def __init__(self):
self.root_window = Tk()
self.vframe = VerticalScrolledFrame(self.root_window)
self.vframe.pack(fill=BOTH, expand=1)
self.window = self.vframe.interior
self.sections = []
self.initialize_window()
def __init__(self):
self.root_window = Tk()
self.vframe = VerticalScrolledFrame(self.root_window)
self.vframe.pack(fill=BOTH, expand=1)
self.window = self.vframe.interior
self.sections = []
self.initialize_window()
def create_window(self):
self.window = ttk.Toplevel(self.parent_window)
self.window.title("NEB Information")
self.window.minsize(500, 500)
self.vframe = VerticalScrolledFrame(self.window)
self.vframe.pack(fill=BOTH, expand=1)
self.neb_window = self.vframe.interior
self.neb_window.grid_rowconfigure(0, weight=1)
self.neb_window.grid_columnconfigure(0, weight=1)
neb_frame = LabelFrame(self.neb_window, text="NEB")
neb_frame.grid(row=0, column=0, padx=20, pady=20)
neb_frame.grid_rowconfigure(0, weight=1)
neb_frame.grid_columnconfigure(0, weight=1)
#frame for images and button
frame1 = Frame(neb_frame)
frame1.grid(row=0, column=0)
frame1.grid_rowconfigure(0, weight=1)
frame1.grid_rowconfigure(1, weight=1)
frame1.grid_columnconfigure(0, weight=1)
frame1.grid_columnconfigure(1, weight=1)
frame1.grid_columnconfigure(2, weight=1)
#add images
label = Label(frame1, text="IMAGES")
label.grid(row=0, column=0, sticky=E, pady=10, padx=10)
images_val = StringVar(frame1)
if self.neb_info['images'][0] is not None:
images_val.set(self.neb_info['images'][0])
images_menu = Entry(frame1, textvariable=images_val)
images_menu.grid(row=0, column=1, sticky=W, pady=10, padx=10)
self.neb_info["images"] = [images_val.get(), images_val]
images_btn = Button(frame1, text="Add Posfiles", command=self.create_window_with_posfiles)
images_btn.grid(row=0, column=2, sticky=W, pady=10, padx=10)
#frame for entities
frame2 = Frame(neb_frame)
frame2.grid(row=1, column=0)
#a label frame to add neb related information
self.neb_entities_frame = LabelFrame(frame2, text="NEB ENTITIES")
self.neb_entities_frame.grid(row=0, column=0, columnspan=3, padx=10, pady=10)
for rownum in xrange(self.num_neb_fields):
self.create_neb_fields(self.neb_entities_frame, rownum)
self.add_button = Button(self.neb_entities_frame, text="Add more neb", command=self.add_elements)
self.add_button.grid(row=self.num_neb_fields + 1, column=0, columnspan=6, pady=10, padx=10)
#save button
save_button = Button(neb_frame, text="Save", command=self.save)
save_button.grid(row=3, column=0, columnspan=2, padx=20, pady=10)
def create_window(self):
self.window = ttk.Toplevel(self.parent_window)
self.window.title("Defects Information")
self.window.minsize(500, 500)
self.vframe = VerticalScrolledFrame(self.window)
self.vframe.pack(fill=BOTH, expand=1)
self.defects_window = self.vframe.interior
self.defects_window.grid_rowconfigure(0, weight=1)
self.defects_window.grid_columnconfigure(0, weight=1)
defects_frame = LabelFrame(self.defects_window, text="Defects")
defects_frame.grid(row=0, column=0, padx=20, pady=20)
defects_frame.grid_rowconfigure(0, weight=1)
defects_frame.grid_rowconfigure(1, weight=1)
defects_frame.grid_columnconfigure(0, weight=1)
defects_frame.grid_columnconfigure(1, weight=1)
#add coordtype
label = Label(defects_frame, text="COORD_TYPE")
label.grid(row=0, column=0, sticky=E, pady=10, padx=10)
coord_type = StringVar(defects_frame)
coord_type.set("fractional")
if self.defects_info['coord_type'][0] is not None:
coord_type.set(self.defects_info['coord_type'][0])
coord_type_option = OptionMenu(defects_frame, coord_type, "fractional", "cartesian")
coord_type_option.grid(row=0, column=1, sticky=W, pady=10, padx=10)
self.defects_info["coord_type"] = [coord_type.get(), coord_type]
#add posfile
label = Label(defects_frame, text="POS FILE")
label.grid(row=1, column=0, sticky=E, pady=10, padx=10)
pos_value = StringVar(defects_frame)
pos_value.set("")
if self.defects_info['posfile'][0] is not None:
pos_value.set(self.defects_info['posfile'][0])
pos_entry = Entry(defects_frame, textvariable=pos_value)
pos_entry.grid(row=1, column=1, sticky=W, pady=10, padx=10)
self.defects_info["posfile"] = [pos_value.get(), pos_value]
#a label frame to add defects related information
self.defects_entities_frame = LabelFrame(defects_frame, text="DEFECT ENTITIES")
self.defects_entities_frame.grid(row=2, column=0, columnspan=2, padx=10, pady=10)
#create field headers
for rownum in xrange(self.num_defect_fields):
self.create_defect_fields(self.defects_entities_frame, rownum)
self.add_button = Button(self.defects_entities_frame, text="Add more defects", command=self.add_elements)
self.add_button.grid(row=self.num_defect_fields + 1, column=0, columnspan=2, pady=10, padx=10)
#save button
save_button = Button(defects_frame, text="Save", command=self.save)
save_button.grid(row=3, column=0, columnspan=2, padx=20, pady=10)
def create_window(self):
self.window = Toplevel(self.parent_window)
self.window.title("Ingredients Information")
self.window.minsize(500, 600)
self.vframe = VerticalScrolledFrame(self.window)
self.vframe.pack(fill=BOTH, expand=1)
self.ingredients_window = self.vframe.interior
self.ingredients_window.grid_rowconfigure(0, weight=1)
self.ingredients_window.grid_rowconfigure(1, weight=1)
self.ingredients_window.grid_rowconfigure(2, weight=1)
self.ingredients_window.grid_columnconfigure(0, weight=1)
#global param frame
global_frame = LabelFrame(self.ingredients_window, text="Global Parameters")
global_frame.grid(row=0, column=0, padx=20, pady=20, sticky=N+S+W+E)
global_label = Label(global_frame, text="Global Parameters")
global_label.grid(row=0, column=0, padx=20, sticky=W)
global_box = Text(global_frame, height=5, width=80)
if self.ingredients_info['global'][0] is not None:
global_box.insert('1.0', self.ingredients_info['global'][0])
else:
global_box.insert('1.0', '\n'.join(["%s %s" % (key, value) for key, value in self.keywords]))
global_box.grid(row=1, column=0, padx=20, pady=5)
self.ingredients_info['global'][1] = global_box
self.ingredients_frame = LabelFrame(self.ingredients_window, text="Ingredients information")
self.ingredients_frame.grid(row=1, column=0, padx=20, pady=5, sticky=N+S+W+E)
self.ingredients_frame.grid_rowconfigure(0, weight=1)
self.ingredients_frame.grid_columnconfigure(0, weight=1)
#ingredients frames
for rownum in xrange(self.num_ing_fields):
self.create_ingredient_fields(self.ingredients_frame, rownum)
self.add_button = Button(self.ingredients_frame, text="Add more Ingredients", command=self.add_ingredients)
self.add_button.grid(row=self.num_ing_fields + 1, column=0, pady=10, padx=10)
#save button
save_button = Button(self.ingredients_window, text="Save", command=self.save)
save_button.grid(row=2, column=0, padx=20, pady=10, sticky=N+S+W+E)
class IngredientsSection:
def __init__(self, parent_window, grid_row):
self.parent_window = parent_window
self.grid_row = grid_row
self.summary_frame = None
self.keywords = [\
('mast_program', 'vasp'), ('mast_kpoints', '2x2x2 M'), ('mast_pp_setup', 'La=La Mn=Mn_pv O=O_s'), ('mast_xc', 'PW91'), ('mast_multiplyencut', '1.5'),\
('mast_setmagmom', '1 -1 1 -1 1 -1 1 -1'), ('mast_charge', '1'),('mast_coordinates', 'im1poscar,im2poscar,im3poscar'), ('mast_strain', '1.01 1.03 0.98'),\
('mast_write_method', 'no_setup'), ('mast_ready_method', 'ready_singlerun'), ('mast_run_method', 'run_singlerun'), ('mast_complete_method', 'complete_singlerun'),\
('mast_update_children_method', 'give_structure'), ('mast_nodes', '3'), ('mast_ppn', '8'), ('mast_queue', 'morgan1'),\
('mast_exec', '//opt/mpiexec/bin/mpiexec //share/apps/bin/vasp5.2_CNEB'), ('mast_walltime', '12'), ('mast_memory', '2'),\
('ibrion', '-1'), ('lcharge', 'False'), ('lwave', 'False'),\
]
self.ingredients_info = {\
'global' : [None, None],\
'ingredients' : [{}, {}],\
}
self.key_boxes = {}
self.num_ing_fields = 1
def content(self):
content_start = "$ingredients\n"
content_end = "$end\n\n"
content_lines = ""
if self.ingredients_info['global'][0]:
content_lines += "begin ingredients_global\n"
content_lines += "%s\n" % self.ingredients_info['global'][0]
content_lines += "end\n\n"
if self.ingredients_info['ingredients'][0]:
for ing_key, ing_data in self.ingredients_info['ingredients'][0].iteritems():
content_lines += "begin %s\n" % ing_data[0]
content_lines += "%s\n" % ing_data[1]
content_lines += "end\n\n"
return content_start + content_lines + content_end
def summary(self):
#the frame which encloses all the contents
self.summary_frame = LabelFrame(self.parent_window, text="Ingredients")
#the frame contents
add_button = Button(self.summary_frame, text="Add Ingredients", command=self.create_window)
add_button.pack(pady=20)
self.summary_frame.grid(row=self.grid_row, column=0, sticky=W+E, padx=20, pady=5)
def create_window(self):
self.window = Toplevel(self.parent_window)
self.window.title("Ingredients Information")
self.window.minsize(500, 600)
self.vframe = VerticalScrolledFrame(self.window)
self.vframe.pack(fill=BOTH, expand=1)
self.ingredients_window = self.vframe.interior
self.ingredients_window.grid_rowconfigure(0, weight=1)
self.ingredients_window.grid_rowconfigure(1, weight=1)
self.ingredients_window.grid_rowconfigure(2, weight=1)
self.ingredients_window.grid_columnconfigure(0, weight=1)
#global param frame
global_frame = LabelFrame(self.ingredients_window, text="Global Parameters")
global_frame.grid(row=0, column=0, padx=20, pady=20, sticky=N+S+W+E)
global_label = Label(global_frame, text="Global Parameters")
global_label.grid(row=0, column=0, padx=20, sticky=W)
global_box = Text(global_frame, height=5, width=80)
if self.ingredients_info['global'][0] is not None:
global_box.insert('1.0', self.ingredients_info['global'][0])
else:
global_box.insert('1.0', '\n'.join(["%s %s" % (key, value) for key, value in self.keywords]))
global_box.grid(row=1, column=0, padx=20, pady=5)
self.ingredients_info['global'][1] = global_box
self.ingredients_frame = LabelFrame(self.ingredients_window, text="Ingredients information")
self.ingredients_frame.grid(row=1, column=0, padx=20, pady=5, sticky=N+S+W+E)
self.ingredients_frame.grid_rowconfigure(0, weight=1)
self.ingredients_frame.grid_columnconfigure(0, weight=1)
#ingredients frames
for rownum in xrange(self.num_ing_fields):
self.create_ingredient_fields(self.ingredients_frame, rownum)
self.add_button = Button(self.ingredients_frame, text="Add more Ingredients", command=self.add_ingredients)
self.add_button.grid(row=self.num_ing_fields + 1, column=0, pady=10, padx=10)
#save button
save_button = Button(self.ingredients_window, text="Save", command=self.save)
save_button.grid(row=2, column=0, padx=20, pady=10, sticky=N+S+W+E)
#individual ingredients
#param_box = self.create_param_box(global_frame, "global")
#ind_frame = LabelFrame(self.ingredients_window, text="Ingredients")
#ind_frame.grid(row=1, column=0, padx=20, pady=20)
#for num in xrange(self.num_ing_fields):
# param_box = self.create_param_box(ind_frame, "individual", ingredient_index=num)
# param_box.grid(row=num, column=0, padx=20, pady=20)
def save(self):
self.ingredients_info['global'][0] = self.ingredients_info['global'][1].get("1.0", END)
for rownum in xrange(self.num_ing_fields):
self.ingredients_info['ingredients'][0][rownum] = [self.ingredients_info['ingredients'][1][rownum][0].get(), self.ingredients_info['ingredients'][1][rownum][1].get("1.0", END)]
self.window.destroy()
self.window = None
self.has_summary = True
self.summary_frame.grid_remove()
self.summary()
def add_ingredients(self):
self.num_ing_fields += 1
self.add_button.grid_remove()
self.create_ingredient_fields(self.ingredients_frame, self.num_ing_fields-1)
self.add_button = Button(self.ingredients_frame, text="Add more Ingredients", command=self.add_ingredients)
self.add_button.grid(row=self.num_ing_fields + 1, column=0, pady=10, padx=10)
def create_ingredient_fields(self, frame, rownum):
if rownum not in self.ingredients_info['ingredients'][1]:
self.ingredients_info['ingredients'][1][rownum] = [None, None]
ing_frame = LabelFrame(frame, text="Ingredient %s" % (rownum + 1))
ing_frame.grid(row=rownum, column=0, padx=10, pady=10, sticky=N+S+W+E)
ing_frame.grid_rowconfigure(0, weight=1)
ing_frame.grid_columnconfigure(0, weight=1)
ing_frame.grid_columnconfigure(1, weight=10)
space_label = Label(ing_frame, text="")
space_label.grid(row=0, column=0, pady=5, sticky=W)
name_label = Label(ing_frame, text="Ingredient Name")
name_label.grid(row=1, column=0, columnspan=2, padx=10, pady=2, sticky=W)
name_value = StringVar()
if rownum in self.ingredients_info['ingredients'][0]:
name_value.set(self.ingredients_info['ingredients'][0][rownum][0])
name_box = Entry(ing_frame, textvariable=name_value)
name_box.grid(row=2, column=0, columnspan=2, padx=10, pady=2, sticky=W)
param_label = Label(ing_frame, text="Ingredient Parameters")
param_label.grid(row=3, column=0, columnspan=2, padx=10, pady=2, sticky=W)
key_option_val = StringVar(ing_frame)
key_option_val.set(self.keywords[0][0])
key_option_menu = Combobox(ing_frame, textvariable=key_option_val, state='readonly')
key_option_menu['values'] = [key for key, value in self.keywords]
key_option_menu.grid(row=4, column=0, sticky=W, pady=10, padx=10)
add_key_btn = Button(ing_frame, text="+")
add_key_btn.grid(row=4, column=1, padx=10, pady=10, sticky=W)
self.key_boxes[rownum] = key_option_val
param_box = Text(ing_frame, height=5, width=80)
if rownum in self.ingredients_info['ingredients'][0]:
param_box.insert('1.0', self.ingredients_info['ingredients'][0][rownum][1])
param_box.grid(row=5, column=0, columnspan=2, padx=10, pady=2, sticky=W)
space_label = Label(ing_frame, text="")
space_label.grid(row=5, column=0, pady=5, sticky=W)
add_key_btn.configure(command=lambda:self.add_param_text(param_box, key_option_val))
self.ingredients_info['ingredients'][1][rownum] = [name_value, param_box]
def add_param_text(self, param_box, option_val):
text = param_box.get("1.0", END)
text += option_val.get()
param_box.delete("1.0", END)
param_box.insert("1.0", text)
def create_param_box(self, parent, box_type, ingredient_index=-1):
values_map = {}
object_map = {}
#global param
if box_type == 'global':
values_map = self.ingredients_info['global'][0]
object_map = self.ingredients_info['global'][1]
#individual ingredients
elif box_type == 'individual':
if ingredient_index >= 0 and len(self.ingredients_info['ingredients'][0]) >= ingredient_index + 1:
values_map = self.ingredients_info['ingredients'][0][ingredient_index]
object_map = self.ingredients_info['ingredients'][1][ingredient_index]
frame = Frame(parent)
self.add_param_fields(frame, 0, object_map)
add_button = Button(frame, text="+")
add_button.configure(command=lambda:self.add_param(add_button, parent, box_type))
add_button.grid(row=0, column=2, pady=20, padx=20)
return frame
def add_param(self, add_button, parent, box_type):
print "success"
add_button.grid_remove()
self.create_param_box(parent, box_type)
def add_param_fields(self, frame, rownum, object_map):
#create the fields
key_option_val = StringVar(frame)
key_option_val.set(self.keywords[0])
key_option_menu = Combobox(frame, textvariable=key_option_val, state='readonly')
key_option_menu['values'] = self.keywords
key_option_menu.grid(row=0, column=0, sticky=W, pady=10, padx=10)
val_text = StringVar(frame)
val_entry = Entry(frame, textvariable=val_text)
val_entry.grid(row=0, column=1, pady=10, padx=10, sticky=W)
object_map.append((key_option_val, val_text))
class MastGui:
def __init__(self):
self.root_window = Tk()
self.vframe = VerticalScrolledFrame(self.root_window)
self.vframe.pack(fill=BOTH, expand=1)
self.window = self.vframe.interior
self.sections = []
self.initialize_window()
def initialize_window(self):
#window properties
self.root_window.title("MAST")
screensizeX = self.root_window.winfo_screenwidth()
screensizeY = self.root_window.winfo_screenheight()
self.root_window.minsize(screensizeX-100, screensizeY - 100)
self.window.grid_rowconfigure(0, weight=1)
self.window.grid_rowconfigure(1, weight=1)
self.window.grid_rowconfigure(2, weight=1)
self.window.grid_rowconfigure(3, weight=1)
self.window.grid_rowconfigure(4, weight=1)
self.window.grid_rowconfigure(5, weight=1)
self.window.grid_rowconfigure(6, weight=1)
self.window.grid_columnconfigure(0, weight=1)
#add sections
self.mast_section = MastSection(self.window, 0)
self.mast_section.summary()
self.sections.append(self.mast_section)
self.structure_section = StructureSection(self.window, 1)
self.structure_section.summary()
self.sections.append(self.structure_section)
self.defects_section = DefectsSection(self.window, 2, self.structure_section)
self.defects_section.summary()
self.sections.append(self.defects_section)
self.neb_section = NEBSection(self.window, 3, self.structure_section, self.defects_section)
self.neb_section.summary()
self.sections.append(self.neb_section)
self.ingredients_section = IngredientsSection(self.window, 4)
self.ingredients_section.summary()
self.sections.append(self.ingredients_section)
self.phonon_section = PhononSection(self.window, 5)
self.phonon_section.summary()
self.create_btn = Button(self.window, text="Create Input File", command=self.create_input)
self.create_btn.grid(row=6, column=0, pady=10, padx=10)
def create_input(self):
input_file = open("mast_input.inp", "w")
for section_obj in self.sections:
output_content = section_obj.content()
input_file.write(output_content)
input_file.close()
self.root_window.destroy()
def run(self):
self.root_window.mainloop()
class DefectsSection:
def __init__(self, parent_window, grid_row, structure_section):
self.parent_window = parent_window
self.grid_row = grid_row
self.summary_frame = None
self.defects_info = {\
'coord_type' : [None, None],\
'posfile' : [None, None],\
'defecttype' : [{}, {}],\
'namemap' : [{}, {}],\
'elementmap' : [{}, {}],\
'infomap' : [{}, {}],\
'chargemap' : [{}, {}],\
}
self.num_defect_fields = 1
self.structure_section = structure_section
self.has_summary=False
self.defect_types = ['vacancy', 'interstitial', 'substitution', 'antisite']
self.fields_hash = {}
def content(self):
content_start = "$defects\n"
content_end = "$end\n\n"
content_lines = ""
if self.defects_info['coord_type'][0]:
content_lines += "coord_type %s\n\n" % self.defects_info['coord_type'][0]
if self.defects_info['posfile'][0]:
content_lines += "posfile %s\n\n" % self.defects_info['posfile'][0]
if self.defects_info['namemap'][0]:
for d_id, d_name in self.defects_info['namemap'][0].iteritems():
content_lines += "begin %s\n" % d_name
if self.defects_info['elementmap'][0][d_id]:
for idx, elt in enumerate(self.defects_info['elementmap'][0][d_id]):
elt = elt.split('(', 1)[1].replace(')', '').strip()
content_lines += "%s %s %s" % (self.defects_info['defecttype'][0][d_id][idx], self.defects_info['infomap'][0][d_id][idx], elt)
if self.defects_info['chargemap'][0][d_id][idx]:
content_lines += " charge=%s" % self.defects_info['chargemap'][0][d_id][idx]
content_lines += "\n"
content_lines += "end\n\n"
return content_start + content_lines + content_end
def get_defects_map(self):
return self.defects_info['namemap'][0]
def summary(self):
#the frame which encloses all the contents
self.summary_frame = LabelFrame(self.parent_window, text="Defects")
self.summary_frame.grid_rowconfigure(0, weight=1)
self.summary_frame.grid_rowconfigure(1, weight=1)
self.summary_frame.grid_columnconfigure(0, weight=1)
self.summary_frame.grid_columnconfigure(1, weight=1)
self.summary_frame.grid_columnconfigure(2, weight=1)
self.summary_frame.grid_columnconfigure(3, weight=1)
self.summary_frame.grid_columnconfigure(4, weight=1)
self.summary_frame.grid_columnconfigure(5, weight=1)
#if it has summary show it
if self.has_summary:
#coord_type
coord_type = Label(self.summary_frame, text="COORD_TYPE :")
coord_type.grid(row=0, column=2, sticky=E, pady=5)
coord_type_value = Label(self.summary_frame, text=self.defects_info['coord_type'][0])
coord_type_value.grid(row=0, column=3, sticky=W, pady=5)
if self.defects_info['posfile'][0] is not None:
pos_label = Label(self.summary_frame, text="POSFILE :")
pos_label.grid(row=1, column=2, sticky=E, pady=5)
pos_value = Label(self.summary_frame, text=self.defects_info['posfile'][0])
pos_value.grid(row=1, column=3, sticky=W, pady=5)
for rownum in xrange(self.num_defect_fields):
if rownum == 0:
continue
if self.defects_info['elementmap'][0]['D' + str(rownum)][0].strip() == "":
continue
id_label = Label(self.summary_frame, text='D'+ str(rownum))
id_label.grid(row=2 + rownum, column=0, padx=10, pady=2, sticky=E)
name_label = Label(self.summary_frame, text=self.defects_info['namemap'][0]['D'+str(rownum)])
name_label.grid(row=2 + rownum, column=1, padx=10, pady=2, sticky=E)
element_label = Label(self.summary_frame, text=self.defects_info['elementmap'][0]['D'+str(rownum)][0])
element_label.grid(row=2 + rownum, column=2, padx=10, pady=2, sticky=W)
type_label = Label(self.summary_frame, text=self.defects_info['defecttype'][0]['D'+str(rownum)][0])
type_label.grid(row=2 + rownum, column=3, padx=10, pady=2, sticky=W)
defect_info_label = Label(self.summary_frame, text=self.defects_info['infomap'][0]['D'+str(rownum)][0])
defect_info_label.grid(row=2 + rownum, column=4, padx=10, pady=2, sticky=W)
charge_label = Label(self.summary_frame, text=self.defects_info['chargemap'][0]['D'+str(rownum)][0])
charge_label.grid(row=2 + rownum, column=5, padx=10, pady=2, sticky=W)
#the frame contents
add_button = Button(self.summary_frame, text="Add Defects", command=self.create_window)
add_button.grid(row=3 + self.num_defect_fields, column=0, columnspan=6, pady=20, padx=20)
self.summary_frame.grid(row=self.grid_row, column=0, padx=20, pady=5, sticky=W+E)
def create_window(self):
self.window = ttk.Toplevel(self.parent_window)
self.window.title("Defects Information")
self.window.minsize(500, 500)
self.vframe = VerticalScrolledFrame(self.window)
self.vframe.pack(fill=BOTH, expand=1)
self.defects_window = self.vframe.interior
self.defects_window.grid_rowconfigure(0, weight=1)
self.defects_window.grid_columnconfigure(0, weight=1)
defects_frame = LabelFrame(self.defects_window, text="Defects")
defects_frame.grid(row=0, column=0, padx=20, pady=20)
defects_frame.grid_rowconfigure(0, weight=1)
defects_frame.grid_rowconfigure(1, weight=1)
defects_frame.grid_columnconfigure(0, weight=1)
defects_frame.grid_columnconfigure(1, weight=1)
#add coordtype
label = Label(defects_frame, text="COORD_TYPE")
label.grid(row=0, column=0, sticky=E, pady=10, padx=10)
coord_type = StringVar(defects_frame)
coord_type.set("fractional")
if self.defects_info['coord_type'][0] is not None:
coord_type.set(self.defects_info['coord_type'][0])
coord_type_option = OptionMenu(defects_frame, coord_type, "fractional", "cartesian")
coord_type_option.grid(row=0, column=1, sticky=W, pady=10, padx=10)
self.defects_info["coord_type"] = [coord_type.get(), coord_type]
#add posfile
label = Label(defects_frame, text="POS FILE")
label.grid(row=1, column=0, sticky=E, pady=10, padx=10)
pos_value = StringVar(defects_frame)
pos_value.set("")
if self.defects_info['posfile'][0] is not None:
pos_value.set(self.defects_info['posfile'][0])
pos_entry = Entry(defects_frame, textvariable=pos_value)
pos_entry.grid(row=1, column=1, sticky=W, pady=10, padx=10)
self.defects_info["posfile"] = [pos_value.get(), pos_value]
#a label frame to add defects related information
self.defects_entities_frame = LabelFrame(defects_frame, text="DEFECT ENTITIES")
self.defects_entities_frame.grid(row=2, column=0, columnspan=2, padx=10, pady=10)
#create field headers
for rownum in xrange(self.num_defect_fields):
self.create_defect_fields(self.defects_entities_frame, rownum)
self.add_button = Button(self.defects_entities_frame, text="Add more defects", command=self.add_elements)
self.add_button.grid(row=self.num_defect_fields + 1, column=0, columnspan=2, pady=10, padx=10)
#save button
save_button = Button(defects_frame, text="Save", command=self.save)
save_button.grid(row=3, column=0, columnspan=2, padx=20, pady=10)
def save(self):
self.defects_info['coord_type'][0] = self.defects_info['coord_type'][1].get()
self.defects_info['posfile'][0] = self.defects_info['posfile'][1].get()
for rownum in xrange(self.num_defect_fields):
self.defects_info['namemap'][0]['D'+str(rownum)] = self.defects_info['namemap'][1]['D'+str(rownum)].get()
num_fields = self.fields_hash.get('D' + str(rownum), 0)
for i in xrange(num_fields):
if 'D' + str(rownum) in self.defects_info['elementmap'][0]:
if i < len(self.defects_info['elementmap'][0]['D' + str(rownum)]):
self.defects_info['elementmap'][0]['D' + str(rownum)][i] = self.defects_info['elementmap'][1]['D'+str(rownum)][i].get()
else:
self.defects_info['elementmap'][0]['D' + str(rownum)].append(self.defects_info['elementmap'][1]['D'+str(rownum)][i].get())
else:
self.defects_info['elementmap'][0]['D'+str(rownum)] = [self.defects_info['elementmap'][1]['D'+str(rownum)][i].get()]
if 'D' + str(rownum) in self.defects_info['infomap'][0]:
if i < len(self.defects_info['infomap'][0]['D' + str(rownum)]):
self.defects_info['infomap'][0]['D' + str(rownum)][i] = self.defects_info['infomap'][1]['D'+str(rownum)][i].get()
else:
self.defects_info['infomap'][0]['D' + str(rownum)].append(self.defects_info['infomap'][1]['D'+str(rownum)][i].get())
else:
self.defects_info['infomap'][0]['D'+str(rownum)] = [self.defects_info['infomap'][1]['D'+str(rownum)][i].get()]
if 'D' + str(rownum) in self.defects_info['chargemap'][0]:
if i < len(self.defects_info['chargemap'][0]['D' + str(rownum)]):
self.defects_info['chargemap'][0]['D' + str(rownum)][i] = self.defects_info['chargemap'][1]['D'+str(rownum)][i].get()
else:
self.defects_info['chargemap'][0]['D' + str(rownum)].append(self.defects_info['chargemap'][1]['D'+str(rownum)][i].get())
else:
self.defects_info['chargemap'][0]['D'+str(rownum)] = [self.defects_info['chargemap'][1]['D'+str(rownum)][i].get()]
if 'D' + str(rownum) in self.defects_info['defecttype'][0]:
if i < len(self.defects_info['defecttype'][0]['D' + str(rownum)]):
self.defects_info['defecttype'][0]['D' + str(rownum)][i] = self.defects_info['defecttype'][1]['D'+str(rownum)][i].get()
else:
self.defects_info['defecttype'][0]['D' + str(rownum)].append(self.defects_info['defecttype'][1]['D'+str(rownum)][i].get())
else:
self.defects_info['defecttype'][0]['D'+str(rownum)] = [self.defects_info['defecttype'][1]['D'+str(rownum)][i].get()]
self.window.destroy()
self.window = None
self.has_summary = True
self.summary_frame.grid_remove()
self.summary()
def add_elements(self):
self.num_defect_fields += 1
self.add_button.grid_remove()
self.create_defect_fields(self.defects_entities_frame, self.num_defect_fields - 1)
self.add_button = Button(self.defects_entities_frame, text="Add more defects", command=self.add_elements)
self.add_button.grid(row=self.num_defect_fields + 1, column=0, columnspan=6, pady=10, padx=10)
def create_defect_fields(self, frame, rownum):
elements_map = self.structure_section.get_elements_map()
elements_options = ["%s (%s)" % (value, key) for key, value in elements_map.iteritems()]
num_fields = self.fields_hash.get('D' + str(rownum), 1)
self.fields_hash['D' + str(rownum)] = num_fields
d_frame = LabelFrame(frame, text="D" + str(rownum))
d_frame.grid(row=rownum, column=0, padx=10, pady=10, sticky=N+S+W+E)
id_label = Label(d_frame, text="D" + str(rownum))
id_label.grid(row=0, column=0, padx=10, pady=10, sticky=W)
name_label = Label(d_frame, text="NAME")
name_label.grid(row=0, column=0, padx=10, pady=10, sticky=W)
element_label = Label(d_frame, text="ELEMENT")
element_label.grid(row=0, column=1, padx=10, pady=10, sticky=W)
vacancy_label = Label(d_frame, text="DEFECT_TYPE")
vacancy_label.grid(row=0, column=2, padx=10, pady=10, sticky=W)
vacancy_label = Label(d_frame, text="DEFECT_INFO")
vacancy_label.grid(row=0, column=3, padx=10, pady=10, sticky=W)
charge_label = Label(d_frame, text="CHARGE")
charge_label.grid(row=0, column=4, padx=10, pady=10, sticky=W)
name_text = StringVar()
if self.defects_info['namemap'][0] and ('D' + str(rownum)) in self.defects_info['namemap'][0]:
name_text.set(self.defects_info['namemap'][0]['D'+str(rownum)])
name_val = Entry(d_frame, textvariable=name_text)
name_val.grid(row=1, column=0, pady=10, padx=10, sticky=W)
self.defects_info['namemap'][1]['D' + str(rownum)] = name_text
for i in xrange(num_fields):
self.create_individual_fields(d_frame, elements_options, rownum, i + 1)
def create_individual_fields(self, d_frame, elements_options, defect_id, rownum):
element = StringVar(d_frame)
element_val = None
if self.defects_info['elementmap'][0] and ('D' + str(defect_id)) in self.defects_info['elementmap'][0] and \
rownum <= len(self.defects_info['elementmap'][0]['D' + str(defect_id)]):
element_val = self.defects_info['elementmap'][0]['D' + str(defect_id)][rownum - 1]
option_menu = OptionMenu(d_frame, element, ())
option_menu.grid(row=rownum, column=1, sticky=W, pady=10, padx=10)
self.add_options(option_menu, elements_options, element, element_val)
if 'D' + str(defect_id) in self.defects_info['elementmap'][1]:
if rownum <= len(self.defects_info['elementmap'][1]['D' + str(defect_id)]):
self.defects_info['elementmap'][1]['D' + str(defect_id)][rownum - 1] = element
else:
self.defects_info['elementmap'][1]['D' + str(defect_id)].append(element)
else:
self.defects_info['elementmap'][1]['D' + str(defect_id)] = [element]
defect_type_text = StringVar(d_frame)
defect_type_val = None
if self.defects_info['defecttype'][0] and ('D' + str(defect_id)) in self.defects_info['defecttype'][0] and \
rownum <= len(self.defects_info['defecttype'][0]['D' + str(defect_id)]):
defect_type_val = self.defects_info['defecttype'][0]['D' + str(defect_id)][rownum - 1]
defect_type_menu = OptionMenu(d_frame, defect_type_text, ())
defect_type_menu.grid(row=rownum, column=2, sticky=W, pady=10, padx=10)
self.add_options(defect_type_menu, self.defect_types, defect_type_text, defect_type_val)
if 'D' + str(defect_id) in self.defects_info['defecttype'][1]:
if rownum <= len(self.defects_info['defecttype'][1]['D' + str(defect_id)]):
self.defects_info['defecttype'][1]['D' + str(defect_id)][rownum - 1] = defect_type_text
else:
self.defects_info['defecttype'][1]['D' + str(defect_id)].append(defect_type_text)
else:
self.defects_info['defecttype'][1]['D' + str(defect_id)] = [defect_type_text]
vacancy_text = StringVar(d_frame)
if self.defects_info['infomap'][0] and ('D' + str(defect_id)) in self.defects_info['infomap'][0] and \
rownum <= len(self.defects_info['infomap'][0]['D' + str(defect_id)]):
vacancy_text.set(self.defects_info['infomap'][0]['D'+str(defect_id)][rownum - 1])
vacancy_val = Entry(d_frame, textvariable=vacancy_text)
vacancy_val.grid(row=rownum, column=3, pady=10, padx=10, sticky=W)
if 'D' + str(defect_id) in self.defects_info['infomap'][1]:
if rownum <= len(self.defects_info['infomap'][1]['D' + str(defect_id)]):
self.defects_info['infomap'][1]['D' + str(defect_id)][rownum - 1] = vacancy_text
else:
self.defects_info['infomap'][1]['D' + str(defect_id)].append(vacancy_text)
else:
self.defects_info['infomap'][1]['D' + str(defect_id)] = [vacancy_text]
charge_text = StringVar(d_frame)
if self.defects_info['chargemap'][0] and ('D' + str(defect_id)) in self.defects_info['chargemap'][0] and \
rownum <= len(self.defects_info['chargemap'][0]['D' + str(defect_id)]):
charge_text.set(self.defects_info['chargemap'][0]['D'+str(defect_id)][rownum - 1])
charge_val = Entry(d_frame, textvariable=charge_text)
charge_val.grid(row=rownum, column=4, pady=10, padx=10, sticky=W)
if 'D' + str(defect_id) in self.defects_info['chargemap'][1]:
if rownum <= len(self.defects_info['chargemap'][1]['D' + str(defect_id)]):
self.defects_info['chargemap'][1]['D' + str(defect_id)][rownum - 1] = charge_text
else:
self.defects_info['chargemap'][1]['D' + str(defect_id)].append(charge_text)
else:
self.defects_info['chargemap'][1]['D' + str(defect_id)] = [charge_text]
add_button = Button(d_frame, text="+")
add_button.grid(row=rownum, column=5, pady=10, padx=10)
add_button.configure(command=lambda:self.add_defect_field(add_button, d_frame, rownum, elements_options, defect_id))
def add_defect_field(self, add_button, d_frame, rownum, elements_options, defect_id):
add_button.grid_remove()
num_fields = self.fields_hash.get('D' + str(defect_id), 1)
self.fields_hash['D' + str(defect_id)] = num_fields + 1
self.create_individual_fields(d_frame, elements_options, defect_id, rownum + 1)
def add_options(self, option_menu, options, element_var, index_val):
menu = option_menu["menu"]
menu.delete(0, "end")
for string in options:
menu.add_command(label=string, command=lambda value=string:element_var.set(value))
if index_val is not None:
element_var.set(index_val)
class DefectsSection:
def __init__(self, parent_window, grid_row, structure_section):
self.parent_window = parent_window
self.grid_row = grid_row
self.summary_frame = None
self.defects_info = {\
'coord_type' : [None, None],\
'posfile' : [None, None],\
'defecttype' : [{}, {}],\
'namemap' : [{}, {}],\
'elementmap' : [{}, {}],\
'infomap' : [{}, {}],\
'chargemap' : [{}, {}],\
}
self.num_defect_fields = 1
self.structure_section = structure_section
self.has_summary = False
self.defect_types = [
'vacancy', 'interstitial', 'substitution', 'antisite'
]
self.fields_hash = {}
def content(self):
content_start = "$defects\n"
content_end = "$end\n\n"
content_lines = ""
if self.defects_info['coord_type'][0]:
content_lines += "coord_type %s\n\n" % self.defects_info[
'coord_type'][0]
if self.defects_info['posfile'][0]:
content_lines += "posfile %s\n\n" % self.defects_info['posfile'][0]
if self.defects_info['namemap'][0]:
for d_id, d_name in self.defects_info['namemap'][0].iteritems():
content_lines += "begin %s\n" % d_name
if self.defects_info['elementmap'][0][d_id]:
for idx, elt in enumerate(
self.defects_info['elementmap'][0][d_id]):
elt = elt.split('(', 1)[1].replace(')', '').strip()
content_lines += "%s %s %s" % (
self.defects_info['defecttype'][0][d_id][idx],
self.defects_info['infomap'][0][d_id][idx], elt)
if self.defects_info['chargemap'][0][d_id][idx]:
content_lines += " charge=%s" % self.defects_info[
'chargemap'][0][d_id][idx]
content_lines += "\n"
content_lines += "end\n\n"
return content_start + content_lines + content_end
def get_defects_map(self):
return self.defects_info['namemap'][0]
def summary(self):
#the frame which encloses all the contents
self.summary_frame = LabelFrame(self.parent_window, text="Defects")
self.summary_frame.grid_rowconfigure(0, weight=1)
self.summary_frame.grid_rowconfigure(1, weight=1)
self.summary_frame.grid_columnconfigure(0, weight=1)
self.summary_frame.grid_columnconfigure(1, weight=1)
self.summary_frame.grid_columnconfigure(2, weight=1)
self.summary_frame.grid_columnconfigure(3, weight=1)
self.summary_frame.grid_columnconfigure(4, weight=1)
self.summary_frame.grid_columnconfigure(5, weight=1)
#if it has summary show it
if self.has_summary:
#coord_type
coord_type = Label(self.summary_frame, text="COORD_TYPE :")
coord_type.grid(row=0, column=2, sticky=E, pady=5)
coord_type_value = Label(self.summary_frame,
text=self.defects_info['coord_type'][0])
coord_type_value.grid(row=0, column=3, sticky=W, pady=5)
if self.defects_info['posfile'][0] is not None:
pos_label = Label(self.summary_frame, text="POSFILE :")
pos_label.grid(row=1, column=2, sticky=E, pady=5)
pos_value = Label(self.summary_frame,
text=self.defects_info['posfile'][0])
pos_value.grid(row=1, column=3, sticky=W, pady=5)
for rownum in xrange(self.num_defect_fields):
if rownum == 0:
continue
if self.defects_info['elementmap'][0][
'D' + str(rownum)][0].strip() == "":
continue
id_label = Label(self.summary_frame, text='D' + str(rownum))
id_label.grid(row=2 + rownum,
column=0,
padx=10,
pady=2,
sticky=E)
name_label = Label(
self.summary_frame,
text=self.defects_info['namemap'][0]['D' + str(rownum)])
name_label.grid(row=2 + rownum,
column=1,
padx=10,
pady=2,
sticky=E)
element_label = Label(
self.summary_frame,
text=self.defects_info['elementmap'][0]['D' +
str(rownum)][0])
element_label.grid(row=2 + rownum,
column=2,
padx=10,
pady=2,
sticky=W)
type_label = Label(
self.summary_frame,
text=self.defects_info['defecttype'][0]['D' +
str(rownum)][0])
type_label.grid(row=2 + rownum,
column=3,
padx=10,
pady=2,
sticky=W)
defect_info_label = Label(
self.summary_frame,
text=self.defects_info['infomap'][0]['D' + str(rownum)][0])
defect_info_label.grid(row=2 + rownum,
column=4,
padx=10,
pady=2,
sticky=W)
charge_label = Label(
self.summary_frame,
text=self.defects_info['chargemap'][0]['D' +
str(rownum)][0])
charge_label.grid(row=2 + rownum,
column=5,
padx=10,
pady=2,
sticky=W)
#the frame contents
add_button = Button(self.summary_frame,
text="Add Defects",
command=self.create_window)
add_button.grid(row=3 + self.num_defect_fields,
column=0,
columnspan=6,
pady=20,
padx=20)
self.summary_frame.grid(row=self.grid_row,
column=0,
padx=20,
pady=5,
sticky=W + E)
def create_window(self):
self.window = ttk.Toplevel(self.parent_window)
self.window.title("Defects Information")
self.window.minsize(500, 500)
self.vframe = VerticalScrolledFrame(self.window)
self.vframe.pack(fill=BOTH, expand=1)
self.defects_window = self.vframe.interior
self.defects_window.grid_rowconfigure(0, weight=1)
self.defects_window.grid_columnconfigure(0, weight=1)
defects_frame = LabelFrame(self.defects_window, text="Defects")
defects_frame.grid(row=0, column=0, padx=20, pady=20)
defects_frame.grid_rowconfigure(0, weight=1)
defects_frame.grid_rowconfigure(1, weight=1)
defects_frame.grid_columnconfigure(0, weight=1)
defects_frame.grid_columnconfigure(1, weight=1)
#add coordtype
label = Label(defects_frame, text="COORD_TYPE")
label.grid(row=0, column=0, sticky=E, pady=10, padx=10)
coord_type = StringVar(defects_frame)
coord_type.set("fractional")
if self.defects_info['coord_type'][0] is not None:
coord_type.set(self.defects_info['coord_type'][0])
coord_type_option = OptionMenu(defects_frame, coord_type, "fractional",
"cartesian")
coord_type_option.grid(row=0, column=1, sticky=W, pady=10, padx=10)
self.defects_info["coord_type"] = [coord_type.get(), coord_type]
#add posfile
label = Label(defects_frame, text="POS FILE")
label.grid(row=1, column=0, sticky=E, pady=10, padx=10)
pos_value = StringVar(defects_frame)
pos_value.set("")
if self.defects_info['posfile'][0] is not None:
pos_value.set(self.defects_info['posfile'][0])
pos_entry = Entry(defects_frame, textvariable=pos_value)
pos_entry.grid(row=1, column=1, sticky=W, pady=10, padx=10)
self.defects_info["posfile"] = [pos_value.get(), pos_value]
#a label frame to add defects related information
self.defects_entities_frame = LabelFrame(defects_frame,
text="DEFECT ENTITIES")
self.defects_entities_frame.grid(row=2,
column=0,
columnspan=2,
padx=10,
pady=10)
#create field headers
for rownum in xrange(self.num_defect_fields):
self.create_defect_fields(self.defects_entities_frame, rownum)
self.add_button = Button(self.defects_entities_frame,
text="Add more defects",
command=self.add_elements)
self.add_button.grid(row=self.num_defect_fields + 1,
column=0,
columnspan=2,
pady=10,
padx=10)
#save button
save_button = Button(defects_frame, text="Save", command=self.save)
save_button.grid(row=3, column=0, columnspan=2, padx=20, pady=10)
def save(self):
self.defects_info['coord_type'][0] = self.defects_info['coord_type'][
1].get()
self.defects_info['posfile'][0] = self.defects_info['posfile'][1].get()
for rownum in xrange(self.num_defect_fields):
self.defects_info['namemap'][0]['D' + str(
rownum)] = self.defects_info['namemap'][1]['D' +
str(rownum)].get()
num_fields = self.fields_hash.get('D' + str(rownum), 0)
for i in xrange(num_fields):
if 'D' + str(rownum) in self.defects_info['elementmap'][0]:
if i < len(
self.defects_info['elementmap'][0]['D' +
str(rownum)]):
self.defects_info['elementmap'][0]['D' + str(
rownum)][i] = self.defects_info['elementmap'][1][
'D' + str(rownum)][i].get()
else:
self.defects_info['elementmap'][0][
'D' + str(rownum)].append(
self.defects_info['elementmap'][1][
'D' + str(rownum)][i].get())
else:
self.defects_info['elementmap'][0]['D' + str(rownum)] = [
self.defects_info['elementmap'][1]['D' + str(rownum)]
[i].get()
]
if 'D' + str(rownum) in self.defects_info['infomap'][0]:
if i < len(self.defects_info['infomap'][0]['D' +
str(rownum)]):
self.defects_info['infomap'][0][
'D' +
str(rownum)][i] = self.defects_info['infomap'][1][
'D' + str(rownum)][i].get()
else:
self.defects_info['infomap'][0][
'D' + str(rownum)].append(
self.defects_info['infomap'][1][
'D' + str(rownum)][i].get())
else:
self.defects_info['infomap'][0]['D' + str(rownum)] = [
self.defects_info['infomap'][1]['D' +
str(rownum)][i].get()
]
if 'D' + str(rownum) in self.defects_info['chargemap'][0]:
if i < len(self.defects_info['chargemap'][0]['D' +
str(rownum)]):
self.defects_info['chargemap'][0]['D' + str(
rownum)][i] = self.defects_info['chargemap'][1][
'D' + str(rownum)][i].get()
else:
self.defects_info['chargemap'][0][
'D' + str(rownum)].append(
self.defects_info['chargemap'][1][
'D' + str(rownum)][i].get())
else:
self.defects_info['chargemap'][0]['D' + str(rownum)] = [
self.defects_info['chargemap'][1]['D' + str(rownum)]
[i].get()
]
if 'D' + str(rownum) in self.defects_info['defecttype'][0]:
if i < len(
self.defects_info['defecttype'][0]['D' +
str(rownum)]):
self.defects_info['defecttype'][0]['D' + str(
rownum)][i] = self.defects_info['defecttype'][1][
'D' + str(rownum)][i].get()
else:
self.defects_info['defecttype'][0][
'D' + str(rownum)].append(
self.defects_info['defecttype'][1][
'D' + str(rownum)][i].get())
else:
self.defects_info['defecttype'][0]['D' + str(rownum)] = [
self.defects_info['defecttype'][1]['D' + str(rownum)]
[i].get()
]
self.window.destroy()
self.window = None
self.has_summary = True
self.summary_frame.grid_remove()
self.summary()
def add_elements(self):
self.num_defect_fields += 1
self.add_button.grid_remove()
self.create_defect_fields(self.defects_entities_frame,
self.num_defect_fields - 1)
self.add_button = Button(self.defects_entities_frame,
text="Add more defects",
command=self.add_elements)
self.add_button.grid(row=self.num_defect_fields + 1,
column=0,
columnspan=6,
pady=10,
padx=10)
def create_defect_fields(self, frame, rownum):
elements_map = self.structure_section.get_elements_map()
elements_options = [
"%s (%s)" % (value, key)
for key, value in elements_map.iteritems()
]
num_fields = self.fields_hash.get('D' + str(rownum), 1)
self.fields_hash['D' + str(rownum)] = num_fields
d_frame = LabelFrame(frame, text="D" + str(rownum))
d_frame.grid(row=rownum,
column=0,
padx=10,
pady=10,
sticky=N + S + W + E)
id_label = Label(d_frame, text="D" + str(rownum))
id_label.grid(row=0, column=0, padx=10, pady=10, sticky=W)
name_label = Label(d_frame, text="NAME")
name_label.grid(row=0, column=0, padx=10, pady=10, sticky=W)
element_label = Label(d_frame, text="ELEMENT")
element_label.grid(row=0, column=1, padx=10, pady=10, sticky=W)
vacancy_label = Label(d_frame, text="DEFECT_TYPE")
vacancy_label.grid(row=0, column=2, padx=10, pady=10, sticky=W)
vacancy_label = Label(d_frame, text="DEFECT_INFO")
vacancy_label.grid(row=0, column=3, padx=10, pady=10, sticky=W)
charge_label = Label(d_frame, text="CHARGE")
charge_label.grid(row=0, column=4, padx=10, pady=10, sticky=W)
name_text = StringVar()
if self.defects_info['namemap'][0] and (
'D' + str(rownum)) in self.defects_info['namemap'][0]:
name_text.set(self.defects_info['namemap'][0]['D' + str(rownum)])
name_val = Entry(d_frame, textvariable=name_text)
name_val.grid(row=1, column=0, pady=10, padx=10, sticky=W)
self.defects_info['namemap'][1]['D' + str(rownum)] = name_text
for i in xrange(num_fields):
self.create_individual_fields(d_frame, elements_options, rownum,
i + 1)
def create_individual_fields(self, d_frame, elements_options, defect_id,
rownum):
element = StringVar(d_frame)
element_val = None
if self.defects_info['elementmap'][0] and ('D' + str(defect_id)) in self.defects_info['elementmap'][0] and \
rownum <= len(self.defects_info['elementmap'][0]['D' + str(defect_id)]):
element_val = self.defects_info['elementmap'][0][
'D' + str(defect_id)][rownum - 1]
option_menu = OptionMenu(d_frame, element, ())
option_menu.grid(row=rownum, column=1, sticky=W, pady=10, padx=10)
self.add_options(option_menu, elements_options, element, element_val)
if 'D' + str(defect_id) in self.defects_info['elementmap'][1]:
if rownum <= len(
self.defects_info['elementmap'][1]['D' + str(defect_id)]):
self.defects_info['elementmap'][1]['D' +
str(defect_id)][rownum -
1] = element
else:
self.defects_info['elementmap'][1][
'D' + str(defect_id)].append(element)
else:
self.defects_info['elementmap'][1]['D' +
str(defect_id)] = [element]
defect_type_text = StringVar(d_frame)
defect_type_val = None
if self.defects_info['defecttype'][0] and ('D' + str(defect_id)) in self.defects_info['defecttype'][0] and \
rownum <= len(self.defects_info['defecttype'][0]['D' + str(defect_id)]):
defect_type_val = self.defects_info['defecttype'][0][
'D' + str(defect_id)][rownum - 1]
defect_type_menu = OptionMenu(d_frame, defect_type_text, ())
defect_type_menu.grid(row=rownum, column=2, sticky=W, pady=10, padx=10)
self.add_options(defect_type_menu, self.defect_types, defect_type_text,
defect_type_val)
if 'D' + str(defect_id) in self.defects_info['defecttype'][1]:
if rownum <= len(
self.defects_info['defecttype'][1]['D' + str(defect_id)]):
self.defects_info['defecttype'][1]['D' + str(defect_id)][
rownum - 1] = defect_type_text
else:
self.defects_info['defecttype'][1][
'D' + str(defect_id)].append(defect_type_text)
else:
self.defects_info['defecttype'][1]['D' + str(defect_id)] = [
defect_type_text
]
vacancy_text = StringVar(d_frame)
if self.defects_info['infomap'][0] and ('D' + str(defect_id)) in self.defects_info['infomap'][0] and \
rownum <= len(self.defects_info['infomap'][0]['D' + str(defect_id)]):
vacancy_text.set(
self.defects_info['infomap'][0]['D' + str(defect_id)][rownum -
1])
vacancy_val = Entry(d_frame, textvariable=vacancy_text)
vacancy_val.grid(row=rownum, column=3, pady=10, padx=10, sticky=W)
if 'D' + str(defect_id) in self.defects_info['infomap'][1]:
if rownum <= len(
self.defects_info['infomap'][1]['D' + str(defect_id)]):
self.defects_info['infomap'][1]['D' + str(defect_id)][
rownum - 1] = vacancy_text
else:
self.defects_info['infomap'][1]['D' + str(defect_id)].append(
vacancy_text)
else:
self.defects_info['infomap'][1]['D' +
str(defect_id)] = [vacancy_text]
charge_text = StringVar(d_frame)
if self.defects_info['chargemap'][0] and ('D' + str(defect_id)) in self.defects_info['chargemap'][0] and \
rownum <= len(self.defects_info['chargemap'][0]['D' + str(defect_id)]):
charge_text.set(
self.defects_info['chargemap'][0]['D' +
str(defect_id)][rownum - 1])
charge_val = Entry(d_frame, textvariable=charge_text)
charge_val.grid(row=rownum, column=4, pady=10, padx=10, sticky=W)
if 'D' + str(defect_id) in self.defects_info['chargemap'][1]:
if rownum <= len(
self.defects_info['chargemap'][1]['D' + str(defect_id)]):
self.defects_info['chargemap'][1]['D' + str(defect_id)][
rownum - 1] = charge_text
else:
self.defects_info['chargemap'][1]['D' + str(defect_id)].append(
charge_text)
else:
self.defects_info['chargemap'][1]['D' +
str(defect_id)] = [charge_text]
add_button = Button(d_frame, text="+")
add_button.grid(row=rownum, column=5, pady=10, padx=10)
add_button.configure(command=lambda: self.add_defect_field(
add_button, d_frame, rownum, elements_options, defect_id))
def add_defect_field(self, add_button, d_frame, rownum, elements_options,
defect_id):
add_button.grid_remove()
num_fields = self.fields_hash.get('D' + str(defect_id), 1)
self.fields_hash['D' + str(defect_id)] = num_fields + 1
self.create_individual_fields(d_frame, elements_options, defect_id,
rownum + 1)
def add_options(self, option_menu, options, element_var, index_val):
menu = option_menu["menu"]
menu.delete(0, "end")
for string in options:
menu.add_command(
label=string,
command=lambda value=string: element_var.set(value))
if index_val is not None:
element_var.set(index_val)
def create_window(self):
self.window = ttk.Toplevel(self.parent_window)
self.window.title("Defects Information")
self.window.minsize(500, 500)
self.vframe = VerticalScrolledFrame(self.window)
self.vframe.pack(fill=BOTH, expand=1)
self.defects_window = self.vframe.interior
self.defects_window.grid_rowconfigure(0, weight=1)
self.defects_window.grid_columnconfigure(0, weight=1)
defects_frame = LabelFrame(self.defects_window, text="Defects")
defects_frame.grid(row=0, column=0, padx=20, pady=20)
defects_frame.grid_rowconfigure(0, weight=1)
defects_frame.grid_rowconfigure(1, weight=1)
defects_frame.grid_columnconfigure(0, weight=1)
defects_frame.grid_columnconfigure(1, weight=1)
#add coordtype
label = Label(defects_frame, text="COORD_TYPE")
label.grid(row=0, column=0, sticky=E, pady=10, padx=10)
coord_type = StringVar(defects_frame)
coord_type.set("fractional")
if self.defects_info['coord_type'][0] is not None:
coord_type.set(self.defects_info['coord_type'][0])
coord_type_option = OptionMenu(defects_frame, coord_type, "fractional",
"cartesian")
coord_type_option.grid(row=0, column=1, sticky=W, pady=10, padx=10)
self.defects_info["coord_type"] = [coord_type.get(), coord_type]
#add posfile
label = Label(defects_frame, text="POS FILE")
label.grid(row=1, column=0, sticky=E, pady=10, padx=10)
pos_value = StringVar(defects_frame)
pos_value.set("")
if self.defects_info['posfile'][0] is not None:
pos_value.set(self.defects_info['posfile'][0])
pos_entry = Entry(defects_frame, textvariable=pos_value)
pos_entry.grid(row=1, column=1, sticky=W, pady=10, padx=10)
self.defects_info["posfile"] = [pos_value.get(), pos_value]
#a label frame to add defects related information
self.defects_entities_frame = LabelFrame(defects_frame,
text="DEFECT ENTITIES")
self.defects_entities_frame.grid(row=2,
column=0,
columnspan=2,
padx=10,
pady=10)
#create field headers
for rownum in xrange(self.num_defect_fields):
self.create_defect_fields(self.defects_entities_frame, rownum)
self.add_button = Button(self.defects_entities_frame,
text="Add more defects",
command=self.add_elements)
self.add_button.grid(row=self.num_defect_fields + 1,
column=0,
columnspan=2,
pady=10,
padx=10)
#save button
save_button = Button(defects_frame, text="Save", command=self.save)
save_button.grid(row=3, column=0, columnspan=2, padx=20, pady=10)
class NEBSection:
def __init__(self, parent_window, grid_row, structure_section, defects_section):
self.parent_window = parent_window
self.grid_row = grid_row
self.structure_section = structure_section
self.defects_section = defects_section
self.has_summary = False
self.neb_info = {\
'images' : [None, None],\
'posfiles' : [{}, {}],\
'startdefect' : [{}, {}],\
'enddefect' : [{}, {}],\
'elementmap' : [{}, {}],\
'startpos' : [{}, {}],\
'endpos' : [{}, {}],\
}
self.num_neb_fields = 1
self.fields_hash = {}
def content(self):
content_start = "$neb\n"
content_end = "$end\n\n"
content_lines = ""
if self.neb_info['startdefect'][0]:
for n_id, s_defect in self.neb_info['startdefect'][0].iteritems():
if n_id not in self.neb_info['enddefect'][0]:
continue
content_lines += "begin %s-%s\n" % (s_defect.split('(', 1)[0].strip(), self.neb_info['enddefect'][0][n_id].split('(', 1)[0].strip())
if n_id in self.neb_info['elementmap'][0]:
for idx, elt in enumerate(self.neb_info['elementmap'][0][n_id]):
elt = elt.split('(', 1)[1].replace(')', '').strip()
content_lines += "%s, %s, %s\n" % (elt, self.neb_info['startpos'][0][n_id][idx], self.neb_info['endpos'][0][n_id][idx])
if n_id in self.neb_info['posfiles'][0]:
content_lines += "posfile %s\n" % ",".join(self.neb_info['posfiles'][0][n_id])
content_lines += "end\n\n"
if self.neb_info['images'][0]:
content_lines += "images %s\n" % self.neb_info['images'][0]
return content_start + content_lines + content_end
def summary(self):
#the frame which encloses all the contents
self.summary_frame = LabelFrame(self.parent_window, text="NEB")
self.summary_frame.grid_rowconfigure(0, weight=1)
self.summary_frame.grid_rowconfigure(1, weight=1)
self.summary_frame.grid_columnconfigure(0, weight=1)
self.summary_frame.grid_columnconfigure(1, weight=1)
self.summary_frame.grid_columnconfigure(2, weight=1)
self.summary_frame.grid_columnconfigure(3, weight=1)
self.summary_frame.grid_columnconfigure(4, weight=1)
self.summary_frame.grid_columnconfigure(5, weight=1)
#if it has summary show it
if self.has_summary:
#coord_type
images = Label(self.summary_frame, text="IMAGES :")
images.grid(row=0, column=2, sticky=E, pady=5)
images_value = Label(self.summary_frame, text=self.neb_info['images'][0])
images_value.grid(row=0, column=3, sticky=W, pady=5)
for rownum in xrange(self.num_neb_fields):
if self.neb_info['startdefect'][0]['N' + str(rownum)].strip() == "":
continue
id_label = Label(self.summary_frame, text='N'+ str(rownum))
id_label.grid(row=2 + rownum, column=0, padx=10, pady=2, sticky=E)
s_defect_label = Label(self.summary_frame, text=self.neb_info['startdefect'][0]['N'+str(rownum)])
s_defect_label.grid(row=2 + rownum, column=1, padx=10, pady=2, sticky=E)
e_defect_label = Label(self.summary_frame, text=self.neb_info['enddefect'][0]['N'+str(rownum)])
e_defect_label.grid(row=2 + rownum, column=2, padx=10, pady=2, sticky=E)
element_label = Label(self.summary_frame, text=self.neb_info['elementmap'][0]['N'+str(rownum)][0])
element_label.grid(row=2 + rownum, column=3, padx=10, pady=2, sticky=E)
s_pos_label = Label(self.summary_frame, text=self.neb_info['startpos'][0]['N'+str(rownum)][0])
s_pos_label.grid(row=2 + rownum, column=4, padx=10, pady=2, sticky=E)
e_pos_label = Label(self.summary_frame, text=self.neb_info['endpos'][0]['N'+str(rownum)][0])
e_pos_label.grid(row=2 + rownum, column=5, padx=10, pady=2, sticky=E)
#the frame contents
add_button = Button(self.summary_frame, text="Add NEB properties", command=self.create_window)
add_button.grid(row=3 + self.num_neb_fields, column=0, columnspan=7, pady=20, padx=20)
self.summary_frame.grid(row=self.grid_row, column=0, sticky=W+E, padx=20, pady=5)
def create_window_with_posfiles(self):
self.neb_info['images'][0] = self.neb_info['images'][1].get()
self.window.destroy()
self.window = None
self.create_window()
def create_window(self):
self.window = ttk.Toplevel(self.parent_window)
self.window.title("NEB Information")
self.window.minsize(500, 500)
self.vframe = VerticalScrolledFrame(self.window)
self.vframe.pack(fill=BOTH, expand=1)
self.neb_window = self.vframe.interior
self.neb_window.grid_rowconfigure(0, weight=1)
self.neb_window.grid_columnconfigure(0, weight=1)
neb_frame = LabelFrame(self.neb_window, text="NEB")
neb_frame.grid(row=0, column=0, padx=20, pady=20)
neb_frame.grid_rowconfigure(0, weight=1)
neb_frame.grid_columnconfigure(0, weight=1)
#frame for images and button
frame1 = Frame(neb_frame)
frame1.grid(row=0, column=0)
frame1.grid_rowconfigure(0, weight=1)
frame1.grid_rowconfigure(1, weight=1)
frame1.grid_columnconfigure(0, weight=1)
frame1.grid_columnconfigure(1, weight=1)
frame1.grid_columnconfigure(2, weight=1)
#add images
label = Label(frame1, text="IMAGES")
label.grid(row=0, column=0, sticky=E, pady=10, padx=10)
images_val = StringVar(frame1)
if self.neb_info['images'][0] is not None:
images_val.set(self.neb_info['images'][0])
images_menu = Entry(frame1, textvariable=images_val)
images_menu.grid(row=0, column=1, sticky=W, pady=10, padx=10)
self.neb_info["images"] = [images_val.get(), images_val]
images_btn = Button(frame1, text="Add Posfiles", command=self.create_window_with_posfiles)
images_btn.grid(row=0, column=2, sticky=W, pady=10, padx=10)
#frame for entities
frame2 = Frame(neb_frame)
frame2.grid(row=1, column=0)
#a label frame to add neb related information
self.neb_entities_frame = LabelFrame(frame2, text="NEB ENTITIES")
self.neb_entities_frame.grid(row=0, column=0, columnspan=3, padx=10, pady=10)
for rownum in xrange(self.num_neb_fields):
self.create_neb_fields(self.neb_entities_frame, rownum)
self.add_button = Button(self.neb_entities_frame, text="Add more neb", command=self.add_elements)
self.add_button.grid(row=self.num_neb_fields + 1, column=0, columnspan=6, pady=10, padx=10)
#save button
save_button = Button(neb_frame, text="Save", command=self.save)
save_button.grid(row=3, column=0, columnspan=2, padx=20, pady=10)
def add_elements(self):
self.num_neb_fields += 1
self.add_button.grid_remove()
self.create_neb_fields(self.neb_entities_frame, self.num_neb_fields - 1)
self.add_button = Button(self.neb_entities_frame, text="Add more neb", command=self.add_elements)
self.add_button.grid(row=self.num_neb_fields + 1, column=0, pady=10, padx=10)
def save(self):
self.neb_info['images'][0] = self.neb_info['images'][1].get()
for rownum in xrange(self.num_neb_fields):
self.neb_info['startdefect'][0]['N'+str(rownum)] = self.neb_info['startdefect'][1]['N'+str(rownum)].get()
self.neb_info['enddefect'][0]['N'+str(rownum)] = self.neb_info['enddefect'][1]['N'+str(rownum)].get()
num_fields = self.fields_hash.get('N' + str(rownum), 0)
for i in xrange(num_fields):
if 'N' + str(rownum) in self.neb_info['elementmap'][0]:
if i < len(self.neb_info['elementmap'][0]['N' + str(rownum)]):
self.neb_info['elementmap'][0]['N' + str(rownum)][i] = self.neb_info['elementmap'][1]['N'+str(rownum)][i].get()
else:
self.neb_info['elementmap'][0]['N' + str(rownum)].append(self.neb_info['elementmap'][1]['N'+str(rownum)][i].get())
else:
self.neb_info['elementmap'][0]['N'+str(rownum)] = [self.neb_info['elementmap'][1]['N'+str(rownum)][i].get()]
if 'N' + str(rownum) in self.neb_info['startpos'][0]:
if i < len(self.neb_info['startpos'][0]['N' + str(rownum)]):
self.neb_info['startpos'][0]['N' + str(rownum)][i] = self.neb_info['startpos'][1]['N'+str(rownum)][i].get()
else:
self.neb_info['startpos'][0]['N' + str(rownum)].append(self.neb_info['startpos'][1]['N'+str(rownum)][i].get())
else:
self.neb_info['startpos'][0]['N'+str(rownum)] = [self.neb_info['startpos'][1]['N'+str(rownum)][i].get()]
if 'N' + str(rownum) in self.neb_info['endpos'][0]:
if i < len(self.neb_info['endpos'][0]['N' + str(rownum)]):
self.neb_info['endpos'][0]['N' + str(rownum)][i] = self.neb_info['endpos'][1]['N'+str(rownum)][i].get()
else:
self.neb_info['endpos'][0]['N' + str(rownum)].append(self.neb_info['endpos'][1]['N'+str(rownum)][i].get())
else:
self.neb_info['endpos'][0]['N'+str(rownum)] = [self.neb_info['endpos'][1]['N'+str(rownum)][i].get()]
#save the posfile values
if not self.neb_info['posfiles'][1]:
continue
for entry in self.neb_info['posfiles'][1]['N' + str(rownum)]:
val_list = self.neb_info['posfiles'][0].setdefault('N' + str(rownum), [])
val_list.append(entry.get())
self.window.destroy()
self.window = None
self.has_summary = True
self.summary_frame.grid_remove()
self.summary()
def create_neb_fields(self, frame, rownum):
elements_map = self.structure_section.get_elements_map()
elements_options = ["%s (%s)" % (value, key) for key, value in elements_map.iteritems()]
defects_map = self.defects_section.get_defects_map()
defects_options = ["%s (%s)" % (value, key) for key, value in defects_map.iteritems()]
num_fields = self.fields_hash.get('N' + str(rownum), 1)
self.fields_hash['N' + str(rownum)] = num_fields
#label frame for this entity
m_frame = LabelFrame(frame, text="N" + str(rownum))
m_frame.grid(row=rownum, column=0, padx=10, pady=10)
e_frame = Frame(m_frame)
e_frame.grid(row=0, column=0)
p_frame = Frame(m_frame)
p_frame.grid(row=1, column=0)
#create field headers
start_label = Label(e_frame, text="START DEFECT")
start_label.grid(row=0, column=0, padx=10, pady=10, sticky=W)
end_label = Label(e_frame, text="END DEFECT")
end_label.grid(row=0, column=1, padx=10, pady=10, sticky=W)
element_label = Label(e_frame, text="ELEMENT")
element_label.grid(row=0, column=2, padx=10, pady=10, sticky=W)
start_pos = Label(e_frame, text="START POSITION")
start_pos.grid(row=0, column=3, padx=10, pady=10, sticky=W)
end_pos = Label(e_frame, text="END POSITION")
end_pos.grid(row=0, column=4, padx=10, pady=10, sticky=W)
start_defect = StringVar(e_frame)
start_defect_val = None
if self.neb_info['startdefect'][0] and ('N' + str(rownum)) in self.neb_info['startdefect'][0]:
start_defect_val = self.neb_info['startdefect'][0]['N' + str(rownum)]
s_option_menu = OptionMenu(e_frame, start_defect, ())
s_option_menu.grid(row=1, column=0, sticky=W, pady=10, padx=10)
self.add_options(s_option_menu, defects_options, start_defect, start_defect_val)
self.neb_info['startdefect'][1]['N' + str(rownum)] = start_defect
end_defect = StringVar(e_frame)
end_defect_val = None
if self.neb_info['enddefect'][0] and ('N' + str(rownum)) in self.neb_info['enddefect'][0]:
end_defect_val = self.neb_info['enddefect'][0]['N' + str(rownum)]
e_option_menu = OptionMenu(e_frame, end_defect, ())
e_option_menu.grid(row=1, column=1, sticky=W, pady=10, padx=10)
self.add_options(e_option_menu, defects_options, end_defect, end_defect_val)
self.neb_info['enddefect'][1]['N' + str(rownum)] = end_defect
for i in xrange(num_fields):
self.create_individual_fields(e_frame, elements_options, rownum, i + 1)
#put the pos file input boxes
#add posfiles if needed
if self.neb_info['images'][0] is not None and self.neb_info['images'][0] != "" and int(self.neb_info['images'][0]) > 0:
label = Label(p_frame, text="POSFILES")
label.grid(row=0, column=0, sticky=E, pady=10, padx=10)
pos_files_frame = Frame(p_frame)
pos_files_frame.grid(row=0, column=1, sticky=W, pady=10, padx=10)
#create boxes
for i in xrange(int(self.neb_info['images'][0])):
entry_val = StringVar(pos_files_frame)
if 'N' + str(rownum) in self.neb_info['posfiles'][0] and len(self.neb_info['posfiles'][0]['N' + str(rownum)]) >= i + 1:
entry_val.set(self.neb_info['posfiles'][0]['N' + str(rownum)][i])
self.neb_info['posfiles'][1]['N' + str(rownum)][i] = entry_val
else:
if not self.neb_info['posfiles'][1] or 'N' + str(rownum) not in self.neb_info['posfiles'][1]:
self.neb_info['posfiles'][1]['N' + str(rownum)] = [entry_val]
else:
self.neb_info['posfiles'][1]['N' + str(rownum)].append(entry_val)
pos_entry = Entry(pos_files_frame, textvariable=entry_val)
pos_entry.grid(row=i, column=0, sticky=W)
def create_individual_fields(self, e_frame, elements_options, neb_id, rownum):
element = StringVar(e_frame)
element_val = None
if self.neb_info['elementmap'][0] and ('N' + str(neb_id)) in self.neb_info['elementmap'][0] and \
rownum <= len(self.neb_info['elementmap'][0]['N' + str(neb_id)]):
element_val = self.neb_info['elementmap'][0]['N' + str(neb_id)][rownum - 1]
option_menu = OptionMenu(e_frame, element, ())
option_menu.grid(row=rownum, column=2, sticky=W, pady=10, padx=10)
self.add_options(option_menu, elements_options, element, element_val)
if 'N' + str(neb_id) in self.neb_info['elementmap'][1]:
if rownum <= len(self.neb_info['elementmap'][1]['N' + str(neb_id)]):
self.neb_info['elementmap'][1]['N' + str(neb_id)][rownum - 1] = element
else:
self.neb_info['elementmap'][1]['N' + str(neb_id)].append(element)
else:
self.neb_info['elementmap'][1]['N' + str(neb_id)] = [element]
startpos_text = StringVar()
if self.neb_info['startpos'][0] and ('N' + str(neb_id)) in self.neb_info['startpos'][0] and \
rownum <= len(self.neb_info['startpos'][0]['N' + str(neb_id)]):
startpos_text.set(self.neb_info['startpos'][0]['N'+str(neb_id)][rownum - 1])
startpos_val = Entry(e_frame, textvariable=startpos_text)
startpos_val.grid(row=rownum, column=3, pady=10, padx=10, sticky=W)
if 'N' + str(neb_id) in self.neb_info['startpos'][1]:
if rownum <= len(self.neb_info['startpos'][1]['N' + str(neb_id)]):
self.neb_info['startpos'][1]['N' + str(neb_id)][rownum - 1] = startpos_text
else:
self.neb_info['startpos'][1]['N' + str(neb_id)].append(startpos_text)
else:
self.neb_info['startpos'][1]['N' + str(neb_id)] = [startpos_text]
endpos_text = StringVar()
if self.neb_info['endpos'][0] and ('N' + str(rownum)) in self.neb_info['endpos'][0] and \
rownum <= len(self.neb_info['endpos'][0]['N' + str(neb_id)]):
endpos_text.set(self.neb_info['endpos'][0]['N'+str(neb_id)][rownum - 1])
endpos_val = Entry(e_frame, textvariable=endpos_text)
endpos_val.grid(row=rownum, column=4, pady=10, padx=10, sticky=W)
if 'N' + str(neb_id) in self.neb_info['endpos'][1]:
if rownum <= len(self.neb_info['endpos'][1]['N' + str(neb_id)]):
self.neb_info['endpos'][1]['N' + str(neb_id)][rownum - 1] = endpos_text
else:
self.neb_info['endpos'][1]['N' + str(neb_id)].append(endpos_text)
else:
self.neb_info['endpos'][1]['N' + str(neb_id)] = [endpos_text]
add_button = Button(e_frame, text="+")
add_button.grid(row=rownum, column=5, pady=10, padx=10)
add_button.configure(command=lambda:self.add_neb_field(add_button, e_frame, rownum, elements_options, neb_id))
def add_neb_field(self, add_button, e_frame, rownum, elements_options, neb_id):
add_button.grid_remove()
num_fields = self.fields_hash.get('N' + str(neb_id), 1)
self.fields_hash['N' + str(neb_id)] = num_fields + 1
self.create_individual_fields(e_frame, elements_options, neb_id, rownum + 1)
def add_options(self, option_menu, options, element_var, index_val):
menu = option_menu["menu"]
menu.delete(0, "end")
for string in options:
menu.add_command(label=string, command=lambda value=string:element_var.set(value))
if index_val is not None:
element_var.set(index_val)
class StructureSection:
def __init__(self, parent_window, grid_row):
self.parent_window = parent_window
self.grid_row = grid_row
self.summary_frame = None
self.structure_info = {\
'coord_type' : [None, None],\
'posfile' : [None, None],\
'elementmap' : [{}, {}],\
'lattice' : [None, None],\
'coordinates': [{}, {}],\
}
self.num_elt_fields = 1
self.has_summary = False
def get_elements_map(self):
return self.structure_info['elementmap'][0]
def content(self):
content_start = "$structure\n"
content_end = "$end\n\n"
content_lines = ""
if self.structure_info['coord_type'][0]:
content_lines += "coord_type %s\n\n" % self.structure_info['coord_type'][0]
if self.structure_info['posfile'][0]:
content_lines += "posfile %s\n\n" % self.structure_info['posfile'][0]
if self.structure_info['elementmap'][0]:
content_lines += "begin elementmap\n"
for elt_key, elt_name in self.structure_info['elementmap'][0].iteritems():
content_lines += "%s %s\n" % (elt_key, elt_name)
content_lines += "end\n\n"
if self.structure_info['coordinates'][0]:
content_lines += "begin coordinates\n"
for elt_key, elt_coord in self.structure_info['coordinates'][0].iteritems():
coord_lines = elt_coord.split('\n')
for line in coord_lines:
if line:
content_lines += "%s %s\n" % (elt_key, line)
content_lines += "end\n\n"
if self.structure_info['lattice'][0]:
content_lines += "begin lattice\n"
content_lines += "%s\n" % self.structure_info['lattice'][0]
content_lines += "end\n\n"
return content_start + content_lines + content_end
def summary(self):
#the frame which encloses all the contents
self.summary_frame = LabelFrame(self.parent_window, text="Structure")
self.summary_frame.grid_rowconfigure(0, weight=1)
self.summary_frame.grid_rowconfigure(1, weight=1)
self.summary_frame.grid_columnconfigure(0, weight=1)
self.summary_frame.grid_columnconfigure(1, weight=1)
self.summary_frame.grid_columnconfigure(2, weight=1)
#if it has summary show it
if self.has_summary:
#coord_type
coord_type = Label(self.summary_frame, text="COORD_TYPE :")
coord_type.grid(row=0, column=1, sticky=E, pady=5)
coord_type_value = Label(self.summary_frame, text=self.structure_info['coord_type'][0])
coord_type_value.grid(row=0, column=2, sticky=W, pady=5)
#posfile
if self.structure_info['posfile'][0].strip() != "":
posfile = Label(self.summary_frame, text="POSFILE :")
posfile.grid(row=1, column=1, sticky=E, pady=5)
posfile_value = Label(self.summary_frame, text=self.structure_info['posfile'][0])
posfile_value.grid(row=1, column=2, sticky=W, pady=5)
#lattice structure
lattice = Label(self.summary_frame, text="LATTICE : ")
lattice.grid(row=2, column=1, sticky=E, pady=5)
lattice_value = Label(self.summary_frame, text=self.structure_info['lattice'][0])
lattice_value.grid(row=2, column=2, sticky=W, pady=5)
for row_num in xrange(self.num_elt_fields + 1):
if row_num == 0:
continue
if self.structure_info['elementmap'][0]['X' + str(row_num)].strip() == "":
continue
id_label = Label(self.summary_frame, text='X'+ str(row_num))
id_label.grid(row=2 + row_num, column=0, padx=10, pady=2, sticky=E)
element_label = Label(self.summary_frame, text=self.structure_info['elementmap'][0]['X'+str(row_num)])
element_label.grid(row=2 + row_num, column=1, padx=10, pady=2, sticky=W)
coordinates_label = Label(self.summary_frame, text=self.structure_info['coordinates'][0]['X'+str(row_num)])
coordinates_label.grid(row=2 + row_num, column=2, padx=10, pady=2, sticky=W)
#the frame contents
add_button = Button(self.summary_frame, text="Add Structure properties", command=self.create_window)
add_button.grid(row=3 + self.num_elt_fields, column=0, columnspan=3, pady=20, padx=20)
self.summary_frame.grid(row=self.grid_row, column=0, padx=20, pady=5, sticky=W+E)
def create_window(self):
self.window = ttk.Toplevel(self.parent_window)
self.window.title("Structure Information")
self.window.minsize(500, 500)
self.vframe = VerticalScrolledFrame(self.window)
self.vframe.pack(fill=BOTH, expand=1)
self.structure_window = self.vframe.interior
self.structure_window.grid_rowconfigure(0, weight=1)
self.structure_window.grid_columnconfigure(0, weight=1)
self.structure_window.grid_rowconfigure(0, weight=1)
self.structure_window.grid_columnconfigure(0, weight=1)
structure_frame = LabelFrame(self.structure_window, text="Structure")
structure_frame.grid(row=0, column=0, padx=20, pady=20)
structure_frame.grid_rowconfigure(0, weight=1)
structure_frame.grid_rowconfigure(1, weight=1)
structure_frame.grid_columnconfigure(0, weight=1)
structure_frame.grid_columnconfigure(1, weight=1)
#add coordtype
label = Label(structure_frame, text="COORD_TYPE")
label.grid(row=0, column=0, sticky=E, pady=10, padx=10)
coord_type = StringVar(structure_frame)
coord_type.set("fractional")
if self.structure_info['coord_type'][0] is not None:
coord_type.set(self.structure_info['coord_type'][0])
coord_type_option = OptionMenu(structure_frame, coord_type, "fractional", "cartesian")
coord_type_option.grid(row=0, column=1, sticky=W, pady=10, padx=10)
self.structure_info["coord_type"] = [coord_type.get(), coord_type]
#pos file
label = Label(structure_frame, text="POSFILE")
label.grid(row=1, column=0, sticky=E, pady=10, padx=10)
text_val = StringVar()
if self.structure_info['posfile'][0] is not None:
text_val.set(self.structure_info['posfile'][0])
text = Entry(structure_frame, textvariable=text_val)
text.grid(row=1, column=1, sticky=W, pady=10, padx=10)
self.structure_info['posfile'] = [text_val.get(), text_val]
#pos file
label = Label(structure_frame, text="LATTICE")
label.grid(row=2, column=0, sticky=E, pady=10, padx=10)
text = Text(structure_frame, height=5, width=30)
if self.structure_info['lattice'][0] is not None:
text.insert('1.0', self.structure_info['lattice'][0])
text.grid(row=2, column=1, sticky=W, pady=10, padx=10)
self.structure_info['lattice'][1] = text
#label frame to add elements info
self.elements_frame = LabelFrame(structure_frame, text="ELEMENTS INFORMATION")
self.elements_frame.grid(row=3, column=0, columnspan=2, pady=10, padx=10)
#create field headers
id_label = Label(self.elements_frame, text="ID")
id_label.grid(row=0, column=0, padx=10, pady=10, sticky=W)
element_label = Label(self.elements_frame, text="ELEMENT")
element_label.grid(row=0, column=1, padx=10, pady=10, sticky=W)
coordinates_label = Label(self.elements_frame, text="COORDINATES")
coordinates_label.grid(row=0, column=2, padx=10, pady=10, sticky=W)
for row_num in xrange(self.num_elt_fields + 1):
if row_num == 0:
continue
self.create_element_fields(self.elements_frame, row_num)
self.add_button = Button(self.elements_frame, text="Add more elements", command=self.add_elements)
self.add_button.grid(row=self.num_elt_fields + 1, column=0, columnspan=3, pady=10, padx=10)
#save button
save_button = Button(structure_frame, text="Save", command=self.save)
save_button.grid(row=4, column=0, columnspan=2, padx=20, pady=10)
def save(self):
self.structure_info['coord_type'][0] = self.structure_info['coord_type'][1].get()
self.structure_info['posfile'][0] = self.structure_info['posfile'][1].get()
self.structure_info['lattice'][0] = self.structure_info['lattice'][1].get("1.0", END)
for row_num in xrange(self.num_elt_fields + 1):
if row_num == 0:
continue
self.structure_info['elementmap'][0]['X'+str(row_num)] = self.structure_info['elementmap'][1]['X'+str(row_num)].get()
self.structure_info['coordinates'][0]['X'+str(row_num)] = self.structure_info['coordinates'][1]['X'+str(row_num)].get("1.0", END)
self.window.destroy()
self.window = None
self.has_summary = True
self.summary_frame.grid_remove()
self.summary()
def add_elements(self):
self.num_elt_fields += 1
self.add_button.grid_remove()
self.create_element_fields(self.elements_frame, self.num_elt_fields)
self.add_button = Button(self.elements_frame, text="Add more elements", command=self.add_elements)
self.add_button.grid(row=self.num_elt_fields + 1, column=0, columnspan=3, pady=10, padx=10)
def create_element_fields(self, elements_frame, row_num):
id_label = Label(elements_frame, text="X" + str(row_num))
id_label.grid(row=row_num, column=0, padx=10, pady=10, sticky=W)
text_val = StringVar()
if self.structure_info['elementmap'][0] and ('X' + str(row_num)) in self.structure_info['elementmap'][0]:
text_val.set(self.structure_info['elementmap'][0]['X'+str(row_num)])
element_name = Entry(elements_frame, textvariable=text_val)
element_name.grid(row=row_num, column=1, pady=10, padx=10, sticky=W)
self.structure_info['elementmap'][1]['X'+ str(row_num)] = text_val
coordinates = Text(elements_frame, height=5, width=30)
if self.structure_info['coordinates'][0] and ('X' + str(row_num)) in self.structure_info['coordinates'][0]:
coordinates.insert('1.0', self.structure_info['coordinates'][0]['X' + str(row_num)])
coordinates.grid(row=row_num, column=2, pady=10, padx=10, sticky=W)
self.structure_info['coordinates'][1]['X'+ str(row_num)] = coordinates
def create_window(self):
self.window = ttk.Toplevel(self.parent_window)
self.window.title("Structure Information")
self.window.minsize(500, 500)
self.vframe = VerticalScrolledFrame(self.window)
self.vframe.pack(fill=BOTH, expand=1)
self.structure_window = self.vframe.interior
self.structure_window.grid_rowconfigure(0, weight=1)
self.structure_window.grid_columnconfigure(0, weight=1)
self.structure_window.grid_rowconfigure(0, weight=1)
self.structure_window.grid_columnconfigure(0, weight=1)
structure_frame = LabelFrame(self.structure_window, text="Structure")
structure_frame.grid(row=0, column=0, padx=20, pady=20)
structure_frame.grid_rowconfigure(0, weight=1)
structure_frame.grid_rowconfigure(1, weight=1)
structure_frame.grid_columnconfigure(0, weight=1)
structure_frame.grid_columnconfigure(1, weight=1)
#add coordtype
label = Label(structure_frame, text="COORD_TYPE")
label.grid(row=0, column=0, sticky=E, pady=10, padx=10)
coord_type = StringVar(structure_frame)
coord_type.set("fractional")
if self.structure_info['coord_type'][0] is not None:
coord_type.set(self.structure_info['coord_type'][0])
coord_type_option = OptionMenu(structure_frame, coord_type, "fractional", "cartesian")
coord_type_option.grid(row=0, column=1, sticky=W, pady=10, padx=10)
self.structure_info["coord_type"] = [coord_type.get(), coord_type]
#pos file
label = Label(structure_frame, text="POSFILE")
label.grid(row=1, column=0, sticky=E, pady=10, padx=10)
text_val = StringVar()
if self.structure_info['posfile'][0] is not None:
text_val.set(self.structure_info['posfile'][0])
text = Entry(structure_frame, textvariable=text_val)
text.grid(row=1, column=1, sticky=W, pady=10, padx=10)
self.structure_info['posfile'] = [text_val.get(), text_val]
#pos file
label = Label(structure_frame, text="LATTICE")
label.grid(row=2, column=0, sticky=E, pady=10, padx=10)
text = Text(structure_frame, height=5, width=30)
if self.structure_info['lattice'][0] is not None:
text.insert('1.0', self.structure_info['lattice'][0])
text.grid(row=2, column=1, sticky=W, pady=10, padx=10)
self.structure_info['lattice'][1] = text
#label frame to add elements info
self.elements_frame = LabelFrame(structure_frame, text="ELEMENTS INFORMATION")
self.elements_frame.grid(row=3, column=0, columnspan=2, pady=10, padx=10)
#create field headers
id_label = Label(self.elements_frame, text="ID")
id_label.grid(row=0, column=0, padx=10, pady=10, sticky=W)
element_label = Label(self.elements_frame, text="ELEMENT")
element_label.grid(row=0, column=1, padx=10, pady=10, sticky=W)
coordinates_label = Label(self.elements_frame, text="COORDINATES")
coordinates_label.grid(row=0, column=2, padx=10, pady=10, sticky=W)
for row_num in xrange(self.num_elt_fields + 1):
if row_num == 0:
continue
self.create_element_fields(self.elements_frame, row_num)
self.add_button = Button(self.elements_frame, text="Add more elements", command=self.add_elements)
self.add_button.grid(row=self.num_elt_fields + 1, column=0, columnspan=3, pady=10, padx=10)
#save button
save_button = Button(structure_frame, text="Save", command=self.save)
save_button.grid(row=4, column=0, columnspan=2, padx=20, pady=10)
class NEBSection:
def __init__(self, parent_window, grid_row, structure_section,
defects_section):
self.parent_window = parent_window
self.grid_row = grid_row
self.structure_section = structure_section
self.defects_section = defects_section
self.has_summary = False
self.neb_info = {\
'images' : [None, None],\
'posfiles' : [{}, {}],\
'startdefect' : [{}, {}],\
'enddefect' : [{}, {}],\
'elementmap' : [{}, {}],\
'startpos' : [{}, {}],\
'endpos' : [{}, {}],\
}
self.num_neb_fields = 1
self.fields_hash = {}
def content(self):
content_start = "$neb\n"
content_end = "$end\n\n"
content_lines = ""
if self.neb_info['startdefect'][0]:
for n_id, s_defect in self.neb_info['startdefect'][0].iteritems():
if n_id not in self.neb_info['enddefect'][0]:
continue
content_lines += "begin %s-%s\n" % (s_defect.split(
'(',
1)[0].strip(), self.neb_info['enddefect'][0][n_id].split(
'(', 1)[0].strip())
if n_id in self.neb_info['elementmap'][0]:
for idx, elt in enumerate(
self.neb_info['elementmap'][0][n_id]):
elt = elt.split('(', 1)[1].replace(')', '').strip()
content_lines += "%s, %s, %s\n" % (
elt, self.neb_info['startpos'][0][n_id][idx],
self.neb_info['endpos'][0][n_id][idx])
if n_id in self.neb_info['posfiles'][0]:
content_lines += "posfile %s\n" % ",".join(
self.neb_info['posfiles'][0][n_id])
content_lines += "end\n\n"
if self.neb_info['images'][0]:
content_lines += "images %s\n" % self.neb_info['images'][0]
return content_start + content_lines + content_end
def summary(self):
#the frame which encloses all the contents
self.summary_frame = LabelFrame(self.parent_window, text="NEB")
self.summary_frame.grid_rowconfigure(0, weight=1)
self.summary_frame.grid_rowconfigure(1, weight=1)
self.summary_frame.grid_columnconfigure(0, weight=1)
self.summary_frame.grid_columnconfigure(1, weight=1)
self.summary_frame.grid_columnconfigure(2, weight=1)
self.summary_frame.grid_columnconfigure(3, weight=1)
self.summary_frame.grid_columnconfigure(4, weight=1)
self.summary_frame.grid_columnconfigure(5, weight=1)
#if it has summary show it
if self.has_summary:
#coord_type
images = Label(self.summary_frame, text="IMAGES :")
images.grid(row=0, column=2, sticky=E, pady=5)
images_value = Label(self.summary_frame,
text=self.neb_info['images'][0])
images_value.grid(row=0, column=3, sticky=W, pady=5)
for rownum in xrange(self.num_neb_fields):
if self.neb_info['startdefect'][0]['N' +
str(rownum)].strip() == "":
continue
id_label = Label(self.summary_frame, text='N' + str(rownum))
id_label.grid(row=2 + rownum,
column=0,
padx=10,
pady=2,
sticky=E)
s_defect_label = Label(
self.summary_frame,
text=self.neb_info['startdefect'][0]['N' + str(rownum)])
s_defect_label.grid(row=2 + rownum,
column=1,
padx=10,
pady=2,
sticky=E)
e_defect_label = Label(
self.summary_frame,
text=self.neb_info['enddefect'][0]['N' + str(rownum)])
e_defect_label.grid(row=2 + rownum,
column=2,
padx=10,
pady=2,
sticky=E)
element_label = Label(
self.summary_frame,
text=self.neb_info['elementmap'][0]['N' + str(rownum)][0])
element_label.grid(row=2 + rownum,
column=3,
padx=10,
pady=2,
sticky=E)
s_pos_label = Label(
self.summary_frame,
text=self.neb_info['startpos'][0]['N' + str(rownum)][0])
s_pos_label.grid(row=2 + rownum,
column=4,
padx=10,
pady=2,
sticky=E)
e_pos_label = Label(
self.summary_frame,
text=self.neb_info['endpos'][0]['N' + str(rownum)][0])
e_pos_label.grid(row=2 + rownum,
column=5,
padx=10,
pady=2,
sticky=E)
#the frame contents
add_button = Button(self.summary_frame,
text="Add NEB properties",
command=self.create_window)
add_button.grid(row=3 + self.num_neb_fields,
column=0,
columnspan=7,
pady=20,
padx=20)
self.summary_frame.grid(row=self.grid_row,
column=0,
sticky=W + E,
padx=20,
pady=5)
def create_window_with_posfiles(self):
self.neb_info['images'][0] = self.neb_info['images'][1].get()
self.window.destroy()
self.window = None
self.create_window()
def create_window(self):
self.window = ttk.Toplevel(self.parent_window)
self.window.title("NEB Information")
self.window.minsize(500, 500)
self.vframe = VerticalScrolledFrame(self.window)
self.vframe.pack(fill=BOTH, expand=1)
self.neb_window = self.vframe.interior
self.neb_window.grid_rowconfigure(0, weight=1)
self.neb_window.grid_columnconfigure(0, weight=1)
neb_frame = LabelFrame(self.neb_window, text="NEB")
neb_frame.grid(row=0, column=0, padx=20, pady=20)
neb_frame.grid_rowconfigure(0, weight=1)
neb_frame.grid_columnconfigure(0, weight=1)
#frame for images and button
frame1 = Frame(neb_frame)
frame1.grid(row=0, column=0)
frame1.grid_rowconfigure(0, weight=1)
frame1.grid_rowconfigure(1, weight=1)
frame1.grid_columnconfigure(0, weight=1)
frame1.grid_columnconfigure(1, weight=1)
frame1.grid_columnconfigure(2, weight=1)
#add images
label = Label(frame1, text="IMAGES")
label.grid(row=0, column=0, sticky=E, pady=10, padx=10)
images_val = StringVar(frame1)
if self.neb_info['images'][0] is not None:
images_val.set(self.neb_info['images'][0])
images_menu = Entry(frame1, textvariable=images_val)
images_menu.grid(row=0, column=1, sticky=W, pady=10, padx=10)
self.neb_info["images"] = [images_val.get(), images_val]
images_btn = Button(frame1,
text="Add Posfiles",
command=self.create_window_with_posfiles)
images_btn.grid(row=0, column=2, sticky=W, pady=10, padx=10)
#frame for entities
frame2 = Frame(neb_frame)
frame2.grid(row=1, column=0)
#a label frame to add neb related information
self.neb_entities_frame = LabelFrame(frame2, text="NEB ENTITIES")
self.neb_entities_frame.grid(row=0,
column=0,
columnspan=3,
padx=10,
pady=10)
for rownum in xrange(self.num_neb_fields):
self.create_neb_fields(self.neb_entities_frame, rownum)
self.add_button = Button(self.neb_entities_frame,
text="Add more neb",
command=self.add_elements)
self.add_button.grid(row=self.num_neb_fields + 1,
column=0,
columnspan=6,
pady=10,
padx=10)
#save button
save_button = Button(neb_frame, text="Save", command=self.save)
save_button.grid(row=3, column=0, columnspan=2, padx=20, pady=10)
def add_elements(self):
self.num_neb_fields += 1
self.add_button.grid_remove()
self.create_neb_fields(self.neb_entities_frame,
self.num_neb_fields - 1)
self.add_button = Button(self.neb_entities_frame,
text="Add more neb",
command=self.add_elements)
self.add_button.grid(row=self.num_neb_fields + 1,
column=0,
pady=10,
padx=10)
def save(self):
self.neb_info['images'][0] = self.neb_info['images'][1].get()
for rownum in xrange(self.num_neb_fields):
self.neb_info['startdefect'][0]['N' + str(
rownum)] = self.neb_info['startdefect'][1]['N' +
str(rownum)].get()
self.neb_info['enddefect'][0]['N' + str(
rownum)] = self.neb_info['enddefect'][1]['N' +
str(rownum)].get()
num_fields = self.fields_hash.get('N' + str(rownum), 0)
for i in xrange(num_fields):
if 'N' + str(rownum) in self.neb_info['elementmap'][0]:
if i < len(
self.neb_info['elementmap'][0]['N' + str(rownum)]):
self.neb_info['elementmap'][0][
'N' +
str(rownum)][i] = self.neb_info['elementmap'][1][
'N' + str(rownum)][i].get()
else:
self.neb_info['elementmap'][0][
'N' + str(rownum)].append(
self.neb_info['elementmap'][1][
'N' + str(rownum)][i].get())
else:
self.neb_info['elementmap'][0]['N' + str(rownum)] = [
self.neb_info['elementmap'][1]['N' +
str(rownum)][i].get()
]
if 'N' + str(rownum) in self.neb_info['startpos'][0]:
if i < len(
self.neb_info['startpos'][0]['N' + str(rownum)]):
self.neb_info['startpos'][0][
'N' +
str(rownum)][i] = self.neb_info['startpos'][1][
'N' + str(rownum)][i].get()
else:
self.neb_info['startpos'][0]['N' + str(rownum)].append(
self.neb_info['startpos'][1]['N' +
str(rownum)][i].get())
else:
self.neb_info['startpos'][0]['N' + str(rownum)] = [
self.neb_info['startpos'][1]['N' +
str(rownum)][i].get()
]
if 'N' + str(rownum) in self.neb_info['endpos'][0]:
if i < len(self.neb_info['endpos'][0]['N' + str(rownum)]):
self.neb_info['endpos'][0][
'N' + str(rownum)][i] = self.neb_info['endpos'][1][
'N' + str(rownum)][i].get()
else:
self.neb_info['endpos'][0]['N' + str(rownum)].append(
self.neb_info['endpos'][1]['N' +
str(rownum)][i].get())
else:
self.neb_info['endpos'][0]['N' + str(rownum)] = [
self.neb_info['endpos'][1]['N' + str(rownum)][i].get()
]
#save the posfile values
if not self.neb_info['posfiles'][1]:
continue
for entry in self.neb_info['posfiles'][1]['N' + str(rownum)]:
val_list = self.neb_info['posfiles'][0].setdefault(
'N' + str(rownum), [])
val_list.append(entry.get())
self.window.destroy()
self.window = None
self.has_summary = True
self.summary_frame.grid_remove()
self.summary()
def create_neb_fields(self, frame, rownum):
elements_map = self.structure_section.get_elements_map()
elements_options = [
"%s (%s)" % (value, key)
for key, value in elements_map.iteritems()
]
defects_map = self.defects_section.get_defects_map()
defects_options = [
"%s (%s)" % (value, key) for key, value in defects_map.iteritems()
]
num_fields = self.fields_hash.get('N' + str(rownum), 1)
self.fields_hash['N' + str(rownum)] = num_fields
#label frame for this entity
m_frame = LabelFrame(frame, text="N" + str(rownum))
m_frame.grid(row=rownum, column=0, padx=10, pady=10)
e_frame = Frame(m_frame)
e_frame.grid(row=0, column=0)
p_frame = Frame(m_frame)
p_frame.grid(row=1, column=0)
#create field headers
start_label = Label(e_frame, text="START DEFECT")
start_label.grid(row=0, column=0, padx=10, pady=10, sticky=W)
end_label = Label(e_frame, text="END DEFECT")
end_label.grid(row=0, column=1, padx=10, pady=10, sticky=W)
element_label = Label(e_frame, text="ELEMENT")
element_label.grid(row=0, column=2, padx=10, pady=10, sticky=W)
start_pos = Label(e_frame, text="START POSITION")
start_pos.grid(row=0, column=3, padx=10, pady=10, sticky=W)
end_pos = Label(e_frame, text="END POSITION")
end_pos.grid(row=0, column=4, padx=10, pady=10, sticky=W)
start_defect = StringVar(e_frame)
start_defect_val = None
if self.neb_info['startdefect'][0] and (
'N' + str(rownum)) in self.neb_info['startdefect'][0]:
start_defect_val = self.neb_info['startdefect'][0]['N' +
str(rownum)]
s_option_menu = OptionMenu(e_frame, start_defect, ())
s_option_menu.grid(row=1, column=0, sticky=W, pady=10, padx=10)
self.add_options(s_option_menu, defects_options, start_defect,
start_defect_val)
self.neb_info['startdefect'][1]['N' + str(rownum)] = start_defect
end_defect = StringVar(e_frame)
end_defect_val = None
if self.neb_info['enddefect'][0] and (
'N' + str(rownum)) in self.neb_info['enddefect'][0]:
end_defect_val = self.neb_info['enddefect'][0]['N' + str(rownum)]
e_option_menu = OptionMenu(e_frame, end_defect, ())
e_option_menu.grid(row=1, column=1, sticky=W, pady=10, padx=10)
self.add_options(e_option_menu, defects_options, end_defect,
end_defect_val)
self.neb_info['enddefect'][1]['N' + str(rownum)] = end_defect
for i in xrange(num_fields):
self.create_individual_fields(e_frame, elements_options, rownum,
i + 1)
#put the pos file input boxes
#add posfiles if needed
if self.neb_info['images'][0] is not None and self.neb_info['images'][
0] != "" and int(self.neb_info['images'][0]) > 0:
label = Label(p_frame, text="POSFILES")
label.grid(row=0, column=0, sticky=E, pady=10, padx=10)
pos_files_frame = Frame(p_frame)
pos_files_frame.grid(row=0, column=1, sticky=W, pady=10, padx=10)
#create boxes
for i in xrange(int(self.neb_info['images'][0])):
entry_val = StringVar(pos_files_frame)
if 'N' + str(rownum) in self.neb_info['posfiles'][0] and len(
self.neb_info['posfiles'][0]['N' +
str(rownum)]) >= i + 1:
entry_val.set(self.neb_info['posfiles'][0]['N' +
str(rownum)][i])
self.neb_info['posfiles'][1]['N' +
str(rownum)][i] = entry_val
else:
if not self.neb_info['posfiles'][1] or 'N' + str(
rownum) not in self.neb_info['posfiles'][1]:
self.neb_info['posfiles'][1]['N' + str(rownum)] = [
entry_val
]
else:
self.neb_info['posfiles'][1]['N' + str(rownum)].append(
entry_val)
pos_entry = Entry(pos_files_frame, textvariable=entry_val)
pos_entry.grid(row=i, column=0, sticky=W)
def create_individual_fields(self, e_frame, elements_options, neb_id,
rownum):
element = StringVar(e_frame)
element_val = None
if self.neb_info['elementmap'][0] and ('N' + str(neb_id)) in self.neb_info['elementmap'][0] and \
rownum <= len(self.neb_info['elementmap'][0]['N' + str(neb_id)]):
element_val = self.neb_info['elementmap'][0]['N' +
str(neb_id)][rownum -
1]
option_menu = OptionMenu(e_frame, element, ())
option_menu.grid(row=rownum, column=2, sticky=W, pady=10, padx=10)
self.add_options(option_menu, elements_options, element, element_val)
if 'N' + str(neb_id) in self.neb_info['elementmap'][1]:
if rownum <= len(
self.neb_info['elementmap'][1]['N' + str(neb_id)]):
self.neb_info['elementmap'][1]['N' + str(neb_id)][rownum -
1] = element
else:
self.neb_info['elementmap'][1]['N' +
str(neb_id)].append(element)
else:
self.neb_info['elementmap'][1]['N' + str(neb_id)] = [element]
startpos_text = StringVar()
if self.neb_info['startpos'][0] and ('N' + str(neb_id)) in self.neb_info['startpos'][0] and \
rownum <= len(self.neb_info['startpos'][0]['N' + str(neb_id)]):
startpos_text.set(
self.neb_info['startpos'][0]['N' + str(neb_id)][rownum - 1])
startpos_val = Entry(e_frame, textvariable=startpos_text)
startpos_val.grid(row=rownum, column=3, pady=10, padx=10, sticky=W)
if 'N' + str(neb_id) in self.neb_info['startpos'][1]:
if rownum <= len(self.neb_info['startpos'][1]['N' + str(neb_id)]):
self.neb_info['startpos'][1]['N' +
str(neb_id)][rownum -
1] = startpos_text
else:
self.neb_info['startpos'][1]['N' +
str(neb_id)].append(startpos_text)
else:
self.neb_info['startpos'][1]['N' + str(neb_id)] = [startpos_text]
endpos_text = StringVar()
if self.neb_info['endpos'][0] and ('N' + str(rownum)) in self.neb_info['endpos'][0] and \
rownum <= len(self.neb_info['endpos'][0]['N' + str(neb_id)]):
endpos_text.set(
self.neb_info['endpos'][0]['N' + str(neb_id)][rownum - 1])
endpos_val = Entry(e_frame, textvariable=endpos_text)
endpos_val.grid(row=rownum, column=4, pady=10, padx=10, sticky=W)
if 'N' + str(neb_id) in self.neb_info['endpos'][1]:
if rownum <= len(self.neb_info['endpos'][1]['N' + str(neb_id)]):
self.neb_info['endpos'][1]['N' + str(neb_id)][rownum -
1] = endpos_text
else:
self.neb_info['endpos'][1]['N' +
str(neb_id)].append(endpos_text)
else:
self.neb_info['endpos'][1]['N' + str(neb_id)] = [endpos_text]
add_button = Button(e_frame, text="+")
add_button.grid(row=rownum, column=5, pady=10, padx=10)
add_button.configure(command=lambda: self.add_neb_field(
add_button, e_frame, rownum, elements_options, neb_id))
def add_neb_field(self, add_button, e_frame, rownum, elements_options,
neb_id):
add_button.grid_remove()
num_fields = self.fields_hash.get('N' + str(neb_id), 1)
self.fields_hash['N' + str(neb_id)] = num_fields + 1
self.create_individual_fields(e_frame, elements_options, neb_id,
rownum + 1)
def add_options(self, option_menu, options, element_var, index_val):
menu = option_menu["menu"]
menu.delete(0, "end")
for string in options:
menu.add_command(
label=string,
command=lambda value=string: element_var.set(value))
if index_val is not None:
element_var.set(index_val)
class MastGui:
def __init__(self):
self.root_window = Tk()
self.vframe = VerticalScrolledFrame(self.root_window)
self.vframe.pack(fill=BOTH, expand=1)
self.window = self.vframe.interior
self.sections = []
self.initialize_window()
def initialize_window(self):
#window properties
self.root_window.title("MAST")
screensizeX = self.root_window.winfo_screenwidth()
screensizeY = self.root_window.winfo_screenheight()
self.root_window.minsize(screensizeX - 100, screensizeY - 100)
self.window.grid_rowconfigure(0, weight=1)
self.window.grid_rowconfigure(1, weight=1)
self.window.grid_rowconfigure(2, weight=1)
self.window.grid_rowconfigure(3, weight=1)
self.window.grid_rowconfigure(4, weight=1)
self.window.grid_rowconfigure(5, weight=1)
self.window.grid_rowconfigure(6, weight=1)
self.window.grid_columnconfigure(0, weight=1)
#add sections
self.mast_section = MastSection(self.window, 0)
self.mast_section.summary()
self.sections.append(self.mast_section)
self.structure_section = StructureSection(self.window, 1)
self.structure_section.summary()
self.sections.append(self.structure_section)
self.defects_section = DefectsSection(self.window, 2,
self.structure_section)
self.defects_section.summary()
self.sections.append(self.defects_section)
self.neb_section = NEBSection(self.window, 3, self.structure_section,
self.defects_section)
self.neb_section.summary()
self.sections.append(self.neb_section)
self.ingredients_section = IngredientsSection(self.window, 4)
self.ingredients_section.summary()
self.sections.append(self.ingredients_section)
self.phonon_section = PhononSection(self.window, 5)
self.phonon_section.summary()
self.create_btn = Button(self.window,
text="Create Input File",
command=self.create_input)
self.create_btn.grid(row=6, column=0, pady=10, padx=10)
def create_input(self):
input_file = open("mast_input.inp", "w")
for section_obj in self.sections:
output_content = section_obj.content()
input_file.write(output_content)
input_file.close()
self.root_window.destroy()
def run(self):
self.root_window.mainloop()
def create_window(self):
self.window = ttk.Toplevel(self.parent_window)
self.window.title("Structure Information")
self.window.minsize(500, 500)
self.vframe = VerticalScrolledFrame(self.window)
self.vframe.pack(fill=BOTH, expand=1)
self.structure_window = self.vframe.interior
self.structure_window.grid_rowconfigure(0, weight=1)
self.structure_window.grid_columnconfigure(0, weight=1)
self.structure_window.grid_rowconfigure(0, weight=1)
self.structure_window.grid_columnconfigure(0, weight=1)
structure_frame = LabelFrame(self.structure_window, text="Structure")
structure_frame.grid(row=0, column=0, padx=20, pady=20)
structure_frame.grid_rowconfigure(0, weight=1)
structure_frame.grid_rowconfigure(1, weight=1)
structure_frame.grid_columnconfigure(0, weight=1)
structure_frame.grid_columnconfigure(1, weight=1)
#add coordtype
label = Label(structure_frame, text="COORD_TYPE")
label.grid(row=0, column=0, sticky=E, pady=10, padx=10)
coord_type = StringVar(structure_frame)
coord_type.set("fractional")
if self.structure_info['coord_type'][0] is not None:
coord_type.set(self.structure_info['coord_type'][0])
coord_type_option = OptionMenu(structure_frame, coord_type,
"fractional", "cartesian")
coord_type_option.grid(row=0, column=1, sticky=W, pady=10, padx=10)
self.structure_info["coord_type"] = [coord_type.get(), coord_type]
#pos file
label = Label(structure_frame, text="POSFILE")
label.grid(row=1, column=0, sticky=E, pady=10, padx=10)
text_val = StringVar()
if self.structure_info['posfile'][0] is not None:
text_val.set(self.structure_info['posfile'][0])
text = Entry(structure_frame, textvariable=text_val)
text.grid(row=1, column=1, sticky=W, pady=10, padx=10)
self.structure_info['posfile'] = [text_val.get(), text_val]
#pos file
label = Label(structure_frame, text="LATTICE")
label.grid(row=2, column=0, sticky=E, pady=10, padx=10)
text = Text(structure_frame, height=5, width=30)
if self.structure_info['lattice'][0] is not None:
text.insert('1.0', self.structure_info['lattice'][0])
text.grid(row=2, column=1, sticky=W, pady=10, padx=10)
self.structure_info['lattice'][1] = text
#label frame to add elements info
self.elements_frame = LabelFrame(structure_frame,
text="ELEMENTS INFORMATION")
self.elements_frame.grid(row=3,
column=0,
columnspan=2,
pady=10,
padx=10)
#create field headers
id_label = Label(self.elements_frame, text="ID")
id_label.grid(row=0, column=0, padx=10, pady=10, sticky=W)
element_label = Label(self.elements_frame, text="ELEMENT")
element_label.grid(row=0, column=1, padx=10, pady=10, sticky=W)
coordinates_label = Label(self.elements_frame, text="COORDINATES")
coordinates_label.grid(row=0, column=2, padx=10, pady=10, sticky=W)
for row_num in xrange(self.num_elt_fields + 1):
if row_num == 0:
continue
self.create_element_fields(self.elements_frame, row_num)
self.add_button = Button(self.elements_frame,
text="Add more elements",
command=self.add_elements)
self.add_button.grid(row=self.num_elt_fields + 1,
column=0,
columnspan=3,
pady=10,
padx=10)
#save button
save_button = Button(structure_frame, text="Save", command=self.save)
save_button.grid(row=4, column=0, columnspan=2, padx=20, pady=10)
class StructureSection:
def __init__(self, parent_window, grid_row):
self.parent_window = parent_window
self.grid_row = grid_row
self.summary_frame = None
self.structure_info = {\
'coord_type' : [None, None],\
'posfile' : [None, None],\
'elementmap' : [{}, {}],\
'lattice' : [None, None],\
'coordinates': [{}, {}],\
}
self.num_elt_fields = 1
self.has_summary = False
def get_elements_map(self):
return self.structure_info['elementmap'][0]
def content(self):
content_start = "$structure\n"
content_end = "$end\n\n"
content_lines = ""
if self.structure_info['coord_type'][0]:
content_lines += "coord_type %s\n\n" % self.structure_info[
'coord_type'][0]
if self.structure_info['posfile'][0]:
content_lines += "posfile %s\n\n" % self.structure_info['posfile'][
0]
if self.structure_info['elementmap'][0]:
content_lines += "begin elementmap\n"
for elt_key, elt_name in self.structure_info['elementmap'][
0].iteritems():
content_lines += "%s %s\n" % (elt_key, elt_name)
content_lines += "end\n\n"
if self.structure_info['coordinates'][0]:
content_lines += "begin coordinates\n"
for elt_key, elt_coord in self.structure_info['coordinates'][
0].iteritems():
coord_lines = elt_coord.split('\n')
for line in coord_lines:
if line:
content_lines += "%s %s\n" % (elt_key, line)
content_lines += "end\n\n"
if self.structure_info['lattice'][0]:
content_lines += "begin lattice\n"
content_lines += "%s\n" % self.structure_info['lattice'][0]
content_lines += "end\n\n"
return content_start + content_lines + content_end
def summary(self):
#the frame which encloses all the contents
self.summary_frame = LabelFrame(self.parent_window, text="Structure")
self.summary_frame.grid_rowconfigure(0, weight=1)
self.summary_frame.grid_rowconfigure(1, weight=1)
self.summary_frame.grid_columnconfigure(0, weight=1)
self.summary_frame.grid_columnconfigure(1, weight=1)
self.summary_frame.grid_columnconfigure(2, weight=1)
#if it has summary show it
if self.has_summary:
#coord_type
coord_type = Label(self.summary_frame, text="COORD_TYPE :")
coord_type.grid(row=0, column=1, sticky=E, pady=5)
coord_type_value = Label(self.summary_frame,
text=self.structure_info['coord_type'][0])
coord_type_value.grid(row=0, column=2, sticky=W, pady=5)
#posfile
if self.structure_info['posfile'][0].strip() != "":
posfile = Label(self.summary_frame, text="POSFILE :")
posfile.grid(row=1, column=1, sticky=E, pady=5)
posfile_value = Label(self.summary_frame,
text=self.structure_info['posfile'][0])
posfile_value.grid(row=1, column=2, sticky=W, pady=5)
#lattice structure
lattice = Label(self.summary_frame, text="LATTICE : ")
lattice.grid(row=2, column=1, sticky=E, pady=5)
lattice_value = Label(self.summary_frame,
text=self.structure_info['lattice'][0])
lattice_value.grid(row=2, column=2, sticky=W, pady=5)
for row_num in xrange(self.num_elt_fields + 1):
if row_num == 0:
continue
if self.structure_info['elementmap'][0][
'X' + str(row_num)].strip() == "":
continue
id_label = Label(self.summary_frame, text='X' + str(row_num))
id_label.grid(row=2 + row_num,
column=0,
padx=10,
pady=2,
sticky=E)
element_label = Label(
self.summary_frame,
text=self.structure_info['elementmap'][0]['X' +
str(row_num)])
element_label.grid(row=2 + row_num,
column=1,
padx=10,
pady=2,
sticky=W)
coordinates_label = Label(
self.summary_frame,
text=self.structure_info['coordinates'][0]['X' +
str(row_num)])
coordinates_label.grid(row=2 + row_num,
column=2,
padx=10,
pady=2,
sticky=W)
#the frame contents
add_button = Button(self.summary_frame,
text="Add Structure properties",
command=self.create_window)
add_button.grid(row=3 + self.num_elt_fields,
column=0,
columnspan=3,
pady=20,
padx=20)
self.summary_frame.grid(row=self.grid_row,
column=0,
padx=20,
pady=5,
sticky=W + E)
def create_window(self):
self.window = ttk.Toplevel(self.parent_window)
self.window.title("Structure Information")
self.window.minsize(500, 500)
self.vframe = VerticalScrolledFrame(self.window)
self.vframe.pack(fill=BOTH, expand=1)
self.structure_window = self.vframe.interior
self.structure_window.grid_rowconfigure(0, weight=1)
self.structure_window.grid_columnconfigure(0, weight=1)
self.structure_window.grid_rowconfigure(0, weight=1)
self.structure_window.grid_columnconfigure(0, weight=1)
structure_frame = LabelFrame(self.structure_window, text="Structure")
structure_frame.grid(row=0, column=0, padx=20, pady=20)
structure_frame.grid_rowconfigure(0, weight=1)
structure_frame.grid_rowconfigure(1, weight=1)
structure_frame.grid_columnconfigure(0, weight=1)
structure_frame.grid_columnconfigure(1, weight=1)
#add coordtype
label = Label(structure_frame, text="COORD_TYPE")
label.grid(row=0, column=0, sticky=E, pady=10, padx=10)
coord_type = StringVar(structure_frame)
coord_type.set("fractional")
if self.structure_info['coord_type'][0] is not None:
coord_type.set(self.structure_info['coord_type'][0])
coord_type_option = OptionMenu(structure_frame, coord_type,
"fractional", "cartesian")
coord_type_option.grid(row=0, column=1, sticky=W, pady=10, padx=10)
self.structure_info["coord_type"] = [coord_type.get(), coord_type]
#pos file
label = Label(structure_frame, text="POSFILE")
label.grid(row=1, column=0, sticky=E, pady=10, padx=10)
text_val = StringVar()
if self.structure_info['posfile'][0] is not None:
text_val.set(self.structure_info['posfile'][0])
text = Entry(structure_frame, textvariable=text_val)
text.grid(row=1, column=1, sticky=W, pady=10, padx=10)
self.structure_info['posfile'] = [text_val.get(), text_val]
#pos file
label = Label(structure_frame, text="LATTICE")
label.grid(row=2, column=0, sticky=E, pady=10, padx=10)
text = Text(structure_frame, height=5, width=30)
if self.structure_info['lattice'][0] is not None:
text.insert('1.0', self.structure_info['lattice'][0])
text.grid(row=2, column=1, sticky=W, pady=10, padx=10)
self.structure_info['lattice'][1] = text
#label frame to add elements info
self.elements_frame = LabelFrame(structure_frame,
text="ELEMENTS INFORMATION")
self.elements_frame.grid(row=3,
column=0,
columnspan=2,
pady=10,
padx=10)
#create field headers
id_label = Label(self.elements_frame, text="ID")
id_label.grid(row=0, column=0, padx=10, pady=10, sticky=W)
element_label = Label(self.elements_frame, text="ELEMENT")
element_label.grid(row=0, column=1, padx=10, pady=10, sticky=W)
coordinates_label = Label(self.elements_frame, text="COORDINATES")
coordinates_label.grid(row=0, column=2, padx=10, pady=10, sticky=W)
for row_num in xrange(self.num_elt_fields + 1):
if row_num == 0:
continue
self.create_element_fields(self.elements_frame, row_num)
self.add_button = Button(self.elements_frame,
text="Add more elements",
command=self.add_elements)
self.add_button.grid(row=self.num_elt_fields + 1,
column=0,
columnspan=3,
pady=10,
padx=10)
#save button
save_button = Button(structure_frame, text="Save", command=self.save)
save_button.grid(row=4, column=0, columnspan=2, padx=20, pady=10)
def save(self):
self.structure_info['coord_type'][0] = self.structure_info[
'coord_type'][1].get()
self.structure_info['posfile'][0] = self.structure_info['posfile'][
1].get()
self.structure_info['lattice'][0] = self.structure_info['lattice'][
1].get("1.0", END)
for row_num in xrange(self.num_elt_fields + 1):
if row_num == 0:
continue
self.structure_info['elementmap'][0][
'X' + str(row_num)] = self.structure_info['elementmap'][1][
'X' + str(row_num)].get()
self.structure_info['coordinates'][0][
'X' + str(row_num)] = self.structure_info['coordinates'][1][
'X' + str(row_num)].get("1.0", END)
self.window.destroy()
self.window = None
self.has_summary = True
self.summary_frame.grid_remove()
self.summary()
def add_elements(self):
self.num_elt_fields += 1
self.add_button.grid_remove()
self.create_element_fields(self.elements_frame, self.num_elt_fields)
self.add_button = Button(self.elements_frame,
text="Add more elements",
command=self.add_elements)
self.add_button.grid(row=self.num_elt_fields + 1,
column=0,
columnspan=3,
pady=10,
padx=10)
def create_element_fields(self, elements_frame, row_num):
id_label = Label(elements_frame, text="X" + str(row_num))
id_label.grid(row=row_num, column=0, padx=10, pady=10, sticky=W)
text_val = StringVar()
if self.structure_info['elementmap'][0] and (
'X' + str(row_num)) in self.structure_info['elementmap'][0]:
text_val.set(self.structure_info['elementmap'][0]['X' +
str(row_num)])
element_name = Entry(elements_frame, textvariable=text_val)
element_name.grid(row=row_num, column=1, pady=10, padx=10, sticky=W)
self.structure_info['elementmap'][1]['X' + str(row_num)] = text_val
coordinates = Text(elements_frame, height=5, width=30)
if self.structure_info['coordinates'][0] and (
'X' + str(row_num)) in self.structure_info['coordinates'][0]:
coordinates.insert(
'1.0',
self.structure_info['coordinates'][0]['X' + str(row_num)])
coordinates.grid(row=row_num, column=2, pady=10, padx=10, sticky=W)
self.structure_info['coordinates'][1]['X' + str(row_num)] = coordinates
def create_window(self):
self.window = ttk.Toplevel(self.parent_window)
self.window.title("NEB Information")
self.window.minsize(500, 500)
self.vframe = VerticalScrolledFrame(self.window)
self.vframe.pack(fill=BOTH, expand=1)
self.neb_window = self.vframe.interior
self.neb_window.grid_rowconfigure(0, weight=1)
self.neb_window.grid_columnconfigure(0, weight=1)
neb_frame = LabelFrame(self.neb_window, text="NEB")
neb_frame.grid(row=0, column=0, padx=20, pady=20)
neb_frame.grid_rowconfigure(0, weight=1)
neb_frame.grid_columnconfigure(0, weight=1)
#frame for images and button
frame1 = Frame(neb_frame)
frame1.grid(row=0, column=0)
frame1.grid_rowconfigure(0, weight=1)
frame1.grid_rowconfigure(1, weight=1)
frame1.grid_columnconfigure(0, weight=1)
frame1.grid_columnconfigure(1, weight=1)
frame1.grid_columnconfigure(2, weight=1)
#add images
label = Label(frame1, text="IMAGES")
label.grid(row=0, column=0, sticky=E, pady=10, padx=10)
images_val = StringVar(frame1)
if self.neb_info['images'][0] is not None:
images_val.set(self.neb_info['images'][0])
images_menu = Entry(frame1, textvariable=images_val)
images_menu.grid(row=0, column=1, sticky=W, pady=10, padx=10)
self.neb_info["images"] = [images_val.get(), images_val]
images_btn = Button(frame1,
text="Add Posfiles",
command=self.create_window_with_posfiles)
images_btn.grid(row=0, column=2, sticky=W, pady=10, padx=10)
#frame for entities
frame2 = Frame(neb_frame)
frame2.grid(row=1, column=0)
#a label frame to add neb related information
self.neb_entities_frame = LabelFrame(frame2, text="NEB ENTITIES")
self.neb_entities_frame.grid(row=0,
column=0,
columnspan=3,
padx=10,
pady=10)
for rownum in xrange(self.num_neb_fields):
self.create_neb_fields(self.neb_entities_frame, rownum)
self.add_button = Button(self.neb_entities_frame,
text="Add more neb",
command=self.add_elements)
self.add_button.grid(row=self.num_neb_fields + 1,
column=0,
columnspan=6,
pady=10,
padx=10)
#save button
save_button = Button(neb_frame, text="Save", command=self.save)
save_button.grid(row=3, column=0, columnspan=2, padx=20, pady=10)
