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Welcome to the OLED-GA_v2 wiki!
This Reference Manual contains descriptions of all input, output and execution features of OLED-GA program. OLED-GA is both an evolutionary search and its computer program implementation, to perform electronic structure calculations of organic molecules to predict the high-performance multiple OLED device. Its main characteristics are:
• It contains different kinds of selection methods, such as, roulette wheel selection (RWS), the stochastic universal sampling (SUS), the linear rank selection (L_Rank), the exponential rank selection (E_Rank), the tournament selection (Tournament).
• It connects semi-empirical scientific program (MOPAC) to perform electronic structure calculations and geometric optimization for all candidates.
• The 3D structure of each potential molecule is generated by using OpenBabel
• It is written in C++
It routinely provides:
• Total energy and orbital energies.
• Select best OLED structures for both HOST and transporting layer.
• Varity of selection methods.
• Controllable GA parameters, such as, mutation rate, crossover rate, population size... etc.
• Statistical analysis of OLED score for each fragment.
Type the command make to generate the executable “OLEDsearch.exe”. Then selected one of the script file to proceed the GA evolutionary search
• ./OLEDcleanrun: This script will clean the exist database and clean the previous calculated results than run an initial OLED-GA search
• ./OLEDrunrestart: This script will keep the exist database and moved the previous calculated results to the directory (OLED-GA/OLEDdata)
• OLED-GA/lib/Seed: Setup the seeds in this directory for building the molecules
• OLED-GA/lib/Reg: Setup the functional fragments for the 1st and 2nd molecular segment in this directory for building the molecules
• OLED-GA/lib/Cap: Setup the capping fragments to form the final molecular segment in this directory for building the molecules
Here follows a description of the variables that you can define in OLED-GA input file. There are two essential input files (saved in /OLED-GA/inp) need to be prepared before OLED-GA search. (ga.inp and mopac.inp)
All the initial parameters for OLED-GA evolutionary search are divided into several parts. Complex input data structures are called blocks and are placed between “$block label” and a “$block label END”. There are three divided blocks in OLED-GA program, that are, $S-Generator, $Fitness, $GA.
$S-Generator block
Mode (integer): It specifies the type of GA scientific search. #1 is for OLED, #2 is
for Transition metal catalytic search, #3 is for chain-like molecule.
Default value: There is no default. But only #1 is work for this version.
Layers (integer): It specifies the how many molecular segments for OLED molecular generation. Ex. #3 means the structure will be generated from a seed and connect 3 molecular segments. Default value: There is a limitation for building layers. Minimum is 3 and maximum is 4.
Library (string): It defined the directory of molecular building blocks. Default value: There is no default.
Best_Restart (logical): If it set to “on” then the program will read the database and
select top 1% candidates from the file “data” for generating the 1st GA pool.
Default value: There is no default.
Reference_Electrode (logical): It defined the idealized energy levels for the transport of holes and electrons across the device. Default value: There is no default.
JobType (logical): It defined the type of job script files (chose SLURM or PBS).
Default value: There is no default.
WriteFragScore (logical): If it set to “on” then the program will count the number of fragments with appearing in a setup FragScoreThreshold and write evaluate the fitness score of fragments for both transporting layer and HOST in output file.
Default value: There is no default.
FragScoreThreshold (double): It defined the minimum value for counting the number of fragments from database. Default value: There is no default.
$Fitness block
Reference (string): It defined the reference structure file for TM catalytic search. Default value: There is no default.
Def_File (string): It defined the essential criteria for TM catalytic search. Default value: There is no default.
$GA block
Population_Size (integer): It defined the size of population for each GA evolutionary process. (the population size only for even number) Default value: There is no default.
Termination (integer): It defined the maximum number of GA evolutionary process. Default value: There is no default.
CrossoverRate (double): It defined the possibility of a pair of genes to do the crossover operation. Use: The value should setup from 0 to 1. Default value: There is no default.
MutationRate (double): It defined the possibility of a gene to do the mutation operation. Use: The value should setup from 0 to 1. Default value: There is no default.
$Selection (double): Several selection methods for a GA process.
• RWS: roulette wheel selection
• SUS: stochastic universal sampling
• E_Rank: exponential rank selection
• L_Rank: linear rank selection
• B_Tournament: tournament selection
For the ranking method, it is essential to set up the rate L_Rank and base of E_Rank.
$Selection End
Method (string): It defined the Hamiltonian for MOPAC calculation Gnorm (double): Exit when gradient norm drops below n kcal/mol/Angstrom Unrestricted (logical): If it set “on” then use restricted Hartree-Fock methods
• Log: This is a main output file, which contains all the information of each gene during GA evolutionary process (such as, gene string codes and their corresponding probabilities, frontier orbital energy levels and scores)
• mm/ETL_#: The potential ETL structures for each generation will be automatically generated by using OpenBabel and saved into those directories. # is the number of generation.
• mm/HTL_#: The potential HTL structures for each generation will be automatically generated by using OpenBabel and saved into those directories. # is the number of generation.
• mopac/ETL_#: The MOPAC calculated results of potential ETL structures for each generation are saved into those directories. # is the number of generation.
• mopac/HTL_#: The MOPAC calculated results of potential HTL structures for each generation are saved into those directories. # is the number of generation.
• Best_ETL, Best_HTL: This output list the best candidate OLED in each GA generation process.
• Bestforfar_ETL, Bestsofar_HTL: This output list the top best candidate OLED so far in each GA generation process.
• OLEDdata: All the structures for both ETL and HTL with the fitness score higher than 900 will be saved into the directory (OLED-GA/).
• Data: All the potential candidates for both ETL and HTL will be saved in this output file as a database.