mirror of https://github.com/abinit/abinit.git
Only 3 broken links reported by linkchecker due to old release notes in site
This commit is contained in:
Matteo Giantomassi
parent
78d126ad2f
commit
e221d890fd
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@ -344,17 +344,9 @@ class Website(object):
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self.abinit_stats = AbinitStats(os.path.join(self.root, "maintainers", "statistics.txt"))
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self.abinit_stats.json_dump(os.path.join(self.root, "developers", "statistics.json"))
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# Build AbinitTestSuite object.
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# Build flat list of tests.
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from doc import tests as tmod
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tests = []
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for t in tmod.abitests.select_tests(suite_args=[], regenerate=True):
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# DO NOT use isinstance to check if ChainOfTests but rely on duck typing.
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# See https://stackoverflow.com/questions/9006740/isinstance-and-type-equivelence-failure-due-to-import-mechanism-python-djan
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#if isinstance(t, ChainOfTests):
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if hasattr(t, "tests"):
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tests.extend(t.tests)
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else:
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tests.append(t)
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tests = tmod.abitests.select_tests(suite_args=[], regenerate=True, flat_list=True)
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# Construct dictionary rpath --> test. Use OrderedDict to have deterministic behaviour.
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self.rpath2test = {}
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@ -6,8 +6,10 @@ from .tools import patch_syspath, AbimkdocsTest
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patch_syspath()
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import os
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from abimkdocs.variables import get_variables_code, ValueWithUnit, ValueWithConditions, MultipleValue, Range
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import json
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from collections import OrderedDict
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from abimkdocs.variables import get_variables_code, ValueWithUnit, ValueWithConditions, MultipleValue, Range
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class VariablesTest(AbimkdocsTest):
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@ -91,25 +93,26 @@ class VariablesTest(AbimkdocsTest):
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raise ValueError("\n".join(errors))
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def test_variables_in_tests(self):
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"""
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Find variables that are not tested by comparing the database of variables
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with the input file of the test.
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Build dictionary with list of untested variables for the different codes.
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Finally compare the new dictionary with the reference one and fail if they don't match.
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"""
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# Build database with all input variables indexed by code name.
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from abimkdocs.variables import get_variables_code
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variables_code = get_variables_code()
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# Build AbinitTestSuite object.
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from doc import tests as tmod
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tests = tmod.abitests.select_tests(suite_args=[], regenerate=True, flat_list=True)
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# Build conter for the different codes, keys are the varnames from the database.
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from collections import Counter
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count_code = {}
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for code, d in variables_code.items():
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count_code[code] = Counter({k: 0 for k in d})
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# Build AbinitTestSuite object.
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from doc import tests as tmod
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tests = []
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for t in tmod.abitests.select_tests(suite_args=[], regenerate=True):
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# DO NOT use isinstance to check if ChainOfTests but rely on duck typing.
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if hasattr(t, "tests"):
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tests.extend(t.tests)
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else:
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tests.append(t)
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black_list = set([
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"atompaw", "cut3d", "multibinit", "fftprof", "conducti", "mrgscr",
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"mrgddb", "mrggkk", "mrgdv", "band2eps", "ujdet", "fold2Bloch", "macroave",
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@ -121,9 +124,10 @@ class VariablesTest(AbimkdocsTest):
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#print(vnset)
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count_code[test.executable].update(vnset)
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untested = {}
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untested = OrderedDict()
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for code, count in count_code.items():
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untested[code] = []
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# Add it if var is not tested and not internal.
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for vname, c in count.items():
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if c == 0 and not variables_code[code][vname].is_internal:
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print(code, vname)
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@ -133,3 +137,15 @@ class VariablesTest(AbimkdocsTest):
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untested[code] = sorted(untested[code])
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print(code, untested[code])
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#assert 0
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ref_json_path = os.path.join(os.path.dirname(__file__), "untested_variables.json")
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update_ref = False
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if update_ref:
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with open(ref_json_path, "wt") as fh:
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json.dump(untested, fh, indent=4)
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else:
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with open(ref_json_path, "rt") as fh:
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ref_untested = json.load(fh)
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self.assertDictEqual(untested, ref_untested,
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msg="Detected mismatch between reference file and new list of untested variables.")
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@ -174,10 +174,12 @@ before it and after it (again, multiple blanks are irrelevant).
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ABINIT has also some (very limited) interpretor capabilities:
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* It can identify one slash sign (/) being placed between two numbers
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(without a separating blank) as being the definition of a fraction (e.g. 1/3 will be interpreted as 0.33333333333333d0) ;
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(without a separating blank) as being the definition of a fraction
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(e.g. 1/3 will be interpreted as 0.33333333333333d0);
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* It can identify sqrt(...) or -sqrt(...) as being the definition of a square root,
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when applied to one valid number - also without a separating blank - (e.g. -sqrt(0.75) will be interpreted as -0.8660254038d0) ;
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when applied to one valid number - also without a separating blank -
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(e.g. -sqrt(0.75) will be interpreted as -0.8660254038d0);
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* Note, however, that these capabilities are NOT recursive.
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At most, a sqrt identifier can contain an expression that uses a fraction (e.g. sqrt(3/4) is OK),
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@ -206,9 +208,16 @@ the input variable is given: a **mnemonics**, possibly some
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**characteristics**, the **variable type** (integer, real, string), and the
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**default value**. Then, follows the description of the variable.
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The **characteristics** can be one of the following: **DEVELOP**,
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**NO_MULTI**, **INTERNAL_ONLY**, **INPUT_ONLY**, **EVOLVING**, **ENERGY**
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, **LENGTH**, **MAGNETIC FIELD**, as described now.
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The **characteristics** can be one of the following:
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- **DEVELOP**,
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- **NO_MULTI**
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- **INTERNAL_ONLY**
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- **INPUT_ONLY**
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- **EVOLVING**
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- **ENERGY**
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- **LENGTH**
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- **MAGNETIC FIELD**
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#### Physical information
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@ -219,23 +228,26 @@ can treat its physical dimensions with some units.
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The use of the atomic unit system (e.g. the Hartree for energy, about 27.211
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eV, and the Bohr for lengths about 0.529 Angstroms) is strictly enforced
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within the code. However, the dimension of some input variables can be
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specified and read correctly. At present, this applies to three types of
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specified and read correctly.
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At present, this applies to three types of
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variables: those that have the dimension of an energy, those that have a
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dimension of length, and those that have a dimension of magnetic field. The
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first class of variables have the characteristics ' **ENERGY** ', and can be
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specified in atomic units (Hartree), or electron-volts, or Rydbergs, or even
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Kelvin. The second class of variables have the characteristics ' **LENGTH** ',
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first class of variables have the characteristics **ENERGY**, and can be
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specified in atomic units (Hartree), or electron-volts, or Rydbergs, or even Kelvin.
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The second class of variables have the characteristics **LENGTH**,
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and can be specified in atomic units (Bohr) and angstrom. The third class of
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variables have the characteristics ' **MAGNETIC FIELD** ', and can be
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variables have the characteristics **MAGNETIC FIELD**, and can be
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specified in atomic units and Tesla. The abinit parser recognize a dimension
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if it is specified after the list of numbers following the input variable
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keyword, in the input file. The specification can be upper or lower case, or a
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mix thereof. Here is the list of recognized chains of characters:
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* 'Ry ' => Rydberg (for energies)
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* 'eV ' => electron-volts (for energies)
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* 'K ' => Kelvin (for energies)
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* 'Angstr...' => Angstrom (for lengths)
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* Ry --> Rydberg (for energies)
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* eV --> electron-volts (for energies)
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* K --> Kelvin (for energies)
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* Angstr --> Angstrom (for lengths)
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Except in the case of 'Angstr', the abbreviation must be used (i.e. 'Rydberg'
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will not be recognized presently). Other character chains, like "au" (for
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@ -263,15 +275,15 @@ even in reduced coordinates, through [[xred]].
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Most of the variables can be used in the multi-dataset mode (see section 3.3),
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but those that must have a unique value throughout all the datasets are
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signaled with the indication ' **NO_MULTI** '.
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signaled with the indication **NO_MULTI**.
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Some of the input variables, with characteristics ' **INPUT_ONLY** ' are only
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Some of the input variables, with characteristics **INPUT_ONLY** are only
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used by the parser, to initialize other input variables, but are not
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transmitted inside the code, beyond the parser. In particular, they are not
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echoed in the output file.
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At variance, some internal variables, with characteristics ' **INTERNAL_ONLY**
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' are documented in the help files, but are not accessible as input variables.
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At variance, some internal variables, with characteristics **INTERNAL_ONLY**
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are documented in the help files, but are not accessible as input variables.
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The documentation is provided because such variables are sometimes mentioned
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in the output file.
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@ -279,11 +291,11 @@ Most of the input variables do not change while a run is performed. Some of
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them, by contrast, may evolve, like the atomic positions, the atomic
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velocities, the cell shape, and the occupation numbers. Their echo, after the
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run has proceeded, will of course differ from their input value. They are
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signaled by the indication ' **EVOLVING** '.
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signaled by the indication **EVOLVING**.
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#### Other information
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'**DEVELOP**' refers to input variables that are not used in production
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**DEVELOP** refers to input variables that are not used in production
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runs, but have been introduced during development time, of a feature that is
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likely not finalized. For non ABINIT developers, it is strongly advised to skip them.
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@ -492,10 +504,10 @@ is equivalent to
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### 3.6 File names in the multi-dataset mode
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The root names for input and output files (potential, density, wavefunctions
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and so on) will receive an appendix: ' **_DS** ' followed by the index of the
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and so on) will receive an appendix: **_DS** followed by the index of the
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dataset. See section 4.
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The ' **get** ' variables can be used to chain the calculations.
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The **get** variables can be used to chain the calculations.
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Let us mention a few of them: [[getwfk]], [[getwfq]], [[getddk]], [[get1wf]],
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[[getden]], [[getcell]], [[getxred]] and [[getxcart]].
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@ -540,10 +552,10 @@ the record of the run in a nicer looking format.
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**abi**
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The other files READ by the code will have a name that is constructed from the
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root "abi". This apply to optionally read wavefunction, density or potential
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files. In the multi-dataset mode, this root will be complemented by ' **_DS**
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' and the dataset index. The list of possible input files, with their name
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created from the root 'abi', is the following (a similar list exist when '
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**_DS** ' and the dataset index are appended to 'abi'):
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files. In the multi-dataset mode, this root will be complemented by **_DS**
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and the dataset index. The list of possible input files, with their name
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created from the root 'abi', is the following (a similar list exist when
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**_DS** and the dataset index are appended to 'abi'):
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* **abi_WFK**
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filename of file containing input wavefunction coefficients created from an
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@ -578,11 +590,11 @@ filename of file containing an approximate hessian, for eventual
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Except "ab_out" and "log", the other files WRITTEN by the code will have a
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name that is constructed from the root "abo". This apply to optionally written
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wavefunction, density, potential, or density of states files. In the multi-
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dataset mode, this root will be complemented by ' **_DS** ' and the dataset
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dataset mode, this root will be complemented by **_DS** and the dataset
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index. Also in the multi-dataset mode, the root "abo" can be used to build the
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name of **input** files, thanks to the 'get' variables. The list of possible
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output files, with their name created from the root 'abo' is the following (a
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similar list exists when ' **_DS** ' and the dataset index are appended to 'abo'):
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similar list exists when **_DS** and the dataset index are appended to 'abo'):
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* **abo_WFK**
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Filename of file containing output wavefunction coefficients, if [[nqpt]]=0.
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@ -4,7 +4,7 @@ This file provides a description of the operations needed to install the
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ABINIT package, to generate the executable and to make the tests.
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It provides also the description of simple modifications of the package, for developers.
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See a recent version of the [new user's guide](../users/new_user_guide.html),
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See a recent version of the [new user's guide](guide/new_user.md),
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for an introduction to the abinit package.
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See a recent version of the [[help:abinit]] file for learning how to use the code.
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Both of them can be found either on the Web, or in the doc subdirectory of the package.
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@ -347,21 +347,15 @@ appropriate library to be installed in order to work properly.
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For further information on these internal tests, see the ~abinit/tests/built-in/README file.
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You might now read the [new user's guide](../users/new_user_guide.html), in
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You might now read the [new user's guide](guide/new_user.md), in
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order to learn how to use the code, and then to follow the four basic
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tutorials, see the [entry page for the tutorials](../tutorial/welcome.html).
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tutorials, see the [entry page for the tutorials](tutorial/index.md).
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This is useful if you consider that the installation has been successful. Or
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you might continue to read the present Web page, and try to perform the speed
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tests, as well as the other tests.
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## How to make the other tests?
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Although it is possible to make the other tests without knowing really how to
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use the code (since all steps involved - the run and subsequent analysis - are
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done automatically), for the other tests, it is recommended to read the
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[new user's guide](../users/new_user_guide.html), and then to follow the four basic
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tutorials, see the [entry page for the tutorials](../tutorial/welcome.html).
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Let us pursue with the testing procedure. Go to the ~abinit/tests directory, and issue:
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make help
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@ -411,8 +405,7 @@ used (automatically), possibly the other input files (like pseudopotentials),
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the output files to be analyzed, the admitted tolerances with respect to
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reference output files, the author of the test, and a brief description of the test.
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To run only the tests in this directory, simply issue, in the ~abinit/tests/
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directory:
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To run only the tests in this directory, simply issue, in the ~abinit/tests/ directory:
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./runtests.py fast
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@ -472,8 +465,7 @@ differences in:
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* the platform description (possibly);
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* the overall execution time (this is ALWAYS printed, even without differences).
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So, a successful execution of one test case may be announced as follows in the
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fldiff.report file:
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So, a successful execution of one test case may be announced as follows in the fldiff.report file:
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Case_1
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2
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@ -491,8 +483,7 @@ fldiff.report file:
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The fldiff.report file will have one such section for each test_case that was
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run. It begins with the number of the test case, then includes a few blocks of
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three lines: the number of the line where something is happening, followed by
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the content of the two lines. Finally, there is a one-line summary for each
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test case.
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the content of the two lines. Finally, there is a one-line summary for each test case.
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More information on the fldiff script can be found in the ~abinit/tests/Scripts/fldiff.pl file.
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@ -8,7 +8,7 @@ import warnings
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import mkdocs.__main__
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if sys.version_info < (3, 6):
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warnings.warn("""Python >= 3.6 is STRONGLY recommended when building the Abinit documentation""")
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warnings.warn("Python >= 3.6 is STRONGLY recommended when building the Abinit documentation\n" * 20)
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# We don't install with setup.py hence we have to add the directory [...]/abinit/tests to $PYTHONPATH
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pack_dir = os.path.dirname(os.path.abspath(__file__))
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@ -726,19 +726,16 @@ class AbinitTests(object):
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return d
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def select_tests(self, suite_args, regenerate=False, keys=None,
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authors=None, ivars=None, with_pickle=True):
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authors=None, ivars=None, with_pickle=True, flat_list=False):
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"""
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Main entry point for client code.
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Return an instance of AbinitTestSuite
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Main entry point for client code. Return an instance of AbinitTestSuite
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Args:
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with_pickle:
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Save the generated database in pickle format.
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with_pickle: Save the generated database in pickle format.
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flat_list: True if a flat list of tests should be returned instead
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of a list that can contain ChainOfTests objects.
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"""
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try:
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tests_todo = self._suite_args_parser(suite_args)
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except:
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raise
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# Load the full database.
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database = self.get_database(regenerate=regenerate, with_pickle=with_pickle)
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@ -797,7 +794,19 @@ class AbinitTests(object):
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exclude_authors=exclude_authors,
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ivars=ivars
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)
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if not flat_list:
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return tests
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else:
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# Build flat list of tests.
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flat = []
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for t in tests:
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if isinstance(t, ChainOfTests):
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# DO NOT use isinstance to check if ChainOfTests but rely on duck typing.
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#if hasattr(t, "tests"):
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flat.extend(t.tests)
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else:
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flat.append(t)
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return flat
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def generate_html_listoftests(self):
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"""Generate the ListOfTests files"""
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