New: move files

TODO.md

@@ -1,56 +0,0 @@
-## Usefull utils
-- createPatch
-- polyDualMesh
-- fvSolution: cellLimited
-- collapseDict: collapseEdges
-- renumberMesh
-- processorField
-
-## Errors
-- salome:
-
-th. 139990926538304 - 
-Trace /volatile/salome/jenkins/workspace/Salome_master_CO7/SALOME-9.6.0-CO7/SOURCES/SMESH/src/SMESH/SMESH_subMesh.cxx [2005] : 
-NETGEN_2D3D failed on sub-shape #1 with error COMPERR_BAD_INPUT_MESH 
-"NgException at Volume meshing: Stop meshing since surface mesh not consistent Some edges multiple times in surface mesh"
-
-th. 140588498282048 - 
-Trace /volatile/salome/jenkins/workspace/Salome_master_CO7/SALOME-9.6.0-CO7/SOURCES/SMESH/src/SMESH/SMESH_subMesh.cxx [2005] : 
-NETGEN_2D3D failed on sub-shape #47 with error COMPERR_WARNING 
-"Thickness 0.001 of viscous layers not reached, average reached thickness is 0.000928207"
-
-th. 139986338838080 - 
-Trace /volatile/salome/jenkins/workspace/Salome_master_CO7/SALOME-9.6.0-CO7/SOURCES/SMESH/src/SMESH/SMESH_subMesh.cxx [2005] : 
-NETGEN_2D3D failed on sub-shape #1 with error COMPERR_BAD_INPUT_MESH 
-"NgException at Volume meshing: Stop meshing since boundary mesh is overlapping Intersecting triangles"
-
-
-## 1.03.21
-- [x] boundary type (wall or symetryPlane)
-- [x] restruct for ways
-- [x] build alpha = 0.01 .. 0.13
-- [x] ! symetryPlane -> cyclicAMI
-
-## 3.03.21
-- [x] configure salome server, ports, etc.
-- [ ] less processes for salome, optimization.
-
-## 4.03.21
-- [x] 3rd direction
-- [x] createPatch(Dict)
-- [ ] views (mesh, ..)
-- [x] alpha for simpleCubic [0.01 .. 0.28]
-- [x] translation vector (cyclicAMI)
-- [ ] BUG: angle between the direction vector and the normal to inlet is ~1.4e-14 
-    - [x] Another solution
-- [ ] BUG: ideasUnvToFoam not working with param '-case PATH'
-    - [x] Temporary sulution via os.chdir(PATH)
-
-## 6.03.21
-- [ ] ERROR: MakeFuseList with alpha > 0.2
-
-## 7.03.21
-- [x] Split the symetryPlane to 4 faces
-
-## 11.03.21
-- [x] Dual test for cyclicAMI

anisotropy.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+python ${DIR}/anisotropy/anisotropy.py

anisotropy/anisotropy.py

@@ -68,24 +68,6 @@ def main():
     logger.info(f"Warnings: {logger.warnings}\tErrors: {logger.errors}")
 
 
-def checkEnv():
-    missed = False
-    
-    try:
-        pythonVersion = "Python {}".format(sys.version.split(" ")[0])
-        salomeVersion = salome_utils.salomeVersion()
-        foamVersion = foam_utils.foamVersion()
-
-    except Exception:
-        logger.critical("Missed environment")
-        missed = True
-
-    else:
-        logger.info(f"environment:\n\t{pythonVersion}\n\t{salomeVersion}\n\t{foamVersion}")
-
-    finally:
-        return missed
-
 
 class Task:
     def __init__(self, **kwargs):
@@ -223,4 +205,3 @@ def postprocessing(tasks):
 if __name__ == "__main__":
     main()
 
-

anisotropy/utils.py

@@ -0,0 +1,163 @@
+import logging
+
+from multiprocessing import Queue, Process, cpu_count
+import socket
+
+
+class struct:
+    def __init__(self, **kwargs):
+        for (k, v) in kwargs.items():
+            setattr(self, k, v)
+
+    def __str__(self):
+        members = []
+
+        for key in self.__dict__.keys():
+            members.append(f"{ key } = ")
+
+            if type(self.__dict__[key]) == str:
+                members[len(members) - 1] += f"\"{ self.__dict__[key] }\""
+
+            else: 
+                members[len(members) - 1] += f"{ self.__dict__[key] }"
+             
+        return f"struct({', '.join(members)})"
+
+    def __repr__(self):
+        return str(self)
+
+
+class Logger:
+    def __init__(self, name, logpath):
+        logging.basicConfig(
+            level = logging.INFO, 
+            format = "%(levelname)s: %(message)s",
+            handlers = [
+                logging.StreamHandler(),
+                logging.FileHandler(logpath)
+            ]
+        )
+
+        self.logger = logging.getLogger(name)
+        self.warnings = 0
+        self.errors = 0
+        self.criticals = 0
+        self.exceptions = 0
+        
+    def info(self, *args):
+        self.logger.info(*args)
+
+    def warning(self, *args):
+        self.warnings += 1
+        self.logger.warning(*args)
+
+    def error(self, *args):
+        self.errors += 1
+        self.logger.error(*args)
+
+    def critical(self, *args):
+        self.criticals += 1
+        self.logger.critical(*args)
+
+    def exception(self, *args):
+        self.exceptions += 1
+        self.logger.exception(*args)
+
+    def fancyline(self):
+        self.logger.info("-" * 80)
+
+
+
+def queue(cmd, qin, qout, *args):
+    
+    while True:
+        # Get item from the queue
+        pos, var = qin.get()
+        
+        # Exit point 
+        if pos is None:
+            break
+
+        # Execute command
+        res = cmd(*var, *args)
+
+        # Put results to the queue
+        qout.put((pos, res))
+
+    return
+
+
+def parallel(np, var, cmd):
+
+    varcount = len(var)
+
+    processes = []
+    nprocs = np if np <= cpu_count() else cpu_count()
+    
+    qin = Queue(1)
+    qout = Queue()
+    
+    logging.info("cpu count: {}".format(np))
+    logging.info("var: {}".format(var))
+    logging.info("cmd: {}".format(cmd))
+
+    # Create processes
+    for n in range(nprocs):
+        pargs = [cmd, qin, qout]
+
+        p = Process(target = queue, args = tuple(pargs))
+
+        processes.append(p)
+    
+    # Start processes
+    for p in processes:
+        p.daemon = True
+        p.start()
+
+    # Fill queue
+    for n in range(varcount):
+        qin.put((n, var[n]))
+
+    for _ in range(nprocs):
+        qin.put((None, None))
+    
+    # Get results
+    results = [[] for n in range(varcount)]
+
+    for n in range(varcount):
+        index, res = qout.get()
+        
+        results[index] = res
+    
+    # Wait until each processor has finished
+    for p in processes:
+        p.join()
+
+    return results
+
+    
+def portIsFree(address, port):
+
+    with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
+        return s.connect_ex((address, port)) == 0
+
+
+def checkEnv():
+    missed = False
+    
+    try:
+        pythonVersion = "Python {}".format(sys.version.split(" ")[0])
+        salomeVersion = salome_utils.salomeVersion()
+        foamVersion = foam_utils.foamVersion()
+
+    except Exception:
+        logger.critical("Missed environment")
+        missed = True
+
+    else:
+        logger.info(f"environment:\n\t{pythonVersion}\n\t{salomeVersion}\n\t{foamVersion}")
+
+    finally:
+        return missed
+
+

config.py

@@ -163,4 +163,3 @@ class faceCentered:
         facesToIgnore = None,
         extrusionMethod = None
     )
-

notes.md

@@ -1,30 +1,8 @@
-## relaxationFactors
 
-| p     | Iterations    | U     |
+- createPatch
-| ---   | ---           | ---   |
+- polyDualMesh
-| 0.05  | 830           | 0.2   |
+- fvSolution: cellLimited
-| 0.1   | 678           | 0.2   |
+- collapseDict: collapseEdges
-| 0.2   | 505           | 0.2   |
+- renumberMesh
-| 0.3   | 305           | 0.3   |
+- processorField
-| 0.3   | 236           | 0.4   |
-| 0.3   | 181           | 0.5   |
 
--->
-
-## SIMPLE.residualControl
-
-| p     | U     | Iterations    |
-| ---   | ---   | ---           |
-| 1e-4  | 1e-4  | 338           |
-| 1e-5  | 1e-5  | 499           |
-
-##
-
-```math
-U = \frac{\Delta p L}{mu} \frac{9}{256} (\sqrt 2 - \frac{1}{1 - \alpha})^2
-L = 2 R_0
-R_0 = 1
-scale = 1e-5
-mu = 1e-3
-\Delta p = 1
-```

openfoam/meshConversion.py

@@ -0,0 +1,4 @@
+
+def ideasUnvToFoam(mesh: str, case: str = None) -> (str, int):
+    return application("ideasUnvToFoam", mesh, case = case, stderr = True)
+

openfoam/meshManipulation.py

@@ -0,0 +1,32 @@
+
+def createPatch(dictfile: str = None, case: str = None):
+    args = ["-overwrite"]
+
+    if dictfile:
+        args.extend(["-dict", dictfile])
+
+    application("createPatch", *args, case = case, stderr = True)
+
+
+def transformPoints(scale: tuple, case: str = None):
+    scale_ = "{}".format(scale).replace(",", "")
+
+    application("transformPoints", "-scale", scale_, case = case, stderr = True)
+
+
+def checkMesh(case: str = None):
+    application("checkMesh", "-allGeometry", "-allTopology", case = case, stderr = True)
+
+    with open("checkMesh.log", "r") as io:
+        warnings = []
+        for line in io:
+            if re.search("\*\*\*", line):
+                warnings.append(line.replace("***", "").strip())
+
+        if warnings:
+            logger.warning("checkMesh:\n\t{}".format("\n\t".join(warnings)))
+
+
+def renumberMesh(case: str = None):
+    application("renumberMesh", "-parallel", "-overwrite", useMPI = True, case = case, stderr = True)
+

openfoam/miscellaneous.py

@@ -0,0 +1,9 @@
+
+def foamDictionary(filepath: str, entry: str, value: str = None, case: str = None):
+    args = [filepath, "-entry", entry]
+
+    if value:
+        args.extend(["-set", value])
+
+    application("foamDictionary", *args, case = case, stderr = False)
+

openfoam/openfoam.py

@@ -123,4 +123,3 @@ def simpleFoam(case: str = None):
 
     return returncode
 
-

openfoam/parallelProcessing.py

@@ -0,0 +1,4 @@
+
+def decomposePar(case: str = None):
+    application("decomposePar", case = case, stderr = True)
+

openfoam/solvers.py

@@ -0,0 +1,15 @@
+
+def potentialFoam(case: str = None):
+    application("potentialFoam", "-parallel", useMPI = True, case = case, stderr = True)
+
+
+def simpleFoam(case: str = None):
+    _, returncode = application("simpleFoam", "-parallel", useMPI = True, case = case, stderr = True)
+
+    with open("simpleFoam.log", "r") as io:
+        for line in io:
+            if re.search("solution converged", line):
+                logger.info("simpleFoam:\n\t{}".format(line.strip()))
+
+    return returncode
+

openfoam/utils.py

@@ -0,0 +1,14 @@
+
+def foamVersion() -> str:
+    return "OpenFOAM-{}".format(os.environ["WM_PROJECT_VERSION"])
+
+
+def foamClean(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 ""
+
+    for d in rmDirs:
+        if os.path.exists(os.path.join(path, d)):
+            shutil.rmtree(os.path.join(path, d))
+

salome/bodyCentered.py

@@ -1,5 +1,5 @@
-import salome
+#import salome
-salome.salome_init()
+#salome.salome_init()
 
 import GEOM
 from salome.geom import geomBuilder
@@ -284,4 +284,3 @@ def bodyCenteredHexagonalPrism(theta = 0.01, fillet = False, direction = [1, 1,
     groups.append(wall)
 
     return shape, groups
-

salome/faceCentered.py

@@ -1,5 +1,5 @@
-import salome
+#import salome
-salome.salome_init()
+#salome.salome_init()
 
 import GEOM
 from salome.geom import geomBuilder
@@ -281,4 +281,3 @@ def faceCenteredHexagonalPrism(theta = 0.01, fillet = False, direction = [1, 1,
     groups.append(wall)
 
     return shape, groups
-

salome/genmesh.py

@@ -1,3 +1,6 @@
+###
+#   This file executes inside salome environment
+##
 from collections import namedtuple
 import os, sys
 import logging

salome/geometry.py

@@ -236,4 +236,3 @@ def boundaryCreate(gobj, dvec, grains):
 
     return boundary
 
-

salome/mesh.py

@@ -189,4 +189,3 @@ def meshExport(mobj, path):
     except:
         logger.error("""meshExport: Cannot export.""")
 
-

salome/simple.py

@@ -1,5 +1,5 @@
-import salome
+#import salome
-salome.salome_init()
+#salome.salome_init()
 
 import GEOM
 from salome.geom import geomBuilder
@@ -261,4 +261,3 @@ def simpleHexagonalPrism(theta = 0.01, fillet = False, direction = [1, 1, 1]):
     groups.append(wall)
 
     return shape, groups
-

salome/utils.py

@@ -80,4 +80,3 @@ def remote(port, cmd):
         stderr = subprocess.PIPE)
 
     return p
-

src/anisotropeCubic.py

@@ -1,103 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import math
-from . import geometry_utils
-
-import GEOM
-geompy = geometry_utils.getGeom()
-
-class StructuredGrains:
-    def __init__(self, radius, stackAngle, theta, layers):
-        self.pos = [0, 0, 0]
-        self.angle = [0, 0, 0]
-        self.radius = radius
-        self.theta = theta
-        self.layers = layers
-        
-        # Parameters and dependencies
-        R = self.radius / (1 - self.theta)
-        
-        C1 = 0.8 #fillet[0]
-        C2 = 0.4 #fillet[1]
-        self.theta1 = 0.01
-        self.theta2 = 0.28
-        
-        Cf = C1 + (C2 - C1) / (self.theta2 - self.theta1) * (self.theta - self.theta1)
-        R_fillet = Cf * (self.radius * math.sqrt(2) - R)
-        
-        ###
-        stackang = [
-            0.5 * math.pi - stackAngle[0], 
-            0.5 * math.pi - stackAngle[1], 
-            0.5 * math.pi - stackAngle[2]
-        ]
-        
-        xvec = geompy.MakeVector(
-            geompy.MakeVertex(0, 0, 0),
-            geompy.MakeVertex(1, 0, 0))
-        yvec = geometry_utils.rotate(xvec, [0.5 * math.pi, 0, 0])
-        zvec = geometry_utils.rotate(xvec, [0, 0.5 * math.pi, 0])
-        
-        grain = geompy.MakeSpherePntR(geompy.MakeVertex(pos[0], pos[1], pos[2]), R)
-        
-        xstack = geompy.MakeMultiTranslation1D(grain, xvec, 2 * self.radius, self.layers[0])
-        ystack = geompy.MakeMultiTranslation1D(xgrain, yvec, 2 * self.radius, self.layers[1])
-        zstack = geompy.MakeMultiTranslation1D(ygrain, zvec, 2 * self.radius, self.layers[2])
-        
-        # Correct position to zero
-        stack = geompy.MakeTranslation(zstack, -2 * self.radius, 0, 0)
-        
-        self.geometry = geompy.ExtractShapes(stack, geompy.ShapeType["SOLID"], True)
-        self.geometry = geompy.MakeFuseList(self.geometry, False, False)
-                
-        if not R_fillet == 0:
-            self.geometry = geompy.MakeFilletAll(self.geometry, R_fillet)
-
-
-class AnisotropeCubic:
-    def __init__(self, scale, grains, style):
-        self.pos = [0, 0, 0]
-        self.angle = [0, 0, 0]
-        self.scale = scale
-        self.grains = grains
-
-        # Bounding box
-        if style == 0:
-            # Square
-            profile = (
-                geompy.Sketcher3D()
-                .addPointAbsolute(0, 0, 0)
-                .addPointAbsolute(0, 0, self.scale[2])
-                .addPointAbsolute(0, self.scale[1], self.scale[2])
-                .addPointAbsolute(0, self.scale[1], 0)
-                .addPointAbsolute(0, 0, 0)
-            )
-            
-            face = geompy.MakeFaceWires([profile.wire()], 1)
-
-        elif style == 1:
-            # Rombus
-            profile = (
-                geompy.Sketcher3D()
-                .addPointAbsolute(self.scale[0], 0.5 * self.scale[1], 0)
-                .addPointAbsolute(0.5 * self.scale[0], 0, 0.5 * self.scale[2])
-                .addPointAbsolute(0, 0.5 * self.scale[1], self.scale[2])
-                .addPointAbsolute(0.5 * self.scale[0], self.scale[1], 0.5 * self.scale[2])
-                .addPointAbsolute(self.scale[0], 0.5 * self.scale[1], 0)
-            )
-
-            face = geompy.MakeFaceWires([profile.wire()], 1)
-            face = geompy.MakeTranslation(face, 
-                0.5 * self.scale[1], 0, 0)
-
-        self.boundingbox = geompy.MakePrismVecH(face,
-            geompy.MakeVectorDXDYDZ(1, 0, 0), 
-            self.scale[0])
-        
-        # Geometry
-        self.geometry = geompy.MakeCutList(box, [self.grains], True)
-
-
-
-

src/applogger.py

@@ -1,41 +0,0 @@
-import logging
-import config
-
-class Logger():
-    def __init__(self):
-        logging.basicConfig(
-            level = logging.INFO, 
-            format = "%(levelname)s: %(message)s",
-            handlers = [
-                logging.StreamHandler(),
-                logging.FileHandler(f"{config.LOG}/anisotrope.log")
-            ]
-        )
-
-        self.logger = logging.getLogger("anisotrope")
-        self.warnings = 0
-        self.errors = 0
-        self.criticals = 0
-        self.exceptions = 0
-        
-    def info(self, *args):
-        self.logger.info(*args)
-
-    def warning(self, *args):
-        self.warnings += 1
-        self.logger.warning(*args)
-
-    def error(self, *args):
-        self.errors += 1
-        self.logger.error(*args)
-
-    def critical(self, *args):
-        self.criticals += 1
-        self.logger.critical(*args)
-
-    def exception(self, *args):
-        self.exceptions += 1
-        self.logger.exception(*args)
-
-    def fancyline(self):
-        self.logger.info("-" * 80)

src/utils.py

@@ -1,77 +0,0 @@
-from multiprocessing import Queue, Process, cpu_count
-import socket
-import logging
-
-def queue(cmd, qin, qout, *args):
-    
-    while True:
-        # Get item from the queue
-        pos, var = qin.get()
-        
-        # Exit point 
-        if pos is None:
-            break
-
-        # Execute command
-        res = cmd(*var, *args)
-
-        # Put results to the queue
-        qout.put((pos, res))
-
-    return
-
-
-def parallel(np, var, cmd):
-
-    varcount = len(var)
-
-    processes = []
-    nprocs = np if np <= cpu_count() else cpu_count()
-    
-    qin = Queue(1)
-    qout = Queue()
-    
-    logging.info("cpu count: {}".format(np))
-    logging.info("var: {}".format(var))
-    logging.info("cmd: {}".format(cmd))
-
-    # Create processes
-    for n in range(nprocs):
-        pargs = [cmd, qin, qout]
-
-        p = Process(target = queue, args = tuple(pargs))
-
-        processes.append(p)
-    
-    # Start processes
-    for p in processes:
-        p.daemon = True
-        p.start()
-
-    # Fill queue
-    for n in range(varcount):
-        qin.put((n, var[n]))
-
-    for _ in range(nprocs):
-        qin.put((None, None))
-    
-    # Get results
-    results = [[] for n in range(varcount)]
-
-    for n in range(varcount):
-        index, res = qout.get()
-        
-        results[index] = res
-    
-    # Wait until each processor has finished
-    for p in processes:
-        p.join()
-
-    return results
-
-    
-def portIsFree(address, port):
-
-    with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
-        return s.connect_ex((address, port)) == 0
-