L-Nafaryus/anisotropy
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Mod: core: improve pipeline

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Fix: openfoam: wrong path expressions
This commit is contained in:
L-Nafaryus 2022-02-18 00:28:05 +05:00
parent c5d2bf1783
commit fc1b8432cb
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GPG Key ID: C76D8DCD2727DBB7
7 changed files with 183 additions and 69 deletions
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5
anisotropy/cli/cli.py
View File

@ -65,7 +65,7 @@ def init(path, verbose):
@click.option(
"-f", "--force", "overwrite",
is_flag = True,
# default = False,
default = None,
help = "Overwrite existing entries"
)
@click.option(
@ -130,11 +130,12 @@ def compute(path, configFile, nprocs, stage, overwrite, params, verbose, executi
"stage": stage,
"overwrite": overwrite
}
for k, v in args.items():
if v is not None:
config.update(**{ k: v })
print(config.options)
if pid:
pid = pathlib.Path(pid).resolve()

107
anisotropy/core/runner.py
View File

@ -12,6 +12,7 @@ from anisotropy.database import Database, tables
from anisotropy import shaping
from anisotropy import meshing
from anisotropy import solving
from anisotropy import openfoam
from . import config as core_config
from . import postprocess
@ -29,7 +30,7 @@ class UltimateRunner(object):
# Configuration file
self.config = config or core_config.default_config()
# Database preparation
self.database = Database(self.config["database"])
self.exec_id = None
@ -51,6 +52,24 @@ class UltimateRunner(object):
# Parameters
self.queue = []
def _query_database(self, tableName: str, to_dict: bool = False):
tableName = tableName.lower()
get_row = {
"shape": self.database.getShape,
"mesh": self.database.getMesh,
"flowonephase": self.database.getFlowOnephase
}[tableName]
# query
args = (
self.config.params["label"],
self.config.params["direction"],
self.config.params["alpha"],
self.exec_id,
to_dict
)
return get_row(*args)
def prepare_database(self):
# create a row in each table for the current case
# shape
@ -128,25 +147,16 @@ class UltimateRunner(object):
def compute_shape(self):
params = self.config.params
shapeParams = self.database.getShape(
params["label"],
params["direction"],
params["alpha"],
self.exec_id
)
shapeParams = self._query_database("shape")
logger.info("Computing shape for {} with direction = {} and alpha = {}".format(
params["label"], params["direction"], params["alpha"]
))
timer = utils.Timer()
# check
if (
self.shapefile.exists() and
shapeParams.shapeStatus == "done" and
not self.config["overwrite"]
):
logger.info("Shape exists. Skipping ...")
# check physical existence
if self.shapefile.exists() and self.config["overwrite"] is not True:
logger.info("Shape exists, skipping ...")
return
#
@ -187,25 +197,16 @@ class UltimateRunner(object):
def compute_mesh(self):
params = self.config.params
meshParams = self.database.getMesh(
params["label"],
params["direction"],
params["alpha"],
self.exec_id
)
meshParams = self._query_database("mesh")
logger.info("Computing mesh for {} with direction = {} and alpha = {}".format(
params["label"], params["direction"], params["alpha"]
))
timer = utils.Timer()
# check
if (
self.meshfile.exists() and
meshParams.meshStatus == "done" and
not self.config["overwrite"]
):
logger.info("Mesh exists. Skipping ...")
# check physical existence
if self.meshfile.exists() and self.config["overwrite"] is not True:
logger.info("Mesh exists, skipping ...")
return
elif not self.shapefile.exists():
@ -246,21 +247,15 @@ class UltimateRunner(object):
def compute_flow(self):
params = self.config.params
query = (
params["label"],
params["direction"],
params["alpha"],
self.exec_id
)
flowParams = self.database.getFlowOnephase(*query)
flowParams = self._query_database("flowonephase")
logger.info("Computing flow for {} with direction = {} and alpha = {}".format(
params["label"], params["direction"], params["alpha"]
))
timer = utils.Timer()
# check
if flowParams.flowStatus == "done" and not self.config["overwrite"]:
# check physical existence
if openfoam.FoamCase(path = self.casepath).is_converged() and not self.config["overwrite"]:
logger.info("Solution exists. Skipping ...")
return
@ -277,7 +272,7 @@ class UltimateRunner(object):
self.database.csave(flowParams)
#
flowParamsDict = self.database.getFlowOnephase(*query, to_dict = True)
flowParamsDict = self._query_database("flowonephase", to_dict = True)
try:
# load shape
@ -309,19 +304,15 @@ class UltimateRunner(object):
def compute_postprocess(self):
params = self.config.params
flowParams = self.database.getFlowOnephase(
params["label"],
params["direction"],
params["alpha"],
self.exec_id
)
flowParams = self._query_database("flowonephase")
logger.info("Computing post process for {} with direction = {} and alpha = {}".format(
params["label"], params["direction"], params["alpha"]
))
if flowParams.flowStatus == "done":
flowParams.flowRate = postprocess.flowRate("outlet", self.casepath)
if flowParams.flowRate is None and self.config["overwrite"] is not True:
flowParams.flowRate = postprocess.flowRate("outlet", self.casepath)
self.database.csave(flowParams)
@ -335,15 +326,43 @@ class UltimateRunner(object):
for current in stages:
if current == "shape":
params = self._query_database("shape")
# check database entry
if params.shapeStatus == "done" and self.config["overwrite"] is not True:
logger.info("Successful shape entry exists, skipping ...")
continue
self.compute_shape()
if current == "mesh":
params = self._query_database("mesh")
# check database entry
if params.meshStatus == "done" and self.config["overwrite"] is not True:
logger.info("Successful mesh entry exists, skipping ...")
continue
self.compute_mesh()
if current == "flow":
params = self._query_database("flowonephase")
# check database entry
if params.flowStatus == "done" and self.config["overwrite"] is not True:
logger.info("Successful flow entry exists, skipping ...")
continue
self.compute_flow()
if current == "postProcess":
params = self._query_database("flowonephase")
# check database entry
# if params.flowStatus == "done" and self.config["overwrite"] is not True:
# logger.info("Successful flow entry exists, skipping ...")
# continue
self.compute_postprocess()
if current == stage or current == "all":

29
anisotropy/database/database.py
View File

@ -57,7 +57,7 @@ class Database(pw.SqliteDatabase):
return self
def csave(self, table: pw.Model, tries: int = 100):
def csave(self, table: pw.Model, tries: int = 5000):
"""Try to save data from model to the database ignoring
peewee.OperationalError. Usefull for concurrent processes.
@ -82,7 +82,12 @@ class Database(pw.SqliteDatabase):
self.close()
break
def getExecution(self, idn: int) -> tables.Execution | None:
def getExecution(
self,
idn: int,
to_dict: bool = False,
**kwargs
) -> tables.Execution | None:
"""Get execution entry from database.
:param idn:
@ -93,7 +98,11 @@ class Database(pw.SqliteDatabase):
query = tables.Execution.select().where(tables.Execution.exec_id == idn)
with self:
table = query.get() if query.exists() else None
if to_dict:
table = query.dicts().get() if query.exists() else None
else:
table = query.get() if query.exists() else None
return table
@ -116,6 +125,7 @@ class Database(pw.SqliteDatabase):
direction: list[float] | ndarray = None,
alpha: float = None,
execution: int = None,
to_dict: bool = False,
**kwargs
) -> tables.Shape | None:
"""Get shape entry from database.
@ -145,7 +155,11 @@ class Database(pw.SqliteDatabase):
)
with self:
table = query.get() if query.exists() else None
if to_dict:
table = query.dicts().get() if query.exists() else None
else:
table = query.get() if query.exists() else None
return table
@ -155,6 +169,7 @@ class Database(pw.SqliteDatabase):
direction: list[float] | ndarray = None,
alpha: float = None,
execution: int = None,
to_dict: bool = False,
**kwargs
) -> tables.Mesh | None:
"""Get mesh entry from database.
@ -185,7 +200,11 @@ class Database(pw.SqliteDatabase):
)
with self:
table = query.get() if query.exists() else None
if to_dict:
table = query.dicts().get() if query.exists() else None
else:
table = query.get() if query.exists() else None
return table

22
anisotropy/gui/layouts/visualization.py
View File

@ -231,7 +231,7 @@ layout = html.Div([
]
)
def plotDraw(clicks, execution, structure, direction, data):
from peewee import JOIN
import peewee as pw
from anisotropy.database import Database, tables
import json
from pandas import DataFrame
@ -263,21 +263,33 @@ def plotDraw(clicks, execution, structure, direction, data):
else:
select = (tables.Shape.alpha, column)
query = (
"""query = (
tables.Shape
.select(*select)
.join(tables.Execution, JOIN.LEFT_OUTER)
.switch(tables.Shape)
.join(tables.Mesh, JOIN.LEFT_OUTER)
#.switch(tables.Shape)
.join(tables.FlowOnephase, JOIN.LEFT_OUTER)
.switch(tables.Shape)
# .join(tables.FlowOnephase, JOIN.LEFT_OUTER)
# .switch(tables.Shape)
.where(
tables.Shape.exec_id == execution,
tables.Shape.label == structure,
)
)
)"""
query = model.select(*select)
idn = db.tables.index(model)
for table in reversed(db.tables[ :idn]):
query = query.join(table, pw.JOIN.LEFT_OUTER)
query = query.switch(tables.Shape)
query = query.where(
tables.Shape.exec_id == execution,
tables.Shape.label == structure,
)
query = query.order_by(tables.Shape.alpha)
if not direction == "all":
query = query.where(tables.Shape.direction == json.loads(direction))

56
anisotropy/openfoam/case.py
View File

@ -6,6 +6,8 @@ import os
import shutil
import re
import pathlib
import io
from lz.reversal import reverse as lz_reverse
from . import FoamFile
@ -72,23 +74,23 @@ class FoamCase(object):
path = pathlib.Path(path or self.path or "")
for file in self._files:
path /= (
path_ = path / (
file.location + "/" + file.object
if file.location else file.object
)
file.read(path.resolve())
file.read(path_.resolve())
def remove(self, path: str = None):
path = pathlib.Path(path or self.path or "")
for file in self._files:
path /= (
path_ = path / (
file.location + "/" + file.object
if file.location else file.object
)
file.remove(path.resolve())
file.remove(path_.resolve())
def clean(self, included: list = ["0", "constant", "system"]):
regxs = [
@ -105,10 +107,16 @@ class FoamCase(object):
for root, dirs, files in os.walk(os.path.abspath("")):
for _dir in dirs:
excluded += [ os.path.join(root, _dir) for regx in regxs if re.match(regx, _dir) ]
excluded += [
os.path.join(root, _dir)
for regx in regxs if re.match(regx, _dir)
]
for file in files:
excluded += [ os.path.join(root, file) for regx in regxs if re.match(regx, file) ]
excluded += [
os.path.join(root, file)
for regx in regxs if re.match(regx, file)
]
for file in excluded:
if os.path.split(file)[1] not in included and os.path.exists(file):
@ -128,3 +136,39 @@ class FoamCase(object):
path = pathlib.Path(self._backpath or "").resolve()
os.chdir(path)
def is_converged(self, path: str = None) -> None | bool:
path = pathlib.Path(path or self.path or "").resolve()
controlDict = FoamFile()
if controlDict.exists(path / "system" / "controlDict"):
controlDict.read(path / "system" / "controlDict")
else:
return None
application = controlDict.get("application")
if application is None:
return None
logfile = (
path / f"{ application }.log"
if (path / f"{ application }.log").exists() else (path / f"log.{ application }")
)
status = False
if logfile.exists():
with open(logfile, "r") as infile:
limit = 30
for line in lz_reverse(infile, batch_size = io.DEFAULT_BUFFER_SIZE):
if not line.find("End") < 0:
status = True
if limit <= 0:
status = False
limit -= 1
return status

4
anisotropy/openfoam/conversion.py
View File

@ -22,6 +22,10 @@ def read_foamfile(filename: str) -> tuple[dict, dict]:
header = ppf.header or {}
content = ppf.content or {}
if type(content) == dict:
if content.get("internalField"):
content["internalField"] = np.asarray(content["internalField"])
return header, content

29
anisotropy/openfoam/file.py
View File

@ -68,11 +68,17 @@ class FoamFile(object):
@property
def location(self) -> str:
return self.header.get("location").replace('"', "")
return (
self.header.get("location").replace('"', "")
if self.header.get("location") else None
)
def __getitem__(self, key):
return self.content[key]
def get(self, key, default = None):
return self.content.get(key, default)
def __setitem__(self, key, value):
self.content[key] = value
@ -99,6 +105,15 @@ class FoamFile(object):
return FoamCase([ self, file ])
def exists(self, filename: str = None) -> bool:
filename = filename or (
self.location + "/" + self.object
if self.location else self.object
)
path = pathlib.Path(filename).resolve()
return path.exists() and path.is_file()
def read(self, filename: str = None):
"""Read a FoamFile.
@ -108,8 +123,8 @@ class FoamFile(object):
:return:
Self.
"""
filename = (
filename or self.location + "/" + self.object
filename = filename or (
self.location + "/" + self.object
if self.location else self.object
)
path = pathlib.Path(filename).resolve()
@ -131,8 +146,8 @@ class FoamFile(object):
Path to the file. If None, use location and object from header with
the current working directory.
"""
filename = (
filename or self.location + "/" + self.object
filename = filename or (
self.location + "/" + self.object
if self.location else self.object
)
path = pathlib.Path(filename).resolve()
@ -146,8 +161,8 @@ class FoamFile(object):
Path to the file. If None, use location and object from header with
the current working directory.
"""
filename = (
filename or self.location + "/" + self.object
filename = filename or (
self.location + "/" + self.object
if self.location else self.object
)
path = pathlib.Path(filename).resolve()