Merge remote-tracking branch 'origin/master' into qc

plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h

@@ -191,7 +191,7 @@ public:
     /**
      * Get the cutoff distance.
      */
-    double getCutoff(void) const;
+    double getCutoff() const;
 
     /**
      * Get the method used for handling long range nonbonded interactions.

plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp

@@ -61,7 +61,7 @@ void AmoebaMultipoleForce::setPolarizationType( AmoebaMultipoleForce::Polarizati
     polarizationType = type;
 }
 
-double AmoebaMultipoleForce::getCutoffDistance( void ) const {
+double AmoebaMultipoleForce::getCutoffDistance() const {
     return cutoffDistance;
 }
 

plugins/amoeba/openmmapi/src/AmoebaVdwForce.cpp

@@ -106,7 +106,7 @@ void AmoebaVdwForce::setCutoff( double inputCutoff ){
     cutoff = inputCutoff;
 }
 
-double AmoebaVdwForce::getCutoff( void ) const {
+double AmoebaVdwForce::getCutoff() const {
     return cutoff;
 }
 

plugins/amoeba/platforms/cuda/src/kernels/amoebaGk.cu

@@ -97,11 +97,11 @@ extern "C" __global__ void computeBornSum(unsigned long long* __restrict__ bornS
         // Extract the coordinates of this tile
         const unsigned int tgx = threadIdx.x & (TILE_SIZE-1);
         const unsigned int tbx = threadIdx.x - tgx;
-        unsigned int x, y;
+        int x, y;
         AtomData1 data;
         data.bornSum = 0;
         if (pos < end) {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-sqrt((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-sqrt((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);
@@ -232,10 +232,10 @@ extern "C" __global__ void computeGKForces(
         // Extract the coordinates of this tile
         const unsigned int tgx = threadIdx.x & (TILE_SIZE-1);
         const unsigned int tbx = threadIdx.x - tgx;
-        unsigned int x, y;
+        int x, y;
         AtomData2 data;
         if (pos < end) {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);
@@ -471,10 +471,10 @@ extern "C" __global__ void computeChainRuleForce(
         // Extract the coordinates of this tile
         const unsigned int tgx = threadIdx.x & (TILE_SIZE-1);
         const unsigned int tbx = threadIdx.x - tgx;
-        unsigned int x, y;
+        int x, y;
         AtomData3 data;
         if (pos < end) {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);
@@ -766,8 +766,8 @@ extern "C" __global__ void computeEDiffForce(
     while (pos < end) {
         // Extract the coordinates of this tile.
 
-        unsigned int x, y;
-        y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+        int x, y;
+        y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
         x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
         if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
             y += (x < y ? -1 : 1);

plugins/amoeba/platforms/cuda/src/kernels/amoebaWcaForce.cu

@@ -207,10 +207,10 @@ extern "C" __global__ void computeWCAForce(unsigned long long* __restrict__ forc
         const unsigned int tgx = threadIdx.x & (TILE_SIZE-1);
         const unsigned int tbx = threadIdx.x - tgx;
         const unsigned int localGroupIndex = threadIdx.x/TILE_SIZE;
-        unsigned int x, y;
+        int x, y;
         AtomData data;
         if (pos < end) {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

plugins/amoeba/platforms/cuda/src/kernels/multipoleElectrostatics.cu

@@ -234,14 +234,14 @@ extern "C" __global__ void computeElectrostatics(
 
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles)
             x = tiles[pos];
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

plugins/amoeba/platforms/cuda/src/kernels/multipoleFixedField.cu

@@ -599,14 +599,14 @@ extern "C" __global__ void computeFixedField(
 
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles)
             x = tiles[pos];
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

plugins/amoeba/platforms/cuda/src/kernels/multipoleInducedField.cu

@@ -337,14 +337,14 @@ extern "C" __global__ void computeInducedField(
 
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles)
             x = tiles[pos];
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

plugins/amoeba/platforms/cuda/src/kernels/pmeMultipoleElectrostatics.cu

@@ -321,14 +321,14 @@ extern "C" __global__ void computeElectrostatics(
 
         // Extract the coordinates of this tile.
         
-        unsigned int x, y;
+        int x, y;
 #ifdef USE_CUTOFF
         if (numTiles <= maxTiles)
             x = tiles[pos];
         else
 #endif
         {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
             x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
             if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                 y += (x < y ? -1 : 1);

serialization/include/openmm/serialization/XmlSerializer.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -79,7 +79,7 @@ public:
 private:
     static void serialize(const SerializationNode& node, std::ostream& stream);
     static void* deserializeStream(std::istream& stream);
-    static TiXmlElement* encodeNode(const SerializationNode& node);
+    static void encodeNode(const SerializationNode& node, std::ostream& stream, int depth);
     static void decodeNode(SerializationNode& node, const TiXmlElement& element);
 };
 

serialization/src/XmlSerializer.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,25 +36,32 @@ using namespace OpenMM;
 using namespace std;
 
 void XmlSerializer::serialize(const SerializationNode& node, std::ostream& stream) {
-    TiXmlDocument doc;
-    TiXmlDeclaration* decl = new TiXmlDeclaration( "1.0", "", "" );
-    doc.LinkEndChild(decl);
-    doc.LinkEndChild(encodeNode(node));
-    TiXmlPrinter printer;
-    printer.SetIndent("\t");
-    doc.Accept(&printer);
-    stream << printer.Str();
+    stream << "<?xml version=\"1.0\" ?>\n";
+    encodeNode(node, stream, 0);
 }
 
-TiXmlElement* XmlSerializer::encodeNode(const SerializationNode& node) {
-    TiXmlElement* element = new TiXmlElement(node.getName());
+void XmlSerializer::encodeNode(const SerializationNode& node, std::ostream& stream, int depth) {
+    for (int i = 0; i < depth; i++)
+        stream << '\t';
+    stream << '<' << node.getName();
     const map<string, string>& properties = node.getProperties();
-    for (map<string, string>::const_iterator iter = properties.begin(); iter != properties.end(); ++iter)
-        element->SetAttribute(iter->first.c_str(), iter->second.c_str());
+    for (map<string, string>::const_iterator iter = properties.begin(); iter != properties.end(); ++iter) {
+        string name, value;
+        TiXmlBase::EncodeString(iter->first, &name);
+        TiXmlBase::EncodeString(iter->second, &value);
+        stream << ' ' << name << "=\"" << value << '\"';
+    }
     const vector<SerializationNode>& children = node.getChildren();
-    for (int i = 0; i < (int) children.size(); i++)
-        element->LinkEndChild(encodeNode(children[i]));
-    return element;
+    if (children.size() == 0)
+        stream << "/>\n";
+    else {
+        stream << ">\n";
+        for (int i = 0; i < (int) children.size(); i++)
+            encodeNode(children[i], stream, depth+1);
+        for (int i = 0; i < depth; i++)
+            stream << '\t';
+        stream << "</" << node.getName() << ">\n";
+    }
 }
 
 void* XmlSerializer::deserializeStream(std::istream& stream) {

tools/ci/after_success.sh

+echo $TRAVIS_PULL_REQUEST $TRAVIS_BRANCH
+
+if [[ "$TRAVIS_PULL_REQUEST" == "true" ]]; then
+    echo "This is a pull request. No deployment will be done."; exit 0
+fi
+
+
+if [[ "$TRAVIS_BRANCH" != "master" ]]; then
+    echo "No deployment on BRANCH='$TRAVIS_BRANCH'"; exit 0
+fi
+
+
+if [[ "2.7 3.3" =~ "$python" ]]; then
+    conda install --yes binstar
+    binstar -t $BINSTAR_TOKEN upload --force -u omnia -p openmm-dev $HOME/miniconda/conda-bld/linux-64/openmm-dev-*
+fi
+
+if [[ "$python" != "2.7" ]]; then
+    echo "No deploy on PYTHON_VERSION=${python}"; exit 0
+fi
+

tools/ci/install.sh

+# Original OpenMM .travis.yml requirements.
+sudo apt-get update -qq
+sudo apt-get install -qq libpcre3 libpcre3-dev gromacs
+sudo apt-get install -qq swig doxygen llvm-3.3
+sudo apt-get install -qq libgl1-mesa-dev opencl-headers fglrx=2:8.960-0ubuntu1 # for opencl support
+export ASAN_SYMBOLIZER_PATH=/usr/bin/llvm-symbolizer-3.3
+
+# New requirements.
+sudo apt-get install -qq -y g++ gfortran csh
+sudo apt-get install -qq -y g++-multilib gcc-multilib
+wget http://repo.continuum.io/miniconda/Miniconda-3.0.5-Linux-x86_64.sh
+bash Miniconda-3.0.5-Linux-x86_64.sh -b
+PIP_ARGS="-U"
+
+export PATH=$HOME/miniconda/bin:$PATH
+
+conda update --yes conda
+conda config --add channels http://conda.binstar.org/omnia
+conda create --yes -n ${python} python=${python} --file tools/ci/requirements-conda.txt
+source activate $python
+$HOME/miniconda/envs/${python}/bin/pip install $PIP_ARGS nose-exclude

tools/ci/requirements-conda.txt

+numpy
+cython
+pip
+nose
+

tools/conda-recipe/README.md

+This is a recipe for building the current development package into a conda binary.
+
+The installation on travis-ci is done by building the conda package, installing
+it, running the tests, and then if successful pushing the package to binstar
+(and the docs to AWS S3). The binstar auth token is an encrypted environment
+variable generated using:
+
+binstar auth -n openmm-travis -o omnia --max-age 22896000 -c --scopes api:write
+
+and then saved in the environment variable BINSTAR_TOKEN.
+
+You can set up travis to store an encrypted token via
+
+gem install travis travis encrypt BINSTAR_TOKEN=xx
+
+where xx is the token output by binstar. The final command should print a line (containing 'secure') for inclusion in your .travis.yml file.

tools/conda-recipe/build.sh

+#!/bin/bash
+
+CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=$PREFIX"
+
+if [[ "$OSTYPE" == "linux-gnu" ]]; then
+    # setting the rpath so that libOpenMMPME.so finds the right libfftw3
+    CMAKE_FLAGS+=" -DCMAKE_INSTALL_RPATH=.."
+    CMAKE_FLAGS+=" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++"
+    #CMAKE_FLAGS+=" -DOPENCL_LIBRARY=/opt/AMDAPP/lib/x86_64/libOpenCL.so" # TEST
+
+elif [[ "$OSTYPE" == "darwin"* ]]; then
+    export MACOSX_DEPLOYMENT_TARGET="10.7"
+    CMAKE_FLAGS+=" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++"
+fi
+
+# Set location for FFTW3 on both linux and mac
+CMAKE_FLAGS+=" -DFFTW_INCLUDES=$PREFIX/include"
+if [[ "$OSTYPE" == "linux-gnu" ]]; then
+    CMAKE_FLAGS+=" -DFFTW_LIBRARY=$PREFIX/lib/libfftw3f.so"
+    CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=$PREFIX/lib/libfftw3f_threads.so"
+elif [[ "$OSTYPE" == "darwin"* ]]; then
+    CMAKE_FLAGS+=" -DFFTW_LIBRARY=$PREFIX/lib/libfftw3f.dylib"
+    CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=$PREFIX/lib/libfftw3f_threads.dylib"
+fi
+
+# Copy source to current directory.
+cp -r $RECIPE_DIR/../.. .
+
+# Build in subdirectory.
+mkdir build
+cd build
+cmake .. $CMAKE_FLAGS
+make -j4
+make install
+
+# Run C tests.
+# Exclude OpenCL tests because @peastman suspects mesa on travis implementation is broken.
+# @jchodera and @pgrinaway suspect travis is working, but AMD OpenCL tests are actually failing due to a bug.
+ctest -j2 -V -E "[A-Za-z]+OpenCL[A-Za-z]+"
+
+# Install Python wrappers.
+export OPENMM_INCLUDE_PATH=$PREFIX/include
+export OPENMM_LIB_PATH=$PREFIX/lib
+cd python
+$PYTHON setup.py install
+cd ..
+
+# Remove one random file
+#rm $PREFIX/bin/TestReferenceHarmonicBondForce
+
+# Copy all tests to bin directory so they will be distributed with install package.
+cp `find . -name "Test*" -type f -maxdepth 1` $PREFIX/bin
+

tools/conda-recipe/meta.yaml

+package:
+  name: openmm
+  version: !!str dev
+
+requirements:
+  build:
+    - cmake
+    - python
+    - fftw3f
+
+  run:
+    - python
+    - fftw3f
+    - numpy
+
+about:
+  home: https://simtk.org/home/openmm
+  license: GPL

tools/conda-recipe/plugin-dir.patch

+diff --git wrappers/python/simtk/openmm/__init__.py wrappers/python/simtk/openmm/__init__.py
+index 7e47b11..0ef290a 100644
+--- wrappers/python/simtk/openmm/__init__.py
++++ wrappers/python/simtk/openmm/__init__.py
+@@ -13,6 +13,10 @@ import os, os.path
+ from simtk.openmm.openmm import *
+ from simtk.openmm.vec3 import Vec3
+ from simtk.openmm import version
+-if os.getenv('OPENMM_PLUGIN_DIR') is None and os.path.isdir(version.openmm_library_path):
++_plugin_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.abspath(__file__)), '..', '..', '..', '..', 'plugins'))
++if os.path.isdir(_plugin_dir):
++    pluginLoadedLibNames = Platform.loadPluginsFromDirectory(_plugin_dir)
++    del _plugin_dir
++elif os.getenv('OPENMM_PLUGIN_DIR') is None and os.path.isdir(version.openmm_library_path):
+     pluginLoadedLibNames = Platform.loadPluginsFromDirectory(os.path.join(version.openmm_library_path, 'plugins'))
+ else:
+     pluginLoadedLibNames = Platform.loadPluginsFromDirectory(Platform.getDefaultPluginsDirectory())
\ No newline at end of file

wrappers/python/simtk/openmm/app/charmmpsffile.py

@@ -158,10 +158,13 @@ class CharmmPsfFile(object):
         title = list()
         for i in range(ntitle):
             title.append(psf.readline().rstrip())
-        # Skip the blank line
-        psf.readline()
+        # Skip all blank lines. Most of the time there is only 1, but I've seen
+        # a file that has 2
+        line = psf.readline().strip()
+        while not line:
+            line = psf.readline().strip()
         # Next is the number of atoms
-        natom = conv(psf.readline().strip(), int, 'natom')
+        natom = conv(line, int, 'natom')
         # Parse all of the atoms
         residue_list = ResidueList()
         atom_list = AtomList()
@@ -1182,8 +1185,11 @@ class CharmmPsfFile(object):
                 if switchDistance >= nonbondedCutoff:
                     raise ValueError('switchDistance is too large compared '
                                      'to the cutoff!')
-                    force.setUseSwitchingFunction(True)
-                    force.setSwitchingDistance(switchDistance)
+                if abs(switchDistance) != switchDistance:
+                    # Detects negatives for both Quantity and float
+                    raise ValueError('switchDistance must be non-negative!')
+                force.setUseSwitchingFunction(True)
+                force.setSwitchingDistance(switchDistance)
 
         else: # periodic
             # Set up box vectors (from inpcrd if available, or fall back to
@@ -1223,8 +1229,11 @@ class CharmmPsfFile(object):
                 if switchDistance >= nonbondedCutoff:
                     raise ValueError('switchDistance is too large compared '
                                      'to the cutoff!')
-                    force.setUseSwitchingFunction(True)
-                    force.setSwitchingDistance(switchDistance)
+                if abs(switchDistance) != switchDistance:
+                    # Detects negatives for both Quantity and float
+                    raise ValueError('switchDistance must be non-negative!')
+                force.setUseSwitchingFunction(True)
+                force.setSwitchingDistance(switchDistance)
 
             if ewaldErrorTolerance is not None:
                 force.setEwaldErrorTolerance(ewaldErrorTolerance)

wrappers/python/simtk/openmm/app/element.py

-#!/bin/env python
-
 """
 element.py: Used for managing elements.