| Name | prips JSON |
| Version |
1.4
JSON |
| download |
| home_page | |
| Summary | PRIPS: Python Runtime Interface Plugin of SPONGE |
| upload_time | 2023-12-31 08:48:22 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | |
| license | |
| keywords |
sponge
molecular dynamics
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# PRIPS: Python Runtime Interface Plugin of SPONGE
SPONGE的python的运行时接口插件
该插件将SPONGE视为一个python解释器，运行python脚本
# 依赖
该插件依赖于cupy。请自行安装好适配你CUDA版本的cupy。
## 为什么需要cupy？
SPONGE的GPU代码需要适配GPU的python端的库，许多库都能满足，如`cupy`、`jax`、`torch`以及`mindspore`。而`cupy`是上述里唯一一个支持“野”指针的库，也即`cupy.cuda.UnownedMemory`，使得它能直接调用SPONGE的内存地址作为自变量，而不需要显式地同步。另外`cupy`作为一个中介，它的数组也可以比较方便地转化为其他库的数组。
# 安装
安装方法：
1. pypi安装
```
pip install prips
```
2. 本地安装
前往gitee库下载解压或克隆源码
```
git clone https://gitee.com/gao_hyp_xyj_admin/sponge_pyplugin.git
```
打开下载并解压或克隆后的文件夹，在有`pyproject.py`的文件夹内呼出合适的shell终端，如windows下的powershell或linux下的shell
```
pip install .
```
# 使用
## SPONGE命令
目前本插件适用的版本为：1.4，也即SPONGE的1.4正式版本
首先在命令行中输入：
```
python -c "import prips"
```
然后正常情况下会输出
```
PRIPS: Python Runtime Interface Plugin of SPONGE
Version: 1.4a0
Path: xxx\prips\_prips.so
Usage:
1. Copy the path printed above
2. Paste it to the value of the command "plugin" of SPONGE
```
在SPONGE的mdin.txt文件夹中加入：
```
plugin = xxx\prips\_prips.so #上方的Path
py = xxxx\example.py #你需要使用的python脚本地址
```
此处的` xxxx\example.py`仅为示例，请修改为你对应的地址。
## SPONGE获取python信息
SPONGE读取python信息使用的方式是读取函数名。
首先，SPONGE会直接逐行运行一遍该python脚本，由此可进行初始化。
然后，SPONGE会读取python脚本里的`After_Initial()`、`Calculate_Force()`和`Mdout_Print()`，分别在其他模块初始完毕、力计算和打印信息的时候调用。例如下面是一个简单的`Example.py`
```python
def Mdout_Print():
print("Hellow SPONGE World!")
```
## python获取SPONGE信息
python由模块`Sponge`获取SPONGE信息。模块`Sponge`是SPONGE作为解释器时的内置模块，在外部用python调用是没有的。
`Sponge`模块内若干个子模块，其中`controller`（程序控制）、`cv_controller`（CV定义）、`md_info`（MD信息）是较为重要的模块。这些子模块的定义与C++版本的定义相同。可以使用`help()`寻求帮助，或阅读下面的API介绍。
```
import Sponge
help(Sponge.controller)
help(Sponge.cv_controller)
help(Sponge.md_info)
```
# 简单例子
以下是一个简单的steer MD的例子，对第一个原子的y方向加上一个力。
```python
import Sponge
my_force_factor = 1
if Sponge.controller.Command_Exist("my_force_factor"):
my_force_factor = float(Sponge.controller.Command("my_force_factor"))
Sponge.controller.Step_Print_Initial("My_Force_Potential", "%2f")
def Calculate_Force():
Sponge.md_info.frc[0][1] += my_force_factor
def Mdout_Print():
Sponge.controller.Step_Print("My_Force_Potential", -my_force_factor * Sponge.md_info.crd[0][1])
```
# API介绍
- [Sponge](#sponge)
- [Sponge.spongeError](#spongespongeerror)
- [Sponge.COLLECTIVE_VARIABLE_NEED](#spongecollective_variable_need)
- [Sponge.controller](#spongecontroller)
- [Sponge.cv_controller](#spongecv_controller)
- [Sponge.md_info](#spongemd_info)
- [Sponge.md_info.sys](#spongemd_infosys)
- [Sponge.NEIGHBOR_LIST](#spongeneighbor_list)
### Sponge
```
Help on built-in module Sponge:
NAME
Sponge
DATA
controller = < IO and CUDA controller of SPONGE >
cv_controller = < cv controller of SPONGE>
fname = r'D:\prips\api_generator.py'
md_info = < MD information container of SPONGE >
FILE
(built-in)
```
### Sponge.spongeError
```
Sponge.spongeError.spongeSuccess = 0
Sponge.spongeError.spongeErrorNotImplemented = 1001
Sponge.spongeError.spongeErrorBadFileFormat = 1002
Sponge.spongeError.spongeErrorConflictingCommand = 1003
Sponge.spongeError.spongeErrorMissingCommand = 1004
Sponge.spongeError.spongeErrorTypeErrorCommand = 1005
Sponge.spongeError.spongeErrorValueErrorCommand = 1006
Sponge.spongeError.spongeErrorSimulationBreakDown = 1007
Sponge.spongeError.spongeErrorMallocFailed = 1008
Sponge.spongeError.spongeErrorOverflow = 1009
Sponge.spongeError.spongeErrorOpenFileFailed = 1010
```
### Sponge.COLLECTIVE_VARIABLE_NEED
```
Sponge.COLLECTIVE_VARIABLE_NEED.CV_NEED_GPU_VALUE = 1
Sponge.COLLECTIVE_VARIABLE_NEED.CV_NEED_CRD_GRADS = 2
Sponge.COLLECTIVE_VARIABLE_NEED.CV_NEED_CPU_VALUE = 4
Sponge.COLLECTIVE_VARIABLE_NEED.CV_NEED_BOX_GRADS = 8
```
### Sponge.controller
```
Help on CONTROLLER in module __main__ object:
class CONTROLLER(builtins.object)
| this **class** is the module to control the input, output and cuda in SPONGE
|
| Methods defined here:
|
| Command(self, arg1, arg2=None)
| Get the simplified value of the command in SPONGE.
| If Only arg1 is given, the command to get the value is "arg1".
| If arg1 and arg2 is given, the command to get the value is "arg1_arg2".
|
| :param arg1: the command or the command prefix
| :param arg2: the command suffix
| :return: a string, the simplified value of the command
|
| Command_Exist(self, arg1, arg2=None)
| Check the command whether exist in SPONGE.
| If Only arg1 is given, the command to check is "arg1".
| If arg1 and arg2 is given, the command to check is "arg1_arg2".
|
| :param arg1: the command or the command prefix
| :param arg2: the command suffix
| :return: True if the command exist, else False
|
| Original_Command(self, arg1, arg2=None)
| Get the original value of the command in SPONGE.
| If Only arg1 is given, the command to get the value is "arg1".
| If arg1 and arg2 is given, the command to get the value is "arg1_arg2".
|
| :param arg1: the command or the command prefix
| :param arg2: the command suffix
| :return: a string, the original value of the command
|
| Step_Print(self, head, content)
| Print a step print item. A step print item is an item to print in the screen and in the mdout file.
|
| :param head: the name of the item
| :param content: the content of the step print item
|
| Step_Print_Initial(self, head, format)
| Initialize a step print item. A step print item is an item to print in the screen and in the mdout file.
|
| :param head: the name of the item
| :param format: the format of the step print item
|
| Throw_SPONGE_Error(self, error, error_by, error_hint)
| Raise error to the screen and the mdinfo file, then exit
|
| Warn(self, warning)
| Print the warning to the screen and the mdinfo file
|
| __init__(self)
|
| __repr__(self)
|
| printf(self, *values, sep=' ', end='\n')
| Print the values to the screen and the mdinfo file
|
| ----------------------------------------------------------------------
| Readonly properties defined here:
|
| working_device
| The working device id
|
| ----------------------------------------------------------------------
| Data descriptors defined here:
|
| __dict__
| dictionary for instance variables (if defined)
|
| __weakref__
| list of weak references to the object (if defined)
```
### Sponge.cv_controller
```
Help on COLLECTIVE_VARIABLE_CONTROLLER in module __main__ object:
class COLLECTIVE_VARIABLE_CONTROLLER(CONTROLLER)
| Method resolution order:
| COLLECTIVE_VARIABLE_CONTROLLER
| CONTROLLER
| builtins.object
|
| Methods defined here:
|
| Ask_For_CV(self, name, N, verbose_level=0)
|
| Command(self, arg1, arg2=None)
|
| Command_Exist(self, arg1, arg2=None)
|
| Get_CV(self, cv_name)
|
| Original_Command(self, arg1, arg2=None)
|
| __repr__(self)
|
| ----------------------------------------------------------------------
| Methods inherited from CONTROLLER:
|
| Step_Print(self, head, content)
| Print a step print item. A step print item is an item to print in the screen and in the mdout file.
|
| :param head: the name of the item
| :param content: the content of the step print item
|
| Step_Print_Initial(self, head, format)
| Initialize a step print item. A step print item is an item to print in the screen and in the mdout file.
|
| :param head: the name of the item
| :param format: the format of the step print item
|
| Throw_SPONGE_Error(self, error, error_by, error_hint)
| Raise error to the screen and the mdinfo file, then exit
|
| Warn(self, warning)
| Print the warning to the screen and the mdinfo file
|
| __init__(self)
|
| printf(self, *values, sep=' ', end='\n')
| Print the values to the screen and the mdinfo file
|
| ----------------------------------------------------------------------
| Readonly properties inherited from CONTROLLER:
|
| working_device
| The working device id
|
| ----------------------------------------------------------------------
| Data descriptors inherited from CONTROLLER:
|
| __dict__
| dictionary for instance variables (if defined)
|
| __weakref__
| list of weak references to the object (if defined)
```
### Sponge.md_info
```
Help on MD_INFORMATION in module __main__ object:
class MD_INFORMATION(builtins.object)
| Contains the information for MD simulations
|
| Methods defined here:
|
| __init__(self)
|
| __repr__(self)
|
| ----------------------------------------------------------------------
| Readonly properties defined here:
|
| atom_numbers
| the total number of atoms
|
| d_mass
| the mass of the atoms
|
| sys
| the system information
|
| ----------------------------------------------------------------------
| Data descriptors defined here:
|
| __dict__
| dictionary for instance variables (if defined)
|
| __weakref__
| list of weak references to the object (if defined)
|
| crd
| the position coordinates of the atoms
|
| d_atom_energy
| the energy of the atoms
|
| d_atom_virial
| the virial of the atoms
|
| d_charge
| the charge of the atoms (In the unit of SPONGE, a unit charge is 18.2223)
|
| frc
| the force of the atoms
|
| vel
| the velocity of the atoms
```
### Sponge.md_info.sys
```
Help on system_information in module __main__ object:
class system_information(builtins.object)
| the system information of MD information
|
| Readonly properties defined here:
|
| box_length
| the length of the box
|
| steps
| the current step of the simulation
|
| ----------------------------------------------------------------------
| Data descriptors defined here:
|
| __dict__
| dictionary for instance variables (if defined)
|
| __weakref__
| list of weak references to the object (if defined)
```
### Sponge.NEIGHBOR_LIST
```
Help on class NEIGHBOR_LIST in module __main__:
class NEIGHBOR_LIST(builtins.object)
| Neighbor List of SPONGE.
| This class should be initialized at After_Initial, because neighbor_list is not initialized when initializing prips
|
| Methods defined here:
|
| __init__(self)
|
| ----------------------------------------------------------------------
| Readonly properties defined here:
|
| atom_numbers
| the number of neighbors for every atom
|
| atom_serials
| the serial of neighbors for every atom
|
| ----------------------------------------------------------------------
| Data descriptors defined here:
|
| __dict__
| dictionary for instance variables (if defined)
|
| __weakref__
| list of weak references to the object (if defined)
```
Raw data
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"home_page": "",
"name": "prips",
"maintainer": "",
"docs_url": null,
"requires_python": "",
"maintainer_email": "",
"keywords": "SPONGE,molecular dynamics",
"author": "",
"author_email": "Yijie Xia <yijiexia@pku.edu.cn>",
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"description": "# PRIPS: Python Runtime Interface Plugin of SPONGE\n\nSPONGE\u7684python\u7684\u8fd0\u884c\u65f6\u63a5\u53e3\u63d2\u4ef6\n\n\u8be5\u63d2\u4ef6\u5c06SPONGE\u89c6\u4e3a\u4e00\u4e2apython\u89e3\u91ca\u5668\uff0c\u8fd0\u884cpython\u811a\u672c\n\n# \u4f9d\u8d56\n\n\u8be5\u63d2\u4ef6\u4f9d\u8d56\u4e8ecupy\u3002\u8bf7\u81ea\u884c\u5b89\u88c5\u597d\u9002\u914d\u4f60CUDA\u7248\u672c\u7684cupy\u3002\n\n## \u4e3a\u4ec0\u4e48\u9700\u8981cupy\uff1f\n\nSPONGE\u7684GPU\u4ee3\u7801\u9700\u8981\u9002\u914dGPU\u7684python\u7aef\u7684\u5e93\uff0c\u8bb8\u591a\u5e93\u90fd\u80fd\u6ee1\u8db3\uff0c\u5982`cupy`\u3001`jax`\u3001`torch`\u4ee5\u53ca`mindspore`\u3002\u800c`cupy`\u662f\u4e0a\u8ff0\u91cc\u552f\u4e00\u4e00\u4e2a\u652f\u6301\u201c\u91ce\u201d\u6307\u9488\u7684\u5e93\uff0c\u4e5f\u5373`cupy.cuda.UnownedMemory`\uff0c\u4f7f\u5f97\u5b83\u80fd\u76f4\u63a5\u8c03\u7528SPONGE\u7684\u5185\u5b58\u5730\u5740\u4f5c\u4e3a\u81ea\u53d8\u91cf\uff0c\u800c\u4e0d\u9700\u8981\u663e\u5f0f\u5730\u540c\u6b65\u3002\u53e6\u5916`cupy`\u4f5c\u4e3a\u4e00\u4e2a\u4e2d\u4ecb\uff0c\u5b83\u7684\u6570\u7ec4\u4e5f\u53ef\u4ee5\u6bd4\u8f83\u65b9\u4fbf\u5730\u8f6c\u5316\u4e3a\u5176\u4ed6\u5e93\u7684\u6570\u7ec4\u3002\n\n# \u5b89\u88c5\n\n\u5b89\u88c5\u65b9\u6cd5\uff1a\n\n1. pypi\u5b89\u88c5\n\n```\npip install prips\n```\n\n2. \u672c\u5730\u5b89\u88c5\n\u524d\u5f80gitee\u5e93\u4e0b\u8f7d\u89e3\u538b\u6216\u514b\u9686\u6e90\u7801\n\n```\ngit clone https://gitee.com/gao_hyp_xyj_admin/sponge_pyplugin.git\n```\n\n\u6253\u5f00\u4e0b\u8f7d\u5e76\u89e3\u538b\u6216\u514b\u9686\u540e\u7684\u6587\u4ef6\u5939\uff0c\u5728\u6709`pyproject.py`\u7684\u6587\u4ef6\u5939\u5185\u547c\u51fa\u5408\u9002\u7684shell\u7ec8\u7aef\uff0c\u5982windows\u4e0b\u7684powershell\u6216linux\u4e0b\u7684shell\n\n```\npip install .\n```\n\n# \u4f7f\u7528\n\n## SPONGE\u547d\u4ee4\n\n\u76ee\u524d\u672c\u63d2\u4ef6\u9002\u7528\u7684\u7248\u672c\u4e3a\uff1a1.4\uff0c\u4e5f\u5373SPONGE\u76841.4\u6b63\u5f0f\u7248\u672c\n\n\u9996\u5148\u5728\u547d\u4ee4\u884c\u4e2d\u8f93\u5165\uff1a\n\n```\npython -c \"import prips\"\n```\n\n\u7136\u540e\u6b63\u5e38\u60c5\u51b5\u4e0b\u4f1a\u8f93\u51fa\n\n```\n PRIPS: Python Runtime Interface Plugin of SPONGE\n\nVersion: 1.4a0\nPath: xxx\\prips\\_prips.so\n\nUsage:\n 1. Copy the path printed above\n 2. Paste it to the value of the command \"plugin\" of SPONGE\n```\n\n\u5728SPONGE\u7684mdin.txt\u6587\u4ef6\u5939\u4e2d\u52a0\u5165\uff1a\n\n```\nplugin = xxx\\prips\\_prips.so #\u4e0a\u65b9\u7684Path\npy = xxxx\\example.py #\u4f60\u9700\u8981\u4f7f\u7528\u7684python\u811a\u672c\u5730\u5740\n```\n\n\u6b64\u5904\u7684` xxxx\\example.py`\u4ec5\u4e3a\u793a\u4f8b\uff0c\u8bf7\u4fee\u6539\u4e3a\u4f60\u5bf9\u5e94\u7684\u5730\u5740\u3002\n\n## SPONGE\u83b7\u53d6python\u4fe1\u606f\n\nSPONGE\u8bfb\u53d6python\u4fe1\u606f\u4f7f\u7528\u7684\u65b9\u5f0f\u662f\u8bfb\u53d6\u51fd\u6570\u540d\u3002\n\u9996\u5148\uff0cSPONGE\u4f1a\u76f4\u63a5\u9010\u884c\u8fd0\u884c\u4e00\u904d\u8be5python\u811a\u672c\uff0c\u7531\u6b64\u53ef\u8fdb\u884c\u521d\u59cb\u5316\u3002\n\u7136\u540e\uff0cSPONGE\u4f1a\u8bfb\u53d6python\u811a\u672c\u91cc\u7684`After_Initial()`\u3001`Calculate_Force()`\u548c`Mdout_Print()`\uff0c\u5206\u522b\u5728\u5176\u4ed6\u6a21\u5757\u521d\u59cb\u5b8c\u6bd5\u3001\u529b\u8ba1\u7b97\u548c\u6253\u5370\u4fe1\u606f\u7684\u65f6\u5019\u8c03\u7528\u3002\u4f8b\u5982\u4e0b\u9762\u662f\u4e00\u4e2a\u7b80\u5355\u7684`Example.py`\n```python\ndef Mdout_Print():\n print(\"Hellow SPONGE World!\")\n```\n\n## python\u83b7\u53d6SPONGE\u4fe1\u606f\n\npython\u7531\u6a21\u5757`Sponge`\u83b7\u53d6SPONGE\u4fe1\u606f\u3002\u6a21\u5757`Sponge`\u662fSPONGE\u4f5c\u4e3a\u89e3\u91ca\u5668\u65f6\u7684\u5185\u7f6e\u6a21\u5757\uff0c\u5728\u5916\u90e8\u7528python\u8c03\u7528\u662f\u6ca1\u6709\u7684\u3002\n\n`Sponge`\u6a21\u5757\u5185\u82e5\u5e72\u4e2a\u5b50\u6a21\u5757\uff0c\u5176\u4e2d`controller`\uff08\u7a0b\u5e8f\u63a7\u5236\uff09\u3001`cv_controller`\uff08CV\u5b9a\u4e49\uff09\u3001`md_info`\uff08MD\u4fe1\u606f\uff09\u662f\u8f83\u4e3a\u91cd\u8981\u7684\u6a21\u5757\u3002\u8fd9\u4e9b\u5b50\u6a21\u5757\u7684\u5b9a\u4e49\u4e0eC++\u7248\u672c\u7684\u5b9a\u4e49\u76f8\u540c\u3002\u53ef\u4ee5\u4f7f\u7528`help()`\u5bfb\u6c42\u5e2e\u52a9\uff0c\u6216\u9605\u8bfb\u4e0b\u9762\u7684API\u4ecb\u7ecd\u3002\n```\nimport Sponge\nhelp(Sponge.controller)\nhelp(Sponge.cv_controller)\nhelp(Sponge.md_info)\n```\n\n# \u7b80\u5355\u4f8b\u5b50\n\n\u4ee5\u4e0b\u662f\u4e00\u4e2a\u7b80\u5355\u7684steer MD\u7684\u4f8b\u5b50\uff0c\u5bf9\u7b2c\u4e00\u4e2a\u539f\u5b50\u7684y\u65b9\u5411\u52a0\u4e0a\u4e00\u4e2a\u529b\u3002\n```python\nimport Sponge\nmy_force_factor = 1\nif Sponge.controller.Command_Exist(\"my_force_factor\"):\n my_force_factor = float(Sponge.controller.Command(\"my_force_factor\"))\nSponge.controller.Step_Print_Initial(\"My_Force_Potential\", \"%2f\")\n\ndef Calculate_Force():\n Sponge.md_info.frc[0][1] += my_force_factor\n\ndef Mdout_Print():\n Sponge.controller.Step_Print(\"My_Force_Potential\", -my_force_factor * Sponge.md_info.crd[0][1])\n```\n\n# API\u4ecb\u7ecd\n\n- [Sponge](#sponge)\n\n - [Sponge.spongeError](#spongespongeerror)\n\n - [Sponge.COLLECTIVE_VARIABLE_NEED](#spongecollective_variable_need)\n\n - [Sponge.controller](#spongecontroller)\n\n - [Sponge.cv_controller](#spongecv_controller)\n\n - [Sponge.md_info](#spongemd_info)\n\n - [Sponge.md_info.sys](#spongemd_infosys)\n\n - [Sponge.NEIGHBOR_LIST](#spongeneighbor_list)\n\n### Sponge\n```\nHelp on built-in module Sponge:\n\nNAME\n Sponge\n\nDATA\n controller = < IO and CUDA controller of SPONGE >\n cv_controller = < cv controller of SPONGE>\n fname = r'D:\\prips\\api_generator.py'\n md_info = < MD information container of SPONGE >\n\nFILE\n (built-in)\n\n\n```\n### Sponge.spongeError\n```\n Sponge.spongeError.spongeSuccess = 0\n Sponge.spongeError.spongeErrorNotImplemented = 1001\n Sponge.spongeError.spongeErrorBadFileFormat = 1002\n Sponge.spongeError.spongeErrorConflictingCommand = 1003\n Sponge.spongeError.spongeErrorMissingCommand = 1004\n Sponge.spongeError.spongeErrorTypeErrorCommand = 1005\n Sponge.spongeError.spongeErrorValueErrorCommand = 1006\n Sponge.spongeError.spongeErrorSimulationBreakDown = 1007\n Sponge.spongeError.spongeErrorMallocFailed = 1008\n Sponge.spongeError.spongeErrorOverflow = 1009\n Sponge.spongeError.spongeErrorOpenFileFailed = 1010\n\n```\n### Sponge.COLLECTIVE_VARIABLE_NEED\n```\n Sponge.COLLECTIVE_VARIABLE_NEED.CV_NEED_GPU_VALUE = 1\n Sponge.COLLECTIVE_VARIABLE_NEED.CV_NEED_CRD_GRADS = 2\n Sponge.COLLECTIVE_VARIABLE_NEED.CV_NEED_CPU_VALUE = 4\n Sponge.COLLECTIVE_VARIABLE_NEED.CV_NEED_BOX_GRADS = 8\n\n```\n### Sponge.controller\n```\nHelp on CONTROLLER in module __main__ object:\n\nclass CONTROLLER(builtins.object)\n | this **class** is the module to control the input, output and cuda in SPONGE\n |\n | Methods defined here:\n |\n | Command(self, arg1, arg2=None)\n | Get the simplified value of the command in SPONGE.\n | If Only arg1 is given, the command to get the value is \"arg1\".\n | If arg1 and arg2 is given, the command to get the value is \"arg1_arg2\".\n |\n | :param arg1: the command or the command prefix\n | :param arg2: the command suffix\n | :return: a string, the simplified value of the command\n |\n | Command_Exist(self, arg1, arg2=None)\n | Check the command whether exist in SPONGE.\n | If Only arg1 is given, the command to check is \"arg1\".\n | If arg1 and arg2 is given, the command to check is \"arg1_arg2\".\n |\n | :param arg1: the command or the command prefix\n | :param arg2: the command suffix\n | :return: True if the command exist, else False\n |\n | Original_Command(self, arg1, arg2=None)\n | Get the original value of the command in SPONGE.\n | If Only arg1 is given, the command to get the value is \"arg1\".\n | If arg1 and arg2 is given, the command to get the value is \"arg1_arg2\".\n |\n | :param arg1: the command or the command prefix\n | :param arg2: the command suffix\n | :return: a string, the original value of the command\n |\n | Step_Print(self, head, content)\n | Print a step print item. A step print item is an item to print in the screen and in the mdout file.\n |\n | :param head: the name of the item\n | :param content: the content of the step print item\n |\n | Step_Print_Initial(self, head, format)\n | Initialize a step print item. A step print item is an item to print in the screen and in the mdout file.\n |\n | :param head: the name of the item\n | :param format: the format of the step print item\n |\n | Throw_SPONGE_Error(self, error, error_by, error_hint)\n | Raise error to the screen and the mdinfo file, then exit\n |\n | Warn(self, warning)\n | Print the warning to the screen and the mdinfo file\n |\n | __init__(self)\n |\n | __repr__(self)\n |\n | printf(self, *values, sep=' ', end='\\n')\n | Print the values to the screen and the mdinfo file\n |\n | ----------------------------------------------------------------------\n | Readonly properties defined here:\n |\n | working_device\n | The working device id\n |\n | ----------------------------------------------------------------------\n | Data descriptors defined here:\n |\n | __dict__\n | dictionary for instance variables (if defined)\n |\n | __weakref__\n | list of weak references to the object (if defined)\n\n```\n### Sponge.cv_controller\n```\nHelp on COLLECTIVE_VARIABLE_CONTROLLER in module __main__ object:\n\nclass COLLECTIVE_VARIABLE_CONTROLLER(CONTROLLER)\n | Method resolution order:\n | COLLECTIVE_VARIABLE_CONTROLLER\n | CONTROLLER\n | builtins.object\n |\n | Methods defined here:\n |\n | Ask_For_CV(self, name, N, verbose_level=0)\n |\n | Command(self, arg1, arg2=None)\n |\n | Command_Exist(self, arg1, arg2=None)\n |\n | Get_CV(self, cv_name)\n |\n | Original_Command(self, arg1, arg2=None)\n |\n | __repr__(self)\n |\n | ----------------------------------------------------------------------\n | Methods inherited from CONTROLLER:\n |\n | Step_Print(self, head, content)\n | Print a step print item. A step print item is an item to print in the screen and in the mdout file.\n |\n | :param head: the name of the item\n | :param content: the content of the step print item\n |\n | Step_Print_Initial(self, head, format)\n | Initialize a step print item. A step print item is an item to print in the screen and in the mdout file.\n |\n | :param head: the name of the item\n | :param format: the format of the step print item\n |\n | Throw_SPONGE_Error(self, error, error_by, error_hint)\n | Raise error to the screen and the mdinfo file, then exit\n |\n | Warn(self, warning)\n | Print the warning to the screen and the mdinfo file\n |\n | __init__(self)\n |\n | printf(self, *values, sep=' ', end='\\n')\n | Print the values to the screen and the mdinfo file\n |\n | ----------------------------------------------------------------------\n | Readonly properties inherited from CONTROLLER:\n |\n | working_device\n | The working device id\n |\n | ----------------------------------------------------------------------\n | Data descriptors inherited from CONTROLLER:\n |\n | __dict__\n | dictionary for instance variables (if defined)\n |\n | __weakref__\n | list of weak references to the object (if defined)\n\n```\n### Sponge.md_info\n```\nHelp on MD_INFORMATION in module __main__ object:\n\nclass MD_INFORMATION(builtins.object)\n | Contains the information for MD simulations\n |\n | Methods defined here:\n |\n | __init__(self)\n |\n | __repr__(self)\n |\n | ----------------------------------------------------------------------\n | Readonly properties defined here:\n |\n | atom_numbers\n | the total number of atoms\n |\n | d_mass\n | the mass of the atoms\n |\n | sys\n | the system information\n |\n | ----------------------------------------------------------------------\n | Data descriptors defined here:\n |\n | __dict__\n | dictionary for instance variables (if defined)\n |\n | __weakref__\n | list of weak references to the object (if defined)\n |\n | crd\n | the position coordinates of the atoms\n |\n | d_atom_energy\n | the energy of the atoms\n |\n | d_atom_virial\n | the virial of the atoms\n |\n | d_charge\n | the charge of the atoms (In the unit of SPONGE, a unit charge is 18.2223)\n |\n | frc\n | the force of the atoms\n |\n | vel\n | the velocity of the atoms\n\n```\n### Sponge.md_info.sys\n```\nHelp on system_information in module __main__ object:\n\nclass system_information(builtins.object)\n | the system information of MD information\n |\n | Readonly properties defined here:\n |\n | box_length\n | the length of the box\n |\n | steps\n | the current step of the simulation\n |\n | ----------------------------------------------------------------------\n | Data descriptors defined here:\n |\n | __dict__\n | dictionary for instance variables (if defined)\n |\n | __weakref__\n | list of weak references to the object (if defined)\n\n```\n### Sponge.NEIGHBOR_LIST\n```\nHelp on class NEIGHBOR_LIST in module __main__:\n\nclass NEIGHBOR_LIST(builtins.object)\n | Neighbor List of SPONGE.\n | This class should be initialized at After_Initial, because neighbor_list is not initialized when initializing prips\n |\n | Methods defined here:\n |\n | __init__(self)\n |\n | ----------------------------------------------------------------------\n | Readonly properties defined here:\n |\n | atom_numbers\n | the number of neighbors for every atom\n |\n | atom_serials\n | the serial of neighbors for every atom\n |\n | ----------------------------------------------------------------------\n | Data descriptors defined here:\n |\n | __dict__\n | dictionary for instance variables (if defined)\n |\n | __weakref__\n | list of weak references to the object (if defined)\n\n```\n\n",
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