Merge branch '49-new_observables' into 'master'

new observables

Closes #49

See merge request !28

data/docker/Dockerfile.partons

+# start from debian jessie
+FROM debian:stretch
+
+# PARTONS version
+ENV PARTONSTAG="v2.0"
+
+# set WORKSPACE env. variable
+ENV WORKSPACE="/root/workspace"
+
+# set working directory
+WORKDIR ${WORKSPACE}
+
+# install git
+# install cmake, build and runtime libraries
+RUN apt-get update && \ 
+    apt-get install -y --no-install-recommends git && \
+    apt-get install -y --no-install-recommends cmake build-essential libeigen3-dev libcln-dev libsfml-dev libqt4-dev libqt4-sql-mysql libgsl-dev && \ 
+    apt-get clean && \
+    apt-get autoclean && \
+    rm -rf /var/lib/apt/lists/*
+
+# pull and install elem-utils
+RUN cd ${WORKSPACE} && \
+    git config --global http.sslVerify false && \
+    git clone --single-branch --depth 1 --branch ${PARTONSTAG} https://drf-gitlab.cea.fr/partons/core/elementary-utils.git && \
+    cd ${WORKSPACE}/elementary-utils/build && \
+    cmake -G"Unix Makefiles" ../ -DCMAKE_BUILD_TYPE=Release && \
+    make 
+
+# pull and install numa
+RUN cd ${WORKSPACE} && \
+    git config --global http.sslVerify false && \
+    git clone --single-branch --depth 1 --branch ${PARTONSTAG} https://drf-gitlab.cea.fr/partons/core/numa.git && \
+    cd ${WORKSPACE}/numa/build && \
+    cmake -G"Unix Makefiles" ../ -DCMAKE_BUILD_TYPE=Release && \
+    make 
+
+# pull and install partons
+RUN cd ${WORKSPACE} && \
+    git config --global http.sslVerify false && \
+    git clone --single-branch --depth 1 --branch ${PARTONSTAG} https://drf-gitlab.cea.fr/partons/core/partons.git && \
+    cd ${WORKSPACE}/partons/build && \
+    cmake -G"Unix Makefiles" ../ -DCMAKE_BUILD_TYPE=Release && \
+    make
+
+# pull and compile partons-example
+RUN cd ${WORKSPACE} && \
+    git config --global http.sslVerify false && \
+    git clone --single-branch --depth 1 --branch ${PARTONSTAG} https://drf-gitlab.cea.fr/partons/core/partons-example.git && \
+    cd ${WORKSPACE}/partons-example/build && \
+    cmake -G"Unix Makefiles" ../ -DCMAKE_BUILD_TYPE=Release && \
+    make 
+
+# creare directories and copy scripts
+RUN mkdir ${WORKSPACE}/.docker && \
+    mkdir ${WORKSPACE}/partons-example/scenarios
+
+COPY ./Dockerfile.partons.mysql ${WORKSPACE}/.docker 
+COPY ./Dockerfile.partons.startup ${WORKSPACE}/.docker 
+
+RUN chmod u+x ${WORKSPACE}/.docker/Dockerfile.partons.mysql && \
+    chmod u+x ${WORKSPACE}/.docker/Dockerfile.partons.startup
+
+# set up database
+RUN echo "mysql-server mysql-server/root_password password partons" | debconf-set-selections && \
+    echo "mysql-server mysql-server/root_password_again password partons" | debconf-set-selections && \
+    apt-get update && \ 
+    apt-get install -y --no-install-recommends mysql-server && \ 
+    apt-get clean && \
+    apt-get autoclean && \
+    rm -rf /var/lib/apt/lists/* && \
+    ${WORKSPACE}/.docker/Dockerfile.partons.mysql && \
+    rm ${WORKSPACE}/.docker/Dockerfile.partons.mysql
+
+# start mysql server each time container is used
+# due to issue: https://github.com/docker/for-linux/issues/72 
+ENTRYPOINT [".docker/Dockerfile.partons.startup"] 

data/docker/Dockerfile.partons.mysql

+#!/bin/bash
+
+# start 
+find /var/lib/mysql -type f -exec touch {} \;
+service mysql start &> /dev/null
+
+# set env.
+__mysql_database="partons"
+__mysql_root="root"
+__mysql_root_password="partons"
+__mysql_user="partons"
+__mysql_user_password="partons"
+
+#define functioni to execute queries 
+function sql_exec() {
+  mysql -u "${__mysql_root}" -D "${__mysql_database}" -p${__mysql_root_password} -e "${1}"
+}
+
+# go to directory with schema
+cd /root/workspace/partons/data/database/sql_schema 
+
+# create database and add user
+mysql -u "${__mysql_root}" -p"${__mysql_root_password}" -e "create database ${__mysql_database}"
+sql_exec "CREATE USER '${__mysql_user}'@'localhost' IDENTIFIED BY '${__mysql_user_password}';"
+sql_exec "GRANT SELECT, INSERT, UPDATE, DELETE ON ${__mysql_database}.* TO '${__mysql_user}'@'localhost';"
+sql_exec "GRANT FILE ON *.* TO '${__mysql_user}'@'localhost';"
+
+# excecute scripts
+#  TODO: if scripts are going to be enumerated this piece of the code
+#+       can be automated, therefore will need less further involvement
+#+       of anyone.
+#+
+#+       Desirable naming might look like following:
+#+       mysql5_common.sql                      -> mysql5_001_common.sql
+#+       mysql5_gpd_layer.sql                   -> mysql5_002_gpd_layer.sql
+#+       mysql5_convol_coeff_function_layer.sql -> mysql5_003_convol_coeff_function_layer.sql
+#+       mysql5_observable_layer.sql            -> mysql5_004_observable_layer.sql
+sql_exec "SOURCE mysql5_common.sql"
+sql_exec "SOURCE mysql5_gpd_layer.sql"
+sql_exec "SOURCE mysql5_convol_coeff_function_layer.sql"
+sql_exec "SOURCE mysql5_observable_layer.sql"

data/docker/Dockerfile.partons.startup

+#!/bin/bash
+
+
+echo "Welcome to PARTONS" 
+echo "See http://partons.cea.fr for description and technical documentation"
+
+#mysql
+find /var/lib/mysql -type f -exec touch {} \;
+service mysql start &> /dev/null
+
+if [ $# -eq 0 ]; then
+   /bin/bash  
+else
+
+   cd /root/workspace/partons-example
+
+   for i in $@; do
+      ./bin/PARTONS_example scenarios/$i 
+   done
+fi

data/docker/README

+to create new image and send it to DockerHub: 
+1) select PARTONS version (code tag) in Dockerfile.partons
+2) execute (remember to change vX.Y): 
+   docker build . -f Dockerfile.partons -t partons/partons:vX.Y  
+3) push (remember to change vX.Y):
+   docker push partons/partons:vX.Y
+4) also tag as latest (remember to change vX.Y):
+   docker image tag partons/partons:vX.Y partons/partons:lates
+5) push:
+   docker push partons/partons:latest
\ No newline at end of file

doc/markdown/partons_download.md

@@ -39,3 +39,21 @@ User      | 25/02/2020 | 2.0              | [Download](http://partons.cea.fr/vm/
 Developer | 25/02/2020 | 2.0              | [Download](http://partons.cea.fr/vm/PARTONS_250220_DEV.ova) | 2.8 GB |
 
 The `Developer` version has a set-up development environment in Eclipse to start contributing to the %PARTONS project, and has more packages installed, which makes the image heavier.
+
+# Docker {#download_docker}
+
+Docker images containing PARTONS with its runtime environment are available via [DockerHub](https://hub.docker.com), see [here](https://hub.docker.com/repository/docker/partons/partons). The basic usage is the following:
+* pull the image (by default containing the latest version of PARTONS)
+~~~~~~~~~~~~~{.sh}
+docker pull partons/partons
+~~~~~~~~~~~~~
+* run interactively
+~~~~~~~~~~~~~{.sh}
+docker run -it --rm partons/partons
+~~~~~~~~~~~~~
+* use image as executable: run specific scenario (here: 'myScenario.xml') stored in your host (here: in 'ABSOLUTEPATH/MYDIR' directory)
+~~~~~~~~~~~~~{.sh}
+docker run -it --rm -v ABSOLUTEPATH/MYDIR:/root/workspace/partons-example/scenarios partons/partons myScenario.xml
+~~~~~~~~~~~~~
+
+For more details please see Docker manual.

include/partons/modules/observable/DVCS/cross_section/DVCSCrossSectionTotal.h

+#ifndef DVCSCROSSSECTIONTOTAL_H
+#define DVCSCROSSSECTIONTOTAL_H
+
+/**
+ * @file DVCSCrossSectionTotal.h
+ * @author Pawel Sznajder (NCBJ)
+ * @date May 17, 2020
+ * @version 1.0
+ */
+
+#include <ElementaryUtils/parameters/Parameters.h>
+#include <stddef.h>
+#include <string>
+#include <utility>
+
+#include "../../../../beans/gpd/GPDType.h"
+#include "../../../../beans/List.h"
+#include "../../../../utils/type/PhysicalType.h"
+#include "DVCSCrossSectionUUMinusPhiIntegrated.h"
+
+namespace PARTONS {
+
+/**
+ * @class DVCSCrossSectionTotal
+ * @brief Unpolarized cross-section for electro-production integrated over \f$xB\f$, \f$Q^{2}\f$, \f$t\f$ and angles.
+ *
+ * Default ranges: \f$1E-4 < xB < 0.7\f$, \f$-1 < t < 0\f$, \f$1 < Q^{2} < 1E3\f$ and \f$0 < y < 1\f$. Full integration over angles.
+ *
+ * Unit: \f$\mathrm{nbarn}\f$.
+ */
+class DVCSCrossSectionTotal: public DVCSCrossSectionUUMinusPhiIntegrated {
+
+public:
+
+    static const std::string DVCS_CROSSSECTION_TOTAL_RANGEXb; ///< String used to set integration xB range via XML scenario.
+    static const std::string DVCS_CROSSSECTION_TOTAL_RANGET; ///< String used to set integration t range via XML scenario.
+    static const std::string DVCS_CROSSSECTION_TOTAL_RANGEQ2; ///< String used to set integration Q2 range via XML scenario.
+    static const std::string DVCS_CROSSSECTION_TOTAL_RANGEY; ///< String used to set integration y range via XML scenario.
+    static const std::string DVCS_CROSSSECTION_TOTAL_N0; ///< String used to set number of MC integration iterations per cycle via XML scenario.
+    static const std::string DVCS_CROSSSECTION_TOTAL_N1; ///< String used to set number of MC integration cycles via XML scenario.
+
+    /**
+     * Unique ID to automatically register the class in the registry.
+     */
+    static const unsigned int classId;
+
+    /**
+     * Function for the integration.
+     */
+    static double DVCSCrossSectionTotalFunction(double* kin, size_t dim,
+            void* par);
+
+    /**
+     * Constructor.
+     * @param className Name of class.
+     */
+    DVCSCrossSectionTotal(const std::string &className);
+
+    /**
+     * Destructor.
+     */
+    virtual ~DVCSCrossSectionTotal();
+
+    virtual DVCSCrossSectionTotal* clone() const;
+    virtual void configure(const ElemUtils::Parameters &parameters);
+
+    size_t getNI0() const;
+    void setNI0(size_t nI0);
+    size_t getNI1() const;
+    void setNI1(size_t nI1);
+    const std::pair<double, double>& getRangeQ2() const;
+    void setRangeQ2(const std::pair<double, double>& rangeQ2);
+    const std::pair<double, double>& getRangeT() const;
+    void setRangeT(const std::pair<double, double>& rangeT);
+    const std::pair<double, double>& getRangexB() const;
+    void setRangexB(const std::pair<double, double>& rangexB);
+    const std::pair<double, double>& getRangeY() const;
+    void setRangeY(const std::pair<double, double>& rangeY);
+
+protected:
+
+    /**
+     * Copy constructor.
+     * @param other Object to be copied.
+     */
+    DVCSCrossSectionTotal(const DVCSCrossSectionTotal &other);
+
+    virtual PhysicalType<double> computeObservable(
+            const DVCSObservableKinematic& kinematic,
+            const List<GPDType>& gpdType);
+
+private:
+
+    /**
+     * Print change of ranges.
+     */
+    void printChangeOfRange(const std::string& func, const std::string& name,
+            const std::pair<double, double>& oldValues,
+            const std::pair<double, double>& newValues) const;
+
+    /**
+     * Parse range.
+     */
+    std::pair<double, double> parseRange(const std::string& str) const;
+
+    size_t m_nI0;   ///< Number of iteration in single cycle.
+    size_t m_nI1;   ///< Number of cycles.
+
+    std::pair<double, double> m_rangexB; ///< xB integration range.
+    std::pair<double, double> m_rangeT; ///< t integration range.
+    std::pair<double, double> m_rangeQ2; ///< Q2 integration range.
+    std::pair<double, double> m_rangeY; ///< y integration range.
+};
+
+struct DVCSCrossSectionTotalParameters {
+
+    DVCSCrossSectionTotal* m_pDVCSCrossSectionTotal; ///< Pointer to DVCSCrossSectionTotal.
+    double m_E; ///< Beam energy.
+    List<GPDType> m_gpdType; ///< GPD types.
+    std::pair<double, double> m_yCut;
+};
+
+} /* namespace PARTONS */
+
+#endif /* DVCSCROSSSECTIONTOTAL_H */

include/partons/modules/observable/DVCS/cross_section/DVCSCrossSectionUUDVCSSubProc.h

+#ifndef DVCSCROSSSECTIONUUDVCSSUBPROC_H
+#define DVCSCROSSSECTIONUUDVCSSUBPROC_H
+
+/**
+ * @file DVCSCrossSectionUUDVCSSubProc.h
+ * @author Pawel Sznajder (IPNO)
+ * @date November 25, 2016
+ * @version 1.0
+ */
+
+#include <string>
+
+#include "../../../../beans/gpd/GPDType.h"
+#include "../../../../beans/List.h"
+#include "../../../../utils/type/PhysicalType.h"
+#include "../DVCSObservable.h"
+
+namespace PARTONS {
+
+/**
+ * @class DVCSCrossSectionUUDVCSSubProc
+ * @brief Unpolarized cross-section for DVCS only.
+ *
+ * Unit: \f$\mathrm{nbarn}/\mathrm{GeV}^4\f$.
+ */
+class DVCSCrossSectionUUDVCSSubProc: public DVCSObservable {
+
+public:
+
+    /**
+     * Unique ID to automatically register the class in the registry.
+     */
+    static const unsigned int classId;
+
+    /**
+     * Constructor.
+     * @param className Name of class.
+     */
+    DVCSCrossSectionUUDVCSSubProc(const std::string &className);
+
+    /**
+     * Destructor.
+     */
+    virtual ~DVCSCrossSectionUUDVCSSubProc();
+
+    virtual DVCSCrossSectionUUDVCSSubProc* clone() const;
+
+protected:
+
+    /**
+     * Copy constructor.
+     * @param other Object to be copied.
+     */
+    DVCSCrossSectionUUDVCSSubProc(const DVCSCrossSectionUUDVCSSubProc &other);
+
+    virtual PhysicalType<double> computeObservable(
+            const DVCSObservableKinematic& kinematic,
+            const List<GPDType>& gpdType);
+};
+
+} /* namespace PARTONS */
+
+#endif /* DVCSCROSSSECTIONUUDVCSSUBPROC_H */

include/partons/modules/observable/DVCS/cross_section/DVCSCrossSectionUUDVCSSubProcPhiIntegrated.h

+#ifndef DVCSCROSSSECTIONUUDVCSSUBPROCPHIINTEGRATED_H
+#define DVCSCROSSSECTIONUUDVCSSUBPROCPHIINTEGRATED_H
+
+/**
+ * @file DVCSCrossSectionUUDVCSSubProcPhiIntegrated.h
+ * @author Luca COLANERI (IPNO)
+ * @date April 24, 2017
+ * @version 1.0
+ */
+
+#include <ElementaryUtils/parameters/Parameters.h>
+#include <string>
+#include <vector>
+
+#include "../../../../beans/gpd/GPDType.h"
+#include "../../../../beans/List.h"
+#include "../../../../utils/type/PhysicalType.h"
+#include "../../../MathIntegratorModule.h"
+#include "DVCSCrossSectionUUDVCSSubProc.h"
+
+namespace PARTONS {
+
+/**
+ * @class DVCSCrossSectionUUDVCSSubProcPhiIntegrated
+ * @brief Unpolarized cross-section for electro-production integrated over \f$\phi\f$.
+ *
+ * Unit: \f$\mathrm{nbarn}/\mathrm{GeV}^4\f$.
+ */
+class DVCSCrossSectionUUDVCSSubProcPhiIntegrated: public DVCSCrossSectionUUDVCSSubProc,
+        public MathIntegratorModule {
+
+public:
+
+    /**
+     * Unique ID to automatically register the class in the registry.
+     */
+    static const unsigned int classId;
+
+    /**
+     * Constructor.
+     * @param className Name of class.
+     */
+    DVCSCrossSectionUUDVCSSubProcPhiIntegrated(const std::string &className);
+
+    /**
+     * Destructor.
+     */
+    virtual ~DVCSCrossSectionUUDVCSSubProcPhiIntegrated();
+
+    virtual DVCSCrossSectionUUDVCSSubProcPhiIntegrated* clone() const;
+    virtual void configure(const ElemUtils::Parameters &parameters);
+
+protected:
+
+    /**
+     * Copy constructor.
+     * @param other Object to be copied.
+     */
+    DVCSCrossSectionUUDVCSSubProcPhiIntegrated(
+            const DVCSCrossSectionUUDVCSSubProcPhiIntegrated &other);
+
+    virtual PhysicalType<double> computeObservable(
+            const DVCSObservableKinematic& kinematic,
+            const List<GPDType>& gpdType);
+
+    /**
+     * Functor to perform the integration.
+     */
+    NumA::FunctionType1D* m_pFunctionToIntegrateObservable;
+
+    /**
+     * Function to be integrated.
+     */
+    virtual double functionToIntegrateObservable(double x,
+            std::vector<double> params);
+
+    /**
+     * Initialize functors.
+     */
+    void initFunctorsForIntegrations();
+};
+
+} /* namespace PARTONS */
+
+#endif /* DVCSCROSSSECTIONUUDVCSSUBPROCPHIINTEGRATED_H */

include/partons/modules/observable/DVCS/cross_section/DVCSCrossSectionUUMinusPhiIntegrated.h

+#ifndef DVCSCROSSSECTIONUUMINUSPHIINTEGRATED_H
+#define DVCSCROSSSECTIONUUMINUSPHIINTEGRATED_H
+
+/**
+ * @file DVCSCrossSectionUUMinusPhiIntegrated.h
+ * @author Luca COLANERI (IPNO)
+ * @date April 24, 2017
+ * @version 1.0
+ */
+
+#include <ElementaryUtils/parameters/Parameters.h>
+#include <string>
+#include <vector>
+
+#include "../../../../beans/gpd/GPDType.h"
+#include "../../../../beans/List.h"
+#include "../../../../utils/type/PhysicalType.h"
+#include "../../../MathIntegratorModule.h"
+#include "DVCSCrossSectionUUMinus.h"
+
+namespace PARTONS {
+
+/**
+ * @class DVCSCrossSectionUUMinusPhiIntegrated
+ * @brief Unpolarized cross-section for electro-production integrated over \f$\phi\f$.
+ *
+ * Unit: \f$\mathrm{nbarn}/\mathrm{GeV}^4\f$.
+ */
+class DVCSCrossSectionUUMinusPhiIntegrated: public DVCSCrossSectionUUMinus,
+        public MathIntegratorModule {
+
+public:
+
+    /**
+     * Unique ID to automatically register the class in the registry.
+     */
+    static const unsigned int classId;
+
+    /**
+     * Constructor.
+     * @param className Name of class.
+     */
+    DVCSCrossSectionUUMinusPhiIntegrated(const std::string &className);
+
+    /**
+     * Destructor.
+     */
+    virtual ~DVCSCrossSectionUUMinusPhiIntegrated();
+
+    virtual DVCSCrossSectionUUMinusPhiIntegrated* clone() const;
+    virtual void configure(const ElemUtils::Parameters &parameters);
+
+protected:
+
+    /**
+     * Copy constructor.
+     * @param other Object to be copied.
+     */
+    DVCSCrossSectionUUMinusPhiIntegrated(
+            const DVCSCrossSectionUUMinusPhiIntegrated &other);
+
+    virtual PhysicalType<double> computeObservable(
+            const DVCSObservableKinematic& kinematic,
+            const List<GPDType>& gpdType);
+
+    /**
+     * Functor to perform the integration.
+     */
+    NumA::FunctionType1D* m_pFunctionToIntegrateObservable;
+
+    /**
+     * Function to be integrated.
+     */
+    virtual double functionToIntegrateObservable(double x,
+            std::vector<double> params);
+
+    /**
+     * Initialize functors.
+     */
+    void initFunctorsForIntegrations();
+};
+
+} /* namespace PARTONS */
+
+#endif /* DVCSCROSSSECTIONUUMINUSPHIINTEGRATED_H */

include/partons/modules/observable/TCS/asymmetry/TCSAfb.h

+#ifndef TCSACU_H
+#define TCSACU_H
+
+/**
+ * @file TCSAfb.h
+ * @author Pawel Sznajder (IPNO)
+ * @date November 25, 2016
+ * @version 1.0
+ */
+
+#include <string>
+
+#include "../../../../beans/gpd/GPDType.h"
+#include "../../../../beans/List.h"
+#include "../../../../utils/type/PhysicalType.h"
+#include "../TCSObservable.h"
+
+namespace PARTONS {
+
+/**
+ * @class TCSAfb
+ * @brief Forward-backward TCS asymmetry.
+ *
+ * Unit: none.
+ */
+class TCSAfb: public TCSObservable {
+
+public:
+
+    /**
+     * Unique ID to automatically register the class in the registry.
+     */
+    static const unsigned int classId;
+
+    /**
+     * Constructor.
+     * @param className Name of class.
+     */
+    TCSAfb(const std::string &className);
+
+    /**
+     * Destructor.
+     */
+    virtual ~TCSAfb();
+
+    virtual TCSAfb* clone() const;
+
+protected:
+
+    /**
+     * Copy constructor.
+     * @param other Object to be copied.
+     */
+    TCSAfb(const TCSAfb &other);
+
+    virtual PhysicalType<double> computeObservable(
+            const TCSObservableKinematic& kinematic,
+            const List<GPDType>& gpdType);
+};
+