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Commit 0b5d58d7 authored by Charlles Abreu's avatar Charlles Abreu
Browse files

Conflict resolution in TestSplineFilter.cpp

parents 9026dbe7 b0d13582
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Showing with 244 additions and 139 deletions
.azure-pipelines/azure-pipelines-windows.yml
View file @ 0b5d58d7
......@@ -2,9 +2,9 @@ jobs:
# Configure, build, install, and test job
- job: 'windows_build'
displayName: 'Windows VS2015'
displayName: 'Windows VS2017'
pool:
vmImage: 'vs2015-win2012r2'
vmImage: 'vs2017-win2016'
timeoutInMinutes: 360
variables:
llvm.version: '7.0.1'
......@@ -54,7 +54,7 @@ jobs:
# Download OpenCL Headers and build the ICD loader
- script: |
setlocal EnableDelayedExpansion
call "C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\vcvarsall.bat" x86_amd64
call "C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
mkdir opencl
cd opencl
wget https://www.khronos.org/registry/cl/specs/opencl-icd-1.2.11.0.tgz -O opencl-icd-1.2.11.0.tgz
......@@ -67,7 +67,9 @@ jobs:
move .\OpenCL-Headers-master\CL\*.h .\inc\CL\
mkdir lib > $null
cd lib
cmake -G Ninja ..
cmake -G Ninja .. ^
-DCMAKE_CXX_COMPILER=cl.exe ^
-DCMAKE_C_COMPILER=cl.exe
cmake --build . ^
-- -j %NUMBER_OF_PROCESSORS%
displayName: "Download and install OpenCL"
......@@ -75,12 +77,14 @@ jobs:
# Configure
- script: |
setlocal EnableDelayedExpansion
call "C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\vcvarsall.bat" x86_amd64
call "C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
mkdir build & cd build
cmake -G Ninja ^
-DOPENCL_INCLUDE_DIR=$(Pipeline.Workspace)/opencl/inc ^
-DOPENCL_LIBRARY=$(Pipeline.Workspace)/opencl/lib/OpenCL.lib ^
-DCMAKE_BUILD_TYPE=$(cmake.build.type) ^
-DCMAKE_CXX_COMPILER=cl.exe ^
-DCMAKE_C_COMPILER=cl.exe ^
-DCMAKE_INSTALL_PREFIX=../install ^
-DOPENMM_BUILD_EXAMPLES=OFF ^
-DOPENMM_BUILD_OPENCL_TESTS=OFF ^
......@@ -89,7 +93,7 @@ jobs:
workingDirectory: $(Build.BinariesDirectory)
# Build
- script: |
call "C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\vcvarsall.bat" x86_amd64
call "C:\Program Files (x86)\Microsoft Visual Studio\2017\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
cmake --build . ^
--config $(cmake.build.type) ^
-- -j %NUMBER_OF_PROCESSORS%
......
.travis.yml
View file @ 0b5d58d7
......@@ -3,7 +3,6 @@ language: python
addons:
apt:
packages:
- gromacs
- doxygen
- python-numpy
- python-scipy
......@@ -104,6 +103,24 @@ jobs:
CXX=$CCACHE/g++
CMAKE_FLAGS=""
- sudo: required
dist: bionic
python: "3.8"
name: "PPC"
arch: ppc64le
env: OPENCL=false
CUDA=false
CMAKE_FLAGS=""
- sudo: required
dist: bionic
python: "3.8"
name: "ARM"
arch: arm64
env: OPENCL=false
CUDA=false
CMAKE_FLAGS=""
before_install:
- START_TIME=$(date +%s)
- wget http://anaconda.org/omnia/ccache/3.2.4/download/${TRAVIS_OS_NAME}-64/ccache-3.2.4-0.tar.bz2
......@@ -114,10 +131,21 @@ before_install:
brew install -y https://raw.githubusercontent.com/Homebrew/homebrew-core/5b680fb58fedfb00cd07a7f69f5a621bb9240f3b/Formula/doxygen.rb;
sudo pip install -U pytest --ignore-installed six;
fi
- if [[ "${TRAVIS_OS_NAME}" == "linux" ]]; then
CMAKE_URL="http://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:${PATH};
# The cmake version installed by apt on ARM and PPC is very old,
# so download a newer version.
- if [[ "${TRAVIS_CPU_ARCH}" == "ppc64le" ]]; then
sudo apt-get install libuv1 rhash libstdc++6;
wget https://anaconda.org/conda-forge/cmake/3.17.0/download/linux-ppc64le/cmake-3.17.0-hfb1cb51_0.tar.bz2;
mkdir $HOME/cmake;
tar -xjvf cmake-3.17.0-hfb1cb51_0.tar.bz2 -C $HOME/cmake;
export PATH=$HOME/cmake/bin:$PATH;
fi
- if [[ "${TRAVIS_CPU_ARCH}" == "arm64" ]]; then
sudo apt-get install libuv1 rhash libstdc++6;
wget https://anaconda.org/conda-forge/cmake/3.17.0/download/linux-aarch64/cmake-3.17.0-h28c56e5_0.tar.bz2;
mkdir $HOME/cmake;
tar -xjvf cmake-3.17.0-h28c56e5_0.tar.bz2 -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;
......@@ -132,17 +160,20 @@ before_install:
${AMDAPPSDK}/bin/x86_64/clinfo;
sudo apt-get install -y libgl1-mesa-dev;
fi
# Install SWIG and Cython for Python wrappers. However, testing CUDA and
# OpenCL, we skip the Python wrapper for speed. We're not using anaconda
# python, but this is a fast way to get an apparently functional precompiled
# build of swig that's more modern than what's in apt.
- if [[ "$OPENCL" == "false" && "$CUDA" == "false" && "$TRAVIS_OS_NAME" == "linux" ]]; then
# Install packages needed for Python: SWIG, Cython, and Gromacs (used by some tests).
# We do this differently on different platforms. Possibly some of this could be unified.
- if [[ "$OPENCL" == "false" && "$CUDA" == "false" && "$TRAVIS_OS_NAME" == "linux" && "${TRAVIS_CPU_ARCH}" != "ppc64le" && "${TRAVIS_CPU_ARCH}" != "arm64" ]]; then
wget http://anaconda.org/omnia/swig/3.0.7/download/linux-64/swig-3.0.7-0.tar.bz2;
mkdir $HOME/swig;
tar -xjvf swig-3.0.7-0.tar.bz2 -C $HOME/swig;
export PATH=$HOME/swig/bin:$PATH;
export SWIG_LIB=$HOME/swig/share/swig/3.0.7;
pip install cython;
sudo apt-get install gromacs;
fi
- if [[ "${TRAVIS_CPU_ARCH}" == "ppc64le" || "${TRAVIS_CPU_ARCH}" == "arm64" ]]; then
sudo apt-get install swig;
pip install cython;
fi
- if [[ "$OPENCL" == "false" && "$CUDA" == "false" && "$TRAVIS_OS_NAME" == "osx" ]]; then
wget http://anaconda.org/omnia/swig/3.0.7/download/osx-64/swig-3.0.7-0.tar.bz2;
......
CMakeLists.txt
View file @ 0b5d58d7
......@@ -41,11 +41,15 @@ if ("${TARGET_ARCH}" MATCHES "x86_64|i386")
endif()
if ("${TARGET_ARCH}" MATCHES "arm")
set(ARM ON)
add_compile_definitions(__ARM__=1)
if ("${TARGET_ARCH}" MATCHES "armv8")
add_definitions(-D__ARM64__=1)
else()
add_definitions(-D__ARM__=1)
endif()
endif()
if ("${TARGET_ARCH}" MATCHES "ppc")
set(PPC ON)
add_compile_definitions(__PPC__=1)
add_definitions(-D__PPC__=1)
endif()
# Where to install
......
cmake_modules/TargetArch.cmake
View file @ 0b5d58d7
......@@ -24,19 +24,40 @@
# OF THE POSSIBILITY OF SUCH DAMAGE.
# Based on the Qt 5 processor detection code, so should be very accurate
# https://qt.gitorious.org/qt/qtbase/blobs/master/src/corelib/global/qprocessordetection.h
# Currently handles arm (v5, v6, v7), x86 (32/64), ia64, and ppc (32/64)
# https://github.com/qt/qtbase/blob/9a6a847/src/corelib/global/qprocessordetection.h
# Currently handles arm / aarch64 (v5, v6, v7, v8), x86 (32/64), ia64, and ppc (32/64)
# Regarding POWER/PowerPC, just as is noted in the Qt source,
# "There are many more known variants/revisions that we do not handle/detect."
set(archdetect_c_code "
#if defined(__arm__) || defined(__TARGET_ARCH_ARM)
#if defined(__ARM_ARCH_7__) \\
#define _STR(x) #x
#define STR(x) _STR(x)
#if defined(__arm__) || defined(__TARGET_ARCH_ARM) || defined(_M_ARM) || \\
defined(_M_ARM64) || defined(__aarch64__) || defined(__ARM64__)
#if defined(__ARM_ARCH) && __ARM_ARCH > 1
#pragma message \"cmake_ARCH armv\" STR(__ARM_ARCH)
#error
#elif defined(__TARGET_ARCH_ARM) && __TARGET_ARCH_ARM > 1
#pragma message \"cmake_ARCH armv\" STR(__TARGET_ARCH_ARM)
#error
#elif defined(_M_ARM) && _M_ARM > 1
#error cmake_ARCH arm ## __M_ARM
#elif defined(__ARM64_ARCH_8__) \\
|| defined(__aarch64__) \\
|| defined(__ARMv8__) \\
|| defined(__ARMv8_A__) \\
|| defined(_M_ARM64)
#error cmake_ARCH armv8
#elif defined(__ARM_ARCH_7__) \\
|| defined(__ARM_ARCH_7A__) \\
|| defined(__ARM_ARCH_7R__) \\
|| defined(__ARM_ARCH_7M__) \\
|| (defined(__TARGET_ARCH_ARM) && __TARGET_ARCH_ARM-0 >= 7)
|| defined(__ARM_ARCH_7S__) \\
|| defined(_ARM_ARCH_7) \\
|| defined(__CORE_CORTEXA__)
#error cmake_ARCH armv7
#elif defined(__ARM_ARCH_6__) \\
|| defined(__ARM_ARCH_6J__) \\
......@@ -44,11 +65,10 @@ set(archdetect_c_code "
|| defined(__ARM_ARCH_6Z__) \\
|| defined(__ARM_ARCH_6K__) \\
|| defined(__ARM_ARCH_6ZK__) \\
|| defined(__ARM_ARCH_6M__) \\
|| (defined(__TARGET_ARCH_ARM) && __TARGET_ARCH_ARM-0 >= 6)
|| defined(__ARM_ARCH_6M__)
#error cmake_ARCH armv6
#elif defined(__ARM_ARCH_5TEJ__) \\
|| (defined(__TARGET_ARCH_ARM) && __TARGET_ARCH_ARM-0 >= 5)
|| defined(__ARM_ARCH_5TE__)
#error cmake_ARCH armv5
#else
#error cmake_ARCH arm
......
devtools/forcefield-scripts/processAmberForceField.py
View file @ 0b5d58d7
......@@ -272,7 +272,7 @@ removeType = [False]*len(types)
for res in residueAtoms:
if res not in residueBonds:
continue
atomBonds = [[] for atom in residueAtoms[res]]
atomBonds = [[] for _ in residueAtoms[res]]
for bond in residueBonds[res]:
atomBonds[bond[0]].append(bond[1])
atomBonds[bond[1]].append(bond[0])
......@@ -361,7 +361,7 @@ for tor in reversed(torsions):
tag = " <Proper class1=\"%s\" class2=\"%s\" class3=\"%s\" class4=\"%s\"" % signature
i = 4
while i < len(tor):
index = i/3
index = i//3
periodicity = int(float(tor[i+2]))
phase = float(tor[i+1])*math.pi/180.0
k = tor[i]*4.184
......@@ -380,7 +380,7 @@ for tor in reversed(impropers):
tag = " <Improper class1=\"%s\" class2=\"%s\" class3=\"%s\" class4=\"%s\"" % signature
i = 4
while i < len(tor):
index = i/3
index = i//3
periodicity = int(float(tor[i+2]))
phase = float(tor[i+1])*math.pi/180.0
k = float(tor[i])*4.184
......
devtools/forcefield-scripts/processCharmmForceField.py
View file @ 0b5d58d7
......@@ -23,7 +23,7 @@ nbfixes = {}
def getFieldPairs(fields):
pairs = []
for i in range(len(fields)/2):
for i in range(len(fields)//2):
pairs.append((fields[2*i], fields[2*i+1]))
return pairs
......@@ -361,7 +361,7 @@ print(' <CMAPTorsionForce>')
for values in sorted(uniqueCmaps, key=lambda x: uniqueCmaps[x]):
print(' <Map>')
size = int(math.sqrt(len(values)))
shift = size/2
shift = size//2
scale = kilocalories_per_mole.conversion_factor_to(kilojoules_per_mole)
# Convert the ordering from the one used by CHARMM to the one used by OpenMM.
reordered = [0]*len(values)
......
docs-source/usersguide/application.rst
View file @ 0b5d58d7
......@@ -1123,6 +1123,13 @@ algorithm\ :cite:`Tuckerman1992`. This allows some forces in the system to be e
frequently than others. For details on how to use it, consult the API
documentation.
Multiple Time Step Langevin Integrator
--------------------------------------
:class:`MTSLangevinIntegrator` is similar to :class:`MTSIntegrator`, but it uses
the Langevin method to perform constant temperature dynamics. For details on
how to use it, consult the API documentation.
Compound Integrator
-------------------
......
libraries/irrxml/include/irrTypes.h
View file @ 0b5d58d7
......@@ -2,6 +2,8 @@
// This file is part of the "Irrlicht Engine".
// For conditions of distribution and use, see copyright notice in irrlicht.h
// NOTE: This file has been changed from the orginal source distribution.
#ifndef __IRR_TYPES_H_INCLUDED__
#define __IRR_TYPES_H_INCLUDED__
......@@ -80,7 +82,8 @@ typedef unsigned short wchar_t;
//! define a break macro for debugging only in Win32 mode.
#if defined(WIN32) && defined(_MSC_VER) && defined(_DEBUG)
#define _IRR_DEBUG_BREAK_IF( _CONDITION_ ) if (_CONDITION_) {_asm int 3}
// NOTE: This line has been changed and originally used '_asm int 3' to break into the debugger.
#define _IRR_DEBUG_BREAK_IF( _CONDITION_ ) if (_CONDITION_) { __debugbreak(); }
#else
#define _IRR_DEBUG_BREAK_IF( _CONDITION_ )
#endif
......
libraries/jama/include/jama_cholesky.h
View file @ 0b5d58d7
......@@ -191,6 +191,9 @@ Array2D<Real> Cholesky<Real>::solve(const Array2D<Real> &B)
if (B.dim1() != n)
return Array2D<Real>();
if (!isspd)
return Arran2D<Real>();
Array2D<Real> X = B.copy();
int nx = B.dim2();
......@@ -224,9 +227,9 @@ Array2D<Real> Cholesky<Real>::solve(const Array2D<Real> &B)
// Solve L*y = b;
for (int j=0; j< nx; j++)
for (int k = 0; k < n; k++)
{
for (int k = 0; k < n; k++)
for (int j=0; j< nx; j++)
{
for (int i = 0; i < k; i++)
X[k][j] -= X[i][j]*L_[k][i];
......@@ -235,9 +238,9 @@ Array2D<Real> Cholesky<Real>::solve(const Array2D<Real> &B)
}
// Solve L'*X = Y;
for (int j=0; j<nx; j++)
for (int k = n-1; k >= 0; k--)
{
for (int k = n-1; k >= 0; k--)
for (int j=0; j<nx; j++)
{
for (int i = k+1; i < n; i++)
X[k][j] -= X[i][j]*L_[i][k];
......
libraries/jama/include/jama_eig.h
View file @ 0b5d58d7
......@@ -663,21 +663,20 @@ class Eigenvalue
// Double QR step involving rows l:n and columns m:n
for (int k = m; k <= n-1; k++) {
int notlast = (k != n-1);
bool notlast = (k != n-1);
if (k != m) {
p = H[k][k-1];
q = H[k+1][k-1];
r = (notlast ? H[k+2][k-1] : 0.0);
x = abs(p) + abs(q) + abs(r);
if (x != 0.0) {
p = p / x;
q = q / x;
r = r / x;
if (x == 0.0) {
continue;
}
p = p / x;
q = q / x;
r = r / x;
}
if (x == 0.0) {
break;
}
s = sqrt(p * p + q * q + r * r);
if (p < 0) {
s = -s;
......
libraries/jama/include/jama_svd.h
View file @ 0b5d58d7
......@@ -12,6 +12,8 @@
// for min(), max() below
#include <cmath>
// for abs() below
#include <limits>
// for numeric_limits
using namespace TNT;
using namespace std;
......@@ -247,6 +249,7 @@ class SVD
int pp = p-1;
int iter = 0;
Real eps(pow(2.0,-52.0));
Real tiny = numeric_limits<Real>::min();
while (p > 0) {
int k=0;
int kase=0;
......@@ -267,7 +270,7 @@ class SVD
if (k == -1) {
break;
}
if (abs(e[k]) <= eps*(abs(s[k]) + abs(s[k+1]))) {
if (abs(e[k]) <= tiny + eps*(abs(s[k]) + abs(s[k+1]))) {
e[k] = 0.0;
break;
}
......@@ -282,7 +285,7 @@ class SVD
}
Real t( (ks != p ? abs(e[ks]) : 0.) +
(ks != k+1 ? abs(e[ks-1]) : 0.));
if (abs(s[ks]) <= eps*t) {
if (abs(s[ks]) <= tiny + eps*t) {
s[ks] = 0.0;
break;
}
......
libraries/lepton/src/MSVC_erfc.h
View file @ 0b5d58d7
......@@ -8,9 +8,13 @@
* (VC11 has _MSC_VER=1700).
*/
#if defined(_MSC_VER)
#if defined(_MSC_VER) || defined(__MINGW32__)
#if !defined(M_PI)
#define M_PI 3.14159265358979323846264338327950288
#endif
#endif
#if defined(_MSC_VER)
#if _MSC_VER <= 1700 // 1700 is VC11, 1800 is VC12
/***************************
* erf.cpp
......
libraries/vecmath/src/vecmath.cpp
View file @ 0b5d58d7
#if defined(__ANDROID__)
#if defined(__ARM__) || defined(__ARM64__)
#include "neon_mathfun.h"
#else
#if !defined(__PNACL__)
......
olla/include/openmm/kernels.h
View file @ 0b5d58d7
......@@ -1063,16 +1063,16 @@ public:
/**
* This kernel is invoked by NoseHooverIntegrator to take one time step.
*/
class IntegrateVelocityVerletStepKernel : public KernelImpl {
class IntegrateNoseHooverStepKernel : public KernelImpl {
public:
static std::string Name() {
return "IntegrateVelocityVerletStep";
return "IntegrateNoseHooverStep";
}
IntegrateVelocityVerletStepKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
IntegrateNoseHooverStepKernel(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
*/
......@@ -1093,6 +1093,49 @@ public:
* @param integrator the NoseHooverIntegrator this kernel is being used for
*/
virtual double computeKineticEnergy(ContextImpl& context, const NoseHooverIntegrator& integrator) = 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;
/**
* Write the chain states to a checkpoint.
*/
virtual void createCheckpoint(ContextImpl& context, std::ostream& stream) const = 0;
/**
* Load the chain states from a checkpoint.
*/
virtual void loadCheckpoint(ContextImpl& context, std::istream& stream) = 0;
};
/**
......@@ -1360,58 +1403,6 @@ 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/CompoundIntegrator.h
View file @ 0b5d58d7
......@@ -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) 2015-2016 Stanford University and the Authors. *
* Portions copyright (c) 2015-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -194,6 +194,16 @@ protected:
double getVelocityTimeOffset() const {
return getIntegrator(0).getVelocityTimeOffset();
}
/**
* This is called while writing checkpoints. It gives the integrator a chance to write
* its own data.
*/
void createCheckpoint(std::ostream& stream) const;
/**
* This is called while loading a checkpoint. The integrator should read in whatever
* data it wrote in createCheckpoint() and update its internal state accordingly.
*/
void loadCheckpoint(std::istream& stream);
private:
int currentIntegrator;
std::vector<Integrator*> integrators;
......
openmmapi/include/openmm/CustomIntegrator.h
View file @ 0b5d58d7
......@@ -668,6 +668,16 @@ protected:
* Get whether computeKineticEnergy() expects forces to have been computed.
*/
bool kineticEnergyRequiresForce() const;
/**
* This is called while writing checkpoints. It gives the integrator a chance to write
* its own data.
*/
void createCheckpoint(std::ostream& stream) const;
/**
* This is called while loading a checkpoint. The integrator should read in whatever
* data it wrote in createCheckpoint() and update its internal state accordingly.
*/
void loadCheckpoint(std::istream& stream);
private:
class ComputationInfo;
class FunctionInfo;
......
openmmapi/include/openmm/Integrator.h
View file @ 0b5d58d7
......@@ -34,6 +34,7 @@
#include "State.h"
#include "Vec3.h"
#include <iosfwd>
#include <map>
#include <vector>
#include "internal/windowsExport.h"
......@@ -151,6 +152,18 @@ protected:
virtual double getVelocityTimeOffset() const {
return 0.0;
}
/**
* This is called while writing checkpoints. It gives the integrator a chance to write
* its own data. The default implementation does nothing.
*/
virtual void createCheckpoint(std::ostream& stream) const {
}
/**
* This is called while loading a checkpoint. The integrator should read in whatever
* data it wrote in createCheckpoint() and update its internal state accordingly.
*/
virtual void loadCheckpoint(std::istream& stream) {
}
private:
double stepSize, constraintTol;
};
......
openmmapi/include/openmm/NoseHooverChain.h
View file @ 0b5d58d7
......@@ -72,7 +72,7 @@ public:
* 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 numYoshidaSuzuki the number of Yoshida Suzuki steps used to propagate this chain (1, 3, 5, or 7).
* @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
......
openmmapi/include/openmm/NoseHooverIntegrator.h
View file @ 0b5d58d7
......@@ -45,13 +45,14 @@ 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.
* thermostats, using the "middle" leapfrog propagation algorithm described in
* J. Phys. Chem. A 2019, 123, 6056-6079.
*/
class OPENMM_EXPORT NoseHooverIntegrator : public Integrator {
public:
/**
* Create a NoseHooverIntegrator. This version creates a bare velocity Verlet integrator
* Create a NoseHooverIntegrator. This version creates a bare leapfrog 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)
......@@ -66,12 +67,12 @@ public:
* @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).
* used in the chain propagation algorithm (must be 1, 3, 5, or 7).
*/
explicit NoseHooverIntegrator(double temperature, double collisionFrequency, double stepSize,
int chainLength = 3, int numMTS = 3, int numYoshidaSuzuki = 3);
int chainLength = 3, int numMTS = 3, int numYoshidaSuzuki = 7);
virtual ~NoseHooverIntegrator();
~NoseHooverIntegrator();
/**
* Advance a simulation through time by taking a series of time steps.
*
......@@ -86,7 +87,7 @@ public:
* @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).
* used in the chain propagation algorithm (must be 1, 3, 5, or 7).
*/
int addThermostat(double temperature, double collisionFrequency,
int chainLength, int numMTS, int numYoshidaSuzuki);
......@@ -110,13 +111,13 @@ public:
* @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).
* used in the chain propagation algorithm (must be 1, 3, 5, or 7).
*/
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);
int chainLength = 3, int numMTS = 3, int numYoshidaSuzuki = 7);
/**
* Get the temperature of the i-th chain for controling absolute particle motion (in Kelvin).
*
......@@ -194,18 +195,6 @@ public:
* @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.
......@@ -232,15 +221,6 @@ public:
*/
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.
......@@ -256,6 +236,18 @@ protected:
* cleanup. It will also get called again if the application calls reinitialize() on the Context.
*/
void cleanup();
/**
* 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
*/
void stateChanged(State::DataType changed) {
if (State::Positions == changed) forcesAreValid = false;
}
/**
* Get the names of all Kernels used by this Integrator.
*/
......@@ -263,17 +255,27 @@ protected:
/**
* Compute the kinetic energy of the system at the current time.
*/
virtual double computeKineticEnergy();
double computeKineticEnergy();
/**
* Computing kinetic energy for this integrator does not require forces.
*/
bool kineticEnergyRequiresForce() const override;
bool kineticEnergyRequiresForce() const;
/**
* This is called while writing checkpoints. It gives the integrator a chance to write
* its own data.
*/
void createCheckpoint(std::ostream& stream) const;
/**
* This is called while loading a checkpoint. The integrator should read in whatever
* data it wrote in createCheckpoint() and update its internal state accordingly.
*/
void loadCheckpoint(std::istream& stream);
std::vector<NoseHooverChain> noseHooverChains;
std::vector<int> allAtoms;
std::vector<std::tuple<int, int, double> > allPairs;
bool forcesAreValid;
Kernel vvKernel, nhcKernel;
Kernel kernel;
bool hasSubsystemThermostats_;
double maxPairDistance_;
};
......
openmmapi/include/openmm/internal/hardware.h
View file @ 0b5d58d7
......@@ -93,7 +93,8 @@ static int getNumProcessors() {
#ifdef WIN32
#define cpuid __cpuid
#else
#if !defined(__ANDROID__) && !defined(__PNACL__) && !defined(__PPC__)
#if !defined(__ANDROID__) && !defined(__PNACL__) && !defined(__PPC__) \
&& !defined(__ARM__) && !defined(__ARM64__)
static void cpuid(int cpuInfo[4], int infoType){
#ifdef __LP64__
__asm__ __volatile__ (
......
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