The Doped Organic Mobility workflow

Summary

The Doped Organic Mobility Workflow realizes the models 2 (MCMD), 3 (CGMD), 4 (QC-POLARON) and 6 (BTE) of the EXTMOS Moda. Starting from a single parameterized molecule containing partial charges and Van-der-Waals parameters (per component), the first WaNo, Deposit, builds a nano-scale (O(10nm)) morphology using X-Y periodicity and feeds it into Quantum Patch to determine electronic structure parameters, such as the single-molecule site energies Ei and overlap matrix elements Ji,f. To achieve sufficiently large morphologies, the input morphology and calculated parameters are input into the RangeExpander WaNo, which stochastically expands the morphology to meso-scale and provides site energies, overlap matrix elements and center of mass positions as input for KMC modules. A KMC simulation is carried out based on this input and provides meso-scale material observables such as the mobility. The workflow is shown below.

Left: The Meso-Scale Organic Mobility Workflow. Starting from a single molecule file, Deposit builds a nano-scale morphology. This morphology is automatically fed into QuantumPatch, which calculates site-energies and optionally overlap matrix elements. This output is stochastically expanded to the meso-scale in RangeExpander, converted in MorphologyAdapter and ultimately used in a Layer simulation in the KMC WaNo. Right: Illustration of the major results of the Meso-Scale Organic Mobility Workflow.

Tutorial: Deposition and mobility analysis of Pentacene using the Doped Organic Mobility Workflow

To deposit and analyze Pentacene using the Meso-Scale Organic Mobility Workflow, the following steps have to be carried out:

Deposit Locate the forcefield and molecule files for pentacene (pentacene.pdb and pentacene.spf) and open the Deposit WaNo by double clicking on it. Specify both files in the Molecule pane as “Molecule” and “Forcefield” respectively. Switch to the “Simulation Parameters” pane and select a sufficiently large box size, such as 25x25x50 and the deposition of 1000 molecules with enabled periodic boundary conditions. Leave the rest at default and switch to the “Resources” pane. Set the amount of CPUs per Node to an adequate number matching your cluster, such as 32. Deposit only utilizes single nodes.

QuantumPatch Leave all settings at their default value except for Basis and Functional. Select an appropriate basis and functional for a single molecule DFT of the chosen molecule. In case of Pentacene the defaults SV(P) and b-p should be sufficient. Set the amount of CPUs per Node to an adequate number matching your cluster, such as 32 and the number of nodes as high as possible. QuantumPatch can use as many cores, as there are molecules in the system, so up to 1000 for this example.

RangeExpander The default settings are adequate for Range Expander. Increase the number of molecules to 105-106 to account for percolation effects. RangeExpander runs on 1 CPU only.

MorphologyAdapter Select the RangeExpander output file you wish to convert. Select an output directory to place the newly created files in.

KMC The default settings will start a simulation with a number of randomly placed electrons in the device. Set the number of hopping sites and the device size to match the parameters of the range expander. Set the input directory to be the same as the output of the conversion WaNo, the default filenames will be correct.

At the end of the simulation the KMC WaNo outputs a set of files, the simplest being the ‘sim_history’ file that contains information about the simulation such as the number of KMC steps, number of charge injections and the estimated mobility. The simulation also outputs the recorded MSD for charge carriers (if requested in the ini file) and a file that counts the number of transport events between sites (again if requested). In case intermediate results are of interest, the atomistic (not-expanded) morphology can be downloaded from the Deposit WaNo.

Parameter explanations of the Doped Organic Mobility Workflow

Deposit

Molecules

Click the + button to create another set of input fields for multiple input molecules

  • Molecule [PDB] PDB structure of the molecule to be deposited.
  • Forcefield [SPF] Forcefield file of the molecule to be deposited.
  • Mixing Ratio Ratio of the specified molecule. Ignored, if only one molecule is specified.

Simulation Parameters

  • Simulation Box [Lx,Ly,Lz] Half box size of the (optionally) x-y periodic simulation box.
  • PBC, PBC Cutoff [Å] Explicit PBC images are created inside a shell of size PBC Cutoff around the simulation box, if enabled.
  • Number of Molecules Number of molecules to be deposited.
  • Initial / Final Temperature [K] Every simulated annealing cycle starts at Initial Temperature and ends at Final Temperature using a geometric cooling schedule. Initial Temperature should be chosen higher than physical to allow for faster deposition.
  • SA Acc Temp [K] After each simulated annealing step the new conformation is accepted using this temperature.
  • Number of Steps Every simulated annealing cycle simulates for Number of Steps MC steps.
  • Number of SA cycles Number of SA cycles simulated annealing cycles are carried out. In case more than 1 CPU is allocated for the Deposit simulation SA cycles are carried out in parallel.

QuantumPatch

DFT Settings

  • Calculate Js If disabled QuantumPatch only calculates site-energies and no overlap integrals
  • Engine Sets the underlying DFT engine.
  • Basis Sets the basis used in the DFT calculation.
  • Functional Sets the functional used in the DFT calculation.
  • Partial Charge Method Partial Charges are calculated either using the ESP or Mulliken method as specified here.

Self-consistency parameters

  • Screened Iterations Shredder carries out a self-consistency loop. The number of iterations until convergence are set here.
  • Damping, Damping Factor If enabled a damping algorithm is used, when determining the partial charges of the molecules in the self-consisteny loop.

Cutoffs

  • Inner Part Cutoff The simulation box of molecules to be simulated is truncated by Inner Part Cutoff Angström from each side before simulation to remove edge effects.
  • Pair Cutoff Only pairs of molecules within pair cutoff Angström in the vicinity of each other are considered during the overlap integral step.
  • Environment Radius Partial charges within this radius around the QM region are considered in the QM calculations.

Hardware Parameters

  • DFT Memory [MB] A single DFT calculation is allowed to use this amount of memory.

RangeExpander

Morphology

  • Number of Molecules Number of sites of the generated system.
  • Morphology Input file with center of mass coordinates of the Deposit/MD morphology. Format: 3 columns with x,y,z coordinates in Angström, no header.
  • Expand Morphology If enabled a morphology of the specified size will be generated, else the specified morphology file is kept.

Transfer Integrals

  • Expand Transfer Integrals If enabled transfer integrals for the generated or loaded morphology will be generated based on distance dependent distributions of transfer integrals from QuantumPatch/Meso-El
  • Max hopping targets Maximum number of possible neighbours of every site. To reproduce microscopic distributions of transfer integrals set this to 45.
  • J distribution (r[A], J[eV], 2 columns) Input file containing the center of mass distance dependent distribution of transfer integrals from QuantumPatch. Format: 2 Columns. First column: center of mass distances of molecule pairs in Angström. Second column: transfer integrals of the pairs in eV.

KMC

  • ini file KMC parameter file. The options in this file are the size of the coarse-grained mesh for calculating charge density: how long to run the KMC simulation for (either in KMC steps or in picoseconds): what dynamic measurements to make during the simulation (MSD, components of displacements etc.) and how often to make those measurements: the names of the other input files: the directories to save and load configurations from, whether to load a state from a previous KMC simulation as a starting point or whether to start with a number of randomly placed carriers, and if so how many carriers should be randomly placed at the start. The parameters are the size of the device, the number of hopping sites, the applied bias at each electrode, the temperature in Kelvin and the permittivity of the material. This file is parsed at the very beginning of the simulation.
  • Morphology file An input file that contains the site “type” (e.g. electrode, trap, transport layer etc.), the number of neighbouring hopping sites, the x, y and z coordinates of the site (currently in nm).
  • Neighbours file An input file that contains the transfer integral and the separation (in nm) between each pair of neighbouring sites.
  • Energetics file A file that contains the HOMO, LUMO and reorganization energy of each site as well as the absorption coefficient of each site.
  • Pair energies file (optional) An input file that contains the difference in site energy between each pair of neighbouring sites.

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