Genetic Algorithm

This code is part of "Designing Mechanosensitive Molecules from Building Blocks: A Genetic Algorithm-Based Approach"

TOC

• Requirements
• Usage
  • Preparation
  • [Config file](#Config file)
  • [Flow Chart](#Flow Chart)
  • Evolution
• [Standalone evaluation of molecules](#Standalone evaluation of molecules)
• [Stretching for molecules build from building blocks](#Stretching for molecules build from building blocks)
• [Stretching for arbitrary isolated molecules](#Stretching for arbitrary isolated molecules)

Requirements

• tmoutproc library from here. Tested with version 0.1
• Queuing system slurm or GE
• Python 3.x
• Turbomole. Version >7.5

Usage

Preparation

• Create directory where the evulution runs
  • Generate directory "generation_data" in it
  • Create config file (see next part)
  • Run evolution: python3 PATH_TO_CODE/genetic/run_evolution.py <config_path> <calculation_path>

Config file

(With exemplary values. Adjust that to your calculations)

[Basics]
genetic_algorithm_path=PATH TO GENETIC ALGORITHM 
turbopath=PATH TO TURBOMOLE
helper_files=PATH TO HELPER FILES
intel_path=PATH TO INTEL Routines
archive_archive_path=PATH TO ARCHIVE OF MOLECULES
calculation_path=PATH TO CURRENT CALCULATION
queuing=(SLURM or GE)

[Genetic Algorithm]
population_size=24
generation_limit=20
evaluation_methods_path=default
genome_length=7
insert_mutation_prob=0.5
coupling_mutation_prob=0.5
block_mutation_prob=0.5
truncate_mutation_prob=0.5
n_tournament_selection=2

[Building Procedure]
CC_bond_lengt=1.58
conjugation_angle=0.45
building_block_path=
generation_data_path=generation_data
ang2Bohr=1.889725989
har2Ev=27.211

[Turbomole Calculations]
partition=epyc,alcc1
cpus_per_task=8
displacement_per_step=0.1
num_stretching_steps_pos=30
num_stretching_steps_neg=30
mem_per_cpu=15G
max_time=05:30:00
kill_time=5700
relax_level=xtb
relax_iterations=730
prerelax= #T or false
define_input=build_calc

Flow Chart

Overview of program sequence: The programm will create a folder structure similar to this:

Evolution

Evolution loop implemented in the algorithm:

Standalone evaluation of molecules

Stretching for molecules build from building blocks

You can bypass the evolution and evaluate molecules directly build from building blocks by running directly genome_to_molecule.py.

Stretching for arbitrary isolated molecules

You can bypass the evolution and evaluate arbitrary molecules by running directly set_up_turbo_calculations.sh. Generate folder structure as shown in the structure above. Place coord, coord.xyz, complexity and limits file, prepare config file and rund set_up_turbo_calculations.sh.

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Matthias Blaschke [email protected]