Merge pull request #34 from sozykinsa/version1_4_beta

Version1 4 beta

.github/workflows/python-app.yml

@@ -27,7 +27,6 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install black flake8
           pip install -r requirements.txt
           pip install -r requirements-dev.txt
       - name: Lint with flake8
@@ -37,6 +36,25 @@ jobs:
           # exit-zero treats all errors as warnings. black defaults to 88 characters
           flake8 . --exclude src/ui/*, --count --exit-zero --max-complexity=18 --max-line-length=120 --statistics
 
+  test-core:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install -r requirements-dev.txt
+    - name: Test with pytest
+      run: |
+        python -m pytest tests_core_atomistic --cov=src/core_atomistic --cov-report=xml --cov-report=term-missing
+
   test-linux:
 
     runs-on: ubuntu-latest
@@ -50,12 +68,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pytest pytest-qt
         pip install -r requirements.txt
         pip install -r requirements-dev.txt
     - name: Test with pytest
       run: |
-        python -m pytest tests --cov=src/core_gui_atomistic --cov-report=xml --cov-report=term-missing --ignore=tests/gui4dft_opengl --ignore=tests/core_gui_atomistic_qt
+        python -m pytest tests --cov=src --cov-report=xml --cov-report=term-missing --ignore=tests/gui4dft_opengl
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1
       with:
@@ -81,12 +98,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pytest pytest-qt pytest-xvfb
         pip install -r requirements.txt
         pip install -r requirements-dev.txt
     - name: Test with pytest
       run: |
-        python -m pytest tests --color=yes --cov=src/core_gui_atomistic --cov=src/src_gui4dft --cov-report=xml --cov-report=term-missing --ignore=tests/gui4dft_opengl
+        python -m pytest tests --color=yes --cov=src/core_atomistic --cov=src/src_gui4dft --cov-report=xml --cov-report=term-missing --ignore=tests/gui4dft_opengl
 
   test-mac:
 
@@ -105,4 +121,4 @@ jobs:
             pip install -r requirements-dev.txt
     - name: Test with pytest
       run: |
-        python -m pytest tests --color=yes --cov=src/core_gui_atomistic --cov=src/src_gui4dft --cov-report=xml --cov-report=term-missing --ignore=tests/gui4dft_opengl
+        python -m pytest tests --color=yes --cov=src/core_atomistic --cov=src/src_gui4dft --cov-report=xml --cov-report=term-missing --ignore=tests/gui4dft_opengl

.gitignore

@@ -14,4 +14,5 @@ executable/build/
 executable/gui4dft.spec
 tests/.coverage
 .coverage
-coverage.xml
+coverage.xml
+/tests_core_atomistic/.pytest_cache

README.md

@@ -5,23 +5,24 @@
 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 >= 3.8). It has some dependences. To install the necessary modules, run in the terminal (command line):
+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>):
 
 pip3 install -r ./requirements.txt
 
-To run the program, type
+To run the program, type (in the <gui4dft path>/src)
 
 python3 gui4dft.py
 
 ## Problems with Install?
 
 You have to set the variable QT_API:
 
-export QT_API=pyside2 (in linux, or https://www.architectryan.com/2018/08/31/how-to-change-environment-variables-on-windows-10/ in Windows)
+export QT_API=pyside6 (in linux, or https://www.architectryan.com/2018/08/31/how-to-change-environment-variables-on-windows-10/ in Windows)
 
 Some operating systems may require additional packages to be installed:
 
-Xubuntu: sudo apt-get install qtbase5-dev
+Ubuntu 22.04: sudo apt-get install -y libxcb-cursor-dev
+Xubuntu: ? sudo apt-get install qtbase5-dev
 
 ## Explanations for the versions of the program
 
@@ -33,7 +34,7 @@ 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. Added support for exporting structural data to input files VASP, CRYSTAL, QE.
+v1.4 - This is the next release in 1.x branch. Pyside6. Added support for exporting structural data to input files VASP, CRYSTAL, QE. 
 
 The master branch contains more or less stable 1.x version functions.
 

requirements-dev-qt.txt

@@ -0,0 +1,2 @@
+pytest-qt
+pytest-xvfb

requirements-dev.txt

@@ -1,6 +1,4 @@
 pytest
 pytest-cov
-pytest-qt
-pytest-xvfb
 black
 flake8

requirements.txt

@@ -1,5 +1,5 @@
 pyopengl
-pyside2
+pyside6
 qtpy
 ase
 numpy

src/core_gui_atomistic/atom.py → src/core_atomistic/atom.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-from core_gui_atomistic import helpers
+from core_atomistic import helpers
 import numpy as np
 
 

src/core_gui_atomistic/atomic_model.py → src/core_atomistic/atomic_model.py

@@ -12,9 +12,9 @@
 from numpy.linalg import inv
 from numpy.linalg import norm
 
-from core_gui_atomistic import helpers
-from core_gui_atomistic.periodic_table import TPeriodTable
-from core_gui_atomistic.atom import Atom
+from core_atomistic import helpers
+from core_atomistic.periodic_table import TPeriodTable
+from core_atomistic.atom import Atom
 from scipy.spatial.distance import cdist
 from scipy.optimize import fmin
 import scipy
@@ -783,6 +783,16 @@ def types_of_atoms(self):
                 types.append([i, elements[i]])
         return types
 
+    def get_charge_to_type_array(self):
+        per_tab = self.mendeley
+        text = ""
+        types = self.types_of_atoms()
+        charge_to_type = np.zeros(200, dtype=int)
+        for i in range(0, len(types)):
+            text += ' ' + str(per_tab.get_let(int(types[i][0])))
+            charge_to_type[int(types[i][0])] = i + 1
+        return charge_to_type, text
+
     def formula(self):
         text = ""
         charges = self.types_of_atoms()

src/core_gui_atomistic/periodic_table.py → src/core_atomistic/periodic_table.py

@@ -1,18 +1,21 @@
 # -*- coding: utf-8 -*-
 
 import numpy as np
-from ase.data import covalent_radii
+from ase.data import covalent_radii, atomic_masses_common
 from ase.data.colors import cpk_colors, jmol_colors
 
 
 class TPeriodTableAtom:
     """Replace color by 'user_color', 'ase_color', 'xxx_color'"""
-    def __init__(self, charge, radius, let, color, mass=1):
+    def __init__(self, charge, radius, let, color, mass=0):
         self.charge = charge
         self.radius = radius
         self.let = let
         # self.color = color
-        self.mass = mass
+        if (mass == 0) and (charge < 119):
+            self.mass = atomic_masses_common[charge]
+        else:
+            self.mass = mass
 
 
 default_color = [0.6, 0.6, 1.0, 1.0]

src/core_gui_atomistic/gui4dft_project_file.py → src/core_atomistic/project_file.py

@@ -1,9 +1,9 @@
 import os
 import numpy as np
-from core_gui_atomistic.atomic_model import AtomicModel
+from core_atomistic.atomic_model import AtomicModel
 
 
-class GUI4dftProjectFile(object):
+class ProjectFile(object):
 
     @staticmethod
     def project_file_writer(model):

src/core_gui_atomistic_qt/guiopenglbase.py → src/core_atomistic_qt/opengl_base.py

@@ -4,12 +4,12 @@
 import OpenGL.GL as gl
 import OpenGL.GLU as glu
 from qtpy.QtWidgets import QOpenGLWidget
-from PySide2.QtCore import QEvent
-from PySide2.QtCore import Qt
-from PySide2.QtGui import QColor, QPainter, QFont
+from qtpy.QtCore import QEvent
+from qtpy.QtCore import Qt
+from qtpy.QtGui import QColor, QPainter, QFont
 from copy import deepcopy
-from core_gui_atomistic.periodic_table import TPeriodTable
-from core_gui_atomistic.atom import Atom
+from core_atomistic.periodic_table import TPeriodTable
+from core_atomistic.atom import Atom
 import math
 import numpy as np
 
@@ -619,9 +619,6 @@ def light_prepare(self) -> None:
         gl.glEnable(gl.GL_LIGHT0)
         gl.glEnable(gl.GL_DEPTH_TEST)
         gl.glEnable(gl.GL_COLOR_MATERIAL)
-        # gl.glDisable(gl.GL_COLOR_MATERIAL)
-
-        # Determine the current lighting model
         gl.glLightModelf(gl.GL_LIGHT_MODEL_TWO_SIDE, gl.GL_TRUE)  # two-side lighting calculation
 
         gl.glEnable(gl.GL_LIGHT0)
@@ -680,7 +677,7 @@ def render_text(self, text_to_render, font=QFont()):
                         fl = False
                 if fl:
                     used_space.append([pos_x, pos_y])
-                    painter.drawText(pos_x - self.property_x_shift, pos_y - self.property_y_shift, st)
+                    painter.drawText(int(pos_x - self.property_x_shift), int(pos_y - self.property_y_shift), st)
         painter.end()
 
     @staticmethod
@@ -861,3 +858,13 @@ def set_atomic_structure(self, structure):
         self.main_model.find_bonds_fast()
         self.add_all_elements()
         self.update()
+
+    def bond_len_correct(self, let1: str, let2: str, d: float):
+        ch1 = self.main_model.mendeley.get_charge_by_letter(let1)
+        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/core_gui_atomistic_qt/pyqtgraphwidget.py → src/core_atomistic_qt/qt_graph.py

@@ -4,9 +4,9 @@
 # ------------------------------------------------------
 # https://www.pythonguis.com/tutorials/pyside-plotting-pyqtgraph/
 
-from PySide2.QtWidgets import QWidget, QVBoxLayout
-from PySide2.QtGui import QFont
-from PySide2.QtCore import Qt
+from qtpy.QtWidgets import QWidget, QVBoxLayout
+from qtpy.QtGui import QFont
+from qtpy.QtCore import Qt
 import pyqtgraph as pg  # pip install pyqtgraph
 import numpy as np
 from typing import List

src/core_gui_atomistic_qt/pyqtgraphwidgetimage.py → src/core_atomistic_qt/qt_image.py

@@ -4,7 +4,7 @@
 # ------------------------------------------------------
 # https://www.pythonguis.com/tutorials/pyside-plotting-pyqtgraph/
 
-from PySide2.QtWidgets import QWidget, QVBoxLayout
+from qtpy.QtWidgets import QWidget, QVBoxLayout
 import pyqtgraph as pg  # pip install pyqtgraph
 
 

src/gui4dft.py

@@ -8,11 +8,11 @@
 import sys
 from pathlib import Path
 
-from PySide2.QtCore import QCoreApplication, Qt
-from PySide2.QtGui import QIcon
-from PySide2.QtWidgets import QApplication
+from qtpy.QtCore import QCoreApplication, Qt
+from qtpy.QtGui import QIcon
+from qtpy.QtWidgets import QApplication
 
-from src_gui4dft.qtbased.mainform import MainForm
+from qtbased.gui4dftform import MainForm
 
 sys.path.append('.')
 

src/src_gui4dft/models/bint.py → src/models/bint.py

@@ -2,8 +2,8 @@
 
 import math
 
-from core_gui_atomistic.atom import Atom
-from core_gui_atomistic.atomic_model import AtomicModel as TAtomicModel
+from core_atomistic.atom import Atom
+from core_atomistic.atomic_model import AtomicModel as TAtomicModel
 
 
 class BiNT(TAtomicModel):

src/src_gui4dft/models/bn_plane.py → src/models/bn_plane.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-from src_gui4dft.models.hexagonal_plane import HexagonalPlane
+from models.hexagonal_plane import HexagonalPlane
 
 
 class BNplane(HexagonalPlane):

src/src_gui4dft/models/capedswcnt.py → src/models/capedswcnt.py

@@ -5,9 +5,9 @@
 import numpy as np
 from pathlib import Path
 
-from core_gui_atomistic.atom import Atom
-from core_gui_atomistic.atomic_model import AtomicModel as TAtomicModel
-from src_gui4dft.models.swnt import SWNT
+from core_atomistic.atom import Atom
+from core_atomistic.atomic_model import AtomicModel as TAtomicModel
+from models.swnt import SWNT
 
 
 class CapedSWNT(TAtomicModel):

src/models/cells/hgy.fdf

@@ -0,0 +1,69 @@
+NumberOfAtoms 24
+NumberOfSpecies 1
+WriteCoorStep True
+%block ChemicalSpeciesLabel
+ 1  6  C
+%endblock ChemicalSpeciesLabel
+LatticeConstant       1.0 Ang
+%block LatticeParameters
+  10.918132  10.928019191942518  30.0  90.0  90.0  120.00000
+%endblock LatticeParameters
+AtomicCoordinatesFormat Ang
+%block AtomicCoordinatesAndAtomicSpecies
+    7.73771075    3.91646015    0.00321888 1
+    5.83793527    5.69686868    0.00319663 1
+    7.00307550    2.64489670    0.00307992 1
+    5.58637353    2.79043812    0.00286192 1
+    6.90851533    5.07320737    0.00327538 1
+    4.51568352    3.41388222    0.00280007 1
+    2.27998040    4.56839740    0.00299596 1
+    3.68665538    4.57067093    0.00292072 1
+    1.45070689    3.41175512    0.00293376 1
+    0.12813302    5.69609889    0.00325181 1
+    1.54433620    5.83873967    0.00311587 1
+    2.24726774    7.05705163    0.00304912 1
+    3.71590058    7.05956093    0.00303845 1
+    4.42123046    5.84219660    0.00303219 1
+    1.66047367    8.35368040    0.00310463 1
+    4.29878106    8.35798568    0.00318221 1
+    9.14444238    3.91853989    0.00325878 1
+    9.88011355    2.64811366    0.00317446 1
+    7.70830376    1.42741070    0.00313964 1
+    9.17704378    1.42984463    0.00319481 1
+    7.12538799    0.12889487    0.00300610 1
+    9.76369877    0.13318502    0.00312341 1
+    9.97401099    5.07495527    0.00337039 1
+   11.29642180    2.79082798    0.00306982 1
+%endblock AtomicCoordinatesAndAtomicSpecies
+SystemName          tpdhg
+SystemLabel         C224
+WriteMullikenPop    1
+PAO.BasisSize  DZP
+MeshCutoff       350.0 Ry
+SpinPolarized True
+MaxSCFIterations       150
+SolutionMethod         diagon
+NetCharge     0.00
+DM.NumberPulay    4
+DM.MixingWeight   0.3
+DM.UseSaveDM      .true.
+NeglNonOverlapInt False
+XC.functional=GGA
+XC.authors=PBE
+WriteCoorXmol     True
+WriteForces .true.
+WriteMullikenPop     1
+MD.TypeOfRun           cg               # Type of dynamics: Conjugate gradients
+MD.NumCGsteps          320              # number of CG steps
+MD.MaxCGDispl          0.10 Ang
+MD.MaxForceTol         0.04 eV/Ang
+MD.UseSaveXV           yes
+MD.VariableCell        .false.
+%block kgrid_Monkhorst_Pack
+  3  0  0   0.0
+  0  3  0   0.0
+  0  0  1   0.0
+%endblock kgrid_Monkhorst_Pack
+%block ProjectedDensityOfStates
+   -24.00  15.00  0.100  1000  eV
+%endblock ProjectedDensityOfStates