Welcome to MCCCS-X’s documentation!

Installation and Running

Docker

Note

For use on supercomputers, use singularity instead

First, docker needs to be installed. Docker Desktop can be installed at https://docs.docker.com/get-docker/

docker pull dejac001/mcccs-mn
docker run -ti -v $PWD:/home/ dejac001/mcccs-mn # run interactively inside container

Then, the image can be accessed interactively by

docker run -ti -v $PWD:/home/ dejac001/mcccs-mn # run interactively inside container

Singularity

module load singularity
singularity pull docker://dejac001/mcccs-mn

Note

It is a good practice to move the singularity image, which is large, to a shared directory (e.g., /home/<groupname>/shared/)

The code can then be run using

module load singularity
cd ${workdir}  # change to working directory where input files are
singularity exec path/to/mcccs-mn_latest.sif topmon

where path/to/mcccs-x_latest.sif is the relative or absolute path to the singularity image made during installation.

To run with multiple processors (e.g. 2), the last line is be replaced with

singularity exec path/to/mcccs-mn_latest.sif mpirun -np 2 topmon

See also

https://www.msi.umn.edu/sites/default/files/Singularity_Containers.pdf

Windows 10

On Windows 10, installing and running can be performed using Docker or Ubuntu. The instructions for Docker are given above. Otherwise, install Windows-Subsystem-for-Linux

then install Ubuntu from the App store and then follow the instructions below for Ubuntu.

Ubuntu

The dockerfiles and docker image is made in ubuntu, so the same commands can be made as those in the docker files.

First, the dependencies need to be installed. The associated dockerfile looks like the following

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FROM ubuntu
MAINTAINER <dejac001@umn.edu>

RUN apt-get update
RUN DEBIAN_FRONTEND="noninteractive" \
   apt-get -y install gfortran cmake git mpi mpich

To install the ubuntu dependencies, type in the commands after RUN.

Second, the code needs to be cloned from the repository. The associated dockerfile looks like

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FROM dejac001/mcccs-x-base
MAINTAINER <dejac001@umn.edu>

RUN cd /lib \
    && git clone https://github.com/dejac001/desorption.git MCCCS-MN \
    && mkdir -p MCCCS-MN/build && cd MCCCS-MN/build/ \
    && cmake -D CMAKE_BUILD_TYPE=RELEASE .. && make -j 2 \
    && ln -sf /lib/MCCCS-MN/build/src/topmon /usr/bin/topmon

Again, installation in ubuntu requires using the same commands after RUN.

Minnesota Supercomputing Institute

Mesabi

module load cmake
git clone https://github.com/dejac001/desorption.git MCCCS-MN
cd /path/to/MCCCS-MN
mkdir build && cd build/
cmake ..
make -j 2

Note

This uses the GNU 4.8.5 fortran compiler. You can try using other compilers too.

Siepmann Group

Metropolis

module purge
git clone https://github.com/dejac001/desorption.git MCCCS-MN && cd MCCCS-MN
module load cmake intel impi
mkdir build && cd build
FC=ifort cmake ..
make -j 2

Input files

Note

See the following for restructured text (.rst) file formats https://docutils.sourceforge.io/docs/user/rst/quickref.html#definition-lists

fort.4

mc_shared

seed

(integer) Random number seed, defaults to ??

nbox

(integer) Number of boxes in simulation, defaults to ??

nmolty

(integer) Number of molecule types in simulation, defaults to ??

analysis

mc_volume

mc_swatch

mc_swap

mc_cbmc

mc_simple

SIMULATION_BOX

MOLECULE_TYPE

MC_SWAP

MC_SWATCH

INTERMOLECULAR_EXCLUSION

UNIFORM_BIASING_POTENTIALS

topmon.inp

Holds many bead parameters

fort.77

Restart file

Algorithms

A mathematical equation can be written like

\[a + b = c^2\]

which is similar to latex

Coupled-Decoupled Configurational-Bias Monte Carlo

See reference [MS99]

CBMC

See references ??

SAFE-CBMC

AVBMC

References

MS99

M G Martin and J I Siepmann. Novel Configurational-bias Monte Carlo Method for Branched Molecules. Transferable Potentials for Phase Equilibria. 2. United-atom Description of Branched Alkanes. J. Phys. Chem. B, 103:4508–4517, 1999.

Indices and tables