fix a bug in lattice.from_1D_representation

pyxtal/__init__.py

@@ -1341,14 +1341,14 @@ def get_std_representation(self, trans):
         """
         pass
 
-    def get_1D_representation(self):
+    def get_1D_representation(self, standard=False):
         """
         Get the 1D representation class for molecular crystals
         """
         if self.molecular:
             rep = representation.from_pyxtal(self)
         else:
-            rep = representation_atom.from_pyxtal(self)
+            rep = representation_atom.from_pyxtal(self, standard=standard)
         return rep
 
     def transform(self, trans, lattice=None):
@@ -3148,6 +3148,7 @@ def update_from_1d_rep(self, x):
         # update cell
         l_type = self.lattice.ltype
         self.lattice = Lattice.from_1d_representation(cell, l_type)
+        #print("lattice dof", N, cell, l_type, self.lattice)
 
         # update position
         start = 0
@@ -3169,7 +3170,7 @@ def get_1d_rep_x(self):
         The above rep is [2.5019, 8.7514, 0.4614]
         """
 
-        rep = self.get_1D_representation()
+        rep = self.get_1D_representation(standard=True)
         cell, xyzs = rep.x[0][1:], rep.x[1:]
         x = cell
         for xyz in xyzs:

pyxtal/lattice.py

@@ -477,7 +477,7 @@ def from_1d_representation(self, v, ltype):
             a, b, c, alpha, beta, gamma = v[0], v[1], v[2], 90, 90, 90
         elif ltype == 'tetragonal':
             a, b, c, alpha, beta, gamma = v[0], v[0], v[1], 90, 90, 90
-        elif ltype == 'hexagonal':
+        elif ltype in ['trigonal', 'hexagonal']:
             a, b, c, alpha, beta, gamma = v[0], v[0], v[1], 90, 90, 120
         else:
             a, b, c, alpha, beta, gamma = v[0], v[0], v[0], 90, 90, 90

pyxtal/representation.py

@@ -21,7 +21,7 @@ def __str__(self):
         return self.to_string()
 
     @classmethod
-    def from_pyxtal(cls, struc, standard=False):
+    def from_pyxtal(cls, struc, standard=True):
         """
         Initialize 1D rep. from the pyxtal object
 

pyxtal/test_all.py

@@ -949,6 +949,12 @@ def test_is_valid_lattice(self):
         self.assertTrue(l9.is_valid_lattice())
         self.assertTrue(not l10.is_valid_lattice())
 
+    def test_from_1d_representation(self):
+        lat = Lattice.from_1d_representation([5.09, 6.11], 'trigonal')
+        self.assertTrue(abs(lat.a-5.09)<1e-3)
+        self.assertTrue(abs(lat.c-6.11)<1e-3)
+        self.assertTrue(abs(lat.gamma-2/3*np.pi)<1e-3)
+
 
 class TestSymmetry(unittest.TestCase):
     def test_from_symops_wo_grou(self):