Peter Murray-Rust Weerapong Phadungsukanan Jens Thomas Toplevel dictionary for computational chemistry Concepts in this dictionary are general throughout computational chemistry and are used extensively in the CompChem convention to describe the structure of computational chemistry. Weerapong Phadungsukanan Modules A calculation module for a computational job A calculation module represents the concept of the model calculation or optimisation or iteration processes for computational job. Module holding concepts relating to environment that the job used or required The computing environment concept refers to a hardware platform, software application, the operating system and any hardware and software configurations used in order to run the job or computational task. The environment also includes the metadata such as machine id, username, starting and finishing date time, tools, compilers, IP, etc. This information is not related to input and output of the model but is supplementary to the software application to run properly and may vary from machine to machine. Therefore, the computing environment is OPTIONAL element in the CompChem convention. A finalization module for a computational job A finalisation module represents the concept of the model results for computational job. A initialisation module for a computational job An initialisation module represents the concept of the model parameters and inputs for computational job. A job or computational task The job concept represents a computational job performed by quantum chemistry software, e.g. geometry optimisation job, frequency analysis job. The job concept is the smallest unit which can fully describe a general picture of computational modelling. A list of computational job A quantum chemistry calculation is often comprised of a series of subtasks, e.g. coarse optimisation -> fine optimisation -> NMR Spectrum Analysis; this is because most quantum chemistry software packages are designed to be modularised and only to perform a single task at a time. The joblist concept is introduced to capture these series of successive subtasks and links the information from one subtask to the next subtask. Environment terms TODO TODO An unspecified date no controlled syntax TODO executable program no controlled syntax TODO host name uncontrolled vocabulary TODO program input no controlled syntax TODO metadata Metadata TODO MOVE The number of processors used to run the job. The number of processors the job was executed on. TODO The program being run This is the name of the computational chemistry package being run. Known values for this are listed in the table below. Program Description Reference nwchem The Northwest Computational Chemistry Package (NWChem) nwchem website gaussian The Gaussian electronic structure coe gaussian website An arbitrary title. A title is not used for reference, though could be used for lexical indexing (e.g. by Solr). It often contains important metadata that is not otherwise available in the output. program version This specifies the version of the code that was used to run the calculation. Ideally it should specify a version in a version control system, although the version number (e.g. 6.1) of the code is acceptable. In NWChem, the version is printed in the Job Information block printed at the start of the output, and is called "nwchem branch" jumbo template Miscellaneous TODO TODO TODO TODO TODO TODO data TODO MOVE A CML id usable throughout cml documents. Need not be unique miscellaneous TODO MOVE parameter TODO MOVE property TODO MOVE TODO TODO TODO TODO TODO TODO A serial number a serial number from 1...n TODO ??? ??? TODO TODO Static Molecular properties serial number of atom TODO Atomic mass normally the mass of an isolated atom, but the isotopic variation may not be clear TODO TODO Mass of the atom May not always be that from a table of atomic masses TODO CML atomType element TODO Reference to CML atomType element This should be the normal usage for atomtype symbols/refs Symbol of the atom This may not always be a CML elementType TODO an atom type An atom type (not the element type). Cf cml:atomType TODO TODO TODO TODO TODO TODO TODO TODO TODO TODO TODO TODO TODO TODO TODO center of mass TODO TODO TODO TODO TODO TODO the type of the element the atomic symbol as in CML:@elementTypeS TODO TODO TODO TODO TODO TODO TODO TODO TODO Irreducible representation TODO TODO TODO TODO TODO TODO TODO TODO number of atoms normally the count of atoms in a molecule or other collection of atoms TODO nuclear dipole TODO TODO TODO TODO The potential energy arising from Coulombic nuclei-nuclei repulsions. T ^ n = - ∑ i ℏ 2 2 M i ∇ R i 2 The nuclear repulsion energy is the sum of the repulsive Coulombic interaction energies between the positively charged nuclei. jumbo template Wikipedia Jens Thomas The molecular point group in Schoenflies notation. The point group of the molecule defines the symmetry operations under which the molecule remains unchanged. CML x3 coordinate TODO CML y3 coordinate TODO CML z3 coordinate TODO Calculation properties The name of a basis set. The basis set name should map to one of the names as listed in the EMSL basis set library. TODO TODO TODO TODO TODO TODO basis function TODO calculationType Type of calculation TODO MOVE TODO TODO change in energy between cycles change in energy between cycles error in DIIS error in DIIS Highest Occupied Molecular Orbital TODO MOVE Lowest Occupied Moecular Orbital TODO MOVE serial number of iteration serial number of iteration TODO MOVE rms density RMS electron density TODO TODO cumulative time TODO MOVE TODO TODO Calculated Energies Coulomb energy TODO 1-electron energy 1-electron energy TODO TODO energy energy of unspecified typeTODO MOVE Exchange correlation energy TODO 1-electron energy TODO TODO TODO Sum of atom energies Sum of atom energies The total energy This may be a code-specific term so may be overridden by code-specific dictionaries Total DFT energy TODO MOVE Total energy TODO MOVE TODO TODO