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="psaxe@molssi.org"
+
+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