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Protocol for glass-transition temperature prediction

This is a repository (v1.0) of the paper:

Kun-Han Lin, Leanne Paterson, Falk May and Denis Andrienko, Glass transition temperature prediction of disordered molecular solids, npj computational materials, accepted

The 26 organic molecules investigated here are common host materials or hole transport materials for organic light-emitting diodes, as shown in the figure below.

alt text

The contents in the repository will be introduced as following.

INPUT_FILES

This folder contains input files for Gaussian (GAUSSIAN/), DDEC6 (DDEC6/) and Gromacs (GROMACS/) computations. In GROMACS folder, there are three input files corresponding to the three steps in generating simulated amorphous morphology and cooling:

a. Geometry optimizaion (em.mdp)  
b. Heating and compressing (heating.mdp)   
c. Cooling (cooling.mdp)   

ANALYZING_SCRIPTS

This folder contains python scripts for generating DDEC parameters, Tg fitting and creating R2-Temperautre plots for various fitting ranges.

Usage of R2-T_plot.py:

python R2-T_plot.py energy.xvg

The input file energy.xvg is the Gromacs output that contains the information of density and temperautre. The output of the python script is the R2-Temperature plot for differnt fitting ranges as shown below:

alt text

Usage of Tg_fit_plot.py:

python Tg_fit_plot.py energy.xvg

The output of the python script is the ρ-Temperature plot and the fitted Tg using different fitting ranges:

Fitting Range1:[ 405.0 , 555.0 )  
Fitting Range2:[ 24.0 , 174.0 )  
Fitting size:  150 Tg:  70.17  
Fitting Range1:[ 412.0 , 612.0 )  
Fitting Range2:[ 14.0 , 214.0 )  
Fitting size:  200 Tg:  81.23  
Fitting Range1:[ 401.0 , 651.0 )  
Fitting Range2:[ 2.0 , 252.0 )  
Fitting size:  250 Tg:  87.60  
Fitting Range1:[ 401.0 , 701.0 )  
Fitting Range2:[ 1.0 , 301.0 )  
Fitting size:  300 Tg:  101.31  
alt text

Usage of gen_VDW.py:

python gen_VDW.py

We generate the VDW parameters according to the protocol proposed by Cole et al. The DDEC6 output file (DDEC_atomic_Rcubed_moments.xyz) should be present in the same folder.
After executing, it generates an output (VDW_parameters.txt) containing the LJ parameters for each atom. In this work, we calculate the LJ parameters for each atomtype defined in forcefield by averaging LJ parameters of atoms belonging to the corresponding atomtype.

index  element  sigma(nm) epsilon(kJ/mol)
1  C  0.3285743291286239  0.2591880549216842
2  C  0.35876550847271765  0.259188054921684
3  C  0.34417631543886273  0.25918805492168406
4  C  0.3467102162365648  0.25918805492168423
5  C  0.33869454454486536  0.2591880549216841
6  N  0.3175683741309179  0.42097226362187506
...

MATERIALS_DATA

This folder contains data of 26 organic semiconductors investigated in this work. The files in the subdirectory are explained in the table below:

Subfolder File Explanation
STRUCTURE nN.xyz XYZ coordinate of the molecule in neutral ground state
GAS_PHASE_QM nN.log Gaussian log file
DDEC6 DDEC* Output files from DDEC6 calculations; see details here
FORCEFIELD .top and .ff topology and forcefield parameters for gromacs simulations
RHO-T energy.xvg Gromacs output containing information of density and temperature during the cooling process