Merge branch 'master' of github.com:/pandegroup/openmm into feature/cuda-docker

appveyor.yml

@@ -28,7 +28,7 @@ install:
   - "set PATH=C:\\fftw;%PATH%"
 
 # Download and install some OpenMM build dependencies (doxygen, swig)
-  - choco install -y doxygen.portable swig > null
+  - choco install -y doxygen.install swig > null
 
 # Download OpenCL Headers and build the ICD loader
   - ps: "[System.Net.ServicePointManager]::SecurityProtocol = [System.Net.SecurityProtocolType]::Tls12;"

devtools/packaging/scripts/windows/Vagrantfile

 Vagrant.configure("2") do |config|
-  config.vm.box = "gusztavvargadr/windows10ee"
+  config.vm.box = "gusztavvargadr/windows-10"
   config.vm.provision :shell, path: "prepare.ps1"
 
   config.vm.provider :virtualbox do |vb|

devtools/packaging/scripts/windows/prepare.ps1

@@ -2,8 +2,8 @@ cd C:\Users\vagrant
 
 # Install CUDA.
 
-wget https://developer.nvidia.com/compute/cuda/9.2/Prod2/network_installers/cuda_9.2.148_win10_network -UseBasicParsing -OutFile cuda_9.2.148_win10_network.exe
-.\cuda_9.2.148_win10_network.exe -s nvcc_9.2 cudart_9.2 cufft_9.2 cufft_dev_9.2 nvrtc_9.2 nvrtc_dev_9.2 | Out-Null
+wget https://developer.nvidia.com/compute/cuda/10.1/Prod/network_installers/cuda_10.1.168_win10_network.exe -UseBasicParsing -OutFile cuda_10.1.168_win10_network.exe
+.\cuda_10.1.168_win10_network.exe -s nvcc_10.1 cudart_10.1 cufft_10.1 cufft_dev_10.1 nvrtc_10.1 nvrtc_dev_10.1 | Out-Null
 
 # Install AMD APP SDK.
 
@@ -14,10 +14,11 @@ wget https://s3.amazonaws.com/omnia-ci/AMD-APP-SDK-v2.9-1.599.381-GA-Full-window
 
 wget https://repo.continuum.io/miniconda/Miniconda3-latest-Windows-x86_64.exe -UseBasicParsing -OutFile Miniconda3-latest-Windows-x86_64.exe
 .\Miniconda3-latest-Windows-x86_64.exe /S /D=C:\Miniconda3 | Out-Null
+[Environment]::SetEnvironmentVariable("Path", $env:Path + ";C:\Miniconda3;C:\Miniconda3\Scripts;C:\Miniconda3\Library\bin", [EnvironmentVariableTarget]::User)
 
 # Install software with conda.
 
-&"C:\Miniconda3\Scripts\conda.exe" config --add channels omnia --add channels conda-forge
+& "C:\Miniconda3\Scripts\conda.exe" config --add channels omnia --add channels conda-forge
 & "C:\Miniconda3\Scripts\conda.exe" install -y fftw3f==3.3.4=vc14_2 jinja2 lxml sphinx sphinxcontrib-autodoc_doxygen sphinxcontrib-lunrsearch conda-build anaconda-client
 & "C:\Miniconda3\Scripts\pip.exe" install sphinxcontrib.bibtex
 

examples/CMakeLists.txt

-# Generate and install examples.
-#
-# This is boilerplate code for generating a set of executables, one per
-# .cpp file in an "examples" subdirectory. 
-#
-# For IDEs that can deal with PROJECT_LABEL properties (at least
-# Visual Studio) the projects for building each of these adhoc
-# executables will be labeled "Example - TheExampleName" if a file
-# TheExampleName.cpp is found in this directory.
-#
-# We check the BUILD_TESTING_{SHARED,STATIC} variables to determine
-# whether to build dynamically linked, statically linked, or both
-# versions of the executable.
-
-
-SET(OpenMM_CWRAPPER "OpenMMCWrapper")
-SET(OpenMM_FWRAPPER "OpenMMFortranWrapper")
-SET(OpenMM_FMODULE  "OpenMMFortranModule")
-
-SET(CPP_EXAMPLES HelloArgon HelloSodiumChloride HelloEthane HelloWaterBox)
-SET(C_EXAMPLES HelloArgonInC HelloSodiumChlorideInC)
-SET(F_EXAMPLES HelloArgonInFortran HelloSodiumChlorideInFortran)
-
-FOREACH(EX_ROOT ${CPP_EXAMPLES})
-    IF (OPENMM_BUILD_SHARED_LIB)
-        # Link with shared library
-        ADD_EXECUTABLE(${EX_ROOT} ${EX_ROOT}.cpp)
-        SET_TARGET_PROPERTIES(${EX_ROOT}
-            PROPERTIES
-            PROJECT_LABEL "Example - ${EX_ROOT}"
-            LINK_FLAGS "${EXTRA_LINK_FLAGS}"
-            COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
-        TARGET_LINK_LIBRARIES(${EX_ROOT} ${SHARED_TARGET})
-    ENDIF (OPENMM_BUILD_SHARED_LIB)
-
-    IF (OPENMM_BUILD_STATIC_LIB)
-        # Link with static library
-        SET(EX_STATIC ${EX_ROOT}Static)
-        ADD_EXECUTABLE(${EX_STATIC} ${EX_ROOT}.cpp)
-        SET_TARGET_PROPERTIES(${EX_STATIC}
-            PROPERTIES
-            PROJECT_LABEL "Example - ${EX_STATIC}"
-            LINK_FLAGS "${EXTRA_LINK_FLAGS}"
-            COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES")
-        TARGET_LINK_LIBRARIES(${EX_STATIC} ${STATIC_TARGET})
-    ENDIF (OPENMM_BUILD_STATIC_LIB)
-
-    INSTALL(FILES ${EX_ROOT}.cpp DESTINATION examples)
-
-ENDFOREACH(EX_ROOT ${CPP_EXAMPLES})
-
-# Only build wrapper examples if wrappers have been built
-IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
-    INCLUDE_DIRECTORIES(BEFORE ${PROJECT_BINARY_DIR}/wrappers)
-
-    FOREACH(EX_ROOT ${C_EXAMPLES})
-        IF (OPENMM_BUILD_SHARED_LIB)
-            # Link with shared library
-            # We need at least one .cpp here to get CMake to include
-            # C++ libraries on the link line.
-            ADD_EXECUTABLE(${EX_ROOT} ${EX_ROOT}.c Empty.cpp)
-            SET_TARGET_PROPERTIES(${EX_ROOT}
-                PROPERTIES
-                PROJECT_LABEL "Example C - ${EX_ROOT}"
-                LINK_FLAGS "${EXTRA_LINK_FLAGS}"
-                COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
-            TARGET_LINK_LIBRARIES(${EX_ROOT} ${SHARED_TARGET})
-            ADD_DEPENDENCIES(${EX_ROOT} ApiWrappers)
-        ENDIF (OPENMM_BUILD_SHARED_LIB)
-
-        IF (OPENMM_BUILD_STATIC_LIB)
-            # Link with static library
-            SET(EX_STATIC ${EX_ROOT}Static)
-            # We need at least one .cpp here to get CMake to include
-            # C++ libraries on the static link line.
-            ADD_EXECUTABLE(${EX_STATIC} ${EX_ROOT}.c Empty.cpp)
-            SET_TARGET_PROPERTIES(${EX_STATIC}
-                PROPERTIES
-                PROJECT_LABEL "Example C - ${EX_STATIC}"
-                LINK_FLAGS "${EXTRA_LINK_FLAGS}"
-                COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES")
-            TARGET_LINK_LIBRARIES(${EX_STATIC} ${STATIC_TARGET})
-            ADD_DEPENDENCIES(${EX_STATIC} ApiWrappers)
-        ENDIF (OPENMM_BUILD_STATIC_LIB)
-  ENDFOREACH(EX_ROOT ${C_EXAMPLES})
-ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
-
-FOREACH(EX_ROOT ${C_EXAMPLES})
-  INSTALL(FILES ${EX_ROOT}.c DESTINATION examples)
-ENDFOREACH(EX_ROOT ${C_EXAMPLES})
-
-FOREACH(EX_ROOT ${F_EXAMPLES})
-    INSTALL(FILES ${EX_ROOT}.f90 DESTINATION examples)
-ENDFOREACH(EX_ROOT ${F_EXAMPLES})
-
-INSTALL(FILES simulateAmber.py simulatePdb.py simulateGromacs.py benchmark.py argon-chemical-potential.py input.inpcrd input.prmtop input.pdb input.gro input.top 5dfr_minimized.pdb 5dfr_solv-cube_equil.pdb
-        DESTINATION examples)
-
-INSTALL(FILES VisualStudio/HelloArgon.vcproj 
-              VisualStudio/HelloArgon.sln 
-              VisualStudio/HelloArgonInC.sln 
-              VisualStudio/HelloArgonInC.vcproj 
-              VisualStudio/HelloArgonInFortran.sln 
-              VisualStudio/HelloArgonInFortran.vfproj 
-        DESTINATION examples/VisualStudio)
-
-INSTALL(FILES README.txt DESTINATION examples)
-INSTALL(FILES Makefile NMakefile DESTINATION examples)
-
-INSTALL(FILES MakefileNotes.txt Empty.cpp DESTINATION examples)
+# Generate and install examples.
+#
+# This is boilerplate code for generating a set of executables, one per
+# .cpp file in an "examples" subdirectory. 
+#
+# For IDEs that can deal with PROJECT_LABEL properties (at least
+# Visual Studio) the projects for building each of these adhoc
+# executables will be labeled "Example - TheExampleName" if a file
+# TheExampleName.cpp is found in this directory.
+#
+# We check the BUILD_TESTING_{SHARED,STATIC} variables to determine
+# whether to build dynamically linked, statically linked, or both
+# versions of the executable.
+
+
+SET(OpenMM_CWRAPPER "OpenMMCWrapper")
+SET(OpenMM_FWRAPPER "OpenMMFortranWrapper")
+SET(OpenMM_FMODULE  "OpenMMFortranModule")
+
+SET(CPP_EXAMPLES HelloArgon HelloSodiumChloride HelloEthane HelloWaterBox)
+SET(C_EXAMPLES HelloArgonInC HelloSodiumChlorideInC)
+SET(F_EXAMPLES HelloArgonInFortran HelloSodiumChlorideInFortran)
+
+FOREACH(EX_ROOT ${CPP_EXAMPLES})
+    IF (OPENMM_BUILD_SHARED_LIB)
+        # Link with shared library
+        ADD_EXECUTABLE(${EX_ROOT} ${EX_ROOT}.cpp)
+        SET_TARGET_PROPERTIES(${EX_ROOT}
+            PROPERTIES
+            PROJECT_LABEL "Example - ${EX_ROOT}"
+            LINK_FLAGS "${EXTRA_LINK_FLAGS}"
+            COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+        TARGET_LINK_LIBRARIES(${EX_ROOT} ${SHARED_TARGET})
+    ENDIF (OPENMM_BUILD_SHARED_LIB)
+
+    IF (OPENMM_BUILD_STATIC_LIB)
+        # Link with static library
+        SET(EX_STATIC ${EX_ROOT}Static)
+        ADD_EXECUTABLE(${EX_STATIC} ${EX_ROOT}.cpp)
+        SET_TARGET_PROPERTIES(${EX_STATIC}
+            PROPERTIES
+            PROJECT_LABEL "Example - ${EX_STATIC}"
+            LINK_FLAGS "${EXTRA_LINK_FLAGS}"
+            COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES")
+        TARGET_LINK_LIBRARIES(${EX_STATIC} ${STATIC_TARGET})
+    ENDIF (OPENMM_BUILD_STATIC_LIB)
+
+    INSTALL(FILES ${EX_ROOT}.cpp DESTINATION examples)
+
+ENDFOREACH(EX_ROOT ${CPP_EXAMPLES})
+
+# Only build wrapper examples if wrappers have been built
+IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
+    INCLUDE_DIRECTORIES(BEFORE ${PROJECT_BINARY_DIR}/wrappers)
+
+    FOREACH(EX_ROOT ${C_EXAMPLES})
+        IF (OPENMM_BUILD_SHARED_LIB)
+            # Link with shared library
+            # We need at least one .cpp here to get CMake to include
+            # C++ libraries on the link line.
+            ADD_EXECUTABLE(${EX_ROOT} ${EX_ROOT}.c Empty.cpp)
+            SET_TARGET_PROPERTIES(${EX_ROOT}
+                PROPERTIES
+                PROJECT_LABEL "Example C - ${EX_ROOT}"
+                LINK_FLAGS "${EXTRA_LINK_FLAGS}"
+                COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+            TARGET_LINK_LIBRARIES(${EX_ROOT} ${SHARED_TARGET})
+            ADD_DEPENDENCIES(${EX_ROOT} ApiWrappers)
+        ENDIF (OPENMM_BUILD_SHARED_LIB)
+
+        IF (OPENMM_BUILD_STATIC_LIB)
+            # Link with static library
+            SET(EX_STATIC ${EX_ROOT}Static)
+            # We need at least one .cpp here to get CMake to include
+            # C++ libraries on the static link line.
+            ADD_EXECUTABLE(${EX_STATIC} ${EX_ROOT}.c Empty.cpp)
+            SET_TARGET_PROPERTIES(${EX_STATIC}
+                PROPERTIES
+                PROJECT_LABEL "Example C - ${EX_STATIC}"
+                LINK_FLAGS "${EXTRA_LINK_FLAGS}"
+                COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES")
+            TARGET_LINK_LIBRARIES(${EX_STATIC} ${STATIC_TARGET})
+            ADD_DEPENDENCIES(${EX_STATIC} ApiWrappers)
+        ENDIF (OPENMM_BUILD_STATIC_LIB)
+  ENDFOREACH(EX_ROOT ${C_EXAMPLES})
+ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
+
+FOREACH(EX_ROOT ${C_EXAMPLES})
+  INSTALL(FILES ${EX_ROOT}.c DESTINATION examples)
+ENDFOREACH(EX_ROOT ${C_EXAMPLES})
+
+FOREACH(EX_ROOT ${F_EXAMPLES})
+    INSTALL(FILES ${EX_ROOT}.f90 DESTINATION examples)
+ENDFOREACH(EX_ROOT ${F_EXAMPLES})
+
+INSTALL(FILES simulateAmber.py simulatePdb.py simulateGromacs.py benchmark.py argon-chemical-potential.py input.inpcrd input.prmtop input.pdb input.gro input.top 5dfr_minimized.pdb 5dfr_solv-cube_equil.pdb apoa1.pdb
+        DESTINATION examples)
+
+INSTALL(FILES VisualStudio/HelloArgon.vcproj 
+              VisualStudio/HelloArgon.sln 
+              VisualStudio/HelloArgonInC.sln 
+              VisualStudio/HelloArgonInC.vcproj 
+              VisualStudio/HelloArgonInFortran.sln 
+              VisualStudio/HelloArgonInFortran.vfproj 
+        DESTINATION examples/VisualStudio)
+
+INSTALL(FILES README.txt DESTINATION examples)
+INSTALL(FILES Makefile NMakefile DESTINATION examples)
+
+INSTALL(FILES MakefileNotes.txt Empty.cpp DESTINATION examples)

wrappers/python/src/swig_doxygen/swig_lib/python/header.i

@@ -20,6 +20,16 @@ PyObject *copyVVec3ToList(std::vector<Vec3> vVec3) {
   return pyList;
 }
 
+int isNumpyAvailable() {
+    static bool initialized = false;
+    static bool available = false;
+    if (!initialized) {
+        initialized = true;
+        available = (_import_array() >= 0);
+    }
+    return available;
+}
+
 } // namespace OpenMM
 %}
 

wrappers/python/src/swig_doxygen/swig_lib/python/typemaps.i

@@ -156,13 +156,49 @@ OpenMM::Vec3 Py_SequenceToVec3(PyObject* obj, int& status) {
 
 %fragment("Py_SequenceToVecDouble", "header", fragment="Py_StripOpenMMUnits") {
 int Py_SequenceToVecDouble(PyObject* obj, std::vector<double>& out) {
-    PyObject* stripped = NULL;
+    PyObject* stripped = Py_StripOpenMMUnits(obj);
     PyObject* item = NULL;
     PyObject* item1 = NULL;
-    PyObject* iterator = NULL;
-    stripped = Py_StripOpenMMUnits(obj);
-    iterator = PyObject_GetIter(stripped);
 
+    if (isNumpyAvailable()) {
+        if (PyArray_Check(stripped) && PyArray_ISCARRAY_RO(stripped) && PyArray_NDIM(stripped) == 1) {
+            int type = PyArray_TYPE(stripped);
+            int length = PyArray_SIZE(stripped);
+            void* data = PyArray_DATA((PyArrayObject*) stripped);
+            if (type == NPY_DOUBLE) {
+                out.resize(length);
+                memcpy(&out[0], data, sizeof(double)*length);
+                Py_DECREF(stripped);
+                return SWIG_OK;
+            }
+            if (type == NPY_FLOAT) {
+                out.resize(length);
+                float* floatData = (float*) data;
+                for (int i = 0; i < length; i++)
+                    out[i] = floatData[i];
+                Py_DECREF(stripped);
+                return SWIG_OK;
+            }
+            if (type == NPY_INT32) {
+                out.resize(length);
+                int* intData = (int*) data;
+                for (int i = 0; i < length; i++)
+                    out[i] = intData[i];
+                Py_DECREF(stripped);
+                return SWIG_OK;
+            }
+            if (type == NPY_INT64) {
+                out.resize(length);
+                long long* longData = (long long*) data;
+                for (int i = 0; i < length; i++)
+                    out[i] = longData[i];
+                Py_DECREF(stripped);
+                return SWIG_OK;
+            }
+        }
+    }
+
+    PyObject* iterator = PyObject_GetIter(stripped);
     if (iterator == NULL) {
         Py_DECREF(stripped);
         return SWIG_ERROR;
@@ -194,16 +230,6 @@ int Py_SequenceToVecDouble(PyObject* obj, std::vector<double>& out) {
 }
 
 %fragment("Py_SequenceToVecVec3", "header", fragment="Py_SequenceToVec3") {
-int isNumpyAvailable() {
-    static bool initialized = false;
-    static bool available = false;
-    if (!initialized) {
-        initialized = true;
-        available = (_import_array() >= 0);
-    }
-    return available;
-}
-
 int Py_SequenceToVecVec3(PyObject* obj, std::vector<Vec3>& out) {
     PyObject* stripped = Py_StripOpenMMUnits(obj);      // new reference
     if (isNumpyAvailable()) {