Deposit GUI

Deposit models the physical vapour deposition process (PVD) of organic small molecule thin-films. Further information on applicability, method and algorithm is available here: Deposit3.pdf
Deposit WaNo Top Deposit WaNo Bottom

Input files and parameters

Tab Simulation Parameters / Simulation Box:

In the „simulation box“ section the dimensions of your final structure are defined. Periodic boundary conditions in x- and y- plane (perpendicular to the direction of deposition) can be applied.

Parameter Description Type Standard
Lx Half the size of the box in x direction in A Float > 20
Ly Half the size of the box in y direction in A Float > 20
Lz Size of the box in z-direction (direction of deposition) in A. Remark: Deposit will stop deposition of molecules, when Lz is reached Float > 40
PBC enabled Enable or disable PBC in x-y-direction. Remark: Simulations with PBC turned on take longer than with PBC turned off. CheckBox Off
PBC Cutoff Periodic images of each deposited molecule are placed outside the box and are taken into account explicitely during the deposition of new molecules when within this Cutoff (in A) to the box edge. Float 20

Tab Simulation Parameters / Simulation Parameters:

The „Simulation Parameters“ section defines settings for the deposition of the molecules. This includes the number of molecules to be deposited and parameters for the Metropolis Monte-Carlo based deposition algorithm.

Parameter Description Type Standard
Number of molecules Number of molecules to be deposited. The deposition stops automatically when the final position of a molecule is above the box size defined by Lz Int N/A
Initial Temperature in K Starting temperature of a single SA cycle (see below). Remark: The initial temperature needs to be large enough to allow a molecule to detatch from a surface in order to sample the surface to find an equilibrated configuration. Float 4000.0
Final Temperature in K Final temperature of a single SA cycle (see below). Float 300.0
SA Acc Temp Of the results of all SA cycles one final configuration is picked with a Metropolis accentance criterion at a certain temperature, the SA Acc Temp. Float 5.0
Number of Steps Number of Monte-Carlo moves during one Simulated Annealing (SA) cycle. Int 20.000
Number of SA cycles Number of simulated annealing (SA) cycles (also called basin hopping cycles) during the deposition of a single molecule. Remark: To minimize real time of Deposit, choose as many CPU as number of SA steps. Int 10-32
Dihedral moves Allow dihedral rotation around single bonds. Remark 1: Use the module „DihedralParametrizer“ to generate customized force fields for the dihedral rotation. Remark 2: To sample the configuration space adequately, the number of steps should be increase by 50% if dihedral moves are enabled. Checkbox Off

Tab Molecules

In the molecules tab the input files are specified. To increase or decrease the number of molecule types to be used during the deposition, use the „+“ and „-“ buttons at the edge of the „Molecules“ box in the „Molecules“ tab.

Parameter Description Type Standard
Restart from existing morphology To continue the deposition of an existing structure from a previous Deposit run, check this box. A new field will appear to specify the input file of the existing structure. Checkbox Off
Restart file This option is only visible when „Restart from existing morphology“ is checked. Chose the „restart.zip“-file from the output of a previous Deposit run, either from your hard drive (first button to the right of the „restart file“ field) or directly from the output of a Deposit run in the same workflow (second button to the right of the „restart file“ field). File N/A
Molecule Import PDB file of the molecule, either from your hard drive or from the Parametrizer or Dihedral Parametrizer WaNo preceding Deposit in the Workflow File N/A
Force field Import SPF file containing the force field of the molecule, either from your hard drive or from the Parametrizer or Dihedral Parametrizer WaNo preceding Deposit in the Workflow File N/A
Mixing ratio If more than one molecule type is to be deposited, specify the mixing ratio using this float. For example, to deposit two molecule types with a mixing ratio of 2:1, put 2.0 in the mixing ratio field of molecule 1 and 1.0 in the mixing ratio field of molecule 2. Float 1.0

Resources, parallelization and performance

For every option not checked in the „Resources“ tab, the server defaults that depend on your HPC machine will be used. Check individual options to modify specific values.

Recommended resources for Deposit:

Resource Recommendation
CPUs per Node: The SA cycles of Deposit run in parallel using MPI. In order to enable parallel execution, allocate as many CPUs per Node as Number of SA cycles (see above) by enabling the property „CPUs per node“ in the „Resources“ tab and setting the value to the same value as for „Number of SA cycles“.
Number of Nodes: 1 (No parallelization on more than a single node available)
Memory: Memory depends on the final size of your sample. A grid of size 300A x 300A x 300A (Lx=Ly=150, Lz=300) needs approx. 64 GB of RAM (allocated per node).
Walltime: Deposition time per molecule is approx. 1minute x (Number of SA Cycles / CPUs per Node) for an average molecule with ~100 atoms and 30.000 MC moves. The deposition time scales approx. linearly with the number of atoms per molecule and the number of MC steps.
Queue: Default

Output Files

Filename File description Interface to module...
Structure.cml Contains atom positions structured as molecules. Quantum Patch
Structure.mol2 Mol2-file for visualization of the deposited structure. Contains all atom positions. None
Restartfile.zip In order to continue the deposition, e.g. to create an interface, read this file into the subsequent Deposit run. Deposit

 

 

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