Update to instruments

.gitignore

@@ -3,6 +3,5 @@ __pycache__
 *.rst
 .sphinx/build/*
 .sphinx/source/media/*
-jobrunner/options.py
 !.sphinx/source/index.rst
 !./README.rst

README.rst

@@ -48,7 +48,7 @@ customization specific to instruments.
 
    pip install PyJobruner --user --install-option="--with-instruments"
 
-This allow for the use of the ``instrument:`` field in the Jobfile
+This allow for the use of the ``instrument`` field in the Jobfile
 
 There maybe situations where users may want to install Jobrunner in
 development mode $\\textemdash$ to design new features, debug, or
@@ -225,7 +225,7 @@ The ``Jobfile`` at this node assigns the use of ``environment.sh``,
 
    # file: Project/Jobfile
 
-   instrument: flashx
+   instrument: Flash-X
 
    # Scripts to include during jobrunner setup and submit commands
    job:

jobrunner/__meta__.py

@@ -1,7 +1,7 @@
 """Metadata for jobrunner"""
 
 __pkgname__ = "PyJobRunner"
-__version__ = "2023.11.01"
+__version__ = "2023.11.2"
 __authors__ = "Akash Dhruv"
 __license__ = "Apache Software License"
 __copyright__ = "Copyright (c) Akash Dhruv 2023. All Rights Reserved."

jobrunner/api/_commands.py

@@ -75,11 +75,11 @@ def submit(dirlist, verbose=False):
         config = lib.ParseJobConfig(basedir, workdir)
 
         # Build inputfile
-        lib.CreateInputFile(config)
         if config.job.input:
             print(f"\n{lib.Color.purple}INPUT: {lib.Color.end}")
             for value in config.job.input:
                 print(f'{" "*4}- {value.replace(basedir,"<ROOT>")}')
+        lib.CreateInputFile(config)
 
         # Build targetfile
         lib.CreateTargetFile(config)

jobrunner/instruments/flashx.py

@@ -2,6 +2,9 @@
 
 import os
 import toml
+import numpy
+import h5py
+from scipy.stats import qmc
 
 
 def CreateParfile(workdir):
@@ -29,6 +32,9 @@ def CreateParfile(workdir):
         # Loop over keys in the input dictionary to and start building the parfile
         for group in input_dict:
 
+            if not group.isupper():
+                raise ValueError(f'[jobrunner] Group "{group}" should be uppercase')
+
             # Indicate which key the following runtime parameters belong to
             parfile.write(f"\n# Runtime parameters for {group}\n")
 
@@ -39,7 +45,7 @@ def CreateParfile(workdir):
                 # more complex configuration which will not be handled.
                 if type(value) == dict:
                     print(
-                        f"[jobrunner] {group}.{key} is a dictionary and will not be handled "
+                        f'{" "*4}[jobrunner] {group}.{key} is a dictionary and will not be handled '
                         + "during Flash-X parfile generation"
                     )
 
@@ -55,3 +61,145 @@ def CreateParfile(workdir):
                     # Deal with rest
                     else:
                         parfile.write(f"{key} = {value}\n")
+
+
+def CreateHeater(workdir):
+    """
+    Create hdf5 input files based on heater configuration. This functionality
+    is only available when "instrument" is defined in the Jobfile, and jobrunner
+    is installed with the option --with-instrument
+    """
+    # Load TOML dictionary for JobWorkDir/job.input, JobWorkDir is a
+    # reserved environment variable for
+    input_dict = toml.load(workdir + os.sep + "job.input")
+
+    # Return immediately if HEATER not present in input dictionary
+    if "HEATER" not in input_dict.keys():
+        return
+
+    # If we are here then HEATER is present in the input dictionary
+    # and we can safely load the corresponding heater dictionary
+    heater_dict = input_dict["HEATER"]
+
+    # Set a counter to track how many heater files are being written
+    # and then loop over items in heater dictionary
+    num_heaters = 0
+    for key, info in heater_dict.items():
+
+        # if info is of type dictionary we have hit a heater configuration
+        # that needs to be written to a file. Start implementing that logic
+        if type(info) == dict:
+
+            # Increase heater counter to track number of heaters
+            num_heaters = num_heaters + 1
+
+            # Set filename and open the hdf5 file in write mode
+            filename = (
+                workdir + os.sep + heater_dict["sim_heaterName"] + "_hdf5_htr_" + key
+            )
+            hfile = h5py.File(filename, "w")
+
+            xsite = numpy.ndarray([info["numSites"]], dtype=float)
+            ysite = numpy.ndarray([info["numSites"]], dtype=float)
+            zsite = numpy.ndarray([info["numSites"]], dtype=float)
+            radii = numpy.ndarray([info["numSites"]], dtype=float)
+
+            if info["numSites"] == 1:
+                xsite[:] = 0.0
+                ysite[:] = 1e-13
+                zsite[:] = 0.0
+                radii[:] = 0.2
+
+            else:
+                halton = qmc.Halton(d=2, seed=1)
+                sample = halton.random(info["numSites"])
+
+                xsite[:] = info["xmin"] + sample[:, 0] * (info["xmax"] - info["xmin"])
+                ysite[:] = 1e-13
+                radii[:] = 0.2
+
+                if info["dim"] == 1:
+                    zsite[:] = 0.0
+                elif info["dim"] == 2:
+                    zsite[:] = info["zmin"] + sample[:, 1] * (
+                        info["zmax"] - info["zmin"]
+                    )
+                else:
+                    raise ValueError(f"[jobrunner] Error in HEATER.{key}.dim")
+
+            hfile.create_dataset(
+                "heater/xMin", data=info["xmin"], shape=(1), dtype="float32"
+            )
+            hfile.create_dataset(
+                "heater/xMax", data=info["xmax"], shape=(1), dtype="float32"
+            )
+            hfile.create_dataset(
+                "heater/zMin", data=info["zmin"], shape=(1), dtype="float32"
+            )
+            hfile.create_dataset(
+                "heater/zMax", data=info["zmax"], shape=(1), dtype="float32"
+            )
+            hfile.create_dataset(
+                "heater/yMin", data=info["ymin"], shape=(1), dtype="float32"
+            )
+            hfile.create_dataset(
+                "heater/yMax", data=info["ymax"], shape=(1), dtype="float32"
+            )
+            hfile.create_dataset(
+                "heater/wallTemp",
+                data=info["wallTemp"],
+                shape=(1),
+                dtype="float32",
+            )
+            hfile.create_dataset(
+                "heater/advAngle",
+                data=info["advAngle"],
+                shape=(1),
+                dtype="float32",
+            )
+            hfile.create_dataset(
+                "heater/rcdAngle",
+                data=info["rcdAngle"],
+                shape=(1),
+                dtype="float32",
+            )
+            hfile.create_dataset(
+                "heater/velContact",
+                data=info["velContact"],
+                shape=(1),
+                dtype="float32",
+            )
+            hfile.create_dataset(
+                "heater/nucWaitTime",
+                data=info["nucWaitTime"],
+                shape=(1),
+                dtype="float32",
+            )
+            hfile.create_dataset(
+                "site/num", data=info["numSites"], shape=(1), dtype="int32"
+            )
+            hfile.create_dataset(
+                "site/x", data=xsite, shape=(info["numSites"]), dtype="float32"
+            )
+            hfile.create_dataset(
+                "site/y", data=ysite, shape=(info["numSites"]), dtype="float32"
+            )
+            hfile.create_dataset(
+                "site/z", data=zsite, shape=(info["numSites"]), dtype="float32"
+            )
+            hfile.create_dataset(
+                "init/radii",
+                data=radii,
+                shape=(info["numSites"]),
+                dtype="float32",
+            )
+            hfile.close()
+
+            print(
+                f'{" "*4}[jobrunner] Wrote heater information to file {filename.replace(workdir + os.sep,"")}'
+            )
+
+    if num_heaters != heater_dict["sim_numHeaters"]:
+        raise ValueError(
+            f"[jobrunner] Number of heater files not equal to sim_numHeaters"
+        )

jobrunner/lib/_filetools.py

@@ -108,8 +108,9 @@ def CreateInputFile(config):
             #        else:
             #            inputfile.write(f'{" "*2}{variable} = {value}\n')
 
-        if config.instrument == "flashx" and options.INSTRUMENTS == 1:
+        if config.instrument == "Flash-X" and options.INSTRUMENTS == 1:
             instruments.flashx.CreateParfile(config.job.workdir)
+            instruments.flashx.CreateHeater(config.job.workdir)
 
 
 def CreateTargetFile(config):