新建
[WIP]DOAS在无定形结构分析中的运用
shenh@dp.tech
推荐镜像 :Basic Image:bohrium-notebook:2023-04-07
推荐机型 :c2_m4_cpu
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目录
数据集
doasdata(v1)
[WIP]DOAS在无定形结构分析中的运用
代码
文本
[1]
## 导入所需要的库
from dpdata import System
import os
import shutil
from pathlib import Path
import glob
from dpdispatcher import Machine, Resources, Task, Submission
import matplotlib.pyplot as plt
import numpy as np
from tqdm import tqdm, trange
代码
文本
0. 本notebook准备的数据集
在这个notebook中我们将会对lammps的轨迹文件进行操作，因此准备有轨迹文件；同时还需要对轨迹中选取的frame进行结构优化，也准备了优化完成的若干frame的lammps输出文件。
代码
文本
[2]
!mv /bohr/doas-2hau/v1/doasdata.tar.gz ./
!tar xvf doasdata.tar.gz
mv: failed to preserve ownership for './doasdata.tar.gz': Operation not permitted mv: cannot remove '/bohr/doas-2hau/v1/doasdata.tar.gz': Read-only file system notedata/ notedata/frames/ notedata/frames/lmp-0/ notedata/frames/lmp-0/dump.atom_energy notedata/frames/lmp-0/in.lmp notedata/frames/lmp-0/lmp.data notedata/frames/lmp-0/log.lammps notedata/frames/lmp-0/output_data.txt notedata/frames/lmp-0/test.py notedata/frames/lmp-1/ notedata/frames/lmp-1/dump.atom_energy notedata/frames/lmp-1/in.lmp notedata/frames/lmp-1/lmp.data notedata/frames/lmp-1/log.lammps notedata/frames/lmp-1/output_data.txt notedata/frames/lmp-1/test.py notedata/frames/lmp-10/ notedata/frames/lmp-10/dump.atom_energy notedata/frames/lmp-10/in.lmp notedata/frames/lmp-10/lmp.data notedata/frames/lmp-10/log.lammps notedata/frames/lmp-10/output_data.txt notedata/frames/lmp-10/test.py notedata/frames/lmp-100/ notedata/frames/lmp-100/dump.atom_energy notedata/frames/lmp-100/in.lmp notedata/frames/lmp-100/lmp.data notedata/frames/lmp-100/log.lammps notedata/frames/lmp-100/output_data.txt notedata/frames/lmp-100/test.py notedata/frames/lmp-101/ notedata/frames/lmp-101/dump.atom_energy notedata/frames/lmp-101/in.lmp notedata/frames/lmp-101/lmp.data notedata/frames/lmp-101/log.lammps notedata/frames/lmp-101/output_data.txt notedata/frames/lmp-101/test.py notedata/frames/lmp-102/ notedata/frames/lmp-102/dump.atom_energy notedata/frames/lmp-102/in.lmp notedata/frames/lmp-102/lmp.data notedata/frames/lmp-102/log.lammps notedata/frames/lmp-102/output_data.txt notedata/frames/lmp-102/test.py notedata/frames/lmp-103/ notedata/frames/lmp-103/dump.atom_energy notedata/frames/lmp-103/in.lmp notedata/frames/lmp-103/lmp.data notedata/frames/lmp-103/log.lammps notedata/frames/lmp-103/output_data.txt notedata/frames/lmp-103/test.py notedata/frames/lmp-104/ notedata/frames/lmp-104/dump.atom_energy notedata/frames/lmp-104/in.lmp notedata/frames/lmp-104/lmp.data notedata/frames/lmp-104/log.lammps notedata/frames/lmp-104/output_data.txt notedata/frames/lmp-104/test.py notedata/frames/lmp-105/ notedata/frames/lmp-105/dump.atom_energy notedata/frames/lmp-105/in.lmp notedata/frames/lmp-105/lmp.data notedata/frames/lmp-105/log.lammps notedata/frames/lmp-105/output_data.txt notedata/frames/lmp-105/test.py notedata/frames/lmp-106/ notedata/frames/lmp-106/dump.atom_energy notedata/frames/lmp-106/in.lmp notedata/frames/lmp-106/lmp.data notedata/frames/lmp-106/log.lammps notedata/frames/lmp-106/output_data.txt notedata/frames/lmp-106/test.py notedata/frames/lmp-107/ notedata/frames/lmp-107/dump.atom_energy notedata/frames/lmp-107/in.lmp notedata/frames/lmp-107/lmp.data notedata/frames/lmp-107/log.lammps notedata/frames/lmp-107/output_data.txt notedata/frames/lmp-107/test.py notedata/frames/lmp-108/ notedata/frames/lmp-108/dump.atom_energy notedata/frames/lmp-108/in.lmp notedata/frames/lmp-108/lmp.data notedata/frames/lmp-108/log.lammps notedata/frames/lmp-108/output_data.txt notedata/frames/lmp-108/test.py notedata/frames/lmp-109/ notedata/frames/lmp-109/dump.atom_energy notedata/frames/lmp-109/in.lmp notedata/frames/lmp-109/lmp.data notedata/frames/lmp-109/log.lammps notedata/frames/lmp-109/output_data.txt notedata/frames/lmp-109/test.py notedata/frames/lmp-11/ notedata/frames/lmp-11/dump.atom_energy notedata/frames/lmp-11/in.lmp notedata/frames/lmp-11/lmp.data notedata/frames/lmp-11/log.lammps notedata/frames/lmp-11/output_data.txt notedata/frames/lmp-11/test.py notedata/frames/lmp-110/ notedata/frames/lmp-110/dump.atom_energy notedata/frames/lmp-110/in.lmp notedata/frames/lmp-110/lmp.data notedata/frames/lmp-110/log.lammps notedata/frames/lmp-110/output_data.txt notedata/frames/lmp-110/test.py notedata/frames/lmp-111/ notedata/frames/lmp-111/dump.atom_energy notedata/frames/lmp-111/in.lmp notedata/frames/lmp-111/lmp.data notedata/frames/lmp-111/log.lammps notedata/frames/lmp-111/output_data.txt notedata/frames/lmp-111/test.py notedata/frames/lmp-112/ notedata/frames/lmp-112/dump.atom_energy notedata/frames/lmp-112/in.lmp notedata/frames/lmp-112/lmp.data notedata/frames/lmp-112/log.lammps notedata/frames/lmp-112/output_data.txt notedata/frames/lmp-112/test.py notedata/frames/lmp-113/ notedata/frames/lmp-113/dump.atom_energy notedata/frames/lmp-113/in.lmp notedata/frames/lmp-113/lmp.data notedata/frames/lmp-113/log.lammps notedata/frames/lmp-113/output_data.txt notedata/frames/lmp-113/test.py notedata/frames/lmp-114/ notedata/frames/lmp-114/dump.atom_energy notedata/frames/lmp-114/in.lmp notedata/frames/lmp-114/lmp.data notedata/frames/lmp-114/log.lammps notedata/frames/lmp-114/output_data.txt notedata/frames/lmp-114/test.py notedata/frames/lmp-115/ notedata/frames/lmp-115/dump.atom_energy notedata/frames/lmp-115/in.lmp notedata/frames/lmp-115/lmp.data notedata/frames/lmp-115/log.lammps notedata/frames/lmp-115/output_data.txt notedata/frames/lmp-115/test.py notedata/frames/lmp-116/ notedata/frames/lmp-116/dump.atom_energy notedata/frames/lmp-116/in.lmp notedata/frames/lmp-116/lmp.data notedata/frames/lmp-116/log.lammps notedata/frames/lmp-116/output_data.txt notedata/frames/lmp-116/test.py notedata/frames/lmp-117/ notedata/frames/lmp-117/dump.atom_energy notedata/frames/lmp-117/in.lmp notedata/frames/lmp-117/lmp.data notedata/frames/lmp-117/log.lammps notedata/frames/lmp-117/output_data.txt notedata/frames/lmp-117/test.py notedata/frames/lmp-118/ notedata/frames/lmp-118/dump.atom_energy notedata/frames/lmp-118/in.lmp notedata/frames/lmp-118/lmp.data notedata/frames/lmp-118/log.lammps notedata/frames/lmp-118/output_data.txt notedata/frames/lmp-118/test.py notedata/frames/lmp-119/ notedata/frames/lmp-119/dump.atom_energy notedata/frames/lmp-119/in.lmp notedata/frames/lmp-119/lmp.data notedata/frames/lmp-119/log.lammps notedata/frames/lmp-119/output_data.txt notedata/frames/lmp-119/test.py notedata/frames/lmp-12/ notedata/frames/lmp-12/dump.atom_energy notedata/frames/lmp-12/in.lmp notedata/frames/lmp-12/lmp.data notedata/frames/lmp-12/log.lammps notedata/frames/lmp-12/output_data.txt notedata/frames/lmp-12/test.py notedata/frames/lmp-120/ notedata/frames/lmp-120/dump.atom_energy notedata/frames/lmp-120/in.lmp notedata/frames/lmp-120/lmp.data notedata/frames/lmp-120/log.lammps notedata/frames/lmp-120/output_data.txt notedata/frames/lmp-120/test.py notedata/frames/lmp-121/ notedata/frames/lmp-121/dump.atom_energy notedata/frames/lmp-121/in.lmp notedata/frames/lmp-121/lmp.data notedata/frames/lmp-121/log.lammps notedata/frames/lmp-121/output_data.txt notedata/frames/lmp-121/test.py notedata/frames/lmp-122/ notedata/frames/lmp-122/dump.atom_energy notedata/frames/lmp-122/in.lmp notedata/frames/lmp-122/lmp.data notedata/frames/lmp-122/log.lammps notedata/frames/lmp-122/output_data.txt notedata/frames/lmp-122/test.py notedata/frames/lmp-123/ notedata/frames/lmp-123/dump.atom_energy notedata/frames/lmp-123/in.lmp notedata/frames/lmp-123/lmp.data notedata/frames/lmp-123/log.lammps notedata/frames/lmp-123/output_data.txt notedata/frames/lmp-123/test.py notedata/frames/lmp-124/ notedata/frames/lmp-124/dump.atom_energy notedata/frames/lmp-124/in.lmp notedata/frames/lmp-124/lmp.data notedata/frames/lmp-124/log.lammps notedata/frames/lmp-124/output_data.txt notedata/frames/lmp-124/test.py notedata/frames/lmp-125/ notedata/frames/lmp-125/dump.atom_energy notedata/frames/lmp-125/in.lmp notedata/frames/lmp-125/lmp.data notedata/frames/lmp-125/log.lammps notedata/frames/lmp-125/output_data.txt notedata/frames/lmp-125/test.py notedata/frames/lmp-126/ notedata/frames/lmp-126/dump.atom_energy notedata/frames/lmp-126/in.lmp notedata/frames/lmp-126/lmp.data notedata/frames/lmp-126/log.lammps notedata/frames/lmp-126/output_data.txt notedata/frames/lmp-126/test.py notedata/frames/lmp-127/ notedata/frames/lmp-127/dump.atom_energy notedata/frames/lmp-127/in.lmp notedata/frames/lmp-127/lmp.data notedata/frames/lmp-127/log.lammps notedata/frames/lmp-127/output_data.txt notedata/frames/lmp-127/test.py notedata/frames/lmp-128/ notedata/frames/lmp-128/dump.atom_energy notedata/frames/lmp-128/in.lmp notedata/frames/lmp-128/lmp.data notedata/frames/lmp-128/log.lammps notedata/frames/lmp-128/output_data.txt notedata/frames/lmp-128/test.py notedata/frames/lmp-129/ notedata/frames/lmp-129/dump.atom_energy notedata/frames/lmp-129/in.lmp notedata/frames/lmp-129/lmp.data notedata/frames/lmp-129/log.lammps notedata/frames/lmp-129/output_data.txt notedata/frames/lmp-129/test.py notedata/frames/lmp-13/ notedata/frames/lmp-13/dump.atom_energy notedata/frames/lmp-13/in.lmp notedata/frames/lmp-13/lmp.data notedata/frames/lmp-13/log.lammps notedata/frames/lmp-13/output_data.txt notedata/frames/lmp-13/test.py notedata/frames/lmp-130/ notedata/frames/lmp-130/dump.atom_energy notedata/frames/lmp-130/in.lmp notedata/frames/lmp-130/lmp.data notedata/frames/lmp-130/log.lammps notedata/frames/lmp-130/output_data.txt notedata/frames/lmp-130/test.py notedata/frames/lmp-131/ notedata/frames/lmp-131/dump.atom_energy notedata/frames/lmp-131/in.lmp notedata/frames/lmp-131/lmp.data notedata/frames/lmp-131/log.lammps notedata/frames/lmp-131/output_data.txt notedata/frames/lmp-131/test.py notedata/frames/lmp-132/ notedata/frames/lmp-132/dump.atom_energy notedata/frames/lmp-132/in.lmp notedata/frames/lmp-132/lmp.data notedata/frames/lmp-132/log.lammps notedata/frames/lmp-132/output_data.txt notedata/frames/lmp-132/test.py notedata/frames/lmp-133/ notedata/frames/lmp-133/dump.atom_energy notedata/frames/lmp-133/in.lmp notedata/frames/lmp-133/lmp.data notedata/frames/lmp-133/log.lammps notedata/frames/lmp-133/output_data.txt notedata/frames/lmp-133/test.py notedata/frames/lmp-134/ notedata/frames/lmp-134/dump.atom_energy notedata/frames/lmp-134/in.lmp notedata/frames/lmp-134/lmp.data notedata/frames/lmp-134/log.lammps notedata/frames/lmp-134/output_data.txt notedata/frames/lmp-134/test.py notedata/frames/lmp-135/ notedata/frames/lmp-135/dump.atom_energy notedata/frames/lmp-135/in.lmp notedata/frames/lmp-135/lmp.data notedata/frames/lmp-135/log.lammps notedata/frames/lmp-135/output_data.txt notedata/frames/lmp-135/test.py notedata/frames/lmp-136/ notedata/frames/lmp-136/dump.atom_energy notedata/frames/lmp-136/in.lmp notedata/frames/lmp-136/lmp.data notedata/frames/lmp-136/log.lammps notedata/frames/lmp-136/output_data.txt notedata/frames/lmp-136/test.py notedata/frames/lmp-137/ notedata/frames/lmp-137/dump.atom_energy notedata/frames/lmp-137/in.lmp notedata/frames/lmp-137/lmp.data notedata/frames/lmp-137/log.lammps notedata/frames/lmp-137/output_data.txt notedata/frames/lmp-137/test.py notedata/frames/lmp-138/ notedata/frames/lmp-138/dump.atom_energy notedata/frames/lmp-138/in.lmp notedata/frames/lmp-138/lmp.data notedata/frames/lmp-138/log.lammps notedata/frames/lmp-138/output_data.txt notedata/frames/lmp-138/test.py notedata/frames/lmp-139/ 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notedata/frames/lmp-142/in.lmp notedata/frames/lmp-142/lmp.data notedata/frames/lmp-142/log.lammps notedata/frames/lmp-142/output_data.txt notedata/frames/lmp-142/test.py notedata/frames/lmp-143/ notedata/frames/lmp-143/dump.atom_energy notedata/frames/lmp-143/in.lmp notedata/frames/lmp-143/lmp.data notedata/frames/lmp-143/log.lammps notedata/frames/lmp-143/output_data.txt notedata/frames/lmp-143/test.py notedata/frames/lmp-144/ notedata/frames/lmp-144/dump.atom_energy notedata/frames/lmp-144/in.lmp notedata/frames/lmp-144/lmp.data notedata/frames/lmp-144/log.lammps notedata/frames/lmp-144/output_data.txt notedata/frames/lmp-144/test.py notedata/frames/lmp-145/ notedata/frames/lmp-145/dump.atom_energy notedata/frames/lmp-145/in.lmp notedata/frames/lmp-145/lmp.data notedata/frames/lmp-145/log.lammps notedata/frames/lmp-145/output_data.txt notedata/frames/lmp-145/test.py notedata/frames/lmp-146/ notedata/frames/lmp-146/dump.atom_energy notedata/frames/lmp-146/in.lmp notedata/frames/lmp-146/lmp.data notedata/frames/lmp-146/log.lammps notedata/frames/lmp-146/output_data.txt notedata/frames/lmp-146/test.py notedata/frames/lmp-147/ notedata/frames/lmp-147/dump.atom_energy notedata/frames/lmp-147/in.lmp notedata/frames/lmp-147/lmp.data notedata/frames/lmp-147/log.lammps notedata/frames/lmp-147/output_data.txt notedata/frames/lmp-147/test.py notedata/frames/lmp-148/ notedata/frames/lmp-148/dump.atom_energy notedata/frames/lmp-148/in.lmp notedata/frames/lmp-148/lmp.data notedata/frames/lmp-148/log.lammps notedata/frames/lmp-148/output_data.txt notedata/frames/lmp-148/test.py notedata/frames/lmp-149/ notedata/frames/lmp-149/dump.atom_energy notedata/frames/lmp-149/in.lmp notedata/frames/lmp-149/lmp.data notedata/frames/lmp-149/log.lammps notedata/frames/lmp-149/output_data.txt notedata/frames/lmp-149/test.py notedata/frames/lmp-15/ notedata/frames/lmp-15/dump.atom_energy notedata/frames/lmp-15/in.lmp notedata/frames/lmp-15/lmp.data notedata/frames/lmp-15/log.lammps notedata/frames/lmp-15/output_data.txt notedata/frames/lmp-15/test.py notedata/frames/lmp-150/ notedata/frames/lmp-150/dump.atom_energy notedata/frames/lmp-150/in.lmp notedata/frames/lmp-150/lmp.data notedata/frames/lmp-150/log.lammps notedata/frames/lmp-150/output_data.txt notedata/frames/lmp-150/test.py notedata/frames/lmp-151/ notedata/frames/lmp-151/dump.atom_energy notedata/frames/lmp-151/in.lmp notedata/frames/lmp-151/lmp.data notedata/frames/lmp-151/log.lammps notedata/frames/lmp-151/output_data.txt notedata/frames/lmp-151/test.py notedata/frames/lmp-152/ notedata/frames/lmp-152/dump.atom_energy notedata/frames/lmp-152/in.lmp notedata/frames/lmp-152/lmp.data notedata/frames/lmp-152/log.lammps notedata/frames/lmp-152/output_data.txt notedata/frames/lmp-152/test.py notedata/frames/lmp-153/ notedata/frames/lmp-153/dump.atom_energy notedata/frames/lmp-153/in.lmp notedata/frames/lmp-153/lmp.data notedata/frames/lmp-153/log.lammps 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notedata/frames/lmp-72/in.lmp notedata/frames/lmp-72/lmp.data notedata/frames/lmp-72/log.lammps notedata/frames/lmp-72/output_data.txt notedata/frames/lmp-72/test.py notedata/frames/lmp-73/ notedata/frames/lmp-73/dump.atom_energy notedata/frames/lmp-73/in.lmp notedata/frames/lmp-73/lmp.data notedata/frames/lmp-73/log.lammps notedata/frames/lmp-73/output_data.txt notedata/frames/lmp-73/test.py notedata/frames/lmp-74/ notedata/frames/lmp-74/dump.atom_energy notedata/frames/lmp-74/in.lmp notedata/frames/lmp-74/lmp.data notedata/frames/lmp-74/log.lammps notedata/frames/lmp-74/output_data.txt notedata/frames/lmp-74/test.py notedata/frames/lmp-75/ notedata/frames/lmp-75/dump.atom_energy notedata/frames/lmp-75/in.lmp notedata/frames/lmp-75/lmp.data notedata/frames/lmp-75/log.lammps notedata/frames/lmp-75/output_data.txt notedata/frames/lmp-75/test.py notedata/frames/lmp-76/ notedata/frames/lmp-76/dump.atom_energy notedata/frames/lmp-76/in.lmp notedata/frames/lmp-76/lmp.data notedata/frames/lmp-76/log.lammps notedata/frames/lmp-76/output_data.txt notedata/frames/lmp-76/test.py notedata/frames/lmp-77/ notedata/frames/lmp-77/dump.atom_energy notedata/frames/lmp-77/in.lmp notedata/frames/lmp-77/lmp.data notedata/frames/lmp-77/log.lammps notedata/frames/lmp-77/output_data.txt notedata/frames/lmp-77/test.py notedata/frames/lmp-78/ notedata/frames/lmp-78/dump.atom_energy notedata/frames/lmp-78/in.lmp notedata/frames/lmp-78/lmp.data notedata/frames/lmp-78/log.lammps notedata/frames/lmp-78/output_data.txt notedata/frames/lmp-78/test.py notedata/frames/lmp-79/ notedata/frames/lmp-79/dump.atom_energy notedata/frames/lmp-79/in.lmp notedata/frames/lmp-79/lmp.data notedata/frames/lmp-79/log.lammps notedata/frames/lmp-79/output_data.txt notedata/frames/lmp-79/test.py notedata/frames/lmp-8/ notedata/frames/lmp-8/dump.atom_energy notedata/frames/lmp-8/in.lmp notedata/frames/lmp-8/lmp.data notedata/frames/lmp-8/log.lammps notedata/frames/lmp-8/output_data.txt notedata/frames/lmp-8/test.py notedata/frames/lmp-80/ notedata/frames/lmp-80/dump.atom_energy notedata/frames/lmp-80/in.lmp notedata/frames/lmp-80/lmp.data notedata/frames/lmp-80/log.lammps notedata/frames/lmp-80/output_data.txt notedata/frames/lmp-80/test.py notedata/frames/lmp-81/ notedata/frames/lmp-81/dump.atom_energy notedata/frames/lmp-81/in.lmp notedata/frames/lmp-81/lmp.data notedata/frames/lmp-81/log.lammps notedata/frames/lmp-81/output_data.txt notedata/frames/lmp-81/test.py notedata/frames/lmp-82/ notedata/frames/lmp-82/dump.atom_energy notedata/frames/lmp-82/in.lmp notedata/frames/lmp-82/lmp.data notedata/frames/lmp-82/log.lammps notedata/frames/lmp-82/output_data.txt notedata/frames/lmp-82/test.py notedata/frames/lmp-83/ notedata/frames/lmp-83/dump.atom_energy notedata/frames/lmp-83/in.lmp notedata/frames/lmp-83/lmp.data notedata/frames/lmp-83/log.lammps notedata/frames/lmp-83/output_data.txt notedata/frames/lmp-83/test.py notedata/frames/lmp-84/ notedata/frames/lmp-84/dump.atom_energy notedata/frames/lmp-84/in.lmp notedata/frames/lmp-84/lmp.data notedata/frames/lmp-84/log.lammps notedata/frames/lmp-84/output_data.txt notedata/frames/lmp-84/test.py notedata/frames/lmp-85/ notedata/frames/lmp-85/dump.atom_energy notedata/frames/lmp-85/in.lmp notedata/frames/lmp-85/lmp.data notedata/frames/lmp-85/log.lammps notedata/frames/lmp-85/output_data.txt notedata/frames/lmp-85/test.py notedata/frames/lmp-86/ notedata/frames/lmp-86/dump.atom_energy notedata/frames/lmp-86/in.lmp notedata/frames/lmp-86/lmp.data notedata/frames/lmp-86/log.lammps notedata/frames/lmp-86/output_data.txt notedata/frames/lmp-86/test.py notedata/frames/lmp-87/ notedata/frames/lmp-87/dump.atom_energy notedata/frames/lmp-87/in.lmp notedata/frames/lmp-87/lmp.data notedata/frames/lmp-87/log.lammps notedata/frames/lmp-87/output_data.txt notedata/frames/lmp-87/test.py notedata/frames/lmp-88/ notedata/frames/lmp-88/dump.atom_energy notedata/frames/lmp-88/in.lmp notedata/frames/lmp-88/lmp.data notedata/frames/lmp-88/log.lammps notedata/frames/lmp-88/output_data.txt notedata/frames/lmp-88/test.py notedata/frames/lmp-89/ notedata/frames/lmp-89/dump.atom_energy notedata/frames/lmp-89/in.lmp notedata/frames/lmp-89/lmp.data notedata/frames/lmp-89/log.lammps notedata/frames/lmp-89/output_data.txt notedata/frames/lmp-89/test.py notedata/frames/lmp-9/ notedata/frames/lmp-9/dump.atom_energy notedata/frames/lmp-9/in.lmp notedata/frames/lmp-9/lmp.data notedata/frames/lmp-9/log.lammps notedata/frames/lmp-9/output_data.txt notedata/frames/lmp-9/test.py notedata/frames/lmp-90/ notedata/frames/lmp-90/dump.atom_energy notedata/frames/lmp-90/in.lmp notedata/frames/lmp-90/lmp.data notedata/frames/lmp-90/log.lammps notedata/frames/lmp-90/output_data.txt notedata/frames/lmp-90/test.py notedata/frames/lmp-91/ notedata/frames/lmp-91/dump.atom_energy notedata/frames/lmp-91/in.lmp notedata/frames/lmp-91/lmp.data notedata/frames/lmp-91/log.lammps notedata/frames/lmp-91/output_data.txt notedata/frames/lmp-91/test.py notedata/frames/lmp-92/ notedata/frames/lmp-92/dump.atom_energy notedata/frames/lmp-92/in.lmp notedata/frames/lmp-92/lmp.data notedata/frames/lmp-92/log.lammps notedata/frames/lmp-92/output_data.txt notedata/frames/lmp-92/test.py notedata/frames/lmp-93/ notedata/frames/lmp-93/dump.atom_energy notedata/frames/lmp-93/in.lmp notedata/frames/lmp-93/lmp.data notedata/frames/lmp-93/log.lammps notedata/frames/lmp-93/output_data.txt notedata/frames/lmp-93/test.py notedata/frames/lmp-94/ notedata/frames/lmp-94/dump.atom_energy notedata/frames/lmp-94/in.lmp notedata/frames/lmp-94/lmp.data notedata/frames/lmp-94/log.lammps notedata/frames/lmp-94/output_data.txt notedata/frames/lmp-94/test.py notedata/frames/lmp-95/ notedata/frames/lmp-95/dump.atom_energy notedata/frames/lmp-95/in.lmp notedata/frames/lmp-95/lmp.data notedata/frames/lmp-95/log.lammps notedata/frames/lmp-95/output_data.txt notedata/frames/lmp-95/test.py notedata/frames/lmp-96/ notedata/frames/lmp-96/dump.atom_energy notedata/frames/lmp-96/in.lmp notedata/frames/lmp-96/lmp.data notedata/frames/lmp-96/log.lammps notedata/frames/lmp-96/output_data.txt notedata/frames/lmp-96/test.py notedata/frames/lmp-97/ notedata/frames/lmp-97/dump.atom_energy notedata/frames/lmp-97/in.lmp notedata/frames/lmp-97/lmp.data notedata/frames/lmp-97/log.lammps notedata/frames/lmp-97/output_data.txt notedata/frames/lmp-97/test.py notedata/frames/lmp-98/ notedata/frames/lmp-98/dump.atom_energy notedata/frames/lmp-98/in.lmp notedata/frames/lmp-98/lmp.data notedata/frames/lmp-98/log.lammps notedata/frames/lmp-98/output_data.txt notedata/frames/lmp-98/test.py notedata/frames/lmp-99/ notedata/frames/lmp-99/dump.atom_energy notedata/frames/lmp-99/in.lmp notedata/frames/lmp-99/lmp.data notedata/frames/lmp-99/log.lammps notedata/frames/lmp-99/output_data.txt notedata/frames/lmp-99/test.py notedata/graph.000.pb notedata/in.lmp notedata/machine.json notedata/output_keep.lammpstrj notedata/resource.json
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1. 从MD轨迹中抓取需要的结构
我们需要从目标轨迹中抓取所需的结构，转换成lammps的结构文件lmp.data并进行结构优化。而在lammps的轨迹文件中通常是没有元素类型信息以及Masses信息的，所以需要我们type_map和mass_map信息。
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[11]
def grasp_struc_from_traj(traj_filename: str, energy_n_frame: int, type_map: dict, mass_map: dict):
strucs = System(traj_filename, 'lammps/dump')
selected_strucs = strucs[::energy_n_frame]
for i, frame in enumerate(selected_strucs):
frame.to('lmp', f'lmp-{i}.data')
with open(f'lmp-{i}.data', 'r') as fp:
lines = fp.readlines()
new_lines = lines[0:8]
new_lines.append('\n')
new_lines.append('Masses\n')
new_lines.append('\n')
for ele_type in type_map.keys():
new_lines.append(f'{int(ele_type[-1]) + 1} {mass_map[type_map[ele_type]]}\n')
new_lines.append('\n')
new_lines += lines[8:]
with open(f'lmp-{i}.data', 'w') as f:
f.writelines(new_lines)
os.makedirs(f'lmp-{i}', exist_ok=True)
shutil.copy(f'lmp-{i}.data', Path(f'lmp-{i}')/'lmp.data')
shutil.copy('graph.000.pb', Path(f'lmp-{i}'))
shutil.copy('in.lmp', Path(f'lmp-{i}'))
return None
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在本次notebook中我们使用的元素类型如下type_map所示
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[12]
os.chdir('notedata')
type_map = {'TYPE_0': 'Si','TYPE_1':'O', 'TYPE_2':'Bi'}
mass_map = {'Si': 28.085, 'O': 15.999, 'Bi': 208.98}
traj_filename = 'output_keep.lammpstrj'
every_n_frame = 100
grasp_struc_from_traj(traj_filename, every_n_frame, type_map, mass_map)
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我们的轨迹文件output_keep.lammpstrj中包含有400个构型，设定enery_n_frame=100，能够提取4个结构，并得到包含有对应输入文件的文件夹。通过调整energy_n_frame的数值可以修改提取结构的数量
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[13]
!tree -L 1 lmp-*
lmp-0 ├── graph.000.pb ├── in.lmp └── lmp.data lmp-0.data [error opening dir] lmp-1 ├── graph.000.pb ├── in.lmp └── lmp.data lmp-1.data [error opening dir] lmp-2 ├── graph.000.pb ├── in.lmp └── lmp.data lmp-2.data [error opening dir] lmp-3 ├── graph.000.pb ├── in.lmp └── lmp.data lmp-3.data [error opening dir] 0 directories, 12 files
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2. 进行结构优化
在本次的notebook中，我们使用dpdispatcher讲所有优化任务提交到远程计算节点中，所以我们需要对machine.json文件中的bohrium账号等信息进行设置。
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[12]
import json
import getpass
from monty.serialization import loadfn, dumpfn
file_path = './machine.json'
j = loadfn(file_path)
email = input('请输入你的 Bohrium 账户： ')
password = getpass.getpass('请输入你的 Bohrium 密码： ')
program_id = int(input('请输入你的 Bohrium 项目 ID【请输入整数】：'))
j['remote_profile']['email'] = email
j['remote_profile']['password'] = password
j['remote_profile']['program_id'] = program_id
with open(file_path, 'w') as f:
json.dump(j, f, indent=4)
请输入你的 Bohrium 账户： shenh@dp.tech 请输入你的 Bohrium 密码： ········ 请输入你的 Bohrium 项目 ID【请输入整数】： 11052
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[53]
def run_minimize():
machine = Machine.load_from_json('machine.json')
resources = Resources.load_from_json('resource.json')
task_list = []
target_folders = [folder for folder in glob.glob('lmp*') if os.path.isdir(folder)]
for folder in target_folders:
task = Task(
command = 'lmp < in.lmp',
task_work_path = folder,
forward_files = ['graph.000.pb', 'in.lmp', 'lmp.data'],
outlog = "log",
errlog = "err"
)
task_list.append(task)
submission = Submission(
work_base='./',
machine = machine,
resources = resources,
task_list = task_list
)
submission.run_submission()
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[54]
run_minimize()
2023-10-10 13:54:06,849 - INFO : info:check_all_finished: False 2023-10-10 13:54:06,851 - INFO : checking all job has been uploaded 2023-10-10 13:54:13,549 - INFO : job: b23cdfa34c2b4e2581180661a9149f257402fcdd submit; job_id is 9122331:job_group_id:11250847
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修改配置文件后，配置文件中携带你的个人账户信息，请注意保密！
通常情况下，该文件不会被分享，你可以运行下面的代码以初始化该配置文件。代码
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[3]
# 运行以下代码以初始化 machine.json 配置文件
import json
import getpass
from monty.serialization import loadfn, dumpfn
file_path = './machine.json'
j = loadfn(file_path)
j['remote_profile']['email'] = 'your email here'
j['remote_profile']['password'] = 'password here'
j['remote_profile']['program_id'] = 11111111
with open(file_path, 'w') as f:
json.dump(j, f, indent=4)
print('初始化配置文件完成！')
--------------------------------------------------------------------------- FileNotFoundError Traceback (most recent call last) Cell In[3], line 8 5 from monty.serialization import loadfn, dumpfn 7 file_path = './machine.json' ----> 8 j = loadfn(file_path) 10 j['remote_profile']['email'] = 'your email here' 11 j['remote_profile']['password'] = 'password here' File /opt/conda/lib/python3.8/site-packages/monty/serialization.py:63, in loadfn(fn, fmt, *args, **kwargs) 61 return msgpack.load(fp, *args, **kwargs) # pylint: disable=E1101 62 else: ---> 63 with zopen(fn, "rt") as fp: 64 if fmt == "yaml": 65 if YAML is None: File /opt/conda/lib/python3.8/site-packages/monty/io.py:45, in zopen(filename, *args, **kwargs) 43 if ext in (".XZ", ".LZMA"): 44 return lzma.open(filename, *args, **kwargs) ---> 45 return open(filename, *args, **kwargs) FileNotFoundError: [Errno 2] No such file or directory: './machine.json'
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至此已经完成从lammps到轨迹中结构优化的过程。
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作图分析
我们提供了400个frame的结构，通过前文的方法获得，在这部分结果的基础上进行作图分析。
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[14]
def get_type_index(type_map, target_element):
for key, value in type_map.items():
if value == target_element:
type_index = int(key[-1]) + 1
return type_index
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[15]
def parse_single(filename: str, target_element: str, type_map:dict):
data = []
type_index = get_type_index(type_map, target_element)
with open(filename, 'r') as file:
lines = file.readlines()
i = 0
while i < len(lines):
line = lines[i].strip()
if line.startswith("ITEM:"):
i += 9
continue
else:
item = line.split()
if int(item[1]) == int(type_index):
data.append(item)
i += 1
length = len(data)
n = length // 2
second_half_data = data[n::]
return second_half_data
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[16]
def plot(target_folders: list, target_element: str, bins: int, type_map: dict):
filename = 'dump.atom_energy'
# output_filename = 'output_data.txt'
data = []
target_energy = []
folders = tqdm(target_folders)
head = [["index", "atom_types", "energy"],]
for folder in folders:
data = parse_single(Path(folder)/filename, target_element, type_map)
head = np.concatenate((head,data),axis=0)
plot_data = list(head[1:,2])
plot_data = [float(data) for data in plot_data]
x_min = float(min(plot_data))
x_max = float(max(plot_data))
plt.hist(plot_data, bins)
xticks = np.linspace(x_min, x_max, 5) # 生成等间距的刻度值
xtick_labels = ['{:.3f}'.format(x) for x in xticks]
plt.xticks(xticks, xtick_labels)
# plt.savefig('aaa.png',dpi=300)
plt.show()
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[18]
# os.chdir('frames')
target_folders = [folder for folder in glob.glob('frames/lmp*') if os.path.isdir(folder)]
len(target_folders)
target_element = 'Bi'
hist_bins = 100
plot(target_folders, target_element, hist_bins, type_map)
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[ ]
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离子迁移
赵钦福
更新于 2024-04-05
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DOAS
赵钦福
更新于 2024-04-05
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