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.

Augmented net — the net obtained by replacing every vertex of a net by its coordination figure — the polygon or polyhedron whose corners are that vertex's edge directions — and every original edge by a single link joining two figures. Written with an -a suffix: skl-a is the augmentation of skl. Every vertex of an augmented net therefore carries exactly one link edge, and contracting the figures back gives the parent net. 456 records here are named that way, 452 of them beside a record under the parent symbol.

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. Usually named with a -c suffix, but the flag on a record is now counted from the graph rather than read off the name: the two disagree on eight records, and five (layers and chains) are left undetermined because a graph cannot say how pieces thread through space. Search results include catenated nets 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.

Curation call — a disagreement inside one record between what a source said and what was computed from that same source's deposit, stated on the record rather than resolved. It names the claim, the finding, the evidence and the decision somebody has to make, and it is derived when the record is served and stored nowhere. open means undecided and nothing was changed; settled means a ruling was taken, which changes what this site presents and never what either source holds. 10 of 3077 records raise one.

Cycle symbol — the shortest cycle through each angle at a vertex, with how many there are: 6(2).6(2).6(2).6(2).6(2).6(2) for dia. The convention MOF+ stores under vs. Not the same quantity as the RCSR vertex symbol, which counts rings.

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.

Genus — the number of independent cycles in one minimal repeat unit of a net, 1 + E − V. pcu 3, nbo 4, fcu 6, sod 7; three is the minimum for a connected 3-periodic net. Undefined for a layer, and left blank there.

Interpenetration — how many copies of a net occupy the same space without bonding. One copy is not catenated; two or more is. Counted here from the lattice the quotient graph's cycles generate.

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.

Periodicity — in how many independent directions a net repeats: 3 for a framework, 2 for a layer, 1 for a chain, 0 for a finite molecule. A record's periodicity is measured, not assumed from the fact that a file has three cell vectors.

Point symbol — the sizes of the shortest cycles at a vertex with no counts, written in Wells' style: 4^12.6^3. Coarser than either vertex symbol.

Quotient graph — a periodic net folded onto one repeat unit: a finite graph whose edges each carry the cell offset they cross into. The object every computation on this site actually works with; the infinite net is recovered from it exactly.

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.

Ring — a cycle that is not the sum of two smaller cycles: a closed path with no shortcut across it. Every ring is a cycle; a cycle with a chord is not a ring, and an angle can have cycles but no ring at all, written *.

Maximum-symmetry embedding — the drawing of a net in which its symmetry is as large as the graph allows: every edge the same length, the cell the ideal cell of the net's own symmetry group, the whole thing scaled so the mean edge is 1. It is a drawing of the net and never a measurement of a material, and it is what a net's space group, transitivity and site symmetries are properties of. 634 records here have no deposit and are drawn from theirs.

Plane group — the symmetry group of a 2-periodic net: one of 17, numbered 1–17, spelled in lower case (p4mm, p6mm). It is not a space group and 11 means p4mm here and P2₁/m in the 230, so the two live in separate columns and separate search fields. 200 records here carry one.

Site symmetry — the point group of the operations of a net's space group that leave a given vertex where it is: the vertex's Wyckoff position in the maximum-symmetry embedding. It is what the coordination number cannot say. dia and nbo are both four-coordinated at every vertex; dia's vertices sit at -43m and are tetrahedral, nbo's at 4/mmm and are square-planar, and no building block fits both. Computed here from the net's own graph and stated on every vertex row that has one.

Space group of a net — the symmetry group of the net's maximum-symmetry embedding, which is a property of the graph and not of any particular drawing of it. A 2-periodic net has a plane group (1–17) instead. For the eleven enantiomorphic pairs the graph fixes the group only up to the pair, because a graph carries no handedness.

Systre — the program (Gavrog, version 19.6.0 here) that computes a net's maximum-symmetry embedding, its space group, its transitivity p/q and its canonical Systre key — a string equal for two graphs exactly when they are the same net. RCSR's archive is a table of those keys.

TD10 — topological density: the average number of vertices within ten steps of a vertex, counting the vertex itself. pcu is 1561.

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. p and q are computed from the net's graph; r and s need a natural tiling, which is not reachable for a 3-periodic net from the library this site runs, so they stay blank rather than being guessed. A 2-periodic net tiles the plane, which has faces and no tiles: its transitivity is a triple and is deliberately not written into an r/s pair.

Vertex symbol — a description of the shortest rings around a vertex, complementing the coordination sequence. In the RCSR convention it names the shortest ring through each angle, with * where there is none; MOF+'s vs names the shortest cycle instead. A record serves both, labelled, and never merges them.

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