lammps python_lammps-tools · PyPI

最新推荐文章于 2024-03-28 16:44:06 发布

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最新推荐文章于 2024-03-28 16:44:06 发布

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文章标签： lammps python

Project description

# lammps-tools

This python tools provide a ease way to process the data associated with lammps. You can use this series of tools to create polymer model, extract data and get data draft plot(TO-DO)

## install

```

pip install lammps_tools

```

## use guide

```

lammps_tools/

data_processing/

dump.py

fix.py

log.py

model_builder/

polymer_generator.py

GP_generator.py

```

## data-processing

This package contains of models to extract data and format by a pythonic way

### dump

**Usage**:

1. Initiate Dump class. It will automatically search target dump file and store where it is.

``` d = Dump(FilePath)```

2. Interate this Instance. Every call will drive it to read a snapshot and return a dict including properties and raw data.

```

for snap in d:

```

**API**:

*Dump(fpath)*

* parameters:

* *fpath*: Note that you must give a str which is a relative path or absoluate path and relative path up to where you run this script not where this script in. Remember Windows platform must convert '/' into '//'.

* *every*: default 0. It specifies the frequency to read snap. If you assign every is n, that means return 0, n, 2n...

* return:

* Dump return a instance but do nothing. Every function takes effect only after you iterate this instance. The reason is once your dump file is very big, this design can save memory.

* Iterate instance will return a dict:

```

snap := {

'TIMESTEP': 1000

'NUMBER_OF_ATOM': 10000

'BOUNDARY_CONDITION': ['pp', 'PP', 'PP']

'BOUNDARY_X': [0.00, 81.24]

'BOUNDARY_Y': [0.00, 81.24]

'BOUNDARY_Z': [0.00, 81.24]

'HEADER': ['id', 'mol', 'type', 'x', 'y', 'z', ....]

'DATA':[

[1, 1, 1, 10.23, 12.32, 13.14],

[2, 1, 1, 16.23, 13.32, 12.87],

[3, 1, 1, 13.23, 17.32, 19.11],

...

]

}

```

### Fix

**Usage**

1. Initiate Fix class as Dump, also need to provide file path.

```

f = Fix(fpath)

```

2. Generally Fix only contains one stage data, so iterate it is unnecessary. But due to lazy function design, you still need read data manually.

```

f.read_data()

```

**API**

*Fix(fpath)*

* parameters:

* *fpath*: Aformentioned

* return:

* Fix return a instance but do nothing. Every function takes effect only after you iterate this instance.

* method:

* Fix.get_col(index)

give a index of fix column and return a list of this.

* Fix.read_data()

return a dict:

```

stage = f.read_data()

stage := {

'NUMBER_OF_DATA': 1234

'DATA':[

[123,234,345,654...],

[234,345,456,567...]

]

}

### Log

**Usage**

1. Initiate Log class as Fix, also need to provide file path.

```

l = Log(fpath)

```

2. Interate this Instance. Every call will drive it to read a stage and return a dict including properties and raw data.

```

for stage in l:

```

**API**

*Log(fpath, summary)*

* parameters:

* *fpath*: Aformentioned

* *summary*: default False. before use .get_col() you must set this to True

* return:

* Log return a instance but do nothing. Every function takes effect only after you iterate this instance.

* Iterate instance will return a dict:

```

stage := {

'STAGE' : 0,

'HEADER' : [Step, Temp, Press,...],

'DATA' : [

[0, 487.3, 1631.12],

...

]

}

* method:

* Log.get_col(item, *stage):

This can return whole item column in log file. Before use this, set *summary* to True.

Or if you pass a single stage as arg, then return this stage' column of item.

## model-builder

### 功能:

* 生成单链

* 生成支化链

* 生成石墨烯片(蜂窝状)(未经测试，使用方法同polymer_generator)

### 更新日志

1. 03/23:

* 逻辑重写, 修改了行走模式, 重构了折返算法 --> 增大了链与链间间隔

2. 04/22：

× 添加了生成石墨烯的脚本，增加了生成lt模板的方法

### 选项:

[DEFAULT]

* 简易名字 := simple_name (yes/no).

```

指定yes文件名为'polymer.lt', 分子名'Polymer';

no则文件名为: 'polymer-{main_chain_length}-{branch_length}\_{branch_number}.lt' , 分子名为 'Polymer-{main_chain_length}-{branch_length}_{(branch_number)}'

```

* 盒子尺寸 := box_*

* 单体文件 := monomer.ltname

[BACKBONE]

* 主链长 := c_chain_length

* 主链键长 := c_bond_length

* 主链元原子 := C_atom

* 主链原子ID := C_ID #当单体为多原子时起作用

* 是否有支链 := isBranch

```

C_atom inherits Forcefield{

write("Data Atoms"){ ###保持元原子坐标在原点不变###

$atom:C_ID $mol:... @atom:C 0 0 0 0

}}

```

[BRANCH]

* 支链长度 := b_chain_length

* 支链键长 := b_bond_length

* 支化点 := b_point = p1, p2, p3...

* 支链元原子 := b_atom

* 支链原子ID := b_ID

```

b_atom inherits Forcefield{

write("Data Atoms"){

$atom:B_ID $mol:... @atom:B 0 0 0 0

}

```

### 使用方法

1. 准备分子链单元的文件, 其中包含主链原子及支链原子(如果有的话)的信息, 名称与monomer_ltname一致

或者生成模板：

```

from lammps_tools.model_builder import polymer_generator

polymer_generator.generate_lt()

```

2. 使用记事本或者vim打开polymer_init.ini文件, 修改参数

3. 新建python文件，导入模块

```

polymer_generator.run()

```

4. 得到单个分子链文件. 同时输出这个链所占据的矩体尺寸, 方便在system.lt中移动生成

5. 写system.lt文件, 使用```moltemplate.sh system.lt ```生成文件

### API

× .run() 配置好ini之后，使用此开始生成

* .generate_lt() 生成moltemplate模板

### 编译树

monomer.lt -> polymer.lt --(fieldforce.lt)--> system.lt

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