Merge pull request #65 from issp-center-dev/release

Release v2.0.0

.travis.yml

@@ -6,6 +6,7 @@ services:
   - docker
 
 before_script:
+  - export ROOTDIR=`pwd`
   - docker-compose rm -f
   - docker-compose pull
   - docker-compose up --build -d
@@ -14,5 +15,8 @@ script:
   - docker exec dcore_container make test
 
 after_script:
+  - cd ${ROOTDIR}
+  - docker cp dcore_container:/home/testuser/opt/DCore/share/doc/dcore ${ROOTDIR}/dcore_doc
   - docker-compose stop
   - docker-compose rm -f
+  - /bin/bash -x ${ROOTDIR}/.travis_scripts/deploy_docs.sh

.travis_scripts/deploy_docs.sh

@@ -0,0 +1,63 @@
+# This is a pull request, finish.
+if [ "_$TRAVIS_PULL_REQUEST" != "_false" ] ;then
+  echo "This is a pull request, do nothing."
+  exit 0;
+fi
+# build doc if and only if master, develop, xxx-autodoc, and tag
+feature_branch=${TRAVIS_BRANCH%-autodoc}
+
+if [ "_$TRAVIS_BRANCH" == "_master" ]; then
+  echo "This is the master branch, deploy docs."
+elif [ "_$TRAVIS_BRANCH" == "_develop" ]; then
+  echo "This is the develop branch, deploy docs."
+elif [ "_${feature_branch}" != "_${TRAVIS_BRANCH}" ]; then
+  echo "This is an auto-documented branch, deploy docs."
+elif [ -n "$TRAVIS_TAG" ]; then
+  echo "This is a versioned tag, deploy docs."
+else
+  echo "Do nothing."
+  exit 0
+fi
+
+
+openssl aes-256-cbc -K $encrypted_0f0c7c69c924_key -iv $encrypted_0f0c7c69c924_iv -in ${ROOTDIR}/.travis_scripts/id_rsa.enc -out ~/.ssh/id_rsa -d
+
+chmod 600 ~/.ssh/id_rsa
+echo -e "Host github.com\n\tStrictHostKeyChecking no\n" >> ~/.ssh/config
+
+git clone [email protected]:${TRAVIS_REPO_SLUG} dcore-repo
+cd dcore-repo
+git checkout gh-pages
+if [ ${feature_branch} != ${TRAVIS_BRANCH} ]; then
+  mkdir -p $feature_branch
+  cp -r ${ROOTDIR}/dcore_doc/* $feature_branch
+  git add $feature_branch
+elif [ "_${TRAVIS_BRANCH}" == "_develop" ]; then
+  mkdir -p develop
+  cp -r ${ROOTDIR}/dcore_doc/* develop
+  git add develop
+elif [ "_${TRAVIS_BRANCH}" == "_master" ]; then
+  mkdir -p master
+  cp -r ${ROOTDIR}/dcore_doc/* master
+  git add master
+elif [ -n ${TRAVIS_TAG}]; then
+  mkdir -p ${TRAVIS_TAG}
+  cp -r ${ROOTDIR}/dcore_doc/* ${TRAVIS_TAG}
+  git add ${TRAVIS_TAG}
+else
+  echo "The deploy script failed to solve where to install documents. The script has some mistake."
+  echo "\$TRAVIS_BRANCH: $TRAVIS_BRANCH"
+  echo "\$TRAVIS_TAG: $TRAVIS_TAG"
+  echo "\$TRAVIS_PULL_REQUEST: $TRAVIS_PULL_REQUEST"
+  echo "\$feature_branch: $feature_branch"
+  exit 1
+fi
+
+git config --global user.email ""
+git config --global user.name "DCore"
+git commit -m "Update by TravisCI (\\#${TRAVIS_BUILD_NUMBER})"
+ST=$?
+if [ $ST == 0 ]; then
+  git push origin gh-pages:gh-pages --follow-tags > /dev/null 2>&1
+fi
+

CMakeLists.txt

@@ -49,6 +49,12 @@ if (BUILD_DCORE)
     set(DCORE_SITE_PACKAGES "${CMAKE_INSTALL_PREFIX}/lib/python2.7/site-packages")
     set(DCORE_DEP_PYTHONPATH "${DCORE_SITE_PACKAGES}:${TRIQS_SITE_PACKAGES}")
 
+    # BSE
+    if (BSE_PATH)
+        set(ENV{PYTHONPATH} ${BSE_PATH}/python:$ENV{PYTHONPATH})
+        set(DCORE_DEP_PYTHONPATH "${DCORE_DEP_PYTHONPATH}:${BSE_PATH}/python")
+    endif()
+
     add_subdirectory(python)
     add_subdirectory(shells)
     add_subdirectory(test)

Dockerfile

@@ -3,9 +3,14 @@ FROM shinaoka/triqs1.4_dmft_alps
 # Copy host directory
 COPY ./ $HOME/src/DCore
 
+RUN pip install sphinx wild-sphinx-theme
+# Workaround for a bug in docutils 0.15
+RUN pip install -U docutils==0.14
+
 WORKDIR $HOME/src/DCore
 RUN mkdir $HOME/build/DCore
 WORKDIR $HOME/build/DCore
 ENV CTEST_OUTPUT_ON_FAILURE=1
-RUN cmake -DCMAKE_VERBOSE_MAKEFILE=ON $HOME/src/DCore -DTRIQS_PATH=$HOME/opt/triqs -DCMAKE_INSTALL_PREFIX=$HOME/opt/DCore \
- && make -j 2 install
+RUN cmake -DCMAKE_VERBOSE_MAKEFILE=ON $HOME/src/DCore -DTRIQS_PATH=$HOME/opt/triqs -DCMAKE_INSTALL_PREFIX=$HOME/opt/DCore -DBUILD_DOC=ON \
+ && make -j 2 all && make -j 2 install
+RUN find .

README.md

@@ -1,7 +1,7 @@
 [![Build Status](https://travis-ci.org/issp-center-dev/DCore.svg?branch=master)](https://travis-ci.org/issp-center-dev/DCore)
 # DCore
 
-DCore is aimed at model calculations and ab-initio calculations by the dynamical mean-field theory (DMFT). This package consists of programs with text-based and hdf5-based interface. These programs enable users to perform DMFT calculations and analyze results without writing computer code. The current version is built on TRIQS Python libraries. We will add supports for impurity solvers based on ALPSCore libraries in future.
+DCore is aimed at model calculations and ab-initio calculations by the dynamical mean-field theory (DMFT). This package consists of programs with text-based and hdf5-based interface. These programs enable users to perform DMFT calculations and analyze results without writing computer code. ALPS and TRIQS impurity solvers are supported.
 
 ## Web page
 

doc/conf.py.in

@@ -13,8 +13,6 @@ extensions = ['sphinx.ext.autodoc',
               'sphinx.ext.todo',
               'sphinx.ext.viewcode',
               'sphinx.ext.autosummary',
-              #'numpydoc',
-              #'sphinxcontrib.spelling'
 ]
 
 source_suffix = '.rst'

doc/impuritysolvers/alpscore_ctseg/ctseg.rst

@@ -43,4 +43,5 @@ Please also refer to `the wiki page <https://github.com/ALPSCore/CT-HYB-SEGMENT/
 
 The DCore interface generates input files for ALPS/CT-HYB-SEGMENT into a working directory at work/imp_shell<ish>_ite<ite> (ish is the index of the shell and ite is the iteration).
 Then, ALPS/CT-HYB-SEGMENT is executed in the working directory, and numerical results are stored there.
-For example, the occupation number and the double occupancy are saved in the file 'observables.dat'.
+For example, the occupation number and the double occupancy are saved in the file 'observables.dat'.
+

doc/index.rst

@@ -22,8 +22,8 @@ The DCore package is published under the
 
 The following files are from the TRIQS (Toolbox for Research on Interacting Quantum Systems).
 
-- https://github.com/issp-center-dev/DCore/blob/develop_v2/python/impurity_solvers/triqs_hubbard_I_impl.py
-- https://github.com/issp-center-dev/DCore/tree/develop_v2/python/converters
+- https://github.com/issp-center-dev/DCore/blob/develop/python/impurity_solvers/triqs_hubbard_I_impl.py
+- https://github.com/issp-center-dev/DCore/tree/develop/python/converters
 
 We would like to express our sincere gratitude to TRIQS's developers.
 
@@ -36,7 +36,7 @@ Authors & Quotation
 
 - ver. 2.0
 
-  H. Shinaoka, J. Otsuki, K. Yoshimi, M. Kawamura, N. Takemori
+  H. Shinaoka, J. Otsuki, K. Yoshimi, M. Kawamura, N. Takemori, Y. Motoyama
 
 - ver. 1.1 (released on 2019/1/25)
 
@@ -48,15 +48,15 @@ Authors & Quotation
 This package depends on TRIQS libraries and applications.
 Please cite relevant papers for these original libraries.
 
-* `TRIQS libraries <https://triqs.ipht.cnrs.fr/1.x/about.html>`_
-* `TRIQS/DFTTools <https://triqs.ipht.cnrs.fr/1.4/applications/dft_tools/about.html>`_
+* `TRIQS libraries <https://triqs.github.io/triqs/2.1.x/about.html>`_
+* `TRIQS/DFTTools <https://triqs.github.io/dft_tools/2.1.x/about.html>`_
 
 In addition to the above two libraries, you may use impurity solvers listed below.
 
-* `TRIQS/cthyb <https://triqs.ipht.cnrs.fr/applications/cthyb/about.html>`_
-* `TRIQS/hubbardI <https://triqs.ipht.cnrs.fr/1.x/applications/hubbardI/about.html>`_
-* `ALPSCore/CT-HYB <https://github.com/ALPSCore/CT-HYB/wiki/Citation>`_
-* `ALPSCore/CT-HYB-SEGMENT <https://github.com/ALPSCore/CT-HYB-SEGMENT>`_
+* `TRIQS/cthyb <https://triqs.github.io/cthyb/2.1.x/about.html>`_
+* `TRIQS/hubbardI <https://triqs.github.io/triqs/1.4/applications/hubbardI/about.html>`_
+* `ALPS/CT-HYB <https://github.com/ALPSCore/CT-HYB/wiki/Citation>`_
+* `ALPS/CT-HYB-SEGMENT <https://github.com/ALPSCore/CT-HYB-SEGMENT>`_
 
 For some of them, they provide a BibTeX entry for each paper in the above cites.
 

doc/install.rst

@@ -34,54 +34,11 @@ You can download the source files in two ways.
 Prerequisites
 -------------
 
-#. You first need to install `TRIQS <https://triqs.github.io/triqs/>`_ library prior to installing all other programs,
-   since ``DCore`` is implemented using ``TRIQS``.
+#. `TRIQS <https://triqs.github.io/triqs/>`_ and `DFTTools/TRIQS <https://triqs.github.io/dft_tools/>`_.
+    They must be installed prior to installing all other programs.
+    If not, please install them following our instruction for :doc:`TRIQS 1.4.x <install_triqs14x>` or :doc:`TRIQS 2.1.x <install_triqs21x>`.
 
-   In the following, we suppose that ``TRIQS`` is installed in directory *path_to_triqs*.
-
-   .. note::
-
-     ``DCore`` supports ``TRIQS`` version **1.4.2** (the current version 2.0 is not supported).
-     Since the installation manual in the TRIQS official website is not compatible with **1.4.2**, we briefly describe below how to install it.
-
-     #. You can download the zip file or tar file from https://github.com/TRIQS/triqs/releases/tag/1.4.2.
-        The version **1.4.2** is not compatible with the latest version of h5py (>=2.8.0).
-        If you encounter any problem, you can clone the repository and checkout **1.4.x** branch, which contains bug fixes.
-        We suppose that source files are located in *path_to_triqs_src* directory.
-
-     #. In an empty directory, type the following command:
-
-        .. code-block:: bash
-
-          $ cmake -DCMAKE_INSTALL_PREFIX=path_to_triqs path_to_triqs_src
-          $ make
-          $ make test
-          $ make install
-
-#. You also need `DFTTools <https://triqs.github.io/dft_tools>`_, which runs on the ``TRIQS`` library.
-
-   .. note::
-
-     The current version in the GitHub repository is not compatible with ``TRIQS`` version 1.4.2.
-     You need to get old code that is compatible with 1.4.2.
-
-     #. Clone the repository, and checkout commit **d005756**.
-
-        .. code-block:: bash
-
-          $ git clone [email protected]:TRIQS/dft_tools.git
-          $ cd dft_tools
-          $ git checkout d005756
-
-     #. To build the source files, make an empty directory, move into it, and then type the following command:
-
-        .. code-block:: bash
-
-          $ cmake -DCMAKE_INSTALL_PREFIX=path_to_triqs\
-            -DTRIQS_PATH=path_to_triqs path_to_dft_tools
-          $ make
-          $ make test
-          $ make install
+    In the following, we suppose that ``TRIQS`` is installed in directory *path_to_triqs*.
 
 #. You will also need at least one impurity solver.
 
@@ -90,7 +47,7 @@ Prerequisites
    * :doc:`ALPS/CT-HYB<impuritysolvers/alpscore_cthyb/cthyb>`
    * :doc:`ALPS/CT-HYB-SEGMENT<impuritysolvers/alpscore_ctseg/ctseg>`
    * :doc:`TRIQS/cthyb<impuritysolvers/triqs_cthyb/cthyb>`
-   * :doc:`Hubbard-I solver<impuritysolvers/triqs_hubbard_one/hubbard_one>`
+   * :doc:`Hubbard-I solver<impuritysolvers/triqs_hubbard_one/hubbard_one>` (not available for TRIQS 2.1.x)
 
    See :doc:`impuritysolvers` for a complete list of supported impurity solvers and their user manuals.
 
@@ -135,12 +92,18 @@ Installation steps
 
      $ make
 
-#. We recommend that you run the tests to check if the compiling is properly finished. Type
+#. We recommend to run the tests to check if DCore is built correctly. Type
 
    ::
 
      $ make test
 
+   If your system MPI wrapper is not "mpirun", please provide the name of the correct one to DCore through cmake by using the flag "-DMPIEXEC".
+   The default value is "mpirun -np #" (# is replaced by the number of processors).
+   For instance, if your wrapper is "mpijob" and you do not need to specify the number of processors explicitly, please use -DMPIEXEC=mpijob.
+   Note that it is not allowed to run MPI programs interactively on some system.
+   In this case, please run tests as a job.
+
    The test results look like
 
    ::

doc/reference/input.rst

@@ -19,7 +19,7 @@ The following table shows which blocks are used by each program.
     [system]         ,     , Yes, Yes, Yes
     [impurity_solver],     , Yes,    , Yes
     [control]        ,     , Yes
-    [tool]           ,     ,    ,    , Yes
+    [tool]           ,     ,    , Yes, Yes
     [mpi]            ,     , Yes,    , Yes
 
 For example, we can see that ``dcore_pre`` needs to be re-executed only when [model] block is changed.

doc/reference/programs.rst

@@ -156,7 +156,7 @@ The computed spectral function can be drawn by
 Using this gnuplot script, you can also see the original (DFT) band structure as follows if either
 *seedname*\_band.dat (Wannier90 output) or dir-wan/dat.iband (RESPACK output) exists.
 
-.. image:: ../tutorial/srvo3_qe/akw_srvo3.png
+.. image:: ../tutorial/srvo3/akw_srvo3.png
    :width: 500
    :align: center
 

doc/support/faqs.rst

@@ -16,7 +16,7 @@ Can **DCore** compute the double occupancy?
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 It depends on impurity solvers.
-For example, ALPSCore/CT-HYB-SEGMENT supports it, but other CT-QMC codes do not at present.
+For example, ALPS/CT-HYB-SEGMENT supports it, but other CT-QMC codes do not at present.
 
 In general, capability of computing **local** physical quantities totally depends on impurity solvers.
 See the documentation of each solver for which local quantities can be computed.
@@ -122,13 +122,13 @@ The argument of ``--ext`` can be png, pdf, eps, jpg, ... (the ones supported by
 Impurity solvers
 ----------------
 
-What is the difference between ALPSCore/CT-HYB and TRIQS/cthyb?
+What is the difference between ALPS/CT-HYB and TRIQS/cthyb?
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 ``ALPS/CT-HYB`` is developed by one of the main developers of DCore, H. Shinaoka.
 Both of ``ALPS/CT-HYB`` and ``TRIQS/cthyb`` implement the hybridization-expansion continuous-time quantum Monte Carlo method.
 The main difference is the reliability of measurement of the single-particle Green's function.
-ALPSCore/CT-HYB uses a more elaborate algorithm (worm sampling).
+ALPS/CT-HYB uses a more elaborate algorithm (worm sampling).
 The non-worm conventional sampling, which is implemented in ``TRIQS/cthyb``,
 may give wrong results in some situations (e.g. SOI coupling with orbital-diagonal bath).
 

doc/tutorial.rst

@@ -15,16 +15,13 @@ Tutorial
 
    tutorial/square/square
    tutorial/bethe-t2g/bethe
-   tutorial/spin_orbit/spin_orbit
    tutorial/afm/afm
 
 **Part-II: DFT+DMFT**
 
 .. toctree::
    :maxdepth: 2
 
-   tutorial/qe
-   tutorial/srvo3_openmx/openmx
-   tutorial/pb/pb
-   tutorial/pb4/pb4
-   tutorial/srvo3_respack/respack
+   tutorial/srvo3/srvo3.rst
+
+More examples are found in the directory "examples".

doc/tutorial/bethe-t2g/bethe.rst

@@ -147,7 +147,7 @@ The reference data extracted from PRL 101, 166405 (2008) are available
 :download:`here <sigma-PRL101-166405.txt>`.
 The plot should look like the following.
 
-.. image:: sigma.svg
+.. image:: sigma.png
    :width: 600
    :align: center
 

doc/tutorial/square/dmft_square_ctseg.ini

@@ -0,0 +1,39 @@
+[model]
+seedname = square
+lattice = square
+norb = 1
+nelec = 1.0
+t = -1.0
+kanamori = [(4.0, 0.0, 0.0)]
+nk = 8
+
+[system]
+beta = 10.0
+n_iw = 1000
+prec_mu = 0.001
+fix_mu = True
+mu = 2
+
+[impurity_solver]
+name = ALPS/cthyb-seg
+exec_path{str} =/path/to/alps_cthyb
+cthyb.TEXT_OUTPUT{int} = 1
+cthyb.MEASUREMENT_freq{int} = 1
+MEASURE_gw{int} = 1
+MAX_TIME{int} = 100
+cthyb.N_MEAS{int} = 50
+cthyb.THERMALIZATION{int}=1000
+cthyb.SWEEPS{int}=100000000
+
+[control]
+max_step = 20
+sigma_mix = 1.0
+time_reversal = True
+
+[tool]
+broadening = 0.4
+knode = [(G,0.0,0.0,0.0),(X,0.5,0.0,0.0),(M,0.5,0.5,0.0),(G,0.0,0.0,0.0)]
+nk_line = 100
+omega_max =6.0
+omega_min =-5.0
+Nomega = 400