关注：

1） Material studio的功能很强大， 量化大师Pickard and Needs主要使用该软件

2)  MS在linux下如何提交任务

3)  Accerys公司人员来访，期望能向他咨询怎样方便的提交任务和返回处理结果。

RunCastep script runs CASTEP as a standalone program.  

输入文件有哪些(.cell; .param; .uspp.....)?

哪些输出文件必须导入到client中进行分析？ (.castep,.....)

如何进行批处理操作？不同压力下对结构进行优化？

1. 问题与回答：

Dear Xiao-qiu,

Thanks for the email. For easy reading the text of my reply is blue in color, just below your questions.

     (1)  If we get a new license key, do we need also to update the version of Materials Studio on Helios ?

We no need to update the version of Materials Studio to install a new license.

     (2)  If we submit a job to Helios using the Materials Studio installed on our own computers, will the jobs still go to the PBS queue?

Due to some network security issues our computer admin people did not liked the concept of submitting the Materials Studio jobs using Windows Client PCs. Materials Studio has its own PBS queue. We did not tried this option as the admin people felt this process is less secure. Rather what I did was I used to generate input files (a set of files needed to run let say CASTEP) using the client Windows PC and transferred these files manually to Helios. With these input files together a Helios PBS script we can run any Materials Studio job.

  （3） I have just installed the new license. All the modules in Materials Studio can be used well with the Helios PBS jobs script.

Xiao-qiu: below is the CASTEP PBS job submission script:

==================================================================
#!/bin/bash
#PBS -N jobname
##PBS -e pbs.err
##PBS -o pbs.out
#PBS -q workq
#PBS -l nodes=1:ppn=8
#PBS -l walltime=480:10:00

NPROCS=`wc -l $PBS_NODEFILE | awk '{print $1}'`

cd $PBS_O_WORKDIR

/home/pld48/Softwares/Accelrys/MaterialsStudio61/MaterialsStudio6.1/etc/CASTEP/bin/RunCASTEP.sh -np $NPROCS INPUT_FILE_NAME_PATH
===================================================================

1.2  Linux下如何运行materials studio中castep

Linux下Castep程序可以通过命令行的方式来运行，具体的方法是：

(1). 首先在Materials Studio界面下搭建相关模型，并且在Calculation对话框中进行相

关设置；

(2). 完成设置后，请按下Calculation对话框下方的Files按钮，选择Save Files；

(3). 使用Windows文件管理器打开相应的文档，在该目录下能够看到带有以下后缀的文件：.cell、.param，请将此文件拷贝到Linux的MS安装目录下的/etc/CASTEP/bin目录下；

(4). 打开.cell文件，在

%BLOCK SPECIES_POT

Al  Al_00.usp

%ENDBLOCK SPECIES_POT

中可以看到所使用的超软赝势，进入Windows下的<ms安装目录>\share\Resources\Quantum\Castep\Potentials\目录中，找到这些赝势文件，并将其拷贝到Linux的MS安装目录下的/etc/CASTEP/bin目录下

5. 进入Linux系统，选定这些文件，点击右键，在权限选项中修改这些文件的权限为可执行、可读写，并运行以下命令执行相关计算：

cd /home/<CASTEP绝对路径>/bin/  切换路径至RunCASTEP.sh 所在路径

<CASTEP绝对路径>：CASTEP安装的绝对路径，例如/home/msi/ms/CASTEP/

./RunCASTEP.sh -np n 文件名   无需后缀  【那么多输入文件，给那个文件名？basename1    - name of the CASTEP job. Input is read from "basename1".param etc.】

-np n 使用多CPU进行并行计算，如果是单CPU，则不用此注释；如果使用多CPU，则需

要使用，例如使用双CPU，则为 -np 2 （-np是关键词，不能修改）。

注意区分大小写

另外建议程序和输入文件都用绝对路径，这样你无论在哪个路径下都可以运行程序。

LINUX下跑CASTEP是没有XSD文件的，有CELL文件就够了，计算结果放在了CASTEP文件中。把数据拷进WINDOWS这边客户端的时候，只要更新结构就有了最新的XSD文件

没这么复杂，CASTEP-ANALYSIS-STRUCTURES-UPDATE.另外，不论提交作业还是返回数据，LINUX的MS下没有XSD，也没必要有。XSD是WIN下的MS的3D窗口中的文件，LINUX没有3D视窗的，呵呵

用更新出来的结果继续分析即可

2. 朝花夕拾

gwusers -add ID 添加用户
gwusers -remove ID 删除用户
gwusers -updated ID 修改ID的密码
gwusers -list 列出所有用户

重启MS网关

msgateway_control_18888 restart

由于之前安装的时候没有将Gateway注册为自动启动服务的话，可执行下面的命令：
1： cp /home/hope/Accelrys/MaterialStudio55/etc/Gateway/masgateway_control_1888  /etc/rc.d/init.d/msgateway_control_18888
2:在执行命令： /sbin/chkconfig --add masgateway_control_1888

3.  Dr. George Fitzgerald简介

Dr. George Fitzgerald discusses the benefits of the Materials studio Collection.

Determination of Zeolite-Confined Nano-titania Catalysis: A Combined Experimental and DFT Study
George Fitzgerald, Accelrys

Abstract: Micro- and mesoporous titanium silicates have been explored in large numbers as potential catalysts for various green oxidation processes. Still, the versatility of the first commercially successful MFI structured TS-1 stands out from this family. A series of thorough studies prove that the unique catalytic activity and selectivity of TS-1 is associated with its hydrophobicity and its isolated tetrahedral Ti4+ ions which are substituted into the silicalite lattice. Such ions are most frequently characterized by a UV band at > 47000 cm-1 (< 213 nm). It has been repeatedly noted, however, that MFI-structured titanium silicates with intense UV bands near 45000 cm-1 (222 nm) can be even more active and selective oxidation catalysts for certain processes.

To learn more about the Materials Studio Collection visit:http://accelrys.com/products/pipeline...

4.  Linux下提交任务的网络问答

在Linux上的MS试算Na的态密度，先在win的MS下建模，设置Catep，calculation的参数，然后保存文件。

将*.cell，*.param，*.usp一同放进Linux下的castep的bin文件夹中，运行，出结果。

然后我将Na.castep，Na_BandStr.castep，Na_DOS.castep导出，放到win下的workplace中，打开castep的Analysis，但是却显示no results files available，请问是怎样的情况？

今天我又试了一下，把win下生成的文件全部导入Linux，计算。再把计算得到的所有文件，包括*.castep，*.param，*.cell等等，全部导到win下的workplace，居然奇迹般的成功了，不知道为什么。

还有就是计算虽然成功了，但是却出现了以下的信息：

$ ./RunCASTEP.sh Na Na_DOS

/home/ybl/Accelrys/MaterialsStudio50/share/bin/runMSserver.sh: eval: line 3: syntax error near unexpected token `('
/home/ybl/Accelrys/MaterialsStudio50/share/bin/runMSserver.sh: eval: line 3: `LD_LIBRARY_PATH=/home/ybl/Accelrys/MaterialsStudio50//lib:/home/ybl/Accelrys/MaterialsStudio50//lib/32:/opt/intel/cce/10.1.018/lib:/opt/intel/fce/10.1.018/lib; export LD_LIBRARY_PATH; OMP_NUM_THREADS=1; export OMP_NUM_THREADS; F_UFMTENDIAN=big; export F_UFMTENDIAN; MPI_VER=mpiexec_saammsg.zju.edu: cannot connect to local mpd (/tmp/mpd2.console_ybl); possible causes:; export MPIVER; MPI_ROOT=/usr/local; export MPI_ROOT; MPI_COMMAND="/usr/local/bin/mpirun -e MPI_REMSH=/usr/bin/ssh -prot -f APPFILE "; export MPI_COMMAND; GATEWAY_TMP="/home/ybl/tmp"; export GATEWAY_TMP; ulimit -Ss unlimited;'

$

不知道什么意思，有什么影响，谢谢指教~~

4. MS手册解读

Manipulating files

CASTEP is a file-based application which means that all input information is provided in various ASCII text files and the output is delivered in a mixture of text and binary files. This section describes some file handling issues which may arise, especially when the CASTEP server is run in a standalone mode and not via a gateway.

Input files

CASTEP allows you to save input files, for subsequent manual editing instead of running the job directly.

To save input files

1. Choose Modules | CASTEP | Calculation from the Materials Studio menu bar.

2. Click the Files... button to open CASTEP Job Files dialog.

3. Click the Save Files button.

Note. The Save Files button is enabled only if a suitable 3D model document is active.

Only one input file, .param, is displayed in the Project Explorer. This file contains the parameters specified using the CASTEP interface. However, it also contains a few parameters that allow you to access functionality which is not supported though the interface. The other input files are hidden, since they are unlikely to be edited manually.

Input files can be run on a server after they have been edited:

To run CASTEP using an existing set of input files

1. Choose Modules | CASTEP | Calculation from the Materials Studio menu bar.

2. Click the Files... button to open CASTEP Job Files dialog.

3. Click the Run Files button.

Note. The Run Files button is enabled only if a suitable .param file is active.

If your server does not support the gateway protocol, you may have to run CASTEP in standalone mode using the RunCASTEP.sh or RunCASTEP.bat files provided with the installation.

In such circumstances it is necessary to copy all the input files from the Materials Studio Project folder to the appropriate directory on the server machine. The scripts required for standalone execution are provided with accompanying RunCASTEP.Readme files that explain, in detail, how to use them. Alternatively, you can obtain help by typing one of the following:

RunCASTEP.sh -hRunCASTEP.sh

Note. The Materials Studio Project folder does not contain the pseudopotential files required to run a job. When transferring input files to the server, you must therefore determine which pseudopotential files are required by examining the .cell file. Then you must locate those potential files in Materials Studio installation, typically in a sub-directory called shareResourcesQuantumCastep and copy the required files to the same directory on the server as the rest of the input files.

Output files

Only one output file, .castep, is displayed in the Project Explorer. 

   However, there are many more files created during a CASTEP run. These are hidden by Materials Studio. All of these output files are placed in the correct Materials Studio Project folder automatically, when the job is run using the Gateway. However, if CASTEP is run in standalone mode, the output files must be copied manually from the server to the appropriate Project folder.

Some output files can be quite large. If these files are not likely to be required to restart the job, then it is recommended that you delete or archive them periodically.

Restarting a CASTEP calculation

It is not possible to restart a completed CASTEP job automatically via the interface. However, there are circumstances in which you may wish to do this, for example, if you are running a geometry optimization which does not converge in the given number of steps, or a you wish to continue your calculation with manually modified runtime parameters. To restart such jobs you should edit .param file and add the CONTINUATION keyword to the file.

Note. Any additional changes to this file may make it impossible to restart the CASTEP job successfully.

Tip. It is possible to remove everything from .param and leave only the CONTINUATION line. This will ensure that all of the settings remain exactly the same as those from the previous run.

Note. In order to restart a job, the output files from the previous run must be present in the Project folder. This check and the subsequent transfer of the files to the server happens automatically whenever CASTEP is used to run an existing file set or to calculate additional properties.

Further information

CASTEP file formats
CASTEP keywords

Instructions for using RunCastep scripts

========================================

NAME

  RunCastep.sh or RunCastep.bat

DESCRIPTION

  RunCastep script runs CASTEP as a standalone program.

  RunCastep.sh is provided for Linux servers, while

  RunCastep.bat is provided for Windows servers.

  Typical usage:

      RunCastep.sh [-h] [ -q <queue name> ]  [-np <number of cores>] <basename1> [ basename2 basename3 basename4 ... ] (Linux)

  or

      RunCastep [-h] [-np <number of cores>] <basename1> [ basename2 basename3 basename4 ... ] (Windows)

RUN OPTIONS

    -h        - displays the help text

    -np       - run in parallel on "number of cores".

                One core is used when the -np option is missing.

    -q <queue name>   - submit the job to the required queue. Gateway

                has to be configured to use this queuing system.

ARGUMENTS

  basename1    - name of the CASTEP job. Input is read from "basename1".param etc.,

                and output is written to "basename1".castep

  basename2, basename3, .. Additional calculations can be started upon successful completion of the first one, as continuation runs. input check file for each subsequent calculation   is copied from the output from the previous run.

【类似于批处理，bat，完成第一个输入文件的计算后，开始第二个DOS、第三个band的后续计算？】

5. CASTEP的文件格式解读

CASTEP file formats

The CASTEP server program is a file-based application. It requires input files and produces a number of output files. The precise number and type of output files produced depends on the details of the CASTEP job being performed.

The table below summarizes information on the format and purpose of all the major file types, and provides links to further information.

     删除、卸载不掉  Material studio2017，重新安装一次后，安装成功，但网关出现问题

且在控制面板->管理工具->服务  找不到MaterialsStudioGateway，此时，重新在安装源文件中安装

BIOVIA Materials Studio Gateway Service (i686)

问题解决！！！

“从控制面板->管理工具->服务，然后查看MaterialsStudioGateway(18888)的状态，看一下gateway是否已启动，若停止，右键启动gateway，建议大家右键选择属性，修改启动类型为“自动”
如果没有找到MaterialsStudioGateway(18888)，可能是因为360的云查杀把gateway列为可疑进程，添加进信任列表，重启应该就可以了”

BIOVIA Materials Studio Gateway Service (i686)

工程师将为您介绍Materials Studio 2017 R2的新功能，并与您深入交流、探讨它们的最新应用及前景，同时在线解答您的疑问。
     

http://www.neotrident.com/news/detail.aspx?id=1062

相较于之前版本，Materials Studio 2017 R2增加了更多令人瞩目的新功能，研究领域进一步扩展，计算效率和计算精度进一步提升。其主要新功能包括：

■ 加入研究化学反应动力学的新模块Cantera；
■  CASTEP计算Raman光谱的效率大幅提升；
■  CASTEP中支持自定义构建新的交换相关泛函；
■  CASTEP中OTFG Norm-conserving 赝势覆盖镧系锕系元素，提高稀土、重金属元素及相关体系的结构和性质计算精度
■  CASTEP支持硬度计算功能；
■  CASTEP支持计算电子顺磁共振（EPR）的g-tensor；
■  DMol³新增泛函Hartree-Fock；
■  DMol³支持硬度计算功能；
■  DFTB+添加多个新的slater-koster库文件；
■  DFTB+支持计算力学性质，得到弹性常数矩阵、体模量，剪切模量，杨氏模量等力学性质；
■  ONETEP增加了隐性溶剂化模型，高效计算大体系在溶液环境下的结构和性质；
■  GULP增加适合研究锂电池的新力场ReaxFF Li；
■  Visualizer中快速调整结构的功能按钮clean，扩展至周期性结构；
■  MS2017 R2结合Pipeline Pliot可直接计算合金的与温度相关的力学性质；合金的热导；聚合物的玻璃化转变温度；聚合物的交联结构；聚合物的机械性质；

（注：Pipeline Pliot是美国Biovia公司旗下的流程定制和信息整合的科学平台，在优化研究创新周期、提高工作效率减少研究经费方面发挥巨大作用。）