Semicrystalline Advanced Options Dialog Box

Semicrystalline Advanced Options Dialog Box Features

• Lamella connection distance text box
• Initial clash vdW scale factor text box
• Placement attempts per chain text box
• Attempts per clash distance text box
• Enforce orthorhombic option
• Enforce full coverage option
• Write debug file for the builder check box

Lamella connection distance text box

Distance beyond which the amorphous chain is not permitted to grow into a crystal chain. This constraint is ignored for a given fraction of bonding events. When the distance is ignored, the current amorphous chain bonds to the crystal chain that has the most neighbors that are already linked to amorphous chains.

Initial clash vdW scale factor text box

Specify the initial scaling factor for detecting clashes. A clash is considered to occur if the nonbonded interatomic distance between two atoms is smaller than the scaled sum of the atomic van der Waals radii of the atoms.

Placement attempts per chain text box

Specify the maximum number of attempts to be made when placing an amorphous chain. For the placement algorithm, in each attempt the chain is oriented at random and placed in the cell at random. If a clash is detected, the attempt is regarded as failed, and a new attempt is made. For the self-avoiding random walk algorithm, the attempt to place a chain is considered to have failed if all monomers have been removed from the polymer in the effort to eliminate clashes and the polymer cannot be rebuilt. The new attempt places the initiator at the largest vacancy in the cell.

If the maximum number of attempts is exceeded, the cell is discarded and a new cell is built.

Attempts per clash distance text box

Specify the maximum number of attempts at building a cell. If a non-clashing cell cannot be built in this number of attempts, the van der Waals scaling factor is lowered. The process continues until a non-clashing cell can be built, or the vdW scale factor is very small.

Enforce orthorhombic option

Enforce orthorhombic symmetry on the output crystal. If you are starting with a triclinic crystal and want to keep the output triclinic, deselect this option.

Enforce full coverage option

Enforce full coverage of the crystal. This means that all crystal chains are connected to chains in the amorphous region, and hence there are no voids in the crystal region due to the deletion of unattached chains at the end of the building process.

When this option is selected, several calculations are done with varying connection distance constraint satisfaction, to ensure that full coverage is achieved. If it is not selected, the result may be a system with less than100% crystal coverage.

Write debug file for the builder check box

Write a log file to allow for monitoring of polymer chain creation and bonding to crystal. It also writes intermediate files with monomer, full crystal, single polymer chain, and preminimized structures. These files may be useful for analyzing a run and determining whether to change any of the settings.

This option is selected by default.