0.1.186

PyPI/setup.cfg

@@ -1,7 +1,7 @@
 [metadata]
 # replace with your username:
 name = guan
-version = 0.1.168
+version = 0.1.186
 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: 0.1.168
+Version: 0.1.186
 Summary: An open source python package
 Home-page: https://py.guanjihuan.com
 Author: guanjihuan

PyPI/src/guan.egg-info/SOURCES.txt

@@ -8,15 +8,13 @@ src/guan/Hamiltonian_of_examples.py
 src/guan/__init__.py
 src/guan/band_structures_and_wave_functions.py
 src/guan/basic_functions.py
-src/guan/custom_classes.py
 src/guan/data_processing.py
 src/guan/decorators.py
 src/guan/density_of_states.py
-src/guan/deprecated.py
 src/guan/figure_plotting.py
 src/guan/file_reading_and_writing.py
-src/guan/functions_using_objects_of_custom_classes.py
 src/guan/machine_learning.py
+src/guan/others.py
 src/guan/quantum_transport.py
 src/guan/topological_invariant.py
 src/guan.egg-info/PKG-INFO

PyPI/src/guan/__init__.py

@@ -13,7 +13,5 @@ from .file_reading_and_writing import *
 from .figure_plotting import *
 from .data_processing import *
 from .decorators import *
-from .custom_classes import *
+from .others import *
-from .functions_using_objects_of_custom_classes import *
-from .deprecated import *
 statistics_of_guan_package()

PyPI/src/guan/band_structures_and_wave_functions.py

@@ -1,12 +1,15 @@
 # Module: band_structures_and_wave_functions
 
 # 计算哈密顿量的本征值
-def calculate_eigenvalue(hamiltonian):
+def calculate_eigenvalue(hamiltonian, hermitian=True):
     import numpy as np
     if np.array(hamiltonian).shape==():
         eigenvalue = np.real(hamiltonian)
     else:
+        if hermitian:
             eigenvalue, eigenvector = np.linalg.eigh(hamiltonian)
+        else:
+            eigenvalue, eigenvector = np.linalg.eig(hamiltonian)
     return eigenvalue
 
 # 输入哈密顿量函数（带一组参数），计算一组参数下的本征值，返回本征值向量组
@@ -65,10 +68,13 @@ def calculate_eigenvalue_with_two_parameters(x_array, y_array, hamiltonian_funct
             i0 += 1
     return eigenvalue_array
 
-# 计算哈密顿量的本征矢（厄密矩阵）
+# 计算哈密顿量的本征矢
-def calculate_eigenvector(hamiltonian):
+def calculate_eigenvector(hamiltonian, hermitian=True):
     import numpy as np
+    if hermitian:
         eigenvalue, eigenvector = np.linalg.eigh(hamiltonian)
+    else:
+        eigenvalue, eigenvector = np.linalg.eig(hamiltonian)
     return eigenvector
 
 # 施密特正交化

PyPI/src/guan/custom_classes.py

@@ -1,11 +0,0 @@
-# Module: custom_classes
-
-# 原子类
-class Atom:
-    def __init__(self, name='atom', index=0, x=0, y=0, z=0, energy=0):
-        self.name = name
-        self.index = index
-        self.x = x
-        self.y = y
-        self.z = z
-        self.energy = energy

PyPI/src/guan/deprecated.py

@@ -1,40 +0,0 @@
-# Module: deprecated
-
-def make_sh_file(sh_filename='a', command_line='python a.py', cpu_num=1, task_name='task', cd_dir=0):
-    import guan
-    print('Warning: The current function name has been deprecated, which will be deleted in the future version. Please change it into guan.make_sh_file_for_qsub().')
-    guan.make_sh_file_for_qsub(sh_filename=sh_filename, command_line=command_line, cpu_num=cpu_num, task_name=task_name, cd_dir=cd_dir)
-
-def plot_without_starting_fig(plt, fig, ax, x_array, y_array, xlabel='x', ylabel='y', title='', fontsize=20, style='', y_min=None, y_max=None, linewidth=None, markersize=None, color=None, fontfamily='Times New Roman'):
-    import guan
-    print('Warning: The current function name has been deprecated, which will be deleted in the future version. Please change it into guan.plot_without_starting_fig_ax().')
-    guan.plot_without_starting_fig_ax(plt, fig, ax, x_array, y_array, xlabel=xlabel, ylabel=ylabel, title=title, fontsize=fontsize, style=style, y_min=y_min, y_max=y_max, linewidth=linewidth, markersize=markersize, color=color, fontfamily=fontfamily)
-
-def draw_dots_and_lines_without_starting_fig(plt, fig, ax, coordinate_array, draw_dots=1, draw_lines=1, max_distance=1, line_style='-k', linewidth=1, dot_style='ro', markersize=3):
-    import guan
-    print('Warning: The current function name has been deprecated, which will be deleted in the future version. Please change it into guan.draw_dots_and_lines_without_starting_fig_ax().')
-    guan.draw_dots_and_lines_without_starting_fig_ax(plt, fig, ax, coordinate_array, draw_dots=draw_dots, draw_lines=draw_lines, max_distance=max_distance, line_style=line_style, linewidth=linewidth, dot_style=dot_style, markersize=markersize)
-
-def get_days_of_the_current_month(str_or_datetime='str'):
-    import guan
-    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_current_month().')
-    date_array = guan.get_date_array_of_the_current_month(str_or_datetime=str_or_datetime)
-    return date_array
-
-def get_days_of_the_last_month(str_or_datetime='str'):
-    import guan
-    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_last_month().')
-    date_array = guan.get_date_array_of_the_last_month(str_or_datetime=str_or_datetime)
-    return date_array
-
-def get_days_of_the_month_before_last(str_or_datetime='str'):
-    import guan
-    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

@@ -1,7 +1,7 @@
 # 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='.pkl'):
+def dump_data(data, filename='a', file_format='.pkl'):
     import pickle
     with open(filename+file_format, 'wb') as f:
         pickle.dump(data, f)
@@ -14,7 +14,7 @@ def load_data(filename, file_format='.pkl'):
     return data
 
 # 使用NumPy保存数组变量到npy文件（二进制文件）
-def save_npy_data(data, filename):
+def save_npy_data(data, filename='a'):
     import numpy as np
     np.save(filename+'.npy', data)
 
@@ -25,7 +25,7 @@ def load_npy_data(filename):
     return data
 
 # 使用NumPy保存数组变量到TXT文件（文本文件）
-def save_txt_data(data, filename):
+def save_txt_data(data, filename='a'):
     import numpy as np
     np.savetxt(filename+'.txt', data)
 
@@ -243,6 +243,177 @@ def write_two_dimensional_data_without_xy_array_and_without_opening_file(matrix,
             f.write(str(element)+'   ')
         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, pbs_q=0, queue_name='bigmem', specific_node=0, node_name='node50.cluster'):
+    sh_content = \
+        '#!/bin/sh\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
+    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（Slurm）
+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' \
+        +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
+    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', cd_dir=0, bsub_q=0, queue_name='score'):
+    sh_content = \
+        '#!/bin/sh\n' \
+        +f'#BSUB -J {task_name}\n'
+    if bsub_q==1:
+        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
+    with open(sh_filename+'.sh', 'w') as f:
+        f.write(sh_content)
+
+# qsub 提交任务（PBS）
+def qsub_task(filename='a', file_format='.sh'):
+    import os
+    os.system('qsub '+filename+file_format)
+
+# sbatch 提交任务（Slurm）
+def sbatch_task(filename='a', file_format='.sh'):
+    import os
+    os.system('sbatch '+filename+file_format)
+
+# bsub 提交任务（LSF）
+def bsub_task(filename='a', file_format='.sh'):
+    import os
+    os.system('bsub < '+filename+file_format)
+
+# 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（Slurm）
+def copy_py_sh_file_and_sbatch_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 = '#SBATCH --job-name='+task_name
+        new_str = '#SBATCH --job-name='+task_name+'_'+str(index)
+        content = content.replace(old_str, new_str)
+        with open(sh_filename+'_'+str(index)+'.sh', 'w') as f: 
+            f.write(content)
+        # sbatch task
+        os.system('sbatch '+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)
+
 # 把矩阵写入.md文件（Markdown表格形式）
 def write_matrix_in_markdown_format(matrix, filename='a'):
     import numpy as np
@@ -250,13 +421,15 @@ def write_matrix_in_markdown_format(matrix, filename='a'):
     dim_0 = matrix.shape[0]
     dim_1 = matrix.shape[1]
     with open(filename+'.md', 'w', encoding='UTF-8') as f:
+        f.write(f'| Row\Column ')
         for i1 in range(dim_1):
             f.write(f'| column {i1+1} ')
         f.write('|\n')
-        for i1 in range(dim_1):
+        for i1 in range(dim_1+1):
             f.write('| :---: ')
         f.write('|\n')
         for i0 in range(dim_0):
+            f.write(f'| row {i0+1} ')
             for i1 in range(dim_1):
                 f.write(f'| {matrix[i0, i1]} ')
             f.write('|\n')

PyPI/src/guan/functions_using_objects_of_custom_classes.py

@@ -1,62 +0,0 @@
-# functions_using_objects_of_custom_classes
-
-# 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):
-    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 = []
-    for atom in atom_object_list:
-        x = atom.x
-        y = atom.y
-        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
-    import guan
-    dim = guan.dimension_of_array(atom_object_list[0].energy)
-    num = len(atom_object_list)
-    hamiltonian = np.zeros((dim*num, dim*num))
-    for i0 in range(num):
-        hamiltonian[i0*dim+0:i0*dim+dim, i0*dim+0:i0*dim+dim] = atom_object_list[i0].energy
-    return hamiltonian

README.md

@@ -26,9 +26,8 @@ import guan
 + file reading and writing
 + figure plotting
 + data processing
-+ custom classes
-+ functions using objects of custom classes
 + decorators
++ others
 
 ## About this package