0.1.175

PyPI/setup.cfg

@@ -1,7 +1,7 @@
 [metadata]
 # replace with your username:
 name = guan
-version = 0.1.169
+version = 0.1.175
 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: 2.4
 Name: guan
-Version: 0.1.169
+Version: 0.1.175
 Summary: An open source python package
 Home-page: https://py.guanjihuan.com
 Author: guanjihuan

PyPI/src/guan/data_processing.py

@@ -1,7 +1,7 @@
 # Module: data_processing
 
 # 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'):
+def logging_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')
@@ -27,6 +27,33 @@ def try_except(function_name, *args, **kwargs):
     except:
         pass
 
+# 打印数组
+def print_array(array, line_break=0):
+    if line_break == 0:
+        for i0 in array:
+            print(i0)
+    else:
+        for i0 in array:
+            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):
+    if show_index==0:
+        for i0 in array:
+            print(i0)
+    else:
+        if index_type==0:
+            index = 0
+            for i0 in array:
+                print(index, i0)
+                index += 1
+        else:
+            index = 0
+            for i0 in array:
+                index += 1
+                print(index, i0)
+
 # 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
@@ -37,6 +64,64 @@ def dimension_of_array(array):
         dim = array.shape[0]
     return dim
 
+# 检查矩阵是否为厄米矩阵（相对误差为1e-5)
+def is_hermitian(matrix):
+    import numpy as np
+    matrix = np.array(matrix)
+    if matrix.shape[0] != matrix.shape[1]:
+        return False
+    return np.allclose(matrix, np.conj(matrix.T))
+
+# 判断一个数是否接近于整数
+def close_to_integer(value, abs_tol=1e-3):
+    import math
+    result = math.isclose(value, round(value), abs_tol=abs_tol)
+    return result
+
+# 从列表中删除某个匹配的元素
+def remove_item_in_one_array(array, item):
+    new_array = [x for x in array if x != item]
+    return new_array 
+
+# 根据子数组的第index个元素对子数组进行排序（index从0开始）
+def sort_array_by_index_element(original_array, index):
+    sorted_array = sorted(original_array, key=lambda x: x[index])
+    return sorted_array
+
+# 随机获得一个整数，左闭右闭
+def get_random_number(start=0, end=1):
+    import random
+    rand_number = random.randint(start, end)   # 左闭右闭 [start, end]
+    return rand_number
+
+# 选取一个种子生成固定的随机整数，左闭右开
+def generate_random_int_number_for_a_specific_seed(seed=0, x_min=0, x_max=10):
+    import numpy as np
+    np.random.seed(seed)
+    rand_num = np.random.randint(x_min, x_max) # 左闭右开[x_min, x_max)
+    return rand_num
+
+# 获取两个模式之间的字符串
+def get_string_between_two_patterns(original_string, start, end, include_start_and_end=0):
+    import re
+    pattern = f'{start}(.*?){end}'
+    result = re.search(pattern, original_string)
+    if result:
+        if include_start_and_end == 0:
+            return result.group(1)
+        else:
+            return start+result.group(1)+end
+    else:
+        return ''
+    
+# 删除某个字符串中两个模式之间的内容，返回新字符串
+def remove_substrings(original_string, start, end):
+    import re
+    escaped_start = re.escape(start)
+    escaped_end = re.escape(end)
+    pattern = f'{escaped_start}.*?{escaped_end}'
+    return re.sub(pattern, '', original_string, flags=re.DOTALL)
+
 # 获取旋转矩阵（输入为角度）
 def get_rotation_matrix(angle_deg):
     import numpy as np
@@ -88,11 +173,6 @@ def convert_matrix_data_into_xyz_data(x_array, y_array, matrix):
             z_array[ix*len_y+iy] = matrix[ix, iy]
     return x_array, y_array, z_array
 
-# 从列表中删除某个匹配的元素
-def remove_item_in_one_array(array, item):
-    new_array = [x for x in array if x != item]
-    return new_array 
-
 # 并行计算前的预处理，把参数分成多份
 def preprocess_for_parallel_calculations(parameter_array_all, task_num=1, task_index=0):
     import numpy as np
@@ -127,78 +207,6 @@ def run_programs_sequentially(program_files=['./a.py', './b.py'], execute='pytho
         end = time.time()
         print('Total running time = '+str((end-start)/60)+' min')
 
-# 判断一个数是否接近于整数
-def close_to_integer(value, abs_tol=1e-3):
-    import math
-    result = math.isclose(value, round(value), abs_tol=abs_tol)
-    return result
-
-# 根据子数组的第index个元素对子数组进行排序（index从0开始）
-def sort_array_by_index_element(original_array, index):
-    sorted_array = sorted(original_array, key=lambda x: x[index])
-    return sorted_array
-
-# 随机获得一个整数，左闭右闭
-def get_random_number(start=0, end=1):
-    import random
-    rand_number = random.randint(start, end)   # 左闭右闭 [start, end]
-    return rand_number
-
-# 选取一个种子生成固定的随机整数，左闭右开
-def generate_random_int_number_for_a_specific_seed(seed=0, x_min=0, x_max=10):
-    import numpy as np
-    np.random.seed(seed)
-    rand_num = np.random.randint(x_min, x_max) # 左闭右开[x_min, x_max)
-    return rand_num
-
-# 获取两个模式之间的字符串
-def get_string_between_two_patterns(original_string, start, end, include_start_and_end=0):
-    import re
-    pattern = f'{start}(.*?){end}'
-    result = re.search(pattern, original_string)
-    if result:
-        if include_start_and_end == 0:
-            return result.group(1)
-        else:
-            return start+result.group(1)+end
-    else:
-        return ''
-    
-# 删除某个字符串中两个模式之间的内容，返回新字符串
-def remove_substrings(original_string, start, end):
-    import re
-    escaped_start = re.escape(start)
-    escaped_end = re.escape(end)
-    pattern = f'{escaped_start}.*?{escaped_end}'
-    return re.sub(pattern, '', original_string, flags=re.DOTALL)
-
-# 打印数组
-def print_array(array, line_break=0):
-    if line_break == 0:
-        for i0 in array:
-            print(i0)
-    else:
-        for i0 in array:
-            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):
-    if show_index==0:
-        for i0 in array:
-            print(i0)
-    else:
-        if index_type==0:
-            index = 0
-            for i0 in array:
-                print(index, i0)
-                index += 1
-        else:
-            index = 0
-            for i0 in array:
-                index += 1
-                print(index, i0)
-
 # 根据一定的字符长度来分割文本
 def split_text(text, width=100):  
     split_text_list = [text[i:i+width] for i in range(0, len(text), width)]

PyPI/src/guan/deprecated.py

@@ -37,4 +37,9 @@ 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
+    return content
+
+def statistics_with_day_and_time(content='', filename='time_logging', file_format='.txt'):
+    import guan
+    print('Warning: The current function name has been deprecated, which will be deleted in the future version. Please change it into guan.logging_with_day_and_time().')
+    guan.logging_with_day_and_time(content=content, filename=filename, file_format=file_format)

PyPI/src/guan/file_reading_and_writing.py

@@ -244,11 +244,16 @@ def write_two_dimensional_data_without_xy_array_and_without_opening_file(matrix,
         f.write('\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):
+def make_sh_file_for_qsub(sh_filename='a', command_line='python a.py', cpu_num=1, task_name='task', cd_dir=0, pbs_q=0, queue_name='bigmem', specific_node=0, node_name='node50.cluster'):
     sh_content = \
         '#!/bin/sh\n' \
-        +'#PBS -N '+task_name+'\n' \
-        +'#PBS -l nodes=1:ppn='+str(cpu_num)+'\n'
+        +f'#PBS -N {task_name}\n'
+    if pbs_q==1:
+        sh_content += f'#PBS -q {queue_name}\n'
+    if specific_node==0:
+        sh_content += f'#PBS -l nodes=1:ppn={cpu_num}\n'
+    else:
+        sh_content += f'#PBS -l nodes={node_name}:ppn={cpu_num}\n'
     if cd_dir==1:
         sh_content += 'cd $PBS_O_WORKDIR\n'
     sh_content += command_line
@@ -256,11 +261,13 @@ def make_sh_file_for_qsub(sh_filename='a', command_line='python a.py', cpu_num=1
         f.write(sh_content)
 
 # 创建一个sh文件用于提交任务（Slurm）
-def make_sh_file_for_sbatch(sh_filename='a', command_line='python a.py', cpu_num=1, task_name='task', cd_dir=0):
+def make_sh_file_for_sbatch(sh_filename='a', command_line='python a.py', cpu_num=1, task_name='task', cd_dir=0, sbatch_partition=0, partition_name='cpu48'):
     sh_content = \
         '#!/bin/sh\n' \
-        +'#SBATCH --job-name='+task_name+'\n' \
-        +'#SBATCH --cpus-per-task='+str(cpu_num)+'\n'
+        +f'#SBATCH --job-name={task_name}\n'
+    if sbatch_partition==1:
+        sh_content += f'#SBATCH --partition={partition_name}\n'
+    sh_content += f'#SBATCH --cpus-per-task={cpu_num}\n'
     if cd_dir==1:
         sh_content += 'cd $PBS_O_WORKDIR\n'
     sh_content += command_line
@@ -271,10 +278,10 @@ def make_sh_file_for_sbatch(sh_filename='a', command_line='python a.py', cpu_num
 def make_sh_file_for_bsub(sh_filename='a', command_line='python a.py', cpu_num=1, task_name='task', cd_dir=0, bsub_q=0, queue_name='score'):
     sh_content = \
         '#!/bin/sh\n' \
-        +'#BSUB -J '+task_name+'\n' \
-        +'#BSUB -n '+str(cpu_num)+'\n'
+        +f'#BSUB -J {task_name}\n'
     if bsub_q==1:
-        sh_content += '#BSUB -q '+queue_name+'\n'
+        sh_content += f'#BSUB -q {queue_name}\n'
+    sh_content += f'#BSUB -n {cpu_num}\n'
     if cd_dir==1:
         sh_content += 'cd $PBS_O_WORKDIR\n'
     sh_content += command_line

PyPI/src/guan/functions_using_objects_of_custom_classes.py

@@ -1,4 +1,21 @@
-# functions_using_objects_of_custom_classes
+# Module: functions_using_objects_of_custom_classes
+
+# 将原子对象列表转成多个独立列表
+def convert_atom_object_list_to_multiple_lists(atom_object_list):
+    name_list = []
+    index_list = []
+    x_list = []
+    y_list = []
+    z_list = []
+    energy_list = []
+    for atom_object in atom_object_list:
+        name_list.append(atom_object.name)
+        index_list.append(atom_object.index)
+        x_list.append(atom_object.x)
+        y_list.append(atom_object.y)
+        z_list.append(atom_object.z)
+        energy_list.append(atom_object.energy)
+    return name_list, index_list, x_list, y_list, z_list, energy_list
 
 # 将原子对象列表转成原子字典列表
 def convert_atom_object_list_to_atom_dict_list(atom_object_list):