LAMMPS Input file Running on HPC Cluster

I have created batch_submit.sh file in my home (rs0043) to submit my input files into the cluster node (sp0045). compilers are loaded accordingly. and then I submit the input file named as in.sp.0.001.mp by using the following command

lmp_serial<in.sp.0.001.mp

For multiple file submission by a single batch_submit I have used batch_submit_all_20.sh where I have created few variables those are substituted by desired values by running the bash file named multijob_within_script_for_multijob. This bash file is self-explanatory and it is run by the following command,

sh multijob_within_script_for_multijob


DONE.

LAMMPS Input File RUNNING

Here I am explaining about the things one needs to know just to run the input file with varying the star data file and strain rate.

To run the lammps input file: (FOR WINDOWS)

1.       Put the input file (i.e. in.sp.0.002.mp) inside a folder. Remember the input file name will always start with “in.” . You can put whatever name you want after that. I tried to use the strain rate value to remember the strain rate value I used inside.

2.       Copy the star data file and paste inside the same folder.

3.       Copy the lammps executable (lmp_serial) and paste into the same folder with input file.

4.       Copy the libOpenCL.dll file and paste it to the same folder location.

5.       Now open the “Run” command

6.       Type “cmd” and hit “enter”

7.       A command prompt will pop up

8.       Navigate to the folder where you have pasted all the above files

9.       Then type lmp_serial<input_file_name (ie. Lmp_serial<in.sp.0.002.mp) and hit “Enter”. The simulation will start running.

(To run in LINUX/Mac):

1.       Same procedure. (except it does not need the .dll file)

2.       In the command prompt after navigating to the desired folder instead of typing lmp_serial<input_file name you just have to type ./lmp_serial<input_file_name. Here you have to create your executable by yourself and you could name it as you like. (I named the executable same as the Windows for remembering easily).

“DONE”

The input file has two things to change that would cause different different output.

1.       Star file name

2.       Strain rate values

STAR FILE NAME

The star data file is generated by Python script and it contains the coordinates of star particles.

The input file Line number 10 (link attached) has command :

read_data  data.star fix molprop NULL Molecules

here data.star is the star data file and the same named star data file should be present in the same folder with input file. I you want to change the name of star data file you have to change in both place (in folder and inside the input file).

STRAIN RATE VALUES

In the line number 118 has the fllowing command:

variable srate1 equal 0.002

the value 0.002 is the strain rate. (I used this value to name input file, remember !)

https://drive.google.com/file/d/1xNu5pZfmT_G8MrzPWFIGuErbAqmthZxP/view?usp=sharing

P-CARD EXPENSES

Subject:	MyExpenses-- please share this with everyone on your team who has a p-card

All,

We have run into the same issue with P-card charges that we did with the travel… YOU HAVE TO KNOW ALL OF THE FUNDING NUMBERS IN ORDER TO SAVE ANYTHING IN THE RECORD. 

So, if you don’t know all 5 numbers, in the short term, we have a few options:

1.       You can fill out the p-card form (make sure that it tells us where to pay, and a SPECIFIC BUSINESS PURPOSE), attach the receipt and turn it in as usual… we will do the rest.

2.       You can upload or email your receipt to your account (receipt@chromerfile.com), making sure that you write EVERYTHING on that receipt that would be on the p-card form… please name it so that we know what charge it goes to…

3.       You can call us and we will give you the last 2 numbers that you must have in order for the charge to save.

Here’s the issue… we still have to get all of the p-card information into MyExpenses, and you still have to mark “received”, sign and date the receipt.  However, you cannot put any of this information into MyExpenses without knowing the entire funding. 

We are open to procedural suggestions, but the above options are the most efficient that we can come up with right out of the chute. 

PLEASE NOTE THAT WE WILL NO LONGER BE SENDING YOU A LIST OF THE CHARGES THAT NEED FUNDING—THIS LIST IS IN YOUR ACCOUNT, SO YOU CAN SEE EVERY CHARGE THAT HAS HIT.

We will help you in whatever way we can… please don’t let these charges sit out there and accumulate!

Thanks,

Pam

Group Presentations Spring Semester 2018

Date:                    speaker：                                              topic: 

Feb 1st                    Rongguang                                            friction


Feb 8th                    Hengxu                                   2D DDD simulation of pillar reloading


Feb 15th                  Stefanos                                   ARO/DOE proposal


Feb 22th                  Michael/Hengxu/Stefanos       Machine learning on indentation (3D DDD)             


Mar 1st                    Michael                             Machine learning on pillar compression (2D DDD)           

Mar 22th                  Josh                                      Crack growth


Mar 29th                 Ryder                                 Nanoindentation of Cu/Ni/Al


April 12th              Ryder/Stefanos                 Nanoindentation of different grain orientations (EBSD)


April 19th              Salehin                                          Jamming


April 26th              Hengxu                                     3D DDD indentation with flat punch


The group meeting is planned to start at 3:30PM (Thursdays).

We have skipped some group meetings due to the planned travels:
March 4th~March 19th, Stefanos and Hengxu, trip to LA (APS and UCLA)

April 2nd~April 6th, Stefanos and Hengxu, trip to Phoenix (MRS Spring)

May 1st~June 10th , Stefanos, trip to Europe (Stockholm, Paris, Groningen)