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

platforms/opencl/tests/TestOpenCLCustomIntegrator.cpp

@@ -292,6 +292,7 @@ void testWithThermostat() {
     system.addForce(forceField);
     AndersenThermostat* thermostat = new AndersenThermostat(temp, collisionFreq);
     system.addForce(thermostat);
+    integrator.setRandomNumberSeed(thermostat->getRandomNumberSeed());
     Context context(system, integrator, platform);
     vector<Vec3> positions(numParticles);
     for (int i = 0; i < numParticles; ++i)
@@ -424,6 +425,7 @@ void testParameter() {
     integrator.addGlobalVariable("temp", 0);
     integrator.addComputeGlobal("temp", "AndersenTemperature");
     integrator.addComputeGlobal("AndersenTemperature", "temp*2");
+    integrator.setRandomNumberSeed(thermostat->getRandomNumberSeed());
     Context context(system, integrator, platform);
     
     // See if the parameter is being used correctly.

platforms/opencl/tests/TestOpenCLMonteCarloAnisotropicBarostat.cpp

@@ -389,7 +389,7 @@ int main(int argc, char* argv[]) {
         testIdealGasAxis(1);
         testIdealGasAxis(2);
         testRandomSeed();
-        testEinsteinCrystal();
+        //testEinsteinCrystal();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

platforms/reference/tests/TestReferenceMonteCarloAnisotropicBarostat.cpp

@@ -389,7 +389,7 @@ int main() {
         testIdealGasAxis(1);
         testIdealGasAxis(2);
         testRandomSeed();
-        testEinsteinCrystal();
+        //testEinsteinCrystal();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

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

@@ -126,7 +126,7 @@ public:
      *
      * @return the cutoff distance, measured in nm
      */
-    double getCutoffDistance(void) const;
+    double getCutoffDistance() const;
 
     /**
      * Set the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use

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);

plugins/cpupme/CMakeLists.txt

@@ -57,7 +57,11 @@ ENDFOREACH(subdir)
 
 INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
 IF (NOT MSVC)
-    SET_SOURCE_FILES_PROPERTIES(${SOURCE_FILES} PROPERTIES COMPILE_FLAGS "-msse4.1")
+    IF (ANDROID)
+        SET_SOURCE_FILES_PROPERTIES(${SOURCE_FILES} PROPERTIES COMPILE_FLAGS "")
+    ELSE (ANDROID)
+        SET_SOURCE_FILES_PROPERTIES(${SOURCE_FILES} PROPERTIES COMPILE_FLAGS "-msse4.1")
+    ENDIF (ANDROID)
 ENDIF (NOT MSVC)
 
 # Include FFTW related files.

plugins/cpupme/src/CpuPmeKernels.cpp

@@ -569,13 +569,20 @@ double CpuCalcPmeReciprocalForceKernel::finishComputation(IO& io) {
 }
 
 bool CpuCalcPmeReciprocalForceKernel::isProcessorSupported() {
-    int cpuInfo[4];
-    cpuid(cpuInfo, 0);
-    if (cpuInfo[0] >= 1) {
-        cpuid(cpuInfo, 1);
-        return ((cpuInfo[2] & ((int) 1 << 19)) != 0); // Require SSE 4.1
-    }
-    return false;
+    // Make sure the CPU supports SSE 4.1 or NEON.
+        
+    #ifdef __ANDROID__
+        uint64_t features = android_getCpuFeatures();
+        return (features & ANDROID_CPU_ARM_FEATURE_NEON) != 0;
+    #else
+        int cpuInfo[4];
+        cpuid(cpuInfo, 0);
+        if (cpuInfo[0] >= 1) {
+            cpuid(cpuInfo, 1);
+            return ((cpuInfo[2] & ((int) 1 << 19)) != 0);
+        }
+        return false;
+    #endif
 }
 
 int CpuCalcPmeReciprocalForceKernel::findFFTDimension(int minimum) {

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) {

tests/TestFindExclusions.cpp

@@ -30,6 +30,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/internal/AssertionUtilities.h"
+#include "openmm/CustomNonbondedForce.h"
 #include "openmm/NonbondedForce.h"
 #include "openmm/OpenMMException.h"
 #include <iostream>
@@ -166,10 +167,62 @@ void testReplaceExceptions() {
     ASSERT(charge == 5.0);
 }
 
+/**
+ * This is the same as testFindExceptions(), except it tests adding exclusions to a CustomNonbondedForce.
+ */
+
+void testFindCustomExclusions() {
+    CustomNonbondedForce nonbonded("r");
+    vector<pair<int, int> > bonds;
+    vector<double> params;
+    for (int i = 0; i < NUM_ATOMS; i++)
+        nonbonded.addParticle(params);
+    // loop over all main-chain atoms (even numbered atoms)
+    for (int i = 0; i < NUM_ATOMS-1; i += 2)
+    {
+        // side-chain bonds
+        bonds.push_back(pair<int, int>(i, i+1));
+        // main-chain bonds
+        if (i < NUM_ATOMS-2) // penultimate atom (NUM_ATOMS-2) has no subsequent main-chain atom
+            bonds.push_back(pair<int, int>(i, i+2));
+    }
+    nonbonded.createExclusionsFromBonds(bonds, 3);
+
+    // Build lists of the expected exclusions.
+
+    vector<set<int> > expectedExclusions(NUM_ATOMS);
+    int totalExclusions = 0;
+    for (int i = 0; i < NUM_ATOMS; i += 2) {
+        addAtomsToExclusions(i, i+1, expectedExclusions, totalExclusions);
+        addAtomsToExclusions(i, i+2, expectedExclusions, totalExclusions);
+        addAtomsToExclusions(i, i+3, expectedExclusions, totalExclusions);
+        addAtomsToExclusions(i, i+4, expectedExclusions, totalExclusions);
+        addAtomsToExclusions(i+1, i+2, expectedExclusions, totalExclusions);
+        addAtomsToExclusions(i, i+5, expectedExclusions, totalExclusions);
+        addAtomsToExclusions(i, i+6, expectedExclusions, totalExclusions);
+        addAtomsToExclusions(i+1, i+3, expectedExclusions, totalExclusions);
+        addAtomsToExclusions(i+1, i+4, expectedExclusions, totalExclusions);
+    }
+    for (int i = 0; i < nonbonded.getNumExclusions(); i++) {
+        int particle1, particle2;
+        nonbonded.getExclusionParticles(i, particle1, particle2);
+    }
+
+    // Compare them to the exceptions that were generated.
+
+    ASSERT_EQUAL(totalExclusions, nonbonded.getNumExclusions());
+    for (int i = 0; i < nonbonded.getNumExclusions(); i++) {
+        int particle1, particle2;
+        nonbonded.getExclusionParticles(i, particle1, particle2);
+        ASSERT(expectedExclusions[particle1].find(particle2) != expectedExclusions[particle1].end());
+    }
+}
+
 int main() {
     try {
         testFindExceptions();
         testReplaceExceptions();
+        testFindCustomExclusions();
     }
     catch(const exception& e) {
         cout << "exception: " << e.what() << endl;

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