From c71338e5c83487b132fee4177e88c876e10a9300 Mon Sep 17 00:00:00 2001
From: qzhu2017 <alecfans@gmail.com>
Date: Wed, 30 Oct 2024 20:50:43 -0400
Subject: [PATCH] add the cut_lattice function

---
 pyxtal/__init__.py     | 23 +++++++++++++++--------
 pyxtal/lattice.py      |  5 +++++
 pyxtal/wyckoff_site.py | 22 +++++++++++++++++++---
 3 files changed, 39 insertions(+), 11 deletions(-)

diff --git a/pyxtal/__init__.py b/pyxtal/__init__.py
index 775709e0..a35a2146 100644
--- a/pyxtal/__init__.py
+++ b/pyxtal/__init__.py
@@ -3282,14 +3282,21 @@ def get_separations(self, hkls=[[1, 0, 0], [0, 1, 0], [0, 0, 1]]):
 
         return np.array(separations)
 
-    #def cut_cell(self, cutoff=5.0):
-    #    """
-    #    An utility to reduce the empty spacing
-    #    """
-    #    seps = self.get_separations()
-    #    id = seps.argmax()
-    #    if seps[id] >= cutoff:
-    #        pass
+    def cut_lattice(self, max_separation=3.0, verbose=False):
+        """
+        An utility to reduce the empty spacing
+        """
+        seps = self.get_separations()
+        ax = seps.argmax()
+        if seps[ax] >= max_separation:
+            cut = seps[ax] - max_separation
+            # update coordinates
+            for mol_site in self.mol_sites:
+                mol_site.cut_lattice(ax, cut)
+            self.lattice.update_para(ax, -cut)
+            if verbose:
+                print(f"Found large separation {ax} {seps[ax]:.2f}")
+                print("Update lattice", self.lattice)
 
 
     def get_structure_factor(self, hkl, coeffs=None):
diff --git a/pyxtal/lattice.py b/pyxtal/lattice.py
index 1f341523..253f3580 100644
--- a/pyxtal/lattice.py
+++ b/pyxtal/lattice.py
@@ -671,6 +671,11 @@ def set_para(self, para=None, radians=False):
         else:
             self.set_matrix()
 
+    def update_para(self, id, change):
+        para = [self.a, self.b, self.c, self.alpha, self.beta, self.gamma]
+        para[id] += change
+        self.set_matrix(para2matrix(para))
+
     def reset_matrix(self, shape="upper"):
         if self.random:
             success = False
diff --git a/pyxtal/wyckoff_site.py b/pyxtal/wyckoff_site.py
index 04e15bb8..d55ffe18 100644
--- a/pyxtal/wyckoff_site.py
+++ b/pyxtal/wyckoff_site.py
@@ -640,9 +640,25 @@ def optimize_orientation_by_energy(self, max_ax=20, max_ori=5, early_quit=3.0, v
             if fun <= early_quit:
                 break
 
-    def update_lattice(self, lattice):
-        # QZ: Symmetrize the angle to the compatible orientation first
-        self.lattice = lattice
+    def cut_lattice(self, ax, cut):
+        """
+        Cut lattice length on the given direction
+
+        Args:
+            ax (int): 0, 1, 2
+            cut (float): the cut
+        """
+        paras = self.lattice.get_para()
+        x0 = self.position[ax]
+        x0 -= np.floor(x0)
+
+        if x0 < 0.25:
+            self.position[ax] = paras[ax] * x0 / (paras[ax]-cut)
+        elif 0.25 <= x0 <= 0.75:
+            self.position[ax] = (paras[ax] * x0 - 0.5 * cut) / (paras[ax]-cut)
+        else:
+            self.position[ax] = (paras[ax] * x0 - cut) / (paras[ax]-cut)
+        #self.lattice.update_para(ax, -cut)
 
     def __str__(self):
         if not hasattr(self.wp, "site_symm"):