Mod: improved cli commands
Mod: new database entries (porosity, volumeCell, ...) + some fixes Fix: foamClean function now cleans numbered directories
This commit is contained in:
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de9d3331d0
commit
4ecacecd34
@ -97,7 +97,7 @@ def init(path):
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from anisotropy import env
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from anisotropy.core.main import Database
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if not os.path.exist(path) or not os.path.isdir(path):
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if not os.path.exists(path) or not os.path.isdir(path):
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click.echo(f"Cannot find directory { path }")
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return
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@ -154,12 +154,12 @@ def update(force, params, path):
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model = Anisotropy()
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model.db = Database(env["db_name"], env["db_path"])
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database = Database(env["db_name"], env["db_path"])
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click.echo("Configuring database ...")
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model.db.setup()
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database.setup()
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if model.db.isempty() or update:
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if database.isempty() or update:
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paramsAll = model.loadFromScratch(env["CONFIG"])
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if args.get("type"):
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@ -172,7 +172,7 @@ def update(force, params, path):
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paramsAll = [ entry for entry in paramsAll if args["theta"] == entry["structure"]["theta"] ]
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for entry in paramsAll:
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model.db.update(entry)
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database.update(entry)
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click.echo("{} entries was updated.".format(len(paramsAll)))
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@ -188,7 +188,7 @@ def update(force, params, path):
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)
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@click.option(
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"-s", "--stage", "stage",
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type = click.Choice(["all", "mesh", "flow"]),
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type = click.Choice(["all", "mesh", "flow", "postProcessing"]),
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default = "all",
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help = "Current computation stage"
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)
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@ -219,7 +219,7 @@ def update(force, params, path):
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def compute(stage, nprocs, force, params, path):
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from anisotropy import env
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from anisotropy.core.main import Anisotropy, Database, logger
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from anisotropy.core.utils import setupLogger, timer, parallel
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from anisotropy.core.utils import setupLogger, parallel
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env.update(
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LOG = os.path.join(path, "logs"),
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@ -236,70 +236,20 @@ def compute(stage, nprocs, force, params, path):
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###
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logger.info("Writing pid ...")
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pidpath = os.path.join(path, "anisotropy.pid")
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with open(os.path.join(path, "anisotropy.pid"), "w") as io:
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with open(pidpath, "w") as io:
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io.write(str(os.getpid()))
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###
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model = Anisotropy()
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model.db = Database(env["db_name"], env["db_path"])
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# Preparations
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##
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database = Database(env["db_name"], env["db_path"])
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logger.info("Loading database ...")
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model.db.setup()
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database.setup()
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###
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def computeCase(stage, type, direction, theta):
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case = Anisotropy()
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case.load(type, direction, theta)
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case.evalParams()
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case.update()
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logger.info(f"Case: type = { type }, direction = { direction }, theta = { theta }")
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logger.info(f"Stage: { stage }")
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if stage == "all" or stage == "mesh":
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if not case.params.get("meshresult", {}).get("meshStatus") == "Done" or force:
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(out, err, returncode), elapsed = timer(case.computeMesh)(path)
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if out: logger.info(out)
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if err: logger.error(err)
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case.load(type, direction, theta)
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if case.params.get("meshresult"):
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case.params["meshresult"]["meshCalculationTime"] = elapsed
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case.update()
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if returncode:
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logger.error("Mesh computation failed. Skipping flow computation ...")
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return
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else:
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logger.info("Mesh exists. Skipping ...")
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if stage == "all" or stage == "flow":
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if not case.params.get("flowresult", {}).get("flowStatus") == "Done" or force:
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(out, err, returncode), elapsed = timer(case.computeFlow)(path)
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if out: logger.info(out)
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if err: logger.error(err)
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case.load(type, direction, theta)
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if case.params.get("flowresult"):
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case.params["flowresult"]["flowCalculationTime"] = elapsed
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case.update()
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if returncode:
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logger.error("Flow computation failed.")
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return
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else:
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logger.info("Flow exists. Skipping ...")
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###
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params = model.db.loadGeneral(
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params = database.loadGeneral(
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args.get("type"),
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args.get("direction"),
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args.get("theta")
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@ -309,8 +259,76 @@ def compute(stage, nprocs, force, params, path):
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for p in params:
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s = p["structure"]
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queueargs.append((stage, s["type"], s["direction"], s["theta"]))
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queueargs.append((s["type"], s["direction"], s["theta"]))
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###
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# Wrap function
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##
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def computeCase(type, direction, theta):
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case = Anisotropy()
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case.db = database
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case.load(type, direction, theta)
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case.evalParams()
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case.update()
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logger.info(f"Case: type = { type }, direction = { direction }, theta = { theta }")
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logger.info(f"Stage mode: { stage }")
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if stage in ["mesh", "all"]:
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case.load(type, direction, theta)
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if not case.params["meshresult"]["meshStatus"] == "Done" or force:
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logger.info("Current stage: mesh")
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out, err, returncode = case.computeMesh(path)
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if out: logger.info(out)
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if err: logger.error(err)
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if returncode:
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logger.error("Mesh computation failed. Skipping flow computation ...")
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return
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else:
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logger.info("Mesh exists. Skipping ...")
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if stage in ["flow", "all"]:
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case.load(type, direction, theta)
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if not case.params["flowresult"]["flowStatus"] == "Done" or force:
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logger.info("Current stage: flow")
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out, err, returncode = case.computeFlow(path)
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if out: logger.info(out)
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if err: logger.error(err)
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if returncode:
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logger.error("Flow computation failed.")
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return
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else:
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logger.info("Flow exists. Skipping ...")
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if stage in ["postProcessing", "all"]:
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case.load(type, direction, theta)
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if case.params["meshresult"]["meshStatus"] == "Done":
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logger.info("Current stage: mesh postProcessing")
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case.porosity()
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else:
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logger.warning("Cannot compute mesh post processing values.")
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if case.params["flowresult"]["flowStatus"] == "Done":
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logger.info("Current stage: flow postProcessing")
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case.flowRate()
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else:
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logger.warning("Cannot compute flow post processing values.")
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###
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# Run
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##
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if nprocs == 1:
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for pos, qarg in enumerate(queueargs):
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computeCase(*qarg)
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@ -318,6 +336,12 @@ def compute(stage, nprocs, force, params, path):
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else:
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parallel(nprocs, queueargs, computeCase)
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if os.path.exists(pidpath):
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logger.info("Removing pid ...")
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os.remove(pidpath)
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logger.info("Computation done.")
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@anisotropy.command(
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help = "Kill process by pid file"
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@ -369,7 +393,7 @@ def computemesh(root, type, direction, theta, path):
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##
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import os, sys
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pyversion = "{}.{}".format(*sys.version_info[:2])
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pyversion = "{}.{}".format(3, 9) #(*sys.version_info[:2])
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sys.path.extend([
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root,
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os.path.join(root, "env/lib/python{}/site-packages".format(pyversion)),
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@ -493,14 +517,14 @@ def show(params, path, printlist, export, fields, output):
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else:
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tables.append(df)
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fig, ax = plt.subplots(nrows = 1, ncols = 1)
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if output == "plot":
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fig, ax = plt.subplots(nrows = 1, ncols = 1)
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for table in tables:
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table.plot(table.keys()[0], table.keys()[1], ax = ax, style = "o")
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for table in tables:
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table.plot(table.keys()[0], table.keys()[1], ax = ax, style = "o")
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plt.legend()
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plt.grid()
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#plt.show()
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plt.legend()
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plt.grid()
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if export:
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supported = ["csv", "jpg"]
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@ -537,19 +561,19 @@ def show(params, path, printlist, export, fields, output):
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# CLI entry
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##
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if __name__ == "__main__":
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try:
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#try:
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anisotropy()
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except KeyboardInterrupt:
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click.echo("Interrupted!")
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#except KeyboardInterrupt:
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# click.echo("Interrupted!")
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finally:
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from anisotropy.salomepl.utils import SalomeManager
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click.echo("Exiting ...")
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#finally:
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# from anisotropy.salomepl.utils import SalomeManager
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# click.echo("Exiting ...")
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if os.path.exists("anisotropy.pid"):
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os.remove("anisotropy.pid")
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# if os.path.exists("anisotropy.pid"):
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# os.remove("anisotropy.pid")
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SalomeManager().killall()
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# SalomeManager().killall()
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sys.exit(0)
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# sys.exit(0)
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@ -16,7 +16,7 @@ from anisotropy import (
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__version__, env,
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openfoam
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)
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from anisotropy.core.utils import setupLogger, timer
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from anisotropy.core.utils import setupLogger, Timer
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from anisotropy.core.database import Database
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from anisotropy import salomepl
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import anisotropy.salomepl.utils
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@ -38,7 +38,7 @@ class Anisotropy(object):
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"""Constructor method"""
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self.env = env
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self.db = Database(self.env["db_name"], self.env["db_path"])
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self.db = None #Database(self.env["db_name"], self.env["db_path"])
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self.params = []
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@ -63,8 +63,8 @@ class Anisotropy(object):
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def version():
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"""Returns versions of all used main programs
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:return: Versions joined by next line symbol
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:rtype: str
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:return:
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Versions joined by next line symbol
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"""
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versions = {
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"anisotropy": __version__,
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@ -86,8 +86,8 @@ class Anisotropy(object):
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def loadFromScratch(self, configpath: str = None) -> list:
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"""Loads parameters from configuration file and expands special values
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:return: List of dicts with parameters
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:rtype: list
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:return:
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List of dicts with parameters
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"""
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config = configpath or self.env["CONFIG"]
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@ -131,8 +131,10 @@ class Anisotropy(object):
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),
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"mesh": mesh,
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"submesh": deepcopy(entry["submesh"]),
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"meshresult": dict(),
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"flow": deepcopy(entry["flow"]),
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"flowapproximation": deepcopy(entry["flowapproximation"])
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"flowapproximation": deepcopy(entry["flowapproximation"]),
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"flowresult": dict(),
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}
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# For `type = fixedValue` only
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@ -251,13 +253,33 @@ class Anisotropy(object):
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manager = salomepl.utils.SalomeManager()
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casepath = self.getCasePath(path)
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return manager.execute(
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self.params["meshresult"]["meshStatus"] = "Computing"
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self.update()
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timer = Timer()
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out, err, returncode = manager.execute(
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scriptpath,
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*salomeargs,
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timeout = self.env["salome_timeout"],
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root = self.env["ROOT"],
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logpath = casepath
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)
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self.load(p["type"], p["direction"], p["theta"])
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if not returncode:
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self.params["meshresult"].update(
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meshStatus = "Done",
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meshCalculationTime = timer.elapsed()
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)
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else:
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self.params["meshresult"].update(
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meshStatus = "Failed"
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)
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self.update()
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return out, err, returncode
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def genmesh(self, path):
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@ -280,7 +302,8 @@ class Anisotropy(object):
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bodyCentered = BodyCentered,
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faceCentered = FaceCentered
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)[p["structure"]["type"]]
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shape, groups = structure(**p["structure"]).build()
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shapeGeometry = structure(**p["structure"])
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shape, groups = shapeGeometry.build()
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[length, surfaceArea, volume] = geompy.BasicProperties(shape, theTolerance = 1e-06)
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@ -312,6 +335,7 @@ class Anisotropy(object):
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if mp["viscousLayers"]:
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mesh.ViscousLayers(**mp, faces = faces)
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# Submesh
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smp = p["submesh"]
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for submesh in smp:
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@ -333,7 +357,7 @@ class Anisotropy(object):
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###
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# Results
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##
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p["meshresult"] = dict()
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#p["meshresult"] = dict()
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if not returncode:
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mesh.removePyramids()
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@ -349,9 +373,9 @@ class Anisotropy(object):
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meshStats = mesh.stats()
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p["meshresult"].update(
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status = "Done",
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surfaceArea = surfaceArea,
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volume = volume,
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volumeCell = shapeGeometry.volumeCell,
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**meshStats
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)
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self.update()
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@ -360,9 +384,9 @@ class Anisotropy(object):
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logger.error(err)
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p["meshresult"].update(
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status = "Failed",
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surfaceArea = surfaceArea,
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volume = volume
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volume = volume,
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volumeCell = shapeGeometry.volumeCell
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)
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self.update()
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@ -370,23 +394,30 @@ class Anisotropy(object):
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def computeFlow(self, path):
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"""Computes a flow on mesh via OpenFOAM
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:return: Process output, error messages and returncode
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:rtype: tuple(str, str, int)
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:return:
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Process output, error messages and returncode
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"""
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###
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# Case preparation
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##
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foamCase = [ "0", "constant", "system" ]
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#self.params["flowresult"] = dict()
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self.params["flowresult"]["flowStatus"] = "Computing"
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self.update()
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timer = Timer()
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flow = self.params["flow"]
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flowapproximation = self.params["flowapproximation"]
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# ISSUE: ideasUnvToFoam cannot import mesh with '-case' flag so 'os.chdir' for that
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casePath = self.getCasePath()
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casePath = self.getCasePath(path)
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if not os.path.exists(casePath):
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logger.warning(f"Cannot find case path. Skipping computation ...\n\t{ casePath }")
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return "", "", 1
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err = f"Cannot find case path { casePath }"
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self.params["flowresult"]["flowStatus"] = "Failed"
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self.update()
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return "", err, 1
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os.chdir(casePath)
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openfoam.foamClean()
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@ -401,14 +432,22 @@ class Anisotropy(object):
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# Mesh manipulations
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##
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if not os.path.exists("mesh.unv"):
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logger.error(f"missed 'mesh.unv'")
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os.chdir(path or self.env["ROOT"])
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return "", "", 1
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err = f"Missed 'mesh.unv'"
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self.params["flowresult"]["flowStatus"] = "Failed"
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self.update()
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return "", err, 1
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out, err, returncode = openfoam.ideasUnvToFoam("mesh.unv")
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if returncode:
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os.chdir(path or self.env["ROOT"])
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self.params["flowresult"]["flowStatus"] = "Failed"
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self.update()
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return out, err, returncode
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openfoam.createPatch(dictfile = "system/createPatchDict")
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@ -424,10 +463,9 @@ class Anisotropy(object):
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"1 (wall)"
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)
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out = openfoam.checkMesh()
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out, err, returncode = openfoam.checkMesh()
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if out:
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logger.info(out)
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if out: logger.warning(out)
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openfoam.transformPoints(flow["scale"])
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@ -442,7 +480,7 @@ class Anisotropy(object):
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str(flow["transportProperties"]["nu"])
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)
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#openfoam.decomposePar()
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# openfoam.decomposePar()
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openfoam.renumberMesh()
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@ -499,33 +537,44 @@ class Anisotropy(object):
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out, err, returncode = openfoam.simpleFoam()
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###
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# Results
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##
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self.params["flowresult"] = dict()
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if not returncode:
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postProcessing = "postProcessing/flowRatePatch(name=outlet)/0/surfaceFieldValue.dat"
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|
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with open(os.path.join(casePath, postProcessing), "r") as io:
|
||||
lastLine = io.readlines()[-1]
|
||||
flowRate = float(lastLine.replace(" ", "").replace("\n", "").split("\t")[1])
|
||||
|
||||
self.params["flowresult"].update(
|
||||
status = "Done",
|
||||
flowRate = flowRate
|
||||
)
|
||||
self.params["flowresult"]["flowCalculationTime"] = timer.elapsed()
|
||||
self.params["flowresult"]["flowStatus"] = "Done"
|
||||
|
||||
else:
|
||||
self.params["flowresult"].update(
|
||||
status = "Failed"
|
||||
)
|
||||
|
||||
self.params["flowresult"]["flowStatus"] = "Failed"
|
||||
|
||||
self.update()
|
||||
|
||||
os.chdir(self.env["ROOT"])
|
||||
os.chdir(path or self.env["ROOT"])
|
||||
|
||||
return out, str(err, "utf-8"), returncode
|
||||
|
||||
|
||||
def flowRate(self):
|
||||
casePath = self.getCasePath()
|
||||
foamPostProcessing = "postProcessing/flowRatePatch(name=outlet)/0/surfaceFieldValue.dat"
|
||||
path = os.path.join(casePath, foamPostProcessing)
|
||||
|
||||
if not os.path.exists(path):
|
||||
logger.warning(f"Unable to compute flow rate. Missed { path }")
|
||||
|
||||
return
|
||||
|
||||
with open(path, "r") as io:
|
||||
lastLine = io.readlines()[-1]
|
||||
flowRate = float(lastLine.replace(" ", "").replace("\n", "").split("\t")[1])
|
||||
|
||||
self.params["flowresult"]["flowRate"] = flowRate
|
||||
self.update()
|
||||
|
||||
return flowRate
|
||||
|
||||
|
||||
def porosity(self):
|
||||
mr = self.params["meshresult"]
|
||||
fr = self.params["flowresult"]
|
||||
|
||||
fr["porosity"] = mr["volume"] / mr["volumeCell"]
|
||||
self.update()
|
||||
|
||||
return fr["porosity"]
|
||||
|
||||
@ -129,6 +129,7 @@ class MeshResult(BaseModel):
|
||||
|
||||
surfaceArea = FloatField(null = True)
|
||||
volume = FloatField(null = True)
|
||||
volumeCell = FloatField(null = True)
|
||||
|
||||
elements = IntegerField(null = True)
|
||||
edges = IntegerField(null = True)
|
||||
|
||||
@ -205,6 +205,13 @@ def timer(func: FunctionType) -> (tuple, float):
|
||||
return inner
|
||||
|
||||
|
||||
class Timer(object):
|
||||
def __init__(self):
|
||||
self.start = time.monotonic()
|
||||
|
||||
def elapsed(self):
|
||||
return time.monotonic() - self.start
|
||||
|
||||
|
||||
def queue(cmd, qin, qout, *args):
|
||||
|
||||
|
||||
@ -22,7 +22,7 @@ def transformPoints(scale, case: str = None):
|
||||
|
||||
|
||||
def checkMesh(case: str = None) -> str:
|
||||
application("checkMesh", "-allGeometry", "-allTopology", case = case, stderr = True)
|
||||
_, err, returncode = application("checkMesh", "-allGeometry", "-allTopology", case = case, stderr = True)
|
||||
out = ""
|
||||
|
||||
with open("checkMesh.log", "r") as io:
|
||||
@ -34,7 +34,7 @@ def checkMesh(case: str = None) -> str:
|
||||
if warnings:
|
||||
out = "checkMesh:\n\t{}".format("\n\t".join(warnings))
|
||||
|
||||
return out
|
||||
return out, err, returncode
|
||||
|
||||
|
||||
def renumberMesh(case: str = None):
|
||||
|
||||
@ -4,12 +4,13 @@
|
||||
|
||||
import os
|
||||
import shutil
|
||||
from .application import application
|
||||
|
||||
def version() -> str:
|
||||
return os.environ["WM_PROJECT_VERSION"]
|
||||
|
||||
|
||||
def foamClean(case: str = None):
|
||||
def foamCleanCustom(case: str = None):
|
||||
rmDirs = ["0", "constant", "system", "postProcessing", "logs"]
|
||||
rmDirs.extend([ "processor{}".format(n) for n in range(os.cpu_count()) ])
|
||||
path = case if case else ""
|
||||
@ -18,6 +19,15 @@ def foamClean(case: str = None):
|
||||
if os.path.exists(os.path.join(path, d)):
|
||||
shutil.rmtree(os.path.join(path, d))
|
||||
|
||||
def foamClean(case: str = None):
|
||||
rmDirs = ["0", "constant", "system"]
|
||||
path = case if case else ""
|
||||
|
||||
for d in rmDirs:
|
||||
if os.path.exists(os.path.join(path, d)):
|
||||
shutil.rmtree(os.path.join(path, d))
|
||||
|
||||
application("foamCleanTutorials", useMPI = False, case = case, stderr = True)
|
||||
|
||||
def uniform(value) -> str:
|
||||
if type(value) == list or type(value) == tuple:
|
||||
|
||||
@ -15,6 +15,7 @@ class BodyCentered(object):
|
||||
self.radius = kwargs.get("radius", self.r0 / (1 - self.theta))
|
||||
self.filletsEnabled = kwargs.get("filletsEnabled", False)
|
||||
self.fillets = kwargs.get("fillets", 0)
|
||||
self.volumeCell = None
|
||||
|
||||
|
||||
def build(self):
|
||||
@ -72,6 +73,7 @@ class BodyCentered(object):
|
||||
vecflow = geompy.GetNormal(inletface)
|
||||
poreCell = geompy.MakePrismVecH(inletface, vecflow, zh)
|
||||
|
||||
[_, _, self.volumeCell] = geompy.BasicProperties(poreCell, theTolerance = 1e-06)
|
||||
|
||||
inletface = geompy.MakeScaleTransform(inletface, oo, scale)
|
||||
poreCell = geompy.MakeScaleTransform(poreCell, oo, scale)
|
||||
@ -127,6 +129,8 @@ class BodyCentered(object):
|
||||
vecflow = geompy.GetNormal(inletface)
|
||||
poreCell = geompy.MakePrismVecH(inletface, vecflow, self.L * sqrt(3))
|
||||
|
||||
[_, _, self.volumeCell] = geompy.BasicProperties(poreCell, theTolerance = 1e-06)
|
||||
|
||||
inletface = geompy.MakeScaleTransform(inletface, oo, scale)
|
||||
poreCell = geompy.MakeScaleTransform(poreCell, oo, scale)
|
||||
|
||||
|
||||
@ -15,6 +15,7 @@ class FaceCentered(object):
|
||||
self.radius = kwargs.get("radius", self.r0 / (1 - self.theta))
|
||||
self.filletsEnabled = kwargs.get("filletsEnabled", False)
|
||||
self.fillets = kwargs.get("fillets", 0)
|
||||
self.volumeCell = None
|
||||
|
||||
|
||||
def build(self):
|
||||
@ -72,6 +73,7 @@ class FaceCentered(object):
|
||||
vecflow = geompy.GetNormal(inletface)
|
||||
poreCell = geompy.MakePrismVecH(inletface, vecflow, 2 * zh)
|
||||
|
||||
[_, _, self.volumeCell] = geompy.BasicProperties(poreCell, theTolerance = 1e-06)
|
||||
|
||||
inletface = geompy.MakeScaleTransform(inletface, oo, scale)
|
||||
poreCell = geompy.MakeScaleTransform(poreCell, oo, scale)
|
||||
@ -127,6 +129,8 @@ class FaceCentered(object):
|
||||
vecflow = geompy.GetNormal(inletface)
|
||||
poreCell = geompy.MakePrismVecH(inletface, vecflow, self.L * sqrt(3))
|
||||
|
||||
[_, _, self.volumeCell] = geompy.BasicProperties(poreCell, theTolerance = 1e-06)
|
||||
|
||||
inletface = geompy.MakeScaleTransform(inletface, oo, scale)
|
||||
poreCell = geompy.MakeScaleTransform(poreCell, oo, scale)
|
||||
|
||||
|
||||
@ -15,6 +15,7 @@ class Simple(object):
|
||||
self.radius = kwargs.get("radius", self.r0 / (1 - self.theta))
|
||||
self.filletsEnabled = kwargs.get("filletsEnabled", False)
|
||||
self.fillets = kwargs.get("fillets", 0)
|
||||
self.volumeCell = None
|
||||
|
||||
|
||||
def build(self):
|
||||
@ -68,6 +69,7 @@ class Simple(object):
|
||||
vecflow = geompy.GetNormal(inletface)
|
||||
poreCell = geompy.MakePrismVecH(inletface, vecflow, height)
|
||||
|
||||
[_, _, self.volumeCell] = geompy.BasicProperties(poreCell, theTolerance = 1e-06)
|
||||
|
||||
inletface = geompy.MakeScaleTransform(inletface, oo, scale)
|
||||
poreCell = geompy.MakeScaleTransform(poreCell, oo, scale)
|
||||
@ -120,6 +122,8 @@ class Simple(object):
|
||||
vecflow = geompy.GetNormal(inletface)
|
||||
poreCell = geompy.MakePrismVecH(inletface, vecflow, self.L * sqrt(3))
|
||||
|
||||
[_, _, self.volumeCell] = geompy.BasicProperties(poreCell, theTolerance = 1e-06)
|
||||
|
||||
inletface = geompy.MakeScaleTransform(inletface, oo, scale)
|
||||
poreCell = geompy.MakeScaleTransform(poreCell, oo, scale)
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user