cif_tcod.dic

Version: 0.015 (2018-02-27)

  1. cif_tcod.dic
    1. TCOD_DATABASE
      1. _tcod_database_code
    2. TCOD_DATA_SOURCE
      1. _tcod_data_source_file
      2. _tcod_data_source_block
    3. TCOD_SOURCE_STRUCTURE_DATABASE
      1. _tcod_source_structure_database_uuid
      2. _tcod_source_structure_database_id
      3. _tcod_source_structure_database_URI
      4. _tcod_source_structure_database_version
    4. TCOD_SOFTWARE_LIBRARY
      1. _tcod_software_library_id
      2. _tcod_software_library
      3. _tcod_software_library_version
      4. _tcod_software_library_compilation_date
      5. _tcod_software_library_compilation_environment
      6. _tcod_software_library_compiler_name
      7. _tcod_software_library_compiler_version
      8. _tcod_software_library_compiler_options
      9. _tcod_software_library_path
      10. _tcod_software_library_binary_uri
      11. _tcod_software_library_source_uri
    5. TCOD_INITIAL_COORDINATE
      1. _tcod_initial_coordinate_db_name
      2. _tcod_initial_coordinate_db_abbrev
      3. _tcod_initial_coordinate_db_URI
      4. _tcod_initial_coordinate_db_code
      5. _tcod_initial_coordinate_URI
    6. TCOD_INITIAL_CELL_PARAM
      1. _tcod_initial_cell_param_db_name
      2. _tcod_initial_cell_param_db_abbrev
      3. _tcod_initial_cell_param_db_URI
      4. _tcod_initial_cell_param_db_code
      5. _tcod_initial_cell_param_URI
    7. TCOD_FF
      1. _tcod_ff_id
      2. _tcod_ff_type
      3. _tcod_ff_name
      4. _tcod_ff_version
      5. _tcod_ff_citation_id
    8. TCOD_FILE
      1. _tcod_file_id
      2. _tcod_file_name
      3. _tcod_file_source_database_name
      4. _tcod_file_source_database_URI
      5. _tcod_file_source_database_version
      6. _tcod_file_source_reference_id
      7. _tcod_file_source_reference_version
      8. _tcod_file_source_reference_uuid
      9. _tcod_file_md5sum
      10. _tcod_file_sha1sum
      11. _tcod_file_format
      12. _tcod_file_interpreter
      13. _tcod_file_role
      14. _tcod_file_contents_type
      15. _tcod_file_contents
      16. _tcod_file_content_encoding
      17. _tcod_file_URI
    9. TCOD_CONTENT_ENCODING
      1. _tcod_content_encoding_id
      2. _tcod_content_encoding_layer_id
      3. _tcod_content_encoding_layer_type
    10. TCOD_COMPUTATION
      1. _tcod_computation_command
      2. _tcod_computation_step
      3. _tcod_computation_environment
      4. _tcod_computation_reference_uuid
      5. _tcod_computation_reference_id
      6. _tcod_computation_reference_URI
      7. _tcod_computation_database_name
      8. _tcod_computation_database_version
      9. _tcod_computation_database_URI
    11. TCOD_TOTAL_ENERGY
      1. _tcod_total_energy
      2. _tcod_total_energy_formula
      3. _tcod_total_energy_details
      4. _tcod_total_energy_gradient
      5. _tcod_total_energy_gradient_formula
      6. _tcod_total_energy_gradient_details
    12. TCOD_ATOM_SITE_RESIDUAL_FORCE
      1. _tcod_atom_site_resid_force_Cartn_x
      2. _tcod_atom_site_resid_force_magnitude

TCOD_DATABASE

Data items from this category are used for TCOD bookkeeping records, such as assigned TCOD number (aka TCOD database code).

_tcod_database_code

Specifies TCOD number assigned upon deposition into TCOD to the crystal structure described in the CIF.

TCOD_DATA_SOURCE

Data items from this category are used to record and trace sources of information deposited into TCOD.

_tcod_data_source_file

Specifies file name of the file that served as a source of data in this TCOD entry. The file should be recoded without the path or other URL components, since these components usually have no sense on the recipient's system. In Unix parlance, the value recorded should be the basename of the original file. For many data sources, however, the basename contains enough information to locate the original source. For instance, CIFs published in IUCr journals have Coeditor Code as a CIF file name, permitting to identify the original paper where the structure is discussed. Other journals may used original article's DOI as a part of the filename for the supplementary CIF file, which also permits one to trace back the original paper.

_tcod_data_source_block

Specifies the name of the data block within the file specified in the _tcod_data_source_file tag that served as a source of data in this TCOD entry. Only the data block name following the 'data_' header keyword should be recorded, not the whole data block header; i.e. the value specified here should be 'I', *not* 'data_I', for a data block with the header 'data_I'.

TCOD_SOURCE_STRUCTURE_DATABASE

_tcod_source_structure_database_uuid

UUID (Universally Unique Identifier, http://en.wikipedia.org/wiki/Universally_unique_identifier) of the database output structure (node, record) that was exported to this entry.

_tcod_source_structure_database_id

_tcod_source_structure_database_URI

_tcod_source_structure_database_version

TCOD_SOFTWARE_LIBRARY

Describes computational libraries.

_tcod_software_library_id

Identifies a software library in a loop

_tcod_software_library

The subroutine library (e.g. linear algebra) that was linked with the code used for the described calculation. Only the library name should be given, e.g. 'pthreads', 'libc', 'lapack'.

If more than one library was used, these items must be looped.

_tcod_software_library_version

A version string (number) of the library linked with the code for this computation.

_tcod_software_library_compilation_date

ISO 8601 (http://en.wikipedia.org/wiki/ISO_8601) format timestamp of the time when the subroutine library file was compiled.

_tcod_software_library_compilation_environment

A set of environment variable definitions, in /bin/sh syntax (i.e. using the "NAME=VALUE" syntax) for all relevant environment variables that were active when compiling this library. You can get the list in this syntax from the Unix/Linux 'printenv' command.

_tcod_software_library_compiler_name

Library compiler name (same syntax as for a package compiler).

_tcod_software_library_compiler_version

Library compiler version (same syntax as for a package compiler).

_tcod_software_library_compiler_options

Library compiler options that were used (same syntax as for a package compiler).

_tcod_software_library_path

A file sytem path of the library file (especially the shared library, *.so or *.dll) linked with the code for this computation.

_tcod_software_library_binary_uri

An URI (Web reference) where the binary software library used for this computation can be fetched.

_tcod_software_library_source_uri

An URI (Web reference) where the source code software library used for this computation can be fetched.

TCOD_INITIAL_COORDINATE

Initial atomic coordinate source.

_tcod_initial_coordinate_db_name

Coordinate source database name (e.g. "Crystallography Open Database")

_tcod_initial_coordinate_db_abbrev

Coordinate source database abbreviated name (e.g. "COD")

_tcod_initial_coordinate_db_URI

Coordinate source database stable URI, e.g. http://www.crystallography.net/

_tcod_initial_coordinate_db_code

Coordinate source database stable stable identifier, e.g. 1518187 (for COD entry 1518187).

_tcod_initial_coordinate_URI

A stable URI of coordinate file, e.g. http://www.crystallography.net/cod/1518187.cif

TCOD_INITIAL_CELL_PARAM

Initial crystallographic unit cell parameter source.

_tcod_initial_cell_param_db_name

Unit cell parameter source database name (e.g. "Crystallography Open Database")

_tcod_initial_cell_param_db_abbrev

Unit cell parameter source database abbreviated name (e.g. "COD")

_tcod_initial_cell_param_db_URI

Unit cell parameter source database stable URI, e.g. http://www.crystallography.net/

_tcod_initial_cell_param_db_code

Unit cell parameter source database stable identifier, e.g. 1518187 (for COD entry 1518187).

_tcod_initial_cell_param_URI

A stable URI of a file with the initial unit cell parameters, e.g. http://www.crystallography.net/cod/1518187.cif

TCOD_FF

_tcod_ff_id

A unique identifier (primary key) of a force field in a loop, in case the COD datablock containing it refers to more than one force field.

_tcod_ff_type

Fixed charge (standard biomolecular and materials: amber, opls, gromos etc.) Polarizable (AMOEBA, iAMOEBA etc.) Distributed multipole based FFs (multipoles instead of fixed point charges S. Price et al.) Hybrid (Different types for interatomic and intraatomic interactions)
Reactive (ReaxFF etc.) L.V. The list is non-exhaustive

Values:

ValueDescription
Fixed-chargedescribe the corresponding model here
Polarizabledescribe the corresponding model here
Distributed-multipoledescribe the corresponding model here
Hybriddescribe the corresponding model here
Reactivedescribe the corresponding model here
othermodel not one of the mentioned above

_tcod_ff_name

Standard name for the FF used. If there is no standard name use 'custom' Examples: charmm, opls, amber, gromos etc. L.V. One must add a reference to the original paper here

_tcod_ff_version

Version of a force field. Usually year of the publication.

_tcod_ff_citation_id

A reference to the citation describing the force field in the _citation_... category loop

TCOD_FILE

_tcod_file_id

Primary key for the _tcod_file_... table.

_tcod_file_name

_tcod_file_source_database_name

_tcod_file_source_database_URI

_tcod_file_source_database_version

_tcod_file_source_reference_id

_tcod_file_source_reference_version

_tcod_file_source_reference_uuid

_tcod_file_md5sum

MD5 checksum of the file.

_tcod_file_sha1sum

SHA1 checksum of the file.

_tcod_file_format

_tcod_file_interpreter

_tcod_file_role

Values:

ValueDescription
inputinput file
output
log
stdin
stdout
stderr

_tcod_file_contents_type

Values:

ValueDescription
scriptexecutable input script
controlcomputation control file
parameterscomputation parameter file
coordinates
structure
edensity
wavefunction
pseudopotential
basisset
forcefield

_tcod_file_contents

_tcod_file_content_encoding

Must match a single _tcod_content_encoding_id from the same datablock.

_tcod_file_URI

A stable URI (Web reference) where the file can be fetched.

TCOD_CONTENT_ENCODING

_tcod_content_encoding_id

_tcod_content_encoding_layer_id

One-based number of an encoding layer in the encoding stack, starting from the innermost layer.

_tcod_content_encoding_layer_type

Values:

ValueDescription
ncrNumeric Character Reference
base64Base64 as described in RFC2045
quoted-printableQuoted-printable as described in RFC2045
gzipGzip as described in RFC1952

TCOD_COMPUTATION

_tcod_computation_command

_tcod_computation_step

One-based position of the computation step, designating the order of execution of this step. Steps with lesser values are to be executed before the steps with greater values of this data item.

_tcod_computation_environment

A set of environment variable definitions, in /bin/sh syntax (i.e. using the "NAME=VALUE" syntax) for all relevant environment variables that are needed to reproduce this computation. You can get the list in this syntax from the Unix/Linux 'printenv' command.

_tcod_computation_reference_uuid

_tcod_computation_reference_id

Reference to a computation description (its primary key) in the remote database that published and stored this computation.

_tcod_computation_reference_URI

Reference to a computation description (its stable REST URI) in the remote database that published and stored this computation.

_tcod_computation_database_name

A name of the database that was used to publish and document this computation.

_tcod_computation_database_version

A version of the database that was used to publish and document this computation.

_tcod_computation_database_URI

A stable URI (of a human-readable description) of the database that was used to publish and document this computation.

TCOD_TOTAL_ENERGY

_tcod_total_energy

Ideally, should correspond to http://www.xml-cml.org/dictionary/compchem/ "total energy" (ID: totalEnergy) whenever applicable.

The total energy for a system of electrons and nuclei. The exact method of computing this parameter depends on the method. The formula used to compute it should be given in the _tcod_total_energy_formula data item; in CIF2 this will be a DRel method (i.e. a formal computable expression in a strictly specified computer language).

CAUTION: total energies are comparable only between computations made by the same method, under the same approximations and with the same or similar input parameters. Therefore, the value of this data item *SHOULD NOT* be used to rank different TCOD entries without proper scaling, analysis and justification.

Units: electron-Volts

_tcod_total_energy_formula

Formula used to compute the _tcod_total_energy value; the exact syntax details are still to be specified.

_tcod_total_energy_details

A human-readable description of the _tcod_total_energy computation ‒ its physical meaning and usability.

_tcod_total_energy_gradient

Gives an total energy gradient at the end of the computation (e.g. at the last optimisation cycle). Derivatives to be taken by nuclei positions and cell parameters.

Units: electron-Volts per Angstroem

_tcod_total_energy_gradient_formula

Formula or computer code used to compute the _tcod_total_energy_gradient value; the exact syntax details are still to be specified.

_tcod_total_energy_gradient_details

A human-readable description of the _tcod_total_energy_gradient computation ‒ its physical meaning and usability.

TCOD_ATOM_SITE_RESIDUAL_FORCE

_tcod_atom_site_resid_force_Cartn_x

These data items describe residual forces on atoms in the final structure. For a converged computation of a stable structure these should be close to 0.

The ..._Cartn_[xyz] referes to the same frame as _atom_site_Cartn_[xyz] coordinates; the ..._fract_[xyz] refer to force projections onto crystal axes. If the _tcod_atom_site_resid_force_magnitude is given as a positive number, then its directions are given by _tcod_atom_site_resid_force_dir_cos_[xy] direction cosini in Cartesian axes of _atom_site_Cartn_[xyz].

Only one set of data items ‒ ..._fract_[xyz], ..._Cartn_[xyz], ..._magnitude + ..._dir_cos_[xy], .._magnitude + ..._dir_cos_[xz] or .._magnitude + ..._dir_cos_[yz] need to be given to fully characterise residual forces; the rest can be computed from these provided values and thus are redundant.

A residual force on a given atom should be computed with all other parameters, including all other atom positions, fixed. The force components for each atom are given as partial derivatives δ E/δ x, δ E/δ y and δ E/δ z, where E is the total energy of the system and x, y, and z are coordinates of the atom for which residual force is computed (the δ is the partial derivative sign).

Units: electronvolts per Angstroem

_tcod_atom_site_resid_force_magnitude

The magnitude of the residual force (see data_tcod_atom_site_residual_force description for details).

Units: electronvolts per Angstroem