Merged changes from main branch

.travis.yml

@@ -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

@@ -21,39 +21,18 @@ 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)
-
-# CMake 2.4 on dart server only needs to know about Dart
 INCLUDE(Dart)
 MARK_AS_ADVANCED(DART_ROOT)
 
-# Avoid dart server problem with cmake 2.4 --cmb
-set(cmv "${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}")
-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 +48,9 @@ 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)
@@ -98,22 +80,7 @@ ELSE(WIN32)
     ENDIF (NOT ANDROID)
 ENDIF(WIN32)
 
-# The build system will set ARCH64 for 64 bit builds, which require
-# use of the lib64/ library directories rather than lib/.
-#SET( ARCH64 OFF CACHE BOOL "ON for 64bit builds, OFF for 32bit builds")
-#MARK_AS_ADVANCED( ARCH64  )
-#IF (ARCH64)
-#    SET(LIB64 64)
-#ELSE (ARCH64)
-#    SET(LIB64) # nothing
-#ENDIF (ARCH64)
-
-IF( CMAKE_SIZEOF_VOID_P EQUAL 8 )
-  SET( LIB64 64 )
-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
@@ -177,37 +144,11 @@ SET(OPENMM_MAJOR_VERSION 7)
 SET(OPENMM_MINOR_VERSION 1)
 SET(OPENMM_BUILD_VERSION 0)
 
-SET(OPENMM_COPYRIGHT_YEARS "2008-2015")
-
-# underbar separated list of dotted authors, no spaces or commas
-SET(OPENMM_AUTHORS "Peter.Eastman")
-
 ADD_DEFINITIONS(-DOPENMM_LIBRARY_NAME=${OPENMM_LIBRARY_NAME}
                 -DOPENMM_MAJOR_VERSION=${OPENMM_MAJOR_VERSION}
                 -DOPENMM_MINOR_VERSION=${OPENMM_MINOR_VERSION}
                 -DOPENMM_BUILD_VERSION=${OPENMM_BUILD_VERSION})
 
-# CMake quotes automatically when building Visual Studio projects but we need
-# to add them ourselves for Linux or Cygwin. Two cases to avoid duplicate quotes
-# in Visual Studio which end up in the binary.
-
-IF (MSVC)
-   SET(NEED_QUOTES FALSE)
-ELSE (MSVC)
-   SET(NEED_QUOTES TRUE)
-ENDIF (MSVC)
-
-##TODO: doesn't work without quotes in nightly build
-SET(NEED_QUOTES TRUE)
-
-IF(NEED_QUOTES)
-   ADD_DEFINITIONS(-DOPENMM_COPYRIGHT_YEARS="${OPENMM_COPYRIGHT_YEARS}"
-                   -DOPENMM_AUTHORS="${OPENMM_AUTHORS}")
-ELSE(NEED_QUOTES)
-   ADD_DEFINITIONS(-DOPENMM_COPYRIGHT_YEARS=${OPENMM_COPYRIGHT_YEARS}
-                   -DOPENMM_AUTHORS=${OPENMM_AUTHORS})
-ENDIF(NEED_QUOTES)
-
 # -DOPENMM_TYPE has to be defined in the target subdirectories.
 # -Dsimbody_EXPORTS defined automatically when Windows DLL build is being done.
 
@@ -283,7 +224,7 @@ 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 +243,6 @@ 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 ${EXTRA_COMPILE_FLAGS})
 IF (CMAKE_SYSTEM_NAME MATCHES "Linux")
     IF (NOT ANDROID)
@@ -319,7 +258,6 @@ IF(OPENMM_BUILD_SHARED_LIB)
     SET_TARGET_PROPERTIES(${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")
@@ -363,63 +301,19 @@ IF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)
     ADD_SUBDIRECTORY(platforms/reference/tests)
 ENDIF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)
 
-# Which hardware platforms to build
+# CUDA platform
 
-# A bit of tedium because we are using custom FindCUDA files that happen to work...
-SET(FINDCUDA_DIR "${CMAKE_CURRENT_SOURCE_DIR}/cmake_modules/FindCUDA")
-SET(CUDA_BUILD_CUBIN OFF)
 FIND_PACKAGE(CUDA QUIET)
 IF(CUDA_FOUND)
-    IF(NOT CUDA_NVCC_FLAGS)
-        SET(FLAGS "")
-        # Note that cmake will insert semicolons between these item automatically...
-        SET(FLAGS ${FLAGS} -gencode arch=compute_11,code=sm_11)
-        SET(FLAGS ${FLAGS} -gencode arch=compute_12,code=sm_12)
-        SET(FLAGS ${FLAGS} -gencode arch=compute_13,code=sm_13)
-        SET(FLAGS ${FLAGS} -gencode arch=compute_20,code=sm_20)
-        SET(FLAGS ${FLAGS} -use_fast_math)
-        IF(MSVC)
-            # Unfortunately the variables CUDA_NVCC_FLAGS_RELEASE and CUDA_NVCC_FLAGS_DEBUG
-            # appear to be unused, at least in CMake 2.6
-            # Release /MD linkage
-            set(FLAGS ${FLAGS} "-Xcompiler \"/MD\" -DOPENMMCUDA_BUILDING_SHARED_LIBRARY")
-        ENDIF(MSVC)
-        SET(CUDA_NVCC_FLAGS  "${FLAGS}"
-            CACHE STRING "Semicolon delimit multiple arguments")
-    ENDIF(NOT CUDA_NVCC_FLAGS)
     SET(OPENMM_BUILD_CUDA_LIB ON CACHE BOOL "Build OpenMMCuda library for Nvidia GPUs")
-
-    # I wish I was not hardcoding /MD here
-    # Avoid strange windows link error with cuda free energy
-    # plugin by specifying /MD to CUDA_NVCC_FLAGS
-    MARK_AS_ADVANCED(CLEAR CUDA_NVCC_FLAGS)
-    IF(MSVC)
-        # Unfortunately the variables CUDA_NVCC_FLAGS_RELEASE and CUDA_NVCC_FLAGS_DEBUG
-        # appear to be unused, at least in CMake 2.6
-        # Release /MD linkage
-        SET(HAS_NVCC_FLAG FALSE)
-        IF(CUDA_NVCC_FLAGS MATCHES "-Xcompiler")
-            SET(HAS_NVCC_FLAG TRUE)
-        ENDIF(CUDA_NVCC_FLAGS MATCHES "-Xcompiler")
-        IF(NOT HAS_NVCC_FLAG)
-            set(new_flags "-Xcompiler \"/MD\" -DOPENMMCUDA_BUILDING_SHARED_LIBRARY")
-            if(CUDA_NVCC_FLAGS)
-                set(new_flags "${CUDA_NVCC_FLAGS};${new_flags}")
-            endif(CUDA_NVCC_FLAGS)
-            SET(CUDA_NVCC_FLAGS "${new_flags}"
-                CACHE STRING "Semicolon delimit multiple arguments" FORCE)
-        ENDIF(NOT HAS_NVCC_FLAG)
-    ENDIF(MSVC)
 ELSE(CUDA_FOUND)
     SET(OPENMM_BUILD_CUDA_LIB OFF CACHE BOOL "Build OpenMMCuda library for Nvidia GPUs")
 ENDIF(CUDA_FOUND)
 IF(OPENMM_BUILD_CUDA_LIB)
     ADD_SUBDIRECTORY(platforms/cuda)
 ENDIF(OPENMM_BUILD_CUDA_LIB)
-MARK_AS_ADVANCED(CUDA_VERBOSE_BUILD)
-MARK_AS_ADVANCED(CUDA_BUILD_CUBIN)
-MARK_AS_ADVANCED(CUDA_BUILD_EMULATION)
-MARK_AS_ADVANCED(CUDA_HOST_COMPILER CUDA_HOST_COMPILER_OPTIONS)
+
+# OpenCL platform
 
 FIND_PACKAGE(OpenCL QUIET)
 IF(OPENCL_FOUND)
@@ -517,7 +411,7 @@ INSTALL_FILES(/include/sfmt            FILES ${SFMT_HEADERS})
 
 ADD_SUBDIRECTORY(serialization)
 FILE(GLOB serialization_files  ${CMAKE_SOURCE_DIR}/serialization/src/*.cpp)
-SET_SOURCE_FILES_PROPERTIES(${serialization_files} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL -DIEEE_8087")
+SET_SOURCE_FILES_PROPERTIES(${serialization_files} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY -DIEEE_8087")
 
 # Python wrappers
 
@@ -535,23 +429,6 @@ IF(OPENMM_BUILD_PYTHON_WRAPPERS)
     ADD_SUBDIRECTORY(wrappers/python)
 ENDIF(OPENMM_BUILD_PYTHON_WRAPPERS)
 
-
-
-
-#
-# Allow automated build and dashboard.
-#
-# redundant INCLUDE(Dart) statement
-# INCLUDE (Dart)
-
-#IF (UNIX AND NOT CYGWIN AND NOT APPLE)
-#  IF (NOT CMAKE_BUILD_TYPE OR CMAKE_BUILD_TYPE MATCHES Debug)
-#    ADD_DEFINITIONS(-fprofile-arcs -ftest-coverage)
-#    LINK_LIBRARIES(gcov)
-#  ENDIF (NOT CMAKE_BUILD_TYPE OR CMAKE_BUILD_TYPE MATCHES Debug)
-#ENDIF (UNIX AND NOT CYGWIN AND NOT APPLE)
-
-
 #
 # Testing
 #
@@ -573,5 +450,3 @@ SET(OPENMM_BUILD_EXAMPLES ON CACHE BOOL "Build example executables")
 IF(OPENMM_BUILD_EXAMPLES)
   ADD_SUBDIRECTORY(examples)
 ENDIF(OPENMM_BUILD_EXAMPLES)
-
-ENDIF(NOT cmv EQUAL "2.4") # This whole file...

appveyor.yml

-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
+  - pip install numpy
 
 # Use cclash for compiler caching (experimental)
   - ps: wget https://github.com/inorton/cclash/releases/download/0.3.14/cclash-0.3.14.zip -OutFile cclash-0.3.14.zip

devtools/packaging/scripts/windows/prepare.ps1

 cd C:\Users\vagrant
 
-# Install everything we can with choco.
-
-choco install -y doxygen.portable swig cmake doxygen.install vcbuildtools git jom
-
 # Install CUDA.
 
 wget https://developer.nvidia.com/compute/cuda/8.0/prod/network_installers/cuda_8.0.44_win10_network-exe -UseBasicParsing -OutFile cuda_8.0.44_win10_network.exe
@@ -21,5 +17,9 @@ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Windows-x86_64.exe -U
 
 # Install software with conda.
 
-& "C:\Miniconda3\Scripts\conda.exe" install -y -c omnia fftw3f jinja2 lxml sphinx sphinxcontrib-autodoc_doxygen sphinxcontrib-lunrsearch conda-build
+& "C:\Miniconda3\Scripts\conda.exe" install -y -c omnia fftw3f jinja2 lxml sphinx sphinxcontrib-autodoc_doxygen sphinxcontrib-lunrsearch conda-build anaconda-client
 & "C:\Miniconda3\Scripts\pip.exe" install sphinxcontrib.bibtex
+
+# Install software with choco.
+
+choco install -y doxygen.portable swig cmake doxygen.install vcbuildtools git jom

docs-source/usersguide/application.rst

@@ -916,8 +916,9 @@ Value                      Meaning
 :code:`NoCutoff`           No cutoff is applied.
 :code:`CutoffNonPeriodic`  The reaction field method is used to eliminate all interactions beyond a cutoff distance.  Not valid for AMOEBA.
 :code:`CutoffPeriodic`     The reaction field method is used to eliminate all interactions beyond a cutoff distance.  Periodic boundary conditions are applied, so each atom interacts only with the nearest periodic copy of every other atom.  Not valid for AMOEBA.
-:code:`Ewald`              Periodic boundary conditions are applied.  Ewald summation is used to compute long range interactions.  (This option is rarely used, since PME is much faster for all but the smallest systems.)  Not valid for AMOEBA.
-:code:`PME`                Periodic boundary conditions are applied.  The Particle Mesh Ewald method is used to compute long range interactions.
+:code:`Ewald`              Periodic boundary conditions are applied.  Ewald summation is used to compute long range Coulomb interactions.  (This option is rarely used, since PME is much faster for all but the smallest systems.)  Not valid for AMOEBA.
+:code:`PME`                Periodic boundary conditions are applied.  The Particle Mesh Ewald method is used to compute long range Coulomb interactions.
+:code:`LJPME`              Periodic boundary conditions are applied.  The Particle Mesh Ewald method is used to compute long range interactions for both Coulomb and Lennard-Jones.
 =========================  ===========================================================================================================================================================================================================================================
 
 
@@ -926,7 +927,7 @@ cutoff distance.  Be sure to specify units, as shown in the examples above. For
 example, :code:`nonbondedCutoff=1.5*nanometers` or
 :code:`nonbondedCutoff=12*angstroms` are legal values.
 
-When using :code:`Ewald` or :code:`PME`\ , you can optionally specify an
+When using :code:`Ewald`, :code:`PME`, or :code:`LJPME`\ , you can optionally specify an
 error tolerance for the force computation.  For example:
 ::
 

docs-source/usersguide/library.rst

@@ -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

docs-source/usersguide/references.bib

@@ -517,3 +517,15 @@
    year = {2014},
    type = {Journal Article}
 }
+
+@article{Wennberg2015
+   author = {Wennberg, Christian L. and Murtola, Teemu and Páll, Szilárd and Abraham, Mark J. and Hess, Berk and Lindahl, Erik},
+   title = {Direct-Space Corrections Enable Fast and Accurate {Lorentz–Berthelot} Combination Rule {Lennard-Jones} Lattice Summation},
+   journal = {Journal of Chemical Theory and Computation},
+   volume = {11},
+   number = {12},
+   pages = {5737-5746},
+   year = {2015},
+   type = {Journal Article}
+}
+

docs-source/usersguide/theory.rst

@@ -412,7 +412,7 @@ and the number of nodes in the mesh along each dimension as
 
 
 .. math::
-   n_\mathit{mesh}=\frac{2\alpha d}{{3d}^{1/5}}
+   n_\mathit{mesh}=\frac{2\alpha d}{{3\delta}^{1/5}}
 
 
 where *d* is the width of the periodic box along that dimension.  Alternatively,
@@ -432,6 +432,38 @@ to numerical round-off error than Ewald summation.  For Platforms that do
 calculations in single precision, making :math:`\delta` too small (typically below about
 5·10\ :sup:`-5`\ ) can actually cause the error to increase.
 
+Lennard-Jones Interaction With Particle Mesh Ewald
+==================================================
+
+The PME algorithm can also be used for Lennard-Jones interactions.  Usually this
+is not necessary, since Lennard-Jones forces are short ranged, but there are
+situations (such as membrane simulations) where neglecting interactions beyond
+the cutoff can measurably affect results.
+
+For computational efficiency, certain approximations are made\ :cite:`Wennberg2015`.
+Interactions beyond the cutoff distance include only the attractive :math:`1/r^6`
+term, not the repulsive :math:`1/r^{12}` term.  Since the latter is much smaller
+than the former at long distances, this usually has negligible effect.  Also,
+the interaction between particles farther apart than the cutoff distance is
+computed using geometric combination rules:
+
+.. math::
+   \sigma=\sqrt{\sigma_1 \sigma_2}
+
+The effect of this approximation is also quite small, and it is still far more
+accurate than ignoring the interactions altogether (which is what would happen
+with PME).
+
+The formula used to compute the number of nodes along each dimension of the mesh
+is slightly different from the one used for Coulomb interactions:
+
+.. math::
+   n_\mathit{mesh}=\frac{\alpha d}{{3\delta}^{1/5}}
+
+As before, this is an empirical formula.  It will usually produce an average
+relative error in the forces less than or similar to :math:`\delta`\ , but that
+is not guaranteed.
+
 .. _gbsaobcforce:
 
 GBSAOBCForce

libraries/lbfgs/src/lbfgs.cpp

@@ -408,6 +408,7 @@ int lbfgs(
         pf = (lbfgsfloatval_t*)vecalloc(param.past * sizeof(lbfgsfloatval_t));
     }
 
+    try {
         /* Evaluate the function value and its gradient. */
         fx = cd.proc_evaluate(cd.instance, x, g, cd.n, 0);
         if (0. != param.orthantwise_c) {
@@ -613,6 +614,26 @@ int lbfgs(
              */
             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:
     /* Return the final value of the objective function. */

olla/include/openmm/kernels.h

@@ -555,7 +555,8 @@ public:
         CutoffNonPeriodic = 1,
         CutoffPeriodic = 2,
         Ewald = 3,
-        PME = 4
+        PME = 4,
+        LJPME = 5
     };
     static std::string Name() {
         return "CalcNonbondedForce";
@@ -596,6 +597,15 @@ public:
      * @param nz      the number of grid points along the Z axis
      */
     virtual void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const = 0;
+    /**
+     * Get the parameters being used for the dispersion terms in LJPME.
+     *
+     * @param alpha   the separation parameter
+     * @param nx      the number of grid points along the X axis
+     * @param ny      the number of grid points along the Y axis
+     * @param nz      the number of grid points along the Z axis
+     */
+    virtual void getLJPMEParameters(double& alpha, int& nx, int& ny, int& nz) const = 0;
 };
 
 /**
@@ -1335,6 +1345,57 @@ public:
 };
 
 
+/**
+ * This kernel performs the dispersion reciprocal space calculation for LJPME.  In most cases, this
+ * calculation is done directly by CalcNonbondedForceKernel so this kernel is unneeded.
+ * In some cases it may want to outsource the work to a different kernel.  In particular,
+ * GPU based platforms sometimes use a CPU based implementation provided by a separate
+ * plugin.
+ */
+class CalcDispersionPmeReciprocalForceKernel : public KernelImpl {
+public:
+    class IO;
+    static std::string Name() {
+        return "CalcDispersionPmeReciprocalForce";
+    }
+    CalcDispersionPmeReciprocalForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
+    }
+    /**
+     * Initialize the kernel.
+     * 
+     * @param gridx        the x size of the PME grid
+     * @param gridy        the y size of the PME grid
+     * @param gridz        the z size of the PME grid
+     * @param numParticles the number of particles in the system
+     * @param alpha        the Ewald blending parameter
+     */
+    virtual void initialize(int gridx, int gridy, int gridz, int numParticles, double alpha) = 0;
+    /**
+     * Begin computing the force and energy.
+     *
+     * @param io                  an object that coordinates data transfer
+     * @param periodicBoxVectors  the vectors defining the periodic box (measured in nm)
+     * @param includeEnergy       true if potential energy should be computed
+     */
+    virtual void beginComputation(IO& io, const Vec3* periodicBoxVectors, bool includeEnergy) = 0;
+    /**
+     * Finish computing the force and energy.
+     * 
+     * @param io   an object that coordinates data transfer
+     * @return the potential energy due to the PME reciprocal space interactions
+     */
+    virtual double finishComputation(IO& io) = 0;
+    /**
+     * Get the parameters being used for PME.
+     * 
+     * @param alpha   the separation parameter
+     * @param nx      the number of grid points along the X axis
+     * @param ny      the number of grid points along the Y axis
+     * @param nz      the number of grid points along the Z axis
+     */
+    virtual void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const = 0;
+};
+
 } // namespace OpenMM
 
 #endif /*OPENMM_KERNELS_H_*/

openmmapi/include/openmm/NonbondedForce.h

@@ -101,15 +101,20 @@ public:
          */
         CutoffPeriodic = 2,
         /**
-         * Periodic boundary conditions are used, and Ewald summation is used to compute the interaction of each particle
+         * Periodic boundary conditions are used, and Ewald summation is used to compute the Coulomb interaction of each particle
          * with all periodic copies of every other particle.
          */
         Ewald = 3,
         /**
-         * Periodic boundary conditions are used, and Particle-Mesh Ewald (PME) summation is used to compute the interaction of each particle
+         * Periodic boundary conditions are used, and Particle-Mesh Ewald (PME) summation is used to compute the Coulomb interaction of each particle
          * with all periodic copies of every other particle.
          */
-        PME = 4
+        PME = 4,
+        /**
+         * Periodic boundary conditions are used, and Particle-Mesh Ewald (PME) summation is used to compute the interaction of each particle
+         * with all periodic copies of every other particle for both Coulomb and Lennard-Jones.  No switching is used for either interaction.
+         */
+        LJPME = 5
     };
     /**
      * Create a NonbondedForce.
@@ -207,6 +212,16 @@ public:
      * @param[out] nz      the number of grid points along the Z axis
      */
     void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
+    /**
+     * Get the parameters to use for dispersion term in LJ-PME calculations.  If alpha is 0 (the default),
+     * these parameters are ignored and instead their values are chosen based on the Ewald error tolerance.
+     *
+     * @param[out] alpha   the separation parameter
+     * @param[out] nx      the number of dispersion grid points along the X axis
+     * @param[out] ny      the number of dispersion grid points along the Y axis
+     * @param[out] nz      the number of dispersion grid points along the Z axis
+     */
+    void getLJPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
     /**
      * Set the parameters to use for PME calculations.  If alpha is 0 (the default), these parameters are
      * ignored and instead their values are chosen based on the Ewald error tolerance.
@@ -217,6 +232,16 @@ public:
      * @param nz      the number of grid points along the Z axis
      */
     void setPMEParameters(double alpha, int nx, int ny, int nz);
+    /**
+     * Set the parameters to use for the dispersion term in LJPME calculations.  If alpha is 0 (the default),
+     * these parameters are ignored and instead their values are chosen based on the Ewald error tolerance.
+     *
+     * @param alpha   the separation parameter
+     * @param nx      the number of grid points along the X axis
+     * @param ny      the number of grid points along the Y axis
+     * @param nz      the number of grid points along the Z axis
+     */
+    void setLJPMEParameters(double alpha, int nx, int ny, int nz);
     /**
      * Get the parameters being used for PME in a particular Context.  Because some platforms have restrictions
      * on the allowed grid sizes, the values that are actually used may be slightly different from those
@@ -230,6 +255,19 @@ public:
      * @param[out] nz      the number of grid points along the Z axis
      */
     void getPMEParametersInContext(const Context& context, double& alpha, int& nx, int& ny, int& nz) const;
+    /**
+     * Get the PME parameters being used for the dispersion term for LJPME in a particular Context.  Because some
+     * platforms have restrictions on the allowed grid sizes, the values that are actually used may be slightly different
+     * from those specified with setPMEParameters(), or the standard values calculated based on the Ewald error tolerance.
+     * See the manual for details.
+     *
+     * @param context      the Context for which to get the parameters
+     * @param[out] alpha   the separation parameter
+     * @param[out] nx      the number of grid points along the X axis
+     * @param[out] ny      the number of grid points along the Y axis
+     * @param[out] nz      the number of grid points along the Z axis
+     */
+    void getLJPMEParametersInContext(const Context& context, double& alpha, int& nx, int& ny, int& nz) const;
     /**
      * Add the nonbonded force parameters for a particle.  This should be called once for each particle
      * in the System.  When it is called for the i'th time, it specifies the parameters for the i'th particle.
@@ -374,7 +412,8 @@ public:
     bool usesPeriodicBoundaryConditions() const {
         return nonbondedMethod == NonbondedForce::CutoffPeriodic ||
                nonbondedMethod == NonbondedForce::Ewald ||
-               nonbondedMethod == NonbondedForce::PME;
+               nonbondedMethod == NonbondedForce::PME ||
+               nonbondedMethod == NonbondedForce::LJPME;
     }
 protected:
     ForceImpl* createImpl() const;
@@ -382,9 +421,9 @@ private:
     class ParticleInfo;
     class ExceptionInfo;
     NonbondedMethod nonbondedMethod;
-    double cutoffDistance, switchingDistance, rfDielectric, ewaldErrorTol, alpha;
+    double cutoffDistance, switchingDistance, rfDielectric, ewaldErrorTol, alpha, dalpha;
     bool useSwitchingFunction, useDispersionCorrection;
-    int recipForceGroup, nx, ny, nz;
+    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;
     std::vector<ParticleInfo> particles;
     std::vector<ExceptionInfo> exceptions;

openmmapi/include/openmm/internal/NonbondedForceImpl.h

@@ -65,6 +65,7 @@ public:
     std::vector<std::string> getKernelNames();
     void updateParametersInContext(ContextImpl& context);
     void getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
+    void getLJPMEParameters(double& alpha, int& nx, int& ny, int& nz) const;
     /**
      * This is a utility routine that calculates the values to use for alpha and kmax when using
      * Ewald summation.
@@ -74,7 +75,7 @@ public:
      * This is a utility routine that calculates the values to use for alpha and grid size when using
      * Particle Mesh Ewald.
      */
-    static void calcPMEParameters(const System& system, const NonbondedForce& force, double& alpha, int& xsize, int& ysize, int& zsize);
+    static void calcPMEParameters(const System& system, const NonbondedForce& force, double& alpha, int& xsize, int& ysize, int& zsize, bool lj);
     /**
      * Compute the coefficient which, when divided by the periodic box volume, gives the
      * long range dispersion correction to the energy.

openmmapi/include/openmm/internal/ThreadPool.h

@@ -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

@@ -105,12 +105,13 @@ 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.
 
@@ -182,6 +183,11 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
                 }
             }
         }
+    }
+    catch (...) {
+        lbfgs_free(x);
+        throw;
+    }
     lbfgs_free(x);
     
     // If necessary, do a final constraint projection to make sure they are satisfied

openmmapi/src/NonbondedForce.cpp

@@ -48,7 +48,8 @@ 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), useSwitchingFunction(false), useDispersionCorrection(true), recipForceGroup(-1), nx(0), ny(0), nz(0) {
+        ewaldErrorTol(5e-4), alpha(0.0), dalpha(0.0), useSwitchingFunction(false), useDispersionCorrection(true), recipForceGroup(-1),
+        nx(0), ny(0), nz(0), dnx(0), dny(0), dnz(0) {
 }
 
 NonbondedForce::NonbondedMethod NonbondedForce::getNonbondedMethod() const {
@@ -106,6 +107,13 @@ void NonbondedForce::getPMEParameters(double& alpha, int& nx, int& ny, int& nz)
     nz = this->nz;
 }
 
+void NonbondedForce::getLJPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
+    alpha = this->dalpha;
+    nx = this->dnx;
+    ny = this->dny;
+    nz = this->dnz;
+}
+
 void NonbondedForce::setPMEParameters(double alpha, int nx, int ny, int nz) {
     this->alpha = alpha;
     this->nx = nx;
@@ -113,10 +121,21 @@ void NonbondedForce::setPMEParameters(double alpha, int nx, int ny, int nz) {
     this->nz = nz;
 }
 
+void NonbondedForce::setLJPMEParameters(double alpha, int nx, int ny, int nz) {
+    this->dalpha = alpha;
+    this->dnx = nx;
+    this->dny = ny;
+    this->dnz = nz;
+}
+
 void NonbondedForce::getPMEParametersInContext(const Context& context, double& alpha, int& nx, int& ny, int& nz) const {
     dynamic_cast<const NonbondedForceImpl&>(getImplInContext(context)).getPMEParameters(alpha, nx, ny, nz);
 }
 
+void NonbondedForce::getLJPMEParametersInContext(const Context& context, double& alpha, int& nx, int& ny, int& nz) const {
+    dynamic_cast<const NonbondedForceImpl&>(getImplInContext(context)).getLJPMEParameters(alpha, nx, ny, nz);
+}
+
 int NonbondedForce::addParticle(double charge, double sigma, double epsilon) {
     particles.push_back(ParticleInfo(charge, sigma, epsilon));
     return particles.size()-1;

openmmapi/src/NonbondedForceImpl.cpp

@@ -90,9 +90,7 @@ void NonbondedForceImpl::initialize(ContextImpl& context) {
         exceptions[particle1].insert(particle2);
         exceptions[particle2].insert(particle1);
     }
-    if (owner.getNonbondedMethod() == NonbondedForce::CutoffPeriodic ||
-            owner.getNonbondedMethod() == NonbondedForce::Ewald ||
-            owner.getNonbondedMethod() == NonbondedForce::PME) {
+    if (owner.getNonbondedMethod() != NonbondedForce::NoCutoff && owner.getNonbondedMethod() != NonbondedForce::CutoffNonPeriodic) {
         Vec3 boxVectors[3];
         system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
         double cutoff = owner.getCutoffDistance();
@@ -151,19 +149,29 @@ void NonbondedForceImpl::calcEwaldParameters(const System& system, const Nonbond
         kmaxz++;
 }
 
-void NonbondedForceImpl::calcPMEParameters(const System& system, const NonbondedForce& force, double& alpha, int& xsize, int& ysize, int& zsize) {
+void NonbondedForceImpl::calcPMEParameters(const System& system, const NonbondedForce& force, double& alpha, int& xsize, int& ysize, int& zsize, bool lj) {
+    if (lj)
+        force.getLJPMEParameters(alpha, xsize, ysize, zsize);
+    else
         force.getPMEParameters(alpha, xsize, ysize, zsize);
     if (alpha == 0.0) {
         Vec3 boxVectors[3];
         system.getDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
         double tol = force.getEwaldErrorTolerance();
         alpha = (1.0/force.getCutoffDistance())*std::sqrt(-log(2.0*tol));
+        if (lj) {
+            xsize = (int) ceil(alpha*boxVectors[0][0]/(3*pow(tol, 0.2)));
+            ysize = (int) ceil(alpha*boxVectors[1][1]/(3*pow(tol, 0.2)));
+            zsize = (int) ceil(alpha*boxVectors[2][2]/(3*pow(tol, 0.2)));
+        }
+        else {
             xsize = (int) ceil(2*alpha*boxVectors[0][0]/(3*pow(tol, 0.2)));
             ysize = (int) ceil(2*alpha*boxVectors[1][1]/(3*pow(tol, 0.2)));
             zsize = (int) ceil(2*alpha*boxVectors[2][2]/(3*pow(tol, 0.2)));
-        xsize = max(xsize, 5);
-        ysize = max(ysize, 5);
-        zsize = max(zsize, 5);
+        }
+        xsize = max(xsize, 6);
+        ysize = max(ysize, 6);
+        zsize = max(zsize, 6);
     }
 }
 
@@ -283,3 +291,7 @@ void NonbondedForceImpl::updateParametersInContext(ContextImpl& context) {
 void NonbondedForceImpl::getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
     kernel.getAs<CalcNonbondedForceKernel>().getPMEParameters(alpha, nx, ny, nz);
 }
+
+void NonbondedForceImpl::getLJPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
+    kernel.getAs<CalcNonbondedForceKernel>().getLJPMEParameters(alpha, nx, ny, nz);
+}

openmmapi/src/ThreadPool.cpp

@@ -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

@@ -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

 
-/* 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

 
-/* 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;