From d0bed2faa092da812e8b2c049b6b74c31768b05a Mon Sep 17 00:00:00 2001 From: Massimiliano Bonomi <massimiliano.bonomi@gmail.com> Date: Wed, 24 Jul 2019 12:11:12 +0200 Subject: [PATCH] modified installation --- user-doc/tutorials/aa-lugano-6a.txt | 71 ++--------------------------- 1 file changed, 4 insertions(+), 67 deletions(-) diff --git a/user-doc/tutorials/aa-lugano-6a.txt b/user-doc/tutorials/aa-lugano-6a.txt index 282c1f86f..8ae3d777d 100644 --- a/user-doc/tutorials/aa-lugano-6a.txt +++ b/user-doc/tutorials/aa-lugano-6a.txt @@ -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: \verbatim -./configure --enable-modules=all --prefix=/Users/gareth/Plumed-tutorial/LAMMPS -make -make install +https://github.com/plumed/conda#install-lammps \endverbatim -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: - -\verbatim -cd lammps-5Jun19 -mkdir build -cd build -export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/Users/gareth/Plumed-tutorial/LAMMPS/lib/pkgconfig -cmake -D PKG_MANYBODY=yes -D PKG_KSPACE=yes -D PKG_MOLECULE=yes -D PKG_RIGID=yes -D PKG_USER-PLUMED=yes ../cmake -\endverbatim - -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: \verbatim touch plumed.dat -- GitLab