For newcomers

Glossary

The vocabulary this site uses, in the sense it uses it.

Atom type — a label that decides which force-field parameters apply to an atom. Written atype@fragment, e.g. c3_c2h1@ph: the same element in a different fragment is a different atom type.

Building block — a node or linker with marked connection points, ready to be placed at a vertex or along an edge of a net. Organic or inorganic; the distinction is a browse facet, not part of the identity.

Catenated net — two or more identical nets interpenetrating without bonding. Named with a -c suffix. Search results include them unless you ask otherwise.

Coordination number — the number of edges meeting at a vertex.

Coordination sequence — how many vertices lie at topological distance 1, 2, 3, … from a given vertex. A fingerprint for identifying a net; four or five shells usually discriminate.

Fit — one parameterisation of a force field against one set of reference systems. Parameters are addressed by fit, because two fits legitimately give different numbers for the same atom types.

Fragment — the unit force-field assignment works on. Structures are matched against fragments by priority, highest first; each fragment then supplies atom types to its atoms.

Framework — an assembled periodic structure: a net with building blocks placed on it. May be a known material or a hypothetical one.

MOF-FF — the force field this site parameterises: a first-principles parameterised force field for metal-organic frameworks.

Net — the underlying periodic graph of a framework: vertices and edges, stripped of chemistry. Also called the topology. Named with three-letter symbols by convention, e.g. pcu.

ric — redundant internal coordinate. The family a parameter belongs to: bnd bond, ang angle, dih dihedral, oop out-of-plane, cha charge, vdw van der Waals.

Reference system — a small model system whose reference calculations a fit was derived from. Every parameter can be traced back to one.

Reverse topological approach (RTA) — building a hypothetical framework by starting from a net and populating it with building blocks, rather than inferring a net from a known structure.

Transitivity (pqrs) — the number of distinct kinds of vertex, edge, face and tile in a net. Low numbers mean high symmetry; frameworks preferentially adopt highly symmetric nets.

Vertex symbol — a description of the shortest rings around a vertex, complementing the coordination sequence.

weaver — the contributor tier. Deposits data and runs assembly jobs. Named for the assembly tooling, not for a role in the abstract.