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NCMAT format
NB: Please also check here for updates to this file.
This document describes the various versions of the NCMAT file format associated
with NCrystal and the extension .ncmat. Note documented here is merely the
format itself, and that different versions of NCrystal might choose to do
slightly different things with the same input file - ideally because newer
versions of the code will introduce improved modelling capabilities, but also
because bugs might get fixed (usually) or introduced (hopefully rarely).
Currently the three versions of the format are NCMAT v1 which is supported by
all NCrystal releases, NCMAT v2 which can be read with NCrystal releases 2.0.0
and beyond, and NCMAT v3 which can be read with NCrystal releases 2.1.0 and
beyond.
The NCMAT v1 format is the original supported format, in which crystal unit cells are defined in @CELL, @SPACEGROUP, and @ATOMPOSITIONS sections, while a @DEBYETEMPERATURE section must provide global or per-element Debye temperatures.
The publication associated with NCrystal release v1.0.0 describes this format in more detail, including how both elastic and inelastic physics is modelled based on what is essentially just the layout of the unit cell and a single dynamic parameter, the Debye temperature:
X.-X. Cai and T. Kittelmann, NCrystal: A library for thermal neutron transport, Computer Physics Communications 246 (2020) 106851, https://doi.org/10.1016/j.cpc.2019.07.015
Example file in NCMAT v1 format, units in the @CELL section are in angstrom and degrees respectively, while the values in the @DEBYETEMPERATURE section are in kelvin:
NCMAT v1
# Some comments about the file can be
# optionally added here.
@CELL
lengths 4.913437 4.913437 5.405118
angles 90. 90. 120.
@SPACEGROUP
154
@ATOMPOSITIONS
Si 0.47 0. 0.666666666667
Si 0. 0.47 0.333333333333
Si 0.53 0.53 0.
O 0.4146 0.2678 0.78543
O 0.2678 0.4146 0.21457
O 0.7322 0.1468 0.452096666667
O 0.5854 0.8532 0.881236666667
O 0.8532 0.5854 0.118763333333
O 0.1468 0.7322 0.547903333333
@DEBYETEMPERATURE
Si 515.5240
O 515.1032
The file must always begin with the format designation, NCMAT v1, on a single
line, with no space added before the initial N. All NCMAT files thus begin
with 5 bytes spelling out NCMAT in ASCII. The entire file must be encoded in
ASCII or UTF-8 encodings, with non-ASCII parts of UTF-8 only allowed in
comments. Line endings can be Unix (LF) or DOS (CFLF), but not the ancient
Macintosh endings (CF).
The four sections appearing in the example file above, @CELL, @SPACEGROUP,
@ATOMPOSITIONS, and @DEBYETEMPERATURE must all be present exactly once in all v1
files - with the exception of @SPACEGROUP which is optional. There is no strict
requirement on the order in which they appear. Comments must be on lines
starting with # marks and are allowed only after the initial line (with the
format version, "NCMAT v1"), and before the first section. Empty lines are
ignored, as is any extraneous white-space within sections. The section markers
(@CELL, etc.) must be on their own lines. When reading NCMAT v1 files with
NCrystal v2.0.0 and later, inelastic scattering will be dealt with as for any
NCMAT v2 file where @DYNINFO sections are absent (see below for what this
means).
The lattice parameters of the crystal. The format is as shown in the example,
but the order of length and angles can be reversed if desired.
Atomic unit cell positions in relative lattice coordinates. Each element appearing must be on separate line, as shown in the example above, and the name must be Capitalised and use the standard chemical element notation.
This optional section contains the space group number of the crystal symmetry, which must be mathematically consistent with the unit cell layout provided in the @CELL and @ATOMPOSITIONS sections. The space group number is given as a single integer with a value from 1 to 230.
Either a single number, the global Debye temperature, must be provided, or one for each of the elements in the material. Each element must be on separate line.
The original parsing code associated with the NCMAT v1 format was somewhat forgiving for certain syntax errors. Thus some clearly broken NCMAT v1 files could be read with the old code, while the new code will raise an error. It is, however, the intention that any v1 file which can be read with newer code will also be readable with older NCrystal code all the way back to NCrystal v1.0.0. All official v1 files in the data libraries published with NCrystal can be read with both new and old parsing code.
The NCMAT v2 format is similar to the NCMAT v1 format, but introduces the possibility of using other models for the modelling of, in particular, inelastic scattering. Support for it is first introduced in NCrystal release 2.0.0. It adds two new optional sections, @DYNINFO and @DENSITY, and makes the @CELL, @ATOMPOSITIONS, and @DEBYETEMPERATURE sections optional in some circumstances. It also introduces support for the element name "D" (deuterium).
The main new feature is the addition of optional @DYNINFO sections. There should exist exactly one for each type of element in the material. Each @DYNINFO section can have one of five different types, influencing what modelling should be used for that element: scatknl, vdos, vdosdebye, freegas or sterile, all described in the following sections. For the special case of crystalline materials with both @ATOMPOSITIONS and @DEBYETEMPERATURE sections, it is allowed to omit all @DYNINFO sections from the file, which then implies vdosdebye type for all elements (which is how NCMAT v1 files will be read in NCrystal v2.0.0 and later). Fields always present in any @DYNINFO sections are:
@DYNINFO
element O
fraction 2/3
type <name-of-type>
Here the element field indicates the name of the element, the type field the
aforementioned type, while the fraction field indicates the relative count of
this type of element in the material as a value between 0 and 1. The fractions
in all DYNINFO sections should add up to to 1, and it is possible to express
fractions as rational numbers for higher precision and readability, e.g. 2/3
(with no spacing allowed, thus no 2 /3). The order of fields in @DYNINFO
sections does not matter, and unless otherwise noted, the values should appear
on the same line as the field name.
The @DYNINFO type sterile, declares a modelling where there is no scattering by thermal neutrons on that element at all (depending on the context, there can still be absorption or scattering by particles other than thermal neutrons). This of course does not represent a realistic model of scattering, but it can nonetheless occasionally be useful if other more detailed information is not available. For instance it might be used when an element of a poly-atomic material is believed to only contribute significantly to absorption cross-sections or density calculations. Example section:
@DYNINFO
element O
fraction 2/3
type sterile
The simplest dynamic model with actual scattering of thermal neutrons, indicates that a basic free-gas model should be chosen for that element. For instance, to enable free-gas modelling of the oxygen in water molecules (which is a typical strategy if one has detailed scattering kernels for the hydrogen but no specific knowledge about the contribution of the oxygen), one would add a section with:
@DYNINFO
element O
fraction 2/3
type freegas
It will depend on the use case or material in question whether a freegas or sterile type represents a more suitable fall-back strategy for a given element.
The most realistic modelling is in the form of 2D scattering kernels, in the form of either S(alpha,beta) or S(Q,omega) tables. For instance, an S(alpha,beta) table is specified with the alphagrid, betagrid, and sab keywords like:
@DYNINFO
element Be
fraction 1
type scatknl
temperature 296.3
alphagrid 8.9330622e-02 1.3293247e-01 2.2332656e-01 2.9245144e-01
<...>
5.9819613e+02 6.2035154e+02 6.6466237e+02 7.0897319e+02
betagrid -7.9349821e+01 -7.4390457e+01 -6.9431093e+01 -6.4471730e+01
<...>
6.4471730e+01 6.9431093e+01 7.4390457e+01 7.9349821e+01
sab 3.3877900e-37 1.3833500e-36 4.5036200e-36 1.4220200e-35
<...>
1.2642200e-19 1.5147000e-19 1.5901900e-19
Of course, the number of entries in the sab field must be equal to the product of the number of entries in the alphagrid and betagrid fields. To allow for more efficient processing, the alphagrid and betagrid fields can have at most 65534 entries, and must have at least 5. In addition to requiring large amounts of space, scattering kernels are complicated by the fact that they describe the relevant dynamics at a certain material temperature only. Thus, a temperature field exists in which this value must be specified. Furthermore, all @DYNINFO sections of type scatknl in a given file must contain the same value of the temperature field, and NCrystal will default the material temperature to that value as well when loading the input file (and might decide to raise an error on attempts to override it when loading the file). It is therefore recommended that NCMAT files with @DYNINFO sections of type scatknl should indicate the temperature in the file name, to avoid user confusion.
At initialisation time, NCrystal will typically integrate the scattering kernel for neutrons at a range of predefined energies, in order to be able to later provide cross-sections and sampling capabilities. By default NCrystal will analyse the scattering kernel at initialisation time in order to select a suitable energy grid. This default behaviour can be modified through specification of the optional egrid field inside the @DYNINFO section. If desired, the exact energy grid can be directly specified by providing at least 10 positive sorted energy values (unit eV):
egrid 1e-5 2e-5 4e-5
<...>
4.0 4.5 5.0
Alternatively, one can specify just the endpoints and number of points of the energy grid by providing just 3 values, corresponding respectively to Elow, Eupper and N of an energy grid running from Elow to Eupper with a total of N grid points spaced evenly in logarithmic space. An example of this would be (first two values are in eV, the third must be integral):
egrid 1e-5 5.0 1000
Replacing any of the three values with 0 indicates that NCrystal should determine it automatically. For instance, the following entries would keep the automatically determined range of the energy grid, but increase the number of grid points:
egrid 0 0 1000
As a final alternative, a single value provided to egrid will be interpreted as Eupper, implying automatic determination of Elow and number of points. Thus, Eupper=20eV can be requested with:
egrid 20.0
Finally, it is possible to specify S'(alpha,beta)=S(alpha,beta)*exp(-beta/2)
values instead of S(alpha,beta) values, by using the sab_scaled keyword
instead of sab. When using sab_scaled it is optionally possible to specify
just the table at non-negative values of beta, and assume
S'(alpha,-beta)=S'(alpha,beta). In this case, the betagrid values must start
at zero and contain only non-negative entries. Irrespective of the input format,
at initialisation time, NCrystal will transform the scattering kernel into a
standard S(alpha,beta) table, for consistent internal treatment.
For convenience and readability, it is allowed to specify parameters of any of
the 1D or 2D "array data" fields on multiple lines. This includes all the
various XXXgrid fields as well as sab and sab_scaled. It is also allowed
to save space by specifying two or more consecutive identical values using the
syntax <value>r<count> (i.e. 0r2000 means the value 0 repeated 2000 times).
Although not supported in the NCMAT v2 format, it might be interesting to note
already that future versions of the NCMAT format are planned to support the
optional specification of scattering kernels as S(Q,omega) tables. This is
planned to simply use qgrid, omegagrid and sqw in place of alphagrid,
betagrid and sab.
As a more convenient alternative to providing a scattering kernel directly, modelling of solid materials might instead be based on a phonon spectrum, or more specifically a vibrational density of state (vdos) spectrum. This is done by specifying the density of phonon states as a function of energy (which is hbar times the phonon frequency). The density values themselves must be provided in the vdos_density field, while the corresponding energy grid will be given as values in the vdos_egrid field (unit eV). As a convenient and efficient shorthand, when only two points are provided in the vdos_egrid field, these will be assumed to be the first and last points of the actual energy grid with the remaining points spaced evenly between those (the total number of points will then be inferred by the number of points in the vdos_density field - which must always be at least 5).
The overall normalisation or unit of the values in the vdos_densiy field does not matter, as NCrystal will renormalise them automatically. The actual density function will be formed by linear interpolation within the grid. For energies below the first grid point, the density values will be assumed to scale as the square of the energy - an approximation which should be suitable for solid materials. For energies above the last grid point, densities will be assumed to be 0. To ensure convergence of subsequent calculations in NCrystal, the first point in the vdos_egrid is required to be at least 1e-5 (i.e. 0.01meV).
An example vdos specification might look like:
@DYNINFO
element V
fraction 1
type vdos
vdos_egrid 0.013300161256 0.38127128934268
vdos_density 0.2594369576 0.3556097936 0.4375132376 0.4857022268 0.4915645468
0.444171744 0.340902404 0.2143757752 0.1140493096 0.0607265688
<...>
0.0593700356 0.0693096064 0.0812168444 0.0885391804 0.082003864
0.0920026688 0.0224714976 0.0040273484
For readability, it is allowed to use multiple lines to specify the parameters of the vdos_egrid and vdos_density fields. At initialisation time, NCrystal will use model-dependent assumptions (to be described elsewhere) to expand the provided density of states into a complete S(alpha,beta) scattering kernel, with subsequent treatment identical to that of any scattering kernel. For that reason, an optional egrid field can be specified as well, with the same meaning as when specifying scattering kernels directly.
As a final note, it should be mentioned that NCrystal calculations internally require the VDOS to be specified on an energy grid with equidistantly spaced points and which if extended downwards would eventually coincide exactly with 0. If the VDOS specified in the input does not exactly conform to this requirement, it will be re-parameterised upon loading (using a procedure which is unlikely to introduce significant numerical errors).
For crystalline materials with a @DEBYETEMPERATURE section, it is allowed to substitute a realistic VDOS spectrum with an idealised one, in which the density of states increases quadratically up to a cutoff energy, after which it becomes 0. In this model due to Debye, phonon states are considered uniformly distributed in momentum space, up to the cutoff - which is the Debye energy, or Boltzmann's constant times the Debye temperature. This is represented with a @DYNINFO type of vdosdebye, e.g.:
@DYNINFO
element V
fraction 1
type vdosdebye
In order to support non-crystalline materials for which a vibrational density of state or scattering kernel is present (like water), it is now optionally allowed to not specify a unit cell at all via @CELL, @ATOMPOSITIONS and @SPACEGROUP sections, and instead configure non-crystalline materials exclusively via the new @DYNINFO sections. However, such materials lack the material densities otherwise calculated from the unit cell information, which is necessary to translate per-atomic cross-sections to macroscopic interaction lengths. Thus, materials without a unit cell, must instead provide their density in the new @DENSITY section:
@DENSITY
0.4 atoms_per_aa3
Other valid units are kg_per_m3 or g_per_cm3 (units must be specified just as
written here, no spaces allowed).
As mentioned, it is since NCMAT v2 possible to omit all of the @SPACEGROUP, @CELL and @ATOMPOSITIONS sections, in order to describe non-crystalline materials. If at least one of the @CELL and @ATOMPOSITIONS is present, they must both be present. The @DEBYETEMPERATURE section should never be specified if there are no @CELL/@ATOMPOSITION sections, and is for now actually also required when there are @CELL/@ATOMPOSITIONS in the file (in later versions this might become optional for elements for which a @DYNINFO section of vdos type is present).
Positions like 0.666667 can now be more precisely described via fractions like "2/3" (no spaces are allowed on either side of the division symbol).
Comments can now appear anywhere in the file, even at the end of other lines
(except the first). Any parts of the line after the # should simply be ignored
by the parser.
Modelling of inelastic scattering with .ncmat files will depend on the
NCrystal material configuration parameter, inelas. By default, modelling will
be based on the content of the @DYNINFO sections (including implicitly defined
@DYNINFO sections when all are omitted for a crystalline
material). Additionally, it is possible to override the @DYNINFO sections
specified in the files, by setting inelas=freegas, inelas=none or
inelas=vdosdebye. In this case, the indicated type will be applied to all
elements. Of course, inelas=vdosdebye can only be used for crystalline
materials with Debye temperatures. Setting inelas=freegas;elas=0 can be used
to enable a pure freegas model for any input file.
The NCMAT v3 format is similar to the NCMAT v2 format, but introduces two new features. The first new feature is the introduction of more flexibility in how atoms can be defined, which both concerns how atoms can be specified in existing sections and also adds a new optional @ATOMDB section. Although not pertaining to the NCMAT format as such, it should nonetheless be noted here that starting with NCrystal v2.1.0 it is also possible to modify atomic definitions for any ncmat file (even those in NCMAT v1 or NCMAT v2 formats), through the usage of the atomdb configuration parameter, using a syntax similar to the one used in @ATOMDB sections (which will be described below). For details about the atomdb configuration parameter see elsewhere (e.g. the NCMatCfg.hh header file).
The other new feature in NCMAT v3 is that it is now possible to add custom sections to NCMAT files. The content of these custom sections will be loaded into the internal material Info objects, but the core NCrystal code will otherwise ignore them. This is primarily intended as a way to facilitate the development of new experimental physics models which might need additional data. Of course, if a such an experimental model matures (and is deemed to be of interest to a wider community), and makes it way into the core NCrystal code, the NCMAT format should evolve further in order to include proper well defined sections for the new data.
In addition to specifying atoms via their element names (H, He, Li, ...) in @DYNINFO, @DEBYETEMPERATURE, and @ATOMPOSITIONS sections, it is now also possible to specify atoms as specific isotopes by prefixing the nucleon number to the element name (H1, H2, He3, Li6, Gd157, ...). Two special aliases are provided: The name D is shorthand for H2 and T is shorthand for H3. This is not only handy, it also provides backwards compatibility with NCMAT content originally written for the NCMAT v2 format, in which D was made available to describe deuterium.
For more complicated atomic setups, one must use an @ATOMDB section (or atomdb
configuration parameter as noted above), which might redefine the meaning of
element names throughout the files (e.g. define particular isotopic abundances
in "B", or define "Al" as actually being a mixture of 99% Al and 1% Cr), or
provide/override physics constants associated with a given isotope or
element. It can also define any of the generic markers: X, X1, X2, ..., X99. If
such are defined, they may be used in place of element names throughout the
existing sections.
The simplest usage of the @ATOMDB section is to provide physics constants
associated with certain natural elements or isotopes. The four constants which
must be provided after the atom symbol are respectively: mass, coherent
scattering length, incoherent cross section, and absorption cross
section. Masses and cross sections must be non-negative. For readability, units
must be indicated by postfixes: Daltons (postfix u), femtometres (postfix
fm), and barns (postfix b). There should be no space between the number and
the unit. An example of this would be:
@ATOMDB
Si 28.09u 0.41491fm 0.004b 0.171b
Si29 28.97649466525u 0.47fm 0.001b 0.101b
Rn222 222.018u -1.23fm 4.56b 7.89b
The first line provides data for silicon in natural abundance, the second line
provides data for the silicon isotope with 29 nucleons, and the last line
provides (nonsense) data for the radon isotope with 222 nucleons. More
accurately, the first two lines override the values for Si and Si29 which
would otherwise be taken from the internal database shipped with NCrystal. On
the contrary, Rn222 is an example of an isotope which is not available in the
internal database (at least not in NCrystal release v2.1.0), so NCMAT files
referring to that isotope must provide values for it in the @ATOMDB
section. It is possible (perhaps for validation purposes) to disable the inbuilt
database, which is done by placing the keyword nodefaults on the first line of
the @ATOMDB section:
@ATOMDB
nodefaults
Si29 28.97649466525u 0.47fm 0.001b 0.101b
In this example, only Si29 will be available for usage in the file. Concerning
isotope labels (as was already mentioned) the labels, D and T are simply taken
to be aliases for the isotope labels H2 and H3 respectively, wherever they are
encountered.
In addition to specifying physics constants associated with elements and isotopes, the @ATOMDB section also allows the definition of mixtures of elements and isotopes. This allows both flexible isotopic compositions, but can also be used to model impurities where for instance a contaminant replace a primary element on certain positions in a crystal lattice. Here is an example which specifies a particular enrichment of boron (95% B10):
@ATOMDB
B is 0.95 B10 0.05 B11
Obviously, the specified fractions must add up to 1. Next is an example which introduces trace amounts of chromium into the positions otherwise occupied by aluminium atoms (assuming the other sections of the NCMAT file defines a crystal involving aluminium atoms):
@ATOMDB
Al is 0.99 Al 0.01 Cr
Lines in the @ATOMDB section are evaluated in order, and in essence can be thought of as defining or redefining the variable which is named at the beginning of the line. This can be used to build up more complicated scenarios. If for instance one would like to model boron carbide (B4C) in which the boron is enriched to 90% boron-10, and where 1 permille of boron atoms are replaced by carbon atoms, one can write (assuming the other sections of the NCMAT file defines a B4C lattice in the obvious manner, putting a B or a C atom at each lattice position):
@ATOMDB
B is 0.9 B10 0.1 B11
B is 0.999 B 0.001 C
As the lines are evaluated in order, a mathematically equivalent but less handy version would be:
@ATOMDB
B is 0.8991 B10 0.0999 B11 0.001 C
To avoid confusion, it is not allowed to use isotope labels to define mixtures:
@ATOMDB
B10 is 0.999 B10 0.001 B11 # This is invalid syntax!
On the other hand, a number of "generic labels" are available, in case one would like to avoid using a standard chemical symbol to denote a mixture. Exactly 100 of such generic markers are available and they are: X, X1, X2, X3, ..., X98, and X99. Apart from Xe (xenon), no standard element starts with X, which should make it easy to identify such custom mixtures in a given NCMAT file. It makes no difference which of the markers X, X1, ..., X99 are used, and the data loaded from a given NCMAT file will contain no indication of the name used in the input.
With generic labels, one can thus define:
@ATOMDB
X is 0.666666666666666666667 H 0.333333333333333333333 O
and then use X in place of an atom name in the other sections of the NCMAT file. Again, to avoid confusion, generic labels (X, X1, ..., X99) can only be used to denote mixtures, and it is not allowed to assign physical properties directly to such a label:
@ATOMDB
X is 12.5u 0.5fm 3b 0.6b # This is invalid syntax!
A mixture consisting of only a single component can be better thought of as an alias:
@ATOMDB
X5 is 1.0 Al
And in fact, for readability, it is allowed to leave out the redundant 1.0 from such a single-component definition, making it more clear that it is essentially just an alias definition:
@ATOMDB
X5 is Al
Finally, it should be noted that some lines in the @ATOMDB section might have no effect. For instance:
#(assume that the rest of the file refers to Al and O only)
@ATOMDB
B is 0.9 B10 0.1 B11 #<---- has no effect, B is not used in file
Al is 0.99 Al 0.01 Cr #<---- has no effect, next line redefines Al.
Al 26.98u 0.3449fm 0.0082b 0.231b
It is syntactically OK to include lines which have no effect, but it is possible that a future version of NCrystal could emit warnings when encountering such lines.
Any number of custom sections can be added. They must have a name of the form
@CUSTOM_ where <name> must consist of 1 or more upper case characters,
A-Z. Multiple custom sections with the same name are allowed. The contents will
be parsed like in all other sections, meaning that comments, superfluous
white-space and empty lines will all be stripped away. The remaining lines and
their contents will be available after loading as lists of lists of strings.
Example of how a custom section might look:
@CUSTOM_MYNEWPHYSICSDATA
#This section is needed for my great new physics model
6.789 Xe 0.95 0x0003450 true
Note that NCrystal might produce warning messages when loading NCMAT files with custom sections, serving as a reminder that such files are likely only intended for a particular development setup and might not be sensible to share with a wider community.
If using EMACS, add the following to your ~/.emacs configuration file to enable a basic syntax highlighting of .ncmat files:
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; Major mode for .ncmat files:
(setq ncmat-sections '("CELL" "ATOMPOSITIONS" "SPACEGROUP" "DEBYETEMPERATURE"
"DYNINFO" "DENSITY" "ATOMDB" "CUSTOM_[A-Z]+"))
(setq ncmat-fields '("lengths" "angles" "element" "fraction" "type" "temperature"
"sab_scaled" "sab" "alphagrid" "betagrid" "egrid" "vdos_egrid" "vdos_density"))
(setq ncmat-highlights
`(("^NCMAT\s*v[0-9]+[a-z0-9]*" . font-lock-function-name-face)
(,(concat "^@\\(" (mapconcat 'identity ncmat-sections "\\|") "\\)") . font-lock-keyword-face)
(,(concat "^\s*\\(" (mapconcat 'identity ncmat-fields "\\|") "\\)") . font-lock-constant-face)
))
(setq ncmat-mode-syntax-table
(let ( (synTable (make-syntax-table)))
(modify-syntax-entry ?# "<" synTable)
(modify-syntax-entry ?\n ">" synTable)
synTable)
)
(define-derived-mode ncmat-mode fundamental-mode "NCMAT"
"major mode for editing .ncmat files."
(setq font-lock-defaults '(ncmat-highlights));keywords
(set-syntax-table ncmat-mode-syntax-table);comments
)
(add-to-list 'auto-mode-alist '("\\.ncmat$" . ncmat-mode))
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