# Mammoth’s documentation!¶

Recently, we have found mammoths genetic material preserved in the permafrost of Siberia. Thanks to genetic engineering, we are able to clone this mammal eradicated since millions of years and use elephants to bear the baby. Using the tiny bits of information present in the code, one can recreate the life of a huge mammal of ancient times.

This is the aim of The Mammoth Project: using bits of information obtained from ab initio calculations of molecules and aggregated systems, we wish to recreate the “life” of these molecules using Classical Molecular Dynamics. These molecules can then evolve to others using the basis of Reactive Molecular Dynamics.

## What is it and why to use it ?¶

Long description with all features …

• orca module in order to read ORCA output files
• mammoth Modules: core, qm2ff.
• the mammoth command for a command line interface (CLI)

Blabla …

## Installation¶

### Install mammoth from source¶

In order to install mammoth from source, you must be able to access to the gitlab repository.

Note that, although not described here, the best practice is to first setup a pyhon virtualenv and then install mammoth in that environment.

#### 1. Clone the repository¶

Run the following command in order to clone the repository:

git clone git@gitlab.com:mammoth_uppa/mammoth.git


Take a look at the requirements.txt to see the mammoth dependencies and needed packages.

#### 2. Installation¶

The installation is supported by setuptools using the file setup.py. There are two options:

• A classic installation if you only want to use mammoth.
• A developper installation if you want to use and contribute to mammoth.
##### 2.1 Classic installation¶

Run the following command:

python setup.py install --prefix=/path/to/the/install/directory


the –prefix option is optional and allows you to install mammoth in a specific directory. Note that the installation directory must be in your PYTHONPATH. This is a better choice if you want to remove easyly all mammoth files.

For example, if you install mammmoth in /home/user/mmtest/, you have first to update PYTHONPATH such as:

export PYTHONPATH=/home/user/mmtest/lib/python3.6/site-packages:\$PYTHONPATH

##### 2.2 Developper installation¶

To install mammoth as a developper, run the following command:

python setup.py develop --prefix=/path/to/the/install/directory


again, the --prefix option allows you to install mammith in a specific directory. Note that the installation directory must be in your PYTHONPATH. See above for more details.

If you install mammoth as a developper, each change you do in the source code of mammoth is immediately available. With the basic installation you would have to install mammoth each time you change something.

#### 3. Uninstall mammoth¶

If you want to remove all files installed by mammoth you have the following options:

• If you have created a virtualenv, just remove it !
• If you have installed mammoth directly follow the instructions here

## Mammoth command line interface¶

The mammoth command reads the given input file and run the desired calculations or do the wanted job. run:

mammoth.py -h