Installation instructions
Untar/unzip the tar.gz
Once you have downloaded the source code, untar and unzip the file:
tar xvfz Amk-SOURCE-2018rev.tar.gz
or clone the code from github:
git clone https://github.com/emartineznunez/AutoMeKin.git
Installing dependencies
Before installing amk for the first time, be aware that the following packages are needed:
- [GNU Bash | https://www.gnu.org/software/bash/] - [GNU bc](https://www.gnu.org/software/bc/) - [GNU Awk (gawk)](https://www.gnu.org/software/gawk/) - [GNU C Compiler (gcc)](https://gcc.gnu.org/) - [Gnuplot](http://www.gnuplot.info/) - [GNU Fortran Compiler (gfortran)](https://gcc.gnu.org/wiki/GFortran) - [GNU Parallel](https://www.gnu.org/software/bash/manual/html_node/GNU-Parallel.html) - [NumPy](https://www.numpy.org/) - [SciPy](https://www.scipy.org/) - [SQLite](https://www.sqlite.org/index.html) (version >= 3) - [Zenity](https://wiki.gnome.org/Projects/Zenity)
You can install the missing ones manually, or you can use the scripts located in amk-SOURCE-2018 and called install-required-packages-distro.sh (where distro=ubuntu-16.4lts, centos7 or sl7), which will do the work for you.The ubuntu-16.4lts script installs all dependencies, but for the RHEL derivatives (centos7 and sl7) you have to install parallel separately, and you have two choices:
a) install-gnu-parallel-from-source.sh. This script installs parallel latest version from source thanks to Ole Tange (the author). Also it can fallback to a user private installation into $HOME/bin if you have not administrator permisions to install it globally.
b) install-gnu-parallel-from-epel.sh. Enables the EPEL repository and installs parallel from it.
The program runs using two levels of theory: semiempirical (or Low-Level LL) and ab initio/DFT (or High-Level HL). So far, the only program interfaced with amk to perform the ab initio/DFT calculations is G09. Therefore, if you want to perform the HL calculations G09 should be installed and should run like in this example: g09<inputfile>outputfile.
These packages might also be useful to analyze the results:
molden, sqlitebrowser
Installation
Once the above packages are installed, either:
Go to AutoMeKin if you cloned it from github
cd AutoMeKin
or go to the amk-SOURCE-2018 folder, if you downloaded the tarball.
cd amk-SOURCE-2018
In both cases, the process continues the same way. Now type:
./configure
This will install amk in $HOME/amk-2018 by default. If you want to install it in a different directory, type:
./configure --prefix=path_to_program
Finally, complete the installation:
make
make install
make clean
The last command (make clean) is only necessary if you want to remove from the src directory the object files and executables created in the compilation process.
For convenience, and once “Environment Modules” has been installed, you should add the following line to your .bashrc file:
module use path_to_program/modules
where path_to_program is the path where you installed amk (e.g., $HOME/amk-2018).
Running the test
To run the formic acid test example (explained in the tutorial ) for a few trajectories follow these steps:
1) Load the module:
module load amk/2018
2) Run the script if amk has been installed in $HOME:
run_test.sh
or
run_test.sh --prefix=path_to_program
otherwise.
This will create a directory named FA_test, where you can check the results (see the tutorial for details). The test may take a few minutes.
Return to AutoMeKin
