Add JDFTx jobs.py to run JDFTx using atomate2/jobflow

src/custodian/jdftx/__init__.py

@@ -0,0 +1,4 @@
+"""
+This package implements various JDFTx Jobs and Error Handlers.
+Used Cp2kJob developed by Nick Winner as a template.
+"""

src/custodian/jdftx/jobs.py

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+"""This module implements basic kinds of jobs for JDFTx runs."""
+
+import logging
+import os
+import subprocess
+
+from custodian.custodian import Job
+
+logger = logging.getLogger(__name__)
+
+
+class JDFTxJob(Job):
+    """A basic JDFTx job. Runs whatever is in the working directory."""
+
+    # If testing, use something like:
+    # job = JDFTxJob()
+    # job.run()  # assumes input files already written to directory
+
+    def __init__(
+        self,
+        jdftx_cmd,
+        input_file="jdftx.in",
+        output_file="jdftx.out",
+        stderr_file="std_err.txt",
+    ) -> None:
+        """
+        This constructor is necessarily complex due to the need for
+        flexibility. For standard kinds of runs, it's often better to use one
+        of the static constructors. The defaults are usually fine too.
+
+        Args:
+            jdftx_cmd (str): Command to run JDFTx as a string.
+            input_file (str): Name of the file to use as input to JDFTx
+                executable. Defaults to "input.in"
+            output_file (str): Name of file to direct standard out to.
+                Defaults to "jdftx.out".
+            stderr_file (str): Name of file to direct standard error to.
+                Defaults to "std_err.txt".
+        """
+        self.jdftx_cmd = jdftx_cmd
+        self.input_file = input_file
+        self.output_file = output_file
+        self.stderr_file = stderr_file
+
+    def setup(self, directory="./") -> None:
+        """No setup required."""
+
+    def run(self, directory="./"):
+        """
+        Perform the actual JDFTx run.
+
+        Returns:
+        -------
+            (subprocess.Popen) Used for monitoring.
+        """
+        cmd = self.jdftx_cmd + " -i " + self.input_file + " -o " + self.output_file
+        logger.info(f"Running {cmd}")
+        with (
+            open(os.path.join(directory, self.output_file), "w") as f_std,
+            open(os.path.join(directory, self.stderr_file), "w", buffering=1) as f_err,
+        ):
+            # use line buffering for stderr
+            return subprocess.run(
+                cmd.split(),
+                cwd=directory,
+                stdout=f_std,
+                stderr=f_err,
+                shell=False,
+                check=False,
+            )
+
+    def postprocess(self, directory="./") -> None:
+        """No post-processing required."""
+
+    def terminate(self, directory="./") -> None:
+        """Terminate JDFTx."""
+        # This will kill any running process with "jdftx" in the name,
+        # this might have unintended consequences if running multiple jdftx processes
+        # on the same node.
+        for cmd in self.jdftx_cmd:
+            if "jdftx" in cmd:
+                try:
+                    os.system(f"killall {cmd}")
+                except Exception as e:
+                    print(f"Unexpected error occurred: {e}")
+                    raise