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 A calculation module for a computational job. A calculation module represents the concept of the model calculation, optimisation or iteration processes for a computational job. Almost any computational procedure is a calculation, and calculations can be nested to any level. As an example, an SCF calculation consists of an initial guess calculation, and a number of iterative calculations, the output of the final iteration constituting the results. An SCF geometry optimisation process consists of multiple calculation steps, each of which consists of an SCF calculation, followed by a gradient calculation. A calculation must contain an initialization module, which defines the inputs to the calculation (and therefore the calculation), and a finalization module, which holds all outputs. The calculation module may contain many other modules describing the process of the calculation, but that may not necessarily be desirable as results. Module holding concepts relating to the 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 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 or calculation. A finalization module represents the concept of the model results for a computational job or calculation. This will usually be the output properties of the final calculation carried out by the job. The finalization module should contain a propertyList with scalar, array and matrix quantities, but may also contain more complex objects such as molecules or orbitals as cml:lists. For a job or calculation with multiple child calculations, the finalization may consist of an aggregation of the key results from the child calculations. For an SCF calculation, the finalization module should contain the calculated energies, together with information on the attained convergence (e.g. norm of the gradient) and the orbitals. For an SCF optimisation, it will contain the above, together with the final molecular coordinates and information on the geometry convergence criteria. An initialization module for a computational job or calculation 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. 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 can be considered as the unit of work that would be submitted to a computational resource. In almost all respects a job is identical to a calculation, in that it has an initialization module, which holds the inputs for the calculation(s) to be run, and a finalization module, which holds all outputs. In addition, a job may contain an environment module, which describes the conditions under which the job was run, such as the program (and version) used, hostname, number of CPUs etc. A list of computational jobs 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 s 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. The date that the executable was compiled. The date that the executable used to run the job was compiled. This can be useful for determining the version of the code that was used. Jumbo NWChem template The date that the job commenced. The date that the job was started. For long-running jobs, this may not be the same as the completion date. Jumbo NWChem template The path to the executable program Many programs print the path of the executable in the output. This can be used to help determine which version of a code was used to run the job. Jumbo NWChem template The name of the host that the program was run on. For multi-processor jobs that were run on multiple hosts this should be the master node or may be undefined. Jumbo NWChem template A cml module for a single literal representation of an input file. The module will usually contain a list of scalars that represent the text of the input file. See the inputFileList for an example. A cml module containing a list of input files. The cml module that is the outer most container for the literal representation of one or more input files. An example for the Gulp code follows below: <module dictRef="compchem:inputFileList"> <module dictRef="compchem:inputFile"> <metadataList> <metadata name="compchem:inputFileName" content="test_cmlDumpDec_4a.in"/> </metadataList> <scalar dataType="xsd:string">opti prop conp </scalar> <scalar dataType="xsd:string">title </scalar> <scalar dataType="xsd:string">alumina test file </scalar> <scalar dataType="xsd:string">end </scalar> <scalar dataType="xsd:string">cell </scalar> <scalar dataType="xsd:string">4.7602 4.7602 12.9933 90.000000 90.000000 120.0 </scalar> <scalar dataType="xsd:string">frac </scalar> <scalar dataType="xsd:string">Al core 0.000000 0.000000 0.352160 </scalar> <scalar dataType="xsd:string">Al shel 0.000000 0.000000 0.352160 </scalar> <scalar dataType="xsd:string">O core 0.306240 0.000000 0.250000 </scalar> <scalar dataType="xsd:string">O shel 0.306240 0.000000 0.250000 </scalar> <scalar dataType="xsd:string">space </scalar> <scalar dataType="xsd:string">167 </scalar> <scalar dataType="xsd:string">species </scalar> <scalar dataType="xsd:string">Al core 0.043 </scalar> <scalar dataType="xsd:string">Al shel 2.957 </scalar> <scalar dataType="xsd:string">O core 0.513 </scalar> <scalar dataType="xsd:string">O shel -2.513 </scalar> <scalar dataType="xsd:string">buckingham </scalar> <scalar dataType="xsd:string">Al shel O shel 2409.505 0.2649 0.00 0.0 10.0 </scalar> <scalar dataType="xsd:string">O shel O shel 25.410 0.6937 32.32 0.0 12.0 </scalar> <scalar dataType="xsd:string">spring </scalar> <scalar dataType="xsd:string">Al 403.98 </scalar> <scalar dataType="xsd:string">O 20.53 </scalar> <scalar dataType="xsd:string">output xr example1 </scalar> <scalar dataType="xsd:string">output marvin example1.mvn </scalar> </module> <module dictRef="compchem:inputFile"> <metadataList> <metadata name="compchem:inputFileName" content="test_cmlDumpDec_4b.in"/> </metadataList> <scalar dataType="xsd:string">fit conp simul opti </scalar> <scalar dataType="xsd:string">cell </scalar> <scalar dataType="xsd:string"> 4.914730 4.914730 5.406570 90.000000 90.000000 120.0 </scalar> <scalar dataType="xsd:string">fractional </scalar> <scalar dataType="xsd:string">Si core 0.468200 0.000000 0.333333 4.000000 </scalar> <scalar dataType="xsd:string">O core 0.413100 0.266100 0.213100 0.869020 </scalar> <scalar dataType="xsd:string">O shel 0.431813 0.264902 0.204106 -2.869020 </scalar> <scalar dataType="xsd:string">space </scalar> <scalar dataType="xsd:string">152 </scalar> <scalar dataType="xsd:string">general 0 6 grad </scalar> <scalar dataType="xsd:string">Si core O shel 1283.037674 0.320500 10.660000 0.0 8.0 1 0 0 </scalar> <scalar dataType="xsd:string">buck </scalar> <scalar dataType="xsd:string">O shel O shel 22764.0 0.149 27.88 0.0000 8.0000 0 0 0 </scalar> <scalar dataType="xsd:string">spring </scalar> <scalar dataType="xsd:string">O 74.92 0 </scalar> <scalar dataType="xsd:string">three </scalar> <scalar dataType="xsd:string">Si core O shel O shel 2.097240 109.470000 1.8000 1.8000 3.2000 0 0 </scalar> <scalar dataType="xsd:string">dump example2.res </scalar> </module> </module> A representation of the name of a single input file. See the inputFileList for an example. The number of processors used to run the job. The number of processors the job was executed on. Jumbo NWChem template The program being run This is the name of the computational chemistry program being run. Known values for this are listed in the table below. Program Description nwchem The Northwest Computational Chemistry Package (NWChem) gaussian The Gaussian electronic structure code Jumbo NWChem template 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, Development) of the code is acceptable. Jumbo NWChem template The type of computational method that is being used in the calculation. Example values are: SCF DFT MP2 This identifies the type of computation that is being carried out and should be a string that identifies the broad class of computation that is being undertaken. There are many different variants of the various computational methods (e.g. DFT with different functionals) and approximations that can be applied to each one (e.g. Resolution of the Identity to DFT and MP2), which would lead to a large number of possibilities and difficulty identifying calculations of a particular class. For this reason, this term only describes the main method. The task that is being carried out by the job or calculation. Example values are: energy frequency geometry_optimization gradient initial_guess iteration step The describes what the job or calcualtion is aiming to do. For a single SCF calculation, the task is an energy, while the task for an individual SCF iteration calculation within the SCF is an iteration. Jobs and calculation both use the task term, although a job would only be expected to use the more general terms (such as energy or geometry_optimization). A CML id Usable throughout cml documents. Need not be unique An index. An integer used as an index.. The serial number of an iteration. The serial number of an iteration. parameter TODO property TODO 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. A Universally Unique IDentifier. A Universally Unique IDentifier as per RFC 4122. Any of the five versions or the special nil identifier are acceptable. This will usually be applied to a cml metadata element as shown below: <metadata name="compchem:UUID" content="d1056d90-a29b-11e1-54a6-d61df6dfef7c"/> Elapsed CPU time. Wikipedia CPU time (or CPU usage, process time) is the amount of time for which a central processing unit (CPU) was used for processing instructions of a computer program, as opposed to, for example, waiting for input/output (I/O) operations. wikipedia entry. Elapsed wallclock time. Wikipedia Wall-clock time is a measure of the real time that elapses from start to end, including time that passes due to programmed (artificial) delays or waiting for resources to become available. In other words, it is the difference between the time at which a task finishes and the time at which the task started as would be measured by a clock, such as one on the wall. wikipedia entry. center of mass TODO TODO The total charge on the system in elementary charge units. TODO the type of the element the atomic symbol as in CML:@elementTypeS TODO TODO TODO TODO TODO TODO TODO Irreducible representation TODO TODO The nuclear electric dipole moment The number of atoms Normally the count of atoms in a molecule or other collection of atoms TODO The total number of electrons in a system. TODO. TODO The total number of alpha spin electrons in a system. TODO. TODO The total number of beta spin electrons in a system. TODO TODO The number of closed shells TODO The number of open shells TODO Wikipedia The molecular point group in Schoenflies notation. The point group of the molecule defines the symmetry operations under which the molecule remains unchanged. wikipedia entry. Jumbo NWChem template Wikipedia The spin multiplicity is equal to the number of alpha electrons, minus beta electrons, plus 1 When all electrons are paired, the spin multiplicity is 1, and the state is a singlet, with one unpaired electron, a doublet, two, a triplet, etc. wikipedia entry. The type of wavefunction. Acceptable values are: closed open restricted open TODO CML x3 coordinate The x-component of the Cartesian coordinates (x,y,z) of an entity. CML y3 coordinate The y-component of the Cartesian coordinates (x,y,z) of an entity. CML z3 coordinate The z-component of the Cartesian coordinates (x,y,z) of an entity. A cml list container for all information related to the basis set. The basis set is the set of functions from which the electron orbitals are constructed. More information can be found on wikipedia or in Jan Labanowsk's CCL article. The model here draws heavily from the work done by the EMSL basis set exchange , which is described in the paper: Basis Set Exchange: A Community Database for Computational Sciences . Their schemas are the basis for what we have done here and we would hope to keep the two efforts aligned as far as possible. Within the context of conventions and dictionaries as detailed in the CML: Evolution and Design paper, we are using existing CML datatypes to hold all complex data structures, with dictionary entries describing the elements. Rather then using matricies to hold the exponents and coefficients, arrays will be used. Attributes (e.g. elementType on contractions) will be moved into separate elements, with the convention used to enforce their appearance. This also means that the attributes will appear as dictionary entries here with an associated explanation. To illustrate this, the mixed basis set for a calculation on water would be printed as follows in the NWChem output: Basis "ao basis" -> "" (cartesian) ----- h1 (Hydrogen) ------------- Exponent Coefficients -------------- --------------------------------------------------------- 1 S 1.30100000E+01 0.019685 1 S 1.96200000E+00 0.137977 1 S 4.44600000E-01 0.478148 2 S 1.22000000E-01 1.000000 3 P 7.27000000E-01 1.000000 h2 (Hydrogen) ------------- Exponent Coefficients -------------- --------------------------------------------------------- 1 S 3.42525091E+00 0.154329 1 S 6.23913730E-01 0.535328 1 S 1.68855400E-01 0.444635 o (Oxygen) ---------- Exponent Coefficients -------------- --------------------------------------------------------- 1 S 4.71055180E+01 -0.014408 1 S 5.91134600E+00 0.129568 1 S 9.76483000E-01 -0.563118 2 S 2.96070000E-01 1.000000 3 P 1.66922190E+01 0.044856 3 P 3.90070200E+00 0.222613 3 P 1.07825300E+00 0.500188 4 P 2.84189000E-01 1.000000 5 P 7.02000000E-02 1.000000 Summary of "ao basis" -> "" (cartesian) ------------------------------------------------------------------------------ Tag Description Shells Functions and Types ---------------- ------------------------------ ------ --------------------- h1 cc-pvdz 3 5 2s1p h2 sto-3g 1 1 1s o Stuttgart RLC ECP 5 11 2s3p This would be marked up as follows: <list dictRef="compchem:basisSet" id="basisSet"> <list dictRef="compchem:basisSetContractions" id="basisSetContractions"> <scalar dataType="xsd:string" id="atomType" dictRef="compchem:atomType">h1</scalar> <scalar dataType="xsd:string" id="elementType" dictRef="compchem:elementType">H</scalar> <scalar dataType="xsd:string" id="basisSetType" dictRef="compchem:basis_set_type">orbital</scalar> <scalar dataType="xsd:string" id="basisSetLabel" dictRef="compchem:basisSetLabel">cc-pvdz</scalar> <scalar dataType="xsd:string" id="basisSetHarmonicType" dictRef="compchem:basisSetHarmonicType">cartesian</scalar> <list dictRef="compchem:basisSetContraction" id="basisSetContraction"> <scalar dataType="xsd:string" dictRef="compchem:basisSetShell">s</scalar> <array size="3" dataType="fpx:real" dictRef="compchem:basisSetExponent">1.301000000000e1 1.962000000000e0 4.446000000000e-1</array> <array size="3" dataType="fpx:real" dictRef="compchem:basisSetCoefficient">1.968500000000e-2 1.379770000000e-1 4.781480000000e-1</array> </list> <list dictRef="compchem:basisSetContraction" id="basisSetContraction"> <scalar dataType="xsd:string" dictRef="compchem:basisSetShell">s</scalar> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetExponent">1.220000000000e-1</array> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetCoefficient">1.000000000000e0</array> </list> <list dictRef="compchem:basisSetContraction" id="basisSetContraction"> <scalar dataType="xsd:string" dictRef="compchem:basisSetShell">p</scalar> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetExponent">7.270000000000e-1</array> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetCoefficient">1.000000000000e0</array> </list> </list> <list dictRef="compchem:basisSetContractions" id="basisSetContractions"> <scalar dataType="xsd:string" id="atomType" dictRef="compchem:atomType">h2</scalar> <scalar dataType="xsd:string" id="elementType" dictRef="compchem:elementType">H</scalar> <scalar dataType="xsd:string" id="basisSetType" dictRef="compchem:basis_set_type">orbital</scalar> <scalar dataType="xsd:string" id="basisSetLabel" dictRef="compchem:basisSetLabel">sto-3g</scalar> <scalar dataType="xsd:string" id="basisSetHarmonicType" dictRef="compchem:basisSetHarmonicType">cartesian</scalar> <list dictRef="compchem:basisSetContraction" id="basisSetContraction"> <scalar dataType="xsd:string" dictRef="compchem:basisSetShell">s</scalar> <array size="3" dataType="fpx:real" dictRef="compchem:basisSetExponent">3.425250910000e0 6.239137300000e-1 1.688554000000e-1</array> <array size="3" dataType="fpx:real" dictRef="compchem:basisSetCoefficient">1.543289700000e-1 5.353281400000e-1 4.446345400000e-1</array> </list> </list> <list dictRef="compchem:basisSetContractions" id="basisSetContractions"> <scalar dataType="xsd:string" id="atomType" dictRef="compchem:atomType">o</scalar> <scalar dataType="xsd:string" id="elementType" dictRef="compchem:elementType">O</scalar> <scalar dataType="xsd:string" id="basisSetType" dictRef="compchem:basis_set_type">orbital</scalar> <scalar dataType="xsd:string" id="basisSetLabel" dictRef="compchem:basisSetLabel">Stuttgart RLC ECP</scalar> <scalar dataType="xsd:string" id="basisSetHarmonicType" dictRef="compchem:basisSetHarmonicType">cartesian</scalar> <list dictRef="compchem:basisSetContraction" id="basisSetContraction"> <scalar dataType="xsd:string" dictRef="compchem:basisSetShell">s</scalar> <array size="3" dataType="fpx:real" dictRef="compchem:basisSetExponent">4.710551800000e1 5.911346000000e0 9.764830000000e-1</array> <array size="3" dataType="fpx:real" dictRef="compchem:basisSetCoefficient">-1.440800000000e-2 1.295680000000e-1 -5.631180000000e-1</array> </list> <list dictRef="compchem:basisSetContraction" id="basisSetContraction"> <scalar dataType="xsd:string" dictRef="compchem:basisSetShell">s</scalar> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetExponent">2.960700000000e-1</array> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetCoefficient">1.000000000000e0</array> </list> <list dictRef="compchem:basisSetContraction" id="basisSetContraction"> <scalar dataType="xsd:string" dictRef="compchem:basisSetShell">p</scalar> <array size="3" dataType="fpx:real" dictRef="compchem:basisSetExponent">1.669221900000e1 3.900702000000e0 1.078253000000e0</array> <array size="3" dataType="fpx:real" dictRef="compchem:basisSetCoefficient">4.485600000000e-2 2.226130000000e-1 5.001880000000e-1</array> </list> <list dictRef="compchem:basisSetContraction" id="basisSetContraction"> <scalar dataType="xsd:string" dictRef="compchem:basisSetShell">p</scalar> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetExponent">2.841890000000e-1</array> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetCoefficient">1.000000000000e0</array> </list> <list dictRef="compchem:basisSetContraction" id="basisSetContraction"> <scalar dataType="xsd:string" dictRef="compchem:basisSetShell">p</scalar> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetExponent">7.020000000000e-2</array> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetCoefficient">1.000000000000e0</array> </list> </list> <list dictRef="compchem:basisSetContractions" id="basisSetContractions"> <scalar dataType="xsd:string" id="atomType" dictRef="compchem:atomType">o</scalar> <scalar dataType="xsd:string" id="elementType" dictRef="compchem:elementType">O</scalar> <scalar dataType="xsd:string" id="basisSetType" dictRef="compchem:basis_set_type">ecporb</scalar> <scalar dataType="xsd:string" id="basisSetLabel" dictRef="compchem:basisSetLabel">Stuttgart RLC ECP</scalar> <scalar dataType="xsd:string" id="basisSetHarmonicType" dictRef="compchem:basisSetHarmonicType">cartesian</scalar> <scalar dataType="xsd:integer" id="numElectronsReplaced" dictRef="compchem:numElectronsReplaced">2</scalar> <list dictRef="compchem:basisSetContraction" id="basisSetContraction"> <scalar dataType="xsd:string" dictRef="compchem:basisSetShell">s</scalar> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetRExponent">2.000000000000e0</array> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetExponent">1.044567000000e1</array> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetCoefficient">5.077106900000e1</array> </list> <list dictRef="compchem:basisSetContraction" id="basisSetContraction"> <scalar dataType="xsd:string" dictRef="compchem:basisSetShell">p</scalar> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetRExponent">2.000000000000e0</array> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetExponent">1.804517400000e1</array> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetCoefficient">-4.903551000000e0</array> </list> <list dictRef="compchem:basisSetContraction" id="basisSetContraction"> <scalar dataType="xsd:string" dictRef="compchem:basisSetShell">d</scalar> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetRExponent">2.000000000000e0</array> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetExponent">8.164798000000e0</array> <array size="1" dataType="fpx:real" dictRef="compchem:basisSetCoefficient">-3.312124000000e0</array> </list> </list> </list> The name of the basis set. This is the name or title of the basis set and should be one of names used within the EMSL Basis Set Exchange. This corresponds to the Dublin core title element of the "basisSet" in the BSE schema. The basisSetLabel will usually be applied within a basisSetContractions list, as this permits different named basis sets to be applied to different atoms. The basisSetLabel may be applied to the whole basis set (i.e. at the same level as the basisSetContrations) if the same basis set was applied to all atoms in the calculation. This is to permit logfiles to be converted to valid CML where the basis set is not printed explictly on each atom. The type of the basis set. This corresponds to the "basisSetType" in the EMSL schema. Valid values are: orbital dftorb dftxfit dftcfit periodic ecporb spinorb polarization diffuse tight rydberg The type of the angular functions used in basis set. This corresponds to the "harmonicType" in the EMSL schema. Valid values are: cartesian spherical For higher angular momentum (l>2), basis functions can be described in cartesian (6 d, 10 f, 15 g, ...) or spherical form (5 d, 7 f, 9 g, ...). Most programs work in cartesians by default, although, particularly for correlated calculations, the higher number of functions in the cartesian form becomes significant, and it becomes more efficient to use the spherical form. This is described more fully in the following paper: Transformation between Cartesian and pure spherical harmonic Gaussians The contraction type of the basis set. This describes how the gaussian functions in the basis are contracted to generate the basis functions. With segmented, each gaussian primitive only contributes to one contraction, whereas with a general contraction, each primitive can contribute to every contraction. This corresponds to the "contractionType" in the EMSL schema. Valid values are: segmented general uncontracted A description of the basis set. TODO The cml:list container for the contractions relating to a particular atom type. This holds all the information relating to a basis set on an atom. It contains an element for the atom_type which is the "tag" that was used to link it to an individual atom in the calculation, an element_type which describes the type of element the contractions relate to, the harmonic_type of the contractions, and then a list of contraction elements. The label for the contraction shell. This corresponds to the "shellType" in the EMSL schema. Valid values are: S P SP D F G H I K L M The cml:list container for an individual contraction. This corresponds to an individual "contraction" element in the EMSL schema, and holds the data for the contraction, including the shell_type, and exponents and coefficients. A cml:array holding the list of exponents for an individual contraction. TODO A cml:array holding the list of R exponents for an individual Effective Core Potential (ECP) contraction. TODO A cml:array holding the list of coefficients for an individual contraction. TODO The number of electrons replaced by an Effective Core Potential (ECP). TODO A cml list container for all information related to an Orbital. This is currently being developed so feel free to get involved. A sketch of the current thinking is below.  <index dataType="xsd:integer">3</index>  <energy dataType="xsd:double">-1.341678D+00</energy>  <symmetry dataType="xsd:string">a2</symmetry>  <degeneracy dataType="xsd:integer">2</degeneracy>  <occupancy dataType="xsd:double">2.0</occupancy> <eigenVectors>  </eigenVectors> A cml list container for all information related to a DFT Functional. A container for a DFT Functional. Currently the only attribute that is used is the dft_functional_title . In the tradition of wikipedia, this is a stub and needs someone who knows about DFT to expand it. The name of the DFT functional used, if a standard functional was used. TODO The Coulomb compoment of the electronic energy in a Density Functional Calculation. TODO The Correlation Energy. TODO The one-electron energy. The one-electron kinetic energy compment of the Hamiltonian operator for a system of electrons and nuclei. The two-electron energy. 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. The Hartree-Fock Self-Consistent Field component of the energy. This is the SCF energy, where the SCF energy is a compment of another energy, such as the MP2 energy. The scf_energy term should NOT be used for the total energy of an SCF calculation, for this the total energy term should be used, as the exact meaning of the SCF energy will be properly determined by the parameters in the initialization module. The total energy for a system of electrons and nuclei. The total energy is formed from the sum of the nuclear, one- and two-electron energies for a system of electrons and nuclei. The meaning of any energy is dependent on the context in which it is found. An energy will usually be located in the finalization module of a calculation, and it is the parameters in the calculation's initialization module that will define the type of energy. So if the calculation's method parameter is MP2, then this will be an MP2 energy, with the exact definition determined by the associated SCF and MP2 parameters in the SCF and MP2 initialization modules. The Exchange correlation energy. TODO