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)

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)

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.

httk.cout(*args)

httk.cerr(*args)

class httk.Code(name, version)

Bases: httk.core.httkobject.HttkObject

Object for keeping track of httk data about a computer software or script

add_ref(ref)

add_refs(refs)

add_tag(tag, val)

add_tags(tags)

classmethod create(name, version, refs=None, tags=None)

Create a Computation object.

get_refs()

get_tag(tag)

get_tags()

class httk.Computation(computation_date, description, code, manifest_hash, signatures, keys, relpath, project_counter, added_date=None)

Bases: httk.core.httkobject.HttkObject

Object for keeping track of httk data about a specific computation run

add_project(project)

add_projects(projects)

add_ref(ref)

add_refs(refs)

add_tag(tag, val)

add_tags(tags)

added_date

classmethod create(computation_date, description, code, manifest_hash, signatures, keys, project_counter, relpath, added_date=None)

Create a Computation object.

get_projects()

get_refs()

get_tag(tag)

get_tags()

class httk.Result(computation)

Bases: httk.core.httkobject.HttkObject

Intended as a base class for results tables for computations

classmethod create(computation)

Create a Computation object.

class httk.ComputationRelated(main_computation, other_computation, relation)

Bases: httk.core.httkobject.HttkObject

Object for keeping track of httk data about a specific computation run

classmethod create(main_computation, other_computation, relation)

Create a Computation object.

class httk.ComputationProject(computation, project)

Bases: httk.core.httkobject.HttkObject

classmethod create(computation, project)

Create a Computation object.

class httk.Author(last_name, given_names)

Bases: httk.core.httkobject.HttkObject

Object for keeping track of tags for other objects

classmethod create(last_name, given_names)

Create a Author object.

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)

Bases: httk.core.httkobject.HttkObject

A reference citation

classmethod create(ref=None, 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)

Create a Reference object.

class httk.Project(name, description, project_key, keys)

Bases: httk.core.httkobject.HttkObject

add_ref(ref)

add_refs(refs)

add_tag(tag, val)

add_tags(tags)

classmethod create(name, description, project_key, keys)

Create a Project object.

get_refs()

get_tag(tag)

get_tags()

class httk.ProjectRef(project, reference)

Bases: httk.core.httkobject.HttkObject

class httk.ProjectTag(project, tag, value)

Bases: httk.core.httkobject.HttkObject

class httk.FracVector(noms, denom=1)

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.

T()

Returns the transpose, A^T.

acos(prec=None, degrees=False, limit=False)

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

argmax()

Return the index of the maximum element across all dimensions in the FracVector.

argmin()

Return the index of the minimum element across all dimensions in the FracVector.

asin(prec=None, degrees=False, limit=False)

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()

Returns the integer that is equal to or just below the value stored in a scalar FracVector.

classmethod chain_vecs(vecs)

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)

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))

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))

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)

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))

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)

Returns the vector cross product of the 3-element 1D vector with the 3-element 1D vector ‘other’, i.e., A x B.

det()

Returns the determinant of the FracVector as a scalar FracVector.

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)

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)

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

classmethod eye(dims)

Create a diagonal one-matrix with the given dimensions

flatten()

Returns a FracVector that has been flattened out to a single rowvector

floor()

Returns the integer that is equal to or just below the value stored in a scalar FracVector.

classmethod from_floats(l, resolution=4294967296)

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)

Return a FracVector created from the tuple representation: (denom, …noms…), returned by the to_tuple() method.

ged_prestacked(other)

ged_stackedinsert(pos, other)

get_append(other)

get_extend(other)

get_insert(pos, other)

get_prepend(other)

get_prextend(other)

get_stacked(other)

inv()

Returns the matrix inverse, A^-1

lengthsqr()

Returns the square of the length of the vector. The same as A * A.T()

limit_denominator(max_denom=1000000000)

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()

Return the maximum element across all dimensions in the FracVector. max(fracvector) works for a 1D vector.

metric_product(vecA, vecB)

Returns the result of the metric product using the present square FracVector as the metric matrix. The same as

vecA*self*vecB.T().

min()

Return the minimum element across all dimensions in the FracVector. max(fracvector) works for a 1D vector.

mul(other)

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()

Return a list of indices of all maximum elements across all dimensions in the FracVector.

nargmin()

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()

Add/remove an integer +/-N to each element to place it in the range [0,1)

normalize_half()

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)

Create a scalar FracVector with a rational approximation of pi to precision prec.

classmethod random(dims, minnom=-100, maxnom=100, denom=100)

Create a zero matrix with the given dimensions

reciprocal()

classmethod set_common_denom(A, B)

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)

Returns a FracVector of reduced resolution where every element is the closest numerical approximation using this denominator.

sign()

Returns the sign of the scalar FracVector: -1, 0 or 1.

simplify()

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)

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)

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

classmethod stack_vecs(vecs)

Optimized stacking of FracVectors.

vecs = a list (or tuple) of fracvectors.

Returns the same thing as:

FracVector.create(vecs)

but only works if all vectors share the same denominator (raises an exception if this is not true)

to_float()

Converts a scalar ExactVector to a single float.

to_floats()

Converts the ExactVector to a list of floats.

to_fraction()

Converts scalar FracVector to a fraction.

to_fractions()

Converts the FracVector to a list of fractions.

to_int()

Converts scalar FracVector to an integer (truncating as necessary).

to_ints()

Converts the FracVector to a list of integers, rounded off as best possible.

to_string(accuracy=8)

Converts the ExactVector to a list of strings.

to_strings(accuracy=8)

Converts the ExactVector to a list of strings.

to_tuple()

Return a FracVector on tuple representation: (denom, …noms…).

classmethod use(old)

Make sure variable is a FracVector, and if not, convert it.

validate()

classmethod zeros(dims)

Create a zero matrix with the given dimensions

class httk.FracScalar(nom, denom)

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.

classmethod create(nom, denom=None, simplify=True)

Create a FracScalar.

FracScalar(something)

something may be any object that can be used in the constructor of the Python Fraction class (also works with strings!).

class httk.MutableFracVector(noms, denom)

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.

classmethod from_FracVector(other)

Create a MutableFracVector from a FracVector.

invalidate()

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_T()

Changes MutableFracVector inline into own transpose: self -> self.T

set_inv()

Changes MutableFracVector inline into own inverse: self -> self^-1

set_negative()

Changes MutableFracVector inline into own negative: self -> -self

set_normalize()

Add/remove an integer +/-N to each element to place it in the range [0,1)

set_normalize_half()

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)

Changes MutableFracVector; reduces resolution.

resolution is the new denominator, each element becomes the closest numerical approximation using this denominator.

set_simplify()

Changes MutableFracVector; reduces any common factor between denominator and all nominators

to_FracVector()

Return a FracVector with the values of this MutableFracVector.

classmethod use(old)

Make sure variable is a MutableFracVector, and if not, convert it.

validate()

class httk.IoAdapterFileReader(f, name=None, deletefilename=None, close=False)

Bases: object

Io adapter for easy handling of io.

close()

classmethod use(other)

class httk.IoAdapterFileWriter(f, name=None, close=False)

Bases: object

Io adapter for access to data as a python file object

close()

classmethod use(other)

class httk.IoAdapterFileAppender(f, name=None)

Bases: object

Io adapter for access to data as a python file object

close()

classmethod use(other)

class httk.IoAdapterString(string=None, name=None)

Bases: object

Universal io adapter, helps handling the passing of filenames, files, and strings to functions that deal with io

close()

string

classmethod use(other)

class httk.IoAdapterStringList(stringlist, name=None)

Bases: object

Universal io adapter, helps handling the passing of filenames, files, and strings to functions that deal with io

classmethod use(other)

class httk.IoAdapterStringList(stringlist, name=None)

Bases: object

Universal io adapter, helps handling the passing of filenames, files, and strings to functions that deal with io

classmethod use(other)

class httk.HttkObject

Bases: object

get_codependent_data()

hexhash

classmethod new_from(other)

to(newtype)

to_tuple(use_hexhash=False)

classmethod types()

classmethod use(old)

httk.httk_typed_property(t)

httk.httk_typed_init(t, **kargs)

httk.httk_typed_property_delayed(t)

httk.httk_typed_init_delayed(t, **kargs)

class httk.HttkPluginWrapper(plugin=None)

Bases: object

class httk.HttkPlugin

Bases: object

class httk.HttkPluginPlaceholder(plugininfo=None)

Bases: object

class httk.Signature(signature_data, key)

Bases: httk.core.httkobject.HttkObject

classmethod create(signature_data, key)

Create a Computation object.

class httk.SignatureKey(keydata, description)

Bases: httk.core.httkobject.HttkObject

classmethod create(keydata, description)

Create a Computation object.

Subpackages

• httk.analysis package
  • Subpackages
    • httk.analysis.matsci package
      • Subpackages
        • httk.analysis.matsci.vis package
          • Submodules
            • httk.analysis.matsci.vis.matplotlibphasediagramvisualizer module
            • httk.analysis.matsci.vis.phasediagramvisualizerplugin module
      • Submodules
        • httk.analysis.matsci.phasediagram module
• httk.atomistic package
  • Subpackages
    • httk.atomistic.atomisticio package
      • Submodules
        • httk.atomistic.atomisticio.structure_cif_io module
        • httk.atomistic.atomisticio.structure_io module
        • httk.atomistic.atomisticio.structureioplugin module
    • httk.atomistic.data package
      • Submodules
        • httk.atomistic.data.periodictable module
        • httk.atomistic.data.spacegroups module
    • httk.atomistic.results package
      • Submodules
        • httk.atomistic.results.relaxedcellresult module
        • httk.atomistic.results.totalenergyresult module
    • httk.atomistic.vis package
      • Submodules
        • httk.atomistic.vis.asestructurevisualizer module
        • httk.atomistic.vis.jmolstructurevisualizer module
        • httk.atomistic.vis.structurephasediagramvisualizerplugin module
        • httk.atomistic.vis.structurevisualizerplugin module
  • 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
  • Submodules
    • httk.config.config module
• httk.core package
  • Subpackages
    • httk.core.vectors package
      • Submodules
        • httk.core.vectors.fracmath module
        • httk.core.vectors.fracvector module
        • httk.core.vectors.mutablefracvector module
        • httk.core.vectors.vector module
        • httk.core.vectors.vectormath module
  • 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
      • LR(1) miniparser
        • Introduction
        • Detailed description
        • Diagnostic output
    • httk.core.project module
    • httk.core.reference module
    • httk.core.signature module
    • httk.core.template module
• httk.db package
  • Subpackages
    • httk.db.backend package
      • Submodules
        • httk.db.backend.sqlite module
    • httk.db.store package
      • Submodules
        • httk.db.store.dictstore module
        • httk.db.store.sqlstore module
        • httk.db.store.trivialstore module
  • Submodules
    • httk.db.filteredcollection module
    • httk.db.httkobjdbplugin module
    • httk.db.storable module
• 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
• httk.graphics package
  • Subpackages
    • httk.graphics.matplotlib package
      • Submodules
        • httk.graphics.matplotlib.arrowplot module
        • httk.graphics.matplotlib.polygonplot module
• httk.httkio package
  • Submodules
    • httk.httkio.cif module
    • httk.httkio.load module
    • httk.httkio.save module
• 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
• httk.iface package
  • Submodules
    • httk.iface.ase_if module
    • httk.iface.cif2cell_if module
    • httk.iface.gulp_if module
    • httk.iface.isotropy_if module
    • httk.iface.jmol_if module
    • httk.iface.openbabel_if_notstable module
    • httk.iface.platon_if module
    • httk.iface.spglib_if module
    • httk.iface.vasp_if module
• httk.task package
  • Submodules
    • httk.task.reader module
    • httk.task.taskmgr module

Submodules

• httk.cli module
• httk.versioning module