Add gpaw

.travis.yml

@@ -1,14 +1,23 @@
 language: python
-
 python:
 - '2.7'
 - '3.8'
-
 install:
 - pip install -r requirements.txt
 - pip install -r test_requirements.txt
 - pip install -e .
-
 script:
-- pytest --cov=src/ --cov-report term-missing --cov-report term:skip-covered --cov-config=tox.ini --cov-fail-under=100 -svv .
-- flake8 src
+- pytest --cov=src/ --cov-report term-missing --cov-report term:skip-covered --cov-config=tox.ini
+  --cov-fail-under=100 -svv .
+- flake8 src
+deploy:
+- provider: pypi
+  user: CitrineInformatics
+  password: "$PYPI_PASSWORD"
+  distributions: sdist bdist_wheel
+  skip_existing: true
+  on:
+    tags: true
+env:
+  global:
+    secure: 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

MANIFEST.in

@@ -1,4 +1,6 @@
-include src/dftinpgen/*.txt
-include src/dftinpgen/data/*.json
-include src/dftinpgen/qe/settings/*.json
-include src/dftinpgen/qe/settings/calculation_presets/*.json
+include src/dftinputgen/*.txt
+include src/dftinputgen/data/*.json
+include src/dftinputgen/qe/settings/*.json
+include src/dftinputgen/qe/settings/calculation_presets/*.json
+include src/dftinputgen/gpaw/settings/*.json
+include src/dftinputgen/gpaw/settings/calculation_presets/*.json

README.md

@@ -56,7 +56,10 @@ documentation.
 
 1. [pw.x](https://www.quantum-espresso.org/Doc/INPUT_PW.html) from the
    [Quantum Espresso package](https://www.quantum-espresso.org/)
-2. (under development) Post-processing utilities for pw.x:
+2. [GPAW](https://wiki.fysik.dtu.dk/gpaw/index.html) including functions for
+`surface relaxation`, `adsorbate vibration calculations`, and `lattice
+parameter optimization` (fcc, bcc, and hcp) 
+3. (under development) Post-processing utilities for pw.x:
    [dos.x](https://www.quantum-espresso.org/Doc/INPUT_DOS.html),
    [bands.x](https://www.quantum-espresso.org/Doc/INPUT_BANDS.html),
    [projwfc.x](https://www.quantum-espresso.org/Doc/INPUT_PROJWFC.html)

docs/src/conf.py

@@ -23,7 +23,9 @@
 author = "Vinay Hegde <[email protected]>"
 
 # The full version, including alpha/beta/rc tags
-release = "0.1.0"
+version_file = os.path.join("..", "..", "src", "dftinputgen", "VERSION.txt")
+with open(version_file, "r") as fr:
+    release = fr.read().strip()
 
 
 # -- General configuration ---------------------------------------------------

docs/src/developer_notes/index.rst

@@ -20,10 +20,20 @@ Code Organization
         settings/
             tags_and_groups.json
             ...
-            base_recipes/
+            calculation_presets/
                 scf.json
                 vc-relax.json
                 ...
+    gpaw/
+        gpaw.py
+        ...
+        settings/
+            tags_and_groups.json
+            ...
+            calculation_presets/
+                bulk_opt.json
+                bulk_opt_hcp.json
+                ...
     vasp/
         ...
 
@@ -33,6 +43,8 @@ Code Organization
 - ``dftinputgen.qe``: derived classes that can generate input files for various
   DFT-based and postprocessing codes in the Quantum Espresso suite (more
   :ref:`here <ssec-qe>`)
+- ``dftinputgen.gpaw``: derived classes that can generate input python scripts
+  for the GPAW package (more :ref:`here <ssec-gpaw>`).
 - ``dftinputgen.vasp``: [under development] derived classes that can generate
   input files for the VASP package.
 - ``dftinputgen.utils``: general-purpose helper functions, e.g. chemical formula

docs/src/module_reference/gpaw/gpaw.rst

@@ -0,0 +1,49 @@
+.. _sssec-gpaw:
+
+Input GPAW
+++++++++++
+
+The :class:`GPAWInputGenerator <dftinputgen.gpaw.GPAWInputGenerator>` class
+(derived from :class:`DftInputGenerator <dftinputgen.base.DftInputGenerator>`)
+implements functionality to generate python scripts for the `GPAW`_
+package. 
+
+Python scripts are written that use `ASE`_ with GPAW specified via a
+calculator object. This calculator object is where all settings for
+the DFT calculation is given. An example of the calculator object
+that is automatically written is given below.
+
+.. code-block:: python
+
+   slab.calc = GPAW(
+   h=0.16,
+   kpts={'size': [4, 4, 1]},
+   occupations={'name': 'fermi-dirac', 'width': 0.05},
+   poissonsolver={'dipolelayer': 'xy'},
+   xc='BEEF-vdW'
+   )
+
+For each calculator setting, a list of valid parameters is looked up from
+a ``GPAW_TAGS`` dictionary which is then defined within the written
+calculator object (more information about the valid calculator parameters
+and defaults provided as ``calculation_presets`` is :ref:`here
+<sssec-gpaw-input-settings>`).
+
+Currently supported calculations include relaxations, bulk optimizations,
+and total energy.
+
+**Note:** The scripts are written assuming that the crystal structure
+is stored in an `ASE readable format`_ (e.g. traj, cif, etc..) with 
+the desired initial magnetic moments defined.
+
+.. _`GPAW`: https://wiki.fysik.dtu.dk/gpaw/index.html
+.. _`ASE`: https://wiki.fysik.dtu.dk/ase/
+.. _`ASE readable format`: https://wiki.fysik.dtu.dk/ase/ase/io/io.html
+
+Interfaces
+==========
+
+.. automodule:: dftinputgen.gpaw.gpaw
+    :members:
+    :inherited-members:
+    :undoc-members:

docs/src/module_reference/gpaw/index.rst

@@ -0,0 +1,21 @@
+.. _ssec-gpaw:
+
+Input generators for GPAW
++++++++++++++++++++++++++
+
+``dftinputgen`` provides an input generator class for the `GPAW`_ package.
+More information :ref:`here <sssec-gpaw>` 
+
+.. _`GPAW`: https://wiki.fysik.dtu.dk/gpaw/index.html
+
+
+.. automodule:: dftinputgen.gpaw
+    :members:
+    :undoc-members:
+
+.. toctree::
+    :maxdepth: 2
+    :hidden:
+
+    gpaw
+    settings

docs/src/module_reference/gpaw/settings.rst

@@ -0,0 +1,33 @@
+.. _sssec-gpaw-input-settings:
+
+Input settings
+++++++++++++++
+
+All input settings have been parsed from the `GPAW manual`_
+(last updated January 2021).
+The calculator parameter names are stored in `tags_and_groups.json`_.
+These parameter names are then made available to the user via
+a module level variable ``GPAW_TAGS``.
+
+The settings module also makes available a few sets of default settings 
+to be used for common DFT calculations such as ``surface_relax``,
+and ``bulk_opt``.
+The defaults are stored in JSON files in the `calculation_presets`_ module.
+These can be accessed by the user via a module level variable ``GPAW_PRESETS``.
+Note that these presets are only reasonable defaults and are not meant to be
+prescriptive.
+
+.. _`GPAW manual`: https://wiki.fysik.dtu.dk/gpaw/documentation/manual.html#parameters
+.. _`tags_and_groups.json`: https://github.com/CitrineInformatics/dft-input-gen/blob/master/src/dftinputgen/qe/settings/tags_and_groups.json 
+.. _`calculation_presets`: https://github.com/CitrineInformatics/dft-input-gen/tree/master/src/dftinputgen/qe/settings/calculation_presets
+
+.. automodule:: dftinputgen.gpaw.settings
+    :members:
+    :undoc-members:
+    :special-members:
+
+.. automodule:: dftinputgen.gpaw.settings.calculation_presets
+    :members:
+    :undoc-members:
+    :special-members:
+

docs/src/module_reference/index.rst

@@ -9,5 +9,6 @@ Module reference
 
     base
     qe/index
+    gpaw/index
     utils
     data

setup.py

@@ -20,6 +20,7 @@
     author_email="[email protected]",
     packages=find_packages(where="src"),
     package_dir={"": "src"},
+    include_package_data=True,
     install_requires=["six", "numpy", "ase <= 3.17"],
     entry_points={"console_scripts": ["dftinputgen = dftinputgen.cli:driver"]},
     classifiers=[

src/dftinputgen/VERSION.txt

@@ -1 +1 @@
-0.1.0
+0.1.2

src/dftinputgen/cli.py

@@ -2,6 +2,8 @@
 
 from dftinputgen.demo.pwx import build_pwx_parser
 from dftinputgen.demo.pwx import generate_pwx_input_files
+from dftinputgen.demo.gpaw import build_gpaw_parser
+from dftinputgen.demo.gpaw import generate_gpaw_input_files
 
 
 def get_parser():
@@ -28,6 +30,12 @@ def get_parser():
     # other subparsers, to be added similarly, go here
     # e.g. ones for gpaw/vasp
 
+    # gpaw subparser
+    gpaw_help = "Generate a python input file for GPAW"
+    gpaw_parser = subparsers.add_parser("gpaw", help=gpaw_help)
+    build_gpaw_parser(gpaw_parser)
+    gpaw_parser.set_defaults(func=generate_gpaw_input_files)
+
     return parser
 
 

src/dftinputgen/demo/gpaw.py

@@ -0,0 +1,117 @@
+"""Demo generating input files for doing a calculation with pw.x."""
+
+import json
+import argparse
+
+from dftinputgen.utils import read_crystal_structure
+from dftinputgen.gpaw import GPAWInputGenerator
+
+
+def _get_default_parser():
+    description = "Input file generation for gpaw."
+    return argparse.ArgumentParser(description=description)
+
+
+def build_gpaw_parser(parser):
+    """Adds GPAW arguments to the input `argparse.ArgumentParser` object."""
+    # Required:
+    crystal_structure = "(REQUIRED) File with the input crystal structure"
+    parser.add_argument(
+        "-i",
+        "--crystal-structure",
+        type=read_crystal_structure,
+        help=crystal_structure,
+        required=True,
+    )
+
+    # Optional:
+    calculation_presets = "Preset group of tags and default values to use"
+    parser.add_argument(
+        "-pre",
+        "--calculation-presets",
+        choices=[
+            "surface_relax",
+            "bulk_opt",
+            "bulk_opt_hcp",
+            "molecule",
+            "surface_adsorbate_vibrations",
+        ],
+        default=None,
+        help=calculation_presets,
+    )
+
+    custom_settings_file = "JSON file with custom DFT settings to use"
+    parser.add_argument(
+        "-file",
+        "--custom-settings-file",
+        default=None,
+        help=custom_settings_file,
+    )
+
+    custom_settings_dict = """JSON string with a dictionary of custom DFT
+    settings to use. Example: '{"pseudo_dir": "/path/to/pseudo_dir/"}'"""
+    parser.add_argument(
+        "-dict",
+        "--custom-settings-dict",
+        default="{}",
+        type=json.loads,
+        help=custom_settings_dict,
+    )
+
+    write_location = "Directory to write the input file(s) in"
+    parser.add_argument("-loc", "--write-location", help=write_location)
+
+    gpaw_input_file = "Name of the GPAW input file to be written"
+    parser.add_argument("-o", "--gpaw-input-file", help=gpaw_input_file)
+
+    gpaw_restart_file = "Name of the GPAW restart file that the written script\
+        will read from"
+    parser.add_argument("-r", "--gpaw-restart-file", help=gpaw_restart_file)
+
+    input_struct_filename = "Name of the input structure that the written\
+        script will read from"
+    parser.add_argument(
+        "-is", "--input_struct_filename", help=input_struct_filename
+    )
+
+    overwrite_files = "To overwrite files or not, that is the question"
+    parser.add_argument("-ov", "--overwrite_files", help=overwrite_files)
+
+    from_scratch = "Whether the calculation should be run from scratch"
+    parser.add_argument("-fs", "--from-scratch", help=from_scratch)
+
+
+def generate_gpaw_input_files(args):
+    """Write input files for the input crystal structure."""
+    gig = GPAWInputGenerator(
+        crystal_structure=args.crystal_structure,
+        calculation_presets=args.calculation_presets,
+        custom_sett_file=args.custom_settings_file,
+        custom_sett_dict=args.custom_settings_dict,
+        write_location=args.write_location,
+        gpaw_input_file=args.gpaw_input_file,
+        gpaw_restart_file=args.gpaw_restart_file,
+        input_struct_filename=args.input_struct_filename,
+        overwrite_files=args.overwrite_files,
+        from_scratch=args.from_scratch,
+    )
+    gig.write_input_files()
+
+
+def run_demo(*sys_args):
+    """End-to-end run of pw.x input file generation."""
+    parser = _get_default_parser()
+    build_gpaw_parser(parser)
+    args = parser.parse_args(*sys_args)
+    generate_gpaw_input_files(args)
+
+
+if __name__ == "__main__":
+    """
+    When run as a script, this module will generate input files to use with
+    GPAW, for a specified crystal structure, calculation presets, and any
+    custom DFT settings on top of preset defaults.
+
+    For a list of optional arguments, run this script with "-h" argument.
+    """
+    run_demo()  # pragma: no cover

src/dftinputgen/gpaw/__init__.py

@@ -0,0 +1 @@
+from dftinputgen.gpaw.gpaw import GPAWInputGenerator  # noqa: F401