@@ -10,10 +10,7 @@ used for the enhanced sampled algorithm.
\section lugano-6a-lo Objectives
Once this tutorial is completed students will
- Know how to compile LAMMPS together with PLUMED
- Have used PLUMED coupled with LAMMPS to perform an investigation of their own design
Once this tutorial is completed students will have used PLUMED coupled with LAMMPS to perform an investigation of their own design.
\section lugano-6a-resources Resources
...
...
@@ -43,75 +40,15 @@ that the method proposed is not a particularly good way to investigate the pheno
\subsection lugano-6a-installation Installing LAMMPS with PLUMED
You can get a copy of LAMMPS from this website:
https://lammps.sandia.gov/download.html
In preparing the material for this exercises I downloaded the latest stable release C++ source. You can try to download the pre-built executables. I did
not do this, however, as I have a Mac and have broken many things on it in the past by using homebrew. I therefore am, as a rule, distrustful of homebrew.
I thus instead made a directory called:
\verbatim
/Users/gareth/Plumed-tutorial/LAMMPS
\endverbatim
On my directory, I copied the downloaded LAMMPS tar ball into this directory and extracted it from the tar ball using the command:
\verbatim
tar -xvf lammps-5Jun19.tar
\endverbatim
Once this operation was completed I found that when I ls the LAMMPS directory I created I have the following files:
\verbatim
lammps-5Jun19 lammps-5Jun19.tar
\endverbatim
Before building LAMMPS I rebuilt a version of PLUMED to link with LAMMPS. I did this using the following commands:
You can find the instructions about how to install LAMMPS patched with PLUMED here:
I set the --prefix flag here to the directory I created to hold my compiled version of LAMMPS here rather than using the default in order to be able to control exactly what version of PLUMED I was linking
LAMMPS with. Setting the prefix in this way ensures that once the above three commands have been run the contents of the LAMMPS directory I created in the first step are as follows:
\verbatim
bin include lammps-5Jun19 lammps-5Jun19.tar lib
\endverbatim
To build LAMMPS we now issue the following commands:
LAMMPS requires cmake, ffmpeg, gsl and xdrfile, which for some reason were not installed on my computer. I therefore installed these packages using the commands:
\verbatim
sudo port install cmake
sudo port install ffmpeg
sudo port install gsl
sudo port install xdrfile
\endverbatim
Finally now that cmake was installed I could build LAMMPS using the command:
\verbatim
make
\endverbatim
This generates an executable called lmp in the build directory, which is used for the remainder of the exercises in this tutorial.
\subsection lugano-6a-setup-equilibration Setting up the simulation and equilibrating
Having compiled LAMMPS we can now run a simulation with LAMMPS. If we take the input lammps-equilibration.in that we downloaded from the tarball we can run this simulation using the following commands:
We can now run a simulation with LAMMPS. If we take the input lammps-equilibration.in that we downloaded from the tarball we can run this simulation using the following commands:
