Fixed some python 3 print bugs as well as include missing iter_equiv_…

…keys_and_pars routines in Cross generators
molmod · Feb 5, 2018 · 845b26e · 845b26e
1 parent 9196186
commit 845b26e
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Showing 2 changed files with 25 additions and 13 deletions.
diff --git a/yaff/pes/generator.py b/yaff/pes/generator.py
@@ -1006,8 +1006,8 @@ def apply(self, par_table, system, ff_args):
         part_valence = ff_args.get_part_valence(system)
         vterms = []
         ics = []
-        for i in xrange(6):
-            for j in xrange(i+1,6):
+        for i in range(6):
+            for j in range(i+1,6):
                 VClass = self.__class__.__dict__['VClass%i%i' %(i,j)]
                 if VClass is not None:
                     vterms.append([i,j,VClass])
@@ -1161,6 +1161,10 @@ class CrossBondDihedralGenerator(ValenceCrossGenerator):
 
     def iter_alt_keys(self, key):
         yield key
+
+    def iter_equiv_keys_and_pars(self, key, pars):
+        yield key, pars
+        yield key[::-1], (pars[0], pars[3], pars[2], pars[1], pars[6], pars[5], pars[4], pars[7])
 
     def iter_indexes(self, system):
         return system.iter_dihedrals()
@@ -1301,7 +1305,7 @@ class CrossBendDihedralGenerator(ValenceCrossGenerator):
     VClass03 = None
     VClass04 = None
     VClass05 = None
-    VClass12 = None  #bend123,dihed0123
+    VClass12 = Cross #bend123,dihed0123
     VClass13 = None
     VClass14 = None
     VClass15 = None
@@ -1313,7 +1317,11 @@ class CrossBendDihedralGenerator(ValenceCrossGenerator):
     VClass45 = None
 
     def iter_alt_keys(self, key):
-        yield key
+        yield key    
+
+    def iter_equiv_keys_and_pars(self, key, pars):
+        yield key, pars
+        yield key[::-1], (pars[0], pars[2], pars[1], pars[4], pars[3], pars[5])
 
     def iter_indexes(self, system):
         return system.iter_dihedrals()
@@ -1343,7 +1351,7 @@ class CrossBendDihedral2Generator(CrossBendDihedralGenerator):
     VClass03 = None
     VClass04 = None
     VClass05 = None
-    VClass12 = None  #bend123,dihed0123
+    VClass12 = Cross #bend123,dihed0123
     VClass13 = None
     VClass14 = None
     VClass15 = None
@@ -1370,7 +1378,7 @@ class CrossBendDihedral3Generator(CrossBendDihedralGenerator):
     VClass03 = None
     VClass04 = None
     VClass05 = None
-    VClass12 = None  #bend123,dihed0123
+    VClass12 = Cross #bend123,dihed0123
     VClass13 = None
     VClass14 = None
     VClass15 = None
@@ -1397,7 +1405,7 @@ class CrossBendDihedral4Generator(CrossBendDihedralGenerator):
     VClass03 = None
     VClass04 = None
     VClass05 = None
-    VClass12 = None  #bend123,dihed0123
+    VClass12 = Cross #bend123,dihed0123
     VClass13 = None
     VClass14 = None
     VClass15 = None
@@ -1424,7 +1432,7 @@ class CrossBendDihedral6Generator(CrossBendDihedralGenerator):
     VClass03 = None
     VClass04 = None
     VClass05 = None
-    VClass12 = None  #bend123,dihed0123
+    VClass12 = Cross #bend123,dihed0123
     VClass13 = None
     VClass14 = None
     VClass15 = None
@@ -1451,7 +1459,7 @@ class CrossBendCosDihedralGenerator(ValenceCrossGenerator):
     VClass03 = None
     VClass04 = None
     VClass05 = None
-    VClass12 = None  #bend123,dihed0123
+    VClass12 = Cross #bend123,dihed0123
     VClass13 = None
     VClass14 = None
     VClass15 = None
@@ -1465,6 +1473,10 @@ class CrossBendCosDihedralGenerator(ValenceCrossGenerator):
     def iter_alt_keys(self, key):
         yield key
 
+    def iter_equiv_keys_and_pars(self, key, pars):
+        yield key, pars
+        yield key[::-1], (pars[0], pars[2], pars[1], pars[4], pars[3], pars[5])
+
     def iter_indexes(self, system):
         return system.iter_dihedrals()
 

diff --git a/yaff/pes/test/test_iclist.py b/yaff/pes/test/test_iclist.py
@@ -170,7 +170,7 @@ def test_iclist_peroxide_dihedral_cos2():
         dlist.forward()
         iclist.forward()
         angle = dihed_angle(system.pos)[0]
-        print 'psi=%.3f deg:    target=%.6f  value=%.6f' %(angle/deg, np.cos(2*angle), iclist.ictab[3]['value'])
+        print('psi=%.3f deg:    target=%.6f  value=%.6f' %(angle/deg, np.cos(2*angle), iclist.ictab[3]['value']))
         assert abs(iclist.ictab[3]['value'] - np.cos(2*angle)) < 1e-5
 
 def test_iclist_peroxide_dihedral_cos3():
@@ -192,7 +192,7 @@ def test_iclist_peroxide_dihedral_cos3():
         dlist.forward()
         iclist.forward()
         angle = dihed_angle(system.pos)[0]
-        print 'psi=%.3f deg:    target=%.6f  value=%.6f' %(angle/deg, np.cos(3*angle), iclist.ictab[3]['value'])
+        print('psi=%.3f deg:    target=%.6f  value=%.6f' %(angle/deg, np.cos(3*angle), iclist.ictab[3]['value']))
         assert abs(iclist.ictab[3]['value'] - np.cos(3*angle)) < 1e-5
 
 def test_iclist_peroxide_dihedral_cos4():
@@ -214,7 +214,7 @@ def test_iclist_peroxide_dihedral_cos4():
         dlist.forward()
         iclist.forward()
         angle = dihed_angle(system.pos)[0]
-        print 'psi=%.3f deg:    target=%.6f  value=%.6f' %(angle/deg, np.cos(4*angle), iclist.ictab[3]['value'])
+        print('psi=%.3f deg:    target=%.6f  value=%.6f' %(angle/deg, np.cos(4*angle), iclist.ictab[3]['value']))
         assert abs(iclist.ictab[3]['value'] - np.cos(4*angle)) < 1e-5
 
 def test_iclist_peroxide_dihedral_cos6():
@@ -236,7 +236,7 @@ def test_iclist_peroxide_dihedral_cos6():
         dlist.forward()
         iclist.forward()
         angle = dihed_angle(system.pos)[0]
-        print 'psi=%.3f deg:    target=%.6f  value=%.6f' %(angle/deg, np.cos(6*angle), iclist.ictab[3]['value'])
+        print('psi=%.3f deg:    target=%.6f  value=%.6f' %(angle/deg, np.cos(6*angle), iclist.ictab[3]['value']))
         assert abs(iclist.ictab[3]['value'] - np.cos(6*angle)) < 1e-5
 
 def test_iclist_grad_dihedral_cos_mil53():