Settings and Options
This section contains a reference of all settings available in the individual modules. Refer to the Examples section to learn how different settings may be applied.
MolPrep
| Setting | Description | Standard Value |
|---|---|---|
| Input Molecule File | Input file in mol, mol2, pdb, cml or xyz format. Refer to the first steps of Simulation Setup for instructions on how to generate input files. | N/A |
| Molecule Identifier | A 3-letter numeric string to label the molecule throughout the workflow in various output files. | ABC (random) |
| Optimize Molecule | Optimize the molecule with DFT (B3LYP, def2-TZVP). Disable this option to use the molecular conformation as provided in the input file. | True (checked) |
| Compute Dihedral Forcefield | Energy profiles for dihedral rotations are computed to sample different conformations during deposition. | True (checked) |
Deposit
Simulation Parameters Tab
Dimensions
| Setting | Description | Standard Value |
|---|---|---|
| Morphology size defined by | The size of the morphology can be either defined by depositing a certain number of molecules (option number of molecules) or by providing a certain box size that is automatically filled with the required number of molecules (option box size). |
box size |
| Number of Molecules | Visible only if Morphology size defined by number of molecules. Sets the number of molecules in the morphology. Number required for ESAnalysis depends on the molecule size. For NPB, 2000 molecules are sufficient. For small molecules such as BPhen, increase to 3000. | 1000-4000 |
| Cubic box | Visible only if Morphology size defined by number of molecules. If set, an approximately cubic morphology is generated. If disabled, X and Y are required. | False |
| X [A] | Box size in x direction in Å. | 100.0 |
| Y [A] | Box size in y direction in Å. Recommended: X=Y. | 100.0 |
| Z [A] | Box size in z direction (deposition axis) in Å. Visible only for Morphology size defined by box size. | 200.0 |
| Set total box height for multilayer | This setting must be enabled if you are depositing a multilayer system, i.e., using multiple Deposit steps. | False (unchecked) |
| Total Z [A] | Visible only if "Set total box height..." above is enabled. Defines the estimated total box height of your multilayer deposition. Needs to be the same value for all sequential Deposit modules. | 200 |
Simulation Parameters
Note
Most of the simulation parameters are calibrated to generate good morphologies. We recommend to modify parameters only as indicated. The simulation parameters listed below are hidden in the WaNo and displayed only if Show simulation parameters (advanced) is enabled.
| Setting | Description | Standard Value |
|---|---|---|
| Initial Temperature [K] | Initial temperature of the simulated annealing cycles. Leave as is. | 4000.0 |
| Final Temperature [K] | Final temperature of the simulated annealing cycles. Leave as is. | 300.0 |
| SA Acc Temp | Acceptance temperature of the simulated annealing cycles. Leave as is. | 5.0 |
| Number of Steps | Number of Monte Carlo steps per SA cycle. Leave as is. | 130000 |
| Number of SA cycles |
Number of simulated annealing (SA) cycles per deposition. SA cycles are executed in parallel.
Optimal performance of deposit is achieved in case of Number of SA cycles = cpus_per_node.
We recommend using no fewer than 20 SA cycles.
|
32 |
| Dihedral moves |
Allow for intramolecular dihedral rotations for flexible molecules. Moves are only executed if
compute Dihedral Forcefield was enabled in MolPrep.
|
True (checked) |
| Postrelaxation Steps | Number of low-temperature Monte Carlo steps at the end of each SA cycle. Leave as is. | 100000 |
Molecules Tab
| Setting | Description | Standard Value |
|---|---|---|
| Restart from existing morphology | Enable to deposit on top of an existing morphology. Note that box parameters need to be identical in both Deposit runs. | False |
| Restartfile | Only visible when Restart enabled. Load file from your hard drive or import from another Deposit run to continue Deposition on the existing morphology. | restartfile.zip |
| Molecules/Molecule | Input molecule file from MolPrep. | molecule.pdb |
| Molecules/Forcefield | Input forcefield file from MolPrep. | molecule_forcefield.spf |
| Molecules/Mixing Ratio |
In case multiple molecular inputs are supplied via the + button, adapt this number to define the mixing ratio.
|
1.0 |
Postprocessing Tab
| Setting | Description | Standard Value |
|---|---|---|
| Extend morphology |
If PBC was enabled, the morphology can be expanded in x and y direction. If checked, the final morphology is expanded and provided in the file structurePBC.cml. The expanded file is required for ESAnalysis
|
True (checked) |
| Cut first layer by (A) | The bottom layer may contain artefacts and is cut during expansion. Increase for larger molecules. | 7.0 |
ESAnalysis
General Tab
General Settings
| Setting | Description | Standard Value |
|---|---|---|
| Morphology |
Morphology file from Deposit. Load from your hard drive or import from the Deposit module in the same workflow. For sufficient environment, use the periodically expanded morphology in structurePBC.cml.
|
structurePBC.cml |
| Compute absolute levels of IP/EA | Computes absolute values for ionization potential and electron affinity for molecules in the core shell. Computationally more expensive than disorder. Not required e.g. for mobility of pristine materials. | True (checked) |
| Compute disorder | Compute distributions of HOMO and LUMO energies on a larger set of molecules. | True (checked) |
| Compute couplings | Compute electronic couplings for molecules in the Disorder shell. Computationally insignificant in comparison to disorder computation. | True (checked) |
Shell setup
| Setting | Description | Standard Value |
|---|---|---|
| Core Shell / Shell size defined by |
Specify how to choose molecules for computation of IP and EA.
|
Number of Molecules |
| Core Shell / Number of molecules | Number of molecules or molecules of each type on which to compute IP and EA. Reasonable values are between 2 and 8, depending on available resources and required statistics. | 8 |
| Core Shell / List of molecule IDs | Specific list of molecule IDs. IDs can be separated by semicolon, applied as a range using a hyphen, or a combination of both. | 43; 57; 79-100 |
| Disorder Shell / Number of molecules | Number of molecules on which to compute HOMO and LUMO disorder. Depending on the available resources, 200-400 molecules are recommended for sufficient statistics. | 200 |
Enginges Tab
| Setting | Description | Standard Value |
|---|---|---|
| Memory per CPU (MB) | Set to the total memory of your node / resource, divided by the number of processors. | 2000 |
| GW Engine | The GW step during IP/EA computation can be performed with Turbomole or PySCF. PySCF is integrated in the Nanoscope, Turbomole requires separate installation and license. | PySCF |
| Functional GW | Functional for the GW step. For PySCF, this step is only calibrated for PBE0. For Turbomole, TMHF is slightly more accurate than PBE0. | PBE0 |
Storage Tab
| Setting | Description | Standard Value |
|---|---|---|
| Storage location |
ESAnalysis typically runs in a scratch directory defined during installation. At the end of the run, a certain set of runtime files are copied back to the work directory where the job was submitted. In the case of limited space in the Workdir, set to Scratch to keep runtime files in scratch and only copy main output files back to the work directory.
|
Workdir |