Update README and add LICENSE

GrupEstructuraElectronicaSimetria · Jul 30, 2021 · 777494c · 777494c
1 parent 3fa982e
commit 777494c
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Showing 4 changed files with 4 additions and 3 deletions.
diff --git a/cosymlib/__init__.py b/cosymlib/__init__.py
@@ -1,4 +1,4 @@
-__version__ = '0.9.5'
+__version__ = '0.9.6'
 
 from cosymlib.molecule import Molecule
 from cosymlib.molecule.geometry import Geometry

diff --git a/cosymlib/file_io/__init__.py b/cosymlib/file_io/__init__.py
@@ -74,7 +74,7 @@ def get_geometry_from_file_xyz(file_name, read_multiple=False):
             if line.lstrip().startswith(comment_line):
                 pass
             elif line.strip() == '':
-                warnings.warn('Line {} is empty'.format(idl + 1), errors.EmptyLineWarning)
+                warnings.warn('Line {} is empty in xyz file'.format(idl + 1), errors.EmptyLineWarning)
             else:
                 try:
                     float(line.split()[1])

diff --git a/cosymlib/tools/__init__.py b/cosymlib/tools/__init__.py
@@ -67,6 +67,7 @@ def generate_connectivity_from_geometry(geometry, thresh=1.2):
 
     radii_matrix = np.array([radius]*len(radius))
     radii_matrix = radii_matrix + radii_matrix.T
+    radii_matrix[(radii_matrix == 0.0)] = np.nan # avoid 0 distance division
 
     try:
         relative_differences = np.abs(radii_matrix - distances_matrix)/radii_matrix

diff --git a/setup.py b/setup.py
@@ -10,7 +10,7 @@ def get_version_number():
 
 
 shape = Extension('cosymlib.shape.shp',
-                  # extra_compile_args=['-std=c99'],
+                  extra_f90_compile_args=['-static-libgcc'],
                   #include_dirs=include_dirs_numpy,
                   sources=['fortran/shp.pyf', 'fortran/shp.f90'])