make tb and negf subpackages of nanonet

freude · May 28, 2020 · f038928 · f038928
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diff --git a/README.md b/README.md
@@ -29,7 +29,11 @@ git clone https://github.com/freude/NanoNet.git
 cd NanoNet
 ```
 
-`Nanonet` requires `openmpi` to be installed in the system. All other dependencies can be installed at once by invoking the following command
+`Nanonet` requires `openmpi` to be installed in the system.
+ ```bash
+ sudo apt-get install libopenmpi-dev
+ ```
+ All other dependencies can be installed at once by invoking the following command
  from within the source directory:
 
 ```bash

diff --git a/jupyter_notebooks/Hukel_model.ipynb b/jupyter_notebooks/Hukel_model.ipynb
diff --git a/jupyter_notebooks/atom_chains.ipynb b/jupyter_notebooks/atom_chains.ipynb
diff --git a/jupyter_notebooks/bismuth_bulk.ipynb b/jupyter_notebooks/bismuth_bulk.ipynb
diff --git a/jupyter_notebooks/block_tridiagonal_and_sorting.ipynb b/jupyter_notebooks/block_tridiagonal_and_sorting.ipynb
diff --git a/jupyter_notebooks/bulk_silicon.ipynb b/jupyter_notebooks/bulk_silicon.ipynb
diff --git a/jupyter_notebooks/bulk_silicon_with_input_file.ipynb b/jupyter_notebooks/bulk_silicon_with_input_file.ipynb
diff --git a/jupyter_notebooks/chain_greens_function.ipynb b/jupyter_notebooks/chain_greens_function.ipynb
diff --git a/jupyter_notebooks/silicon_nanowire.ipynb b/jupyter_notebooks/silicon_nanowire.ipynb
diff --git a/nanonet/__init__.py b/nanonet/__init__.py
diff --git a/negf/__init__.py → nanonet/negf/__init__.py b/negf/__init__.py → nanonet/negf/__init__.py
diff --git a/negf/cfr.py → nanonet/negf/cfr.py b/negf/cfr.py → nanonet/negf/cfr.py
diff --git a/negf/continued_fraction_representation.py → ...negf/continued_fraction_representation.py b/negf/continued_fraction_representation.py → ...negf/continued_fraction_representation.py
diff --git a/negf/field.py → nanonet/negf/field.py b/negf/field.py → nanonet/negf/field.py
diff --git a/negf/greens_functions.py → nanonet/negf/greens_functions.py b/negf/greens_functions.py → nanonet/negf/greens_functions.py
diff --git a/negf/hamiltonian_chain.py → nanonet/negf/hamiltonian_chain.py b/negf/hamiltonian_chain.py → nanonet/negf/hamiltonian_chain.py
@@ -1,7 +1,7 @@
 import numpy as np
 from scipy.linalg import block_diag
-from tb.aux_functions import yaml_parser
-from negf.field import Field
+from nanonet.tb.aux_functions import yaml_parser
+from nanonet.negf.field import Field
 
 
 def fd(energy, ef, temp):

diff --git a/negf/invdisttree.py → nanonet/negf/invdisttree.py b/negf/invdisttree.py → nanonet/negf/invdisttree.py
diff --git a/negf/poisson.py → nanonet/negf/poisson.py b/negf/poisson.py → nanonet/negf/poisson.py
diff --git a/negf/recursive_greens_functions.py → nanonet/negf/recursive_greens_functions.py b/negf/recursive_greens_functions.py → nanonet/negf/recursive_greens_functions.py
diff --git a/negf/surf_greens_function.py → nanonet/negf/surf_greens_function.py b/negf/surf_greens_function.py → nanonet/negf/surf_greens_function.py
diff --git a/negf/transport.py → nanonet/negf/transport.py b/negf/transport.py → nanonet/negf/transport.py
diff --git a/tb/__init__.py → nanonet/tb/__init__.py b/tb/__init__.py → nanonet/tb/__init__.py
diff --git a/tb/abstract_interfaces.py → nanonet/tb/abstract_interfaces.py b/tb/abstract_interfaces.py → nanonet/tb/abstract_interfaces.py
diff --git a/tb/aux_functions.py → nanonet/tb/aux_functions.py b/tb/aux_functions.py → nanonet/tb/aux_functions.py
@@ -4,7 +4,6 @@
 from __future__ import print_function
 from __future__ import absolute_import
 from itertools import product
-import math
 import numpy as np
 import yaml
 
@@ -183,7 +182,7 @@ def get_k_coords(special_points, num_of_points, label):
     :rtype:                  numpy.ndarray
     """
 
-    from tb.special_points import SPECIAL_K_POINTS_BI, SPECIAL_K_POINTS_SI
+    from nanonet.tb.special_points import SPECIAL_K_POINTS_BI, SPECIAL_K_POINTS_SI
 
     if isinstance(label, str):
         if label == 'Bi':
@@ -379,7 +378,7 @@ def find_nonzero_lines(mat, order):
     left_block = max(h_l_h, h_r_v)
     right_block = max(h_r_h, h_l_v)
 
-    from tb.sorting_algorithms import split_matrix_0, cut_in_blocks, split_matrix
+    from nanonet.tb.sorting_algorithms import split_matrix_0, cut_in_blocks, split_matrix
 
     blocks = split_matrix_0(h_0, left=left_block, right=right_block)
     h_0_s, h_l_s, h_r_s = cut_in_blocks(h_0, blocks)

diff --git a/tb/block_tridiagonalization.py → nanonet/tb/block_tridiagonalization.py b/tb/block_tridiagonalization.py → nanonet/tb/block_tridiagonalization.py
@@ -111,7 +111,7 @@ def cut_in_blocks(h_0, blocks):
     Examples
     --------
     >>> import numpy as np
-    >>> from tb.block_tridiagonalization import cut_in_blocks
+    >>> from nanonet.tb.block_tridiagonalization import cut_in_blocks
     >>> a = np.array([[1, 1, 0, 0], [1, 1, 1, 0], [0, 1, 1, 1], [0, 0, 1, 1]])
     >>> a
     array([[1, 1, 0, 0],
@@ -466,7 +466,7 @@ def compute_edge(mat):
     Examples
     --------
     >>> import numpy as np
-    >>> from tb.block_tridiagonalization import compute_edge
+    >>> from nanonet.tb.block_tridiagonalization import compute_edge
     >>> input_matrix = np.array([[1, 1, 0, 0], [1, 1, 1, 0], [0, 1, 1, 1], [0, 0, 1, 1]])
     >>> input_matrix
     array([[1, 1, 0, 0],
@@ -533,7 +533,7 @@ def compute_blocks(left_block, right_block, edge, edge1):
     Examples
     --------
     >>> import numpy as np
-    >>> from tb.block_tridiagonalization import compute_edge
+    >>> from nanonet.tb.block_tridiagonalization import compute_edge
     >>> input_matrix = np.array([[1, 1, 0, 0], [1, 1, 1, 0], [0, 1, 1, 1], [0, 0, 1, 1]])
     >>> input_matrix
     array([[1, 1, 0, 0],

diff --git a/tb/constants.py → nanonet/tb/constants.py b/tb/constants.py → nanonet/tb/constants.py
diff --git a/tb/diatomic_matrix_element.py → nanonet/tb/diatomic_matrix_element.py b/tb/diatomic_matrix_element.py → nanonet/tb/diatomic_matrix_element.py
diff --git a/tb/gf.py → nanonet/tb/gf.py b/tb/gf.py → nanonet/tb/gf.py
@@ -4,7 +4,7 @@
 import pickle
 import matplotlib.pyplot as plt
 import numpy as np
-import tb
+import nanonet.tb as tb
 
 
 def main():

diff --git a/tb/gf_script.py → nanonet/tb/gf_script.py b/tb/gf_script.py → nanonet/tb/gf_script.py
diff --git a/tb/hamiltonian.py → nanonet/tb/hamiltonian.py b/tb/hamiltonian.py → nanonet/tb/hamiltonian.py
@@ -9,13 +9,13 @@
 import inspect
 from operator import mul
 import numpy as np
-from tb.abstract_interfaces import AbstractBasis
-from tb.structure_designer import StructDesignerXYZ, CyclicTopology
-from tb.diatomic_matrix_element import me
-from tb.orbitals import Orbitals
-from tb.aux_functions import dict2xyz
-from tb.block_tridiagonalization import split_into_subblocks_optimized, cut_in_blocks
-import verbosity
+from nanonet.tb.abstract_interfaces import AbstractBasis
+from nanonet.tb.structure_designer import StructDesignerXYZ, CyclicTopology
+from nanonet.tb.diatomic_matrix_element import me
+from nanonet.tb.orbitals import Orbitals
+from nanonet.tb.aux_functions import dict2xyz
+from nanonet.tb.block_tridiagonalization import split_into_subblocks_optimized, cut_in_blocks
+import nanonet.verbosity as verbosity
 
 
 unique_distances = set()

diff --git a/tb/hamiltonian_initializer.py → nanonet/tb/hamiltonian_initializer.py b/tb/hamiltonian_initializer.py → nanonet/tb/hamiltonian_initializer.py
diff --git a/tb/hamiltonian_sparse.py → nanonet/tb/hamiltonian_sparse.py b/tb/hamiltonian_sparse.py → nanonet/tb/hamiltonian_sparse.py
@@ -7,8 +7,8 @@
 import numpy as np
 import scipy.sparse.linalg as splin
 import scipy.sparse as sp
-from tb.orbitals import Orbitals
-from tb.hamiltonian import Hamiltonian
+from nanonet.tb.orbitals import Orbitals
+from nanonet.tb.hamiltonian import Hamiltonian
 
 
 class HamiltonianSp(Hamiltonian):

diff --git a/tb/orbitals.py → nanonet/tb/orbitals.py b/tb/orbitals.py → nanonet/tb/orbitals.py
@@ -4,7 +4,7 @@
 `SiliconSP3D5S`, `HydrogenS`, `Bismuth`.
 """
 import sys
-from tb.aux_functions import print_table
+from nanonet.tb.aux_functions import print_table
 
 
 class Orbitals(object):

diff --git a/tb/plotting.py → nanonet/tb/plotting.py b/tb/plotting.py → nanonet/tb/plotting.py
diff --git a/tb/reduced_mode_space.py → nanonet/tb/reduced_mode_space.py b/tb/reduced_mode_space.py → nanonet/tb/reduced_mode_space.py
@@ -5,7 +5,7 @@
 import pickle
 import os.path
 import numpy as np
-from negf.greens_functions import surface_greens_function_poles
+from nanonet.negf.greens_functions import surface_greens_function_poles
 
 
 # def object_function(vec, energy, initial_basis, extended_basis, h_0, h_0_reduced):

diff --git a/tb/sorting_algorithms.py → nanonet/tb/sorting_algorithms.py b/tb/sorting_algorithms.py → nanonet/tb/sorting_algorithms.py
diff --git a/tb/special_points.py → nanonet/tb/special_points.py b/tb/special_points.py → nanonet/tb/special_points.py
diff --git a/tb/structure_designer.py → nanonet/tb/structure_designer.py b/tb/structure_designer.py → nanonet/tb/structure_designer.py
@@ -9,8 +9,8 @@
 import logging
 import numpy as np
 import scipy.spatial
-from tb.abstract_interfaces import AbstractStructureDesigner
-from tb.aux_functions import xyz2np, count_species, is_in_coords, print_dict
+from nanonet.tb.abstract_interfaces import AbstractStructureDesigner
+from nanonet.tb.aux_functions import xyz2np, count_species, is_in_coords, print_dict
 
 
 class StructDesignerXYZ(AbstractStructureDesigner):

diff --git a/tb/tb_script.py → nanonet/tb/tb_script.py b/tb/tb_script.py → nanonet/tb/tb_script.py
@@ -4,7 +4,7 @@
 import pickle
 import matplotlib.pyplot as plt
 import numpy as np
-import tb
+import nanonet.tb as tb
 
 
 def preprocess_data(param_file, k_points_file, xyz, code_name):

diff --git a/tb/tbmpi_script.py → nanonet/tb/tbmpi_script.py b/tb/tbmpi_script.py → nanonet/tb/tbmpi_script.py
@@ -2,7 +2,7 @@
 from __future__ import print_function
 from __future__ import absolute_import
 from mpi4py import MPI
-import tb
+import nanonet.tb as tb
 from .tb_script import create_parser, preprocess_data, postprocess_data
 
 

diff --git a/verbosity/__init__.py → nanonet/verbosity/__init__.py b/verbosity/__init__.py → nanonet/verbosity/__init__.py
diff --git a/verbosity/verbosity.py → nanonet/verbosity/verbosity.py b/verbosity/verbosity.py → nanonet/verbosity/verbosity.py
diff --git a/setup.py b/setup.py
@@ -1,4 +1,4 @@
-from setuptools import setup
+from setuptools import setup, find_namespace_packages
 
 
 setup(name='nanonet',
@@ -7,7 +7,7 @@
       author='M. V. Klymenko, J. A. Vaitkus, J. S. Smith, J. H. Cole',
       author_email='mike.klymenko@rmit.edu.au',
       license='MIT',
-      packages=['tb', 'negf', 'verbosity'],
+      packages=find_namespace_packages(include=['nanonet.*']),
       entry_points={
         'console_scripts': ['tb = tb.tb_script:main', 'tbmpi = tb.tbmpi_script:main', 'gf = tb.gf_script:main'],
       },

diff --git a/test/reduced_mode_space.py b/test/reduced_mode_space.py
@@ -1,7 +1,7 @@
 import numpy as np
 import matplotlib.pyplot as plt
-import tb
-from tb.reduced_mode_space import bs, reduce_mode_space
+import nanonet.tb as tb
+from nanonet.tb.reduced_mode_space import bs, reduce_mode_space
 import pickle
 
 

diff --git a/test/test_aux_functions.py b/test/test_aux_functions.py
@@ -1,5 +1,5 @@
 import unittest
-from tb.aux_functions import xyz2np
+from nanonet.tb.aux_functions import xyz2np
 
 
 class Test(unittest.TestCase):

diff --git a/test/test_block_tridiagonalization.py b/test/test_block_tridiagonalization.py
@@ -1,6 +1,6 @@
 import unittest
 import doctest
-import tb.block_tridiagonalization as btd
+import nanonet.tb.block_tridiagonalization as btd
 suite = doctest.DocTestSuite(btd)
 unittest.TextTestRunner(verbosity=2).run(suite)
 

diff --git a/test/test_greens_functions.py b/test/test_greens_functions.py
@@ -1,10 +1,9 @@
 import sys
-import matplotlib.pyplot as plt
 import numpy as np
-import tb
-import negf
-from negf.hamiltonian_chain import HamiltonianChain
-from negf.recursive_greens_functions import recursive_gf
+import nanonet.tb as tb
+import nanonet.negf as negf
+from nanonet.negf.hamiltonian_chain import HamiltonianChain
+from nanonet.negf.recursive_greens_functions import recursive_gf
 
 np.warnings.filterwarnings('ignore')
 
@@ -682,7 +681,7 @@ def expected_dens_of_complex_chain():
 
 
 def test_double_barrier_density_recursive(single_period_test=complex_chain, periods=20):
-    from negf.field import Field1D
+    from nanonet.negf.field import Field1D
 
     def qw(coord, coords_of_steps, jumps, width=1):
         ans = 0

diff --git a/test/test_hamiltonian_module.py b/test/test_hamiltonian_module.py
@@ -1,5 +1,5 @@
 import numpy as np
-import tb
+import nanonet.tb as tb
 
 
 def test_simple_atomic_chain():

diff --git a/test/test_hamiltonian_sparse_module.py b/test/test_hamiltonian_sparse_module.py
@@ -1,5 +1,5 @@
 import numpy as np
-import tb
+import nanonet.tb as tb
 from test.test_hamiltonian_module import expected_bulk_silicon_band_structure
 
 

diff --git a/test/test_matrix_splitting_from_aux_functions.py b/test/test_matrix_splitting_from_aux_functions.py
@@ -1,6 +1,6 @@
 import unittest
 import numpy as np
-from tb.aux_functions import compute_edge, blocksandborders_constrained
+from nanonet.tb.aux_functions import compute_edge, blocksandborders_constrained
 
 
 class Test(unittest.TestCase):

diff --git a/test/test_scripts_and_initializer.py b/test/test_scripts_and_initializer.py
@@ -1,6 +1,6 @@
 import unittest
-import tb.tb_script as tb_script
-import tb.tbmpi_script as tbmpi_script
+import nanonet.tb.tb_script as tb_script
+import nanonet.tb.tbmpi_script as tbmpi_script
 
 
 class Test(unittest.TestCase):