.. _science_calculators_morphology: Nanomatch Morphology Calculator =============================== .. list-table:: :header-rows: 1 :align: center * - Properties - Notes * - :ref:`science_properties_HOMOLUMO` - byproduct * - Dipole (property not yet described / available) - byproduct * - :ref:`science_properties_morphology` - recommended Workflow -------- The **Nanomatch Morphology Calculator** workflow is essentially the first part of the **Nanomatch Mobility Calculator** workflow (:ref:`science_calculators_mobility`), which is terminated after the morphology is generated and analyzed. .. list-table:: Nanomatch Morphology Calculator Workflow :widths: 30 30 30 :header-rows: 1 * - **Nanomatch Software** - **Scientific Role** - **Illustration** * - `Parametrizer `_ - | Geometry optimization - .. image:: mobility/parametrizer.png :width: 300px :align: center * - `DihedralParametrizer `_ - | Computation of intramolecular | forcefields - .. image:: mobility/dhp.png :width: 300px :align: center * - `Deposit `_ - | Simulation of the physical | vapor deposition (PVD) | to obtain atomistic morphology - .. image:: mobility/deposit.png :width: 300px :align: center Implemented Scientific Methods ------------------------------ The following scientific methods are implemented in the **Nanomatch Morphology Calculator**: Molecular Structure Optimization ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ *obabel*, *xtb*, and *Density Functional Theory (DFT)* are used to generate initial 3D conformers, pre-optimize and optimize the geometry, and compute partial charges via an electrostatic potential (ESP) fit for single molecules in a vacuum. DFT optimization is performed with def2-TZVP/B3LYP level of theory. Morphology Generation ~~~~~~~~~~~~~~~~~~~~~ The *DEPOSIT protocol* [1]_ simulates physical vapor deposition to generate thin-film morphologies with atomistic resolution. This involves Monte Carlo (MC) based basin hopping with simulated annealing (SA) to model intermolecular interactions during deposition. In total, 1000 molecules are deposited into a box with a base size of 100x100 Å. Output ------ Displayed Results ~~~~~~~~~~~~~~~~~ The data below will be displayed as the workflow ends (backend name: `result.yml`): .. code-block:: yaml ZUOUZKKEUPVFJK-UHFFFAOYSA-N: HOMO: value: -6.304540838835274 LUMO: value: -0.9858224534777202 dipole: results: dipole_vector: - -1.3524802844422331e-05 - 3.1223022592016277e-06 - 1.662349335263646e-05 value: 2.1656629345848317e-05 morphology: results: average_neighbors: unit: Angstrom value: 17.6 mass_density: std: 0.01 unit: g/cm3 value: 1.14 molecular_volume: unit: nm3 value: 0.23 number_density: std: 9.9e+19 unit: 1/cm3 value: 4.36e+21 rdf_first_peak: unit: Angstrom value: 4.921630094043887 value: 'file: structure.cml' The table below explains each parameter, its meaning, units, and other relevant information (field "value" is occasionally omitted). .. list-table:: :header-rows: 1 * - Parameter - Description - Units - Value - Additional Information * - HOMO - Highest Occupied Molecular Orbital - eV - -6.304540838835274 - HOMO * - LUMO - Lowest Unoccupied Molecular Orbital - eV - -0.9858224534777202 - LUMO * - dipole_vector - Components of the dipole moment vector - Debye (D) - (-1.3524802844422331e-05, 3.1223022592016277e-06, 1.662349335263646e-05) - Vector representation of the dipole moment * - dipole - Magnitude of the dipole moment - Debye (D) - 2.1656629345848317e-05 - Magnitude of the dipole moment * - average_neighbors - Average distance to neighboring molecules - Å - 17.6 - Average distance to neighboring molecules * - mass_density - Mass per unit volume - g/cm³ - 1.14 - Standard deviation (`std`): 0.01 (example value) * - molecular_volume - Volume occupied by a single molecule - nm³ - 0.23 - * - number_density - Number of molecules per unit volume - 1/cm³ - 4.36e+21 - Standard deviation (`std`): 9.9e+19 (example value) * - rdf_first_peak - Position of the first peak in the radial distribution function - Å - 4.921630094043887 - Indicates the most probable intermolecular distance .. _science_calculators_morphology_files: Files ~~~~~ In addition to parsed output, the following files are available upon the workflow completion: .. list-table:: :header-rows: 1 :widths: 5 15 15 50 * - No. - File - Description - Example * - 1 - output_molecule.mol2 - | Molecule output file in MOL2 | format. - `output_molecule.mol2 <../../../../../docs/build/html/_static/science/calculators/mobility/output_molecule.mol2>`_ * - 2 - summary_RDF.png - | Radial distribution function | (RDF). - .. image:: mobility/summary_RDF.png :width: 300px :align: center * - 3 - structure.cml - | Molecular structure in | CML format. - `structure.cml <../../../../../docs/build/html/_static/science/calculators/mobility/structure.cml>`_ * - 4 - | visualization_2D | _and_3D.png - | 2D and 3D visualizations | of the molecules | (center of geometries) - .. image:: mobility/visualization_2D_and_3D.png :width: 300px :align: center References ---------- .. _ref1: .. [1] Neumann, T., Friederich, P., Symalla, F., Meded, V., Wenzel, W., "Simulating Charge Transport in Organic Semiconductors: From Quantum Chemistry to Device Simulation," Journal of Computational Chemistry, 34 (31), 2013, 2716-2725. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.23445.