Add doc to VASP converter concerning block structure

doc/guide/SrVO3.rst

@@ -183,7 +183,7 @@ will be stored in a separate subgroup in the hdf5 file, called `dmft_output`.
 Note that this script performs 15 DMFT cycles, but does not check for
 convergence. Of course, it would be possible to build in convergence criteria.
 A simple check for convergence can be also done if you store multiple quantities
-of each iteration and analyze the convergence by hand. In general, it is advisable
+of each iteration and analyse the convergence by hand. In general, it is advisable
 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.

doc/guide/conversion.rst

@@ -263,6 +263,15 @@ For the conversion to a h5 file we use on the python level (in analogy to the Wi
     Converter = VaspConverter(filename = filename)
     Converter.convert_dft_input()
 
+As usual, the resulting h5-file can then be used with the SumkDFT class.
+
+Note that the automatic detection of the correct blockstructure might fail for VASP inputs.
+This can be circumvented by increase the :class:`SumkDFT <dft.sumk_dft.SumkDFT>` threshold to e.g.::
+     
+    SK.analyse_block_structure(threshold = 1e-4)
+
+However, only do this after a careful study of the density matrix and the dos in the wannier basis.
+
 A general H(k)
 --------------
 
@@ -445,7 +454,7 @@ In our `Pnma`-LaVO\ :sub:`3` example, for instance, we could use::
 where the ``x=-1,1,0`` option indicates that the V--O bonds in the octahedra are
 rotated by (approximatively) 45 degrees with respect to the axes of the `Pbnm` cell.
 
-The converter will analyze the matrix elements of the local Hamiltonian
+The converter will analyse the matrix elements of the local Hamiltonian
 to find the symmetry matrices `rot_mat` needed for the global-to-local
 transformation of the basis set for correlated orbitals
 (see section :ref:`hdfstructure`).

python/sumk_dft.py

@@ -58,7 +58,7 @@ class SumkDFT(object):
                          If True, the local Green's function matrix for each spin is divided into smaller blocks 
                           with the block structure determined from the DFT density matrix of the corresponding correlated shell.
 
-                         Alternatively and additionally, the block structure can be analyzed using :meth:`analyse_block_structure <dft.sumk_dft.SumkDFT.analyse_block_structure>`
+                         Alternatively and additionally, the block structure can be analysed using :meth:`analyse_block_structure <dft.sumk_dft.SumkDFT.analyse_block_structure>`
                          and manipulated using the SumkDFT.block_structre attribute (see :class:`BlockStructure <dft.block_structure.BlockStructure>`).
         dft_data : string, optional
                    Name of hdf5 subgroup in which DFT data for projector and lattice Green's function construction are stored.

test/CMakeLists.txt

@@ -5,7 +5,7 @@ file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/${all_h5_files} DESTINATION ${CMAKE_CURREN
 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)
+set(all_tests wien2k_convert hk_convert w90_convert sumkdft_basic srvo3_Gloc srvo3_transp sigma_from_file blockstructure analyse_block_structure_from_gf analyse_block_structure_from_gf2)
 
 foreach(t ${all_tests})
   add_test(NAME ${t} COMMAND python ${CMAKE_CURRENT_SOURCE_DIR}/${t}.py)

test/analyse_block_structure_from_gf.py

@@ -32,13 +32,13 @@ 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:
+with HDFArchive('analyse_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:
+with HDFArchive('analyse_block_structure_from_gf.out.h5','r') as ar,\
+     HDFArchive('analyse_block_structure_from_gf.ref.h5','r') as ar2:
     assert ar['bs1'] == ar2['bs1'], 'bs1 not equal'
     a1 = ar['bs2']
     a2 = ar2['bs2']

test/analyse_block_structure_from_gf2.py

@@ -3,7 +3,7 @@ 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
+# here we test the SK.analyse_block_structure_from_gf function
 # with GfReFreq, GfReTime