Vibrational Analysis
Cycling movement/oscillation about an equilibrium point. In quantum mechanics, vibrational analysis is used to decompose complex internal motion of groups of atoms in a molecule into patterns of motion (normal modes) where all parts of the system move sinusoidally with the same frequency and with a fixed phase relation. Frequency is defined as the number of occurrences of a repeating event per unit of time. Definition given by Dr Daniel Nurkowski <danieln@cmclinnovations.com>.
A class for the computations of vibrational spectrum of molecules.
A class for VibrationalAnalysis.
Lumo plus one energy
Space And Time Unit.
The property that defines the contents of a file generated from file that is output of the calculation. Foe example, xml and png files by parsing Gaussian file (calculations). Created by Nenad Krdzavac (nk510@cam.ac.uk)
Output source
Auxiliary Concept
A generic class representing Auxiliary concepts.
Mass Unit
A class for the Pople split valence 6-311+G* basis set.
6-311+G* Basis Set
Electronic and ZPEEnergy
Frequency is defined as the number of occurrences of a repeating event per unit of time. Definition given by Dr Daniel Nurkowski <danieln@cmclinnovations.com>.
Frequency
Length Unit
Publication Concept
A generic class representing concepts related to publications.
Methodology Feature
A class for specific features or properties of a given methodology.
Mechanics Unit
Float Value
A class for float value, containing value and unit.
The geometry type classifies molecules, depending on their geometries, into three categories: atomic, linear and nonlinear. The geometry type can be inferred from molecules geometry or rather from molecule's rotational constants. For atomic molecules all rotational constants are zero (Gaussian does not event print them), for linear molecules there are two, equal to each other, and one equal to zero rotational constants and for nonlinear molecules there should be three non-zero rotational constants. Definition given by Dr Daniel Nurkowski <danieln@cmclinnovations.com>.
Geometry Type
Molecular Methodology
A class for general methodologies of computational chemistry.
A class for MolecularMethodology.
Homo minus two energy
These are inversely proportional to moments of inertia and determine the magnitude of spacing between rotational energy levels. The rotational constants can be calculated from molecule's geometry and atoms it contains as eigenvalues of the moments of inertia tensor. Definition given by Dr Daniel Nurkowski <danieln@cmclinnovations.com>.
Rotational Constants
Scf energy
Calculation Result
A class for specific concepts related to the results of computational chemistry procedures.
Lumo energy
LUMO stands for Lowest Unoccupied Molecular Orbital. Definition given by Angiras Menon. Email: am2145@cam.ac.uk
Polarized split Valence Basis Set
A class for the Pople basis sets with polarization functions.
Science And Engineering Unit
A class for various types of energies associated with molecular system.
System Energies
Pople Basis Set
A class for the Pople basis sets.
Homo minus one energy
Calculation Concept
A class for generic concepts that describe calculations in computational chemistry.
Value
This is super class for the expression of various types of values.
Energy And Work Unit
Level of theory
The level of theory is the set of underlying approximations used to describe the chemical system. Higher levels of theory are often more accurate however they come at much greater computational cost. Definition given by Dr Daniel Nurkowski <danieln@cmclinnovations.com>.
Zero point energy
Lumo plus two energy
Molar Energy Unit
Multiple Determinant
A class for the methods of quantum chemistry using multiple Slater determinants.
Computation module
Frequency Unit.
Quantum Mechanics
A class for QuantumMechanics.
A class for Quantum Mechanical methods.
Homo energy
HOMO stands for Highest Occupied Molecular Orbital. Definition given by Angiras Menon. Email: am2145@cam.ac.uk
Split Valence Basis Set
A class for the Pople split valence basis sets.
Gaussian calculations performed by Gaussian software.
Gaussian calculation
A class for SourcePackage.
A class for quantum chemistry packages used to peform computations.
Source Package
SourcePackage
Single Reference State
A class for Single Reference (SR) coupled-cluster methods.
Initialization module
Molecular Computation
A class for the specific type of calculation (like optimization, single point, etc) conducted by a computational chemistry program.
A class for MolecularComputation.
Unit
A unit of measure, or unit, is a particular quantity value that has been chosen as a scale for measuring other quantities the same kind (more generally of equivalent dimension). For example, the meter is a quantity of length that has been rigorously defined and standardized by the BIPM (International Board of Weights and Measures). Any measurement of the length can be expressed as a number multiplied by the unit meter. More formally, the value of a physical quantity Q with respect to a unit (U) is expressed as the scalar multiple of a real number (n) and U: Q = nU.
Physical Unit.
Integer Value
A class that represents integer value, containing value and unit.
Geometry Optimization
A class for calculations in computational chemistry that aim to find molecular geometry of lowest energy.
Chemistry Unit
Gaussian-n
A collection of composite calculations (mainly quadratic CI plus others) that try to approximate full CI.
Basis Set
A class for the basis set. In computational chemistry basis set is a set of functions which are combined to create molecular orbitals.
Basis set is a set of functions that are used to describe electronic wavefunctions. Definition given by Dr Daniel Nurkowski <danieln@cmclinnovations.com>.
The symmetry number or symmetry order of an object is the number of different but indistinguishable (or equivalent) arrangements (or views) of the object, i.e. the order of its symmetry group. In statistical
thermodynamics, the symmetry number corrects for any overcounting of equivalent molecular conformations in the partition function and depends on the assumptions made while deriving the partition function. As an example, the Rigid Rotor Harmonic Oscillator (RRHO) approximation treats an object, in this case a molecule, as a rigid body which does not allow certain symmetry operations like reflections or inversion. These forbidden operations need to be subtracted from the point group order in order to obtain a correct symmetry number of an object that is subject to constraints. Definition given by Dr Daniel Nurkowski <danieln@cmclinnovations.com>.
Rotational Symmetry
A class for the Pople basis sets with diffuse functions.
Diffuse Basis Set
has coordinates
A property that describes atom coordinates.
has result
A property that describes generic results of the computations.
Molecule Property
A property that specifies the Molecule Property.
Generic Datatype Property for Molecular Features related to computations
The upper property for various properties related to Molecular Data
has unique species
generalization
This property relates a quantity kind to its generalization. A quantity kind, PARENT, is a generalization of the quantity kind CHILD only if
1. PARENT and CHILD have the same dimensions in every system of quantities;
2. Every unit that is a measure of quantities of kind CHILD is also a valid measure of quantities of kind PARENT.
has electronic energy
A property that describes the electronic energy.
Mass of an element in gaussian is given in unified atomic mass untis. These are usually represented with a symbol "u" or "Da" as another name of that unit is Dalton. Definition given by Dr Daniel Nurkowski <danieln@cmclinnovations.com>.
specialization
This property relates a quantity kind to its specialization(s). For example, linear velocity and angular velocity are both specializations of velocity.
A property that descibes the formal charge. The formal charge is the charge assigned to an atom in a molecule, assuming that electrons in a chemical bond are shared equally between atoms, regardless of relative electronegativity. Note: It is proposed by Dr Daniel Nurkowski to add gc:Molecule as a domain side of formal charge object property (date: 11.10.2018.)
has formal charge
Atom Coordinate X
A property that describes Atom X coordinate
Atom Coordinate Z
A property that describes Atom Z coordinate
has atom
A property that describes atoms comprised by a molecule or residue
Atom Coordinate Y
A property that describes Atom Y coordinate
Molecule
A property that specifies a molecule.
Output File
A property that specifies the Output file.
Calculation
A property that specifies the calculation.
has initialization.
An initialization module represents the concept of the model parameters and inputs for computational job. The module defines the calculation, so that it should be possible to reproduce the calculation based soley on the data in this module. The initialization module should contain a parameterList with scalar, array and matrix quantities, and the starting molecule, but may also contain more complex objects as cml:lists, such as the basis set.
Generic Molecular Property
The upper property for various properties related to molecular systems.
A property that describes what element the given atom is.
is element
Parameter
A property that specifies a parameter.
has environment
has system energies result
A property that describes system energies.
true
has cotational constants value
Generic Datatype Property for Molecular Data
The upper property for various properties related to Molecular Data
has cotational constants count
A property that describes total number of rotational constants value.
has rotational symmetry number
has run date
abbreviation
An abbreviation for a unit is a short (usually 5 characters or less) string that is used in place of the full name for the unit in contexts where space is limited, or where using the abbreviation will enhance readability.
hasspin multiplicity value
The spin multiplicity is equal to the number of alpha electrons, minus beta electrons, plus 1.
Date
Date may be used to express temporal information at any level of granularity. Recommended best practice is to use an encoding scheme, such as the W3CDTF profile of ISO 8601 [W3CDTF].
A point or period of time associated with an event in the lifecycle of the resource.
1999-07-02
literal
has level of theory value
Number of Atoms
A property that determines the number of atoms in a given collection
A property that determines the number of atoms in a given collection
symbol
The symbol for a unit is a glyph that is used to represent the unit in a compact form. For example, the symbol for the US Dollar is $. This contrasts with unit:abbreviation, which gives a short alphanumeric abbreviation for the unit. (I.e. USD for US Dollar).
has name
The name of an entity.
A property that defines the name of molecular system elements, i.e. atom or residue.
code
A unit code is a numeric string that uniquely identifies a unit
has source package name
This is the name of the computational chemistry program being run.
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, Development) of the code is acceptable.
has source package version
has count
conversion multiplier
has unit
A property that describes a unit of the value.
has value
A Superproperty of typed numerical values.
conversion offset
has vibration count
A property that describes the number of vibrational frequencies.
Angstrom
Å
0085
1.0E-10
0.0
Å
cm-1
A wavenumber - the unit of frequency.
Molar Energy
0910
0.0
1.0e0
J/mol
Joule per Mole
J/mol
Da
0.0
1.66090210E-27
0485
Da
Dalton
Gigahertz
GHz
0.0
1.0E9
3035
GHz
Atomic Unit
Atomic Unit this is measure in units of elementary atomic charge called atomicUnits (a.u) .
The elementary unit of charge (e) is called an atomic unit (a.u.) of charge and is so many Coulombs (1.6 *10**(-19) Coulombs. (float)
E_h
A hartree (symbol E_h) is the atomic unit of energy. The hartree energy is equal to the absolute value of the electric potential energy of the hydrogen atom in its ground state.
0.0
4.35974394E-18
E_h
Hartree