0.1.164

PyPI/setup.cfg

@@ -1,7 +1,7 @@
 [metadata]
 # replace with your username:
 name = guan
-version = 0.1.158
+version = 0.1.164
 author = guanjihuan
 author_email = guanjihuan@163.com
 description = An open source python package

PyPI/src/guan.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: guan
-Version: 0.1.158
+Version: 0.1.164
 Summary: An open source python package
 Home-page: https://py.guanjihuan.com
 Author: guanjihuan

PyPI/src/guan/data_processing.py

@@ -86,6 +86,116 @@ def run(function_name, *args, **kwargs):
         pass
     return return_data
 
+# 获取运行的日期和时间并写入文件
+def statistics_with_day_and_time(content='', filename='time_logging', file_format='.txt'):
+    import datetime
+    datetime_today = str(datetime.date.today())
+    datetime_time = datetime.datetime.now().strftime('%H:%M:%S')
+    with open(filename+file_format, 'a', encoding="utf-8") as f2:
+       if content == '':
+           f2.write(datetime_today+' '+datetime_time+'\n')
+       else:
+           f2.write(datetime_today+' '+datetime_time+' '+content+'\n')
+
+# 创建一个sh文件用于提交任务（PBS）
+def make_sh_file_for_qsub(sh_filename='a', command_line='python a.py', cpu_num=1, task_name='task', cd_dir=0):
+    sh_content = \
+        '#!/bin/sh\n' \
+        +'#PBS -N '+task_name+'\n' \
+        +'#PBS -l nodes=1:ppn='+str(cpu_num)+'\n'
+    if cd_dir==1:
+        sh_content += 'cd $PBS_O_WORKDIR\n'
+    sh_content += command_line
+    with open(sh_filename+'.sh', 'w') as f:
+        f.write(sh_content)
+
+# 创建一个sh文件用于提交任务（LSF）
+def make_sh_file_for_bsub(sh_filename='a', command_line='python a.py', cpu_num=1, task_name='task', queue_name='score', cd_dir=0):
+    sh_content = \
+        '#!/bin/sh\n' \
+        +'#BSUB -J '+task_name+'\n' \
+        +'#BSUB -q '+queue_name+'\n' \
+        +'#BSUB -n '+str(cpu_num)+'\n'
+    if cd_dir==1:
+        sh_content += 'cd $PBS_O_WORKDIR\n'
+    sh_content += command_line
+    with open(sh_filename+'.sh', 'w') as f:
+        f.write(sh_content)
+
+# 复制.py和.sh文件，然后提交任务，实现半手动并行（PBS）
+def copy_py_sh_file_and_qsub_task(parameter_array, py_filename='a', old_str_in_py='parameter = 0', new_str_in_py='parameter = ', sh_filename='a', task_name='task'):
+    import os
+    parameter_str_array = []
+    for i0 in parameter_array:
+        parameter_str_array.append(str(i0))
+    index = 0
+    for parameter_str in parameter_str_array:
+        index += 1
+        # copy python file
+        old_file = py_filename+'.py'
+        new_file = py_filename+'_'+str(index)+'.py'
+        os.system('cp '+old_file+' '+new_file)
+        with open(new_file, 'r') as f:
+            content  = f.read()
+        old_str = old_str_in_py
+        new_str = new_str_in_py+parameter_str
+        content = content.replace(old_str, new_str)
+        with open(py_filename+'_'+str(index)+'.py', 'w') as f:
+            f.write(content)
+        # copy sh file
+        old_file = sh_filename+'.sh'
+        new_file = sh_filename+'_'+str(index)+'.sh'
+        os.system('cp '+old_file+' '+new_file)
+        with open(new_file, 'r') as f:
+            content  = f.read()
+        old_str = 'python '+py_filename+'.py'
+        new_str = 'python '+py_filename+'_'+str(index)+'.py'
+        content = content.replace(old_str, new_str)
+        old_str = '#PBS -N '+task_name
+        new_str = '#PBS -N '+task_name+'_'+str(index)
+        content = content.replace(old_str, new_str)
+        with open(sh_filename+'_'+str(index)+'.sh', 'w') as f: 
+            f.write(content)
+        # qsub task
+        os.system('qsub '+new_file)
+
+# 复制.py和.sh文件，然后提交任务，实现半手动并行（LSF）
+def copy_py_sh_file_and_bsub_task(parameter_array, py_filename='a', old_str_in_py='parameter = 0', new_str_in_py='parameter = ', sh_filename='a', task_name='task'):
+    import os
+    parameter_str_array = []
+    for i0 in parameter_array:
+        parameter_str_array.append(str(i0))
+    index = 0
+    for parameter_str in parameter_str_array:
+        index += 1
+        # copy python file
+        old_file = py_filename+'.py'
+        new_file = py_filename+'_'+str(index)+'.py'
+        os.system('cp '+old_file+' '+new_file)
+        with open(new_file, 'r') as f:
+            content  = f.read()
+        old_str = old_str_in_py
+        new_str = new_str_in_py+parameter_str
+        content = content.replace(old_str, new_str)
+        with open(py_filename+'_'+str(index)+'.py', 'w') as f:
+            f.write(content)
+        # copy sh file
+        old_file = sh_filename+'.sh'
+        new_file = sh_filename+'_'+str(index)+'.sh'
+        os.system('cp '+old_file+' '+new_file)
+        with open(new_file, 'r') as f:
+            content  = f.read()
+        old_str = 'python '+py_filename+'.py'
+        new_str = 'python '+py_filename+'_'+str(index)+'.py'
+        content = content.replace(old_str, new_str)
+        old_str = '#BSUB -J '+task_name
+        new_str = '#BSUB -J '+task_name+'_'+str(index)
+        content = content.replace(old_str, new_str)
+        with open(sh_filename+'_'+str(index)+'.sh', 'w') as f: 
+            f.write(content)
+        # bsub task
+        os.system('bsub < '+new_file)
+
 # 获取矩阵的维度（考虑单一数值的矩阵维度为1）
 def dimension_of_array(array):
     import numpy as np
@@ -180,105 +290,6 @@ def preprocess_for_parallel_calculations(parameter_array_all, task_num=1, task_i
             parameter_array = parameter_array_all[task_index*num_parameter:num_all]
     return parameter_array
 
-# 创建一个sh文件用于提交任务（PBS）
-def make_sh_file_for_qsub(sh_filename='a', command_line='python a.py', cpu_num=1, task_name='task', cd_dir=0):
-    sh_content = \
-        '#!/bin/sh\n' \
-        +'#PBS -N '+task_name+'\n' \
-        +'#PBS -l nodes=1:ppn='+str(cpu_num)+'\n'
-    if cd_dir==1:
-        sh_content += 'cd $PBS_O_WORKDIR\n'
-    sh_content += command_line
-    with open(sh_filename+'.sh', 'w') as f:
-        f.write(sh_content)
-
-# 创建一个sh文件用于提交任务（LSF）
-def make_sh_file_for_bsub(sh_filename='a', command_line='python a.py', cpu_num=1, task_name='task', queue_name='score', cd_dir=0):
-    sh_content = \
-        '#!/bin/sh\n' \
-        +'#BSUB -J '+task_name+'\n' \
-        +'#BSUB -q '+queue_name+'\n' \
-        +'#BSUB -n '+str(cpu_num)+'\n'
-    if cd_dir==1:
-        sh_content += 'cd $PBS_O_WORKDIR\n'
-    sh_content += command_line
-    with open(sh_filename+'.sh', 'w') as f:
-        f.write(sh_content)
-
-# 复制.py和.sh文件，然后提交任务，实现半手动并行（PBS）
-def copy_py_sh_file_and_qsub_task(parameter_array, py_filename='a', old_str_in_py='parameter=0', new_str_in_py='parameter=', sh_filename='a', qsub_task_name='task'):
-    import os
-    parameter_str_array = []
-    for i0 in parameter_array:
-        parameter_str_array.append(str(i0))
-    index = 0
-    for parameter_str in parameter_str_array:
-        index += 1
-        # copy python file
-        old_file = py_filename+'.py'
-        new_file = py_filename+'_'+str(index)+'.py'
-        os.system('cp '+old_file+' '+new_file)
-        with open(new_file, 'r') as f:
-            content  = f.read()
-        old_str = old_str_in_py
-        new_str = new_str_in_py+parameter_str
-        content = content.replace(old_str, new_str)
-        with open(py_filename+'_'+str(index)+'.py', 'w') as f:
-            f.write(content)
-        # copy sh file
-        old_file = sh_filename+'.sh'
-        new_file = sh_filename+'_'+str(index)+'.sh'
-        os.system('cp '+old_file+' '+new_file)
-        with open(new_file, 'r') as f:
-            content  = f.read()
-        old_str = 'python '+py_filename+'.py'
-        new_str = 'python '+py_filename+'_'+str(index)+'.py'
-        content = content.replace(old_str, new_str)
-        old_str = qsub_task_name
-        new_str = qsub_task_name+'_'+str(index)
-        content = content.replace(old_str, new_str)
-        with open(sh_filename+'_'+str(index)+'.sh', 'w') as f: 
-            f.write(content)
-        # qsub task
-        os.system('qsub '+new_file)
-
-# 复制.py和.sh文件，然后提交任务，实现半手动并行（LSF）
-def copy_py_sh_file_and_bsub_task(parameter_array, py_filename='a', old_str_in_py='parameter=0', new_str_in_py='parameter=', sh_filename='a', bsub_task_name='task'):
-    import os
-    parameter_str_array = []
-    for i0 in parameter_array:
-        parameter_str_array.append(str(i0))
-    index = 0
-    for parameter_str in parameter_str_array:
-        index += 1
-        # copy python file
-        old_file = py_filename+'.py'
-        new_file = py_filename+'_'+str(index)+'.py'
-        os.system('cp '+old_file+' '+new_file)
-        with open(new_file, 'r') as f:
-            content  = f.read()
-        old_str = old_str_in_py
-        new_str = new_str_in_py+parameter_str
-        content = content.replace(old_str, new_str)
-        with open(py_filename+'_'+str(index)+'.py', 'w') as f:
-            f.write(content)
-        # copy sh file
-        old_file = sh_filename+'.sh'
-        new_file = sh_filename+'_'+str(index)+'.sh'
-        os.system('cp '+old_file+' '+new_file)
-        with open(new_file, 'r') as f:
-            content  = f.read()
-        old_str = 'python '+py_filename+'.py'
-        new_str = 'python '+py_filename+'_'+str(index)+'.py'
-        content = content.replace(old_str, new_str)
-        old_str = bsub_task_name
-        new_str = bsub_task_name+'_'+str(index)
-        content = content.replace(old_str, new_str)
-        with open(sh_filename+'_'+str(index)+'.sh', 'w') as f: 
-            f.write(content)
-        # bsub task
-        os.system('bsub < '+new_file)
-
 # 自动先后运行程序
 def run_programs_sequentially(program_files=['./a.py', './b.py'], execute='python ', show_time=0):
     import os
@@ -350,7 +361,8 @@ def print_array(array, line_break=0):
             print(i0)
     else:
         for i0 in array:
-            print(i0+'\n')
+            print(i0)
+            print()
 
 # 以显示编号的样式，打印数组
 def print_array_with_index(array, show_index=1, index_type=0):
@@ -457,8 +469,8 @@ def combine_two_pdf_files(input_file_1='a.pdf', input_file_2='b.pdf', output_fil
     with open(output_file, 'wb') as combined_file:
         output_pdf.write(combined_file)
 
-# 将PDF文件转成文本
+# 使用pdfminer3k将PDF文件转成文本
-def pdf_to_text(pdf_path):
+def pdf_to_text_with_pdfminer3k(pdf_path):
     from pdfminer.pdfparser import PDFParser, PDFDocument
     from pdfminer.pdfinterp import PDFResourceManager, PDFPageInterpreter
     from pdfminer.converter import PDFPageAggregator
@@ -488,6 +500,16 @@ def pdf_to_text(pdf_path):
                     content  = content + x.get_text().strip()
     return content
 
+# 使用PyPDF2将PDF文件转成文本
+def pdf_to_text_with_PyPDF2_for_all_pages(pdf_path):
+    import guan
+    num_pages = guan.get_pdf_page_number(pdf_path)
+    content = ''
+    for i0 in range(num_pages):
+        page_text = guan.pdf_to_txt_for_a_specific_page(pdf_path, page_num=i0+1)
+        content += page_text + '\n\n'
+    return content
+
 # 获取PDF文件页数
 def get_pdf_page_number(pdf_path):
     import PyPDF2
@@ -576,17 +598,6 @@ def get_time(colon=True):
         datetime_time = datetime_time.replace(':', '')
     return datetime_time
 
-# 获取运行的日期和时间并写入文件
-def statistics_with_day_and_time(content='', filename='a', file_format='.txt'):
-    import datetime
-    datetime_today = str(datetime.date.today())
-    datetime_time = datetime.datetime.now().strftime('%H:%M:%S')
-    with open(filename+file_format, 'a', encoding="utf-8") as f2:
-       if content == '':
-           f2.write(datetime_today+' '+datetime_time+'\n')
-       else:
-           f2.write(datetime_today+' '+datetime_time+' '+content+'\n')
-
 # 获取本月的所有日期
 def get_date_array_of_the_current_month(str_or_datetime='str'):
     import datetime

PyPI/src/guan/deprecated.py

@@ -32,3 +32,9 @@ def get_days_of_the_month_before_last(str_or_datetime='str'):
     print('Warning: The current function name has been deprecated, which will be deleted in the future version. Please change it into guan.get_date_array_of_the_month_before_last().')
     date_array = guan.get_date_array_of_the_month_before_last(str_or_datetime=str_or_datetime)
     return date_array
+
+def pdf_to_text(pdf_path):
+    import guan
+    print('Warning: The current function name has been deprecated, which will be deleted in the future version. Please change it into guan.pdf_to_text_with_pdfminer3k().')
+    content = guan.pdf_to_text_with_pdfminer3k(pdf_path)
+    return content

PyPI/src/guan/file_reading_and_writing.py

@@ -1,15 +1,15 @@
 # Module: file_reading_and_writing
 
 # 使用pickle将变量保存到文件（支持几乎所有对象类型）
-def dump_data(data, filename, file_format='.txt'):
+def dump_data(data, filename, file_format='.pkl'):
     import pickle
-    with open(filename+file_format, 'wb', encoding='UTF-8') as f:
+    with open(filename+file_format, 'wb') as f:
         pickle.dump(data, f)
 
 # 使用pickle从文件中恢复数据到变量（支持几乎所有对象类型）
-def load_data(filename, file_format='.txt'):
+def load_data(filename, file_format='.pkl'):
     import pickle
-    with open(filename+file_format, 'rb', encoding='UTF-8') as f:
+    with open(filename+file_format, 'rb') as f:
         data = pickle.load(f)
     return data
 

PyPI/src/guan/functions_using_objects_of_custom_classes.py

@@ -1,5 +1,20 @@
 # functions_using_objects_of_custom_classes
 
+# 将原子对象列表转出原子字典列表
+def convert_atom_object_list_to_atom_dict_list(atom_object_list):
+    atom_dict_list = []
+    for atom_object in atom_object_list:
+        atom_dict = {
+            'name': atom_object.name,
+            'index': atom_object.index, 
+            'x': atom_object.x,
+            'y': atom_object.y,
+            'z': atom_object.z,
+            'energy': atom_object.energy,
+        }
+        atom_dict_list.append(atom_dict)
+    return atom_dict_list
+
 # 从原子对象列表中获取 (x, y) 坐标数组
 def get_coordinate_array_from_atom_object_list(atom_object_list):
     coordinate_array = []
@@ -9,6 +24,32 @@ def get_coordinate_array_from_atom_object_list(atom_object_list):
         coordinate_array.append([x, y])
     return coordinate_array
 
+# 从原子对象列表中获取 x 和 y 的最大值和最小值
+def get_max_min_x_y_from_atom_object_list(atom_object_list):
+    import guan
+    coordinate_array = guan.get_coordinate_array_from_atom_object_list(atom_object_list)
+    x_array = []
+    for coordinate in coordinate_array:
+        x_array.append(coordinate[0])
+    y_array = []
+    for coordinate in coordinate_array:
+        y_array.append(coordinate[1])
+    max_x = max(x_array)
+    min_x = min(x_array)
+    max_y = max(y_array)
+    min_y = min(y_array)
+    return max_x, min_x, max_y, min_y
+
+# 从原子对象列表中获取满足坐标条件的索引
+def get_index_via_coordinate_from_atom_object_list(atom_object_list, x=0, y=0, z=0, eta=1e-3):
+    for atom in atom_object_list:
+        x_i = atom.x
+        y_i = atom.y
+        z_i = atom.z
+        index = atom.index
+        if abs(x-x_i)<eta and abs(y-y_i)<eta and abs(z-z_i)<eta:
+            return index
+
 # 根据原子对象列表来初始化哈密顿量
 def initialize_hamiltonian_from_atom_object_list(atom_object_list):
     import numpy as np