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AUTOMATON: A novel program for the search of global minimum structures of atomic clusters and molecules in the gas phase.

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Automaton

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AUTOMATON is a hybrid program that combines a probabilistic cellular automata and a genetic algorithm for the global minimum search of clusters and molecules. The main procedure consists of two major steps: first, a discrete population is generated combining rules of a simplified Cellular Automata model with geometrical optimizations (to the nearest stationary point) using an ab initio or DFT method; second, this population is primarily evolved through genetic operations, and then followed by geometrical optimizations, towards the nearest stationary point. Additionally, AUTOMATON includes a structure-recognition routine, which is used at different stages of the search process to identify and eliminate duplicate structures.

• Osvaldo Yañez, Rodrigo Báez-Grez, Diego Inostroza, Walter A. Rabanal-León, Ricardo Pino-Rios, Jorge Garza, and W. Tiznado. Journal of Chemical Theory and Computation 2019 15 (2), 1463-1475. DOI: 10.1021/acs.jctc.8b00772 https://pubs.acs.org/doi/abs/10.1021/acs.jctc.8b00772

• Osvaldo Yañez, Diego Inostroza, Brandon Usuga‑Acevedo, Alejandro Vásquez‑Espinal, Ricardo Pino‑Rios, Mauricio Tabilo‑Sepulveda, Jorge Garza, Jorge Barroso, Gabriel Merino, William Tiznado. Theoretical Chemistry Accounts 2020 139 (41), 1-8. DOI: 10.1007/s00214-020-2548-5 https://link.springer.com/article/10.1007/s00214-020-2548-5

Last update: February, 11-2020

Getting Started

1) Step Zero

Before starting the installation, it is important to know that AUTOMATON is not a full or autonomous software; instead, it needs an assisting program to calculate energies and perform optimizations like Gaussian, Mopac or Lammps. AUTOMATON uses these pre-installed tools for the minima local search on the potential energy surface (PES).

1. Installing external softwares.

• Mopac (http://openmopac.net/Download_MOPAC_Executable_Step2.html)

• Gaussian (http://gaussian.com/)

• Lammps (https://lammps.sandia.gov/download.html#ubuntu)

NOTE: mpiexec for Lammps (https://www.mpich.org/static/docs/v3.1/www1/mpiexec.html)

2. Installing Perl environment.

Once the programs for both energy calculations and geometry optimizations are working correctly, the Perl environment needs to be installed as well. Perl is a highly capable, feature-rich programming language that runs on many platforms from portable to mainframes. It can be installed from:

There are some additional libraries and softwares that must also be installed to allow AUTOMATON to work:

-Install CPAN modules (http://www.cpan.org/modules/INSTALL.html or https://egoleo.wordpress.com/2008/05/19/how-to-install-perl-modules-through-cpan-on-ubuntu-hardy-server/)

user$ cpan Parallel::ForkManager
  
user$ cpan Math::Matrix

2) Downloading and Installing AUTOMATON

AUTOMATON can be directly downloaded as a zip file from the page:

-https://github.com/HumanOsv/Automaton

Alternatively, it can be downloaded using the Git tools using the following command:

user$ git clone https://github.com/HumanOsv/Automaton.git

user$ cd ./Automaton

Note: before downloading using Git tools, make sure to be in your final installation path.

We recommend to install using Git tools to update future AUTOMATON software easily. To update the program, use the following command:

user$ git pull master

Alternatively, AUTOMATON could be installed as follows: choose a final installation path, and then extract the ZIP file (containing the software). Provide all the basic permissions for use and, optionally, set AUTOMATON.pl file as a system call.

3) Running AUTOMATON

To run AUTOMATON the following files are necessary in the working directory:

• Input.dat              : The AUTOMATON input file, see below for more information.

• AUTOMATON.pl           : The executable file for structure prediction. **

• ReaxFF file (optional) : Reactive MD-force field file of Lammps.

Note: AUTOMATON.pl can be called from another path if correctly set

Now, use the following commands to execute this program:

user$  perl AUTOMATON.pl Config.in > out.log

Alternatively, the user can set AUTOMATON to run in the background using one of the following methods:

user$ nohup perl AUTOMATON.pl Config.in > out.log
user$ setsid perl AUTOMATON.pl Config.in > out.log

4) Input File

The main input file, known as input.dat, contains all the necessary parameters for a correct calculation. Each variable is explained below.

Number of structures (3N or 5N, N = Atoms number)

numb_conf = 60

Use of genetic operators; mating and mutation operator.

mutations = YES
crossing_over = YES

Rules of Cellular Automata using Chemistry intelligence (Others Elements > Hydrogen > Alkali > Alkaline Earth > Halogens)

clever_automata = NO

Maximun Cycles and Energy (kcal/mol) AUTOMATON

maximun_cycles = 30
maximun_energy = 100

Chemical formula for the system ( example: H 02 Pb 03 Ca 04 ).

chemical_formula = H 06 C 06

NOTE: Respect the spaces.

The size of the box (Angstroms) with format "length, width, height". AUTOMATON builds an automatic cuadricular box using the sum of all covalents radii of the system.

box_size = 

Software that will be used (mopac/gaussian/lammps).

software = gaussian

Configuring the program for chemistry packages

Procesor and memory (GB) that will be used for each calculation.

core_mem = 8,8

The charge and multiplicity of the candidate.

charge_multi = 0,1

Keywords for gaussian, mopac, or lammps

1. Gaussian

header = PBE1PBE/SDDAll scf=(maxcycle=512) opt=(cartesian,maxcycle=512)

2. Mopac

header = AUX LARGE PM6

3. Lammps (ReaxFF file)

header = reaxxFF.Co

General Note: Respect the spaces of separation between the symbol "=".

Correct : software = gaussian
Wrong   : software=gaussian

5) AUTOMATON outputs

After a successful run of the program, several output files will be generated in your working directory.

01Final_coords.xyz         : Final coordinates XYZ file format of each species ordered less energy at higher energy.
02Duplicate_coords.xyz     : Candidates that are a duplicate of a candidate in the population, in XYZ file format.
Output.log                 : Print summary information after each set of this many iterations.
PostCoords-NumberCycle.xyz : Local optimization for each structure.
PreCoords-NumberCycle.xyz  : Non-optimized structures.

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