Merge pull request #80 from issp-center-dev/develop

Version 2.1.0

CMakeLists.txt

@@ -1,11 +1,16 @@
 # Version number of the application
-set (DCORE_VERSION "2.0.2")
+set (DCORE_VERSION "2.1.0")
 
 # Append triqs installed files to the cmake load path
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake)
 
 option(BUILD_DCORE "Build DCore" ON)
 
+option(MPIEXEC "Default value of mpi.command" OFF)
+if(NOT MPIEXEC)
+  set(MPIEXEC "mpirun -np \#")
+endif()
+
 # start configuration 
 cmake_minimum_required(VERSION 2.8)
 project(DCore NONE)

doc/CMakeLists.txt

@@ -26,7 +26,7 @@ file(GLOB_RECURSE all_doc_files RELATIVE ${CMAKE_SOURCE_DIR}/doc * EXCLUDE *.swp
 add_custom_command(OUTPUT ${CMAKE_BINARY_DIR}/doc_source.tar DEPENDS ${all_doc_files} COMMAND ${CMAKE_COMMAND} -E tar cf ${CMAKE_BINARY_DIR}/doc_source.tar ${all_doc_files} WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/doc)
 add_custom_target(make_doc_local_copy_dir ALL COMMAND ${CMAKE_COMMAND} -E make_directory ${CMAKE_BINARY_DIR}/doc_source)
 add_custom_target(copy_tar_doc ALL DEPENDS ${CMAKE_BINARY_DIR}/doc_source.tar make_doc_local_copy_dir COMMAND ${CMAKE_COMMAND} -E tar xf ${CMAKE_BINARY_DIR}/doc_source.tar WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/doc_source)
-add_custom_target(make_option_tables ALL DEPENDS copy_tar_doc COMMAND ${PYTHON_INTERPRETER} ${CMAKE_SOURCE_DIR}/python/option_tables.py ${CMAKE_BINARY_DIR}/doc_source/reference)
+add_custom_target(make_option_tables ALL DEPENDS copy_tar_doc COMMAND ${PYTHON_INTERPRETER} ${CMAKE_BINARY_DIR}/python/dcore/option_tables.py ${CMAKE_BINARY_DIR}/doc_source/reference)
 add_custom_target(make_doc_local_copy ALL DEPENDS make_option_tables)
 
 # create documentation target

doc/impuritysolvers/pomerol/dmft_square_pomerol.ini

@@ -0,0 +1,34 @@
+[model]
+seedname = square
+lattice = square
+norb = 1
+nelec = 1.0
+t = -1.0
+kanamori = [(4.0, 0.0, 0.0)]
+nk = 8
+
+[system]
+T = 0.1
+n_iw = 1000
+mu = 2.0
+fix_mu = True
+
+[impurity_solver]
+name = pomerol
+exec_path{str} = pomerol2dcore
+n_bath{int} = 3
+fit_gtol{float} = 1e-6
+
+[control]
+max_step = 100
+sigma_mix = 0.5
+time_reversal = True
+converge_tol = 1e-5
+
+[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

doc/impuritysolvers/pomerol/pomerol.rst

@@ -1,20 +1,20 @@
-Hubbard-I approximation: ``pomerol``
-====================================
+Exact diagonalization solver: ``pomerol``
+=========================================
 
-``pomerol`` is an exact diagonalization library implemented in c++.
-``DCore`` provides an interface to ``pomerol`` library to use it as a solver for the Hubbard-I approximation.
+``pomerol`` is an exact diagonalization (ED) library implemented in c++.
+``DCore`` provides an interface to ``pomerol`` library to compute an approximate solution of DMFT with discritized hybridization function.
 
 Features
 --------
 
-- All interactions available in ``DCore`` are supported.
-
-- [todo] tail evaluation of Gf
+- Arbitrary temperature
 
-- [todo] dynamical susceptibility
+- All interactions available in ``DCore`` are supported.
 
 - [experimental] two-particle Green's function
 
+- [todo] tail evaluation of Gf
+
 Install
 -------
 
@@ -27,8 +27,46 @@ The following library/program needs to be installed:
 How to use
 ----------
 
+Mandatory parameters:
+
 ::
 
     [impurity_solver]
     name = pomerol
     exec_path{str} = /install_directory/bin/pomerol2dcore
+
+Optional parameters:
+
+::
+
+    n_bath{int} = 3  # 0 for default
+    fit_gtol{float} = 1e-6  # 1e-5 for default
+
+The default value of ``n_bath`` is 0, namely, no bath site is taken into account (Hubbard-I approximation).
+For ``n_bath>0``, hybridization function Delta(iw) is fitted by
+
+.. math::
+
+    \Delta^{n_\mathrm{bath}}_{o_1 o_2}(i\omega) = \sum_{l=1}^{n_\mathrm{bath}} \frac{V_{o_1 l} V_{l o_2}}{i\omega - \epsilon_l}
+
+Then, the finite-size system consisting of the impurity site and ``n_bath`` bath sites are solve by ED method.
+The size of the Hilbert space increases exponentially according to :math:`2^{n_\textrm{spn-orb}}` where :math:`n_\textrm{spn-orb}=2*n_\mathrm{orb} + 2*n_\mathrm{bath}`.
+Because of storage limitation, :math:`n_\textrm{spn-orb} \simeq 16` is the limits in this solver.
+
+Example
+-------
+
+:doc:`The square-lattice model in tutorial <../../tutorial/square/square>` is solved by the pomerol solver using the following input parameter set:
+
+:download:`dmft_square_pomerol.ini <dmft_square_pomerol.ini>`
+
+.. literalinclude:: dmft_square_pomerol.ini
+   :language: ini
+
+It is recommended to set ``convergence_tol`` parameter in [control] block to stop the DMFT loop automatically.
+The figure below shows the renormalization factor as a function of ``n_bath``.
+Convergence to the CTHYB result is obtained around ``n_bath=3``.
+
+.. image:: renorm.png
+   :width: 700
+   :align: center

doc/install.rst

@@ -6,6 +6,10 @@
 Installation
 ============
 
+Install script
+--------------
+You may use `MateriAppsInstaller <https://github.com/wistaria/MateriAppsInstaller>`_, a collection of install scripts, to install prerequisites (TRIQS 1.4.x) and DCore.
+
 Download
 --------
 
@@ -34,7 +38,7 @@ You can download the source files in two ways.
 Prerequisites
 -------------
 
-#. `TRIQS <https://triqs.github.io/triqs/>`_ and `DFTTools/TRIQS <https://triqs.github.io/dft_tools/>`_.
+#. `TRIQS <https://triqs.github.io/triqs/>`_ and `TRIQS/DFTTools <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>`.
 
@@ -82,6 +86,11 @@ Installation steps
    Please set CMAKE_INSTALL_PREFIX to the directory where DCore will be installed.
    If the cmake command succeeded, you will see the following message.
 
+   DCore invokes some MPI parallelized impurity solver in a DMFT loop.
+   If your system MPI command 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"``.
+
    ::
 
      -- Build files have been written to: /.../dcore.build
@@ -98,9 +107,7 @@ Installation steps
 
      $ 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.
+   Some of tests invoke an MPI parallelized impourity solver.
    Note that it is not allowed to run MPI programs interactively on some system.
    In this case, please run tests as a job.
 

doc/reference/input.rst

@@ -312,3 +312,6 @@ This block includes parameters that are solely used by ``dcore_post``.
 This block includes parameters which are read by ``dcore`` and ``dcore_post``.
 
 .. include:: mpi_desc.txt
+
+When an option ``-DMPIEXEC=<MPIRUN>`` is passed to the ``cmake`` command,
+The default value of ``command`` will be replaced with ``<MPIRUN>``.

doc/tutorial/square/square.rst

@@ -125,7 +125,7 @@ We can plot it using gnuplot as follows:
    :align: center
 
 Another impurity solver: CTHYB-SEG
----------------------------
+----------------------------------
 
 The input file for ALPS/cthyb-seg is given as below.
 

python/CMakeLists.txt

@@ -7,7 +7,7 @@ configure_file(${CMAKE_SOURCE_DIR}/cmake/sitecustomize.py ${CMAKE_CURRENT_BINARY
 
 # Install path
 install(DIRECTORY ${CMAKE_SOURCE_DIR}/python/ DESTINATION
-${CMAKE_INSTALL_PREFIX}/lib/python2.7/site-packages/dcore FILES_MATCHING PATTERN *.py)
+    ${DCORE_SITE_PACKAGES}/dcore FILES_MATCHING PATTERN *.py)
 
 # Copy all Python files for ctest into a build directory
 file(GLOB_RECURSE all_py_files RELATIVE ${CMAKE_SOURCE_DIR}/python *.py)
@@ -21,6 +21,9 @@ add_custom_command(OUTPUT ${CMAKE_BINARY_DIR}/py_source.tar
 
 add_custom_target(copy_tar_py ALL DEPENDS ${CMAKE_BINARY_DIR}/py_source.tar)
 
+configure_file(mpi_command.py.in ${CMAKE_CURRENT_BINARY_DIR}/dcore/mpi_command.py @ONLY)
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/dcore/mpi_command.py DESTINATION ${DCORE_SITE_PACKAGES}/dcore)
+
 # add version file
 configure_file(version.py.in version.py)
 install(FILES ${CMAKE_CURRENT_BINARY_DIR}/version.py DESTINATION ${DCORE_SITE_PACKAGES}/dcore)

python/dcore.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 #
 # DCore -- Integrated DMFT software for correlated electrons
 # Copyright (C) 2017 The University of Tokyo
@@ -53,6 +52,7 @@ def dcore(filename, np=1):
 if __name__ == '__main__':
     from .option_tables import generate_all_description
     import argparse
+    from .version import version
 
     parser = argparse.ArgumentParser(
         prog='dcore.py',
@@ -69,6 +69,7 @@ def dcore(filename, np=1):
                         type=str,
                         help="input file name.")
     parser.add_argument('--np', default=1, help='Number of MPI processes', required=True)
+    parser.add_argument('--version', action='version', version='DCore {}'.format(version))
 
     args = parser.parse_args()
     if os.path.isfile(args.path_input_file) is False:

python/dcore_bse.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 #
 # DCore -- Integrated DMFT software for correlated electrons
 # Copyright (C) 2017 The University of Tokyo
@@ -74,9 +73,9 @@ def calc_g2_in_impurity_model(solver_name, solver_params, mpirun_command, basis_
 
     # Solve the model
     if flag_box:
-        xloc, chiloc = sol.calc_Xloc_ph(rot, mpirun_command, num_wf, num_wb, s_params)
+        xloc, chiloc = sol.calc_G2loc_ph(rot, mpirun_command, num_wf, num_wb, s_params)
     else:
-        xloc, chiloc = sol.calc_Xloc_ph_sparse(rot, mpirun_command, freqs, num_wb, s_params)
+        xloc, chiloc = sol.calc_G2loc_ph_sparse(rot, mpirun_command, freqs, num_wb, s_params)
 
     # Check results for x_loc
     print("\n checking x_loc...")
@@ -663,6 +662,7 @@ def dcore_bse(filename, np=1):
 if __name__ == '__main__':
     import argparse
     from .option_tables import generate_all_description
+    from .version import version
 
     parser = argparse.ArgumentParser(
         prog='dcore_bse.py',
@@ -678,6 +678,7 @@ def dcore_bse(filename, np=1):
                         help="input file name."
                         )
     parser.add_argument('--np', help='Number of MPI processes', required=True)
+    parser.add_argument('--version', action='version', version='DCore {}'.format(version))
 
     args = parser.parse_args()
     if os.path.isfile(args.path_input_file) is False:

python/dcore_check.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 #
 # DCore -- Integrated DMFT software for correlated electrons
 # Copyright (C) 2017 The University of Tokyo
@@ -18,8 +17,6 @@
 #
 from __future__ import print_function
 
-from itertools import *
-
 from .pytriqs_gf_compat import *
 
 from dmft_core import DMFTCoreSolver
@@ -300,6 +297,7 @@ def dcore_check(ini_file, prefix, fig_ext, max_n_iter):
 if __name__ == '__main__':
     from .option_tables import generate_all_description
     import argparse
+    from .version import version
 
     parser = argparse.ArgumentParser(
         prog='dcore_check.py',
@@ -331,6 +329,7 @@ def dcore_check(ini_file, prefix, fig_ext, max_n_iter):
                         type=int,
                         help='Max number of iterations to be processed'
                         )
+    parser.add_argument('--version', action='version', version='DCore {}'.format(version))
     # for backward compatibility
     # parser.add_argument('--output',
     #                     action='store',

python/dcore_post.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 #
 # DCore -- Integrated DMFT software for correlated electrons
 # Copyright (C) 2017 The University of Tokyo
@@ -442,6 +441,7 @@ def dcore_post(filename, np=1, prefix="./"):
 if __name__ == '__main__':
     from .option_tables import generate_all_description
     import argparse
+    from .version import version
 
     parser = argparse.ArgumentParser(
         prog='dcore_post.py',
@@ -458,6 +458,7 @@ def dcore_post(filename, np=1, prefix="./"):
                         help="input file name."
                         )
     parser.add_argument('--np', help='Number of MPI processes', required=True)
+    parser.add_argument('--version', action='version', version='DCore {}'.format(version))
     parser.add_argument('--prefix',
                         action='store',
                         default='post/',

python/dcore_pre.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 #
 # DCore -- Integrated DMFT software for correlated electrons
 # Copyright (C) 2017 The University of Tokyo
@@ -262,8 +261,8 @@ def __generate_local_potential(p):
     # set factor
     try:
         fac = ast.literal_eval(local_potential_factor)
-        if isinstance(fac, float):
-            fac = [fac] * n_inequiv_shells
+        if isinstance(fac, float) or isinstance(fac, int):
+            fac = [float(fac)] * n_inequiv_shells
         elif isinstance(fac, list) or isinstance(fac, tuple):
             assert len(fac) == n_inequiv_shells
         else:
@@ -390,6 +389,7 @@ def dcore_pre(filename):
 if __name__ == '__main__':
     from .option_tables import generate_all_description
     import argparse
+    from .version import version
 
     parser = argparse.ArgumentParser(
         prog='dcore_pre.py',
@@ -405,6 +405,7 @@ def dcore_pre(filename):
                         type=str,
                         help="input file name."
                         )
+    parser.add_argument('--version', action='version', version='DCore {}'.format(version))
 
     args = parser.parse_args()
     if os.path.isfile(args.path_input_file) is False: