httk package¶
The high-throughput toolkit (httk)
- A set of tools and utilities meant to help with:
- Project management, preparation of large-scale computational project.
- Execution of large-scale computational projects
- interface with supercomputer cluster queuing systems, etc.
- aid with scripting multi-stage runs
- retrieval of data from supercomputers
- Storage of data in databases
- Search, retrieval and ‘processing’ of data in storage
- Analysis (especially as a helpful interface against 3:rd party software)
-
httk.
load
(ioa, ext=None)[source]¶ A very generic file reader method.
Load a file into a suitable httk object. Try to do the most sane thing possible given the input file. If you know what to expect from the input file, it may be safer to use a targeted method for that file type.
-
httk.
save
(obj, ioa, ext=None)[source]¶ A very generic file writer method.
Load a file into a suitable httk object. Try to do the most sane thing possible given the input file. If you know what to expect from the input file, it may be safer to use a targeted method for that file type.
-
class
httk.
Code
(name, version)[source]¶ Bases:
httk.core.httkobject.HttkObject
Object for keeping track of httk data about a computer software or script
-
class
httk.
Computation
(computation_date, description, code, manifest_hash, signatures, keys, relpath, project_counter, added_date=None)[source]¶ Bases:
httk.core.httkobject.HttkObject
Object for keeping track of httk data about a specific computation run
-
added_date
¶
-
classmethod
create
(computation_date, description, code, manifest_hash, signatures, keys, project_counter, relpath, added_date=None)[source]¶ Create a Computation object.
-
-
class
httk.
Result
(computation)[source]¶ Bases:
httk.core.httkobject.HttkObject
Intended as a base class for results tables for computations
-
class
httk.
ComputationRelated
(main_computation, other_computation, relation)[source]¶ Bases:
httk.core.httkobject.HttkObject
Object for keeping track of httk data about a specific computation run
-
class
httk.
Author
(last_name, given_names)[source]¶ Bases:
httk.core.httkobject.HttkObject
Object for keeping track of tags for other objects
-
class
httk.
Reference
(ref, authors=None, editors=None, journal=None, journal_issue=None, journal_volume=None, page_first=None, page_last=None, title=None, year=None, book_publisher=None, book_publisher_city=None, book_title=None)[source]¶ Bases:
httk.core.httkobject.HttkObject
A reference citation
-
class
httk.
Project
(name, description, project_key, keys)[source]¶ Bases:
httk.core.httkobject.HttkObject
-
class
httk.
FracVector
(noms, denom=1)[source]¶ Bases:
httk.core.vectors.vector.Vector
FracVector is a general immutable N-dimensional vector (tensor) class for performing linear algebra with fractional numbers.
A FracVector consists of a multidimensional tuple of integer nominators, and a single shared integer denominator.
Since FracVectors are immutable, every operation on a FracVector returns a new FracVector with the result of the operation. A created FracVector never changes. Hence, they are safe to use as keys in dictionaries, to use in sets, etc.
Note: most methods returns FracVector results that are not simplified (i.e., the FracVector returned does not have the smallest possible integer denominator). To return a FracVector with the smallest possible denominator, just call FracVector.simplify() at the last step.
-
acos
(prec=None, degrees=False, limit=False)[source]¶ Return a FracVector where every element is the arccos of the element in the source FracVector.
prec = precision (should be set as a fraction) limit = True requires the denominator to be smaller or equal to precision
-
asin
(prec=None, degrees=False, limit=False)[source]¶ Return a FracVector where every element is the arcsin of the element in the source FracVector.
prec = precision (should be set as a fraction) limit = True requires the denominator to be smaller or equal to precision
-
ceil
()[source]¶ Returns the integer that is equal to or just below the value stored in a scalar FracVector.
-
classmethod
chain_vecs
(vecs)[source]¶ Optimized chaining of FracVectors.
vecs: a list (or tuple) of fracvectors.
- Returns the same thing as
- FracVector.create(vecs,chain=True)
- i.e., removes outermost dimension and chain the sub-sequences. If input=[[1 2 3],[4,5,6]], then
- FracVector.chain(input) -> [1,2,3,4,5,6]
but this method assumes all vectors share the same denominator (it raises an exception if this is not true)
-
cos
(prec=None, degrees=False, limit=False)[source]¶ Return a FracVector where every element is the cosine of the element in the source FracVector.
prec = precision (should be set as a fraction) limit = True requires the denominator to be smaller or equal to precision
-
classmethod
create
(noms, denom=None, simplify=True, chain=False, min_accuracy=Fraction(1, 10000))[source]¶ Create a FracVector from various types of sequences.
Simplest use:
FracVector.create(some_kind_of_sequence)
where ‘some_kind_of_sequence’ can be any nested list or tuple of objects that can be used in the constructor of the Python Fraction class (also works with strings!). If any object found while traveling the items has a .to_fractions() method, it will be called and is expected to return a fraction or list or tuple of fractions.
Optional parameters:
- Invocation with denominator: FracVector.create(nominators,denominator) nominators is any sequence, and denominator a common denominator to divide all nominators with
- simplify: boolean, return a FracVector with the smallest possible denominator.
- chain: boolean, remove outermost dimension and chain the sub-sequences. I.e., if input=[[1 2 3],[4,5,6]], then FracVector.create(input) -> [1,2,3,4,5,6]
Relevant: FracVector itself implements .to_fractions(), and hence, the same constructor allows stacking several FracVector objects like this:
vertical_fracvector = FracVector.create([[fracvector1],[fracvector2]]) horizontal_fracvector = FracVector.create([fracvector1,fracvector2],chain=True)
- min_accuracy: set to a boolean to adjust the minimum accuracy assumed in string input. The default is 1/10000, i.e. 0.33 = 0.3300 = 33/100, whereas 0.3333 = 1/3. Set it to None to assume infinite accuracy, i.e., convert exactly whatever string is given (unless a standard deviation is given as a parenthesis after the string.)
-
classmethod
create_cos
(data, degrees=False, limit=False, find_best_rational=True, prec=Fraction(1, 1000000))[source]¶ Creating a FracVector as the cosine of the argument data. If data are composed by strings, the standard deviation of the numbers are taken into account, and the best possible fractional approximation to the cosines of the data are returned within the standard deviation.
This is not the same as FracVector.create(data).cos(), which creates the best possible fractional approximations of data and then takes cos on that.
-
classmethod
create_exp
(data, prec=Fraction(1, 1000000), limit=False)[source]¶ Creating a FracVector as the exponent of the argument data. If data are composed by strings, the standard deviation of the numbers are taken into account, and the best possible fractional approximation to the cosines of the data are returned within the standard deviation.
This is not the same as FracVector.create(data).exp(), which creates the best possible fractional approximations of data and then takes exp on that.
-
classmethod
create_sin
(data, degrees=False, limit=False, prec=Fraction(1, 1000000))[source]¶ Creating a FracVector as the sine of the argument data. If data are composed by strings, the standard deviation of the numbers are taken into account, and the best possible fractional approximation to the cosines of the data are returned within the standard deviation.
This is not the same as FracVector.create(data).sin(), which creates the best possible fractional approximations of data and then takes cos on that.
-
cross
(other)[source]¶ Returns the vector cross product of the 3-element 1D vector with the 3-element 1D vector ‘other’, i.e., A x B.
-
dim
¶ This property returns a tuple with the dimensionality of each dimension of the FracVector (the noms are assumed to be a nested list of rectangular shape).
-
dot
(other)[source]¶ Returns the vector dot product of the 1D vector with the 1D vector ‘other’, i.e., A . B or A cdot B. The same as A * B.T().
-
exp
(prec=None, limit=False)[source]¶ Return a FracVector where every element is the exponent of the element in the source FracVector.
prec = precision (should be set as a fraction) limit = True requires the denominator to be smaller or equal to precision
-
floor
()[source]¶ Returns the integer that is equal to or just below the value stored in a scalar FracVector.
-
classmethod
from_floats
(l, resolution=4294967296)[source]¶ Create a FracVector from a (nested) list or tuple of floats. You can convert a numpy array with this method if you use A.tolist()
resolution: the resolution used for interpreting the given floating point numbers. Default is 2^32.
-
classmethod
from_tuple
(t)[source]¶ Return a FracVector created from the tuple representation: (denom, …noms…), returned by the to_tuple() method.
-
limit_denominator
(max_denom=1000000000)[source]¶ Returns a FracVector of reduced resolution.
resolution: each element in the returned FracVector is the closest numerical approximation that can is allowed by a fraction with maximally this denominator. Note: since all elements must be put on a common denominator, the result may have a larger denominator than max_denom
-
max
()[source]¶ Return the maximum element across all dimensions in the FracVector. max(fracvector) works for a 1D vector.
-
metric_product
(vecA, vecB)[source]¶ - Returns the result of the metric product using the present square FracVector as the metric matrix. The same as
- vecA*self*vecB.T().
-
min
()[source]¶ Return the minimum element across all dimensions in the FracVector. max(fracvector) works for a 1D vector.
-
mul
(other)[source]¶ Returns the result of multiplying the vector with ‘other’ using matrix multiplication.
Note that for two 1D FracVectors, A.dot(B) is not the same as A.mul(B), but rather: A.mul(B.T()).
-
nargmax
()[source]¶ Return a list of indices of all maximum elements across all dimensions in the FracVector.
-
nargmin
()[source]¶ Return a list of indices for all minimum elements across all dimensions in the FracVector.
-
static
nested_map
(op, *ls)¶ Map an operator over a nested tuple. (i.e., the same as the built-in map(), but works recursively on a nested tuple)
-
static
nested_map_fractions
(op, *ls)¶ Map an operator over a nested tuple, but checks every element for a method to_fractions() and uses this to further convert objects into tuples of Fraction.
-
nom
¶ Returns the integer nominator of a scalar FracVector.
-
normalize_half
()[source]¶ Add/remove an integer +/-N to each element to place it in the range [-1/2,1/2)
- This is useful to find the shortest vector C between two points A, B in a space with periodic boundary conditions [0,1):
- C = (A-B).normalize_half()
-
classmethod
pi
(prec=Fraction(1, 1000000), limit=False)[source]¶ Create a scalar FracVector with a rational approximation of pi to precision prec.
-
classmethod
random
(dims, minnom=-100, maxnom=100, denom=100)[source]¶ Create a zero matrix with the given dimensions
-
classmethod
set_common_denom
(A, B)[source]¶ Used internally to combine two different FracVectors.
Returns a tuple (A2,B2,denom) where A2 is numerically equal to A, and B2 is numerically equal to B, but A2 and B2 are both set on the same shared denominator ‘denom’ which is the product of the denominator of A and B.
-
set_denominator
(set_denom=1000000000)[source]¶ Returns a FracVector of reduced resolution where every element is the closest numerical approximation using this denominator.
-
simplify
()[source]¶ Returns a reduced FracVector. I.e., each element has the same numerical value but the new FracVector represents them using the smallest possible shared denominator.
-
sin
(prec=None, degrees=False, limit=False)[source]¶ Return a FracVector where every element is the sine of the element in the source FracVector.
prec = precision (should be set as a fraction) limit = True requires the denominator to be smaller or equal to precision
-
sqrt
(prec=None, limit=False)[source]¶ Return a FracVector where every element is the sqrt of the element in the source FracVector.
prec = precision (should be set as a fraction) limit = True requires the denominator to be smaller or equal to precision
-
-
class
httk.
FracScalar
(nom, denom)[source]¶ Bases:
httk.core.vectors.fracvector.FracVector
Represents the fractional number nom/denom. This is a subclass of FracVector with the purpose of making it clear when a scalar fracvector is needed/used.
-
class
httk.
MutableFracVector
(noms, denom)[source]¶ Bases:
httk.core.vectors.fracvector.FracVector
,httk.core.vectors.vector.MutableVector
Same as FracVector, only, this version allow assignment of elements, e.g.,
mfracvec[2,7] = 5
and, e.g.,
mfracvec[:,7] = [1,2,3,4]
Other than this, the FracVector methods exist and do the same, i.e., they return copies of the fracvector, rather than modifying it.
However, methods have also been added named with set_* prefixes which performs mutating operations, e.g.,
A.set_T()
replaces A with its own transpose, whereas
A.T()
just returns a new MutableFracVector that is the transpose of A, leaving A unmodified.
-
invalidate
()[source]¶ Internal method to call when MutableFracVector is changed in such a way that cached properties are invalidated (e.g., _dim)
-
static
nested_inmap
(op, *ls)¶ Like inmap, but work for nested lists
-
static
nested_map
(op, *ls)¶ Map an operator over a nested list. (i.e., the same as the built-in map(), but works recursively on a nested list)
-
static
nested_map_fractions
(op, *ls)¶ Map an operator over a nested list, but checks every element for a method to_fractions() and uses this to further convert objects into lists of Fraction.
-
set_normalize_half
()[source]¶ Add/remove an integer +/-N to each element to place it in the range [-1/2,1/2)
- This is useful to find the shortest vector C between two points A, B in a space with periodic boundary conditions [0,1):
- C = (A-B).normalize_half()
-
set_set_denominator
(resolution=1000000000)[source]¶ Changes MutableFracVector; reduces resolution.
resolution is the new denominator, each element becomes the closest numerical approximation using this denominator.
-
-
class
httk.
IoAdapterFileReader
(f, name=None, deletefilename=None, close=False)[source]¶ Bases:
object
Io adapter for easy handling of io.
-
class
httk.
IoAdapterFileWriter
(f, name=None, close=False)[source]¶ Bases:
object
Io adapter for access to data as a python file object
-
class
httk.
IoAdapterFileAppender
(f, name=None)[source]¶ Bases:
object
Io adapter for access to data as a python file object
-
class
httk.
IoAdapterString
(string=None, name=None)[source]¶ Bases:
object
Universal io adapter, helps handling the passing of filenames, files, and strings to functions that deal with io
-
string
¶
-
-
class
httk.
IoAdapterStringList
(stringlist, name=None)[source]¶ Bases:
object
Universal io adapter, helps handling the passing of filenames, files, and strings to functions that deal with io
-
class
httk.
IoAdapterStringList
(stringlist, name=None)[source] Bases:
object
Universal io adapter, helps handling the passing of filenames, files, and strings to functions that deal with io
-
classmethod
use
(other)[source]
-
classmethod
Subpackages¶
- httk.analysis package
- httk.atomistic package
- Subpackages
- Submodules
- httk.atomistic.assignment module
- httk.atomistic.assignments module
- httk.atomistic.cell module
- httk.atomistic.cellshape module
- httk.atomistic.cellutils module
- httk.atomistic.cli module
- httk.atomistic.compound module
- httk.atomistic.formulautils module
- httk.atomistic.representativesites module
- httk.atomistic.representativestructure module
- httk.atomistic.siteassignment module
- httk.atomistic.sites module
- httk.atomistic.sitesutils module
- httk.atomistic.spacegroup module
- httk.atomistic.spacegrouputils module
- httk.atomistic.structure module
- httk.atomistic.structurephasediagram module
- httk.atomistic.structureutils module
- httk.atomistic.supercellutils module
- httk.atomistic.unitcellsites module
- httk.atomistic.unitcellstructure module
- httk.config package
- httk.core package
- Subpackages
- Submodules
- httk.core.basic module
- httk.core.citation module
- httk.core.code module
- httk.core.computation module
- httk.core.console module
- httk.core.crypto module
- httk.core.ed25519 module
- httk.core.geometry module
- httk.core.httkobject module
- httk.core.ioadapters module
- httk.core.miniparser module
- httk.core.project module
- httk.core.reference module
- httk.core.signature module
- httk.core.template module
- httk.db package
- httk.external package
- Submodules
- httk.external.aflow_ext module
- httk.external.ase_glue module
- httk.external.cif2cell_ext module
- httk.external.command module
- httk.external.gulp_ext module
- httk.external.isotropy_ext module
- httk.external.jmol module
- httk.external.numpy_ext module
- httk.external.platon_ext module
- httk.external.pymatgen_glue module
- httk.external.pyspglib_ext module
- httk.external.subimport module
- Submodules
- httk.graphics package
- httk.httkio package
- httk.httkweb package
- Submodules
- httk.httkweb.app_curses module
- httk.httkweb.app_qt5 module
- httk.httkweb.functionhandler_httk module
- httk.httkweb.helpers module
- httk.httkweb.publish module
- httk.httkweb.render_httk module
- httk.httkweb.render_rst module
- httk.httkweb.serve module
- httk.httkweb.templateengine_httk module
- httk.httkweb.templateengine_templator module
- httk.httkweb.webgenerator module
- Submodules
- httk.iface package
- httk.task package