Merge pull request #37 from paulsaxe/main

Finalized support for Docker.

.github/workflows/Release.yaml

@@ -13,3 +13,14 @@ jobs:
  with:
  src : dftbplus_step
  secrets: inherit
+
+ docker:
+ name: Docker
+ needs: release
+ uses: molssi-seamm/devops/.github/workflows/Docker.yaml@main
+ with:
+ image : molssi-seamm/seamm-dftbplus
+ description: A DFTB+ executable packaged for use with SEAMM or standalone
+ # Can limit platforms, e.g., linux/amd64, linux/arm64
+ # platforms: linux/amd64
+ secrets: inherit

HISTORY.rst

@@ -1,6 +1,12 @@
 =======
 History
 =======
+2024.4.24 -- Finalized support for Docker containers
+ * Fixed issues and tested running in containers.
+ * Add CI to make a Docker image for DFTB+
+ * Fixed issue with changes in input for DFTB+: CalculateGradients has become
+ PrintGradients it seems.
+
 2024.1.18 -- Support for running in containers and writing input only.
  * Added new property: scaled dipole.
  * Added option to write the input file and not run DFTB+

Makefile

@@ -1,7 +1,7 @@
 MODULE := dftbplus_step
 .PHONY: help clean clean-build clean-docs clean-pyc clean-test lint format typing test
 .PHONY: dependencies test-all coverage html docs servedocs release check-release
-.PHONY: dist install uninstall
+.PHONY: dist install uninstall image uninstall-image
 .DEFAULT_GOAL := help
 
 define BROWSER_PYSCRIPT
@@ -104,3 +104,9 @@ install: uninstall ## install the package to the active Python's site-packages
 
 uninstall: clean ## uninstall the package
  pip uninstall --yes $(MODULE)
+
+image: uninstall-image ## Make the Docker image
+ cd devtools/docker && docker image build -t ghcr.io/molssi-seamm/seamm-dftbplus:latest .
+
+uninstall-image: ## Remove the docker image
+ docker image rm --force ghcr.io/molssi-seamm/seamm-dftbplus:latest

devtools/docker/Dockerfile

@@ -0,0 +1,19 @@
+FROM molssi/mamba141
+
+LABEL org.opencontainers.image.authors="[email protected]"
+
+COPY ./environment.yml /root/environment.yml
+
+RUN mamba env update -f /root/environment.yml
+
+RUN apt-get install -qy curl
+
+RUN mkdir /root/Parameters \
+ && cd /root/Parameters \
+ && curl 'https://dftb.org/fileadmin/DFTB/public/slako-unpacked.tar.xz' -o slako-unpacked.tar.xz \
+ && tar -x -o -p -f slako-unpacked.tar.xz \
+ && chmod -R go+rX . \
+ && rm slako-unpacked.tar.xz
+
+WORKDIR /home
+CMD ["dftb+"]

devtools/docker/environment.yml

@@ -0,0 +1,10 @@
+name: base
+channels:
+ - conda-forge
+dependencies:
+ - python
+ # Executables, etc.
+ - dftbplus
+ - dftbplus-tools
+ - dftbplus-python
+

dftbplus_step/base.py

@@ -107,6 +107,11 @@ def model(self):
  def model(self, value):
  self.parent.model = value
 
+ @property
+ def exe_config(self):
+ """The configuration for the DFTB+ executable."""
+ return self.parent.exe_config
+
  def band_structure(
  self, input_path, sym_points, sym_names, Efermi=[0.0, 0.0], DOS=None
  ):
@@ -158,13 +163,6 @@ def create_band_structure_data(
  full_config.read(ini_dir / "dftbplus.ini")
 
  executor = self.parent.flowchart.executor
- executor_type = executor.name
- if executor_type not in full_config:
- raise RuntimeError(
- f"No section for '{executor_type}' in DFTB+ ini file "
- f"({ini_dir / 'dftbplus.ini'})"
- )
- config = dict(full_config.items(executor_type))
 
  if spin_polarized:
  cmd = ["dp_bands", "-s", input_path, "band"]
@@ -173,7 +171,7 @@ def create_band_structure_data(
 
  result = executor.run(
  cmd=cmd,
- config=config,
+ config=self.exe_config,
  directory=self.directory,
  files={},
  return_files=["*"],
@@ -271,34 +269,16 @@ def create_dos_data(self, input_path, Efermi=[0.0]):
 
  logger.info("Preparing DOS")
 
- seamm_options = self.parent.global_options
-
  # Total DOS
  executor = self.parent.flowchart.executor
 
- # Read configuration file for DFTB+
- ini_dir = Path(seamm_options["root"]).expanduser()
- full_config = configparser.ConfigParser()
- full_config.read(ini_dir / "dftbplus.ini")
- executor_type = executor.name
- if executor_type not in full_config:
- raise RuntimeError(
- f"No section for '{executor_type}' in DFTB+ ini file "
- f"({ini_dir / 'dftbplus.ini'})"
- )
- config = dict(full_config.items(executor_type))
-
  result = executor.run(
  cmd=[
  "dp_dos",
  str(input_path),
  "dos_total.dat",
- ">",
- "DOS.out",
- "2>",
- "dos_stderr.txt",
  ],
- config=config,
+ config=self.exe_config,
  directory=self.directory,
  files={},
  return_files=["*"],
@@ -369,12 +349,8 @@ def create_dos_data(self, input_path, Efermi=[0.0]):
  "-w",
  str(path),
  str(out),
- ">",
- "DOS.out",
- "2>",
- "dos_stderr.txt",
  ],
- config=config,
+ config=self.exe_config,
  directory=self.directory,
  files={},
  return_files=["*"],
@@ -788,26 +764,14 @@ def run(self, current_input):
  "results.tag",
  "*.xml",
  "eigenvec.bin",
- ] # yapf: disable
+ ]
 
  # Run the calculation
  executor = self.parent.flowchart.executor
 
- # Read configuration file for DFTB+
- ini_dir = Path(seamm_options["root"]).expanduser()
- full_config = configparser.ConfigParser()
- full_config.read(ini_dir / "dftbplus.ini")
- executor_type = executor.name
- if executor_type not in full_config:
- raise RuntimeError(
- f"No section for '{executor_type}' in DFTB+ ini file "
- f"({ini_dir / 'dftbplus.ini'})"
- )
- config = dict(full_config.items(executor_type))
-
  result = executor.run(
  cmd=["{code}", ">", "DFTB+.out", "2>", "stderr.txt"],
- config=config,
+ config=self.exe_config,
  directory=self.directory,
  files=files,
  return_files=return_files,
@@ -816,7 +780,7 @@ def run(self, current_input):
  env=env,
  )
 
- if result is None:
+ if not result:
  logger.error("There was an error running DFTB+")
  return None
 

dftbplus_step/choose_parameters.py

@@ -74,7 +74,7 @@ def get_input(self):
 
  # Get the metadata for the Slater-Koster parameters
  metadata = self.parent._metadata
- slako_dir = Path(self.parent.options["slako_dir"]).expanduser()
+ slako_dir = Path(self.exe_config["slako-dir"]).expanduser()
 
  # Create the directory
  directory = Path(self.directory)

dftbplus_step/data/configuration.txt

@@ -1,27 +1,4 @@
 [dftbplus-step]
-
-# Information about where/how the executables are installed
-# installation may be 'user', 'conda' or 'module'. If a module is
-# specified it will be loaded and those executables used. In this
-# case, any path specified using dftbplus-path will be ignored.
-
-installation = 
-conda-environment = 
-modules = 
-
-# The path to the executable. Can be empty or not present, in which
-# case the default PATH is used. If a path is given, dftb+
-# from this location will be used.
-#
-# Ignored if a module is used. The default is to use the PATH
-# environment variable.
-
-dftbplus-path = 
-
-# The path to the Slater-Koster functions
-
-slako-dir = 
-
 # Whether to use MPI to run parallel
 
 # use-mpi = False

dftbplus_step/data/dftbplus.ini

@@ -0,0 +1,80 @@
+# Configuration options for how to run DFTB+
+
+[docker]
+# The code to use. This may maybe more than just the name of the code, and variables in
+# braces {} will be expanded. For example:
+# code = mpiexec -np {NTASKS} lmp_mpi
+# would expand {NTASKS} to the number of tasks and run the command
+
+code = dftb+
+
+# The name and location of the Docker container to use, optionally with the version
+
+container = ghcr.io/molssi-seamm/seamm-dftbplus:{version}
+
+# In addition, you can specify the platform to use. This is useful on e.g. Macs with
+# app silicon (M1, M3...) where the default platform is linux/arm64 but some containers
+# are only available for linux/amd64.
+
+# platform = linux/amd64
+
+# The path to the Slater-Koster functions
+
+slako-dir = /root/Parameters/slako
+
+
+[local]
+# The type of local installation to use. Options are:
+# conda: Use a conda environment
+# modules: Use the modules system
+# local: Use a local installation
+# docker: Use a Docker container
+# By default SEAMM installs DFTB+ using conda.
+
+installation = conda
+
+# The command line to use, which should start with the executable followed by any options.
+# Variables in braces {} will be expanded. For example:
+#
+# code = mpiexec -np {NTASKS} lmp_mpi
+#
+# would expand {NTASKS} to the number of tasks and run the command.
+# For a 'local' installation, the command line should include the full path to the
+# executable or it should be in the path. 
+
+code = dftb+
+
+######################### conda section ############################
+# The full path to the conda executable:
+
+# conda = 
+
+# The Conda environment to use. This is either the name or full path.
+
+conda-environment = seamm-dftbplus
+
+######################### modules section ############################
+# The modules to load to run DFTB+, as a list of strings.
+# For example, to load the modules dftbplus and openmpi, you would use:
+# modules = dftbplus openmpi
+
+# modules = 
+
+######################### local section ############################
+# The full path to the DFTB+ executable should be in the 'code' option.
+
+######################### docker section ############################
+# The name and location of the Docker container to use, optionally with the version.
+# {version} will be expanded to the version of the plug-in.
+
+# container = ghcr.io/molssi-seamm/seamm-dftbplus:{version}
+
+# In addition, you can specify the platform to use. This is useful on e.g. Macs with
+# app silicon (M1, M3...) where the default platform is linux/arm64 but some containers
+# are only available for linux/amd64.
+
+# platform = linux/amd64
+
+# The path to the Slater-Koster functions
+
+slako-dir = ~/SEAMM/Parameters/slako