GUI4dft v1.4

.github/workflows/python-app.yml

@@ -20,10 +20,10 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 3.9
+      - name: Set up Python 3.10.11
         uses: actions/setup-python@v2
         with:
-          python-version: 3.9
+          python-version: 3.10.11
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
@@ -42,10 +42,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10.11
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: 3.10.11
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -61,10 +61,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10.11
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: 3.10.11
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -91,10 +91,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10.11
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: 3.10.11
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -110,10 +110,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10.11
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: 3.10.11
     - name: Install dependencies
       run: |
             python -m pip install --upgrade pip

README.md

@@ -5,7 +5,7 @@
 GUI4dft (Graphical User Interface for support of Density Functional Theory calculations) - first free SIESTA oriented GUI. It is a cross-platform program. 
 
 ## Install
-GUI4DFT program is written in Python 3 (version >= 3.9). It has some dependences. To install the necessary modules, run in the terminal (in the <gui4dft path>):
+GUI4DFT program is written in Python 3 (version 3.9 or 3.10). It has some dependences. To install the necessary modules, run in the terminal (in the <gui4dft path>):
 
 pip3 install -r ./requirements.txt
 
@@ -34,7 +34,9 @@ v1.2 - Contains some additional features. For example, it allows visualizing the
 
 v1.3 - This version uses pyqtgraph instead of matplotlib and pyside2 instead of PyQt5. The colors of the atoms and covalent radii are taken from the ASE module. The project is covered with tests.
 
-v1.4 - This is the next release in 1.x branch. Pyside6. Added support for exporting structural data to input files VASP, CRYSTAL, QE. 
+v1.4 - Pyside6. Added support for exporting structural data to input files VASP, CRYSTAL, QE. 
+
+v1.5 - This is the next release in 1.x branch. Python 3.12.
 
 The master branch contains more or less stable 1.x version functions.
 

src/core_atomistic/atom.py

@@ -12,6 +12,7 @@ def __init__(self, at_data):
         self.xyz = np.array([at_data[0], at_data[1], at_data[2]])
         self.let = at_data[3]
         self.charge = int(at_data[4])
+        self.cluster: int = 0
         self.is_visible: bool = True
         self.selected: bool = False
         self.active: bool = False

src/core_atomistic/atomic_model.py

@@ -46,13 +46,14 @@
     def __getitem__(self, i):
         return self.atoms[i]
 
-    def add_atom_with_data(self, xyz: np.ndarray, charge: int, tag: str = "") -> None:
+    def add_atom_with_data(self, xyz: np.ndarray, charge: int, let: str = "", tag: str = "") -> None:
         """
         xyz: coords
         charge: atomic number
         tag: additional information
         """
-        let = self.mendeley.get_let(charge)
+        if let == "":
+            let = self.mendeley.get_let(charge)
         atom = Atom([*xyz, let, charge])
         atom.tag = tag
         self.atoms.append(atom)
@@ -130,7 +131,7 @@
     def twist_z(self, alpha):
         cm = self.center_mass()
         self.move(-cm)
-        z0 = self.minZ()
+        z0 = self.min_z()
         z1 = np.linalg.norm(self.lat_vector3)
 
         for i in range(0, len(self.atoms)):
@@ -182,15 +183,17 @@
                 str2 = ani_file.readline()
         else:
             str2 = ani_file.readline()
-        atoms = []
+        new_model = AtomicModel()
         mendeley = TPeriodTable()
         reg = re.compile('[^a-zA-Z ]')
         for i1 in range(0, number_of_atoms):
             str1 = helpers.spacedel(str2)
             s = str1.split(' ')
-            d1 = float(s[indexes[1]])
-            d2 = float(s[indexes[2]])
-            d3 = float(s[indexes[3]])
+            xyz = np.array([s[indexes[1]], s[indexes[2]], s[indexes[3]]], dtype=float)
+            if max(indexes) < len(s) - 1:
+                tag = s[max(indexes) + 1]
+            else:
+                tag = ""
             c = s[indexes[0]]
             if c.isnumeric():
                 charge = int(c)
@@ -199,10 +202,9 @@
                 c = reg.sub('', s[indexes[0]])
                 charge = mendeley.get_charge_by_letter(c)
             if (charge > 0) or is_allow_charge_incorrect:
-                atoms.append([d1, d2, d3, c, charge])
+                new_model.add_atom_with_data(xyz, charge, let=c, tag=tag)
             if i1 < number_of_atoms -1:
                 str2 = ani_file.readline()
-        new_model = AtomicModel(atoms)
         new_model.set_lat_vectors_default()
         return new_model
 
@@ -395,6 +397,12 @@
         self.rotate_y(betta)
         self.rotate_z(gamma)
 
+    def sub_model(self, inds):
+        new_model_atoms = []
+        for i in inds:
+            new_model_atoms.append(self.atoms[i])
+        return AtomicModel(new_model_atoms)
+
     def projection_to_cylinder(self, atomslist, radius):
         """This method returns projections on cylinder with radius for atom at."""
         row = []
@@ -490,15 +498,15 @@
         cif_text += "\n\n\n\n#End data_GUI4dft_Data\n\n\n"
         return cif_text
 
-    def minX(self):
+    def min_x(self):
         """Minimum X-coordinate."""
         minx = self.atoms[0].x
         for atom in self.atoms:
             if float(atom.x) < float(minx):
                 minx = atom.x
         return float(minx)
 
-    def maxX(self):
+    def max_x(self):
         """Maximum X-coordinate."""
         maxx = self.atoms[0].x
         for atom in self.atoms:
@@ -508,9 +516,9 @@
 
     def size_x(self):
         """The length of the molecule along the X axis."""
-        return self.maxX() - self.minX()
+        return self.max_x() - self.min_x()
 
-    def minY(self):
+    def min_y(self):
         """Minimum Y-coordinate."""
         miny = self.atoms[0].y
 
@@ -519,7 +527,7 @@
                 miny = atom.y
         return float(miny)
 
-    def maxY(self):
+    def max_y(self):
         """Maximum Y-coordinate."""
         maxy = self.atoms[0].y
 
@@ -530,9 +538,9 @@
 
     def size_y(self):
         """The length of the molecule along the Y axis."""
-        return self.maxY() - self.minY()
+        return self.max_y() - self.min_y()
 
-    def minZ(self):
+    def min_z(self):
         """Minimum Z-coordinate."""
         minz = self.atoms[0].z
 
@@ -541,7 +549,7 @@
                 minz = atom.z
         return float(minz)
 
-    def maxZ(self):
+    def max_z(self):
         """Maximum Z-coordinate."""
         maxz = self.atoms[0].z
 
@@ -552,7 +560,11 @@
 
     def size_z(self):
         """The length of the molecule along the Z axis."""
-        return self.maxZ() - self.minZ()
+        return self.max_z() - self.min_z()
+
+    def set_cluster(self, cluster, k):
+        for atom in cluster:
+            self.atoms[atom].cluster = k
 
     def sort_atoms_by_type(self):
         for i in range(0, self.n_atoms()):
@@ -642,6 +654,16 @@
             clusters.append(cluster)
         return clusters
 
+    def find_clusters_by_tag(self):
+        clusters = []
+        tags = np.array(self.get_tags(), dtype=int)
+        size = max(tags)
+        for i in range(0, size):
+            clusters.append([])
+        for i in range(0, len(self.atoms)):
+            clusters[tags[i] - 1].append(i)
+        return clusters
+
     def find_bonds_exact(self):
         """The method returns list of bonds of the molecule."""
         if self.bonds_per:
@@ -838,7 +860,7 @@
         self.go_to_positive_array_translate(self.atoms)
 
     def go_to_positive_coordinates(self):
-        d_vec = np.array([self.minX(), self.minY(), self.minZ()])
+        d_vec = np.array([self.min_x(), self.min_y(), self.min_z()])
         self.move_array(self.atoms, d_vec)
         self.go_to_positive_array(self.atoms)
 

src/core_atomistic/helpers.py

@@ -177,7 +177,6 @@ def list_of_values(filename, prop):
     return list_of_val
 
 
-
 def write_text_to_file(f_name, text):  # pragma: no cover
     if len(f_name) > 0:
         with open(f_name, 'w') as f:

src/core_atomistic_qt/opengl_base.py

@@ -20,6 +20,9 @@ def __init__(self, parent=None):
         self.main_model = None
         self.perspective_angle: int = 35
         self.background_color = np.array((1.0, 1.0, 1.0), dtype=float)
+        self.periodic_table = TPeriodTable()
+        self.color_of_atoms = self.periodic_table.get_all_colors()
+        self.color_of_bonds_by_atoms: bool = True
         self.is_check_atom_selection: bool = False
         self.quality: int = 1
         # opengl lists
@@ -773,9 +776,9 @@ def auto_zoom(self):
         if self.is_orthographic:
             self.scale_factor = aspect * 6.0 / model_size
         else:
-            x_max = self.main_model.maxX()
-            y_max = self.main_model.maxY()
-            z_max = self.main_model.maxZ()
+            x_max = self.main_model.max_x()
+            y_max = self.main_model.max_y()
+            z_max = self.main_model.max_z()
             rad = self.main_model.get_covalent_radii().max()
             h, w = self.height(), self.width()
             size = x_max + rad if h > w else y_max + rad
@@ -864,7 +867,6 @@ def bond_len_correct(self, let1: str, let2: str, d: float):
         ch2 = self.main_model.mendeley.get_charge_by_letter(let2)
         self.main_model.mendeley.Bonds[ch1][ch2] = d
         self.main_model.mendeley.Bonds[ch2][ch1] = d
-        #self.main_model.set_mendeley(self.periodic_table)
         self.main_model.find_bonds_fast()
         self.add_all_elements()
         self.update()

src/models/capedswcnt.py

@@ -38,8 +38,8 @@ def __init__(self, n, m, leng, ncell, type, dist1, angle1, dist2, angle2):
                     for i in range(0, size1):
                         capatoms[i].z = -capatoms[i].z
 
-                minz = self.minZ()
-                maxz = capatoms.maxZ()
+                minz = self.min_z()
+                maxz = capatoms.max_z()
 
                 capatoms.move(np.array([0, 0, minz - maxz - zaz]))
                 capatoms.rotate_z(angle1)
@@ -52,8 +52,8 @@ def __init__(self, n, m, leng, ncell, type, dist1, angle1, dist2, angle2):
                 if not self.invert():
                     for i in range(0, size1):
                         capatoms[i].z = -capatoms[i].z
-                maxz = self.maxZ()
-                minz = capatoms.minZ()
+                maxz = self.max_z()
+                minz = capatoms.min_z()
 
                 zaz = dist2