Micro and Nano Mechanics Group - User contributions [en]

Tutorials

2011-09-27T23:52:23Z

Agarcia: /* Science Outreach */

== Simulation Codes ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[MD++ Manuals]]
!width="200" | [[ParaDiS Manuals]]
!width="300" | [[ParaDiS Workshop Notes]]
|-
!width="200" | [[DDLab Manuals]]
!width="200" | [[VASP Manuals]]
!width="300" | [[How to compile Qbox]]
|-
!width="200" |
!width="200" |
!width="300" | [[How to compile pimc++]]
|}

== Computers ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[Unix Basics]]
!width="200" | [[Computer Setup]]
!width="200" | [[Computing Clusters | Parallel Clusters]]
|-
!width="200" | [[Install Ubuntu]]
!width="200" | [[Install FFTW3]]
!width="200" | [[Install HDF5]]
|-
!width="200" | [[Install GSL]]
!width="200" | [[Standard Tcl Library | Tcl Library]]
!width="200" | [[Install the GNU Compiler Collection (GCC)]]
|}

== Scientific Background ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[Dislocations]]
|}

== Science Outreach ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [http://www.youtube.com/watch?v=SgM-Xes16Sw Outreach interview]
!width="200" | [[How to install MD++ in Ubuntu | Install MD++ in Ubuntu]]
!width="200" | [[Introduction to Molecular Dynamics Simulations of Fullerenes | MD of Fullerenes]]
|-
!width="200" | [[Images of Fullerenes]]
!width="200" | [[Android Applications and Information]]
|

|}

 

== [[Tutorial:Members_Only | Members Only]] ==

Videos of bucky balls in motion

2009-08-12T22:38:30Z

Agarcia:

work in progress!

A set of bucky balls in motion

{video:youtube|<l1MjiJP-RV0>}

Videos of bucky balls in motion

2009-08-09T21:58:07Z

Agarcia: New page: work in progress!

work in progress!

Tutorials

2009-08-09T20:57:37Z

Agarcia: /* Science Outreach */

== Simulation Codes ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[MD++ Manuals]]
|
|
|-
!width="200" | [[ParaDiS Manuals]]
!width="200" | [[ParaDiS Workshop Notes]]
!width="200" | [[DDLab Manuals]]
|-
!width="200" | [[How to compile VASP]]
!width="200" | [[How to compile Qbox]]
|
|}

== Computers ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[Unix Basics]]
!width="200" | [[Computer Setup]]
!width="200" | [[Computing Clusters | Parallel Clusters]]
|-
!width="200" | [[How to install Ubuntu]]
!width="200" | [[Install FFTW3]]
!width="200" | [[Install HDF5]]
|-
!width="200" | [[Standard Tcl Library]]
!width="200" |
!width="200" |
|}

== Scientific Background ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[Dislocations]]
|}

== Science Outreach ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [http://www.youtube.com/watch?v=SgM-Xes16Sw Outreach interview]
!width="200" | [[How to install MD++ in Ubuntu | Install MD++ in Ubuntu]]
!width="200" | [[Introduction to Molecular Dynamics Simulations of Fullerenes | MD of Fullerenes]]
|-
!width="200" | [[Simulating Solids in MD++]]
!width="200" | [[Images of Fullerenes]]
!width="200" | [[Videos of bucky balls in motion]]
|}

 

== [[Tutorial:Members_Only | Members Only]] ==

Tutorials

2009-08-09T20:55:17Z

Agarcia: /* Science Outreach */

== Simulation Codes ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[MD++ Manuals]]
|
|
|-
!width="200" | [[ParaDiS Manuals]]
!width="200" | [[ParaDiS Workshop Notes]]
!width="200" | [[DDLab Manuals]]
|-
!width="200" | [[How to compile VASP]]
!width="200" | [[How to compile Qbox]]
|
|}

== Computers ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[Unix Basics]]
!width="200" | [[Computer Setup]]
!width="200" | [[Computing Clusters | Parallel Clusters]]
|-
!width="200" | [[How to install Ubuntu]]
!width="200" | [[Install FFTW3]]
!width="200" | [[Install HDF5]]
|-
!width="200" | [[Standard Tcl Library]]
!width="200" |
!width="200" |
|}

== Scientific Background ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[Dislocations]]
|}

== Science Outreach ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [http://www.youtube.com/watch?v=SgM-Xes16Sw Outreach interview]
!width="200" | [[How to install MD++ in Ubuntu | Install MD++ in Ubuntu]]
!width="200" | [[Introduction to Molecular Dynamics Simulations of Fullerenes | MD of Fullerenes]]
|-
!width="200" | [[Simulating Solids in MD++]]
!width="200" | [[Images of Fullerenes]]
|
|}

 

== [[Tutorial:Members_Only | Members Only]] ==

Tutorials

2009-08-06T18:10:10Z

Agarcia:

== Simulation Codes ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[MD++ Manuals]]
|
|
|-
!width="200" | [[ParaDiS Manuals]]
!width="200" | [[ParaDiS Workshop Notes]]
!width="200" | [[DDLab Manuals]]
|-
!width="200" | [[How to compile VASP]]
!width="200" | [[How to compile Qbox]]
|
|}

== Computers ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[Unix Basics]]
!width="200" | [[Computer Setup]]
!width="200" | [[Computing Clusters | Parallel Clusters]]
|-
!width="200" | [[How to install Ubuntu]]
!width="200" | [[Install FFTW3]]
!width="200" | [[Install HDF5]]
|-
!width="200" | [[Standard Tcl Library]]
!width="200" |
!width="200" |
|}

== Scientific Background ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[Dislocations]]
|}

== Science Outreach ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [http://www.youtube.com/watch?v=SgM-Xes16Sw Outreach interview]
!width="200" | [[How to install MD++ in Ubuntu | Install MD++ in Ubuntu]]
!width="200" | [[Introduction to Molecular Dynamics Simulations of Fullerenes | MD of Fullerenes]]
|-
!width="200" | [[Simulating Solid Compounds in MD++]]
!width="200" | [[Images of Fullerenes]]
|
|
|}

 

== [[Tutorial:Members_Only | Members Only]] ==

Tutorials

2009-08-06T18:07:01Z

Agarcia:

== Simulation Codes ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[MD++ Manuals]]
|
|
|-
!width="200" | [[ParaDiS Manuals]]
!width="200" | [[ParaDiS Workshop Notes]]
!width="200" | [[DDLab Manuals]]
|-
!width="200" | [[How to compile VASP]]
!width="200" | [[How to compile Qbox]]
|
|}

== Computers ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[Unix Basics]]
!width="200" | [[Computer Setup]]
!width="200" | [[Computing Clusters | Parallel Clusters]]
|-
!width="200" | [[How to install Ubuntu]]
!width="200" | [[Install FFTW3]]
!width="200" | [[Install HDF5]]
|-
!width="200" | [[Standard Tcl Library]]
!width="200" |
!width="200" |
|}

== Scientific Background ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [[Dislocations]]
|}

== Science Outreach ==

{| class="wikitable" cellpadding="2"
|-
!width="200" | [http://www.youtube.com/watch?v=SgM-Xes16Sw Outreach interview]
!width="200" | [[Introduction to Molecular Dynamics Simulations of Fullerenes | MD of Fullerenes]]
!width="200" | [[Images of Fullerenes]]
|width="200" | [[Simulating Solid Compounds in MD++]]
!width="200" | [[How to install MD++ in Ubuntu | Install MD++ in Ubuntu]]
|
|
|}

 

== [[Tutorial:Members_Only | Members Only]] ==

How to install MD++ in Ubuntu

2009-07-30T22:01:53Z

Agarcia:

How to install MD++

What is MD++?

MD++ is simulation code developed by Dr. Wei Cai. The code is used to simulate systems of molecules using energy potentials that approximate the atomistic interaction in the system. To write a code for a specific element that does not fit any of the potentials that have been written, it is actually very complex. For a complete list of potentials and the type of atoms that they can be used for may be found in Appendix B of this packet. To download the latest version of MD++,
please go to: [http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/ MD++]

To install in MD++, follow these steps:

make a directory(or folder) in the home directory and call it Codes.

...$ mkdir Codes

Open a terminal emulator. Switch to the Codes directory by typing:

...$ cd Codes/

Copy latest version of MD++ package into the Codes directory.

Now, to install MD++ type:

...$ tar -zxvf md++-2007-02-27.tar.gz

Now, compile all potential files by typing:

...$ make all build=R

To compile a specific pontetial (for example the Finnis-Sinclair Pontetial for Molybedum) type:

...$ make fs build=R

To clear a potential, type:

...$ make fs clean

To clear all potentials, type

...$ make all clean

Now, run an example to check if MD++ is working properly by typing:

...$ bin/md_gpp scripts/Examples/Example01-m0.script

Note: All these actions needs to be done from the MD++ directory, unless specified.

If you run into problems with running MD++ in ubuntu,
make sure that you download the necessary X11-86 files, tcl files and cpp compiler from the synpatic package manager.
----

[[w:http:Tutorials|Back to Tutorials]]

----

How to install MD++ in Ubuntu

2009-07-30T22:00:43Z

Agarcia:

How to install MD++

What is MD++?

MD++ is simulation code developed by Dr. Wei Cai. The code is used to simulate systems of molecules using energy potentials that approximate the atomistic interaction in the system. To write a code for a specific element that does not fit any of the potentials that have been written, it is actually very complex. For a complete list of potentials and the type of atoms that they can be used for may be found in Appendix B of this packet. To download the latest version of MD++,
please go to: [http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/ MD++]

To install in MD++, follow these steps:

make a directory(or folder) in the home directory and call it Codes.

...$ mkdir Codes

Open a terminal emulator. Switch to the Codes directory by typing:

...$ cd Codes/

Copy latest version of MD++ package into the Codes directory.

Now, to install MD++ type:

...$ tar -zxvf md++-2007-02-27.tar.gz

Now, compile all potential files by typing:

...$ make all build=R

To compile a specific pontetial (for example the Finnis-Sinclair Pontetial for Molybedum) type:

...$ make fs build=R

To clear a potential, type:

...$ make fs clean

To clear all potentials, type

...$ make all clean

Now, run an example to check if MD++ is working properly by typing:

...$ bin/md_gpp scripts/Examples/Example01-m0.script

Note: All these actions needs to be done from the MD++ directory, unless specified.

----

[[w:http:Tutorials|Back to Tutorials]]

----
If you run into problems with running MD++ in ubuntu,
make sure that you download the necessary X11-86 files, tcl files and cpp compiler.

Alfonso Garcia

2009-07-29T00:58:40Z

Agarcia:

==Alfonso Garcia==

Hello, my name is Alfonso Garcia and I am an educator working with professor Wei Cai in developing
teaching materials for high school students to learn molecular dynamic simulations. I am interested in doing
simulations of fullerenes. We are in the process of implement the REBO potential in MD++ to be able to
simulate buckyballs, nanotubes and graphene sheets in MD++.

Alfonso Garcia

2009-07-29T00:57:26Z

Agarcia:

==Alfonso Garcia==

Hello, my name is Alfonso Garcia and I am an educator working with professor Wei Cai in bringing developing
teaching materials for high school students to learn molecular dynamic simulations. I am interested in doing
simulations of fullerenes. We are in the process of implement the REBO potential in MD++ to be able to
simulate buckyballs, nanotubes and graphene sheets in MD++.

Alfonso Garcia

2009-07-29T00:56:19Z

Agarcia: New page: ==Alfonso Garcia== Hello, my name is Alfonso Garcia and I am an educator working with professor Wei Cai in bringing developing teaching materials for high school students to learn molec...

==Alfonso Garcia==

Hello, my name is Alfonso Garcia and I am an educator working with professor Wei Cai in bringing developing
teaching materials for high school students to learn molecular dynamic simulations. I am interested in doing simulations of fullerenes. We are in the process of implement the REBO potential in MD++ to be able to simulate buckyballs, nanotubes and graphene sheets in MD++.

Group Members

2009-07-29T00:51:08Z

Agarcia:

__NOTOC__
===Professor===
:[[Wei Cai]]

===Research Associate===
:[[Sylvie Aubry]]

===Postdoc===
:[[Alfredo Correa]]
:[[Yongxing Shen | Yongxing Shen (guest)]]

===Graduate Students===
:[[William Cash]]
:[[Keonwook Kang]]
:[[Haneesh Kesari]]
:[[Hark Lee]]
:[[Eunseok Lee]]
:[[Seokwoo Lee]]
:[[Seunghwa Ryu]]
:[[Chris Weinberger]]
:[[Jie Yin]]
:[[William Fong | William Fong (guest)]]

==Educator==
:[[Alfonso Garcia]]

How to install MD++ in Ubuntu

2009-07-29T00:26:22Z

Agarcia:

How to install MD++ in Ubuntu

2009-07-29T00:12:46Z

Agarcia:

How to install MD++ in Ubuntu

2009-07-28T23:55:02Z

Agarcia:

Downloadable Files

2008-08-14T18:21:35Z

Agarcia:

Under Construction!

These files maybe downloaded and used to learn about MD++ simulation.

Examples jpg (images) Files and mpg (movies) Files
test
Script Files
test
Other Necessary files
test
Other Useful files
test

Downloadable Files

2008-08-14T18:19:58Z

Agarcia: New page: Underconstruction! These files maybe downloaded to be used as examples to learn about MD++ simulation. Examples jpg (images) Files and mpg (movies) Files test Script Files test Other Ne...

Underconstruction!
These files maybe downloaded to be used as examples to learn about MD++ simulation.

Examples jpg (images) Files and mpg (movies) Files
test
Script Files
test
Other Necessary files
test
Other Useful files
test

Tutorials

2008-08-14T18:15:38Z

Agarcia: /* Other Resources */

==Tutorials==

[[Dislocations]]

[[Unix Basics]]

[[Computer Setup]]

[[MD++ Manuals]]

[[DDLab Manuals]]

[[ParaDiS Manuals]]

[[ParaDiS Workshop Notes]]

[[Computing Clusters]]

== Other Resources ==

[[ How to install Ubuntu]]

[[ How to install MD++ in Ubuntu]]

[[ Useful Information about the Potential Files Used in MD++]]

[[ Introduction to Molecular Dynamics Simulations of Fullerenes]]

[[Atom Eye]]

[[Images of Fullerenes]]

[[Files for Download]]

[[Making Amimations Using a MD++ Script File]]

[[Downloadable Files]]

Making Amimations Using a MD++ Script File

2008-08-08T22:23:06Z

Agarcia:

'''Making a simulation using MD++ scripts'''

To make a simulation movie, follow these three major steps:

Step 1

Make cfg files using the scipt file. To do so,

add this command to your script file before your iterations. This command will create the cfg files. Savecfgfreq sets the frequency of generating the cfg files.

savecfg = 1 savecfgfreq = 50 intercfgfile = inter.cfg

Next, run the script file. When the script file is run, the cfg files will be created.

Example: ...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script

Check to see if the cfg files were created by going to the runs directory and then to the directory were your your saving your files for the simulation.

Example: ...MD++$ls runs/buckyball/ (Check that the cfg files were created.)

Note: Before running another simulation make sure that the cfg are removed. Otherwise, you code will refer to this cfg files to create new animation movies.

Example: ...MD++$ rm runs/buckyball/inter00* (to remove your cfg files type this command)

Step 2

Open the first cfg file in Atom Eye. This file should start inter0001.cfg. Make the necessary changes to your initial frame like change the color of your background, change color of atoms species, etc.

Example: ...MD++$ Tools/AtomEye/A.i686 runs/buckyball/inter0001.cfg &

Now, press the "y" key to start creating the jpg files. This a frame for each cfg file and put them in directory in the MD++ directory and name it Jpgs. This new directory will be used by a compression program called MEncoder.

Step 3

Get the multimedia player software Mplayer in Ubuntu. This MPlayer comes with MEncoder which will allow compression of the jpg files into a movie. Other commercial software can also be used like Adobe Premiere or Animation Shop. To create an animation in using the Mplayer in Ubuntu, download the script file vidcompress to the MD++ directory. First setup the permissions to access the vidcompress file.

Example: ...MD++$ chmod 755 vidcompress

Run the vidcompress script file by typing:

Example: ...MD++$ ./vidcompress

This will compress the jpg files to make the movie and will see the movie in the MD++ directory named AtomEye.mpg. Lastly, open the movie using the MPlayer or another media player that opens mpg files.

Important Note: To make another animation movie, you must remove the src_anim file, rename the Jpgs directory and the movie itself. Otherwise, this will create another animation movie of the jpg files.

Example: ...MD++$ mplayer AtomEye.mpg

References

1. [http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/ MD++]

2. [http://mt.seas.upenn.edu/Archive/Graphics/A/#making_movie Atom Eye]

Making Amimations Using a MD++ Script File

2008-08-08T21:58:42Z

Agarcia:

'''Making a simulation using MD++ scripts'''

To make a simulation movie, follow these three major steps:

Step 1

Make cfg files using the scipt file. To do so,

add this command to your script file before your iterations. This command will create the cfg files. Savecfgfreq sets the frequency of generating the cfg files.

savecfg = 1 savecfgfreq = 50 intercfgfile = inter.cfg

Next, run the script file. When the script file is run, the cfg files will be created.

Example: ...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script

Check to see if the cfg files were created by going to the runs directory and then to the directory were your your saving your files for the simulation.

Example: ...MD++$ls runs/buckyball/ (Check that the cfg files were created.)

Note: Before running another simulation make sure that the cfg are removed. Otherwise, you code will refer to this cfg files to create new animation movies.

Example: ...MD++$ rm runs/buckyball/inter00* (to remove your cfg files type this command)

Step 2

Open the first cfg file in Atom Eye. This file should start inter0001.cfg. Make the necessary changes to your initial frame like change the color of your background, change color of atoms species, etc.

Example: ...MD++$ Tools/AtomEye/A.i686 runs/buckyball/inter0001.cfg &

Now, press the "y" key to start creating the jpg files. This a frame for each cfg file and put them in directory in the MD++ directory and name it Jpgs. This new directory will be used by a compression program called vidcompress.

Step 3

Get this compression software like Mplayer in Ubuntu. Or other commercial software like Adobe Premiere or Animation Shop. To create an animation in using the Mplayer in Ubuntu, download the execution files vidcompress to the MD++ directory. First setup the permissions to access the vidcompress file.

Example: ...MD++$ chmod 755 vidcompress

Run the vidcompress execution file.

Example: ...MD++$ ./vidcompress

Lastly, run the movie.

Example: ...MD++$ mplayer AtomEye.mpg

References

1. [http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/ MD++]

2. [http://mt.seas.upenn.edu/Archive/Graphics/A/#making_movie Atom Eye]

Making Amimations Using a MD++ Script File

2008-08-08T21:52:53Z

Agarcia:

'''Making a simulation using MD++ scripts'''

To make a simulation movie, follow these three major steps:

Step 1

Make cfg files using the scipt file. To do so,

add this command to your script file before your iterations. This command will create the cfg files. Savecfgfreq sets the frequency of generating the cfg files.

savecfg = 1 savecfgfreq = 50 intercfgfile = inter.cfg

Next, run the script file. When the script file is run, the cfg files will be created.

Example: ...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script

Check to see if the cfg files were created by going to the runs directory and then to the directory were your your saving your files for the simulation.

Example: ...MD++$ls runs/buckyball/ (Check that the cfg files were created.)

Note: Before running another simulation make sure that the cfg are removed. Otherwise, you code will refer to this cfg files to create new animation movies.

Example: ...MD++$ rm runs/buckyball/inter00* (to remove your cfg files type this command)

Step 2

Open the first cfg file in Atom Eye. This file should start inter0001.cfg. Make the necessary changes to your initial frame like change the color of your background, change color of atoms species, etc.

Example: ...MD++$ Tools/AtomEye/A.i686 runs/buckyball/inter0001.cfg &

Now, press the "y" key to start creating the jpg files. This a frame for each cfg file and put them in directory in the MD++ directory and name it Jpgs. This new directory will be used by a compression program called vidcompress.

Step 3

Get this compression software like Mplayer in Ubuntu. Or other commercial software like Adobe Premiere or Animation Shop. To create an animation in using the Mplayer in Ubuntu, download the execution files vidcompress to the MD++ directory. First setup the permissions to access the vidcompress file.

Example: ...MD++$ chmod 755 vidcompress

Run the vidcompress execution file.

Example: ...MD++$ ./vidcompress

Lastly, run the movie.

Example: ...MD++$ mplayer Nameofanimation.mpg

References

1. [http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/ MD++]

2. [http://mt.seas.upenn.edu/Archive/Graphics/A/#making_movie Atom Eye]

Making Amimations Using a MD++ Script File

2008-08-08T21:35:19Z

Agarcia:

'''Making a simulation using MD++ scripts'''

To make a simulation movie, follow these three major steps:

Step 1

Make cfg files using the scipt file. To do so,

add this command to your script file before your iterations. This command will create the cfg files. Savecfgfreq sets the frequency of generating the cfg files.

savecfg = 1 savecfgfreq = 50 intercfgfile = inter.cfg

Next, run the script file. When the script file is run, the cfg files will be created.

Example: ...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script

Check to see if the cfg files were created by going to the runs directory and then to the directory were your your saving your files for the simulation.

Example: ...MD++$ls runs/buckyball/ (Check that the cfg files were created.)

Note: Before running another simulation make sure that the cfg are removed. Otherwise, you code will refer to this cfg files to create new animation movies.

Example: ...MD++$ rm runs/buckyball/inter00* (to remove your cfg files type this command)

Step 2

Open the first cfg file in Atom Eye. This file should start inter0001.cfg. Make the necessary changes to your initial frame like change the color of your background, change color of atoms species, etc.

Example: ...MD++$ Tools/AtomEye/A.i686 runs/buckyball/inter0001.cfg &

Now, press the "y" key to start creating the jpg files. This a frame for each cfg file and put them in directory in the MD++ directory and name it Jpgs. This new directory will be used by a compression program called vidcompress.

Step 3

Get this compression file from the and place it in the MD++ directory: [vidcompress]

Example: ...MD++$ chmod 755 vidcompress

Run the vidcompress execution file.

Example: ...MD++$ ./vidcompress

Run Animation

Lastly, run the movie.
Example: ...MD++$ mplayer Nameofanimation.mpg

References

1. [http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/ MD++]

2. [http://mt.seas.upenn.edu/Archive/Graphics/A/#making_movie Atom Eye]

Making Amimations Using a MD++ Script File

2008-08-01T22:45:33Z

Agarcia:

Making Amimations Using a MD++ Script File

2008-08-01T22:43:53Z

Agarcia:

Making Amimations Using a MD++ Script File

2008-08-01T22:40:50Z

Agarcia:

'''Making a simulation using MD++ scripts'''

To make your simulation movie, you need to follow these three major steps:

1. Make cfg files using the scipt file. To do so,

add this command to your script file before your iterations. This command will create the cfg files.

savecfg = 1 savecfgfreq = 50 intercfgfile = inter.cfg

Next, run the script file.

Example: ...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script

Example: ...MD++$ls runs/buckyball/ (Check that the cfg files were created.)

Example: ...MD++$ rm runs/buckyball/inter00* (to remove your cfg files type this command)

2. Select make the necessary changes to your initial frame and they run the simulation.

Example: ...MD++$ Tools/AtomEye/A.i686 runs/buckyball/inter0001.cfg &

Now, presse the key "y" to start creating the jpg files.

3. Get this compression file and place it in the MD++ directory: [vidcompress]

Example: ...MD++$ chmod 755 vidcompress

Run the vidcompress execution file.

Example: ...MD++$ ./vidcompress

Lastly, run the movie.
Example: ...MD++$ mplayer Nameofanimation.mpg

References

1. [http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/ MD++]

2. [http://mt.seas.upenn.edu/Archive/Graphics/A/#making_movie Atom Eye]

Making Amimations Using a MD++ Script File

2008-08-01T22:39:31Z

Agarcia:

Making a simulation using a MD++ script

To make your simulation movie, you need to follow these three major steps:

1. Make cfg files using the scipt file. To do so,

add this command to your script file before your iterations. This command will create the cfg files.

savecfg = 1 savecfgfreq = 50 intercfgfile = inter.cfg

Next, run the script file.

Example: ...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script

Example: ...MD++$ls runs/buckyball/ (Check that the cfg files were created.)

Example: ...MD++$ rm runs/buckyball/inter00* (to remove your cfg files type this command)

2. Select make the necessary changes to your initial frame and they run the simulation.

Example: ...MD++$ Tools/AtomEye/A.i686 runs/buckyball/inter0001.cfg &

Now, presse the key "y" to start creating the jpg files.

3. Get this compression file and place it in the MD++ directory: [vidcompress]

Example: ...MD++$ chmod 755 vidcompress

Run the vidcompress execution file.

Example: ...MD++$ ./vidcompress

Lastly, run the movie.
Example: ...MD++$ mplayer Nameofanimation.mpg

References

1. [http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/ MD++]

2. [http://mt.seas.upenn.edu/Archive/Graphics/A/#making_movie Atom Eye]

Making Amimations Using a MD++ Script File

2008-08-01T22:38:42Z

Agarcia:

Making a simulation using a MD++ script

To make your simulation movie, you need to follow these three major steps:

1. Make cfg files using the scipt file. To do so,

add this command to your script file before your iterations. This command will create the cfg files.

savecfg = 1 savecfgfreq = 50 intercfgfile = inter.cfg

Next, run the script file.

Example: ...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script

Example: ...MD++$ls runs/buckyball/ (Check that the cfg files were created.)

Example: ...MD++$ rm runs/buckyball/inter00* (to remove your cfg files type this command)

2. Select make the necessary changes to your initial frame and they run the simulation.

Example: ...MD++$ Tools/AtomEye/A.i686 runs/buckyball/inter0001.cfg &

Now, presse the key "y" to start creating the jpg files.

3. Get this compression file and place it in the MD++ directory: [vidcompress]

Example: ...MD++$ chmod 755 vidcompress

Run the vidcompress execution file.

Example: ...MD++$ ./vidcompress

Lastly, run the movie.
Example: ...MD++$ mplayer Nameofanimation.mpg

References

1. [http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/ MD++]
2. [Atom Eye; http://mt.seas.upenn.edu/Archive/Graphics/A/#making_movie]

Making Amimations Using a MD++ Script File

2008-07-30T01:48:43Z

Agarcia:

Making a simulation using a MD++ script

To make your simulation movie, you need to follow these three major steps:

1. Make cfg files using the scipt file. To do so,

add this command to your script file before your iterations. This command will create the cfg files.

savecfg = 1 savecfgfreq = 50 intercfgfile = inter.cfg

Next, run the script file.

Example: ...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script

Example: ...MD++$ls runs/buckyball/ (Check that the cfg files were created.)

Example: ...MD++$ rm runs/buckyball/inter00* (to remove your cfg files type this command)

2. Select make the necessary changes to your initial frame and they run the simulation.

Example: ...MD++$ Tools/AtomEye/A.i686 runs/buckyball/inter0001.cfg &

Now, presse the key "y" to start creating the jpg files.

3. Get this compression file and place it in the MD++ directory: [vidcompress]

Example: ...MD++$ chmod 755 vidcompress

Run the vidcompress execution file.

Example: ...MD++$ ./vidcompress

Lastly, run the movie.
Example: ...MD++$ mplayer Nameofanimation.mpg

References

1. [MD++; http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/]
2. [Atom Eye; http://mt.seas.upenn.edu/Archive/Graphics/A/#making_movie]

Making Amimations Using a MD++ Script File

2008-07-30T01:48:09Z

Agarcia:

Making a simulation using a MD++ script

To make your simulation movie, you need to follow these three major steps:

1. Make cfg files using the scipt file. To do so,

add this command to your script file before your iterations. This command will create the cfg files.

savecfg = 1 savecfgfreq = 50 intercfgfile = inter.cfg

Next, run the script file.

Example: ...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script

Example: ...MD++$ls runs/buckyball/ (Check that the cfg files were created.)

Example: ...MD++$ rm runs/buckyball/inter00* (to remove your cfg files type this command)

2. Select make the necessary changes to your initial frame and they run the simulation.

Example: ...MD++$ Tools/AtomEye/A.i686 runs/buckyball/inter0001.cfg &

Now, presse the key "y" to start creating the jpg files.

3. Get this compression file and place it in the MD++ directory: [vidcompress]

Example: ...MD++$ chmod 755 vidcompress

Run the vidcompress execution file.

Example: ...MD++$ ./vidcompress

Lastly, run the movie.
Example: ...MD++$ mplayer Nameofanimation.mpg

References

1. [MD++| http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/]
2. [Atom Eye| http://mt.seas.upenn.edu/Archive/Graphics/A/#making_movie]

Making Amimations Using a MD++ Script File

2008-07-30T01:45:56Z

Agarcia:

Making a simulation using a MD++ script

To make your simulation movie, you need to follow these three major steps:

1. Make cfg files using the scipt file. To do so,

add this command to your script file before your iterations. This command will create the cfg files.

savecfg = 1 savecfgfreq = 50 intercfgfile = inter.cfg

Next, run the script file.

Example: ...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script

Example: ...MD++$ls runs/buckyball/ (Check that the cfg files were created.)

Example: ...MD++$ rm runs/buckyball/inter00* (to remove your cfg files type this command)

2. Select make the necessary changes to your initial frame and they run the simulation.

Example: ...MD++$ Tools/AtomEye/A.i686 runs/buckyball/inter0001.cfg &

Now, presse the key "y" to start creating the jpg files.

3. Get this compression file and place it in the MD++ directory: [vidcompress]

Example: ...MD++$ chmod 755 vidcompress

Run the vidcompress execution file.

Example: ...MD++$ ./vidcompress

Lastly, run the movie.
Example: ...MD++$ mplayer Nameofanimation.mpg

References

1. MD++ []
2. Atom Eye [http://mt.seas.upenn.edu/Archive/Graphics/A/#making_movie]

Making Amimations Using a MD++ Script File

2008-07-30T01:42:10Z

Agarcia:

Making a simulation using a MD++ script

To make your simulation movie, you need to follow these three major steps:

1. Make cfg files using the scipt file. To do so,

add this command to your script file before your iterations. This command will create the cfg files.

savecfg = 1 savecfgfreq = 50 intercfgfile = inter.cfg

Next, run the script file.

Example: ...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script

Example: ...MD++$ls runs/buckyball/ (Check that the cfg files were created.)

Example: ...MD++$ rm runs/buckyball/inter00* (to remove your cfg files type this command)

2. Select make the necessary changes to your initial frame and they run the simulation.

Example: ...MD++$ Tools/AtomEye/A.i686 runs/buckyball/inter0001.cfg &

Now, presse the key "y" to start creating the jpg files.

3. Get this compression file and place it in the MD++ directory: [vidcompress]

References

1. MD++ ()
2. Atom Eye (http://mt.seas.upenn.edu/Archive/Graphics/A/#making_movie)

Example: ...MD++$ chmod 755 vidcompress

Run the vidcompress execution file

Example: ...MD++$ ./vidcompress

Lastly, run the movie.
Example: ...MD++$ mplayer Nameofanimation.mpg

Making Amimations Using a MD++ Script File

2008-07-29T23:08:12Z

Agarcia:

Making a simulation using a MD++ script

To make your simulation movie, you need to follow these three major steps:

1. Make cfg files using the scipt file. To do so,

add this command to your script file before your iterations. This command will create the cfg files.

savecfg = 1 savecfgfreq = 50 intercfgfile = inter.cfg

Next, run the script file.

Example: ...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script

Example: ...MD++$ls runs/buckyball/ (Check that the cfg files were created.)

Example: ...MD++$ rm runs/buckyball/inter00* (to remove your cfg files type this command)

2. Select make the necessary changes to your initial frame and they run the simulation.

Example: ...MD++$ Tools/AtomEye/A.i686 runs/buckyball/inter0001.cfg &

Now, presse the key "y" to start creating the jpg files.

3. Get this compression file and place it in the MD++ directory: [vidcompress]

Example: ...MD++$ chmod 755 vidcompress

Run the vidcompress execution file

Example: ...MD++$ ./vidcompress

Lastly, run the movie.
Example: ...MD++$ mplayer Nameofanimation.mpg

Making Amimations Using a MD++ Script File

2008-07-29T23:07:08Z

Agarcia:

Making a simulation using a MD++ script

To make your simulation movie, you need to follow these three major steps:

1. Make cfg files using the scipt file. To do so,

add this command to your script file before your iterations. This command will create the cfg files.

savecfg = 1 savecfgfreq = 50 intercfgfile = inter.cfg

Next, run the script file

Example: ...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script

Example: ...MD++$ls runs/buckyball/ (Check that the cfg files were created.)

Example: ...MD++$ rm runs/buckyball/inter00* (to remove your cfg files type this command)

2. Select make the necessary changes to your initial frame and they run:

Example: ...MD++$ Tools/AtomEye/A.i686 runs/buckyball/inter0001.cfg &

Now, presse the key "y" to start creating the jpg files

3. Get this compression file and place it in the MD++ directory: [vidcompress]

Example: ...MD++$ chmod 755 vidcompress

Run the vidcompress execution file

Example: ...MD++$ ./vidcompress

Lastly, run the movie.
Example: ...MD++$ mplayer Nameofanimation.mpg

Making Amimations Using a MD++ Script File

2008-07-29T23:06:19Z

Agarcia:

Making a simulation using a MD++ script

To make your simulation movie, you need to follow these three major steps:

1. Make cfg files using the scipt file. To do so, do t

add this command to your script file before your iterations. This command will create the cfg files.

savecfg = 1 savecfgfreq = 50 intercfgfile = inter.cfg

Next, run the script file

Example: ...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script

Example: ...MD++$ls runs/buckyball/ (Check that the cfg files were created.)

Example: ...MD++$ rm runs/buckyball/inter00* (to remove your cfg files type this command)

2. Select make the necessary changes to your initial frame and they run:

Example: ...MD++$ Tools/AtomEye/A.i686 runs/buckyball/inter0001.cfg &

Now, presse the key "y" to start creating the jpg files

3. Get this compression file and place it in the MD++ directory: [vidcompress]

Example: ...MD++$ chmod 755 vidcompress

Run the vidcompress execution file

Example: ...MD++$ ./vidcompress

Lastly, run the movie.
Example: ...MD++$ mplayer Nameofanimation.mpg

Making Amimations Using a MD++ Script File

2008-07-29T23:05:21Z

Agarcia:

Making a simulation using a MD++ script

To make your simulation movie, you need add the following three major steps:

1. Make cfg files using the scipt file. To do so, do t

add this command to your script file before your iterations. This command will create the cfg files.

savecfg = 1 savecfgfreq = 50 intercfgfile = inter.cfg

Next, run the script file

Example: ...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script

Example: ...MD++$ls runs/buckyball/ (Check that the cfg files were created.)

Example: ...MD++$ rm runs/buckyball/inter00* (to remove your cfg files type this command)

2. Select make the necessary changes to your initial frame and they run:

Example: ...MD++$ Tools/AtomEye/A.i686 runs/buckyball/inter0001.cfg &

Now, presse the key "y" to start creating the jpg files

3. Get this compression file and place it in the MD++ directory: [vidcompress]

Example: ...MD++$ chmod 755 vidcompress

Run the vidcompress execution file

Example: ...MD++$ ./vidcompress

Lastly, run the movie.
Example: ...MD++$ mplayer Nameofanimation.mpg

Making Amimations Using a MD++ Script File

2008-07-29T22:06:55Z

Agarcia:

Making a simulation using a MD++ script

To make your simulation movie, you need add the following command:

...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script

...MD++$ls runs/buckyball/

...MD++$ rm runs/buckyball/inter00* (to remove your cfg files type this command)

Select make the necessary changes to your initial frame and they run:

...MD++$ Tools/AtomEye/A.i686 runs/buckyball/inter0001.cfg &

Get this file: [vidcompress]

...MD++$ chmod 755 vidcompress

...MD++$ ./vidcompress

...MD++$ mplayer AtomEye.mpg

Making Amimations Using a MD++ Script File

2008-07-29T22:05:46Z

Agarcia: New page: Making a simulation using a MD++ script To make your simulation movie, you need add the following command: ...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script ...MD++$ls runs/b...

Making a simulation using a MD++ script

To make your simulation movie, you need add the following command:

...MD++$ bin/tersoff_gpp scripts/myscripts/buckyball.script

...MD++$ls runs/buckyball/

...MD++$ rm runs/buckyball/inter00*

Select make the necessary changes to your initial frame and they run:

...MD++$ Tools/AtomEye/A.i686 runs/buckyball/inter0001.cfg &

Get this file: vidcompress

...MD++$ chmod 755 vidcompress

...MD++$ ./vidcompress

...MD++$ mplayer AtomEye.mpg

Tutorials

2008-07-29T20:24:00Z

Agarcia: /* Other Resources */

Files for Download

2008-07-25T21:45:58Z

Agarcia: New page: These the files needed to for the activities mentioned in above.

These the files needed to for the activities mentioned in above.

Tutorials

2008-07-25T21:44:58Z

Agarcia: /* Other Resources */

Introduction to Molecular Dynamics Simulations of Fullerenes

2008-07-25T01:51:09Z

Agarcia:

Why do we want to simulate fullerenes?
Fullerenes are a group of molecules made with only carbon atoms. These molecules exhibit very
special properties. The reason why scientists are interested in understanding the behavior of fullerenes
is because they have extra ordinary properties in superconductivity, electricity and elasticity. They
could have numerous applications to improve many of our existing products and develop new products. There
are lots of unexplained answers regarding the behavior of fullerenes. It is believed that making
simulations of these molecules is the most safe and efficient approach.

Procedure for simulating a bucky ball
Brainstorming:
What would you need to make a simulation of a bucky ball?
-The coordinates of each atom in space
-The program that will create the graphics
What do need to change the physical properties of the bucky ball like the temperature,
velocity, pressure of the system, etc.?
-Appropriate potential energy approximation
-MD++ code

Note: all the files needed for this activity are in a folder called etp07nanostructurefiles.

Step 1
Obtain the coordinates of the bucky ball. They are located in a file called buckyball.xyz . Make
sure that you keep this file in that format. Place the buckyball.xyz file in the runs directory.
It is assumed that you have installed MD++ properly. From the desktop, go to the menu bar and click
on places and open the home folder. Open the Codes folder. Then open the MD++ folder. Open the
runs folder. Make a new folder and name it buckyball. Copy the buckyball.xyz file into the runs folder.

Step 2
Obtain the octave execution file of the bucky ball. They are located in a file called readbuckyball.oct.
Make sure that you keep this file in that format. Place the octave file in the runs directory. Again
from the desktop, go to the menu bar and click on places and open the home folder. Open the Codes
folder. Open the MD++ folder. Open the runs folder. Copy the readbuckyball.oct file into the runs folder.

Step 3
From the runs directory, run the octave file by typing:
./readbuckyball.oct
This will create a cn file called buckyball.cn. Go back to the MD++ directory.

Step 4
Now copy the script file called buckyball.script. Go to the scripts directory. Make a directory and call
it myscripts. Now copy the the file buckyball.script into the myscripts folder.

Step 5
Now open the terminal emulator ( the icon that has the $ sign). Go to the MD++ directory by typing:
cd Codes/MD++/
To run the simulation of the bucky ball type:
bin/md_gpp scripts/myscripts/buckyball.script
A new graphics window will pop-up with the simulation of a bucky ball in 3D!!!

Note: All simulations are run from MD++ directory.
Note: md_gpp is just a visualization tool. It is not a potential.

Exercises
Now, here are a few exercises to learn the process.
1.Repeat the same process to simulate a nanotube.
2.Repeat the same process to simulate a graphene sheet.
Analysis Questions
1.Compare the coordinate files for the three molecules. Describe the differences and write them down
for discussion.
2.Compare the octave files for the three molecules. Explain the differences and write them down
for discussion.
3.Compare the script files for the three molecules. Explain the differences and write them down
for discussion.

Additional Problem
1. After comparing the above files and given the coordinates file for a nanocapsule, make a simulation of
an nanocapsule. (Hint: Copy and Paste files and make the appropriate changes)

Challenge Exercises
1.Make a temperature dependent bucky ball. Go to the open the script file for the bucky ball and
activate the commands needed to simulate the bucky ball under a desired temperature. For this
temperature dependent simulation a potential call Tersoff potential will be needed. Do the following
step before running the simulation.

Further Step
Open the terminal emulator. Go to the MD++ directory by typing:
cd Codes/MD++
now type:
make tersoff build=R TCL=no
This will compile the Tersoff potential in the bin directory. Now that the script file for the
bucky ball has been modified, type:

bin/tersoff_gpp scripts/myscripts/buckyball.script
This will pop-up a new graphics window with a temperature-dependent bucky ball simulation. The
other simulations can also be made temperature dependent by copying and pasting the sections.

Acknowledgments
Professor Dr. Wei Cai for hosting me as fellow
Keonwook Kang, Graduate Stduent in prof. Wei Cai group
Haneesh
Mechanical Engineering and Computation Department, Durand Hall, Stanford University

References
1.MD++
source: http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/
2.Fullerenes
source: http://en.wikipedia.org/wiki/Fullerene
3.Fullerene Science Module
source: http://www.chemistry.wustl.edu/~edudev/Fullerene/fullerene.html
4.What are fullerenes?
source: http://www.nottingham.ac.uk/~ppzjld/what.htm
5.Carbon Cages: LBL Scientists Study Fullerenes
source: http://lbl.gov/Science-Articles/Archive/fullerenes.html

----

[[w:http:Tutorials|Back to Tutorials]]

----

Introduction to Molecular Dynamics Simulations of Fullerenes

2008-07-25T01:50:31Z

Agarcia:

Introduction to Molecular Dynamics Simulations of Fullerenes

2008-07-25T01:49:05Z

Agarcia:

Introduction to Molecular Dynamics Simulations of Fullerenes

2008-07-25T01:48:13Z

Agarcia:

Introduction to Molecular Dynamics Simulations of Fullerenes

2008-07-25T01:47:07Z

Agarcia:

Introduction to Molecular Dynamics Simulations of Fullerenes

2008-07-25T01:46:07Z

Agarcia:

Introduction to Molecular Dynamics Simulations of Fullerenes

2008-07-25T01:34:37Z

Agarcia:

Introduction to Molecular Dynamics Simulations of Fullerenes

2008-07-25T01:27:41Z

Agarcia:

Images of Fullerenes

2008-07-23T01:36:10Z

Agarcia:

Images generated with the visualizing tool in MD++

[[Image:bb2.gif|600px]]

Bucky Ball

[[Image:buckyball2.jpg|600px]]

Carbon Nanotube

[[Image:buckyball2.jpg|600px]]

Carbon graphene sheet

[[Image:buckyball2.jpg|600px]]

Images generated with the visualizing tool called Atom Eye

[[Image:buckyball2.jpg|600px]]

Bucky Ball.

[[Image:nanotube.jpg|600px]]

Carbon Nanotube.

[[Image:graphenebuckyball.jpg|600px]]

This is an image of a bucky ball on top of the surface of a graphene sheet.