adjust the generation of lattice for very long molecules

pyxtal/lattice.py

@@ -76,6 +76,7 @@ def __init__(self, ltype, volume=None, matrix=None, PBC=None, **kwargs):
                 "min_l",
                 "mid_l",
                 "max_l",
+                "min_special", #min special for mole
             ]:
                 setattr(self, key, value)
                 self.kwargs[key] = value
@@ -1127,6 +1128,7 @@ def generate_cellpara(
     minvec=1.2,
     minangle=np.pi / 6,
     max_ratio=10.0,
+    min_special=None,
     maxattempts=100,
     **kwargs,
 ):
@@ -1153,6 +1155,7 @@ def generate_cellpara(
         a 6-length array representing the lattice of the unit cell. If
         generation fails, outputs a warning message and returns empty
     """
+    min_special = kwargs.get("min_special", min_special) #; print("min_special", min_special)
     maxangle = np.pi - minangle
     for _n in range(maxattempts):
         # Triclinic
@@ -1185,6 +1188,11 @@ def generate_cellpara(
             a = vec[0] * np.cbrt(abc) / np.cbrt(xyz)
             b = vec[1] * np.cbrt(abc) / np.cbrt(xyz)
             c = vec[2] * np.cbrt(abc) / np.cbrt(xyz)
+            if min_special is not None and c < min_special:
+                coef = random.uniform(0.8, 1.2) * min_special / c
+                c *= coef
+                b /= np.sqrt(coef)
+                a /= np.sqrt(coef)
         # Orthorhombic
         # elif sg <= 74:
         elif ltype in ["orthorhombic"]:

pyxtal/molecular_crystal.py

@@ -264,6 +264,7 @@ def set_lattice(self, lattice):
                         unique_axis=unique_axis,
                         thickness=self.thickness,
                         area=self.area,
+                        min_special=max([mol.get_max_length() for mol in self.molecules]),
                     )
                     good_lattice = True
                     break

pyxtal/molecule.py

@@ -368,6 +368,16 @@ def get_box(self, padding=None):
                 dims[i] = max([dims[i] + r, 3.4])  # for planar molecules
         return Box(dims)
 
+    def get_lengths(self):
+        if not hasattr(self, 'box'):
+            self.box = self.get_box()
+        return self.box.width, self.box.height, self.box.length
+
+    def get_max_length(self):
+        w, h, l = self.get_lengths()
+        return max([w, h, l])
+
+
     def get_box_coordinates(self, xyz, padding=0, resolution=1.0):
         """
         create the points cloud to describe the molecular box

pyxtal/optimize/base.py

@@ -143,7 +143,7 @@ def __init__(
                         ff_style,
                     )
                     params0 = self.parameters.params_init.copy()
-                    self.parameters.export_parameters(self.wdir + "/" + self.ff_parameters, params0)
+                    self.parameters.export_parameters(self.workdir + "/" + self.ff_parameters, params0)
 
                 self.prepare_chm_info(params0)
 

pyxtal/wyckoff_site.py

@@ -805,9 +805,9 @@ def _create_matrix(self, center=False, ignore=False):
             ijk_lists = []
             for id in range(3):
                 if self.PBC[id]:
-                    if not ignore and abc[id] > 25 and self.radius < 10:
+                    if not ignore and abc[id] > 50.0 and self.radius < 10:
                         ijk_lists.append([0])
-                    elif abc[id] < 7.0:
+                    elif abc[id] < 8.5:
                         ijk_lists.append([-3, -2, -1, 0, 1, 2, 3])
                     else:
                         ijk_lists.append([-1, 0, 1])
@@ -866,7 +866,6 @@ def get_dists_auto(self, ignore=False):
             a distance matrix (M, N, N)
             list of molecular xyz (M, N, 3)
         """
-        len(self.numbers)
         coord1, _ = self._get_coords_and_species(first=True, unitcell=True)
 
         return self.get_distances(coord1, coord1, center=False, ignore=ignore)
@@ -918,7 +917,6 @@ def short_dist(self):
         Returns:
             True or False
         """
-        len(self.numbers)
         tols_matrix = self.tols_matrix
         # Check periodic images
         d, _ = self.get_dists_auto()