朝花夕拾-重新认识Materials Studio
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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(. . .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=480:10:00NPROCS=`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castepLinux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_POTAl &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_188882:在执行命令： /sbin/chkconfig --add masgateway_control_18883. &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, AccelrysAbstract: 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: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/ export LD_LIBRARY_PATH; OMP_NUM_THREADS=1; export OMP_NUM_THREADS; F_UFMTENDIAN= 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/ 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 -S'$不知道什么意思，有什么影响，谢谢指教~~4. MS手册解读Manipulating filesCASTEP 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 filesCASTEP allows you to save input files, for subsequent manual editing instead of running the job directly.Choose Modules | CASTEP | Calculation from the Materials Studio menu bar. Click the Files... button to open CASTEP Job Files dialog. 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, , 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:Choose Modules | CASTEP | Calculation from the Materials Studio menu bar. Click the Files... button to open CASTEP Job Files dialog. Click the Run Files button. Note. The Run Files button is enabled only if a suitable
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.shNote. 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 share\Resources\Quantum\Castep and copy the required files to the same directory on the server as the rest of the input files.Output filesOnly 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 calculationIt 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
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 informationCASTEP file formatsCASTEP keywordsInstructions for using RunCastep scripts========================================NAME & RunCastep.sh or RunCastep.batDESCRIPTION & 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 formatsThe 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.File typeInput or OutputBrief description.paramInputGeneral input file (text).cellInputStructure input file (text).castepOutputReport on the calculation (text).checkOutputCharge density, wavefunctions, structure, etc. (binary).bandsOutputEigenvalues (text).cst_espOutputElectrostatic potentials (binary)OutputGeometry optimization trajectory data (text).mdOutputMolecular dynamics trajectory data (text).tsOutputTransition state search trajectory data (text).phononOutputPhonon data (text)OutputWeights required to calculate PDOS (binary).cst_omeOutputMatrix elements required to calculate optical properties (binary).elfOutputElectron localization function, ELF (binary).otfgN/AInformation required for generating pseudopotential files on the fly stored on the client (text)
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Copyright &MPI - C++ Examples
C++ Examples
is a directory of C++ programs which
illustrate the use of the Message Passing Interface
for parallel programming.
MPI allows a user to write a program in a familiar language, such as
C, C++, FORTRAN, or Python, and carry out a computation in
parallel on an arbitrary number of cooperating computers.
Overview of MPI
A remarkable feature of MPI is that the user writes
a single program which runs on all the computers.
because each computer is assigned a unique identifying number,
it is possible for different actions to occur on different
machines, even though they run the same program:
if ( I am processor A ) then
add a bunch of numbers
else if ( I am processor B ) then
multipy a matrix times a vector
Another feature of MPI is that the data stored on each
computer is entirely separate from that stored on other computers.
If one computer needs data from another, or wants to send
a particular value to all the other computers, it must
explicitly call the appropriate library routine requesting
a data transfer.
Depending on the library routine called,
it may be necessary for both sender and receiver to be
"on the line" at the same time (which means that one will
probably have to wait for the other to show up), or it is
possible for the sender to send the message to a buffer, for
later delivery, allowing the sender to proceed immediately
to further computation.
Here is a simple example of what a piece of the program would
look like, in which the number X is presumed to have been
computed by processor A and needed by processor B:
if ( I am processor A ) then
call MPI_Send ( X )
else if ( I am processor B ) then
call MPI_Recv ( X )
Often, an MPI program is written so that one computer
supervises the work, creating data, issuing it to the
worker computers, and gathering and printing the results at the
Other models are also possible.
It should be clear that a program using MPI to execute in parallel
will look much different from a corresponding sequential version.
The user must divide the problem data among the different processes,
rewrite the algorithm to divide up work among the processes,
and add explicit calls to transfer values as needed from the
process where a data item "lives" to a process that needs that
A C++ program, subroutine or function that calls any
MPI function, or uses an MPI-defined variable, must include
include "mpi.h"
so that the types of the MPI variables are defined.
You probably compile and link your program with a single command,
g++ myprog.C
Depending on the computer that you are using, you may be able
to compile an MPI program with a similar command, which automatically
locates the include file and the compiled libraries that you will
This command is likely to be:
mpiCC myprog.c
Interactive MPI Runs
Some systems allow users to run an MPI program interactively.
You do this with the mpirun command:
mpirun -np 4 a.out
This command requests that the executable program a.out
be run, right now, using 4 processors.
The mpirun command may be a convenience for beginners,
with very small jobs, but this is not the way to go once you
have a large lengthy program to run!
Also, what actually happens
can vary from machine to machine.
When you ask for 4 processors,
for instance,
in the best case, mpirun automatically finds three other
machines just like the one you are one, copies your program
to them, and starts your program on all four.
in a less good case, there are four processors on your current
machine, so the memory is divided up among them and your program
in a worse case, there are less than four processors available,
so, as necessary, one processor will "time share", and run two
or more of your processes alternately.
The latest versions of MPI no longer support the special C++ MPI bindings,
so the examples given here have reverted to using the C MPI bindings.
Licensing:
The computer code and data files described and made available on this web page
are distributed under
Languages:
MPI examples are available in
Related Data and Programs:
a C++ program which
creates new communicators involving a subset of initial
set of MPI processes in the default communicator MPI_COMM_WORLD.
a C++ program which
solves the 1D Time Dependent Heat Equation using MPI.
a C++ program which
prints out "Hello, world!" using the MPI parallel programming environment.
a C++ library which
contains "stub" MPI routines which allow
a user to compile, load, and possibly run an MPI program on a
serial machine.
a C++ program which
demonstrates how to "multitask", that is, to execute several unrelated
and distinct tasks simultaneously, using MPI for parallel execution.
a C++ program which
computes an approximate solution to the Poisson equation in a rectangle,
and is intended as the starting point for the creation of a parallel version.
a C++ program which
counts the number of primes between 1 and N, using MPI for parallel execution.
C programs which
illustrate the use of the POSIX thread library to carry out
parallel program execution.
a C++ program which
approximates an integral using a quadrature rule, and carries out the
computation in parallel using MPI.
a C++ program which
demonstrates one way to generate the same sequence of random numbers
for both sequential execution and parallel execution under MPI.
a C++ program which
uses the MPI parallel programming environment, and measures the time
necessary to copy a set of data around a ring of processes.
a C++ program which
demonstrates, for a particular circuit, an exhaustive search
for solutions of the circuit satisfiability problem, using MPI to
carry out the calculation in parallel.
a C++ program which
searches integers between A and B for a value J such that F(J) = C,
using MPI for parallel execution.
a C++ library which
implements a simple procedure for smoothly dividing T tasks among
P such a method can be useful in MPI and other parallel
environments, particularly when T is not an exact multiple of P,
and when the processors can be indexed starting from 0 or from 1.
a C++ program which
uses finite differences and MPI to estimate a solution to the
wave equation.
Reference:
William Gropp, Steven Huss-Lederman, Andrew Lumsdaine, Ewing Lusk,
Bill Nitzberg, William Saphir, Marc Snir,
MPI: The Complete Reference,
Volume II: The MPI-2 Extensions,
Second Edition,
MIT Press, 1998,
ISBN13: 978-0-262-57123-4,
LC: QA76.642.M65.
William Gropp, Ewing Lusk, Anthony Skjellum,
Using MPI: Portable Parallel Programming with the
Message-Passing Interface,
Second Edition,
MIT Press, 1999,
LC: QA76.642.G76.
William Gropp, Ewing Lusk, Rajiv Thakur,
Using MPI-2: Advanced Features of the Message-Passing
Interface,
Second Edition,
MIT Press, 1999,
LC: QA76.642.G762.
Stan Openshaw, Ian Turton,
High Performance Computing and the Art of Parallel Programming:
an Introduction for Geographers, Social Scientists, and
Engineers,
Routledge, 2000,
LC: QA76.88.O64.
Peter Pacheco,
Parallel Programming with MPI,
Morgan Kaufman, 1996,
LC: QA76.642.P3.
Sudarshan Raghunathan,
Making a Supercomputer Do What You Want: High Level Tools for
Parallel Programming,
Computing in Science and Engineering,
Volume 8, Number 5, September/October 2006, pages 70-80.
Marc Snir, Steve Otto, Steven Huss-Lederman, David Walker,
Jack Dongarra,
MPI: The Complete Reference,
Volume I: The MPI Core,
Second Edition,
MIT Press, 1998,
ISBN: 0-262-69216-3,
LC: QA76.642.M65.
Scott Vetter, Yukiya Aoyama, Jun Nakano,
RS/600 SP: Practical MPI Programming,
IBM Redbooks, 1999,
Examples and Tests:
BONES passes a vector of real data from one process to
It was used as an example in an introductory MPI workshop.
BUFFON demonstrates how parallel Monte Carlo
processes can set up distinct random number streams.
DAY1 works out exercise #3 assigned after day 1 of a
workshop on MPI.
The instructions were to have process 1 generate some
integers, send them to process 3 which used some of those values to
generate some real numbers which were then sent
back to process 1.
INTERVALS estimates an integral by dividing an interval
into subintervals, and having the servant processes estimate
the integral over each subinterval.
MATVEC computes a matrix-vector product c = A * b,
giving each process a copy of the vector b, and using self-scheduling
to let any process have the next row of A to work on when it is ready.
Arrays are allocated dynamically.
The "math.h" include file
is needed, as is the run-time math library.
MONTE CARLO computes PI by the Monte Carlo method, testing
whether points in the unit square are in the unit circle.
QUADRATURE integrates a function f(x)
SEARCH searches a list of numbers for all
occurrences of a target value.
SUM adds a list of numbers.
TYPE sets up a user-defined datatype, and sends and
receives data in this form.
You can go up one level to .
Last revised on 24 October 2011.