add possibility to not use dihedral angles

jhrmnn · Jul 19, 2018 · f621ec1 · f621ec1
1 parent 1916a45
commit f621ec1
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Showing 3 changed files with 20 additions and 11 deletions.
diff --git a/berny/coords.py b/berny/coords.py
@@ -208,7 +208,7 @@ def get_clusters(C):
 
 
 class InternalCoords(object):
-    def __init__(self, geom, allowed=None, superweakdih=False):
+    def __init__(self, geom, allowed=None, dihedral=True, superweakdih=False):
         self._coords = []
         n = len(geom)
         geom = geom.supercell()
@@ -232,14 +232,15 @@ def __init__(self, geom, allowed=None, superweakdih=False):
                 ang = Angle(i, j, k, C=C)
                 if ang.eval(geom.coords) > pi/4:
                     self.append(ang)
-        for bond in self.bonds:
-            self.extend(get_dihedrals(
-                [bond.i, bond.j],
-                geom.coords,
-                bondmatrix,
-                C,
-                superweak=superweakdih,
-            ))
+        if dihedral:
+            for bond in self.bonds:
+                self.extend(get_dihedrals(
+                    [bond.i, bond.j],
+                    geom.coords,
+                    bondmatrix,
+                    C,
+                    superweak=superweakdih,
+                ))
         if geom.lattice is not None:
             self._reduce(n)
 

diff --git a/berny/core.py b/berny/core.py
@@ -18,6 +18,7 @@
     'stepmax': 1.8e-3,
     'steprms': 1.2e-3,
     'trust': 0.3,
+    'dihedral': True,
     'superweakdih': False,
 }
 """
@@ -29,6 +30,9 @@
     Initial trust radius in atomic units. It is the maximum RMS of the
     quadratic step (see below).
 
+- dihedral:
+    Form dihedral angles.
+
 - superweakdih:
     Form dihedral angles containing two or more noncovalent bonds.
 """
@@ -89,7 +93,11 @@ def __init__(self, geom, params):
 
     def init(s, log=no_log):
         s.trust = s.params['trust']
-        s.coords = InternalCoords(s.geom, superweakdih=s.params['superweakdih'])
+        s.coords = InternalCoords(
+            s.geom,
+            dihedral=s.params['dihedral'],
+            superweakdih=s.params['superweakdih'],
+        )
         s.H = s.coords.hessian_guess(s.geom)
         s.weights = s.coords.weights(s.geom)
         for line in str(s.coords).split('\n'):

diff --git a/setup.py b/setup.py
@@ -3,7 +3,7 @@
 
 setup(
     name='pyberny',
-    version='0.3.2',
+    version='0.3.3',
     description='Molecular/crystal structure optimizer',
     long_description=open('README.md').read(),
     long_description_content_type='text/markdown',