Using Globus

• Go to htpps://www.globus.org/ 
• Click on Log in 
• Select organization (West Virginia University) 
• You will be redirected to your mix account in order to log-in.
• A new screen will pop-up. Click on endpoint and type wvu#hpcdtn (both right and left panels)
• The pre-selected path is /gpfs/. For datadepot use /depot/
• You can transfer files from hpc to datadepot storage or other public available endpoints

SHARING FILES? 

• Connect online to globus
• Select endpoint and set path to /depot/ 
• Go to the directory you want to share and select the specific folder.
• Click on share (you will need to have permission from whomever is operating your endpoint.

• A new screen will pop-up:

• Host path is the name of the folder you selected for sharing (change it by clicking on browse - required )
• Share display name is the name of the shared folder you want others to see (required).
• If you want add a description and some keywords for the people you're sharing the folder.
• If all goes well, a new screen will pop-up:

• The path will reflect your choice of shared folder. (/) means you want to share all subfolders that exist inside the folder you selected for sharing. If you want, click on browse and select a specific subfolder.
• Select if you want to make your shared folder available to: Single user,group,public,all globus users.
• For single user you will have to type their e-mails. For groups you will have to type in the group name. Click on add.
• Select if the users you're sharing to will have readable and writable permissions.
• Click on add permission.
• Your folder is shared!

UPLOADING FILES FROM YOUR PC? MAKE IT AN ENDPOINT!

• If you want to transfer files from your campus storage platform to your personal computer/laptop you will have to connect your PC to globus (endpoint).
• Info for MAC OS X and how to make your Mac an endpoint: https://docs.globus.org/how-to/globus-connect-personal-mac/
• Info for Linux OS and how to make your linux machine an endpoint: https://docs.globus.org/how-to/globus-connect-personal-linux/
• The globus personal connect application should always be running if you want your PC to be an endpoint and move files from storage platforms to your PC and vice-versa!

installatio of OOF2

Details of installation for different system can be found here:

https://www.ctcms.nist.gov/oof/oof2/prerequisites.html


For Mac:

Two commonly used package managers on OS X are MacPorts and fink. Both should work. If you have neither installed already, it will be easier to use MacPorts.
Neither fink nor MacPorts will install the version of swig that OOF2 2.1.11 or earlier requires. See Installing SWIG, below, if you need it to install it. If you aren't building your own OOF2 extensions, and if you use --skip-swig when building OOF2, you don't need to install SWIG. If you're using OOF2 2.1.12 or later, you don't need to install SWIG.
To run OOF2, you will need to install X11, which Apple no longer supplies, but which can be downloaded from Mac OS Forge. It's slightly easier to get X11 from MacPorts, if you're using MacPorts.
When the instructions below tell you to type a command, type it in a Terminal window. You can copy and paste the lines from this page.

Macintosh OS X with MacPorts

1. Install MacPorts from http://www.macports.org/install.php, following their instructions. It's easiest to use the .pkg installer. If you get error messages when running "sudo port -v selfupdate", open a new Terminal window and try again.
   
2. Type these commands. Some of them may take a while to run, depending on whether or not your computer already has some of the dependencies installed.
   

         sudo port install pkgconfig
         sudo port install xorg-server
         sudo port install py27-numpy -atlas 
         sudo port install py27-pygtk
         sudo port select python python27
         sudo port install libgnomecanvas
         sudo port install google-perftools
   

   Note: If you prefer to use Python 2.5 or Python 2.6 instead of Python 2.7, replace the '27's in the commands with '25's or '26's.
   Note: The numpy line is there to tell MacPorts to install the version of numpy that doesn't use atlas. Atlas is a substitute for the blas libraries distributed with OS X, and takes a very very long time to install. If you either already have atlas installed or don't mind waiting for it to build, you can skip the py27-numpy installation step completely. In that case, the default, atlas-using, version of numpy will be installed automatically when you install py27-gtk.
   
3. The version of ImageMagick provide with older versions of MacPorts on older versions of OS X was incompatible with OOF2. You really should update your system, but if for some reason you're using OS X 10.6 or earlier, do this:
   
   1. Type these commands:
      

            mkdir -p ~/ports/graphics/ImageMagick
            cp /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/graphics/ImageMagick/Portfile \
                   ~/ports/graphics/ImageMagick
            cd ~/ports
            sudo portindex 

      Note: If you're using MacPorts version earlier than 2.0.4, replace the path in the second line with

      /opt/local/var/macports/sources/rsync.macports.org/release/ports/graphics/ImageMagick/Portfile

      
      
   2. Using any text editor (not a word processor!) edit ~/ports/graphics/ImageMagick/Portfile, appending these three lines:
      

            variant no_openmp description {Disable OpenMP} {
               configure.args-append   --disable-openmp
            } 

      
      
   3. Type this command:
      

            sudo port install ImageMagick +no_openmp

      
      
   
   
4. If you're using OS X 10.7 or later, type this commmand:
   

         sudo port install ImageMagick

   
   
5. If you're using Python 2.6 or 2.7, and you get this message when trying to build OOF2
   

     Can't find pygtk-2.0! Version 2.6 or later required

   then you need to work around a MacPorts bug by setting the PKG_CONFIG_PATH environment variable to /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/pkgconfig before building. Replace the 2.7 with 2.6 if you're using python 2.6. For example, if you're using the bash shell, type

     export PKG_CONFIG_PATH=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/pkgconfig
   

   You can put the line in your .profile file in your home directory to make the change permanent, if you find yourself rebuilding OOF2 frequently for some reason.
   

Macintosh OS X with fink

We haven't used fink recently, so these instructions may be out of date. Please let us know if they are.

1. Install Xcode from Mac OS Forge.
2. Install fink, by going to http://www.finkproject.org/download/srcdist.php and following the instructions there. If the bootstrap script asks you to choose a mode and you're on a 64-bit capable Mac, choose 64bit-only.
   If you already have fink installed in 32 bit mode, you don't need to reinstall everything just to change to 64 bit mode. You may need to force ImageMagick to build in 32 bit mode in step 5.
   
3. Enable the "unstable" fink packages.
   (a) Run "sudo fink configure", and answer "y" when asked about the unstable tree.
   (b) Run these commands:
   

          sudo fink selfupdate
          sudo fink selfupdate-rsync
          sudo fink index -f
          sudo fink scanpackages 

   
   
4. Use fink to install the libraries that ImageMagick will require by typing these commands:
   

          sudo fink install libjpeg
          sudo fink install lcms
          sudo fink install libpng14-shlibs 

   
   
5. Build ImageMagick without OpenMP, which is incompatible with OOF2 on OS X. (NOTE! It may not be necessary to do this step. We haven't tried building OOF2 with fink using a recent version of either fink or OS X. You could try installing ImageMagick with fink by typing sudo fink install imagemagick7-dev and skipping this step. You'll know if it worked if you can successfully load and display an image in OOF2.)
   
   • Go to http://www.imagemagick.org. Click "Download". Choose a site to download it from. Download the file with the latest version number and the .bz2 suffix.
     
   • Uncompress and untar the package:
     

            tar -xjf ImageMagick-<version>.tar.bz2
     

     where <version> is 6.6.7-10 or something like that.
     
   • Run these commands:
     

             cd ImageMagick-<version>
             ./configure LDFLAGS=-L/sw/lib CPPFLAGS=-I/sw/include --disable-openmp

     
     
   • Check the output from the configure command. If it says that support for some image format that you need hasn't been included, you probably need to go back to step 4 and install more packages from fink. The "Packages" link on the fink website will let you search for the package name.
     (If the output indicates no support for formats for which you are sure the libraries have been installed, and if it's possible that you have a 32 bit version of fink, try reconfiguring ImageMagick with CPPFLAGS="-I/sw/include -m32" (including the quotation marks!) instead of CPPFLAGS=-I/sw/include. The OOF developers haven't tested this. Please let us know if it works or not.)
     
   • Build and install ImageMagick by running these commands:
     

             make
             sudo make install 

     
     
   
   
6. Use fink to install the other packages that OOF2 requires by typing these commands, some of which may take a while to run:

          sudo fink install python 
          sudo fink install pygtk2-gtk-py27-dev
          sudo fink install libgnomecanvas2-dev
   

Installing SWIG on OS X

NOTE: for OOF2 version 2.1.12 and later, it is no longer necessary to install swig.
The only obstacle to installing swig 1.1 build 883 on a Mac is that the Mac's file system is not case sensitive, and swig's build procedure tries to make a subdirectory named SWIG and a file named swig in the same directory. You can install swig on a case-insensitive disk, you just can't build it there. There are at least three ways to get around this inconvenience:

• Build swig on a disk with a different type of file system. Format the disk with the Unix File System, using Apple's Disk Utility application.
• Use Disk Utility to create a disk image, formatted with the Unix File System. After you open the disk image, it will act just like a real disk, and you can use it to build swig.
• Hack the swig source files so that it doesn't have a case problem. If you don't mind a second hand swig, you can download our modified version here:
  • swig1.1-883-mac.tar.gz

NetBSD

OOF2 version 2.0.5 and 2.1.1 or later will work on NetBSD. OOF2 version 2.1.0 does not work. These commands were sufficient to install OOF2 on a 32-bit version of NetBSD 5.1. Execute them from a root account. echo /usr/X11R7/lib >> /etc/ld.so.conf pkg_add pkg-config pkg_add py-gobject-shared pkg_add py26-gtk2 pkg_add libgnomecanvas pkg_add ImageMagick pkg_add freetype2 pkg_add fontconfig The first line may not be necessary if you set LD_LIBRARY_PATH. Installing the prerequisites will provide a program called "python2.6" in /usr/pkg/bin. You can use this to build oof2, but you'll have to invoke it explicitly: python2.6 setup.py build --skip-swig --library-dirs=/usr/pkg/lib install You could also create an alias or symbolic link called "python" that points to /usr/pkg/bin/python2.6, and then you can follow the instructions in README.md without change.

---

Installing Anaconda and Pymks

Go to https://www.continuum.io/downloads and click on your OS distribution (Mac,Linux,Windows).

For MacOS:

Download the graphical installer for Python 2.7 and install anaconda.

For Linux:

Download the Python 2.7 installer.

Open a terminal and type
cd ~/path_of_downloaded_anaconda_file/
bash Anaconda    (and press the tab key to get the full name)

The final command will run the installation and you're going to be asked a series of questions.
In general, Anaconda will be installed in /home/your_username/anaconda2.

If you want to install it somewhere else you will need to give a full path like: /home/your_username/Python_tools/anaconda2

For all other questions type yes (that is critical for smooth installation and easy use of Anaconda)

After you've installed Anaconda follow the instruction for PyMKS:

MacOS and Linux:

Open a terminal and type:

conda --add-channels pymks
pip install pymks
conda install vtk
pip install mayavi

With these 4 commands you have full functionality of Pymks in Jupyter-notebook using:
import pymks

If you want to run the jupyter notebook you can type in terminal jupyter-notebook, or anaconda-navigator and you can see the full set of tools installed with Anaconda.

MacOS users can open the the Anaconda Navigator in Applications and run Jupyter Notebook from there.

Accessing iLabs

1.    The iLab system for accessing WVU core facilities is now operational.  The main page can be found here:
https://wvu.corefacilities.org <http://wvu.corefacilities.org>

. Avoid using Internet Explorer to access this page.  Chrome or Firefox work better than IE.

2.    User manuals will be posted on the HSC Core Facilities website as soon as possible:

http://www.hsc.wvu.edu/resoff/research/shared-research-resources/

.  Contact individual core directors for additional help accessing core services.

3.    PIs or their designates must approve their staff before they can log in as users in iLab. Follow the instructions below.
4.    If you are a department administrator and need access to a specific department/PI for financial purposes, please email Melissa McDilda at mmcdilda@hsc.wvu.edu <mailto:mmcdilda@hsc.wvu.edu> with the details.


*NOTE: The PI of a sponsored award has the primary responsibility to ensure that all spending on his/her sponsored award(s) meets the award terms and is relevant and necessary to the project purpose, reasonable in amount, and in compliance with all laws, regulations, University policies, and sponsor guidelines.*

*Account Approval for Your Current Users**
*
Whenever you have a new lab member, ask that person to:
1.    Log in to the main WVU iLab page at

http://wvu.corefacilities.org

.
2.    Select “Internal WVU user”.
3.    Enter the WVU ID and password.
4.    Complete the prompts.
You will receive a notice from iLab (no_reply@iLabsolutions.com <mailto:no_reply@iLabsolutions.com>) that a new user is requesting to join your lab. Follow the instructions in the email.

If you would prefer to delegate these notifications/approvals to a financial manager, please email Melissa McDilda at mmcdilda@hsc.wvu.edu <mailto:mmcdilda@hsc.wvu.edu> with your financial manager’s name & email. Please cc: the core manager, too.


1.    Click on the link in the email to log in.
2.    Once logged in, click on the “my labs” link in the left navigation menu.
3.    To approve lab membership requests, select the “Membership Requests & POETA/GL(s)” tab. New membership requests will show at the top of this page. Click “Approve” to accept a member into your lab or “Reject” to not accept.
4.    To assign funding string(s) (POETA/GL(s)) to a member of your lab, find the member in the above list where it says “Manage POETA/GL(s)”. Select the checkbox(es) to the right of their name for the POETA/GL(s)(s) you want to assign to them.
5.    Set the auto-approval amount if you do not want to approve service requests below a certain dollar amount. To do this, select the “Members” panel and enter a dollar amount in the “Auto Pre-Approval” amount and click “save settings”.


*Additional Help*

More detailed instructions are available in iLab by using the “HELP” link in the upper right corner of the website or by navigating to http://help.ilab.agilent.com.

On the Help page, select “Core Facility Management” then select scroll over and click on the “Lab Administrators” section.
For any questions not addressed on the Help site, click on the “HELP” link in the upper right hand corner and submit a ticket or contact: ilab-support@agilent.com <mailto:ilab-support@agilent.com>.

Summer HPC HandsOn

A 3 day long program on learning some details to work on HPC cluster just held in 12-15 June this year. Several topics were discussed and solved throughout this summer program. As I registered for this program I got the opportunity to attend this seminar and here I am giving the two important link which covers almost everything that is taught in this Summer HPC Hands On program. :)

https://wvuhpc.github.io/HandsOnHPC/


https://github.com/WVUHPC/SummerHandsOn

Sending Data Files

If you are sending large or any data file:
1) Please save and import them on to your Google Drive.
2) Please zip the file.
3) Left click and go to sharable link and turn on this feature.
4) Copy and paste the link in to an email and let the sender know what it is.

This process will allow you to backup your data on the Google Drive as well as manage the data more easily when it comes to sending data as you are sending a link and not an attachment that is >25MB. Thank you and please use this method when you are sending data to anyone.

Spring MRS-2017 Notes

Hakan

Hakan will serve as a judge in the Graduate Student Awards Committee with Prof. Kiran Solanki (ASU), Dr. Hua Zhou (Argonne National Laboratory).

Talk Details:

Session: CM5.12: Plasticity
Session Chairs: Marc Legros, Reiner Moenig
Time: April 20th 2017- 4PM
Title: Using nanoindentation as a mechanical spectroscopy tool- investigating incipient plasticity using in-situ 4-pt bend stage



Hengxu

Talk Details:

SESSION CM6.3: Discrete Dislocation Dynamics

Session Chairs: Wei Cai and Yao Shen

Time: 4:30 PM, April 18, 2017

 Title:  2D Discrete Dislocation Dynamics Simulations of Nanoindentation with tensile pre-stress:  Can we probe ‘mobile’ dislocations through nanoindentation?

Slides can be downloaded here:
https://drive.google.com/file/d/0B0bdwsoc2sM-WkxSQk9OcDBZV1U/view?usp=sharing

Two questions/comments from audiences:
1,
question:
why the hardness hardness increases with indentation depth, this is different with Nix-Gao model prediction
Answer: There are two kinds of indentation size effect: wedge indentation (Nix-Gao model), indentation size effect is related to the indentation depth: hardness decreases with indentation depth; spherical indentation: indentation size effect is related to the indenter radius: indentation hardness increases with decreasing indenter radius. Here, hardness does increase with indentation depth.
2,
question: why nanoindentation is so important, I have seen many people discussing indentations.
Answer: There are two main advantages of indentation as far as I know. First of all, indentation is 'non-destructive', the measurement only leaves a very small 'damage' on the sample surface, while for example in a simple tension/compression test, the sample is destroyed after the test. Secondly, nanoindentation test is very convenient method to probe material mechanical properties at small length scale. For example, tensile test at small length scale is very difficult regarding the equipment and the sample preparation. Moreover, the famous nano-pillar compression test is actually based on nano indenter, just using a flat punch instead of normally used Berkervich/Sphere indenter.

MSE Seminar

MS&E Seminar, Friday, April 21 @ 3pm - Prof. Yue Qi

Topic: Undestanding Oxygen Vacancy for Solid Oxide Fuel Cell and Battery Materials -- Charge Transfer, Polaron Shape, Strain, and Interactions

To Do List: 4/17/17 - 4/21/17

Hakan: When exactly is your MRS talk? Please send me your MRS talk to check it, and please update the News&Events section of the wiki page with the facts of your talk at MRS, judge, etc. for other group members (including me) to check and admire. :) Please share links to the program, your session etc, in the news&events section of the wiki page. On your projects, you know what you have to do :)

Hengxu: When exactly is your MRS talk? Please send me your MRS talk to check it, and please update the News&Events section of the wiki page with the facts of your talk at MRS, judge, etc. for other group members (including me) to check and admire. :) Please share links to the program, your session etc, in the news&events section of the wiki page. On your projects, you know what you have to do :) ...I hope! ...an addition to what I asked you yesterday, can you post on the wiki directions for installing the 3D-DDD code?

Josh: We should meet on Monday (or the sooner you can make it) to discuss on the next steps regarding your draft, and also arrange a chat with Chris during the week. Thanks for the hard work while I was gone!

Ryder: Let's meet first thing Monday morning to start getting things done for Ni and also work on the code (show you some things etc.). We need to work very hard over the next few weeks on your project, just because it is so interesting (to me at least) to see what comes out! :)

Michalis: Do you have an updated version of your draft? Tomorrow, we should chat with Andrew, and we should work more on your draft afterwards. We should finish it before May 20. I think we are in a good pace from what I remember. Also, please try to coordinate with Hengxu, he is supposed to send you a DDD example this week to try and see whether you can make it work.

Salehin: Have you made any progress since last time? Let's meet on Monday, and let's plan a meeting with Sierros this week. We have a lot of things to do, please let's make a list on Monday, and keep track of them every few days.

All: there is new furniture and chairs coming for the lab this and next week. Please be aware, especially on April 25th when the conference table is coming.

Stefanos is  going to Europe next month. He is leaving for Europe on May 19 and will be coming back in late June. What this means is that whatever needs to be finished, should be finished in the coming month! :)

Comment on the Nanoindentation Protocol and its relation to nanoblitz

 For nanoblitz, we cannot set a exact depth value as we did in the std hardness protocol, but we can decrease the load to 0.2mN or so to reach around 50nm depth

Hakan Yavas:
    Yes, fast protocol, hardness and nanoblitz are here
Ryder Bolin:
    There is suppose to be more nano blitz load and disp
Hakan Yavas:
    Ok, I saw it
Ryder Bolin:
    You saw that data?
Hakan Yavas:
    By the way, you did not get any hardness measurements
Stefanos Papanikolaou:
    ?
Hakan Yavas:
    It seems that the tip did not touch the surface
Ryder Bolin:
    Yes we did
    For nano?
    Cause the hard protocol has it
    Never mind I see it. Could you explain to me why this happened?
Hakan Yavas:
    You only have the hardness up to 0.3nm
Ryder Bolin:
    I removed backlash every time I set something up. You can ask stefanos he was there
    Hakan look at the nano indenter protocol and see if you can find what's going on.


Hakan Yavas:
    I am checking it
    when did you calibrate the tip?
Stefanos Papanikolaou:
    Ryder?
Ryder Bolin:
    Maybe 2 months ago I believe
Stefanos Papanikolaou:
    before we moved the machine?
Ryder Bolin:
    After nano mechanics ran checks on silica remember.
Hakan Yavas:
    December 6th
    Wrong tip calibration may cause this
Ryder Bolin:
    Nano mechanics ran is a complete work up. I had the check functionality and noise
Hakan Yavas:
    ryder, to do a proper tip calibration please follow the routine from the manual page 71
Ryder Bolin:
    Okay I'll run another calibration
Hakan Yavas:
    as I stated previously you should redo the tip calibration after getting large batch of data- so we can get more reliable data. hardness is a function of indented tip area and software calculates stiffness etc. using this parameter. it is very crucial
    + before running a tip calibration please clean the silica surface to remove possible contaminations and dirts- this will increase the calibration efficiency
Ryder Bolin:
    Okay I'll take care of it.


Re-calculation before exporting::::

Stefanos Papanikolaou:
    il momento della verita
Hakan Yavas:
    Also exported
Stefanos Papanikolaou:
    Ryder?
Ryder Bolin:
    Show me
    No show me how you exported
Hakan Yavas:
    Ok
    Before exporting it I recalculated the results
    Did you see it
Ryder Bolin:
    Oh okay try that with load.
    I saw
    Okay it worked thanks
Hakan Yavas:
    That works right
Ryder Bolin:
    Yes!
Hakan Yavas:
    Great

Useful Info on LAMMPS:

Professor.....among the last four column 1st one is the z coordinate value. In our case it is a 2d simulation so this value is always zero.

The last three values are as following.......

"The final 3 nx,ny,nz values on a line of the Atoms entry are optional. LAMMPS only reads them if the "true flag" command is specified in the input command script. Otherwise they are initialized to 0 by LAMMPS. Their meaning, for each dimension, is that "n" box-lengths are added to xyz to get the atom's "true" un-remapped position. This can be useful in pre- or post-processing to enable the unwrapping of long-chained molecules which wind thru the periodic box one or more times. The value of "n" can be positive, negative, or zero. For 2-d simulations specify nz as 0"

link: http://lammps.sandia.gov/doc/2001/data_format.html 

This is what true flag command says.....

"read atom positions  and dump atom positions in one of 2 formats

• flag = 0 -> read/dump only atom positions (remapped to periodic box)
• flag = 1 -> dump atom positions plus integer box counts
• flag = 2 -> read atom positions plus integer box counts
• flag = 3 -> read/dump atom positions plus integer box counts

for each dimension, box count of "n" means add that many box lengths
  to get "true" un-remapped position, "n" can be positive, negative, or zero
 

Default = 0"

Welcome to the laboratory page of Stefanos Papanikolaou's research assistants. Every weekly to-do list will be posted here, as well as a recording of our latest projects and achievements.

Paper Deadline Target

• Indentation papers (2).
• Joshua Thibault's paper.Joshua Thibault
• Michalis Tzimas's paper.

The target for all 4 papers has been set to the end of March