New lineshapes and spin factors

.ci/build_docs.sh

@@ -0,0 +1,111 @@
+#!/bin/sh
+################################################################################
+# Title         : generateDocumentationAndDeploy.sh
+# Date created  : 2016/02/22
+# Notes         :
+__AUTHOR__="Jeroen de Bruijn"
+# Preconditions:
+# - Packages doxygen doxygen-doc doxygen-latex doxygen-gui graphviz
+#   must be installed.
+# - Doxygen configuration file must have the destination directory empty and
+#   source code directory with a $(TRAVIS_BUILD_DIR) prefix.
+# - An gh-pages branch should already exist. See below for mor info on hoe to
+#   create a gh-pages branch.
+#
+# Required global variables:
+# - TRAVIS_BUILD_NUMBER : The number of the current build.
+# - TRAVIS_COMMIT       : The commit that the current build is testing.
+# - DOXYFILE            : The Doxygen configuration file.
+# - TRAVIS_REPO_SLUG    : The username / reponame for the repository.
+# - GH_REPO_TOKEN       : Secure token to the github repository.
+#
+# For information on how to encrypt variables for Travis CI please go to
+# https://docs.travis-ci.com/user/environment-variables/#Encrypted-Variables
+# or https://gist.github.com/vidavidorra/7ed6166a46c537d3cbd2
+# For information on how to create a clean gh-pages branch from the master
+# branch, please go to https://gist.github.com/vidavidorra/846a2fc7dd51f4fe56a0
+#
+# This script will generate Doxygen documentation and push the documentation to
+# the gh-pages branch of a repository specified by GH_REPO_REF.
+# Before this script is used there should already be a gh-pages branch in the
+# repository.
+# 
+################################################################################
+
+################################################################################
+##### Setup this script and get the current gh-pages branch.               #####
+if [[ $TRAVIS_OS_NAME == "osx" ]]; then return ; fi
+
+echo 'Setting up the script...'
+# Exit with nonzero exit code if anything fails
+set -e
+
+GH_REPO_ORG=`echo $TRAVIS_REPO_SLUG | cut -d "/" -f 1`
+GH_REPO_NAME=`echo $TRAVIS_REPO_SLUG | cut -d "/" -f 2`
+GH_REPO_REF="github.com/$GH_REPO_ORG/$GH_REPO_NAME.git"
+
+# Create a clean working directory for this script.
+# Get the current gh-pages branch
+cd doc
+git clone -b gh-pages https://git@$GH_REPO_REF html
+cd html
+
+##### Configure git.
+# Set the push default to simple i.e. push only the current branch.
+git config --global push.default simple
+# Pretend to be an user called Travis CI.
+git config user.name "Travis CI"
+git config user.email "[email protected]"
+
+# Remove everything currently in the gh-pages branch.
+# GitHub is smart enough to know which files have changed and which files have
+# stayed the same and will only update the changed files. So the gh-pages branch
+# can be safely cleaned, and it is sure that everything pushed later is the new
+# documentation.
+rm -rf *
+
+# Need to create a .nojekyll file to allow filenames starting with an underscore
+# to be seen on the gh-pages site. Therefore creating an empty .nojekyll file.
+# Presumably this is only needed when the SHORT_NAMES option in Doxygen is set
+# to NO, which it is by default. So creating the file just in case.
+echo "" > .nojekyll
+
+################################################################################
+##### Generate the Doxygen code documentation and log the output.          #####
+echo 'Generating Doxygen code documentation...'
+# Redirect both stderr and stdout to the log file AND the console.
+cd ..
+
+doxygen --version
+
+doxygen $DOXYFILE 2>&1 | tee doxygen.log
+
+################################################################################
+##### Upload the documentation to the gh-pages branch of the repository.   #####
+# Only upload if Doxygen successfully created the documentation.
+# Check this by verifying that the html directory and the file html/index.html
+# both exist. This is a good indication that Doxygen did it's work.
+if [ -d "html" ] && [ -f "html/index.html" ]; then
+
+    cd html
+    echo 'Uploading documentation to the gh-pages branch...'
+    # Add everything in this directory (the Doxygen code documentation) to the
+    # gh-pages branch.
+    # GitHub is smart enough to know which files have changed and which files have
+    # stayed the same and will only update the changed files.
+    git add --all
+
+    # Commit the added files with a title and description containing the Travis CI
+    # build number and the GitHub commit reference that issued this build.
+    git commit -m "Deploy code docs to GitHub Pages Travis build: ${TRAVIS_BUILD_NUMBER}" -m "Commit: ${TRAVIS_COMMIT}"
+
+    # Force push to the remote gh-pages branch.
+    # The ouput is redirected to /dev/null to hide any sensitive credential data
+    # that might otherwise be exposed.
+    git push --force "https://${GH_REPO_TOKEN}@${GH_REPO_REF}" > /dev/null 2>&1
+else
+    echo '' >&2
+    echo 'Warning: No documentation (html) files have been found!' >&2
+    echo 'Warning: Not going to push the documentation to GitHub!' >&2
+    exit 1
+fi

.ci/build_root.sh

@@ -0,0 +1,19 @@
+pushd $DEPS_DIR 
+set -evx
+
+os=$1
+if [[ $os == "osx" ]] ; then 
+  wget -nv http://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda_${os}.sh
+elif [[ $os == "linux" ]] ; then 
+  wget -nv http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda_${os}.sh
+fi
+
+bash miniconda_${os}.sh -b -p $DEPS_DIR/miniconda
+export PATH="$DEPS_DIR/miniconda/bin:$PATH"
+hash -r
+conda config --add channels conda-forge
+
+conda create --yes -n env_${os} root doxygen -c conda-forge
+
+set +evx 
+popd

.ci/build_root_linux.sh

@@ -0,0 +1,20 @@
+pushd $DEPS_DIR 
+
+if [[ $1 == "osx" ]] ; then 
+  wget -nv http://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh
+elif [[ $1 == "linux" ]] ; then 
+  wget -nv http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+fi
+
+bash miniconda.sh -b -p $DEPS_DIR/miniconda
+export PATH="$DEPS_DIR/miniconda/bin:$PATH"
+hash -r
+conda config --add channels conda-forge
+conda config --set channel_priority strict
+
+# conda install --quiet --yes -c conda-forge/label/gcc8 root_base doxygen
+conda create --quiet --yes -n my_root_env root doxygen zstd=1.3.7 -c conda-forge
+# conda init bash
+# source "$DEPS_DIR/miniconda/bin/thisroot.sh"
+# export CXX="$DEPS_DIR/miniconda/bin/g++"
+popd

.ci/build_root_osx.sh

@@ -0,0 +1,17 @@
+pushd $DEPS_DIR 
+
+wget -nv https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O ~/miniconda.sh
+bash ~/miniconda.sh -b -p $DEPS_DIR/miniconda
+export PATH="$DEPS_DIR/miniconda/bin:$PATH"
+hash -r
+conda config --add channels conda-forge
+conda install --quiet --yes -c conda-forge root
+. $DEPS_DIR/miniconda/etc/profile.d/conda.sh
+conda activate root
+#         . "/home/tim/miniconda/etc/profile.d/conda.sh"
+#     else
+#         export PATH="/home/tim/miniconda/bin:$PATH"
+
+# source "$DEPS_DIR/miniconda/bin/thisroot.sh"
+popd
+

.ci/travis_linux.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+set -evx
+# from https://stackoverflow.com/questions/55342122/conda-activate-on-travis-ci
+export PATH="$DEPS_DIR/miniconda/bin:$PATH"
+. $(conda info --root)/etc/profile.d/conda.sh
+conda activate env_${TRAVIS_OS_NAME}
+
+echo -en 'travis_fold:start:script.build\\r'
+echo "Building..."
+echo "Building under OS: $TRAVIS_OS_NAME, CXX =$CXX"
+echo "Directories: DEPS_DIR=$DEPS_DIR; TRAVIS_BUILD_DIR=$TRAVIS_BUILD_DIR"
+mkdir -p build
+cd build
+cmake .. -DENABLE_INSTALL=0
+cmake --build . -- -j2
+
+set +evx
+
+cd ..
+
+./build/bin/AmpGen.exe options/example_b2kstarll.opt --CompilerWrapper::Verbose --nEvents 10000
+

.ci/travis_osx.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+. $(conda info --root)/etc/profile.d/conda.sh
+conda activate env_${TRAVIS_OS_NAME}
+
+echo -en 'travis_fold:start:script.build\\r'
+echo "Building..."
+echo "Building under OS: $TRAVIS_OS_NAME"
+
+mkdir -p build
+cd build
+echo "CMake-ing, CXX = $CXX"
+cmake .. -DCMAKE_CXX_COMPILER=clang -DUSE_SIMD=0 -DUSE_OPENMP=0 -DENABLE_INSTALL=0
+echo "Building ..."
+cmake --build . -- -j2 
+cd ..
+echo "Running test job ..."
+./build/bin/AmpGen.exe options/example_b2kstarll.opt --CompilerWrapper::Verbose --nEvents 10000

.travis.yml

@@ -0,0 +1,51 @@
+language: cpp
+
+matrix: 
+  include:
+    - os: osx 
+      osx_image: xcode10.1
+      compiler: clang
+      addons:
+        homebrew:
+          packages:
+            - libomp
+    - os: linux
+      env:
+        - MATRIX_EVAL="CC=gcc-8 && CXX=g++-8"
+
+
+
+cache:
+  ccache: true
+  apt: true
+  directories:
+  - "${TRAVIS_BUILD_DIR}/deps/root"
+  - "${TRAVIS_BUILD_DIR}/deps/doxygen"
+
+# Blacklist
+branches:
+  except:
+    - gh-pages
+
+# Environment variables
+env:
+  global:
+    - GH_REPO_NAME: AmpGen
+    - DOXYFILE: $TRAVIS_BUILD_DIR/doc/doxyfile
+    - GH_REPO_REF: github.com/GooFit/AmpGen.git
+    - DEPS_DIR: "${TRAVIS_BUILD_DIR}/deps"
+
+before_install:
+  - eval "${MATRIX_EVAL}"
+  - chmod +x .ci/build_root.sh 
+  - source .ci/build_root.sh ${TRAVIS_OS_NAME} 
+
+# Build your code e.g. by calling make
+script:
+  - chmod +x .ci/travis_${TRAVIS_OS_NAME}.sh
+  - source .ci/travis_${TRAVIS_OS_NAME}.sh
+
+# Generate and deploy documentation
+after_success:
+  - chmod +x .ci/build_docs.sh
+  - source .ci/build_docs.sh

AmpGen/ASTResolver.h

@@ -17,54 +17,60 @@ namespace AmpGen {
   class MinuitParameter;
   class MinuitParameterSet;
   class MinuitParameterLink;
-  /// \class ASTResolver
-  /// Traverses trees in IExpression::resolveDependencies()
-  /// to keep track of the dependencies of the tree
-  /// such as sub-trees, external parameters and the event type map.
 
+  /** @ingroup ExpressionEngine class ASTResolver
+      @brief (Internal) class to aide in the resolution of the dependencies of expression trees. 
+
+      Traverses trees in IExpression::resolve() to keep track of the dependencies of the tree
+      such as sub-trees, external parameters and the mapping between particle kinematics and the
+      event vector.
+  */ 
   class ASTResolver 
   { 
     public: 
-      ASTResolver(const std::map<std::string, size_t>& evtMap = {} , const MinuitParameterSet* mps = nullptr );
-      bool hasSubExpressions() const;
-      void reduceSubTrees(); 
-      void cleanup();
-      void getOrderedSubExpressions( Expression& expression, std::vector<std::pair<uint64_t,Expression>>& dependentSubexpressions );
+      ASTResolver(const std::map<std::string, unsigned>& evtMap = {} , const MinuitParameterSet* mps = nullptr );
+      std::vector<std::pair<uint64_t,Expression>> getOrderedSubExpressions( const Expression& expression);
 
       template <class TYPE> void resolve( const TYPE& obj ){}
       template <class TYPE, class ...ARGS> size_t addCacheFunction( const std::string& name, const ARGS&... args )
       {
         auto it = m_cacheFunctions.find(name);
         if( it != m_cacheFunctions.end() ) return it->second->address();
-        auto cacheFunction = std::make_shared<TYPE>(nParameters, args... );
+        auto cacheFunction = std::make_shared<TYPE>(m_nParameters, name, args... );
         m_cacheFunctions[name] = cacheFunction;
-        nParameters += cacheFunction->size();
-        return nParameters - cacheFunction->size();
+        m_nParameters += cacheFunction->size();
+        return m_nParameters - cacheFunction->size();
       }
-      size_t nParams() const { return nParameters ; }       
-      bool enableCuda() const { return enable_cuda ; }
-      bool enableCompileConstants() const { return enable_compileTimeConstants ;} 
+      size_t nParams() const { return m_nParameters ; }       
+      bool enableCuda() const { return m_enable_cuda ; }
+      bool enableAVX()  const { return m_enable_avx; }
+      bool enableCompileConstants() const { return m_enable_compileTimeConstants ;} 
+      void setEnableAVX(){ m_enable_avx = true ; }
       std::map<std::string, std::shared_ptr<CacheTransfer>> cacheFunctions() const;
       void addResolvedParameter(const IExpression* param, const std::string& thing);
       void addResolvedParameter(const IExpression* param, const size_t& address, const size_t& arg=0);
       std::string resolvedParameter( const IExpression* param ) const; 
+
+      void clear();
 
+      std::map<const IExpression*, std::string> parameters() const { return m_resolvedParameters; }
     private: 
-      std::map<const IExpression* , std::string> m_resolvedParameters; 
-      std::map<std::string, std::shared_ptr<CacheTransfer>> m_cacheFunctions;
-      std::map<std::string, size_t>      evtMap;                      /// event specification 
-      std::map<std::string, std::string> parameterMapping;            /// Mapping of parameters to compile parameters
-      const MinuitParameterSet*          mps;                         /// Set of MinuitParameters 
-      std::map<const SubTree*, uint64_t> tempTrees;                   /// temporary store of sub-trees for performing cse reduction 
-      std::map<uint64_t, Expression>     subTrees;                    /// Unordered sub-trees 
-      unsigned int                       nParameters;                 /// Number of parameters
-      bool                               enable_cuda;                 /// flag to generate CUDA code <<experimental>>
-      bool                               enable_compileTimeConstants; /// flag to enable compile time constants <<experimental>>
-
+      std::map<const IExpression*, std::string>             m_resolvedParameters;          /// Map of parameters that have been resolved
+      std::map<std::string, std::shared_ptr<CacheTransfer>> m_cacheFunctions;              /// Container of functions for calculating function cache
+      std::map<std::string, unsigned>                       m_evtMap;                      /// Event specification 
+      std::map<std::string, std::string>                    m_parameterMapping;            /// Mapping of parameters to compile parameters
+      const MinuitParameterSet*                             m_mps;                         /// Set of MinuitParameters 
+      std::map<const IExpression*, const SubTree*>          m_tempTrees;                   /// temporary store of sub-trees for performing cse reduction 
+      unsigned int                                          m_nParameters;                 /// Number of parameters
+      bool                                                  m_enable_cuda                 {false}; /// flag to generate CUDA code <<experimental>>
+      bool                                                  m_enable_compileTimeConstants {false}; /// flag to enable compile time constants <<experimental>> 
+      bool                                                  m_enable_avx                  {false}; /// flag to generate code using AVX instructions <<experimental>>
+      bool                                                  m_check_hashes                {false}; /// flag to check that hashes are unique 
   };
 
   template <> void ASTResolver::resolve<Parameter>( const Parameter& obj );
   template <> void ASTResolver::resolve<SubTree>  ( const SubTree  & obj );
   template <> void ASTResolver::resolve<Spline>   ( const Spline   & obj );
   template <> void ASTResolver::resolve<MinuitParameterLink>( const MinuitParameterLink& obj );  
+  template <> void ASTResolver::resolve<LambdaExpression>( const LambdaExpression& obj);
 }

AmpGen/AddCPConjugate.h

@@ -0,0 +1,6 @@
+
+namespace AmpGen {
+  class MinuitParameterSet; 
+
+  void AddCPConjugate(MinuitParameterSet&);
+}