Dalton

To use, add the dalton module to add it to your environment. You give this command to see how to load Dalton and its prerequisites:
使用时，将 dalton 模块添加到您的环境中。您可以输入此命令以查看如何加载 Dalton 及其先决条件：

ml spider dalton

Notes  注释

• HPC2N has compiled the program with GCC compilers and Intel MPI (impi).
  HPC2N 已使用 GCC 编译器和 Intel MPI（impi）编译了该程序。
• This is an OpenMP + MPI hybrid build.
  这是一个 OpenMP + MPI 混合构建。
• Dalton provides a few environment variables that refers to various directories, please use them, if needed, and not hard coded pathnames as this will make your life easier when Dalton gets upgraded.
  Dalton 提供了一些环境变量，指向不同的目录，如有需要，请使用这些变量，而不要硬编码路径名，这样在 Dalton 升级时会简化您的工作。

You can find most of the environment variables with
您可以找到大多数环境变量

dalton -h

while a few (like path to the install directory) are found with
而少数（如安装目录的路径）则可通过

env | grep -i dalton

NOTE: that DALTON_TMPDIR needs to be defined by the userr.
注意：DALTON_TMPDIR 需由用户定义。

DALTON 道尔顿

There are several options to the script, which can be viewed by typing dalton -h or just dalton. Some of the more important ones include:
脚本有多个选项，可通过输入 dalton -h 或仅输入 dalton 来查看。其中一些较为重要的选项包括：

• -b directory Prepend this directory to the list of directories where the program should look for basis sets. Needed in case you want to use local modifications of a given basis. The job directory and the basis set library will always be included in the basis set directory list (in that search order).
  -b 目录 将此目录添加到程序查找基组的目录列表前端。当你希望使用某个基组的本地修改版本时，此选项是必要的。作业目录和基组库始终会被包含在基组目录列表中（按此搜索顺序）。
• -f dal_mol[_pot] extract dal_mol[_pot].tar.gz archive from WRKDIR into DALTON_TMPDIR before calculation starts
  -f 在计算开始前，将 dal_mol[_pot]提取的 dal_mol[_pot].tar.gz 存档从 WRKDIR 解压至 DALTON_TMPDIR
• -mb mem set dalton max usable work memory to mem Megabytes.
  -mb mem 将达尔顿最大可用工作内存设置为 mem 兆字节。
• -N num Use num MPI processes
  -N num 使用 num 个 MPI 进程
• -o filename Redirect the output normally printed in the DALTON.OUT file in the temporary directory to the file “filename” in the WRKDIR directory. On a computer system with distributed scratch disk but a commonly mounted home directory, this allows you to follow the calculation without having to log into the compute nodes.
  -o 文件名 将通常打印在临时目录中 DALTON.OUT 文件的输出重定向到 WRKDIR 目录中的“文件名”。在具有分布式临时磁盘但共享挂载主目录的计算机系统上，这使您无需登录计算节点即可跟踪计算进度。
• -w wrkdir Change the working directory to “wrkdir”, that is, change the directory in which the program searches for input files and places the DALTON.OUT file to “wrkdir”.
  -w wrkdir 将工作目录更改为“wrkdir”，即更改程序在其中搜索输入文件并将 DALTON.OUT 文件放置的目录为“wrkdir”。

Serial 串行

To run the program, load the module, then use this command:
要运行程序，请加载模块，然后使用以下命令：

dalton [options] dalinp{.dal} [molinp{.mol} [potinp{.pot}]]

to run using the shell script dalton, which is the recommended way of running. 
使用 shell 脚本 dalton 运行，这是推荐的运行方式。

Example: Say you have the input file myinput.dal, and the molecule input molinput.mol, you would type this to run
示例：假设您有输入文件 myinput.dal 和分子输入文件 molinput.mol，您可以输入以下命令来运行

dalton myinput molinput

When the job is finished, the output is copied back as myinput_molinput.out. In addition, the program will copy back a file named myinput_nmolinput.tar.gz. This file contains, in tar'ed and gzip'ed form, a number of useful intergace and post-processing files which may be needed for post-DALTON programs, or for restarting calculations.
任务完成后，输出结果会被复制回名为 myinput_molinput.out 的文件。此外，程序还会复制回一个名为 myinput_nmolinput.tar.gz 的文件。该文件以 tar 和 gzip 格式包含了许多有用的接口和后处理文件，这些文件可能用于 DALTON 程序的后处理，或用于重新启动计算。

Note If it is anything but a short program, you should ALWAYS run it as a batch script.
注意 如果程序不是简短的，您应始终将其作为批处理脚本运行。

Example, batch script 示例，批处理脚本

#!/bin/bash
# Change to your own project id
#SBATCH -A SNICXXXX-YY-ZZ
# Asking for 1 task
#SBATCH -n 1
# Asking for 30 minutes run time 
#SBATCH --time=00:30:00

#Load the Dalton moduleand its prerequisites
ml GCC/6.2.0-2.27  
ml impi/2017.1.132
ml DALTON/2016.2

dalton [options] dalinp{.dal} [molinp{.mol} [potinp{.pot}]]

Submit the script with
提交脚本

sbatch <jobscript>

MPI 消息传递接口

Note srun and mpirun both works
注意，srun 和 mpirun 均可使用

Example script 示例脚本

Assuming you have an input file dalton_in.dal (if you have a molecule input file, add that one as well)
假设你有一个输入文件 dalton_in.dal（如果你有一个分子输入文件，也请一并添加）

Change n and DALTON_NUM_MPI_PROCS accordingly.
相应地调整 n 和 DALTON_NUM_MPI_PROCS。

#!/bin/bash
#SBATCH -J DALTON-test
#SBATCH -A SNICXXXX-YY-ZZ
#SBATCH -n 8
#SBATCH --time=10:30:00

#Load the Dalton moduleand its prerequisites
ml GCC/6.2.0-2.27 
ml impi/2017.1.132
ml DALTON/2016.2 

#You can call the tmp dir anything
export DALTON_TMPDIR=<what-you-want>

export DALTON_NUM_MPI_PROCS=8

dalton -N 8 -noappend -t `pwd`/<any tmpdir> [options] dalinp{.dal} [molinp{.mol} [potinp{.pot}]

Submit the script with
提交脚本

sbatch <jobscript>