# RepTate: Rheology of Entangled Polymers: Toolkit for the Analysis of Theory and Experiments
# --------------------------------------------------------------------------------------------------------
#
# Authors:
# Jorge Ramirez, jorge.ramirez@upm.es
# Victor Boudara, victor.boudara@gmail.com
#
# Useful links:
# http://blogs.upm.es/compsoftmatter/software/reptate/
# https://github.com/jorge-ramirez-upm/RepTate
# http://reptate.readthedocs.io
#
# --------------------------------------------------------------------------------------------------------
#
# Copyright (2017-2023): Jorge Ramirez, Victor Boudara, Universidad Politécnica de Madrid, University of Leeds
#
# This file is part of RepTate.
#
# RepTate is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# RepTate is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with RepTate. If not, see <http://www.gnu.org/licenses/>.
#
# --------------------------------------------------------------------------------------------------------
"""Module TheoryBobNLVE
BobLVE file calculates the LVE of a given polymer configuration
by Chinmay Das et al.
"""
import os
import numpy as np
import RepTate
from RepTate.gui.QTheory import QTheory
import time
import ctypes
from RepTate.theories.BobCtypesHelper import BobCtypesHelper, BobError
from PySide6.QtWidgets import QApplication, QToolBar, QToolButton, QMenu
from PySide6.QtWidgets import QDialog, QFileDialog, QMessageBox
from PySide6.QtGui import QDesktopServices, QIcon
from PySide6.QtCore import QUrl, Signal, QSize
from RepTate.theories.theory_helpers import FlowMode
from RepTate.gui import bob_LVE
[docs]
class TheoryBobNLVE(QTheory):
"""Predict the nonlinear rheology of "branch-on-branch" polymers, read from a polymer configuration file,
using BoB v2.5 (Chinmay Das and Daniel Read).
Polymer configuration files can be generated from the React application in RepTate.
The original documentation of BoB can be found here: `<https://sourceforge.net/projects/bob-rheology/files/bob-rheology/bob2.3/bob2.3.pdf/download>`_.
"""
thname = 'BOB'
description = 'Branch-On-Branch rheology'
citations = ['Das C. et al., J. Rheol. 2006, 50, 207-234']
doi = ["http://dx.doi.org/10.1122/1.2167487"]
html_help_file = 'https://reptate.readthedocs.io/manual/Applications/NLVE/Theory/theory.html#bob-nlve'
single_file = False # False if the theory can be applied to multiple files simultaneously
signal_param_dialog = Signal(object)
def __init__(self, name='ThBobLVE', parent_dataset=None, axarr=None):
"""**Constructor**"""
super().__init__(name, parent_dataset, axarr)
self.function = self.calculate # main theory function
self.has_modes = False # True if the theory has modes
self.signal_param_dialog.connect(self.launch_param_dialog)
self.polyconf_file_out = None # full path of target polyconf file
self.bch = BobCtypesHelper(self)
self.autocalculate = False
self.freqint = 1.1 # BoB theory points spaced by log10(freqint)
self.do_priority_seniority = False
self.init_flow_mode()
self.success_dialog = False
self.argv = None
self.inp_counter = 0 # counter for the 'virtual' input file for BoB
self.virtual_input_file = [] # 'virtual' input file for BoB
# temp_dir = os.path.join('theories', 'temp')
# #create temp folder if does not exist
# if not os.path.exists(temp_dir):
# os.makedirs(temp_dir)
self.selected_file = None
self.setup_dialog()
# add widgets specific to the theory
tb = QToolBar()
tb.setIconSize(QSize(24, 24))
self.tbutflow = QToolButton()
self.tbutflow.setPopupMode(QToolButton.MenuButtonPopup)
menu = QMenu(self)
self.shear_flow_action = menu.addAction(
QIcon(':/Icon8/Images/new_icons/icon-shear.png'), "Shear Flow")
self.extensional_flow_action = menu.addAction(
QIcon(':/Icon8/Images/new_icons/icon-uext.png'),
"Extensional Flow")
if self.flow_mode == FlowMode.shear:
self.tbutflow.setDefaultAction(self.shear_flow_action)
else:
self.tbutflow.setDefaultAction(self.extensional_flow_action)
self.tbutflow.setMenu(menu)
tb.addWidget(self.tbutflow)
#BOB settings buttons
self.bob_settings_button = tb.addAction(
QIcon(':/Icon8/Images/new_icons/icons8-BoB-settings.png'),
"Edit BoB's input polyconf. file and material parameters")
self.thToolsLayout.insertWidget(0, tb)
connection_id = self.shear_flow_action.triggered.connect(
self.select_shear_flow)
connection_id = self.extensional_flow_action.triggered.connect(
self.select_extensional_flow)
connection_id = self.bob_settings_button.triggered.connect(
self.launch_param_dialog)
[docs]
def select_shear_flow(self):
self.flow_mode = FlowMode.shear
self.tbutflow.setDefaultAction(self.shear_flow_action)
[docs]
def select_extensional_flow(self):
self.flow_mode = FlowMode.uext
self.tbutflow.setDefaultAction(self.extensional_flow_action)
[docs]
def get_file_name(self):
"""Open a dialog to choose a file containing the polymer configuration for BoB"""
# file browser window
options = QFileDialog.Options()
dir_start = os.path.join(RepTate.root_dir, "data", "React")
dilogue_name = "Select a Polymer Configuration File"
ext_filter = "Data Files (*.dat)"
selected_file, _ = QFileDialog.getOpenFileName(
self, dilogue_name, dir_start, ext_filter, options=options)
self.selected_file = selected_file
self.d.selected_file.setText(os.path.basename(selected_file))
[docs]
def num_file_lines(self, fname):
"""Return the number of lines in the file `fname`"""
with open(fname) as f:
i = 0
for _, l in enumerate(f):
i += 1
return i + 1
[docs]
def setup_dialog(self):
"""Load the form dialog from bob_LVE.py"""
self.dialog = QDialog(self)
self.dialog.ui = bob_LVE.Ui_Dialog()
self.dialog.ui.setupUi(self.dialog)
self.d = self.dialog.ui
self.d.pb_pick_file.clicked.connect(self.get_file_name)
self.d.selected_file.setStyleSheet("color : blue ;")
# connect button OK
self.d.pb_ok.clicked.connect(self.handle_pb_ok)
self.d.pb_ok.setDefault(True)
# connect button Cancel
self.d.pb_cancel.clicked.connect(self.dialog.reject)
# connect button Help
self.d.pb_help.clicked.connect(
self.handle_help_button)
[docs]
def handle_pb_ok(self):
"""Define the OK button role. If something is wrong, keep the dialog open"""
if self.selected_file is None:
QMessageBox.warning(
self, 'Select Input Polyconf',
'Please select a file for BoB to read the polymer configuration')
else:
self.dialog.accept()
[docs]
def launch_param_dialog(self):
"""Show a dialog to get the filename of the polymer configuration.
This function is called via a Signal for multithread compatibility"""
if not self.dialog.exec_():
self.success_dialog = False
return
conffile = self.selected_file
if not self.is_ascii(conffile):
# ok_path = os.path.join('theories', 'temp', 'target_polyconf.dat')
# copy2(conffile, ok_path)
# conffile = ok_path
self.Qprint("<font color=orange><b>\"%s\" contains non-ascii characters. BoB might not like it...</b></font>" % conffile)
print("\"%s\" contains non-ascii characters. BoB might not like it..." % conffile)
if conffile == '' or os.path.splitext(conffile)[1] == '':
self.Qprint("<font color=red><b>Set the output filepath to write the polyconf file</b></font>")
return
nlines = self.num_file_lines(conffile)
# inpf = os.path.join('theories', 'temp', 'temp_inpf.dat')
inpf = 'inpf.dat' # dummy name
self.create_bob_input_file(nlines, inpf)
# BoB main arguments
self.argv = ["./bob", "-i", inpf, "-c", conffile]
self.success_dialog = True
[docs]
def is_ascii(self, s):
"""Check if `s` contains non ASCII characters"""
try:
s.encode('ascii')
return True
except UnicodeEncodeError:
return False
[docs]
def init_flow_mode(self):
"""Find if data files are shear or extension"""
try:
f = self.theory_files()[0]
if f.file_type.extension == 'shear':
self.flow_mode = FlowMode.shear
else:
self.flow_mode = FlowMode.uext
except Exception as e:
print("in RP init:", e)
self.flow_mode = FlowMode.shear #default mode: shear
[docs]
def request_stop_computations(self):
"""Called when user wants to terminate the current computation"""
self.Qprint('<font color=red><b>Stop current calculation requested</b></font>')
self.bch.set_flag_stop_bob(ctypes.c_bool(True))
[docs]
def do_error(self, line=""):
"""This theory does not calculate the error"""
pass
[docs]
def calculate(self, f=None):
"""Create polymer configuration file and calculate distribution characteristics"""
ft = f.data_table
tt = self.tables[f.file_name_short]
tt.num_columns = ft.num_columns
tt.num_rows = ft.num_rows
tt.data = np.zeros((tt.num_rows, tt.num_columns))
self.freqmax = 1.0 / f.data_table.mincol(0)
self.freqmin = 1.0 / f.data_table.maxcol(0)
#show form if not filled yet
if not self.success_dialog:
self.signal_param_dialog.emit(self)
self.success_dialog = None
while self.success_dialog is None: # wait for the end of QDialog
# TODO: find a better way to wait for the dialog thread to finish
time.sleep(0.5)
if not self.success_dialog:
self.Qprint('Operation cancelled')
return
QApplication.processEvents()
self.bch.link_c_callback()
self.bch.set_do_priority_seniority(ctypes.c_bool(self.do_priority_seniority))
# Run BoB C++ code
self.start_time_cal = time.time()
flowrate = float(f.file_parameters["gdot"])
tmin = ft.data[0, 0]
tmax = ft.data[-1, 0]
is_shear = self.flow_mode == FlowMode.shear
self.Qprint("<hr><h3>rate %.3g s<sup>-1</sup></h3>" % flowrate)
try:
time_arr, stress_arr = self.bch.return_bob_nlve(self.argv, flowrate, tmin, tmax, is_shear)
except BobError:
self.Qprint('Operation cancelled')
return
#copy results to RepTate data file
if time:
tt.num_columns = ft.num_columns
tt.num_rows = len(time_arr)
tt.data = np.zeros((tt.num_rows, tt.num_columns))
tt.data[:, 0] = time_arr[:]
tt.data[:, 1] = stress_arr[:]
# tt.data[:, 2] =
[docs]
def do_fit(self, line=''):
self.Qprint("Fitting not allowed in this theory")
