big grid

backend/latmathcher/__init__.py

@@ -2,3 +2,4 @@
 
 from .latmatcher import LatMatch
 from .pipeline import PipelineLatMatch, atoms_to_greed
+from .utils import generate_xyz_text

backend/latmathcher/latmatcher.py

@@ -53,6 +53,11 @@ class LatMatch:
 
         n = int(np.ceil(eta))
         for (nx, ny) in np.mgrid[-n:n, -n:n].T.reshape(n ** 2 * 4, 2):
+            # print("nx:",nx)
+            # print("ny:", ny)
+            # print("dx:", dx)
+            # print("dy:", dy)
+            # print("etc:", etac)
             d2 = (dx + nx) ** 2 + (dy + ny) ** 2
             cost += np.mean(np.exp(- d2 / (2 * etac))) / n ** 2
         return -cost

backend/latmathcher/utils.py

@@ -0,0 +1,15 @@
+
+
+
+def generate_xyz_text(atoms):
+    """
+    Generate the text content of an XYZ format from a list of atoms.
+    :param atoms: List of atoms with their symbols and coordinates
+    :return: XYZ format as a string
+    """
+    xyz_content = f"{len(atoms)}\n"
+    xyz_content += "XYZ file content generated from atoms_to_greed function\n"
+    for atom in atoms:
+        symbol, coordinates = atom
+        xyz_content += f"{symbol} {coordinates[0]:.3f} {coordinates[1]:.3f} {coordinates[2]:.3f}\n"
+    return xyz_content

interface_connection/latmatcher_interface.py

@@ -1,7 +1,7 @@
 
 
 from backend.latmathcher.plots import plot_atom_list
-from backend.latmathcher import atoms_to_greed
+from backend.latmathcher import atoms_to_greed, generate_xyz_text
 from backend.latmathcher import PipelineLatMatch
 from backend.db_utils.utils import structure_ato_list
 from backend.db_utils.parse_c2db import from_c2db_structure, read_c2db_json
@@ -100,9 +100,10 @@ def compute_supercell_a(file_material_a, file_material_b,inter_distance , max_an
 
 
     # Write the content to a file
-    with open(file12, 'w') as file:
-        file.write(xyz_content)
-
+    # with open(file12, 'w') as file:
+    #     file.write(xyz_content)
+    atoms= atoms_to_greed(super_xyz, lat_v=min_supercel.sc_vec3, dim=(5,5,0))
+    xyz_content=generate_xyz_text(atoms)
 
     plot=plot_supercel(super_xyz, min_supercel)
     return file12, str(rez[0]), str((rez[1], rez[2])),plot, xyz_content
@@ -134,8 +135,8 @@ def  plot_supercel(super_xyz, min_supercel):
     y = [0.0, min_supercel.sc_vec3[1][0], min_supercel.sc_vec3[1][0] + min_supercel.sc_vec3[1][1],
          min_supercel.sc_vec3[1][1], 0.0]
     plt.gca().add_patch(patches.Polygon(xy=list(zip(x, y)), fill=True, alpha=0.4, color="green"))
-    plt.ylim(-15, 15)
-    plt.xlim(-10, 20)
+    plt.ylim(min(y)-10, max(y)+10)
+    plt.xlim(min(x)-10, max(x)+10)
     # super_a = [super_xyz[i] for i in range(len(new_structure["host_guest"])) if
     #            new_structure["host_guest"][i] == "host"]
     # super_b = [super_xyz[i] for i in range(len(new_structure["host_guest"])) if