Micro and Nano Mechanics Group - User contributions [en]

Compile LAMMPS on GPU on Sherlock

2015-07-22T22:45:47Z

Mjorda: /* Compile LAMMPS with gpu */

<P ALIGN="CENTER">
<FONT SIZE="+3" color="darkred"><STRONG>
Compile LAMMPS on GPU on Sherlock </STRONG></font></P>
<DIV>
<P ALIGN="CENTER"><STRONG>Mikael Jorda</STRONG></P>
</DIV>
<P ALIGN="CENTER"> Created july 2015</P>

This tutorial explains how to install, compile and use LAMMPS with GPUs on the cluster Sherlock
<HR>

==Installing and compiling LAMMPS on sherlock==
In order to use LAMMPS on GPU, you must compile it with the cuda library. The process is a little bit different from the usual compilation of LAMMPS.

===Download LAMMPS===

Go to the LAMMPS website (http://lammps.sandia.gov/download.html) and download the most recent stable version of the code. Put it in your Codes directory and unzip it
tar -zxvf lammps-stable.tar.gz

'''or'''

The following command can be used to checkout a specific reversion of LAMMPS from our '''svn''' server.

svn checkout -r 23 http://micro.stanford.edu/svn/LAMMPS ~/Codes/LAMMPS.svn/

1. Copy Makefile.mc2 into Codes/LAMMPS.svn/src/MAKE/ directory using the following commands
cd ~/Codes/LAMMPS
wget http://micro.stanford.edu/mediawiki/images/f/fb/Makefile.mc2.txt -O ./src/MAKE/Makefile.mc2

2. In any directory, type the following command
Export TARGET=sherlock
(or add it to your bash_profile not to have to type it every time you connect to the cluster)

3. In your home directory, make a folder named '''usr'''
mkdir ~/usr

4. Download the fftw library and unzip it using the following commands
cd ~/usr
wget http://micro.stanford.edu/mediawiki/images/9/9e/Fftw.tar -O fftw.tar
tar –zxvf fftw.tar

5. Make sure you have the modules for using '''mpi''' complier and '''cuda''', you can load the modules by adding the below two lines to your '''bash_profile''' file.
vi ~/.bash_profile (You can use whatever text editor to open the file and add the following lines)

module load mpich/3.1.4
module load cuda

Save the file and log out. Next time when you log in, the compilers should work for you.

===Compile LAMMPS with gpu===

You need first to build the GPU library. Go to your lammps/lib/gpu folder.
Copy the generic linux makefile
cd ~/Codes/LAMMPS/lib/gpu
cp Makefile.linux Makefile.sherlock

You have to modify 3 lines in this file. Open it and replace the values of CUDA_HOME, CUDA_ARCH and CUDA_PREC with the following
vi Makefile.sherlock

CUDA_HOME = /share/sw/free/cuda/6.5
CUDA_ARCH = -arch=sm_35
CUDA_PREC = -D_DOUBLE_DOUBLE

==Using the GPU for a LAMMPS run==

===Modify the input script===

===Request GPUs on Sherlock===

Compile LAMMPS on GPU on Sherlock

2015-07-22T22:44:51Z

Mjorda: /* Compile LAMMPS with gpu */

<P ALIGN="CENTER">
<FONT SIZE="+3" color="darkred"><STRONG>
Compile LAMMPS on GPU on Sherlock </STRONG></font></P>
<DIV>
<P ALIGN="CENTER"><STRONG>Mikael Jorda</STRONG></P>
</DIV>
<P ALIGN="CENTER"> Created july 2015</P>

This tutorial explains how to install, compile and use LAMMPS with GPUs on the cluster Sherlock
<HR>

==Installing and compiling LAMMPS on sherlock==
In order to use LAMMPS on GPU, you must compile it with the cuda library. The process is a little bit different from the usual compilation of LAMMPS.

===Download LAMMPS===

Go to the LAMMPS website (http://lammps.sandia.gov/download.html) and download the most recent stable version of the code. Put it in your Codes directory and unzip it
tar -zxvf lammps-stable.tar.gz

'''or'''

The following command can be used to checkout a specific reversion of LAMMPS from our '''svn''' server.

svn checkout -r 23 http://micro.stanford.edu/svn/LAMMPS ~/Codes/LAMMPS.svn/

1. Copy Makefile.mc2 into Codes/LAMMPS.svn/src/MAKE/ directory using the following commands
cd ~/Codes/LAMMPS
wget http://micro.stanford.edu/mediawiki/images/f/fb/Makefile.mc2.txt -O ./src/MAKE/Makefile.mc2

2. In any directory, type the following command
Export TARGET=sherlock
(or add it to your bash_profile not to have to type it every time you connect to the cluster)

3. In your home directory, make a folder named '''usr'''
mkdir ~/usr

4. Download the fftw library and unzip it using the following commands
cd ~/usr
wget http://micro.stanford.edu/mediawiki/images/9/9e/Fftw.tar -O fftw.tar
tar –zxvf fftw.tar

5. Make sure you have the modules for using '''mpi''' complier and '''cuda''', you can load the modules by adding the below two lines to your '''bash_profile''' file.
vi ~/.bash_profile (You can use whatever text editor to open the file and add the following lines)

module load mpich/3.1.4
module load cuda

Save the file and log out. Next time when you log in, the compilers should work for you.

===Compile LAMMPS with gpu===

You need first to build the GPU library. Go to your lammps/lib/gpu folder.
Copy the generic linux mkefile
cd ~/Codes/LAMMPS/lib/gpu
cp Makefile.linux Makefile.sherlock

You have to modify 3 lines in this file. Open it and replace the values of CUDA_HOME, CUDA_ARCH and CUDA_PREC with the following
vi Makefile.sherlock

CUDA_HOME = /share/sw/free/cuda/6.5
CUDA_ARCH = -arch=sm_35
CUDA_PREC = -D_DOUBLE_DOUBLE

==Using the GPU for a LAMMPS run==

===Modify the input script===

===Request GPUs on Sherlock===

Compile LAMMPS on GPU on Sherlock

2015-07-22T22:39:16Z

Mjorda: /* Download LAMMPS */

<P ALIGN="CENTER">
<FONT SIZE="+3" color="darkred"><STRONG>
Compile LAMMPS on GPU on Sherlock </STRONG></font></P>
<DIV>
<P ALIGN="CENTER"><STRONG>Mikael Jorda</STRONG></P>
</DIV>
<P ALIGN="CENTER"> Created july 2015</P>

This tutorial explains how to install, compile and use LAMMPS with GPUs on the cluster Sherlock
<HR>

==Installing and compiling LAMMPS on sherlock==
In order to use LAMMPS on GPU, you must compile it with the cuda library. The process is a little bit different from the usual compilation of LAMMPS.

===Download LAMMPS===

Go to the LAMMPS website (http://lammps.sandia.gov/download.html) and download the most recent stable version of the code. Put it in your Codes directory and unzip it
tar -zxvf lammps-stable.tar.gz

'''or'''

The following command can be used to checkout a specific reversion of LAMMPS from our '''svn''' server.

svn checkout -r 23 http://micro.stanford.edu/svn/LAMMPS ~/Codes/LAMMPS.svn/

1. Copy Makefile.mc2 into Codes/LAMMPS.svn/src/MAKE/ directory using the following commands
cd ~/Codes/LAMMPS
wget http://micro.stanford.edu/mediawiki/images/f/fb/Makefile.mc2.txt -O ./src/MAKE/Makefile.mc2

2. In any directory, type the following command
Export TARGET=sherlock
(or add it to your bash_profile not to have to type it every time you connect to the cluster)

3. In your home directory, make a folder named '''usr'''
mkdir ~/usr

4. Download the fftw library and unzip it using the following commands
cd ~/usr
wget http://micro.stanford.edu/mediawiki/images/9/9e/Fftw.tar -O fftw.tar
tar –zxvf fftw.tar

5. Make sure you have the modules for using '''mpi''' complier and '''cuda''', you can load the modules by adding the below two lines to your '''bash_profile''' file.
vi ~/.bash_profile (You can use whatever text editor to open the file and add the following lines)

module load mpich/3.1.4
module load cuda

Save the file and log out. Next time when you log in, the compilers should work for you.

===Compile LAMMPS with gpu===

You need first to build the GPU library. Go to your lammps/lib/gpu folder.
Copy the generic linux mkefile
cp Makefile.linux Makefile.sherlock

You have to modify 3 parameters in this file

==Using the GPU for a LAMMPS run==

===Modify the input script===

===Request GPUs on Sherlock===

Compile LAMMPS on GPU on Sherlock

2015-07-22T22:31:10Z

Mjorda: /* Compile LAMMPS with gpu */

Compile LAMMPS on GPU on Sherlock

2015-07-22T22:20:44Z

Mjorda: /* Download LAMMPS */

Compile LAMMPS on GPU on Sherlock

2015-07-22T22:13:12Z

Mjorda:

Compile LAMMPS on GPU on Sherlock

2015-07-22T22:11:41Z

Mjorda:

Compile LAMMPS on GPU on Sherlock

2015-07-22T22:09:57Z

Mjorda:

Compile LAMMPS on GPU on Sherlock

2015-07-22T22:04:27Z

Mjorda: Created page with "<P ALIGN="CENTER"> <FONT SIZE="+3" color="darkred"><STRONG> Compile LAMMPS on GPU on Sherlock </STRONG></font></P> <DIV> <P ALIGN="CENTER"><STRONG>Mikael Jorda</STRONG></P> <..."

Tutorial:Members Only

2015-07-22T21:59:37Z

Mjorda: /* Manuals for Group Members */

== Manuals for Group Members ==

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Scientific Articles
|-
| [https://micro.stanford.edu/journal-repository Journal Repository]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | ParaDiS
|-
| [[ParaDiS Cylinder Code Manuals ]]
|-
| [[ParaDiS ThinFilm Code Manuals]]
|-
| [[ParaDiS Aniso Code Manuals]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | MD++
|-
| [[Foward Flux Sampling in MD++]]
|-
| [[Torsion and Bending PBC in MD++]]
|-
| [[A Polygonal Dislocation Loop in MD++]]
|-
| [[Use of Ewald Summation in MD++]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | LAMMPS
|-
| [[Use Au-Si MEAM Potential in LAMMPS]]
|-
| [[Compile LAMMPS on GPU on Sherlock]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Phase Field
|-
| [[Summary of Nanowire Growth Mechanism]]
|-
| [[Single Phase Field Model with Isotropic Surface Energy]]
|-
| [[Single Phase Field Model with Anisotropic Surface Energy]]
|-
| [[Multi Phase Field Model with Isotropic Interface Energy]]
|-
| [[Multi Phase Field Model with Anisotropic Interface Energy]]
|-
| [[Multi Phase Field Model (Revised Formulation)]]
|-
| [[Parallelization of the Phase Field Model]]
|-
| [[Phase Field Model for Grain Evolution]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | VASP
|-
| [[VASP Computing Bulk Modulus of Au]]
|-
| [[VASP Computing Bulk Modulus of ZrO2]]
|-
| [[VASP Computing Bulk Modulus of YSZ]]
|-
| [[VASP Computing Density of States of YSZ]]
|-
| [[VASP Computing Generalized Stacking Fault Energy of Au]]
|-
| [[VASP Computing Ideal Shear Strength of Au]]
|-
| [[VASP terminology]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Qbox
|-
| [[Qbox Computing Bulk Modulus of Au]]
|-
| [[Qbox Computing Bulk Modulus of ZrO2]]
|-
| [[Qbox Implemention of Magnetic Field]]
|-
| [[Qbox Generating Pseudopotentials]]
|-
| [[Ab Initio Simulations of Condensed Matter under Arbitrary Magnetic Field | MPBC/Qbox draft1]]
|-
| [[Predicting Molecular and Electronic Response to Magnetic Field from First Principles | MPBC/Qbox draft2]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | C++
|-
| [[BOOST Library]]
|-
| [[Install GCC]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | LaTeX
|-
| [[Install LaTeX from Scratch]]
|-
| [[Beamer Presentations]]
|-
| [[TikZ package]]
|-
| [[PGFPLOTS]]
|-
| [[Asymptote]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Tools
|-
| [[Atom Eye]]
|-
| [[Gnuplot]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Computers
|-
| [[Micro Maintenance]]
|-
| [[Libraries in SU-AHPCRC]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Fatigue Literature Review
|-
| [[2D Dislocation Dynamics]]
|-
| [[3D Dislocation Dynamics]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Outreach
|-
| [[Simulating Solids in MD++]]
|-
| [[Videos of bucky balls in motion]]
|}

Tutorials

2015-07-22T21:59:03Z

Mjorda: /* Simulation Codes */

== 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" | [[How to compile LAMMPS]]
!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]]
|

|}

<br> <br>

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

Tutorials

2015-07-22T21:57:55Z

Mjorda: /* Simulation Codes */

== 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" | [[How to compile LAMMPS]]
!width="200" | [[How to compile LAMMPS with gpu on Sherlock]]
!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]]
|

|}

<br> <br>

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

Tutorial:Members Only

2015-07-08T21:16:36Z

Mjorda: /* Manuals for Group Members */

== Manuals for Group Members ==

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Scientific Articles
|-
| [https://micro.stanford.edu/journal-repository Journal Repository]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | ParaDiS
|-
| [[ParaDiS Cylinder Code Manuals ]]
|-
| [[ParaDiS ThinFilm Code Manuals]]
|-
| [[ParaDiS Aniso Code Manuals]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | MD++
|-
| [[Foward Flux Sampling in MD++]]
|-
| [[Torsion and Bending PBC in MD++]]
|-
| [[A Polygonal Dislocation Loop in MD++]]
|-
| [[Use of Ewald Summation in MD++]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | LAMMPS
|-
| [[Use Au-Si MEAM Potential in LAMMPS]]
|-
| [[Compile LAMMPS on GPU]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Phase Field
|-
| [[Summary of Nanowire Growth Mechanism]]
|-
| [[Single Phase Field Model with Isotropic Surface Energy]]
|-
| [[Single Phase Field Model with Anisotropic Surface Energy]]
|-
| [[Multi Phase Field Model with Isotropic Interface Energy]]
|-
| [[Multi Phase Field Model with Anisotropic Interface Energy]]
|-
| [[Multi Phase Field Model (Revised Formulation)]]
|-
| [[Parallelization of the Phase Field Model]]
|-
| [[Phase Field Model for Grain Evolution]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | VASP
|-
| [[VASP Computing Bulk Modulus of Au]]
|-
| [[VASP Computing Bulk Modulus of ZrO2]]
|-
| [[VASP Computing Bulk Modulus of YSZ]]
|-
| [[VASP Computing Density of States of YSZ]]
|-
| [[VASP Computing Generalized Stacking Fault Energy of Au]]
|-
| [[VASP Computing Ideal Shear Strength of Au]]
|-
| [[VASP terminology]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Qbox
|-
| [[Qbox Computing Bulk Modulus of Au]]
|-
| [[Qbox Computing Bulk Modulus of ZrO2]]
|-
| [[Qbox Implemention of Magnetic Field]]
|-
| [[Qbox Generating Pseudopotentials]]
|-
| [[Ab Initio Simulations of Condensed Matter under Arbitrary Magnetic Field | MPBC/Qbox draft1]]
|-
| [[Predicting Molecular and Electronic Response to Magnetic Field from First Principles | MPBC/Qbox draft2]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | C++
|-
| [[BOOST Library]]
|-
| [[Install GCC]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | LaTeX
|-
| [[Install LaTeX from Scratch]]
|-
| [[Beamer Presentations]]
|-
| [[TikZ package]]
|-
| [[PGFPLOTS]]
|-
| [[Asymptote]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Tools
|-
| [[Atom Eye]]
|-
| [[Gnuplot]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Computers
|-
| [[Micro Maintenance]]
|-
| [[Libraries in SU-AHPCRC]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Fatigue Literature Review
|-
| [[2D Dislocation Dynamics]]
|-
| [[3D Dislocation Dynamics]]
|}

{| class="wikitable" cellpadding="2" style="text-align:center"
|-
!width="500" | Outreach
|-
| [[Simulating Solids in MD++]]
|-
| [[Videos of bucky balls in motion]]
|}

M11 MD++ Powered by Python

2015-01-15T02:24:39Z

Mjorda:

MD++ with Python scripting language ([http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/PDF_Manuals/M11_MD++_v3.pdf Python])

example scripts

<UL>
<LI> [http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/Python/si.py si.py]
<LI> [http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/Python/si2.py si2.py]
<LI> [http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/Python/si-arg.py si-arg.py]
<LI> [http://micro.stanford.edu/~caiwei/Forum/2004-12-12-MD++/Python/si-temp.py si-temp.py]
</UL>

M11 MD++ Powered by Python

2015-01-15T01:50:48Z

Mjorda:

M11 MD++ Powered by Python

2015-01-15T01:49:32Z

Mjorda:

File:Si.txt

2015-01-15T01:48:21Z

Mjorda:

M11 MD++ Powered by Python

2015-01-15T01:41:05Z

Mjorda:

M11 MD++ Powered by Python

2015-01-15T01:35:41Z

Mjorda: Created page with "MD++ with Python scripting language (Python) example scripts <UL> <LI> si.py <LI> si2.py <LI> si-arg.py <LI> si-temp.py </UL>"

MD++ with Python scripting language ([[M11_MD++_v3.pdf |Python]])

example scripts

<UL>
<LI> [[si.py]]
<LI> [[si2.py]]
<LI> [[si-arg.py]]
<LI> [[si-temp.py]]
</UL>

MD++ Manuals

2015-01-15T01:25:23Z

Mjorda:

<H4>Manuals</H4>
<UL>
<LI> [http://micro.stanford.edu/MDpp/docs/list MD++ Documentation]
<LI>[[M01 Introduction to MD++]]
<LI>[[M02 Making a Perfect Crystal]]
<LI>[[M03 Equilibrium Lattice Constant and Bulk Modulus]]
<LI>[[M04 Energy Minimization of Vacancy]]
<LI>[[M05 Finite Temperature Simulation]]
<LI>[[M06 Visualization ]]
<LI>[[M07 Computing Elastic Constants | M07 Computing Elastic Constants at ''T'' = 0]]
<LI>[[M08 MD++ Powered by Tcl Language]]
<LI>[[M09 Computing Ideal Strength]]
<LI>[[M10 DisregistryAnalysis | M10 Visualize Disregistry vector]]
<LI>[[M11 MD++ Powered by Python]]
<LI>[http://micro.stanford.edu/~caiwei/me346/ Molecular Simulations Lecture Notes]
<LI>[[Comprehensive Nuclear Materials MD Case Studies | Case Studies of Crystals and Dislocations]]
<LI>[[MD++ An Example Script File | An Example Script File]]
<LI>[[MD++ An Example Tcl File | An Example Tcl File]]
</UL>

<H4>Technical details</H4>
<UL>
<LI>[[ MD++ QnA | MD++ FAQs]]
<LI>[[MD Potential Files]]
<LI>[[Making Amimations Using a MD++ Script File | Making Movies in MD++]]
<LI>[[Output File Formats in MD++]]
<LI>[[Running MD++ on Mac OS]]
</UL>

<H4>Advanced topics</H4>
<UL>
<LI>[[media:ewald_notes.pdf | Notes on Ewald Summation]]
<LI>[[Computing Melting Point by Free Energy Method]]
<LI>[[M04A Conjugate Gradient Method in MD++ | Conjugate Gradient Methods in MD++]]
<LI>[[Computing Elastic Constants 2 | Computing Elastic Constants at Finite Temperature]]
<LI>[[M10 Angular momentum is conserved or not | Conservation of Angular Momentum]]
<LI>[[Use MEAM in MD++]]
<LI>[[media:Day1_Ising_Demo.pdf | Monte Carlo Simulation of 2D Ising Model]]
<LI>[[Phonon dispersion relation | Phonon Dispersion Relation of Graphene]]
</UL>