modified name reading from fchk

added density getter functions in molecule class added a new print option for density measure files + updated version
GrupEstructuraElectronicaSimetria · Aug 5, 2020 · 105f8dc · 105f8dc
1 parent f8399e4
commit 105f8dc
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Showing 3 changed files with 46 additions and 2 deletions.
diff --git a/cosymlib/__init__.py b/cosymlib/__init__.py
@@ -1,4 +1,4 @@
-__version__ = '0.8.4'
+__version__ = '0.8.5'
 
 from cosymlib.molecule import Molecule, Geometry
 from cosymlib import file_io
@@ -278,6 +278,42 @@ def print_electronic_symmetry_measure(self, group, axis=None, axis2=None, center
 
         output.write(txt)
 
+    def print_electronic_density_measure(self, group, axis=None, axis2=None, center=None, output=sys.stdout):
+
+        txt = ''
+        txt2 = ''
+        first = True
+        for molecule in self._molecules:
+            dens_measure = molecule.get_dens_symmetry(group, axis=axis, axis2=axis2, center=center)
+
+            if first:
+                sep_line = '          ' + '---------' * len(dens_measure['labels']) + '\n'
+
+                txt += '\nDensity: CSM-like values\n'
+                txt += sep_line
+                txt += '           ' + '  '.join(['{:^7}'.format(s) for s in dens_measure['labels']])
+                txt += '\n'
+                txt += sep_line
+
+                txt2 += '--------------\n'
+                txt2 += 'Total CSM {}\n'.format(group)
+                txt2 += '--------------\n'
+
+            txt += '{:<9} '.format(molecule.name) + '  '.join(['{:7.3f}'.format(s) for s in dens_measure['csm_coef']])
+            txt += '\n'
+            first = False
+            axes_information = molecule.get_symmetry_axes(group, axis=axis, axis2=axis2, center=center)
+            txt2 += '{:<9} '.format(molecule.name) + '{:7.3f}\n'.format(dens_measure['csm'])
+            txt2 += '\ncenter: ' + '  '.join(['{:12.8f}'.format(s) for s in axes_information['center']])
+            txt2 += '\n'
+            txt2 += 'axis  : ' + '  '.join(['{:12.8f}'.format(s) for s in axes_information['axis']])
+            txt2 += '\n'
+            txt2 += 'axis2 : ' + '  '.join(['{:12.8f}'.format(s) for s in axes_information['axis2']])
+
+        txt += '\n' + txt2
+
+        output.write(txt)
+
     def print_wnfsym_sym_matrices(self, group, axis=None, axis2=None, center=None, output=sys.stdout):
 
         txt = ''

diff --git a/cosymlib/file_io/__init__.py b/cosymlib/file_io/__init__.py
@@ -126,7 +126,7 @@ def get_molecule_from_file_fchk(file_name, read_multiple=False):
     input_molecule = [[] for _ in range(len(key_list))]
     read = False
     with open(file_name, mode='r') as lines:
-        name = lines.readline().strip('\n')
+        name = lines.readline().split()[0]#.strip('\n')
         line = lines.readline().split()
         basis_set = line[-1]
         if 'R' in line[1]:

diff --git a/cosymlib/molecule/__init__.py b/cosymlib/molecule/__init__.py
@@ -89,6 +89,14 @@ def get_symmetry_matrix(self, group, axis=None, axis2=None, center=None):
     def get_wf_symmetry(self, group, axis=None, axis2=None, center=None):
         return self._symmetry.wf_measure(group)
 
+    @set_parameters
+    def get_dens_symmetry(self, group, axis=None, axis2=None, center=None):
+        return self._symmetry.dens_measure(group)
+
+    @set_parameters
+    def get_symmetry_axes(self, group, axis=None, axis2=None, center=None):
+        return self._symmetry.axes(group)
+
     @set_parameters
     def get_ideal_group_table(self, group, axis=None, axis2=None, center=None):
         return self._symmetry.wf_ideal_group_table(group)