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# uincode version, keep ü
pinyin = ['a', 'o', 'e', 'er', 'ai', 'ao', 'ou', 'an', 'en', 'ang', 'eng', 'yi', 'ya', 'yao', 'ye', 'you', 'yan', 'yin', 'yang', 'ying', 'yong', 'wu', 'wa', 'wo', 'wai', 'wei', 'wan', 'wen', 'wang', 'weng', 'yu', 'yue', 'yuan', 'yun', 'ba', 'bo', 'bai', 'bei', 'bao', 'ban', 'ben', 'bang', 'beng', 'bi', 'biao', 'bie', 'bian', 'bin', 'bing', 'bu', 'pa', 'po', 'pai', 'pei', 'pao', 'pou', 'pan', 'pen', 'pang', 'peng', 'pi', 'piao', 'pie', 'pian', 'pin', 'ping', 'pu', 'ma', 'mo', 'me', 'mai', 'mei', 'mao', 'mou', 'man', 'men', 'mang', 'meng', 'mi', 'miao', 'mie', 'miu', 'mian', 'min', 'ming', 'mu', 'fa', 'fo', 'fei', 'fou', 'fan', 'fen', 'fang', 'feng', 'fu', 'da', 'de', 'dai', 'dei', 'dao', 'dou', 'dan', 'den', 'dang', 'deng', 'dong', 'di', 'diao', 'die', 'diu', 'dian', 'ding', 'du', 'duo', 'dui', 'duan', 'dun', 'ta', 'te', 'tai', 'tei', 'tao', 'tou', 'tan', 'tang', 'teng', 'tong', 'ti', 'tiao', 'tie', 'tian', 'ting', 'tu', 'tuo', 'tui', 'tuan', 'tun', 'na', 'ne', 'nai', 'nei', 'nao', 'n

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#!/bin/bash

# This script runs a command and kills it if there is no output for a certain time

# Define the command to run and the output file
COMMAND="lmp_mpi -in input.lmp"
OUTPUT_FILE="lammps.log"

# Define the timeout value in seconds
TIMEOUT=60

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Note

1. The latest OneAPI that supports CentOS 7 is 2022.3.1
2. Use lscpu to check the arch of CPU.

Build

# download source code
wget https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/2022.11.001/elpa-2022.11.001.tar.gz
tar -xvf elpa-2022.11.001.tar.gz

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Note

1. use mkl's fftw build

Build

wget https://www.cp2k.org/static/downloads/plumed-src-2.8.2.tgz --no-check-certificate
tar -xvf plumed-src-2.8.2.tgz
cd plumed-2.8.2

./configure FC=mpiifort CC=mpiicc CXX=mpiicpc CXXFLAGS="-O3 -mtune=icelake-server" --enable-mpi \

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Note

1. Use autoconfig when <= 2.6, and cmake > 2.7
2. Patch fortran Makefile
3. Use CP2K's toolchain as reference: https://github.com/cp2k/cp2k/blob/master/tools/toolchain/scripts/stage3/install_libint.sh

Build

# download
wget https://www.cp2k.org/static/downloads/libint-v2.6.0-cp2k-lmax-5.tgz --no-check-certificate
tar -xvf libint-v2.6.0-cp2k-lmax-5.tgz

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Installation

https://medium.com/@anarmammadli/how-to-install-openpbs-20-0-1-on-ubuntu-b1cc62cfb0ec

Issue

• pbs_server doesn't run
• postgresql doesn't run
• Similar issues
  • https://community.openpbs.org/t/can-not-start-pbs-server-all-other-jobs-are-running/3048

Fix

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Improve Download Speed

Use BBR congestion control

Ubuntu

Update /etc/sysctl.conf

net.core.default_qdisc=fq
net.ipv4.tcp_congestion_control=bbr

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import numpy as np

def sample_data_frame(path: str, frame_lines: int, nsample: int, out_path: str,
                      total_lines: int = -1, encoding='utf-8',
                      write_buffer_size=10 * 1024 * 1024,
                      ):
    """
    Sample data frame from file randomly

    A data file is composed of multiple frames, each frame has fixed number of lines.

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POC: use typescript as container of structured data for LLM

Prompt

The following is Typescript code that describe the data structure of reactions. The reactions to be exported are not implement yet.

/**
 * This is a typescript prompt file to export reactions data.
 */

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Build DeepMD-kit + LAMMPS in a conda envrionment

Steps

Create conda environment

conda create -p 2.2.5/gpu python==3.10.13  tensorflow=2.10.*=gpu*

Note:

• Install tensorflow with conda instead of pip will have less trouble (for example, conda will install the right cudnn for you)