;
class SumForceTask;
CpuCalcForcesAndEnergyKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data, ContextImpl& context);
/**
* Initialize the kernel.
......
platforms/cpu/include/CpuLangevinDynamics.h
View file @ 1945dd6c
/* Portions copyright (c) 2013-2016 Stanford University and Simbios.
/* Portions copyright (c) 2013-2017 Stanford University and Simbios.
* Authors: Peter Eastman
* Contributors:
*
......@@ -35,9 +35,6 @@ namespace OpenMM {
class CpuLangevinDynamics : public ReferenceStochasticDynamics {
public:
class Update1Task;
class Update2Task;
class Update3Task;
/**
* Constructor.
*
......
platforms/cpu/include/CpuNeighborList.h
View file @ 1945dd6c
......@@ -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) 2013-2016 Stanford University and the Authors. *
* Portions copyright (c) 2013-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -45,7 +45,6 @@ namespace OpenMM {
class OPENMM_EXPORT_CPU CpuNeighborList {
public:
class ThreadTask;
class Voxels;
CpuNeighborList(int blockSize);
void computeNeighborList(int numAtoms, const AlignedArray<float>& atomLocations, const std::vector<std::set<int> >& exclusions,
......
platforms/cpu/include/CpuNonbondedForce.h
View file @ 1945dd6c
/* Portions copyright (c) 2006-2015 Stanford University and Simbios.
/* Portions copyright (c) 2006-2017 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -39,7 +39,6 @@ namespace OpenMM {
class CpuNonbondedForce {
public:
class ComputeDirectTask;
/**---------------------------------------------------------------------------------------
......
platforms/cpu/include/CpuSETTLE.h
View file @ 1945dd6c
......@@ -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) 2013 Stanford University and the Authors. *
* Portions copyright (c) 2013-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -45,8 +45,6 @@ namespace OpenMM {
*/
class OPENMM_EXPORT_CPU CpuSETTLE : public ReferenceConstraintAlgorithm {
public:
class ApplyToPositionsTask;
class ApplyToVelocitiesTask;
CpuSETTLE(const System& system, const ReferenceSETTLEAlgorithm& settle, ThreadPool& threads);
~CpuSETTLE();
......
platforms/cpu/src/CpuBondForce.cpp
View file @ 1945dd6c
......@@ -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) 2014-2016 Stanford University and the Authors. *
* Portions copyright (c) 2014-2017 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -35,25 +35,6 @@
using namespace OpenMM;
using namespace std;
class CpuBondForce::ComputeForceTask : public ThreadPool::Task {
public:
ComputeForceTask(CpuBondForce& owner, vector<RealVec>& atomCoordinates, RealOpenMM** parameters, vector<RealVec>& forces,
vector<RealOpenMM>& threadEnergy, RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn) : owner(owner), atomCoordinates(atomCoordinates),
parameters(parameters), forces(forces), threadEnergy(threadEnergy), totalEnergy(totalEnergy), referenceBondIxn(referenceBondIxn) {
}
void execute(ThreadPool& threads, int threadIndex) {
RealOpenMM* energy = (totalEnergy == NULL ? NULL : &threadEnergy[threadIndex]);
owner.threadComputeForce(threads, threadIndex, atomCoordinates, parameters, forces, energy, referenceBondIxn);
}
CpuBondForce& owner;
vector<RealVec>& atomCoordinates;
RealOpenMM** parameters;
vector<RealVec>& forces;
vector<RealOpenMM>& threadEnergy;
RealOpenMM* totalEnergy;
ReferenceBondIxn& referenceBondIxn;
};
CpuBondForce::CpuBondForce() {
}
......@@ -188,8 +169,10 @@ void CpuBondForce::calculateForce(vector<RealVec>& atomCoordinates, RealOpenMM**
// Have the worker threads compute their forces.
vector<RealOpenMM> threadEnergy(threads->getNumThreads(), 0);
ComputeForceTask task(*this, atomCoordinates, parameters, forces, threadEnergy, totalEnergy, referenceBondIxn);
threads->execute(task);
threads->execute([&] (ThreadPool& threads, int threadIndex) {
RealOpenMM* energy = (totalEnergy == NULL ? NULL : &threadEnergy[threadIndex]);
threadComputeForce(threads, threadIndex, atomCoordinates, parameters, forces, energy, referenceBondIxn);
});
threads->waitForThreads();
// Compute any "extra" bonds.
......
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