diff --git a/README.md b/README.md
index 4ef46595c6cddc03285dc434df4e2e66668d9712..0fff59352ad0c35e6a80840cf13dfa817110f9b1 100644
--- a/README.md
+++ b/README.md
@@ -1,95 +1,50 @@
-This is the main repository of the [NOMAD](http://nomad-lab.eu) parser for
+This is the main repository of the [NOMAD](https://www.nomad-coe.eu/) parser for
[BigDFT](http://bigdft.org/).
-# Standalone Installation
-The parser is designed to be usable as a separate python package. Here is an
-example of the call syntax:
-
+# Example
```python
- from bigdftparser import bigdftparser
+ from bigdftparser import BigDFTParser
import matplotlib.pyplot as mpl
- # 0. Initialize a parser by giving a path to the BigDFT output file and a list of
- # default units
- path = "path/to/main.file"
+ # 1. Initialize a parser with a set of default units.
default_units = ["eV"]
- parser = bigdftparser(path, default_units=default_units)
+ parser = BigDFTParser(default_units=default_units)
- # 1. Parse
- results = parser.parse()
+ # 2. Parse a file
+ path = "path/to/main.file"
+ results = parser.parse(path)
- # 2. Query the results with using the id's created specifically for NOMAD.
+ # 3. Query the results with using the id's created specifically for NOMAD.
scf_energies = results["energy_total_scf_iteration"]
mpl.plot(scf_energies)
mpl.show()
```
-To install this standalone version, you need to first clone the
-*git@gitlab.mpcdf.mpg.de:nomad-lab/python-common.git* repository and the
-*git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-meta-info.git* repository into the
-same folder. Then install the *python-common* package according to the
-instructions found in the README. After that, you can install this package by
-running either of the following two commands depending on your python version:
+# Installation
+The code is python 2 and python 3 compatible. First download and install
+the nomadcore package:
```sh
-python setup.py develop --user # for python2
-python3 setup.py develop --user # for python3
+git clone https://gitlab.mpcdf.mpg.de/nomad-lab/python-common.git
+cd python-common
+pip install -r requirements.txt
+pip install -e .
```
-# Scala access
-The scala layer in the Nomad infrastructure can access the parser functionality
-through the scalainterface.py file, by calling the following command:
+Then download the metainfo definitions to the same folder where the
+'python-common' repository was cloned:
-```python
- python scalainterface.py path/to/main/file
+```sh
+git clone https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info.git
```
-This scala interface is in it's own file to separate it from the rest of the
-code.
-
-# Support of different versions
-The parser is designed to support multiple versions of BigDFT with a
-[DRY](https://en.wikipedia.org/wiki/Don%27t_repeat_yourself) approach: The
-initial parser class is based on BigDFT 1.8.0, and other versions will be
-subclassed from it. By sublassing, all the previous functionality will be
-preserved, new functionality can be easily created, and old functionality
-overridden only where necesssary.
+Finally download and install the parser:
-# Developer Info
-This section describes some of the guidelines that are used in the development
-of this parser.
-
-## Documentation
-This parser tries to follow the [google style
-guide](https://google.github.io/styleguide/pyguide.html?showone=Comments#Comments)
-for documenting python code. Documenting makes it much easier to follow the
-logic behind your parser.
-
-## Testing
-The parsers can become quite complicated and maintaining them without
-systematic testing is impossible. There are general tests that are
-performed automatically in the scala layer for all parsers. This is essential,
-but can only test that the data is outputted in the correct format and
-according to some general rules. These tests cannot verify that the contents
-are correct.
-
-In order to truly test the parser output, regression testing is needed. The
-tests for this parser are located in the **regtest** folder. Tests provide one
-way to test each parseable quantity and python has a very good [library for
-unit testing](https://docs.python.org/2/library/unittest.html). When the parser
-supports a new quantity it is quite fast to create unit tests for it. These
-tests will validate the parsing, and also easily detect bugs that may rise when
-the code is modified in the future.
-
-## Profiling
-The parsers have to be reasonably fast. For some codes there is already
-significant amount of data in the NoMaD repository and the time taken to parse
-it will depend on the performance of the parser. Also each time the parser
-evolves after system deployment, the existing data may have to be reparsed at
-least partially.
+```sh
+git clone https://gitlab.mpcdf.mpg.de/nomad-lab/parser-big-dft.git
+cd parser-big-dft
+pip install -e .
+```
-By profiling what functions take the most computational time and memory during
-parsing you can identify the bottlenecks in the parser. There are already
-existing profiling tools such as
-[cProfile](https://docs.python.org/2/library/profile.html#module-cProfile)
-which you can plug into your scripts very easily.
+# Notes
+The parser is based on BigDFT 1.8.
diff --git a/parser/parser-big-dft/bigdftparser/parser.py b/parser/parser-big-dft/bigdftparser/parser.py
index 5efab8b340bb3f9da2b94d6a728f835f41c885bd..46703e71bcb2ae0c7c7adf7c982e1362f02a2e58 100644
--- a/parser/parser-big-dft/bigdftparser/parser.py
+++ b/parser/parser-big-dft/bigdftparser/parser.py
@@ -6,7 +6,6 @@ from nomadcore.baseclasses import ParserInterface
logger = logging.getLogger("nomad")
-#===============================================================================
class BigDFTParser(ParserInterface):
"""This class handles the initial setup before any parsing can happen. It
determines which version of BigDFT was used to generate the output and then
@@ -15,8 +14,8 @@ class BigDFTParser(ParserInterface):
After the implementation has been setup, you can parse the files with
parse().
"""
- def __init__(self, main_file, metainfo_to_keep=None, backend=None, default_units=None, metainfo_units=None, debug=True, log_level=logging.ERROR, store=True):
- super(BigDFTParser, self).__init__(main_file, metainfo_to_keep, backend, default_units, metainfo_units, debug, log_level, store)
+ def __init__(self, metainfo_to_keep=None, backend=None, default_units=None, metainfo_units=None, debug=True, log_level=logging.ERROR, store=True):
+ super(BigDFTParser, self).__init__(metainfo_to_keep, backend, default_units, metainfo_units, debug, log_level, store)
def setup_version(self):
"""Setups the version by looking at the output file and the version
@@ -78,4 +77,4 @@ class BigDFTParser(ParserInterface):
except AttributeError:
logger.exception("A parser class '{}' could not be found in the module '[]'.".format(class_name, parser_module))
raise
- self.main_parser = parser_class(self.parser_context.main_file, self.parser_context)
+ self.main_parser = parser_class(self.parser_context)
diff --git a/parser/parser-big-dft/bigdftparser/scalainterface.py b/parser/parser-big-dft/bigdftparser/scalainterface.py
index c602f237345a07d55640d66940e81341efbe93b4..bd2edf21eb9367039eb57dfcc884b2cdbf909e9f 100644
--- a/parser/parser-big-dft/bigdftparser/scalainterface.py
+++ b/parser/parser-big-dft/bigdftparser/scalainterface.py
@@ -13,5 +13,5 @@ if __name__ == "__main__":
# Initialise the parser with the main filename and a JSON backend
main_file = sys.argv[1]
- parser = BigDFTParser(main_file, backend=JsonParseEventsWriterBackend)
- parser.parse()
+ parser = BigDFTParser(backend=JsonParseEventsWriterBackend)
+ parser.parse(main_file)
diff --git a/parser/parser-big-dft/bigdftparser/versions/bigdft18/mainparser.py b/parser/parser-big-dft/bigdftparser/versions/bigdft18/mainparser.py
index 78d7d1091e9f6e7c118cccacfba23e8a6b698a85..e0f8f9deb149e20c8467c9802e7f7ccb4ba086bb 100644
--- a/parser/parser-big-dft/bigdftparser/versions/bigdft18/mainparser.py
+++ b/parser/parser-big-dft/bigdftparser/versions/bigdft18/mainparser.py
@@ -7,15 +7,14 @@ from bigdftparser.generic.libxc_codes import LIB_XC_MAPPING
LOGGER = logging.getLogger("nomad")
-#===============================================================================
class BigDFTMainParser(AbstractBaseParser):
"""The main parser class that is called for all run types. Parses the NWChem
output file.
"""
- def __init__(self, file_path, parser_context):
+ def __init__(self, parser_context):
"""
"""
- super(BigDFTMainParser, self).__init__(file_path, parser_context)
+ super(BigDFTMainParser, self).__init__(parser_context)
# Map keys in the output to funtions that handle the values
self.key_to_funct_map = {
@@ -30,7 +29,7 @@ class BigDFTMainParser(AbstractBaseParser):
"Energy (Hartree)": lambda x: self.backend.addRealValue("energy_total", float(x), unit="hartree"),
}
- def parse(self):
+ def parse(self, filepath):
"""The output file of a BigDFT run is a YAML document. Here we directly
parse this document with an existing YAML library, and push its
contents into the backend. This function will read the document in
@@ -39,7 +38,7 @@ class BigDFTMainParser(AbstractBaseParser):
"""
self.prepare()
self.print_json_header()
- with open(self.file_path, "r") as fin:
+ with open(filepath, "r") as fin:
try:
# Open default sections and output default information
section_run_id = self.backend.openSection("section_run")
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/forces_posinp.xyz b/regtests/bigdft_1.8/periodicity/free/forces_posinp.xyz
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/forces_posinp.xyz
rename to regtests/bigdft_1.8/periodicity/free/forces_posinp.xyz
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/input_minimal.yaml b/regtests/bigdft_1.8/periodicity/free/input_minimal.yaml
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/input_minimal.yaml
rename to regtests/bigdft_1.8/periodicity/free/input_minimal.yaml
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/output.out b/regtests/bigdft_1.8/periodicity/free/output.out
similarity index 100%
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rename to regtests/bigdft_1.8/periodicity/free/output.out
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/posinp.xyz b/regtests/bigdft_1.8/periodicity/free/posinp.xyz
similarity index 100%
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rename to regtests/bigdft_1.8/periodicity/free/posinp.xyz
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/time.yaml b/regtests/bigdft_1.8/periodicity/free/time.yaml
similarity index 100%
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rename to regtests/bigdft_1.8/periodicity/free/time.yaml
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/forces_posinp.xyz b/regtests/bigdft_1.8/periodicity/periodic/forces_posinp.xyz
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rename to regtests/bigdft_1.8/periodicity/periodic/forces_posinp.xyz
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/input_minimal.yaml b/regtests/bigdft_1.8/periodicity/periodic/input_minimal.yaml
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rename to regtests/bigdft_1.8/periodicity/periodic/input_minimal.yaml
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/output.out b/regtests/bigdft_1.8/periodicity/periodic/output.out
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rename to regtests/bigdft_1.8/periodicity/periodic/output.out
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diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/time.yaml b/regtests/bigdft_1.8/periodicity/periodic/time.yaml
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rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/time.yaml
rename to regtests/bigdft_1.8/periodicity/periodic/time.yaml
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/surface/forces_posinp.xyz b/regtests/bigdft_1.8/periodicity/surface/forces_posinp.xyz
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diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/surface/input_minimal.yaml b/regtests/bigdft_1.8/periodicity/surface/input_minimal.yaml
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diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/single_point/forces_posinp.xyz b/regtests/bigdft_1.8/single_point/forces_posinp.xyz
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diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/abinit_1/forces_posinp.xyz b/regtests/bigdft_1.8/xc_functionals/abinit_1/forces_posinp.xyz
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diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/abinit_1/input.dft b/regtests/bigdft_1.8/xc_functionals/abinit_1/input.dft
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rename to regtests/bigdft_1.8/xc_functionals/abinit_1/input.dft
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/abinit_1/input_minimal.yaml b/regtests/bigdft_1.8/xc_functionals/abinit_1/input_minimal.yaml
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diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/abinit_100/forces_posinp.xyz b/regtests/bigdft_1.8/xc_functionals/abinit_100/forces_posinp.xyz
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diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/abinit_100/input.yaml b/regtests/bigdft_1.8/xc_functionals/abinit_100/input.yaml
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diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/abinit_100/input_minimal.yaml b/regtests/bigdft_1.8/xc_functionals/abinit_100/input_minimal.yaml
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diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/abinit_100/output.out b/regtests/bigdft_1.8/xc_functionals/abinit_100/output.out
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diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/abinit_100/posinp.xyz b/regtests/bigdft_1.8/xc_functionals/abinit_100/posinp.xyz
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rename to regtests/bigdft_1.8/xc_functionals/abinit_100/posinp.xyz
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/abinit_100/psppar.N b/regtests/bigdft_1.8/xc_functionals/abinit_100/psppar.N
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diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/abinit_100/time.yaml b/regtests/bigdft_1.8/xc_functionals/abinit_100/time.yaml
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diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/abinit_11/forces_posinp.xyz b/regtests/bigdft_1.8/xc_functionals/abinit_11/forces_posinp.xyz
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rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_001/output.out
rename to regtests/bigdft_1.8/xc_functionals/libxc_001/output.out
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_001/posinp.xyz b/regtests/bigdft_1.8/xc_functionals/libxc_001/posinp.xyz
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_001/posinp.xyz
rename to regtests/bigdft_1.8/xc_functionals/libxc_001/posinp.xyz
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_001/psppar.N b/regtests/bigdft_1.8/xc_functionals/libxc_001/psppar.N
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_001/psppar.N
rename to regtests/bigdft_1.8/xc_functionals/libxc_001/psppar.N
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_001/time.yaml b/regtests/bigdft_1.8/xc_functionals/libxc_001/time.yaml
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_001/time.yaml
rename to regtests/bigdft_1.8/xc_functionals/libxc_001/time.yaml
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_010/forces_posinp.xyz b/regtests/bigdft_1.8/xc_functionals/libxc_010/forces_posinp.xyz
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_010/forces_posinp.xyz
rename to regtests/bigdft_1.8/xc_functionals/libxc_010/forces_posinp.xyz
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_010/input.yaml b/regtests/bigdft_1.8/xc_functionals/libxc_010/input.yaml
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_010/input.yaml
rename to regtests/bigdft_1.8/xc_functionals/libxc_010/input.yaml
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_010/input_minimal.yaml b/regtests/bigdft_1.8/xc_functionals/libxc_010/input_minimal.yaml
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_010/input_minimal.yaml
rename to regtests/bigdft_1.8/xc_functionals/libxc_010/input_minimal.yaml
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_010/output.out b/regtests/bigdft_1.8/xc_functionals/libxc_010/output.out
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_010/output.out
rename to regtests/bigdft_1.8/xc_functionals/libxc_010/output.out
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_010/posinp.xyz b/regtests/bigdft_1.8/xc_functionals/libxc_010/posinp.xyz
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_010/posinp.xyz
rename to regtests/bigdft_1.8/xc_functionals/libxc_010/posinp.xyz
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_010/psppar.N b/regtests/bigdft_1.8/xc_functionals/libxc_010/psppar.N
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_010/psppar.N
rename to regtests/bigdft_1.8/xc_functionals/libxc_010/psppar.N
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_010/time.yaml b/regtests/bigdft_1.8/xc_functionals/libxc_010/time.yaml
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_010/time.yaml
rename to regtests/bigdft_1.8/xc_functionals/libxc_010/time.yaml
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101/forces_posinp.xyz b/regtests/bigdft_1.8/xc_functionals/libxc_101/forces_posinp.xyz
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101/forces_posinp.xyz
rename to regtests/bigdft_1.8/xc_functionals/libxc_101/forces_posinp.xyz
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101/input.yaml b/regtests/bigdft_1.8/xc_functionals/libxc_101/input.yaml
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101/input.yaml
rename to regtests/bigdft_1.8/xc_functionals/libxc_101/input.yaml
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101/input_minimal.yaml b/regtests/bigdft_1.8/xc_functionals/libxc_101/input_minimal.yaml
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101/input_minimal.yaml
rename to regtests/bigdft_1.8/xc_functionals/libxc_101/input_minimal.yaml
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101/output.out b/regtests/bigdft_1.8/xc_functionals/libxc_101/output.out
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101/output.out
rename to regtests/bigdft_1.8/xc_functionals/libxc_101/output.out
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101/posinp.xyz b/regtests/bigdft_1.8/xc_functionals/libxc_101/posinp.xyz
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101/posinp.xyz
rename to regtests/bigdft_1.8/xc_functionals/libxc_101/posinp.xyz
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101/psppar.N b/regtests/bigdft_1.8/xc_functionals/libxc_101/psppar.N
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101/psppar.N
rename to regtests/bigdft_1.8/xc_functionals/libxc_101/psppar.N
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101/time.yaml b/regtests/bigdft_1.8/xc_functionals/libxc_101/time.yaml
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101/time.yaml
rename to regtests/bigdft_1.8/xc_functionals/libxc_101/time.yaml
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101130/forces_posinp.xyz b/regtests/bigdft_1.8/xc_functionals/libxc_101130/forces_posinp.xyz
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101130/forces_posinp.xyz
rename to regtests/bigdft_1.8/xc_functionals/libxc_101130/forces_posinp.xyz
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101130/input.yaml b/regtests/bigdft_1.8/xc_functionals/libxc_101130/input.yaml
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101130/input.yaml
rename to regtests/bigdft_1.8/xc_functionals/libxc_101130/input.yaml
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101130/input_minimal.yaml b/regtests/bigdft_1.8/xc_functionals/libxc_101130/input_minimal.yaml
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101130/input_minimal.yaml
rename to regtests/bigdft_1.8/xc_functionals/libxc_101130/input_minimal.yaml
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101130/output.out b/regtests/bigdft_1.8/xc_functionals/libxc_101130/output.out
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101130/output.out
rename to regtests/bigdft_1.8/xc_functionals/libxc_101130/output.out
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101130/posinp.xyz b/regtests/bigdft_1.8/xc_functionals/libxc_101130/posinp.xyz
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101130/posinp.xyz
rename to regtests/bigdft_1.8/xc_functionals/libxc_101130/posinp.xyz
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101130/psppar.N b/regtests/bigdft_1.8/xc_functionals/libxc_101130/psppar.N
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101130/psppar.N
rename to regtests/bigdft_1.8/xc_functionals/libxc_101130/psppar.N
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101130/time.yaml b/regtests/bigdft_1.8/xc_functionals/libxc_101130/time.yaml
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/xc_functionals/libxc_101130/time.yaml
rename to regtests/bigdft_1.8/xc_functionals/libxc_101130/time.yaml
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/yaml_test/data.yml b/regtests/bigdft_1.8/yaml_test/data.yml
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/yaml_test/data.yml
rename to regtests/bigdft_1.8/yaml_test/data.yml
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/yaml_test/node_data.yml b/regtests/bigdft_1.8/yaml_test/node_data.yml
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/yaml_test/node_data.yml
rename to regtests/bigdft_1.8/yaml_test/node_data.yml
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/yaml_test/node_reader.py b/regtests/bigdft_1.8/yaml_test/node_reader.py
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/yaml_test/node_reader.py
rename to regtests/bigdft_1.8/yaml_test/node_reader.py
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/yaml_test/output.out b/regtests/bigdft_1.8/yaml_test/output.out
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/yaml_test/output.out
rename to regtests/bigdft_1.8/yaml_test/output.out
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/yaml_test/yaml_creator.py b/regtests/bigdft_1.8/yaml_test/yaml_creator.py
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/yaml_test/yaml_creator.py
rename to regtests/bigdft_1.8/yaml_test/yaml_creator.py
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/yaml_test/yaml_reader.py b/regtests/bigdft_1.8/yaml_test/yaml_reader.py
similarity index 100%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/yaml_test/yaml_reader.py
rename to regtests/bigdft_1.8/yaml_test/yaml_reader.py
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/run_tests.py b/regtests/regtests.py
similarity index 74%
rename from parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/run_tests.py
rename to regtests/regtests.py
index 75f1d7e838862798f1175a6043d1b321d256c13e..294f523445594b5b0555937b0685b08a9ae6acb6 100644
--- a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/run_tests.py
+++ b/regtests/regtests.py
@@ -1,15 +1,3 @@
-"""
-This is a module for unit testing the BigDFT parser. The unit tests are run with
-a custom backend that outputs the results directly into native python object for
-easier and faster analysis.
-
-Each property that has an enumerable list of different possible options is
-assigned a new test class, that should ideally test through all the options.
-
-The properties that can have non-enumerable values will be tested only for one
-specific case inside a test class that is designed for a certain type of run
-(MD, optimization, QM/MM, etc.)
-"""
import os
import unittest
import logging
@@ -18,41 +6,32 @@ from bigdftparser import BigDFTParser
from nomadcore.unit_conversion.unit_conversion import convert_unit
-#===============================================================================
-def get_results(folder, metainfo_to_keep=None):
- """Get the given result from the calculation in the given folder by using
- the Analyzer in the nomadtoolkit package. Tries to optimize the parsing by
- giving the metainfo_to_keep argument.
+def get_result(folder, metaname=None):
+ """Get the results from the calculation in the given folder. By default goes through different
Args:
folder: The folder relative to the directory of this script where the
parsed calculation resides.
- metaname: The quantity to extract.
+ metaname(str): Optional quantity to return. If not specified, returns
+ the full dictionary of results.
"""
dirname = os.path.dirname(__file__)
- filename = os.path.join(dirname, folder, "output.out")
- parser = BigDFTParser(filename, None, debug=True, log_level=logging.WARNING)
- results = parser.parse()
- return results
+ filename = os.path.join("bigdft_{}".format(VERSION), dirname, folder, "output.out")
+ parser = BigDFTParser(None, debug=True, log_level=logging.CRITICAL)
+ results = parser.parse(filename)
-
-#===============================================================================
-def get_result(folder, metaname, optimize=True):
- if optimize:
- results = get_results(folder, None)
+ if metaname is None:
+ return results
else:
- results = get_results(folder)
- result = results[metaname]
- return result
+ return results[metaname]
-#===============================================================================
class TestSinglePoint(unittest.TestCase):
"""Tests that the parser can handle single point calculations.
"""
@classmethod
def setUpClass(cls):
- cls.results = get_results("single_point", "section_run")
+ cls.results = get_result("single_point")
# cls.results.print_summary()
def test_program_name(self):
@@ -177,42 +156,40 @@ class TestSinglePoint(unittest.TestCase):
# self.assertEqual(kind["method_atom_kind_label"][0], "H")
-#===============================================================================
class TestPeriodicity(unittest.TestCase):
"""Tests that the parser can handle different boundary conditions.
"""
def test_periodic(self):
- results = get_results("periodicity/periodic")
+ results = get_result("periodicity/periodic")
result = results["configuration_periodic_dimensions"]
self.assertTrue(np.array_equal(result, np.array([True, True, True])))
def test_surface(self):
- results = get_results("periodicity/surface")
+ results = get_result("periodicity/surface")
result = results["configuration_periodic_dimensions"]
self.assertTrue(np.array_equal(result, np.array([True, False, True])))
def test_free(self):
- results = get_results("periodicity/free")
+ results = get_result("periodicity/free")
result = results["configuration_periodic_dimensions"]
self.assertTrue(np.array_equal(result, np.array([False, False, False])))
-#===============================================================================
class TestXCFunctionals(unittest.TestCase):
"""Tests that the parser can handle different XC functional codes.
"""
def test_abinit_1(self):
- results = get_results("xc_functionals/abinit_1")
+ results = get_result("xc_functionals/abinit_1")
result = results["XC_functional"]
self.assertEqual(result, "1.0*LDA_XC_TETER93")
def test_abinit_11(self):
- results = get_results("xc_functionals/abinit_11")
+ results = get_result("xc_functionals/abinit_11")
result = results["XC_functional"]
self.assertEqual(result, "1.0*GGA_C_PBE_1.0*GGA_X_PBE")
def test_abinit_12(self):
- results = get_results("xc_functionals/abinit_12")
+ results = get_result("xc_functionals/abinit_12")
result = results["XC_functional"]
self.assertEqual(result, "1.0*GGA_X_PBE")
@@ -247,37 +224,40 @@ class TestXCFunctionals(unittest.TestCase):
# self.assertEqual(result, "1.0*GGA_XC_HCTH_407")
def test_abinit_100(self):
- results = get_results("xc_functionals/abinit_100")
+ results = get_result("xc_functionals/abinit_100")
result = results["XC_functional"]
self.assertEqual(result, "1.0*HF_X")
def test_libxc_001(self):
- results = get_results("xc_functionals/libxc_001")
+ results = get_result("xc_functionals/libxc_001")
result = results["XC_functional"]
self.assertEqual(result, "1.0*LDA_X")
def test_libxc_010(self):
- results = get_results("xc_functionals/libxc_010")
+ results = get_result("xc_functionals/libxc_010")
result = results["XC_functional"]
self.assertEqual(result, "1.0*LDA_C_PZ_MOD")
def test_libxc_101(self):
- results = get_results("xc_functionals/libxc_101")
+ results = get_result("xc_functionals/libxc_101")
result = results["XC_functional"]
self.assertEqual(result, "1.0*GGA_X_PBE")
def test_libxc_101130(self):
- results = get_results("xc_functionals/libxc_101130")
+ results = get_result("xc_functionals/libxc_101130")
result = results["XC_functional"]
self.assertEqual(result, "1.0*GGA_C_PBE_1.0*GGA_X_PBE")
-#===============================================================================
if __name__ == '__main__':
- suites = []
- suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSinglePoint))
- suites.append(unittest.TestLoader().loadTestsFromTestCase(TestPeriodicity))
- suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctionals))
- alltests = unittest.TestSuite(suites)
- unittest.TextTestRunner(verbosity=0).run(alltests)
+ VERSIONS = ["1.8"]
+
+ for VERSION in VERSIONS:
+ suites = []
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSinglePoint))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestPeriodicity))
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctionals))
+
+ alltests = unittest.TestSuite(suites)
+ unittest.TextTestRunner(verbosity=0).run(alltests)