azplugins is a component (plugin) for HOOMD-blue, which expands its functionality for tackling a variety of problems in soft matter physics. It is hosted on GitHub.

First, you will need a working installation of HOOMD-blue, see how to install hoomd. Then, follow essentially the same steps as for installing HOOMD-blue, as outlined here.

First, clone the code into your programs folder (i.e., execute this in a terminal in your home/programs folder):

git clone https://github.com/mphowardlab/azplugins.git

This should create a folder named “azplugins”. Go into that folder and create a “build” folder:

cd azplugins 
mkdir build 
cd build 

Now, we need to compile and install azplugins. Execute:

cmake ..

Two options might be needed at this point. -DHOOMD_ROOT=path to your hoomd installation and -DCMAKE_INSTALL_PREFIX=where you want azplugins to be installed (usually a folder in your home/programs folder). If this executes without any errors, you can compile and install:

 
make install

If you encounter an error indicating issues with generating cuda files (assuming you need GPU compatibility) it is likely a version incompatibility, with gcc or cuda. For azplugins 0.12.0 and earlier, try gcc7 and CUDA10 by passing the following options to the earlier cmake command: -DCMAKE_C_COMPILER=gcc-7 -DCMAKE_CXX_COMPILER=g++-7 -DCUDA_VERSION=10.0

depending on your installation type, you should now be able to use azplugins (with import azplugins or from hoomd import azplugins). See also here: https://azplugins.readthedocs.io/en/latest/installation.html

The page for the flow branch of azplugins is https://github.com/mphowardlab/azplugins/tree/feature/sllod-couette .

In order to install it, first you need to go to the azplugins folder including the code(not the folder with installation files). From the terminal, type 'git checkout feature/sllod-couette'. By doing that, one opens the repository branch including couette-flow from the terminal.

Then type 'git log'. If the message 'Remove unresolved merge marker' appears, you can continue your installation. If no, then you need to update the code from the latest git repository, by typing 'git pull' on your terminal.After this, by typing again 'git log', the message 'Remove unresolved merge marker' should now appear. (in general, check that you have the latest log message)

Moving on, next thing needed is to recompile by going into the build folder. Through the terminal, access build folder in azplugins folder, and then do 'cmake ..'. Two options are needed at this point. -DHOOMD_ROOT=‘path to your hoomd installation’ and ‘-DCMAKE_INSTALL_PREFIX=‘where you want azplugins to be installed, ie azplugins-1.__'.

After this, do 'make install'.

If none of this works, then probably the paths added as options are not correct. One solution would be to remove the branch folder completely and start from scratch, as it is easier to update the branch features this way.

To install azplugins on the campus cluster you follow a similar installation procedure as the one on Mac. First of all, you go into the folder you install programs, let's say this folder is called 'programs'. Then you do the following:

git clone https://github.com/mphowardlab/azplugins.git

This creates a folder named azplugins. You can then go in the azplugins folder and type:

mkdir build && cd build

Now, in the build folder, make sure you are in the right branch of the git repository, for example to study flow you must do:

git checkout feature/sllod-couette 

and then make sure you have are on the latest version by pressing

git pull.

You can check if you are in the right version by typing

git log

After you make sure you are in the right branch and version, load all the needed modules for your installation:

module load cuda/10.0
module load gcc/7.2.0
module load anaconda/3.0

Then, check the modules are loaded using module list. If everything is in place, proceed with your installation by doing:

cmake .. -DHOOMD_ROOT='/home/tk16/programs/hoomd-2.9.0/hoomd'

Since we use anaconda, there is no need to specify a python path, and everything should be straightforward.

Sometimes the flags might differ. You can also use the following command to install azplugins to your designated folder/path.

-DCMAKE_INSTALL_PREFIX='path to your destination to install azplugins'

If no errors occur, do:

make install -j4