Merge tag '1.5'

Release 1.5

.clang-format

@@ -0,0 +1,45 @@
+BasedOnStyle: LLVM
+
+AccessModifierOffset: 0
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: true
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlinesLeft: false
+AlignOperands: false
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortBlocksOnASingleLine: true
+AllowShortCaseLabelsOnASingleLine: true
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: true
+AllowShortLoopsOnASingleLine: true
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: false
+BinPackArguments: true
+BinPackParameters: true 
+BreakBeforeBinaryOperators: NonAssignment
+BreakBeforeBraces: Attach
+BreakBeforeTernaryOperators: false
+BreakConstructorInitializersBeforeComma: false
+BreakStringLiterals: false
+ColumnLimit: 150
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 3
+ContinuationIndentWidth: 3
+Cpp11BracedListStyle: true
+DerivePointerBinding : false
+IndentCaseLabels: true
+IndentWidth: 2
+Language: Cpp
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation : All
+PointerAlignment: Right
+ReflowComments: false
+SortIncludes: false
+SpaceAfterControlStatementKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceInEmptyParentheses: false
+SpacesInParentheses: false
+Standard: Cpp11
+TabWidth: 2
+UseTab: Never

.dockerignore

@@ -0,0 +1,3 @@
+.git
+Dockerfile
+Jenkinsfile

.travis.yml

@@ -0,0 +1,48 @@
+
+language: cpp
+sudo: required
+dist: trusty
+
+compiler:
+  - gcc
+    #  - clang
+
+before_install:
+  - sudo add-apt-repository 'deb http://apt.llvm.org/trusty/ llvm-toolchain-trusty-5.0 main' -y
+  - wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key|sudo apt-key add -
+  - sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y
+  - sudo apt-get update
+  - sudo apt-get install -y --allow-unauthenticated g++-7 clang-5.0
+  - export LIBRARY_PATH=/usr/lib/llvm-5.0/lib:$LIBRARY_PATH
+  - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-7 60 --slave /usr/bin/g++ g++ /usr/bin/g++-7
+  - sudo update-alternatives --install /usr/bin/clang clang /usr/bin/clang-5.0 60 --slave /usr/bin/clang++ clang++ /usr/bin/clang++-5.0
+  - sudo apt-get install -y --allow-unauthenticated libboost-all-dev cmake git libgfortran3 gfortran openmpi-bin openmpi-common openmpi-doc libopenmpi-dev libblas-dev liblapack-dev libfftw3-dev libgmp-dev hdf5-tools libhdf5-serial-dev python-h5py python-dev python-numpy python-scipy python-jinja2 python-virtualenv python-matplotlib python-tornado python-zmq python-mpi4py python-mako clang-format-5.0 libclang-5.0-dev python-clang-5.0 python-sphinx libjs-mathjax valgrind libnfft3-dev
+
+install: true
+
+script:
+  # ===== Set up Cpp2Py
+  - git clone https://github.com/triqs/cpp2py
+  - mkdir cpp2py/build && cd cpp2py/build
+  - git checkout master
+  - cmake .. -DCMAKE_CXX_COMPILER=/usr/bin/${CXX} -DPYTHON_INTERPRETER=/usr/bin/python -DCMAKE_INSTALL_PREFIX=$TRAVIS_BUILD_DIR/root_install
+  - make -j8 install
+  - cd $TRAVIS_BUILD_DIR
+  - source root_install/share/cpp2pyvars.sh
+  # ===== Set up TRIQS
+  - git clone https://github.com/TRIQS/triqs --branch unstable
+  - mkdir triqs/build && cd triqs/build
+  - git checkout unstable
+  - cmake .. -DCMAKE_CXX_COMPILER=/usr/bin/${CXX} -DBuild_Tests=OFF -DCMAKE_INSTALL_PREFIX=$TRAVIS_BUILD_DIR/root_install -DCMAKE_BUILD_TYPE=Debug
+  - make -j8 install
+  - cd $TRAVIS_BUILD_DIR
+  - source root_install/share/triqsvars.sh
+  # ===== Set up dft_tools and Test using fsanitize=address
+  - mkdir build && cd build
+  - cmake .. -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_COMPILER=/usr/bin/${CXX} -DCMAKE_CXX_FLAGS='-fsanitize=address -fno-omit-frame-pointer -fuse-ld=gold'
+  - make -j8
+  - export ASAN_SYMBOLIZER_PATH=/usr/lib/llvm-5.0/bin/llvm-symbolizer
+  - export ASAN_OPTIONS=symbolize=1:detect_leaks=0
+  - export CTEST_OUTPUT_ON_FAILURE=1
+  - if [ "$CXX" = g++ ]; then export LD_PRELOAD=/usr/lib/gcc/x86_64-linux-gnu/7/libasan.so; elif [ "$CXX" = clang++ ]; then export LD_PRELOAD=/usr/lib/llvm-5.0/lib/clang/5.0.1/lib/linux/libclang_rt.asan-x86_64.so; fi
+  - cd test && ctest

CMakeLists.txt

@@ -1,50 +1,83 @@
 # Version number of the application
-set (DFT_TOOLS_VERSION "1.4")
-set (DFT_TOOLS_RELEASE "1.4.0")
+set (DFT_TOOLS_VERSION "1.5")
+set (DFT_TOOLS_RELEASE "1.5.0")
 
-# Append triqs installed files to the cmake load path
-list(APPEND CMAKE_MODULE_PATH ${TRIQS_PATH}/share/triqs/cmake)
-
-# start configuration 
-cmake_minimum_required(VERSION 2.8)
-project(dft_tools CXX Fortran)
-set(CMAKE_BUILD_TYPE Release)
-enable_testing()
-
-# Load TRIQS, including all predefined variables from TRIQS installation
-find_package(TRIQS REQUIRED)
-
-# Check that versions are compatible
-if(NOT DFT_TOOLS_VERSION EQUAL TRIQS_VERSION)
-  message(FATAL_ERROR "The application version is not compatible with the TRIQS library (TRIQS library version: ${TRIQS_VERSION} while this application version: ${DFT_TOOLS_VERSION})")
+# Default to Release build type
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "Type of build" FORCE)
 endif()
+message( STATUS "-------- BUILD-TYPE: ${CMAKE_BUILD_TYPE} -------------")
+
+# start configuration
+cmake_minimum_required(VERSION 2.8)
+project(dft_tools C CXX Fortran)
+
+# Use shared libraries
+set(BUILD_SHARED_LIBS ON)
+
+# Load TRIQS and Cpp2Py
+find_package(TRIQS 1.5 EXACT REQUIRED)
+find_package(Cpp2Py REQUIRED)
+
 if (NOT ${TRIQS_WITH_PYTHON_SUPPORT})
  MESSAGE(FATAL_ERROR "dft_tools require Python support in TRIQS")
 endif()
 
-# Get hash
-triqs_get_git_hash(${CMAKE_SOURCE_DIR} "DFT_TOOLS")
-if(${GIT_RESULT} EQUAL 0)
-  message(STATUS "Hash: ${DFT_TOOLS_GIT_HASH}")
-endif(${GIT_RESULT} EQUAL 0)
+# Default Install directory to TRIQS_ROOT if not given. Checks an absolute name is given.
+if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT OR (NOT IS_ABSOLUTE ${CMAKE_INSTALL_PREFIX}))
+  message(STATUS " No install prefix given (or invalid). Defaulting to TRIQS_ROOT")
+  set(CMAKE_INSTALL_PREFIX ${TRIQS_ROOT} CACHE PATH "default install path" FORCE)
+endif()
+message(STATUS "-------- CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX} -------------")
 
-# We want to be installed in the TRIQS tree
-set(CMAKE_INSTALL_PREFIX ${TRIQS_PATH})
+# Macro defined in TRIQS which picks the hash of repo.
+triqs_get_git_hash_of_source_dir(DFT_TOOLS_GIT_HASH)
+message(STATUS "Git hash: ${DFT_TOOLS_GIT_HASH}")
 
 add_subdirectory(fortran/dmftproj) 
 
 # Add the compiling options (-D... ) for C++
 message(STATUS "TRIQS : Adding compilation flags detected by the library (C++11/14, libc++, etc...) ")
-add_definitions(${TRIQS_CXX_DEFINITIONS})
 
 add_subdirectory(c++)
 add_subdirectory(python)
 add_subdirectory(shells)
-add_subdirectory(test)
-option(BUILD_DOC "Build documentation" OFF)
-if(${BUILD_DOC})
-  if(NOT TRIQS_WITH_DOCUMENTATION)
+
+#------------------------
+# tests
+#------------------------
+ 
+enable_testing()
+ 
+option(Build_Tests "Build the tests of the library " ON)
+if (Build_Tests)
+  message(STATUS "-------- Preparing tests  -------------")
+ add_subdirectory(test)
+endif()
+
+#------------------------
+# Documentation
+#------------------------
+option(Build_Documentation "Build documentation" OFF)
+if(${Build_Documentation})
+  if(NOT ${TRIQS_WITH_DOCUMENTATION})
     message("Error: TRIQS library has not been compiled with its documentation")
   endif()
   add_subdirectory(doc)
-endif(${BUILD_DOC})
+endif()
+
+#--------------------------------------------------------
+# Packaging
+#--------------------------------------------------------
+option(BUILD_DEBIAN_PACKAGE "Build a deb package" OFF)
+if(BUILD_DEBIAN_PACKAGE)
+  if(NOT CMAKE_INSTALL_PREFIX STREQUAL "/usr")
+    message(FATAL_ERROR "CMAKE_INSTALL_PREFIX must be /usr for packaging")
+  endif()
+  SET(CPACK_GENERATOR "DEB")
+  SET(CPACK_PACKAGE_VERSION ${DFT_TOOLS_VERSION})
+  SET(CPACK_PACKAGE_CONTACT "https://github.com/TRIQS/dft_tools")
+  EXECUTE_PROCESS(COMMAND dpkg --print-architecture OUTPUT_VARIABLE CMAKE_DEBIAN_PACKAGE_ARCHITECTURE OUTPUT_STRIP_TRAILING_WHITESPACE)
+  SET(CPACK_DEBIAN_PACKAGE_DEPENDS "libc6 (>= 2.23), libgcc1 (>= 1:6), libstdc++6, python, libpython2.7, libopenmpi1.10, libhdf5-10, libgmp10, libfftw3-double3, libibverbs1, libgfortran3, zlib1g, libsz2, libhwloc5, libquadmath0, libaec0, libnuma1, libltdl7, libblas3, liblapack3, python-numpy, python-h5py, python-jinja2, python-mako, python-mpi4py, python-matplotlib, python-scipy, cpp2py (= ${DFT_TOOLS_VERSION}), triqs (= ${DFT_TOOLS_VERSION})")
+  INCLUDE(CPack)
+endif()

Dockerfile

@@ -0,0 +1,12 @@
+# See ../triqs/packaging for other options
+FROM flatironinstitute/triqs:master-ubuntu-clang
+
+ARG APPNAME=dft_tools
+COPY . $SRC/$APPNAME
+WORKDIR $BUILD/$APPNAME
+RUN chown build .
+USER build
+ARG BUILD_DOC=0
+RUN cmake $SRC/$APPNAME -DTRIQS_ROOT=${INSTALL} -DBuild_Documentation=${BUILD_DOC} && make -j2 && make test
+USER root
+RUN make install

Jenkinsfile

@@ -0,0 +1,140 @@
+def projectName = "dft_tools"
+def documentationPlatform = "ubuntu-clang"
+def triqsBranch = env.CHANGE_TARGET ?: env.BRANCH_NAME
+def triqsProject = '/TRIQS/triqs/' + triqsBranch.replaceAll('/', '%2F')
+def publish = !env.BRANCH_NAME.startsWith("PR-")
+
+properties([
+  disableConcurrentBuilds(),
+  buildDiscarder(logRotator(numToKeepStr: '10', daysToKeepStr: '30')),
+  pipelineTriggers([
+    upstream(
+      threshold: 'SUCCESS',
+      upstreamProjects: triqsProject
+    )
+  ])
+])
+
+/* map of all builds to run, populated below */
+def platforms = [:]
+
+def dockerPlatforms = ["ubuntu-clang", "ubuntu-gcc", "centos-gcc"]
+/* .each is currently broken in jenkins */
+for (int i = 0; i < dockerPlatforms.size(); i++) {
+  def platform = dockerPlatforms[i]
+  platforms[platform] = { -> node('docker') {
+    stage(platform) { timeout(time: 1, unit: 'HOURS') {
+      checkout scm
+      /* construct a Dockerfile for this base */
+      sh """
+        ( echo "FROM flatironinstitute/triqs:${triqsBranch}-${env.STAGE_NAME}" ; sed '0,/^FROM /d' Dockerfile ) > Dockerfile.jenkins
+        mv -f Dockerfile.jenkins Dockerfile
+      """
+      /* build and tag */
+      def img = docker.build("flatironinstitute/${projectName}:${env.BRANCH_NAME}-${env.STAGE_NAME}", "--build-arg BUILD_DOC=${platform==documentationPlatform} .")
+      if (!publish || platform != documentationPlatform) {
+        /* but we don't need the tag so clean it up (except for documentation) */
+        sh "docker rmi --no-prune ${img.imageName()}"
+      }
+    } }
+  } }
+}
+
+def osxPlatforms = [
+  ["gcc", ['CC=gcc-7', 'CXX=g++-7']],
+  ["clang", ['CC=/usr/local/opt/llvm/bin/clang', 'CXX=/usr/local/opt/llvm/bin/clang++', 'CXXFLAGS=-I/usr/local/opt/llvm/include', 'LDFLAGS=-L/usr/local/opt/llvm/lib']]
+]
+for (int i = 0; i < osxPlatforms.size(); i++) {
+  def platformEnv = osxPlatforms[i]
+  def platform = platformEnv[0]
+  platforms["osx-$platform"] = { -> node('osx && triqs') {
+    stage("osx-$platform") { timeout(time: 1, unit: 'HOURS') {
+      def srcDir = pwd()
+      def tmpDir = pwd(tmp:true)
+      def buildDir = "$tmpDir/build"
+      def installDir = "$tmpDir/install"
+      def triqsDir = "${env.HOME}/install/triqs/${triqsBranch}/${platform}"
+      dir(installDir) {
+        deleteDir()
+      }
+
+      checkout scm
+      dir(buildDir) { withEnv(platformEnv[1]+[
+          "PATH=$triqsDir/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin",
+          "CPATH=$triqsDir/include",
+          "LIBRARY_PATH=$triqsDir/lib",
+          "CMAKE_PREFIX_PATH=$triqsDir/share/cmake"]) {
+        deleteDir()
+        sh "cmake $srcDir -DCMAKE_INSTALL_PREFIX=$installDir -DTRIQS_ROOT=$triqsDir"
+        sh "make -j3"
+        try {
+          sh "make test"
+        } catch (exc) {
+          archiveArtifacts(artifacts: 'Testing/Temporary/LastTest.log')
+          throw exc
+        }
+        sh "make install"
+      } }
+    } }
+  } }
+}
+
+try {
+  parallel platforms
+  if (publish) { node("docker") {
+    stage("publish") { timeout(time: 1, unit: 'HOURS') {
+      def commit = sh(returnStdout: true, script: "git rev-parse HEAD").trim()
+      def workDir = pwd()
+      dir("$workDir/gh-pages") {
+        def subdir = env.BRANCH_NAME
+        git(url: "ssh://git@github.com/TRIQS/${projectName}.git", branch: "gh-pages", credentialsId: "ssh", changelog: false)
+        sh "rm -rf ${subdir}"
+        docker.image("flatironinstitute/${projectName}:${env.BRANCH_NAME}-${documentationPlatform}").inside() {
+          sh "cp -rp \$INSTALL/share/doc/${projectName} ${subdir}"
+        }
+        sh "git add -A ${subdir}"
+        sh """
+          git commit --author='Flatiron Jenkins <jenkins@flatironinstitute.org>' --allow-empty -m 'Generated documentation for ${env.BRANCH_NAME}' -m '${env.BUILD_TAG} ${commit}'
+        """
+        // note: credentials used above don't work (need JENKINS-28335)
+        sh "git push origin gh-pages"
+      }
+      dir("$workDir/docker") { try {
+        git(url: "ssh://git@github.com/TRIQS/docker.git", branch: env.BRANCH_NAME, credentialsId: "ssh", changelog: false)
+        sh "echo '160000 commit ${commit}\t${projectName}' | git update-index --index-info"
+        sh """
+          git commit --author='Flatiron Jenkins <jenkins@flatironinstitute.org>' --allow-empty -m 'Autoupdate ${projectName}' -m '${env.BUILD_TAG}'
+        """
+        // note: credentials used above don't work (need JENKINS-28335)
+        sh "git push origin ${env.BRANCH_NAME}"
+      } catch (err) {
+        echo "Failed to update docker repo"
+      } }
+    } }
+  } }
+} catch (err) {
+  if (env.BRANCH_NAME != "jenkins") emailext(
+    subject: "\$PROJECT_NAME - Build # \$BUILD_NUMBER - FAILED",
+    body: """\$PROJECT_NAME - Build # \$BUILD_NUMBER - FAILED
+
+$err
+
+Check console output at \$BUILD_URL to view full results.
+
+Building \$BRANCH_NAME for \$CAUSE
+\$JOB_DESCRIPTION
+
+Chages:
+\$CHANGES
+
+End of build log:
+\${BUILD_LOG,maxLines=60}
+    """,
+    to: 'mzingl@flatironinstitute.org, hstrand@flatironinstitute.org, nils.wentzell@gmail.com, dsimon@flatironinstitute.org',
+    recipientProviders: [
+      [$class: 'DevelopersRecipientProvider'],
+    ],
+    replyTo: '$DEFAULT_REPLYTO'
+  )
+  throw err
+}

c++/plovasp/atm/CMakeLists.txt

@@ -1,7 +1,6 @@
-# Linking and include info
 add_library(atm_c dos_tetra3d.hpp dos_tetra3d.cpp argsort.hpp argsort.cpp)
-set_target_properties(atm_c PROPERTIES LINKER_LANGUAGE CXX)
-include_directories(${CMAKE_CURRENT_SOURCE_DIR}/c++/plovasp/atm ${TRIQS_INCLUDE_ALL})
+target_link_libraries(atm_c triqs)
+target_compile_options(atm_c PRIVATE -std=c++17)
 
 install(TARGETS atm_c DESTINATION lib)
 

c++/plovasp/atm/test/CMakeLists.txt

@@ -1,24 +1,13 @@
-find_package(TriqsTest)
 enable_testing()
 
-# Linking and include info
-#add_library(atm_c dos_tetra3d.hpp dos_tetra3d.cpp argsort.h argsort.c)
-#set_target_properties(atm_c PROPERTIES LINKER_LANGUAGE CXX)
-#include_directories(${CMAKE_CURRENT_SOURCE_DIR}/c++/plovasp/atm ${TRIQS_INCLUDE_ALL})
-
 FILE(GLOB TestList RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.cpp)
 FOREACH( TestName1  ${TestList} )
  STRING(REPLACE ".cpp" "" TestName ${TestName1})
- add_executable( ${TestName}  ${CMAKE_CURRENT_SOURCE_DIR}/${TestName}.cpp )
- target_link_libraries( ${TestName} atm_c ${TRIQS_LIBRARY_ALL} )
+ add_executable( ${TestName}  ${TestName}.cpp )
+ target_link_libraries( ${TestName} atm_c triqs)
  triqs_set_rpath_for_target( ${TestName} )
- triqs_add_cpp_test( ${TestName} )
- if (TESTS_C_WITH_VALGRIND)
-  add_test ( ${TestName}_valgrind valgrind --error-exitcode=1 ${CMAKE_CURRENT_BINARY_DIR}/${TestName})
- endif()
+ add_test(NAME ${TestName} COMMAND ${CMAKE_CURRENT_BINARY_DIR}/${t})
 ENDFOREACH( TestName1  ${TestList} )
 
-#add_executable(test_atm test2py.cpp)
-#target_link_libraries(test_atm atm_c)
 
-#add_subdirectory(test)
+

dft_dmft_cthyb.py

@@ -1,10 +1,10 @@
 import pytriqs.utility.mpi as mpi
 from pytriqs.operators.util import *
 from pytriqs.archive import HDFArchive
-from pytriqs.applications.impurity_solvers.cthyb import *
-from pytriqs.gf.local import *
-from pytriqs.applications.dft.sumk_dft import *
-from pytriqs.applications.dft.converters.wien2k_converter import *
+from triqs_cthyb import *
+from pytriqs.gf import *
+from triqs_dft_tools.sumk_dft import *
+from triqs_dft_tools.converters.wien2k_converter import *
 
 dft_filename='Gd_fcc'
 U = 9.6
@@ -52,7 +52,7 @@ spin_names = ["up","down"]
 orb_names = [i for i in range(n_orb)]
 
 # Use GF structure determined by DFT blocks
-gf_struct = SK.gf_struct_solver[0] 
+gf_struct = [(block, indices) for block, indices in SK.gf_struct_solver[0].iteritems()]
 # Construct U matrix for density-density calculations
 Umat, Upmat = U_matrix_kanamori(n_orb=n_orb, U_int=U, J_hund=J)
 # Construct Hamiltonian and solver

doc/CMakeLists.txt

@@ -1,29 +1,23 @@
 # generate the conf.py
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/conf.py.in ${CMAKE_CURRENT_BINARY_DIR}/conf.py)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/conf.py.in ${CMAKE_CURRENT_BINARY_DIR}/conf.py @ONLY)
 
-# all rst files of the documentation
-file(GLOB_RECURSE doc_sources *.rst)
+# ---------------------------------
+# Top Sphinx target
+# ---------------------------------
+# Sources
+file(GLOB_RECURSE sources *.rst)
 
 # create documentation target
 set(sphinx_top ${CMAKE_CURRENT_BINARY_DIR}/html/index.html)
-add_custom_command(OUTPUT ${sphinx_top} DEPENDS ${doc_sources} py_copy
-                   COMMAND ${CMAKE_BINARY_DIR}/build_pytriqs ${TRIQS_SPHINXBUILD_EXECUTABLE} -c . -b html ${CMAKE_CURRENT_SOURCE_DIR} html)
-add_custom_target(doc_sphinx ALL DEPENDS ${sphinx_top})
+add_custom_command(OUTPUT ${sphinx_top} DEPENDS ${sources}
+  		   COMMAND ${TRIQS_SPHINXBUILD_EXECUTABLE} -c . -j8 -b html ${CMAKE_CURRENT_SOURCE_DIR} html)
+add_custom_target(doc_sphinx ALL DEPENDS ${sphinx_top} ${CMAKE_CURRENT_BINARY_DIR})
 
-# install
+# ---------------------------------
+# Install
+# ---------------------------------
 install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/ COMPONENT documentation DESTINATION share/doc/dft_tools
- FILES_MATCHING 
- PATTERN "*.html" 
- PATTERN "*.png"
- PATTERN "*.js"
+ FILES_MATCHING
+ REGEX "\\.(html|pdf|png|gif|jpg|js|xsl|css|py|txt|inv|bib)$"
  PATTERN "_*"
- PATTERN "*.jpg" 
- PATTERN "*.gif" 
- PATTERN "*.xsl" 
- PATTERN "*.css"
- PATTERN "*.pdf"
- PATTERN "*.py"
- PATTERN "*.txt"
- PATTERN "*.inv"
- PATTERN "*.bib"
  )

doc/documentation.rst

@@ -1,4 +1,4 @@
-.. module:: pytriqs.applications.dft
+.. module:: triqs_dft_tools
 
 .. _documentation:
 

doc/guide/SrVO3.rst

@@ -23,11 +23,11 @@ Loading modules
 
 First, we load the necessary modules::
 
-  from pytriqs.applications.dft.sumk_dft import *
-  from pytriqs.gf.local import *
+  from triqs_dft_tools.sumk_dft import *
+  from pytriqs.gf import *
   from pytriqs.archive import HDFArchive
   from pytriqs.operators.util import *
-  from pytriqs.applications.impurity_solvers.cthyb import *
+  from triqs_cthyb import *
 
 The last two lines load the modules for the construction of the
 :ref:`CTHYB solver <triqscthyb:welcome>`.
@@ -56,7 +56,7 @@ Initializing the solver
 -----------------------
 
 We also have to specify the :ref:`CTHYB solver <triqscthyb:welcome>` related settings.
-We assume that the DMFT script for SrVO3 is executed on 16 cores. A sufficient set 
+We assume that the DMFT script for SrVO3 is executed on 16 cores. A sufficient set
 of parameters for a first guess is::
 
   p = {}
@@ -80,7 +80,7 @@ each material individually. A guide on how to set the tail fit parameters is giv
 
 
 The next step is to initialize the
-:class:`solver class <pytriqs.applications.impurity_solvers.cthyb.Solver>`.
+:class:`solver class <triqs_cthyb.Solver>`.
 It consist of two parts:
 
 #. Calculating the multi-band interaction matrix, and constructing the
@@ -94,7 +94,7 @@ The first step is done using methods of the :ref:`TRIQS <triqslibs:welcome>` lib
   spin_names = ["up","down"]
   orb_names = [i for i in range(n_orb)]
   # Use GF structure determined by DFT blocks:
-  gf_struct = SK.gf_struct_solver[0]
+  gf_struct = [(block, indices) for block, indices in SK.gf_struct_solver[0].iteritems()]
   # Construct U matrix for density-density calculations:
   Umat, Upmat = U_matrix_kanamori(n_orb=n_orb, U_int=U, J_hund=J)
 
@@ -102,7 +102,7 @@ We assumed here that we want to use an interaction matrix with
 Kanamori definitions of :math:`U` and :math:`J`.
 
 Next, we construct the Hamiltonian and the solver::
-  
+
   h_int = h_int_density(spin_names, orb_names, map_operator_structure=SK.sumk_to_solver[0], U=Umat, Uprime=Upmat)
   S = Solver(beta=beta, gf_struct=gf_struct)
 
@@ -125,7 +125,7 @@ some additional refinements::
 
   for iteration_number in range(1,loops+1):
       if mpi.is_master_node(): print "Iteration = ", iteration_number
-  
+
       SK.symm_deg_gf(S.Sigma_iw,orb=0)                        # symmetrizing Sigma
       SK.set_Sigma([ S.Sigma_iw ])                            # put Sigma into the SumK class
       chemical_potential = SK.calc_mu( precision = prec_mu )  # find the chemical potential for given density
@@ -137,17 +137,17 @@ some additional refinements::
           dm = S.G_iw.density()
           SK.calc_dc(dm, U_interact = U, J_hund = J, orb = 0, use_dc_formula = dc_type)
           S.Sigma_iw << SK.dc_imp[0]['up'][0,0]
-  
+
       # Calculate new G0_iw to input into the solver:
       S.G0_iw << S.Sigma_iw + inverse(S.G_iw)
       S.G0_iw << inverse(S.G0_iw)
 
       # Solve the impurity problem:
       S.solve(h_int=h_int, **p)
-  
+
       # Solved. Now do post-solution stuff:
       mpi.report("Total charge of impurity problem : %.6f"%S.G_iw.total_density())
-  
+
       # Now mix Sigma and G with factor mix, if wanted:
       if (iteration_number>1 or previous_present):
           if mpi.is_master_node():
@@ -158,7 +158,7 @@ some additional refinements::
               del ar
           S.G_iw << mpi.bcast(S.G_iw)
           S.Sigma_iw << mpi.bcast(S.Sigma_iw)
-  
+
       # Write the final Sigma and G to the hdf5 archive:
       if mpi.is_master_node():
           ar = HDFArchive(dft_filename+'.h5','a')
@@ -188,8 +188,8 @@ to start with a lower statistics (less measurements), but then increase it at a
 point close to converged results (e.g. after a few initial iterations). This helps
 to keep computational costs low during the first iterations.
 
-Using the Kanamori Hamiltonian and the parameters above (but on 16 cores), 
-your self energy after the **first iteration** should look like the 
+Using the Kanamori Hamiltonian and the parameters above (but on 16 cores),
+your self energy after the **first iteration** should look like the
 self energy shown below.
 
 .. image:: images_scripts/SrVO3_Sigma_iw_it1.png
@@ -208,12 +208,12 @@ Therefore disabled the tail fitting first::
     p["perform_tail_fit"] = False
 
 and perform only one DMFT iteration. The resulting self energy can be tail fitted by hand::
-    
+
     Sigma_iw_fit = S.Sigma_iw.copy()
     Sigma_iw_fit << tail_fit(S.Sigma_iw, fit_max_moment = 4, fit_min_n = 40, fit_max_n = 160)[0]
 
 Plot the self energy and adjust the tail fit parameters such that you obtain a
-proper fit. The :meth:`tail_fit function <pytriqs.gf.local.tools.tail_fit>` is part
+proper fit. The :meth:`fit_tail function <pytriqs.gf.tools.tail_fit>` is part
 of the :ref:`TRIQS <triqslibs:welcome>` library.
 
 For a self energy which is going to zero for :math:`i\omega \rightarrow 0` our suggestion is

doc/guide/analysis.rst

@@ -27,7 +27,7 @@ Initialisation
 All tools described below are collected in an extension of the :class:`SumkDFT <dft.sumk_dft.SumkDFT>` class and are
 loaded by importing the module :class:`SumkDFTTools <dft.sumk_dft_tools.SumkDFTTools>`::
 
-  from pytriqs.applications.dft.sumk_dft_tools import *
+  from triqs_dft_tools.sumk_dft_tools import *
 
 The initialisation of the class is equivalent to that of the :class:`SumkDFT <dft.sumk_dft.SumkDFT>`
 class::
@@ -37,7 +37,7 @@ class::
 Note that all routines available in :class:`SumkDFT <dft.sumk_dft.SumkDFT>` are also available here.
 
 If required, we have to load and initialise the real frequency self energy. Most conveniently,
-you have your self energy already stored as a real frequency :class:`BlockGf <pytriqs.gf.local.BlockGf>` object
+you have your self energy already stored as a real frequency :class:`BlockGf <pytriqs.gf.BlockGf>` object
 in a hdf5 file::
 
   ar = HDFArchive('case.h5', 'a')
@@ -45,10 +45,10 @@ in a hdf5 file::
 
 You may also have your self energy stored in text files. For this case the :ref:`TRIQS <triqslibs:welcome>` library offers
 the function :meth:`read_gf_from_txt`, which is able to load the data from text files of one Greens function block
-into a real frequency :class:`ReFreqGf <pytriqs.gf.local.ReFreqGf>` object. Loading each block separately and
-building up a :class:´BlockGf <pytriqs.gf.local.BlockGf>´ is done with::
+into a real frequency :class:`ReFreqGf <pytriqs.gf.ReFreqGf>` object. Loading each block separately and
+building up a :class:´BlockGf <pytriqs.gf.BlockGf>´ is done with::
 
-  from pytriqs.gf.local.tools import *
+  from pytriqs.gf.tools import *
   # get block names
   n_list = [n for n,nl in SK.gf_struct_solver[0].iteritems()]
   # load sigma for each block - in this example sigma is composed of 1x1 blocks

doc/guide/conversion.rst

@@ -107,7 +107,7 @@ Now we convert these files into an hdf5 file that can be used for the
 DMFT calculations. For this purpose we
 use the python module :class:`Wien2kConverter <dft.converters.wien2k_converter.Wien2kConverter>`. It is initialized as::
 
-  from pytriqs.applications.dft.converters.wien2k_converter import *
+  from triqs_dft_tools.converters.wien2k_converter import *
   Converter = Wien2kConverter(filename = case)
 
 The only necessary parameter to this construction is the parameter `filename`.
@@ -338,7 +338,7 @@ matrix of the imaginary part, and then move on to the next :math:`\mathbf{k}`-po
 
 The converter itself is used as::
 
-  from pytriqs.applications.dft.converters.hk_converter import *
+  from triqs_dft_tools.converters.hk_converter import *
   Converter = HkConverter(filename = hkinputfile)
   Converter.convert_dft_input()
   
@@ -372,7 +372,7 @@ as a placeholder for the actual prefix chosen by the user when creating the
 input for :program:`wannier90`.
 Once these two files are available, one can use the converter as follows::
 
-    from pytriqs.applications.dft.converters import Wannier90Converter
+    from triqs_dft_tools.converters import Wannier90Converter
     Converter = Wannier90Converter(seedname='seedname')
     Converter.convert_dft_input()
 

doc/guide/dftdmft_singleshot.rst

@@ -22,7 +22,7 @@ The first thing is the :class:`SumkDFT <dft.sumk_dft.SumkDFT>` class.
 It contains all basic routines that are necessary to perform a summation in k-space
 to get the local quantities used in DMFT. It is initialized by::
 
-    from pytriqs.applications.dft.sumk_dft import *
+    from triqs_dft_tools.sumk_dft import *
     SK = SumkDFT(hdf_file = filename + '.h5')
 
 

doc/guide/images_scripts/Ce-gamma.py

@@ -1,5 +1,5 @@
-from pytriqs.applications.dft.sumk_dft import *
-from pytriqs.applications.dft.converters.wien2k_converter import *
+from triqs_dft_tools.sumk_dft import *
+from triqs_dft_tools.converters.wien2k_converter import *
 from pytriqs.applications.impurity_solvers.hubbard_I.hubbard_solver import Solver
 
 import os

doc/guide/images_scripts/Ce-gamma_DOS.py

@@ -1,5 +1,5 @@
-from pytriqs.applications.dft.sumk_dft_tools import *
-from pytriqs.applications.dft.converters.wien2k_converter import *
+from triqs_dft_tools.sumk_dft_tools import *
+from triqs_dft_tools.converters.wien2k_converter import *
 from pytriqs.applications.impurity_solvers.hubbard_I.hubbard_solver import Solver
 
 # Creates the data directory, cd into it:

doc/guide/images_scripts/dft_dmft_cthyb.py

@@ -1,9 +1,9 @@
 import pytriqs.utility.mpi as mpi
 from pytriqs.operators.util import *
 from pytriqs.archive import HDFArchive
-from pytriqs.applications.impurity_solvers.cthyb import *
-from pytriqs.gf.local import *
-from pytriqs.applications.dft.sumk_dft import *
+from triqs_cthyb import *
+from pytriqs.gf import *
+from triqs_dft_tools.sumk_dft import *
 
 dft_filename='SrVO3'
 U = 4.0
@@ -30,7 +30,7 @@ p["fit_min_n"] = 30
 p["fit_max_n"] = 60
 
 # If conversion step was not done, we could do it here. Uncomment the lines it you want to do this.
-#from pytriqs.applications.dft.converters.wien2k_converter import *
+#from triqs_dft_tools.converters.wien2k_converter import *
 #Converter = Wien2kConverter(filename=dft_filename, repacking=True)
 #Converter.convert_dft_input()
 #mpi.barrier()
@@ -58,7 +58,7 @@ spin_names = ["up","down"]
 orb_names = [i for i in range(n_orb)]
 
 # Use GF structure determined by DFT blocks
-gf_struct = SK.gf_struct_solver[0]
+gf_struct = [(block, indices) for block, indices in SK.gf_struct_solver[0].iteritems()]
 
 # Construct U matrix for density-density calculations
 Umat, Upmat = U_matrix_kanamori(n_orb=n_orb, U_int=U, J_hund=J)

doc/guide/images_scripts/dft_dmft_cthyb_slater.py

@@ -1,10 +1,10 @@
 import pytriqs.utility.mpi as mpi
 from pytriqs.operators.util import *
 from pytriqs.archive import HDFArchive
-from pytriqs.applications.impurity_solvers.cthyb import *
-from pytriqs.gf.local import *
-from pytriqs.applications.dft.sumk_dft import *
-from pytriqs.applications.dft.converters.wien2k_converter import *
+from triqs_cthyb import *
+from pytriqs.gf import *
+from triqs_dft_tools.sumk_dft import *
+from triqs_dft_tools.converters.wien2k_converter import *
 
 dft_filename='SrVO3'
 U = 9.6
@@ -31,7 +31,7 @@ p["fit_min_n"] = 30
 p["fit_max_n"] = 60
 
 # If conversion step was not done, we could do it here. Uncomment the lines it you want to do this.
-#from pytriqs.applications.dft.converters.wien2k_converter import *
+#from triqs_dft_tools.converters.wien2k_converter import *
 #Converter = Wien2kConverter(filename=dft_filename, repacking=True)
 #Converter.convert_dft_input()
 #mpi.barrier()
@@ -59,7 +59,7 @@ spin_names = ["up","down"]
 orb_names = [i for i in range(n_orb)]
 
 # Use GF structure determined by DFT blocks
-gf_struct = SK.gf_struct_solver[0]
+gf_struct = [(block, indices) for block, indices in SK.gf_struct_solver[0].iteritems()]
 
 # Construct Slater U matrix 
 Umat = U_matrix(n_orb=n_orb, U_int=U, J_hund=J, basis='cubic',)

doc/guide/transport.rst

@@ -84,8 +84,8 @@ Using the transport code
 
 First we have to read the Wien2k files and store the relevant information in the hdf5 archive::
 
-    from pytriqs.applications.dft.converters.wien2k_converter import *
-    from pytriqs.applications.dft.sumk_dft_tools import *
+    from triqs_dft_tools.converters.wien2k_converter import *
+    from triqs_dft_tools.sumk_dft_tools import *
 
     Converter = Wien2kConverter(filename='case', repacking=True)
     Converter.convert_transport_input()

doc/index.rst

@@ -1,6 +1,6 @@
 .. index:: DFTTools
 
-.. module:: pytriqs.applications.dft
+.. module:: triqs_dft_tools
 
 .. _dft:
 

doc/install.rst

@@ -83,7 +83,7 @@ Finally, you will have to change the calls to :program:`python_with_DMFT` to
 
  
 Version compatibility 
---------------------- 
+---------------------
  
 Be careful that the version of the TRIQS library and of the dft tools must be 
 compatible (more information on the :ref:`TRIQS website <triqslibs:welcome>`. 
@@ -97,3 +97,18 @@ Checkout the version of the code that you want, for instance::
      $ git co 1.2 
  
 Then follow the steps 2 to 5 described above to compile the code. 
+
+Custom CMake options
+--------------------
+
+Functionality of ``dft_tools`` can be tweaked using extra compile-time options passed to CMake::
+
+    cmake -DOPTION1=value1 -DOPTION2=value2 ... ../cthyb.src
+
++---------------------------------------------------------------+-----------------------------------------------+
+| Options                                                       | Syntax                                        |
++===============================================================+===============================================+
+| Disable testing (not recommended)                             | -DBuild_Tests=OFF                             |
++---------------------------------------------------------------+-----------------------------------------------+
+| Build the documentation locally                               | -DBuild_Documentation=ON                      |
++---------------------------------------------------------------+-----------------------------------------------+

fortran/dmftproj/CMakeLists.txt

@@ -6,7 +6,8 @@ set(SOURCES modules.f dmftproj.f readcomline.f set_ang_trans.f setsym.f
 
 # The main target and what to link with...
 add_executable(dmftproj ${SOURCES})
-target_link_libraries(dmftproj ${TRIQS_LIBRARY_LAPACK})
+find_package(LAPACK)
+target_link_libraries(dmftproj ${LAPACK_LIBRARIES})
 
 # where to install
 install (TARGETS dmftproj DESTINATION bin)

python/CMakeLists.txt

@@ -1,16 +1,19 @@
 # where will the python end up in triqs?
-set(python_destination pytriqs/applications/dft)
+set(PYTHON_LIB_DEST ${CPP2PY_PYTHON_LIB_DEST_ROOT}/triqs_dft_tools)
 
 # site_customize for build
-set(package_name "pytriqs.applications")
-configure_file(${CMAKE_SOURCE_DIR}/cmake/sitecustomize.py ${CMAKE_CURRENT_BINARY_DIR}/sitecustomize.py @ONLY)
+set(package_name "triqs_dft_tools")
 
-# make a local pytriqs copy
-triqs_prepare_local_pytriqs(${python_destination})
-
-# VASP converter
-add_subdirectory(converters/plovasp)
+# Create a temporary copy of the python modules so that we can run before installation with the test
+FILE(GLOB PYTHON_SOURCES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.py )
+foreach(f ${PYTHON_SOURCES})
+ configure_file(${f} ${f} COPYONLY)
+endforeach()
 
 # add version file
-configure_file(version.py.in version.py)
-install(FILES ${CMAKE_CURRENT_BINARY_DIR}/version.py DESTINATION ${TRIQS_PYTHON_LIB_DEST_ROOT}/${python_destination})
+configure_file(version.py.in version.py @ONLY)
+
+# install files
+install(FILES ${PYTHON_SOURCES} ${CMAKE_CURRENT_BINARY_DIR}/version.py DESTINATION ${PYTHON_LIB_DEST})
+
+add_subdirectory(converters)

python/block_structure.py

@@ -1,13 +1,14 @@
 import copy
 import numpy as np
-from pytriqs.gf.local import GfImFreq, BlockGf
+from pytriqs.gf import GfImFreq, BlockGf
 from ast import literal_eval
+import pytriqs.utility.mpi as mpi
 from warnings import warn
 
 class BlockStructure(object):
     """ Contains information about the Green function structure.
 
-    This class contains information about the structure of the solver 
+    This class contains information about the structure of the solver
     and sumk Green functions and the mapping between them.
 
     Parameters
@@ -33,19 +34,21 @@ class BlockStructure(object):
     solver_to_sumk_block : list of dict
         solver_to_sumk_block[ish][from_block] = to_block
 
-        maps from the solver block to the sumk block 
+        maps from the solver block to the sumk block
         for *inequivalent* correlated shell ish
     """
     def __init__(self,gf_struct_sumk=None,
                       gf_struct_solver=None,
                       solver_to_sumk=None,
                       sumk_to_solver=None,
-                      solver_to_sumk_block=None):
+                      solver_to_sumk_block=None,
+                      deg_shells=None):
         self.gf_struct_sumk = gf_struct_sumk
         self.gf_struct_solver = gf_struct_solver
         self.solver_to_sumk = solver_to_sumk
         self.sumk_to_solver = sumk_to_solver
         self.solver_to_sumk_block = solver_to_sumk_block
+        self.deg_shells = deg_shells
 
     @classmethod
     def full_structure(cls,gf_struct,corr_to_inequiv):
@@ -99,20 +102,21 @@ class BlockStructure(object):
                 gf_struct_sumk = gs_sumk_all,
                 solver_to_sumk = copy.deepcopy(solver_to_sumk),
                 sumk_to_solver = solver_to_sumk,
-                solver_to_sumk_block = s2sblock)
+                solver_to_sumk_block = s2sblock,
+                deg_shells = [[] for ish in range(len(gf_struct))])
 
     def pick_gf_struct_solver(self,new_gf_struct):
-        """ Pick selected orbitals within blocks. 
+        """ Pick selected orbitals within blocks.
 
         This throws away parts of the Green's function that (for some
-        reason - be sure that you know what you're doing) shouldn't be 
+        reason - be sure that you know what you're doing) shouldn't be
         included in the calculation.
 
         To drop an entire block, just don't include it.
         To drop a certain index within a block, just don't include it.
 
-        If it was before: 
-        
+        If it was before:
+
         [{'up':[0,1],'down':[0,1],'left':[0,1]}]
 
         to choose the 0th index of the up block and the 1st index of
@@ -130,11 +134,11 @@ class BlockStructure(object):
         Parameters
         ----------
         new_gf_struct : list of dict
-            formatted the same as gf_struct_solver: 
+            formatted the same as gf_struct_solver:
 
             new_gf_struct[ish][block]=list of indices in that block.
         """
-        
+
         for ish in range(len(self.gf_struct_solver)):
             gf_struct = new_gf_struct[ish]
 
@@ -154,24 +158,24 @@ class BlockStructure(object):
                     new_ind = gf_struct[blk].index(ind)
                     self.sumk_to_solver[ish][k]=(blk,new_ind)
                 else:
-                    self.sumk_to_solver[ish][k]=(None,None) 
+                    self.sumk_to_solver[ish][k]=(None,None)
             # reindexing gf_struct so that it starts with 0
             for k in gf_struct:
                 gf_struct[k]=range(len(gf_struct[k]))
             self.gf_struct_solver[ish]=gf_struct
 
     def pick_gf_struct_sumk(self,new_gf_struct):
-        """ Pick selected orbitals within blocks. 
+        """ Pick selected orbitals within blocks.
 
         This throws away parts of the Green's function that (for some
-        reason - be sure that you know what you're doing) shouldn't be 
+        reason - be sure that you know what you're doing) shouldn't be
         included in the calculation.
 
         To drop an entire block, just don't include it.
         To drop a certain index within a block, just don't include it.
 
-        If it was before: 
-        
+        If it was before:
+
         [{'up':[0,1],'down':[0,1],'left':[0,1]}]
 
         to choose the 0th index of the up block and the 1st index of
@@ -188,11 +192,11 @@ class BlockStructure(object):
         Parameters
         ----------
         new_gf_struct : list of dict
-            formatted the same as gf_struct_solver: 
+            formatted the same as gf_struct_solver:
 
             new_gf_struct[ish][block]=list of indices in that block.
 
-            However, the indices are not according to the solver Gf 
+            However, the indices are not according to the solver Gf
             but the sumk Gf.
         """
 
@@ -218,7 +222,7 @@ class BlockStructure(object):
         Parameters
         ----------
         mapping : list of dict
-            the dict consists of elements 
+            the dict consists of elements
             (from_block,from_index) : (to_block,to_index)
             that maps from one structure to the other
         """
@@ -254,7 +258,7 @@ class BlockStructure(object):
     def create_gf(self,ish=0,gf_function=GfImFreq,**kwargs):
         """ Create a zero BlockGf having the gf_struct_solver structure.
 
-        When using GfImFreq as gf_function, typically you have to 
+        When using GfImFreq as gf_function, typically you have to
         supply beta as keyword argument.
 
         Parameters
@@ -284,7 +288,7 @@ class BlockStructure(object):
         .. warning::
 
             Elements that are zero in the new structure due to
-            the new block structure will be just ignored, thus 
+            the new block structure will be just ignored, thus
             approximated to zero.
 
         Parameters
@@ -292,15 +296,24 @@ class BlockStructure(object):
         G : BlockGf
             the Gf that should be converted
         G_struct : GfStructure
-            the structure ofthat G 
+            the structure of that G
         ish : int
             shell index
-        show_warnings : bool
-            whether to show warnings when elements of the Green's 
+        show_warnings : bool or float
+            whether to show warnings when elements of the Green's
             function get thrown away
+            if float, set the threshold for the magnitude of an element
+            about to be thrown away to trigger a warning
+            (default: 1.e-10)
         **kwargs :
             options passed to the constructor for the new Gf
         """
+
+        warning_threshold = 1.e-10
+        if isinstance(show_warnings, float):
+            warning_threshold = show_warnings
+            show_warnings = True
+
         G_new = self.create_gf(ish=ish,**kwargs)
         for block in G_struct.gf_struct_solver[ish].keys():
             for i1 in G_struct.gf_struct_solver[ish][block]:
@@ -311,22 +324,24 @@ class BlockStructure(object):
                     i2_sol = self.sumk_to_solver[ish][i2_sumk]
                     if i1_sol[0] is None or i2_sol[0] is None:
                         if show_warnings:
-                            warn(('Element {},{} of block {} of G is not present '+
-                                'in the new structure').format(i1,i2,block))
+                            if mpi.is_master_node():
+                                warn(('Element {},{} of block {} of G is not present '+
+                                    'in the new structure').format(i1,i2,block))
                         continue
                     if i1_sol[0]!=i2_sol[0]:
-                        if show_warnings:
-                            warn(('Element {},{} of block {} of G is approximated '+
-                                'to zero to match the new structure.').format(
-                                    i1,i2,block))
+                        if show_warnings and np.max(np.abs(G[block][i1,i2].data)) > warning_threshold:
+                            if mpi.is_master_node():
+                                warn(('Element {},{} of block {} of G is approximated '+
+                                    'to zero to match the new structure. Max abs value: {}').format(
+                                        i1,i2,block,np.max(np.abs(G[block][i1,i2].data))))
                         continue
                     G_new[i1_sol[0]][i1_sol[1],i2_sol[1]] = \
                             G[block][i1,i2]
         return G_new
 
     def approximate_as_diagonal(self):
-        """ Create a structure for a GF with zero off-diagonal elements. 
-        
+        """ Create a structure for a GF with zero off-diagonal elements.
+
         .. warning::
 
             In general, this will throw away non-zero elements of the
@@ -351,7 +366,8 @@ class BlockStructure(object):
     def __eq__(self,other):
         def compare(one,two):
             if type(one)!=type(two):
-                return False
+                if not (isinstance(one, (bool, np.bool_)) and isinstance(two, (bool, np.bool_))):
+                    return False
             if one is None and two is None:
                 return True
             if isinstance(one,list) or isinstance(one,tuple):
@@ -361,10 +377,10 @@ class BlockStructure(object):
                     if not compare(x,y):
                         return False
                 return True
-            elif isinstance(one,int): 
-                return one==two
-            elif isinstance(one,str):
+            elif isinstance(one,(int,bool, str, np.bool_)):
                 return one==two
+            elif isinstance(one,np.ndarray):
+                return np.all(one==two)
             elif isinstance(one,dict):
                 if set(one.keys()) != set(two.keys()):
                     return False
@@ -375,8 +391,9 @@ class BlockStructure(object):
             warn('Cannot compare {}'.format(type(one)))
             return False
 
-        for prop in [ "gf_struct_sumk", "gf_struct_solver", 
-                "solver_to_sumk", "sumk_to_solver", "solver_to_sumk_block"]:
+        for prop in [ "gf_struct_sumk", "gf_struct_solver",
+                "solver_to_sumk", "sumk_to_solver", "solver_to_sumk_block",
+                "deg_shells"]:
             if not compare(getattr(self,prop),getattr(other,prop)):
                 return False
         return True
@@ -388,8 +405,8 @@ class BlockStructure(object):
         """ Reduce to dict for HDF5 export."""
 
         ret = {}
-        for element in [ "gf_struct_sumk", "gf_struct_solver", 
-                         "solver_to_sumk_block"]:
+        for element in [ "gf_struct_sumk", "gf_struct_solver",
+                         "solver_to_sumk_block","deg_shells"]:
             ret[element] = getattr(self,element)
 
         def construct_mapping(mapping):
@@ -436,6 +453,18 @@ class BlockStructure(object):
                 keys = sorted(element[ish].keys(),key=keyfun)
                 for k in keys:
                     s+='  '+str(k)+str(element[ish][k])+'\n'
+        s += "deg_shells\n"
+        for ish in range(len(self.deg_shells)):
+            s+=' shell '+str(ish)+'\n'
+            for l in range(len(self.deg_shells[ish])):
+                s+='  equivalent group '+str(l)+'\n'
+                if isinstance(self.deg_shells[ish][l],dict):
+                    for key, val in self.deg_shells[ish][l].iteritems():
+                        s+='   '+key+('*' if val[1] else '')+':\n'
+                        s+='    '+str(val[0]).replace('\n','\n    ')+'\n'
+                else:
+                    for key in self.deg_shells[ish][l]:
+                        s+='   '+key+'\n'
         return s
 
 from pytriqs.archive.hdf_archive_schemes import register_class

python/converters/CMakeLists.txt

@@ -0,0 +1,10 @@
+# Create a temporary copy of the python modules so that we can run before installation with the test
+FILE(GLOB PYTHON_SOURCES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.py)
+foreach(f ${PYTHON_SOURCES})
+ configure_file(${f} ${f} COPYONLY)
+endforeach()
+
+# install files
+install(FILES ${PYTHON_SOURCES} DESTINATION ${PYTHON_LIB_DEST}/converters)
+
+add_subdirectory(plovasp)

python/converters/converter_tools.py

@@ -19,10 +19,8 @@
 # TRIQS. If not, see <http://www.gnu.org/licenses/>.
 #
 ##########################################################################
-from pytriqs.cmake_info import hdf5_command_path
 import pytriqs.utility.mpi as mpi
 
-
 class ConverterTools:
 
     def __init__(self):
@@ -73,7 +71,7 @@ class ConverterTools:
         mpi.report("Repacking the file %s" % self.hdf_file)
 
         retcode = subprocess.call(
-            [hdf5_command_path + "/h5repack", "-i%s" % self.hdf_file, "-otemphgfrt.h5"])
+            ["h5repack", "-i%s" % self.hdf_file, "-otemphgfrt.h5"])
         if retcode != 0:
             mpi.report("h5repack failed!")
         else:

python/converters/plovasp/CMakeLists.txt

@@ -1,11 +1,19 @@
-set(python_destination pytriqs/applications/dft/converters/plovasp)
+# === Build and install atm module 
+add_cpp2py_module(atm)
+target_link_libraries(atm atm_c triqs)
+target_compile_options(atm PRIVATE -std=c++17)
+target_include_directories(atm PRIVATE ${CMAKE_SOURCE_DIR}/c++)
 
-include_directories(${CMAKE_CURRENT_SOURCE_DIR} ${TRIQS_INCLUDE_ALL})
-triqs_python_extension(atm ${python_destination})
-target_link_libraries(atm atm_c ${TRIQS_LIBRARY_ALL})
-triqs_set_rpath_for_target(atm)
+install(TARGETS atm DESTINATION ${PYTHON_LIB_DEST}/converters/plovasp)
+
+# === Copy Python files to current build directory and register for install
+set(PYTHON_SOURCES __init__.py  converter.py elstruct.py  inpconf.py  plotools.py  proj_group.py  proj_shell.py  sc_dmft.py  vaspio.py)
+foreach(f ${PYTHON_SOURCES})
+ configure_file(${f} ${f} COPYONLY)
+endforeach()
+
+# install files
+install(FILES ${PYTHON_SOURCES} DESTINATION ${PYTHON_LIB_DEST}/converters/plovasp)
 
 # This we need in order for tests to work
-add_custom_command(TARGET atm POST_BUILD COMMAND ln -fs ${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_PROJECT_NAME}/atm.so ${CMAKE_BINARY_DIR}/python/dft/converters/plovasp)
-
-install (TARGETS atm DESTINATION ${TRIQS_PYTHON_LIB_DEST_ROOT}/${python_destination})
+#add_custom_command(TARGET atm POST_BUILD COMMAND ln -fs ${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_PROJECT_NAME}/atm.so ${CMAKE_BINARY_DIR}/python/dft/converters/plovasp)

python/converters/plovasp/atm_desc.py

@@ -1,6 +1,6 @@
 # Generated automatically using the command :
 # c++2py.py -m atm -o atm --moduledoc "Analytical Tetrahedron Method for DOS" ../../../c++/plovasp/atm/dos_tetra3d.hpp
-from wrap_generator import *
+from cpp2py.wrap_generator import *
 
 # The module
 module = module_(full_name = "atm", doc = "Analytical Tetrahedron Method for calculating DOS", app_name = "atm")
@@ -8,11 +8,11 @@ module = module_(full_name = "atm", doc = "Analytical Tetrahedron Method for cal
 # All the triqs C++/Python modules
 
 # Add here all includes beyond what is automatically included by the triqs modules
-module.add_include("../../../c++/plovasp/atm/dos_tetra3d.hpp")
+module.add_include("plovasp/atm/dos_tetra3d.hpp")
 
 # Add here anything to add in the C++ code at the start, e.g. namespace using
 module.add_preamble("""
-#include <triqs/python_tools/converters/arrays.hpp>
+#include <triqs/cpp2py_converters/arrays.hpp>
 """)
 
 module.add_function ("array_view<double,2> dos_tetra_weights_3d (array_view<double,1> eigk, double en, array_view<long,2> itt)", doc = """DOS of a band by analytical tetrahedron method\n\n   Returns corner weights for all tetrahedra for a given band and real energy.""")

python/converters/plovasp/examples/ce/hf_solver.py

@@ -21,9 +21,9 @@
 ################################################################################
 
 from types import *
-#from pytriqs.applications.dft.U_matrix import *
+#from triqs_dft_tools.U_matrix import *
 from U_matrix import *
-from pytriqs.gf.local import *
+from pytriqs.gf import *
 #from hubbard_I import gf_hi_fullu, sigma_atomic_fullu
 import pytriqs.utility.mpi as mpi
 from itertools import izip

python/converters/plovasp/examples/ce/test_ham_hf.py

@@ -1,6 +1,6 @@
-#from pytriqs.applications.dft.sumk_dft import *
+#from triqs_dft_tools.sumk_dft import *
 from sumk_dft import *
-#from pytriqs.applications.dft.converters.wien2k_converter import *
+#from triqs_dft_tools.converters.wien2k_converter import *
 from converters.vasp_converter import *
 #from pytriqs.applications.impurity_solvers.hubbard_I.hubbard_solver import Solver
 from hf_solver import Solver

python/converters/plovasp/examples/srvo3/conv_example.py

@@ -1,6 +1,6 @@
 
 import numpy as np
-from pytriqs.gf.local import *
+from pytriqs.gf import *
 #from sumk_dft import SumkDFT
 from sumk_dft_tools import SumkDFTTools
 from converters.vasp_converter import VaspConverter

python/converters/wien2k_converter.py

@@ -502,7 +502,7 @@ class Wien2kConverter(ConverterTools):
         - symmetries from :file:`case.outputs`,
 
         if those Wien2k files are present and stores the data in the hdf5 archive.
-        This function is automatically called by :meth:`convert_dft_input <pytriqs.applications.dft.converters.wien2k_converter.Wien2kConverter.convert_dft_input>`. 
+        This function is automatically called by :meth:`convert_dft_input <triqs_dft_tools.converters.wien2k_converter.Wien2kConverter.convert_dft_input>`. 
 
         """
 

python/sumk_dft.py

@@ -23,14 +23,17 @@
 from types import *
 import numpy
 import pytriqs.utility.dichotomy as dichotomy
-from pytriqs.gf.local import *
+from pytriqs.gf import *
 import pytriqs.utility.mpi as mpi
+from pytriqs.utility.comparison_tests import assert_arrays_are_close
 from pytriqs.archive import *
 from symmetry import *
 from block_structure import BlockStructure
 from sets import Set
 from itertools import product
 from warnings import warn
+from scipy import compress
+from scipy.optimize import minimize
 
 
 class SumkDFT(object):
@@ -521,7 +524,7 @@ class SumkDFT(object):
             set_up_G_latt = True
         else:                                       # Check that existing GF is consistent
             G_latt = getattr(self, "G_latt_" + iw_or_w)
-            GFsize = [gf.N1 for bname, gf in G_latt]
+            GFsize = [gf.target_shape[0] for bname, gf in G_latt]
             unchangedsize = all([self.n_orbitals[ik, ntoi[spn[isp]]] == GFsize[
                                 isp] for isp in range(self.n_spin_blocks[self.SO])])
             if not unchangedsize:
@@ -593,13 +596,13 @@ class SumkDFT(object):
             Sigma_imp) == self.n_inequiv_shells, "put_Sigma: give exactly one Sigma for each inequivalent corr. shell!"
 
         # init self.Sigma_imp_(i)w:
-        if all(type(gf) == GfImFreq for bname, gf in Sigma_imp[0]):
+        if all( (isinstance(gf, Gf) and isinstance (gf.mesh, MeshImFreq)) for bname, gf in Sigma_imp[0]):
             # Imaginary frequency Sigma:
             self.Sigma_imp_iw = [BlockGf(name_block_generator=[(block, GfImFreq(indices=inner, mesh=Sigma_imp[0].mesh))
                                                                for block, inner in self.gf_struct_sumk[icrsh]], make_copies=False)
                                  for icrsh in range(self.n_corr_shells)]
             SK_Sigma_imp = self.Sigma_imp_iw
-        elif all(type(gf) == GfReFreq for bname, gf in Sigma_imp[0]):
+        elif all( isinstance(gf, Gf) and isinstance (gf.mesh, MeshReFreq) for bname, gf in Sigma_imp[0]):
             # Real frequency Sigma:
             self.Sigma_imp_w = [BlockGf(name_block_generator=[(block, GfReFreq(indices=inner, mesh=Sigma_imp[0].mesh))
                                                               for block, inner in self.gf_struct_sumk[icrsh]], make_copies=False)
@@ -848,6 +851,412 @@ class SumkDFT(object):
                             elif (ind1 < 0) and (ind2 < 0):
                                 self.deg_shells[ish].append([block1, block2])
 
+    def _get_hermitian_quantity_from_gf(self, G):
+        """ Convert G to a Hermitian quantity
+
+        For G(tau) and G(iw), G(tau) is returned.
+        For G(t) and G(w), the spectral function is returned.
+
+        Parameters
+        ----------
+        G : list of BlockGf of GfImFreq, GfImTime, GfReFreq or GfReTime
+            the input Green's function
+
+        Returns
+        -------
+        gf : list of BlockGf of GfImTime or GfReFreq
+            the output G(tau) or A(w)
+        """
+        # make a GfImTime from the supplied GfImFreq
+        if all(isinstance(g_sh._first(), GfImFreq) for g_sh in G):
+            gf = [BlockGf(name_block_generator = [(name, GfImTime(beta=block.mesh.beta,
+                indices=block.indices,n_points=len(block.mesh)+1)) for name, block in g_sh],
+                make_copies=False) for g_sh in G]
+            for ish in range(len(gf)):
+                for name, g in gf[ish]:
+                    g.set_from_inverse_fourier(G[ish][name])
+        # keep a GfImTime from the supplied GfImTime
+        elif all(isinstance(g_sh._first(), GfImTime) for g_sh in G):
+            gf = G
+        # make a spectral function from the supplied GfReFreq
+        elif all(isinstance(g_sh._first(), GfReFreq) for g_sh in G):
+            gf = [g_sh.copy() for g_sh in G]
+            for ish in range(len(gf)):
+                for name, g in gf[ish]:
+                    g << 1.0j*(g-g.conjugate().transpose())/2.0/numpy.pi
+        elif all(isinstance(g_sh._first(), GfReTime) for g_sh in G):
+            def get_delta_from_mesh(mesh):
+                w0 = None
+                for w in mesh:
+                    if w0 is None:
+                        w0 = w
+                    else:
+                        return w-w0
+            gf = [BlockGf(name_block_generator = [(name, GfReFreq(
+                window=(-numpy.pi*(len(block.mesh)-1) / (len(block.mesh)*get_delta_from_mesh(block.mesh)), 
+                numpy.pi*(len(block.mesh)-1) / (len(block.mesh)*get_delta_from_mesh(block.mesh))),
+                n_points=len(block.mesh), indices=block.indices)) for name, block in g_sh], make_copies=False)
+                for g_sh in G]
+
+            for ish in range(len(gf)):
+                for name, g in gf[ish]:
+                    g.set_from_fourier(G[ish][name])
+                    g << 1.0j*(g-g.conjugate().transpose())/2.0/numpy.pi
+        else:
+            raise Exception("G must be a list of BlockGf of either GfImFreq, GfImTime, GfReFreq or GfReTime")
+        return gf
+
+
+
+    def analyse_block_structure_from_gf(self, G, threshold=1.e-5, include_shells=None, analyse_deg_shells = True):
+        r"""
+        Determines the block structure of local Green's functions by analysing
+        the structure of the corresponding non-interacting Green's function.
+        The resulting block structures for correlated shells are
+        stored in the :class:`SumkDFT.block_structure <dft.block_structure.BlockStructure>`
+        attribute.
+
+        This is a safer alternative to analyse_block_structure, because
+        the full non-interacting Green's function is taken into account
+        and not just the density matrix and Hloc.
+
+        Parameters
+        ----------
+        G : list of BlockGf of GfImFreq, GfImTime, GfReFreq or GfReTime
+            the non-interacting Green's function for each inequivalent correlated shell
+        threshold : real, optional
+                    If the difference between matrix elements is below threshold,
+                    they are considered to be equal.
+        include_shells : list of integers, optional
+                         List of correlated shells to be analysed.
+                         If include_shells is not provided all correlated shells will be analysed.
+        analyse_deg_shells : bool
+                             Whether to call the analyse_deg_shells function
+                             after having finished the block structure analysis
+
+        Returns
+        -------
+        G : list of BlockGf of GfImFreq or GfImTime
+            the Green's function transformed into the new block structure
+        """
+
+        gf = self._get_hermitian_quantity_from_gf(G)
+
+        # initialize the variables
+        self.gf_struct_solver = [{} for ish in range(self.n_inequiv_shells)]
+        self.sumk_to_solver = [{} for ish in range(self.n_inequiv_shells)]
+        self.solver_to_sumk = [{} for ish in range(self.n_inequiv_shells)]
+        self.solver_to_sumk_block = [{}
+                                     for ish in range(self.n_inequiv_shells)]
+
+        # the maximum value of each matrix element of each block and shell
+        max_gf = [{name:numpy.max(numpy.abs(g.data),0) for name, g in gf[ish]} for ish in range(self.n_inequiv_shells)]
+
+        if include_shells is None:
+            # include all shells
+            include_shells = range(self.n_inequiv_shells)
+
+        for ish in include_shells:
+            for sp in self.spin_block_names[self.corr_shells[self.inequiv_to_corr[ish]]['SO']]:
+                n_orb = self.corr_shells[self.inequiv_to_corr[ish]]['dim']
+
+                # gives an index list of entries larger that threshold
+                maxgf_bool = (abs(max_gf[ish][sp]) > threshold)
+
+                # Determine off-diagonal entries in upper triangular part of the
+                # Green's function
+                offdiag = Set([])
+                for i in range(n_orb):
+                    for j in range(i + 1, n_orb):
+                        if maxgf_bool[i, j]:
+                            offdiag.add((i, j))
+
+                # Determine the number of non-hybridising blocks in the gf
+                blocs = [[i] for i in range(n_orb)]
+                while len(offdiag) != 0:
+                    pair = offdiag.pop()
+                    for b1, b2 in product(blocs, blocs):
+                        if (pair[0] in b1) and (pair[1] in b2):
+                            if blocs.index(b1) != blocs.index(b2):     # In separate blocks?
+                                # Merge two blocks
+                                b1.extend(blocs.pop(blocs.index(b2)))
+                                break                                  # Move on to next pair in offdiag
+
+                # Set the gf_struct for the solver accordingly
+                num_blocs = len(blocs)
+                for i in range(num_blocs):
+                    blocs[i].sort()
+                    self.gf_struct_solver[ish].update(
+                        [('%s_%s' % (sp, i), range(len(blocs[i])))])
+
+                # Construct sumk_to_solver taking (sumk_block, sumk_index) --> (solver_block, solver_inner)
+                # and solver_to_sumk taking (solver_block, solver_inner) -->
+                # (sumk_block, sumk_index)
+                for i in range(num_blocs):
+                    for j in range(len(blocs[i])):
+                        block_sumk = sp
+                        inner_sumk = blocs[i][j]
+                        block_solv = '%s_%s' % (sp, i)
+                        inner_solv = j
+                        self.sumk_to_solver[ish][(block_sumk, inner_sumk)] = (
+                            block_solv, inner_solv)
+                        self.solver_to_sumk[ish][(block_solv, inner_solv)] = (
+                            block_sumk, inner_sumk)
+                        self.solver_to_sumk_block[ish][block_solv] = block_sumk
+
+        # transform G to the new structure
+        full_structure = BlockStructure.full_structure(
+            [{sp:range(self.corr_shells[self.inequiv_to_corr[ish]]['dim'])
+                for sp in self.spin_block_names[self.corr_shells[self.inequiv_to_corr[ish]]['SO']]}
+                for ish in range(self.n_inequiv_shells)],None)
+        G_transformed = [
+            self.block_structure.convert_gf(G[ish],
+                full_structure, ish, mesh=G[ish].mesh.copy(), show_warnings=threshold,
+                gf_function=type(G[ish]._first()))
+            for ish in range(self.n_inequiv_shells)]
+
+        if analyse_deg_shells:
+            self.analyse_deg_shells(G_transformed, threshold, include_shells)
+        return G_transformed
+
+    def analyse_deg_shells(self, G, threshold=1.e-5, include_shells=None):
+        r"""
+        Determines the degenerate shells of local Green's functions by analysing
+        the structure of the corresponding non-interacting Green's function.
+        The results are stored in the
+        :class:`SumkDFT.block_structure <dft.block_structure.BlockStructure>`
+        attribute.
+
+        Due to the implementation and numerics, the maximum difference between
+        two matrix elements that are detected as equal can be a bit higher
+        (e.g. a factor of two) than the actual threshold.
+
+        Parameters
+        ----------
+        G : list of BlockGf of GfImFreq or GfImTime
+            the non-interacting Green's function for each inequivalent correlated shell
+        threshold : real, optional
+                    If the difference between matrix elements is below threshold,
+                    they are considered to be equal.
+        include_shells : list of integers, optional
+                         List of correlated shells to be analysed.
+                         If include_shells is not provided all correlated shells will be analysed.
+        """
+
+        # initialize
+        self.deg_shells = [[] for ish in range(self.n_inequiv_shells)]
+
+        # helper function
+        def null(A, eps=1e-15):
+            """ Calculate the null-space of matrix A """
+            u, s, vh = numpy.linalg.svd(A)
+            null_mask = (s <= eps)
+            null_space = compress(null_mask, vh, axis=0)
+            return null_space.conjugate().transpose()
+
+        gf = self._get_hermitian_quantity_from_gf(G)
+
+        if include_shells is None:
+            # include all shells
+            include_shells = range(self.n_inequiv_shells)
+
+        # We consider two blocks equal, if their Green's functions obey
+        # maybe_conjugate1( v1^dagger G1 v1 ) = maybe_conjugate2( v2^dagger G2 v2 )
+        # where maybe_conjugate is a function that conjugates the Green's
+        # function if the flag 'conjugate' is set and the v are unitary
+        # matrices
+        #
+        # for each pair of blocks, we check whether there is a transformation
+        # maybe_conjugate( T G1 T^dagger ) = G2
+        # where our goal is to find T
+        # we just try whether there is such a T with and without conjugation
+        for ish in include_shells:
+            for block1 in self.gf_struct_solver[ish].iterkeys():
+                for block2 in self.gf_struct_solver[ish].iterkeys():
+                    if block1==block2: continue
+
+                    # check if the blocks are already present in the deg_shells
+                    ind1 = -1
+                    ind2 = -2
+                    for n, ind in enumerate(self.deg_shells[ish]):
+                        if block1 in ind:
+                            ind1 = n
+                            v1 = ind[block1]
+                        if block2 in ind:
+                            ind2 = n
+                            v2 = ind[block2]
+
+                    # if both are already present, go to the next pair of blocks
+                    if ind1 >= 0 and ind2 >= 0:
+                        continue
+
+                    gf1 = gf[ish][block1]
+                    gf2 = gf[ish][block2]
+
+                    # the two blocks have to have the same shape
+                    if gf1.target_shape != gf2.target_shape:
+                        continue
+
+                    # Instead of directly comparing the two blocks, we
+                    # compare its eigenvalues. As G(tau) is Hermitian,
+                    # they are real and the eigenvector matrix is unitary.
+                    # Thus, if the eigenvalues are equal we can transform
+                    # one block to make it equal to the other (at least
+                    # for tau=0).
+
+                    e1 = numpy.linalg.eigvalsh(gf1.data[0])
+                    e2 = numpy.linalg.eigvalsh(gf2.data[0])
+                    if numpy.any(abs(e1-e2) > threshold): continue
+
+                    for conjugate in [False,True]:
+                        if conjugate:
+                            gf2 = gf2.conjugate()
+
+                        # we want T gf1 T^dagger = gf2
+                        # while for a given tau, T could be calculated
+                        # by diagonalizing gf1 and gf2, this does not
+                        # work for all taus simultaneously because of
+                        # numerical imprecisions
+
+                        # rather, we rewrite the equation to
+                        # T gf1 = gf2 T
+                        # which is the Sylvester equation.
+                        # For that equation, one can use the Kronecker
+                        # product to get a linear problem, which consists
+                        # of finding the null space of M vec T = 0.
+
+                        M = numpy.kron(numpy.eye(*gf1.target_shape),gf2.data[0])-numpy.kron(gf1.data[0].transpose(),numpy.eye(*gf1.target_shape))
+                        N = null(M, threshold)
+
+                        # now we get the intersection of the null spaces
+                        # of all values of tau
+                        for i in range(1,len(gf1.data)):
+                            M = numpy.kron(numpy.eye(*gf1.target_shape),gf2.data[i])-numpy.kron(gf1.data[i].transpose(),numpy.eye(*gf1.target_shape))
+                            # transform M into current null space
+                            M = numpy.dot(M, N)
+                            N = numpy.dot(N, null(M, threshold))
+                            if numpy.size(N) == 0:
+                                break
+
+                        # no intersection of the null spaces -> no symmetry
+                        if numpy.size(N) == 0: continue
+
+                        # reshape N: it then has the indices matrix, matrix, number of basis vectors of the null space
+                        N = N.reshape(gf1.target_shape[0], gf1.target_shape[1], -1).transpose([1, 0, 2])
+
+                        """
+                        any matrix in the null space can now be constructed as
+                        M = 0
+                        for i in range(N.shape[-1]):
+                            M += y[i]*N[:,:,i]
+                        with coefficients (complex numbers) y[i].
+
+                        We want to get a set of coefficients y so that M is unitary.
+                        Unitary means M M^dagger = 1.
+                        Thus,
+                            sum  y[i] N[:,:,i] y[j].conjugate() N[:,:,j].conjugate().transpose() = eye.
+                        The object N[:,:,i] N[:,:,j] is a four-index object which we call Z.
+                        """
+                        Z = numpy.einsum('aci,bcj->abij', N, N.conjugate())
+
+                        """
+                        function chi2
+                        This function takes a real parameter vector y and reinterprets it as complex.
+                        Then, it calculates the chi2 of
+                            sum  y[i] N[:,:,i] y[j].conjugate() N[:,:,j].conjugate().transpose() - eye.
+                        """
+                        def chi2(y):
+                            # reinterpret y as complex number
+                            y = y.view(numpy.complex_)
+                            ret = 0.0
+                            for a in range(Z.shape[0]):
+                                for b in range(Z.shape[1]):
+                                    ret += numpy.abs(numpy.dot(y, numpy.dot(Z[a, b], y.conjugate()))
+                                                  - (1.0 if a == b else 0.0))**2
+                            return ret
+
+                        # use the minimization routine from scipy
+                        res = minimize(chi2, numpy.ones(2 * N.shape[-1]))
+
+                        # if the minimization fails, there is probably no symmetry
+                        if not res.success: continue
+                        # check if the minimization returned zero within the tolerance
+                        if res.fun > threshold: continue
+
+                        # reinterpret the solution as a complex number
+                        y = res.x.view(numpy.complex_)
+
+                        # reconstruct the T matrix
+                        T = numpy.zeros(N.shape[:-1], dtype=numpy.complex_)
+                        for i in range(len(y)):
+                            T += N[:, :, i] * y[i]
+
+                        # transform gf1 using T
+                        G_transformed = gf1.copy()
+                        G_transformed.from_L_G_R(T, gf1, T.conjugate().transpose())
+
+                        # it does not make sense to check the tails for an
+                        # absolute error because it will usually not hold;
+                        # we could just check the relative error
+                        # (here, we ignore it, reasoning that if the data
+                        # is the same, the tails have to coincide as well)
+                        try:
+                            assert_arrays_are_close(G_transformed.data, gf2.data, threshold)
+                        except (RuntimeError, AssertionError):
+                            # the symmetry does not hold
+                            continue
+
+                        # Now that we have found a valid T, we have to
+                        # rewrite it to match the convention that
+                        # C1(v1^dagger G1 v1) = C2(v2^dagger G2 v2),
+                        # where C conjugates if the flag is True
+
+                        # For each group of degenerate shells, the list
+                        # SK.deg_shells[ish] contains a dict. The keys
+                        # of the dict are the block names, the values
+                        # are tuples. The first entry of the tuple is
+                        # the transformation matrix v, the second entry
+                        # is the conjugation flag
+
+                        # the second block is already present
+                        # set v1 and C1 so that they are compatible with
+                        # C(T gf1 T^dagger) = gf2
+                        # and with
+                        # C1(v1^dagger G1 v1) = C2(v2^dagger G2 v2)
+                        if (ind1 < 0) and (ind2 >= 0):
+                            if conjugate:
+                                self.deg_shells[ish][ind2][block1] = numpy.dot(T.conjugate().transpose(), v2[0].conjugate()), not v2[1]
+                            else:
+                                self.deg_shells[ish][ind2][block1] = numpy.dot(T.conjugate().transpose(), v2[0]), v2[1]
+                        # the first block is already present
+                        # set v2 and C2 so that they are compatible with
+                        # C(T gf1 T^dagger) = gf2
+                        # and with
+                        # C1(v1^dagger G1 v1) = C2(v2^dagger G2 v2)
+                        elif (ind1 >= 0) and (ind2 < 0):
+                            if conjugate:
+                                self.deg_shells[ish][ind1][block2] = numpy.dot(T.conjugate(), v1[0].conjugate()), not v1[1]
+                            else:
+                                self.deg_shells[ish][ind1][block2] = numpy.dot(T, v1[0]), v1[1]
+                        # the blocks are not already present
+                        # we arbitrarily choose v1=eye and C1=False and
+                        # set v2 and C2 so that they are compatible with
+                        # C(T gf1 T^dagger) = gf2
+                        # and with
+                        # C1(v1^dagger G1 v1) = C2(v2^dagger G2 v2)
+                        elif (ind1 < 0) and (ind2 < 0):
+                            d = dict()
+                            d[block1] = numpy.eye(*gf1.target_shape), False
+                            if conjugate:
+                                d[block2] = T.conjugate(), True
+                            else:
+                                d[block2] = T, False
+                            self.deg_shells[ish].append(d)
+
+                        # a block was found, break out of the loop
+                        break
+
+
     def density_matrix(self, method='using_gf', beta=40.0):
         """Calculate density matrices in one of two ways.
 
@@ -1212,20 +1621,52 @@ class SumkDFT(object):
         Parameters
         ----------
         gf_to_symm : gf_struct_solver like
-                     Input GF.
+                     Input and output GF (i.e., it gets overwritten)
         orb : int
               Index of an inequivalent shell.
 
         """
 
+        # when reading block_structures written with older versions from
+        # an h5 file, self.deg_shells might be None
+        if self.deg_shells is None: return
+
         for degsh in self.deg_shells[orb]:
-            ss = gf_to_symm[degsh[0]].copy()
-            ss.zero()
+            # ss will hold the averaged orbitals in the basis where the
+            # blocks are all equal
+            # i.e. maybe_conjugate(v^dagger gf v)
+            ss = None
             n_deg = len(degsh)
-            for bl in degsh:
-                ss += gf_to_symm[bl] / (1.0 * n_deg)
-            for bl in degsh:
-                gf_to_symm[bl] << ss
+            for key in degsh:
+                if ss is None:
+                    ss = gf_to_symm[key].copy()
+                    ss.zero()
+                    helper = ss.copy()
+                # get the transformation matrix
+                if isinstance(degsh, dict):
+                    v, C = degsh[key]
+                else:
+                    # for backward compatibility, allow degsh to be a list
+                    v = numpy.eye(*ss.target_shape)
+                    C = False
+                # the helper is in the basis where the blocks are all equal
+                helper.from_L_G_R(v.conjugate().transpose(), gf_to_symm[key], v)
+                if C:
+                    helper << helper.transpose()
+                # average over all shells
+                ss += helper / (1.0 * n_deg)
+            # now put back the averaged gf to all shells
+            for key in degsh:
+                if isinstance(degsh, dict):
+                    v, C = degsh[key]
+                else:
+                    # for backward compatibility, allow degsh to be a list
+                    v = numpy.eye(*ss.target_shape)
+                    C = False
+                if C:
+                    gf_to_symm[key].from_L_G_R(v, ss.transpose(), v.conjugate().transpose())
+                else:
+                    gf_to_symm[key].from_L_G_R(v, ss, v.conjugate().transpose())
 
     def total_density(self, mu=None, iw_or_w="iw", with_Sigma=True, with_dc=True, broadening=None):
         r"""
@@ -1610,3 +2051,9 @@ class SumkDFT(object):
     def __set_solver_to_sumk_block(self,value):
         self.block_structure.solver_to_sumk_block = value
     solver_to_sumk_block = property(__get_solver_to_sumk_block,__set_solver_to_sumk_block)
+
+    def __get_deg_shells(self):
+        return self.block_structure.deg_shells
+    def __set_deg_shells(self,value):
+        self.block_structure.deg_shells = value
+    deg_shells = property(__get_deg_shells,__set_deg_shells)

python/sumk_dft_tools.py

@@ -21,13 +21,16 @@
 import sys
 from types import *
 import numpy
-from pytriqs.gf.local import *
+from pytriqs.gf import *
 import pytriqs.utility.mpi as mpi
 from symmetry import *
 from sumk_dft import SumkDFT
 from scipy.integrate import *
 from scipy.interpolate import *
 
+if not hasattr(numpy, 'full'):
+    # polyfill full for older numpy:
+    numpy.full = lambda a, f: numpy.zeros(a) + f
 
 class SumkDFTTools(SumkDFT):
     """
@@ -767,8 +770,8 @@ class SumkDFTTools(SumkDFT):
                     self.Sigma_imp_w[icrsh] = BlockGf(
                         name_list=spn, block_list=glist(), make_copies=False)
                     for i, g in self.Sigma_imp_w[icrsh]:
-                        for iL in g.indices:
-                            for iR in g.indices:
+                        for iL in g.indices[0]:
+                            for iR in g.indices[0]:
                                 for iom in xrange(n_om):
                                     g.data[iom, int(iL), int(iR)] = Sigma_save[
                                         i].data[ioffset + iom, int(iL), int(iR)]

python/symmetry.py

@@ -23,7 +23,7 @@
 import copy
 import numpy
 from types import *
-from pytriqs.gf.local import *
+from pytriqs.gf import *
 from pytriqs.archive import *
 import pytriqs.utility.mpi as mpi
 

python/trans_basis.py

@@ -1,6 +1,6 @@
-from pytriqs.applications.dft.sumk_dft import *
-from pytriqs.applications.dft.converters import Wien2kConverter
-from pytriqs.gf.local import *
+from triqs_dft_tools.sumk_dft import *
+from triqs_dft_tools.converters import Wien2kConverter
+from pytriqs.gf import *
 from pytriqs.archive import *
 import pytriqs.utility.mpi as mpi
 import numpy

shells/plovasp.bash.in

@@ -1,4 +1,4 @@
 #!/bin/bash
 
-@CMAKE_INSTALL_PREFIX@/bin/pytriqs -m pytriqs.applications.dft.converters.plovasp.converter $@
+@CMAKE_INSTALL_PREFIX@/bin/pytriqs -m triqs_dft_tools.converters.plovasp.converter $@
 

shells/vasp_dmft.bash.in

@@ -83,5 +83,5 @@ stdbuf -o 0 $MPIRUN_CMD -np $NPROC "$VASP_DIR" &
 
 PYTRIQS=@CMAKE_INSTALL_PREFIX@/bin/pytriqs
 
-$MPIRUN_CMD -np $NPROC $PYTRIQS -m pytriqs.applications.dft.converters.plovasp.sc_dmft $(jobs -p) $NITER $DMFT_SCRIPT 'plo.cfg' || kill %1
+$MPIRUN_CMD -np $NPROC $PYTRIQS -m triqs_dft_tools.converters.plovasp.sc_dmft $(jobs -p) $NITER $DMFT_SCRIPT 'plo.cfg' || kill %1
 

test/CMakeLists.txt

@@ -1,20 +1,19 @@
-# load triqs helper to set up tests
-find_package(TriqsTest)
-
 # Copy h5 files to binary dir
 FILE(GLOB all_h5_files RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.h5)
 file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/${all_h5_files} DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
 # Copy other files
-FILE(COPY SrVO3.pmat SrVO3.struct SrVO3.outputs SrVO3.oubwin SrVO3.ctqmcout SrVO3.symqmc SrVO3.sympar SrVO3.parproj hk_convert_hamiltonian.hk LaVO3-Pnma_hr.dat LaVO3-Pnma.inp DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+FILE(COPY SrVO3.pmat SrVO3.struct SrVO3.outputs SrVO3.oubwin SrVO3.ctqmcout SrVO3.symqmc SrVO3.sympar SrVO3.parproj SrIrO3_rot.h5 hk_convert_hamiltonian.hk LaVO3-Pnma_hr.dat LaVO3-Pnma.inp DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+# List all tests
+set(all_tests wien2k_convert hk_convert w90_convert sumkdft_basic srvo3_Gloc srvo3_transp sigma_from_file blockstructure analyze_block_structure_from_gf analyze_block_structure_from_gf2)
+
+foreach(t ${all_tests})
+  add_test(NAME ${t} COMMAND python ${CMAKE_CURRENT_SOURCE_DIR}/${t}.py)
+endforeach()
+
+# Set the PythonPath : put the build dir first (in case there is an installed version). 
+set_property(TEST ${all_tests} PROPERTY ENVIRONMENT PYTHONPATH=${CMAKE_BINARY_DIR}/python:$ENV{PYTHONPATH} )
 
-triqs_add_python_test(wien2k_convert)
-triqs_add_python_test(hk_convert)
-triqs_add_python_test(w90_convert)
-triqs_add_python_test(sumkdft_basic)
-triqs_add_python_test(srvo3_Gloc)
-triqs_add_python_test(srvo3_transp)
-triqs_add_python_test(sigma_from_file)
-triqs_add_python_test(blockstructure)
 
 # VASP converter tests
 add_subdirectory(plovasp)

test/analyze_block_structure_from_gf.py

@@ -0,0 +1,232 @@
+from pytriqs.gf import *
+from sumk_dft import SumkDFT
+from scipy.linalg import expm
+import numpy as np
+from pytriqs.utility.comparison_tests import assert_gfs_are_close, assert_arrays_are_close, assert_block_gfs_are_close
+from pytriqs.archive import *
+import itertools
+
+# The full test checks all different possible combinations of conjugated
+# blocks. This takes a few minutes. For a quick test, just checking one
+# random value suffices.
+# (this parameter affects the second test)
+full_test = False
+
+#######################################################################
+# First test                                                          #
+# where we check the analyse_block_structure_from_gf function         #
+# for the SrIrO3_rot.h5 file                                          #
+#######################################################################
+
+beta = 40
+SK = SumkDFT(hdf_file = 'SrIrO3_rot.h5')
+Sigma = SK.block_structure.create_gf(beta=beta)
+SK.put_Sigma([Sigma])
+G = SK.extract_G_loc()
+
+# the original block structure
+block_structure1 = SK.block_structure.copy()
+
+G_new = SK.analyse_block_structure_from_gf(G)
+
+# the new block structure
+block_structure2 = SK.block_structure.copy()
+
+with HDFArchive('analyze_block_structure_from_gf.out.h5','w') as ar:
+    ar['bs1'] = block_structure1
+    ar['bs2'] = block_structure2
+
+# check whether the block structure is the same as in the reference
+with HDFArchive('analyze_block_structure_from_gf.out.h5','r') as ar,\
+     HDFArchive('analyze_block_structure_from_gf.ref.h5','r') as ar2:
+    assert ar['bs1'] == ar2['bs1'], 'bs1 not equal'
+    a1 = ar['bs2']
+    a2 = ar2['bs2']
+    assert a1==block_structure2, "writing/reading block structure incorrect"
+    # we set the deg_shells to None because the transformation matrices
+    # have a phase freedom and will, therefore, not be equal in general
+    a1.deg_shells = None
+    a2.deg_shells = None
+    assert a1==a2, 'bs2 not equal'
+
+# check if deg shells are correct
+assert len(SK.deg_shells[0])==1, "wrong number of equivalent groups"
+
+# check if the Green's functions that are found to be equal in the
+# routine are indeed equal
+for d in SK.deg_shells[0]:
+    assert len(d)==2, "wrong number of shells in equivalent group"
+    # the convention is that for every degenerate shell, the transformation
+    # matrix v and the conjugate bool is saved
+    # then,
+    # maybe_conjugate1( v1^dagger G1 v1 ) = maybe_conjugate2( v2^dagger G2 v2 )
+    # therefore, to test, we calculate
+    #   maybe_conjugate( v^dagger G v )
+    # for all degenerate shells and check that they are all equal
+    normalized_gfs = []
+    for key in d:
+        normalized_gf = G_new[0][key].copy()
+        normalized_gf.from_L_G_R(d[key][0].conjugate().transpose(), G_new[0][key], d[key][0])
+        if d[key][1]:
+            normalized_gf << normalized_gf.transpose()
+        normalized_gfs.append(normalized_gf)
+    for i in range(len(normalized_gfs)):
+        for j in range(i+1,len(normalized_gfs)):
+            assert_arrays_are_close(normalized_gfs[i].data, normalized_gfs[j].data, 1.e-5)
+            # the tails have to be compared using a relative error
+            for o in range(normalized_gfs[i].tail.order_min,normalized_gfs[i].tail.order_max+1):
+                if np.abs(normalized_gfs[i].tail[o][0,0]) < 1.e-10:
+                    continue
+                assert np.max(np.abs((normalized_gfs[i].tail[o]-normalized_gfs[j].tail[o])/(normalized_gfs[i].tail[o][0,0]))) < 1.e-5, \
+                        "tails are different"
+
+#######################################################################
+# Second test                                                         #
+# where a Green's function is constructed from a random model         #
+# and the analyse_block_structure_from_gf function is tested for that #
+# model                                                               #
+#######################################################################
+
+# helper function to get random Hermitian matrix
+def get_random_hermitian(dim):
+    herm = np.random.rand(dim,dim)+1.0j*np.random.rand(dim,dim)
+    herm = herm + herm.conjugate().transpose()
+    return herm
+
+# helper function to get random unitary matrix
+def get_random_transformation(dim):
+    herm = get_random_hermitian(dim)
+    T = expm(1.0j*herm)
+    return T
+
+# we will conjugate the Green's function blocks according to the entries
+# of conjugate_values
+# for each of the 5 blocks that will be constructed, there is an entry
+# True or False that says whether it will be conjugated
+if full_test:
+    # in the full test we check all combinations
+    conjugate_values = list(itertools.product([False, True], repeat=5))
+else:
+    # in the quick test we check a random combination
+    conjugate_values = [np.random.rand(5)>0.5]
+
+for conjugate in conjugate_values:
+    # construct a random block-diagonal Hloc
+    Hloc = np.zeros((10,10), dtype=np.complex_)
+    # the Hloc of the first three 2x2 blocks is equal
+    Hloc0 = get_random_hermitian(2)
+    Hloc[:2,:2] = Hloc0
+    Hloc[2:4,2:4] = Hloc0
+    Hloc[4:6,4:6] = Hloc0
+    # the Hloc of the last two 2x2 blocks is equal
+    Hloc1 = get_random_hermitian(2)
+    Hloc[6:8,6:8] = Hloc1
+    Hloc[8:,8:] = Hloc1
+    # construct the hybridization delta
+    # this is equal for all 2x2 blocks
+    V = get_random_hermitian(2) # the hopping elements from impurity to bath
+    b1 = np.random.rand() # the bath energy of the first bath level
+    b2 = np.random.rand() # the bath energy of the second bath level
+    delta = G[0]['ud'][:2,:2].copy()
+    delta[0,0] << (V[0,0]*V[0,0].conjugate()*inverse(Omega-b1)+V[0,1]*V[0,1].conjugate()*inverse(Omega-b2))/2.0
+    delta[0,1] << (V[0,0]*V[1,0].conjugate()*inverse(Omega-b1)+V[0,1]*V[1,1].conjugate()*inverse(Omega-b2))/2.0
+    delta[1,0] << (V[1,0]*V[0,0].conjugate()*inverse(Omega-b1)+V[1,1]*V[0,1].conjugate()*inverse(Omega-b2))/2.0
+    delta[1,1] << (V[1,0]*V[1,0].conjugate()*inverse(Omega-b1)+V[1,1]*V[1,1].conjugate()*inverse(Omega-b2))/2.0
+    # construct G
+    G[0].zero()
+    for i in range(0,10,2):
+        G[0]['ud'][i:i+2,i:i+2] << inverse(Omega-delta)
+    G[0]['ud'] << inverse(inverse(G[0]['ud']) - Hloc)
+
+    # for testing symm_deg_gf below, we need this
+    # we construct it so that for every group of degenerate blocks of G[0], the
+    # mean of the blocks of G_noisy is equal to G[0]
+    G_noisy = G[0].copy()
+    noise1 = np.random.randn(*delta.target_shape)
+    G_noisy['ud'][:2,:2].data[:,:,:] += noise1
+    G_noisy['ud'][2:4,2:4].data[:,:,:] -= noise1/2.0
+    G_noisy['ud'][4:6,4:6].data[:,:,:] -= noise1/2.0
+    noise2 = np.random.randn(*delta.target_shape)
+    G_noisy['ud'][6:8,6:8].data[:,:,:] += noise2
+    G_noisy['ud'][8:,8:].data[:,:,:] -= noise2
+
+    # for testing backward-compatibility in symm_deg_gf, we need the
+    # un-transformed Green's functions
+    G_pre_transform = G[0].copy()
+    G_noisy_pre_transform = G_noisy.copy()
+
+    # transform each block using a random transformation matrix
+    for i in range(0,10,2):
+        T = get_random_transformation(2)
+        G[0]['ud'][i:i+2,i:i+2].from_L_G_R(T, G[0]['ud'][i:i+2,i:i+2], T.conjugate().transpose())
+        G_noisy['ud'][i:i+2,i:i+2].from_L_G_R(T, G_noisy['ud'][i:i+2,i:i+2], T.conjugate().transpose())
+        # if that block shall be conjugated, go ahead and do it
+        if conjugate[i//2]:
+            G[0]['ud'][i:i+2,i:i+2] << G[0]['ud'][i:i+2,i:i+2].transpose()
+            G_noisy['ud'][i:i+2,i:i+2] << G_noisy['ud'][i:i+2,i:i+2].transpose()
+
+    # analyse the block structure
+    G_new = SK.analyse_block_structure_from_gf(G, 1.e-7)
+
+    # transform G_noisy etc. to the new block structure
+    G_noisy = SK.block_structure.convert_gf(G_noisy, block_structure1, beta = G_noisy.mesh.beta)
+    G_pre_transform = SK.block_structure.convert_gf(G_pre_transform, block_structure1, beta = G_noisy.mesh.beta)
+    G_noisy_pre_transform = SK.block_structure.convert_gf(G_noisy_pre_transform, block_structure1, beta = G_noisy.mesh.beta)
+
+    assert len(SK.deg_shells[0]) == 2, "wrong number of equivalent groups found"
+    assert sorted([len(d) for d in SK.deg_shells[0]]) == [2,3], "wrong number of members in the equivalent groups found"
+    for d in SK.deg_shells[0]:
+        if len(d)==2:
+            assert 'ud_3' in d, "shell ud_3 missing"
+            assert 'ud_4' in d, "shell ud_4 missing"
+        if len(d)==3:
+            assert 'ud_0' in d, "shell ud_0 missing"
+            assert 'ud_1' in d, "shell ud_1 missing"
+            assert 'ud_2' in d, "shell ud_2 missing"
+
+        # the convention is that for every degenerate shell, the transformation
+        # matrix v and the conjugate bool is saved
+        # then,
+        # maybe_conjugate1( v1^dagger G1 v1 ) = maybe_conjugate2( v2^dagger G2 v2 )
+        # therefore, to test, we calculate
+        #   maybe_conjugate( v^dagger G v )
+        # for all degenerate shells and check that they are all equal
+        normalized_gfs = []
+        for key in d:
+            normalized_gf = G_new[0][key].copy()
+            normalized_gf.from_L_G_R(d[key][0].conjugate().transpose(), G_new[0][key], d[key][0])
+            if d[key][1]:
+                normalized_gf << normalized_gf.transpose()
+            normalized_gfs.append(normalized_gf)
+        for i in range(len(normalized_gfs)):
+            for j in range(i+1,len(normalized_gfs)):
+                # here, we use a threshold that is 1 order of magnitude less strict
+                # because of numerics
+                assert_gfs_are_close(normalized_gfs[i], normalized_gfs[j], 1.e-6)
+
+    # now we check symm_deg_gf
+    # symmetrizing the GF has is has to leave it unchanged
+    G_new_symm = G_new[0].copy()
+    SK.symm_deg_gf(G_new_symm, 0)
+    assert_block_gfs_are_close(G_new[0], G_new_symm, 1.e-6)
+
+    # symmetrizing the noisy GF, which was carefully constructed,
+    # has to give the same result as G_new[0]
+    SK.symm_deg_gf(G_noisy, 0)
+    assert_block_gfs_are_close(G_new[0], G_noisy, 1.e-6)
+
+    # check backward compatibility of symm_deg_gf
+    # first, construct the old format of the deg shells
+    for ish in range(len(SK.deg_shells)):
+        for gr in range(len(SK.deg_shells[ish])):
+            SK.deg_shells[ish][gr] = SK.deg_shells[ish][gr].keys()
+
+    # symmetrizing the GF as is has to leave it unchanged
+    G_new_symm << G_pre_transform
+    SK.symm_deg_gf(G_new_symm, 0)
+    assert_block_gfs_are_close(G_new_symm, G_pre_transform, 1.e-6)
+
+    # symmetrizing the noisy GF pre transform, which was carefully constructed,
+    # has to give the same result as G_pre_transform
+    SK.symm_deg_gf(G_noisy_pre_transform, 0)
+    assert_block_gfs_are_close(G_noisy_pre_transform, G_pre_transform, 1.e-6)

test/analyze_block_structure_from_gf2.py

@@ -0,0 +1,115 @@
+from pytriqs.gf import *
+from sumk_dft import SumkDFT
+import numpy as np
+from pytriqs.utility.comparison_tests import assert_block_gfs_are_close
+
+# here we test the SK.analyze_block_structure_from_gf function
+# with GfReFreq, GfReTime
+
+
+# helper function to get random Hermitian matrix
+def get_random_hermitian(dim):
+    herm = np.random.rand(dim,dim)+1.0j*np.random.rand(dim,dim)
+    herm = herm + herm.conjugate().transpose()
+    return herm
+
+# helper function to get random unitary matrix
+def get_random_transformation(dim):
+    herm = get_random_hermitian(dim)
+    T = expm(1.0j*herm)
+    return T
+
+# construct a random block-diagonal Hloc
+Hloc = np.zeros((10,10), dtype=np.complex_)
+# the Hloc of the first three 2x2 blocks is equal
+Hloc0 = get_random_hermitian(2)
+Hloc[:2,:2] = Hloc0
+Hloc[2:4,2:4] = Hloc0
+Hloc[4:6,4:6] = Hloc0
+# the Hloc of the last two 2x2 blocks is equal
+Hloc1 = get_random_hermitian(2)
+Hloc[6:8,6:8] = Hloc1
+Hloc[8:,8:] = Hloc1
+# construct the hybridization delta
+# this is equal for all 2x2 blocks
+V = get_random_hermitian(2) # the hopping elements from impurity to bath
+b1 = np.random.rand() # the bath energy of the first bath level
+b2 = np.random.rand() # the bath energy of the second bath level
+delta = GfReFreq(window=(-5,5), indices=range(2), n_points=1001)
+delta[0,0] << (V[0,0]*V[0,0].conjugate()*inverse(Omega-b1)+V[0,1]*V[0,1].conjugate()*inverse(Omega-b2+0.02j))/2.0
+delta[0,1] << (V[0,0]*V[1,0].conjugate()*inverse(Omega-b1)+V[0,1]*V[1,1].conjugate()*inverse(Omega-b2+0.02j))/2.0
+delta[1,0] << (V[1,0]*V[0,0].conjugate()*inverse(Omega-b1)+V[1,1]*V[0,1].conjugate()*inverse(Omega-b2+0.02j))/2.0
+delta[1,1] << (V[1,0]*V[1,0].conjugate()*inverse(Omega-b1)+V[1,1]*V[1,1].conjugate()*inverse(Omega-b2+0.02j))/2.0
+# construct G
+G = BlockGf(name_block_generator=[('ud',GfReFreq(window=(-5,5), indices=range(10), n_points=1001))], make_copies=False)
+for i in range(0,10,2):
+    G['ud'][i:i+2,i:i+2] << inverse(Omega-delta+0.02j)
+G['ud'] << inverse(inverse(G['ud']) - Hloc)
+
+
+SK = SumkDFT(hdf_file = 'SrIrO3_rot.h5', use_dft_blocks=False)
+G_new = SK.analyse_block_structure_from_gf([G])
+G_new_symm = G_new[0].copy()
+SK.symm_deg_gf(G_new_symm, 0)
+assert_block_gfs_are_close(G_new[0], G_new_symm)
+
+
+assert SK.gf_struct_sumk == [[('ud', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9])], [('ud', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9])]],\
+    "wrong gf_struct_sumk"
+for i in range(5):
+    assert 'ud_{}'.format(i) in SK.gf_struct_solver[0], "missing block"
+    assert SK.gf_struct_solver[0]['ud_{}'.format(i)] == range(2), "wrong block size"
+for i in range(10):
+    assert SK.sumk_to_solver[0]['ud',i] == ('ud_{}'.format(i/2), i%2), "wrong mapping"
+
+assert len(SK.deg_shells[0]) == 2, "wrong number of equivalent groups found"
+assert sorted([len(d) for d in SK.deg_shells[0]]) == [2,3], "wrong number of members in the equivalent groups found"
+for d in SK.deg_shells[0]:
+    if len(d)==2:
+        assert 'ud_3' in d, "shell ud_3 missing"
+        assert 'ud_4' in d, "shell ud_4 missing"
+    if len(d)==3:
+        assert 'ud_0' in d, "shell ud_0 missing"
+        assert 'ud_1' in d, "shell ud_1 missing"
+        assert 'ud_2' in d, "shell ud_2 missing"
+
+
+
+def get_delta_from_mesh(mesh):
+    w0 = None
+    for w in mesh:
+        if w0 is None:
+            w0 = w
+        else:
+            return w-w0
+
+Gt = BlockGf(name_block_generator = [(name,
+            GfReTime(window=(-np.pi*(len(block.mesh)-1) / (len(block.mesh)*get_delta_from_mesh(block.mesh)), np.pi*(len(block.mesh)-1) / (len(block.mesh)*get_delta_from_mesh(block.mesh))),
+                n_points=len(block.mesh),
+                indices=block.indices)) for name, block in G], make_copies=False)
+
+Gt['ud'].set_from_inverse_fourier(G['ud'])
+
+G_new = SK.analyse_block_structure_from_gf([Gt])
+G_new_symm = G_new[0].copy()
+SK.symm_deg_gf(G_new_symm, 0)
+assert_block_gfs_are_close(G_new[0], G_new_symm)
+
+assert SK.gf_struct_sumk == [[('ud', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9])], [('ud', [0, 1, 2, 3, 4, 5, 6, 7, 8, 9])]],\
+    "wrong gf_struct_sumk"
+for i in range(5):
+    assert 'ud_{}'.format(i) in SK.gf_struct_solver[0], "missing block"
+    assert SK.gf_struct_solver[0]['ud_{}'.format(i)] == range(2), "wrong block size"
+for i in range(10):
+    assert SK.sumk_to_solver[0]['ud',i] == ('ud_{}'.format(i/2), i%2), "wrong mapping"
+
+assert len(SK.deg_shells[0]) == 2, "wrong number of equivalent groups found"
+assert sorted([len(d) for d in SK.deg_shells[0]]) == [2,3], "wrong number of members in the equivalent groups found"
+for d in SK.deg_shells[0]:
+    if len(d)==2:
+        assert 'ud_3' in d, "shell ud_3 missing"
+        assert 'ud_4' in d, "shell ud_4 missing"
+    if len(d)==3:
+        assert 'ud_0' in d, "shell ud_0 missing"
+        assert 'ud_1' in d, "shell ud_1 missing"
+        assert 'ud_2' in d, "shell ud_2 missing"

test/blockstructure.py

@@ -1,8 +1,8 @@
-from pytriqs.applications.dft.sumk_dft import *
+from sumk_dft import *
 from pytriqs.utility.h5diff import h5diff
-from pytriqs.gf.local import *
+from pytriqs.gf import *
 from pytriqs.utility.comparison_tests import assert_block_gfs_are_close
-from pytriqs.applications.dft import BlockStructure
+from block_structure import BlockStructure
 
 SK = SumkDFT('blockstructure.in.h5',use_dft_blocks=True)
 
@@ -21,7 +21,8 @@ sk_pick1 = BlockStructure(gf_struct_sumk = SK.gf_struct_sumk,
                           gf_struct_solver = SK.gf_struct_solver,
                           solver_to_sumk = SK.solver_to_sumk,
                           sumk_to_solver = SK.sumk_to_solver,
-                          solver_to_sumk_block = SK.solver_to_sumk_block)
+                          solver_to_sumk_block = SK.solver_to_sumk_block,
+                          deg_shells = SK.deg_shells)
 assert sk_pick1 == pick1, 'constructing block structure from SumkDFT properties failed'
 
 # check pick_gf_struct_sumk

test/hk_convert.py

@@ -21,11 +21,12 @@
 ################################################################################
 
 
-from pytriqs.applications.dft.converters import *
 from pytriqs.archive import *
 from pytriqs.utility.h5diff import h5diff
 import pytriqs.utility.mpi as mpi
 
+from converters import *
+
 Converter = HkConverter(filename='hk_convert_hamiltonian.hk',hdf_filename='hk_convert.out.h5')
 
 Converter.convert_dft_input()

test/plovasp/CMakeLists.txt

@@ -1,5 +1,5 @@
 # load triqs helper to set up tests
-set(TestSuites
+set(all_tests
     inpconf
 #    plocar_io
     plotools
@@ -8,10 +8,11 @@ set(TestSuites
     vaspio
     atm)
     
-FILE(COPY ${TestSuites} DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+FILE(COPY ${all_tests} DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
 FILE(COPY run_suite.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
 
-foreach(test_suite ${TestSuites})
-    add_test(${test_suite}
-      ${PythonBuildExecutable} run_suite.py ${test_suite})
-endforeach(test_suite ${TestSuites})
+foreach(t ${all_tests})
+  add_test(NAME ${t} COMMAND python run_suite.py ${t})
+endforeach()
+
+set_property(TEST ${all_tests} PROPERTY ENVIRONMENT PYTHONPATH=${CMAKE_BINARY_DIR}/python:$ENV{PYTHONPATH} )

test/plovasp/atm/test_atm.py

@@ -2,7 +2,7 @@
 import os
 
 import numpy as np
-from pytriqs.applications.dft.converters.plovasp.atm import dos_tetra_weights_3d
+from converters.plovasp.atm import dos_tetra_weights_3d
 import mytest
 
 ################################################################################

test/plovasp/inpconf/test_general.py

@@ -7,7 +7,7 @@ _rpath = os.path.dirname(rpath.__file__) + '/'
 
 import arraytest
 import numpy as np
-from pytriqs.applications.dft.converters.plovasp.inpconf import ConfigParameters
+from converters.plovasp.inpconf import ConfigParameters
 
 ################################################################################
 #

test/plovasp/inpconf/test_groups.py

@@ -7,7 +7,7 @@ _rpath = os.path.dirname(rpath.__file__) + '/'
 
 import arraytest
 import numpy as np
-from pytriqs.applications.dft.converters.plovasp.inpconf import ConfigParameters
+from converters.plovasp.inpconf import ConfigParameters
 
 ################################################################################
 #

test/plovasp/inpconf/test_input.py

@@ -7,7 +7,7 @@ _rpath = os.path.dirname(rpath.__file__) + '/'
 
 import arraytest
 import numpy as np
-from pytriqs.applications.dft.converters.plovasp.inpconf import ConfigParameters
+from converters.plovasp.inpconf import ConfigParameters
 
 ################################################################################
 #

test/plovasp/inpconf/test_parameter_set.py

@@ -7,7 +7,7 @@ _rpath = os.path.dirname(rpath.__file__) + '/'
 
 import arraytest
 import numpy as np
-from pytriqs.applications.dft.converters.plovasp.inpconf import ConfigParameters
+from converters.plovasp.inpconf import ConfigParameters
 
 ################################################################################
 #

test/plovasp/inpconf/test_shells.py

@@ -7,7 +7,7 @@ _rpath = os.path.dirname(rpath.__file__) + '/'
 
 import arraytest
 import numpy as np
-from pytriqs.applications.dft.converters.plovasp.inpconf import ConfigParameters
+from converters.plovasp.inpconf import ConfigParameters
 
 ################################################################################
 #

test/plovasp/inpconf/test_special_parsers.py

@@ -7,7 +7,7 @@ _rpath = os.path.dirname(rpath.__file__) + '/'
 
 import arraytest
 import numpy as np
-from pytriqs.applications.dft.converters.plovasp.inpconf import ConfigParameters
+from converters.plovasp.inpconf import ConfigParameters
 
 ################################################################################
 #

test/plovasp/plotools/test_consistency.py

@@ -1,8 +1,8 @@
 
-import pytriqs.applications.dft.converters.plovasp.vaspio
-from pytriqs.applications.dft.converters.plovasp.inpconf import ConfigParameters
-from pytriqs.applications.dft.converters.plovasp.plotools import check_data_consistency
-from pytriqs.applications.dft.converters.plovasp.elstruct import ElectronicStructure
+import converters.plovasp.vaspio
+from converters.plovasp.inpconf import ConfigParameters
+from converters.plovasp.plotools import check_data_consistency
+from converters.plovasp.elstruct import ElectronicStructure
 import mytest
 
 ################################################################################

test/plovasp/proj_group/test_block_map.py

@@ -4,9 +4,9 @@ import rpath
 _rpath = os.path.dirname(rpath.__file__) + '/'
 
 import numpy as np
-from pytriqs.applications.dft.converters.plovasp.inpconf import ConfigParameters
-from pytriqs.applications.dft.converters.plovasp.proj_shell import ProjectorShell
-from pytriqs.applications.dft.converters.plovasp.proj_group import ProjectorGroup
+from converters.plovasp.inpconf import ConfigParameters
+from converters.plovasp.proj_shell import ProjectorShell
+from converters.plovasp.proj_group import ProjectorGroup
 import mytest
 
 ################################################################################

test/plovasp/proj_group/test_one_site.py

@@ -4,11 +4,11 @@ import rpath
 _rpath = os.path.dirname(rpath.__file__) + '/'
 
 import numpy as np
-from pytriqs.applications.dft.converters.plovasp.vaspio import VaspData
-from pytriqs.applications.dft.converters.plovasp.elstruct import ElectronicStructure
-from pytriqs.applications.dft.converters.plovasp.inpconf import ConfigParameters
-from pytriqs.applications.dft.converters.plovasp.proj_shell import ProjectorShell
-from pytriqs.applications.dft.converters.plovasp.proj_group import ProjectorGroup
+from converters.plovasp.vaspio import VaspData
+from converters.plovasp.elstruct import ElectronicStructure
+from converters.plovasp.inpconf import ConfigParameters
+from converters.plovasp.proj_shell import ProjectorShell
+from converters.plovasp.proj_group import ProjectorGroup
 from pytriqs.archive import HDFArchive
 import mytest
 

test/plovasp/proj_group/test_select_bands.py

@@ -4,11 +4,11 @@ import rpath
 _rpath = os.path.dirname(rpath.__file__) + '/'
 
 import numpy as np
-from pytriqs.applications.dft.converters.plovasp.vaspio import VaspData
-from pytriqs.applications.dft.converters.plovasp.elstruct import ElectronicStructure
-from pytriqs.applications.dft.converters.plovasp.inpconf import ConfigParameters
-from pytriqs.applications.dft.converters.plovasp.proj_shell import ProjectorShell
-from pytriqs.applications.dft.converters.plovasp.proj_group import ProjectorGroup
+from converters.plovasp.vaspio import VaspData
+from converters.plovasp.elstruct import ElectronicStructure
+from converters.plovasp.inpconf import ConfigParameters
+from converters.plovasp.proj_shell import ProjectorShell
+from converters.plovasp.proj_group import ProjectorGroup
 import mytest
 
 ################################################################################

test/plovasp/proj_group/test_two_site.py

@@ -4,11 +4,11 @@ import rpath
 _rpath = os.path.dirname(rpath.__file__) + '/'
 
 import numpy as np
-from pytriqs.applications.dft.converters.plovasp.vaspio import VaspData
-from pytriqs.applications.dft.converters.plovasp.elstruct import ElectronicStructure
-from pytriqs.applications.dft.converters.plovasp.inpconf import ConfigParameters
-from pytriqs.applications.dft.converters.plovasp.proj_shell import ProjectorShell
-from pytriqs.applications.dft.converters.plovasp.proj_group import ProjectorGroup
+from converters.plovasp.vaspio import VaspData
+from converters.plovasp.elstruct import ElectronicStructure
+from converters.plovasp.inpconf import ConfigParameters
+from converters.plovasp.proj_shell import ProjectorShell
+from converters.plovasp.proj_group import ProjectorGroup
 from pytriqs.archive import HDFArchive
 import mytest
 

test/plovasp/proj_shell/test_projshells.py

@@ -4,11 +4,11 @@ import rpath
 _rpath = os.path.dirname(rpath.__file__) + '/'
 
 import numpy as np
-from pytriqs.applications.dft.converters.plovasp.vaspio import VaspData
-from pytriqs.applications.dft.converters.plovasp.elstruct import ElectronicStructure
-from pytriqs.applications.dft.converters.plovasp.inpconf import ConfigParameters
-from pytriqs.applications.dft.converters.plovasp.proj_shell import ProjectorShell
-from pytriqs.applications.dft.converters.plovasp.proj_group import ProjectorGroup
+from converters.plovasp.vaspio import VaspData
+from converters.plovasp.elstruct import ElectronicStructure
+from converters.plovasp.inpconf import ConfigParameters
+from converters.plovasp.proj_shell import ProjectorShell
+from converters.plovasp.proj_group import ProjectorGroup
 import mytest
 
 ################################################################################

test/plovasp/vaspio/test_doscar.py

@@ -7,7 +7,7 @@ _rpath = os.path.dirname(rpath.__file__) + '/'
 
 import mytest
 import numpy as np
-from pytriqs.applications.dft.converters.plovasp.vaspio import Doscar
+from converters.plovasp.vaspio import Doscar
 
 ################################################################################
 #

test/plovasp/vaspio/test_eigenval.py

@@ -7,7 +7,7 @@ _rpath = os.path.dirname(rpath.__file__) + '/'
 
 import mytest
 import numpy as np
-from pytriqs.applications.dft.converters.plovasp.vaspio import Eigenval
+from converters.plovasp.vaspio import Eigenval
 
 ################################################################################
 #

test/plovasp/vaspio/test_kpoints.py

@@ -7,7 +7,7 @@ _rpath = os.path.dirname(rpath.__file__) + '/'
 
 import mytest
 import numpy as np
-from pytriqs.applications.dft.converters.plovasp.vaspio import Kpoints
+from converters.plovasp.vaspio import Kpoints
 
 ################################################################################
 #

test/plovasp/vaspio/test_poscar.py

@@ -7,7 +7,7 @@ _rpath = os.path.dirname(rpath.__file__) + '/'
 
 import mytest
 import numpy as np
-from pytriqs.applications.dft.converters.plovasp.vaspio import Poscar
+from converters.plovasp.vaspio import Poscar
 
 ################################################################################
 #

test/sigma_from_file.py

@@ -20,9 +20,9 @@
 ################################################################################
 
 from pytriqs.archive import *
-from pytriqs.gf.local import *
-from pytriqs.gf.local.tools import *
-from pytriqs.applications.dft.sumk_dft_tools import *
+from pytriqs.gf import *
+from pytriqs.gf.tools import *
+from sumk_dft_tools import *
 from pytriqs.utility.comparison_tests import *
 import numpy as np
 

test/srvo3_Gloc.py

@@ -20,9 +20,9 @@
 ################################################################################
 
 from pytriqs.archive import *
-from pytriqs.gf.local import *
-from pytriqs.applications.dft.sumk_dft import *
-from pytriqs.applications.dft.converters.wien2k_converter import *
+from pytriqs.gf import *
+from sumk_dft import *
+from converters.wien2k_converter import *
 from pytriqs.operators.util import set_operator_structure
 from pytriqs.utility.comparison_tests import *
 from pytriqs.utility.h5diff import h5diff
@@ -40,8 +40,8 @@ orb_names = ['%s'%i for i in range(num_orbitals)]
 orb_hybridized = False
 
 gf_struct = set_operator_structure(spin_names,orb_names,orb_hybridized)
-glist = [ GfImFreq(indices=inner,beta=beta) for block,inner in gf_struct.iteritems()]
-Sigma_iw = BlockGf(name_list = gf_struct.keys(), block_list = glist, make_copies = False)
+glist = [ GfImFreq(indices=inner,beta=beta) for block,inner in gf_struct]
+Sigma_iw = BlockGf(name_list = [block for block,inner in gf_struct], block_list = glist, make_copies = False)
 
 SK.set_Sigma([Sigma_iw])
 Gloc = SK.extract_G_loc()

test/srvo3_transp.py

@@ -20,9 +20,9 @@
 ################################################################################
 
 from numpy import *
-from pytriqs.applications.dft.converters.wien2k_converter import *
-from pytriqs.applications.dft.sumk_dft import *
-from pytriqs.applications.dft.sumk_dft_tools import *
+from converters.wien2k_converter import *
+from sumk_dft import *
+from sumk_dft_tools import *
 from pytriqs.utility.comparison_tests import *
 from pytriqs.utility.h5diff import h5diff 
 

test/sumkdft_basic.py

@@ -21,7 +21,7 @@
 ################################################################################
 
 from pytriqs.archive import *
-from pytriqs.applications.dft.sumk_dft_tools import SumkDFTTools
+from sumk_dft_tools import SumkDFTTools
 import pytriqs.utility.mpi as mpi
 from pytriqs.utility.comparison_tests import *
 from pytriqs.utility.h5diff import h5diff 

test/w90_convert.py

@@ -21,7 +21,7 @@
 ################################################################################
 
 
-from pytriqs.applications.dft.converters import *
+from converters import *
 from pytriqs.archive import *
 from pytriqs.utility.h5diff import h5diff
 import pytriqs.utility.mpi as mpi

test/wien2k_convert.py

@@ -21,11 +21,12 @@
 ################################################################################
 
 from pytriqs.archive import *
-from pytriqs.applications.dft.converters import Wien2kConverter
 from pytriqs.utility.comparison_tests import *
 from pytriqs.utility.h5diff import h5diff 
 import pytriqs.utility.mpi as mpi
 
+from converters import Wien2kConverter
+
 Converter = Wien2kConverter(filename='SrVO3')
 Converter.hdf_file = 'wien2k_convert.out.h5'
 Converter.convert_dft_input()