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LAMMPS

Installation​

On Ares​

When you are on Ares, you should ideally find the lammps application already installed as a module. To see if there is a lammps module in ares run the below command:

module spider lammps
#module -r spider '.*lammps*.'

To load the module use. (Note that this loads the default lammps version)

module load lammps

Using spack​

You can view the lammps in list of provided packages in spack using:

spack list lammps

To list the details of lammps(version, description, dependencies, etc.)

spack info lammps

To install lammps with adios2 dependency using spack

spack install lammps+adios

Building from source​

You can download the source and the documentation as a tarball

mkdir Build_lammps
cd Build_lammps
wget -c https://download.lammps.org/tars/lammps-stable.tar.gz
tar -xzvf lammps*.tar.gz

Now change the directory to the LAMMPS distribution directory that just got uncompressed

cd /path/to/lammps 
mkdir build; cd build  # create and use a build directory

Building LAMMPS with ADIOS2​

Using CMake​

We are going to install LAMMPS with ADIOS2 using CMake. Note that LAMMPS requires CMake version 3.10 or later. You can check your cmake version using:

cmake --version

In order to build lammps with adios2, the adios2 library need to be on your system or be downloaded and built. Then, you need to tell LAMMPS where it is found on your system.

# This can be done by providing the adios2 installation directory in PATH variable
export PATH=/path/of/adios2:$PATH
#This is ADIOS2 installed path in my system: ~/spack/opt/spack/linux-ubuntu22.04-skylake/gcc-11.4.0/adios2-2.9.0-fsrkmnhkjp4ozmq5fsy2ryeaqcuuzhu

One important thing to note here is that if you have ADIOS2 built either with or without MPI then the same has to be matched while building LAMMPS.

#if ADIOS2 was built with MPI 
cmake ../cmake -D PKG_ADIOS=yes -D BUILD_MPI=yes  
#if ADIOS2 was built without MPI then
#cmake ../cmake -D PKG_ADIOS=yes -D BUILD_MPI=no

Now the build files would been written to your build folder. Now compile them using:

make 
#make -j N

If the compilation is successful, you should see a library liblammps.a and the LAMMPS executable lmp inside the build folder.

Now you can either use LAMMPS by running the executable using from this directory using:

./lmp

Or, you can install the LAMMPS executable into your system with:

make install #copies compiled files into installation location

Usage​

In order to show the usage of lammps with adios2, we can use either dump atom/adios or dump custom/adios commands. What these commands do is that these dump a snapshot of atom coordinates every N timesteps in ADIOS-bases "BP" file format, or using a different I/O solutions in adios to a stream that can be read on-line by another program. Here is the syntax for each:

dump ID group-ID atom/adios N file.bp
dump ID group-ID custom/adios N file.bp args

Example usages: Save the below file as lj_fluid.in

# create a Lennard-Jones fluid
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 20 0 20 0 20
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no

# define a group of atoms
group fluid type 1

# dump atom coordinates every 100 timesteps to atoms.bp
dump adios1 fluid atom/adios 100 atoms.bp

# dump custom quantities every 50 timesteps to custom.bp
dump adios2 fluid custom/adios 50 custom.bp id type x y z vx vy vz

# run the simulation for 1000 timesteps
run 1000

Then run lammps by giving this input file as argument as shown:

lmp -in lj_fluid.in

If this is successful, you should see the below files in the current directory:

custom.bp
atoms.bp

Note that a file adios2_config.xml with specific configuration settings is expected in the current working directory. If the file is not present, LAMMPS will create a minimal default file.