#!/user/bin/env python3 # -*- coding: utf-8 -*- # Copyright (c) 2024 Zhibin Gao's Group. All rights reserved. # Author: Zhibin Gao # Email: zhibin.gao@xjtu.edu.cn import os import warnings import glob import io import sys # Add parent directory to system path current_dir = os.path.dirname(os.path.abspath(__file__)) parent_dir = os.path.dirname(current_dir) if parent_dir not in sys.path: sys.path.append(parent_dir) # Import custom modules import streamlit_scripts.file_op as fo import streamlit_scripts.chang_model as cm import streamlit_scripts.calculate_K as calk import predict # Should import correctly now # Import third party libraries import streamlit as st import pandas as pd from pymatgen.core.structure import Structure from pymatgen.symmetry.analyzer import SpacegroupAnalyzer def display_results(df): """ Display calculation results Args: df: DataFrame containing calculation results Returns: template: HTML template string containing results """ # Define lattice thermal conductivity formula formula=r"$$\kappa_L=A\frac{M V^{\frac{1}{3}} \theta_a^3}{\gamma^2 T n} $$" try: # Generate results display template template=f""" The number of atoms of the crystal structure is {df["Number of Atoms"][0]}.
The volume of the crystal structure is {df["Volume (Å3)"][0]} Å$^3$.
The total atomic mass of the crystal structure is {df["the total atomic mass (amu)"][0]} amu.
The Bulk modulus of the crystal structure is {df["Bulk modulus (GPa)"][0]} GPa.
The Shear modulus of the crystal structure is {df["Shear modulus (GPa)"][0]} GPa.
The sound velocity of the crystal structure is {df["Speed of sound (m s-1)"][0]} m/s.
The Acoustic Debye Temperature of the crystal structure is {df["Acoustic Debye Temperature (K)"][0]} K.
The Grüneisen parameter of the crystal structure is {df["Grüneisen parameter"][0]}.
The formula of the lattice thermal conductivity is: {formula}.
The calculated lattice thermal conductivity is {df["Kappa_Slack (W m-1 K-1)"][0]} W/(m·K).
""" except Exception as e: st.write(e) return template def app(): """Main application function""" # Set page title st.title("KappaP") # Get paths sour_path = os.path.abspath('.') root_dir_path = st.session_state.root_dir_path model_path = os.path.join(sour_path, "model") if st.session_state.uploaded_files: # Check if uploaded CIF files are valid and ensure primitive structures are used cif_path_list = glob.glob(os.path.join(root_dir_path, '*.cif')) valid_structures = {} for cif_path in cif_path_list: try: file_name = os.path.basename(cif_path) # First try to get converted primitive structure from session state if hasattr(st.session_state, 'primitive_structures') and file_name in st.session_state.primitive_structures: valid_structures[file_name] = st.session_state.primitive_structures[file_name] print(f"Using cached primitive structure for {file_name}") else: # If not in session state, read and convert structure = Structure.from_file(cif_path) analyzer = SpacegroupAnalyzer(structure) primitive_structure = analyzer.get_primitive_standard_structure() valid_structures[file_name] = primitive_structure print(f"Created new primitive structure for {file_name}") except Exception as e: st.write(f"{file_name} Invalid CIF file: {str(e)}") os.remove(cif_path) st.write(f"Invalid CIF file {file_name} has been deleted.") if not valid_structures: st.error("No valid CIF files found.") return # Create id_prop.csv cif_path_list, cif_name_list = fo.create_id_prop(root_dir_path) if len(cif_name_list) > 0: # Get crystal info for first file first_cif_name = cif_name_list[0] first_cif_path = os.path.join(root_dir_path, first_cif_name) # Get crystal info using get_crystalline_content cry_content = fo.get_crystalline_content(first_cif_path) results_csv_path = os.path.join(sour_path, "test_results.csv") # Get model paths and names model_path_list, model_name_list = cm.get_model_path(model_path) # Predict using first model try: cm.copy_model(model_path_list[0], sour_path) predict.main(root_dir_path) pre_df = cm.get_pre_dataframe(results_csv_path, model_name_list[0]) finally: cm.clean_model(sour_path) # Predict using remaining models and merge results for model_path, model_name in zip(model_path_list[1:], model_name_list[1:]): try: cm.copy_model(model_path, sour_path) predict.main(root_dir_path) pre_df1 = cm.get_pre_dataframe(results_csv_path, model_name) pre_df = pd.merge(pre_df, pre_df1, left_index=True, right_index=True) finally: cm.clean_model(sour_path) try: st.write("---") # Get crystal data all_cry_df = fo.get_dir_crystalline_data(root_dir_path) if all_cry_df.empty: st.error("Failed to extract crystal data from CIF files.") return # Merge crystal data and predictions whole_info_df = pd.merge(all_cry_df, pre_df, left_index=True, right_index=True) if whole_info_df.empty: st.error("Failed to merge crystal data with predictions.") return # Calculate physical parameters Debye_df = calk.cal_Debye_T(whole_info_df) gamma_df = calk.cal_gamma(Debye_df) A_df = calk.cal_A(gamma_df, 1) K_slack_df = calk.cal_K_Slack(A_df) # Select columns to display ls = ["Number of Atoms", "Density (g cm-3)", "Volume (Å3)", "the total atomic mass (amu)", "Bulk modulus (GPa)", "Shear modulus (GPa)", "Sound velocity of the transverse wave (m s-1)", "Sound velocity of the longitude wave (m s-1)", "Speed of sound (m s-1)", "Poisson ratio", "Grüneisen parameter", "Acoustic Debye Temperature (K)", "Kappa_Slack (W m-1 K-1)"] final_df = K_slack_df.loc[:, ls] # Check if results are empty if final_df.empty: st.error("No data was generated. Please check your input files.") return # Display results st.dataframe(final_df) st.write("---") # Display filename first_index = final_df.index[0] if len(final_df.index) > 0 else "No file" st.write(f"The file name of displaying crystalline is: {first_index}") # Display crystal structure info st.write("The information of uploaded crystal structure is:") st.write(cry_content, unsafe_allow_html=True) st.write("---") # Display calculation results if not final_df.empty: template = display_results(final_df) st.markdown(template, unsafe_allow_html=True) st.write("---") except Exception as e: st.error(f"An error occurred: {str(e)}") st.write("Please check your input files and try again.") finally: # Clean up temporary files fo.del_cif_file(root_dir_path) fo.del_temp_file(sour_path) else: # Prompt user to upload files st.info('Please upload CIF files in the sidebar first.') # Display declaration declaration = """

We strive to have clear documentation and examples to help everyone with using KappaP on their own. We will happily fix issues in the documentation and examples should you find any, however, we will not be able to offer extensive user support and training, except for our collaborators.

""" st.markdown(declaration, unsafe_allow_html=True)