Changed C compiler to icc for Intel config (#63)

* updated gitignore * ran black * use icc in Intel config * patch version bump * rephrased readme
mdolab · Mar 2, 2023 · d3f6a4c · d3f6a4c
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diff --git a/.gitignore b/.gitignore
@@ -5,6 +5,7 @@
 *.o
 *.so
 *.out
+doc/_build
 
 # auto generated files
 src/libcgns_utils-f2pywrappers2.f90

diff --git a/README.md b/README.md
@@ -3,8 +3,7 @@
 [![Documentation Status](https://readthedocs.com/projects/mdolab-cgnsutilities/badge/?version=latest)](https://mdolab-cgnsutilities.readthedocs-hosted.com/en/latest/?badge=latest)
 [![codecov](https://codecov.io/gh/mdolab/cgnsutilities/branch/main/graph/badge.svg?token=ZCO3MR2LNL)](https://codecov.io/gh/mdolab/cgnsutilities)
 
-This repository contains a single program called `cgns_utils` that
-provides many useful functions for working with cgns grids. 
+This repository contains many useful functions for working with CGNS grids and a CLI program called `cgns_utils` to call these functions.
 
 ## License
 

diff --git a/cgnsutilities/__init__.py b/cgnsutilities/__init__.py
@@ -1 +1 @@
-__version__ = "2.7.0"
+__version__ = "2.7.1"
diff --git a/cgnsutilities/cgns_utils.py b/cgnsutilities/cgns_utils.py
@@ -1040,7 +1040,6 @@ def main():
 
         # Check if the user gave a reference name. Otherwise, use the input name as reference
         if args.outFile is None:
-
             # Get the base name
             outFile = os.path.splitext(os.path.basename(args.gridFile))[0]
 
@@ -1060,7 +1059,6 @@ def main():
                 pickle.dump(curGrid.convArray, fid)
 
         elif args.outType == "tecplot":
-
             # Create a single 2D array that will contain all data
             data = []
 

diff --git a/cgnsutilities/cgnsutilities.py b/cgnsutilities/cgnsutilities.py
@@ -212,12 +212,10 @@ def printBlockInfo(self):
         print("Total Nodes:", allBlocksInfo["totalNodes"])
 
     def addBlock(self, blk):
-
         """Add a block to the grid"""
         self.blocks.append(blk)
 
     def removeBlocks(self, blockIDs):
-
         """
         This function will remove certain blocks from the grid.
         The user should ensure that the final mesh is still valid
@@ -311,7 +309,6 @@ def extractSurface(self, fileName):
             f = open(fileName, "w")
             f.write("%d\n" % len(patches))
             for i in range(len(patches)):
-
                 f.write("%d %d 1\n" % (patches[i].shape[0], patches[i].shape[1]))
             for i in range(len(patches)):
                 patches[i][:, :, 0].flatten("F").tofile(f, sep="\n", format="%20.15g")
@@ -333,7 +330,6 @@ def extractSpecifiedSurface(self, fileName, blkid, imin, imax, jmin, jmax, kmin,
             f = open(fileName, "w")
             f.write("%d\n" % len(patches))
             for i in range(len(patches)):
-
                 f.write("%d %d 1\n" % (patches[i].shape[0], patches[i].shape[1]))
             for i in range(len(patches)):
                 patches[i][:, :, 0].flatten("F").tofile(f, sep="\n", format="%20.15g")
@@ -488,7 +484,6 @@ def writeBCs(self, bcFile):
             bcFile = self.name + ".bc"
 
         with open(bcFile, "w") as fid:
-
             for idx_block, block in enumerate(self.blocks):
                 blockID = idx_block + 1
                 block.writeBCs(blockID, fid)
@@ -642,7 +637,6 @@ def double2D(self):
             blk.double2D()
 
     def getBoundingBox(self):
-
         # Get the bounds of each grid.
         xMin = 1e20 * np.ones(3)
         xMax = -1.0 * np.ones(3)
@@ -826,7 +820,6 @@ def cartesian(self, cartFile, outFile):
 
         # Define tangent bunching law
         def tanDist(Sp1, Sp2, N):
-
             """
             This is the tangential spacing developed by Ney Secco.
             This bunching law is coarse at the ends and fine at the middle
@@ -903,7 +896,6 @@ def func(P):
             return S
 
         def generateGrid(xmin, xmax, extension1, extension2, nNodes, binVol, weightGR):
-
             """
             Function that optimizes bunching law to match grid resolution
 
@@ -1072,7 +1064,6 @@ def func(P):
         print("Mesh successfully generated and stored in: " + outFile)
 
     def split(self, extraSplits):
-
         """Recursively propagate splits due to boundary conditions or
         B2B information"""
 
@@ -1319,7 +1310,6 @@ def fillOpenBCs(self, bocoType, famName):
             blockID = myIDs[i] - 1
 
             if types[i] == 0:  # Boco
-
                 # Check if face already has a BC
                 has_bc = False
                 for boco in self.blocks[blockID].bocos:
@@ -1426,7 +1416,6 @@ def translate(self, dx, dy, dz):
             blk.coords[:, :, :] += [dx, dy, dz]
 
     def rotate(self, vx, vy, vz, theta):
-
         """
         This rotates the grid around an axis that passes through the origin.
         vx, vy, vz are the components of the rotation vector
@@ -1647,7 +1636,6 @@ def coarsen(self):
         new_dims = copy.deepcopy(self.dims)
         for i in range(3):
             if self.dims[i] > 2:
-
                 if self.dims[i] % 2 == 0:
                     print(f"INFO: unevenly coarsing block {self.name} along dimension {i} (size {self.dims[i]}) ")
 
@@ -1896,7 +1884,6 @@ def revolve(self, normalDirection, rotationAxis, startAngle, endAngle, nThetas):
         for i in range(self.dims[0]):
             for j in range(self.dims[1]):
                 for k in range(nThetas):
-
                     tc = self.coords[i, j, 0, :].copy()
 
                     angleRad = startAngleRad + angleRadStep * k
@@ -2193,7 +2180,6 @@ def writeBCs(self, blk_num, file_handle):
 
             data_arr_str = ""
             for data_arr in boco.dataSets:
-
                 # use the BC dictionary in reverse to find the bc type string
                 for bctype in BC:
                     if data_arr.type == BC[bctype]:
@@ -2267,7 +2253,6 @@ def rebunch(self, spacing, extraCells, nStar):
         newNodes = np.zeros((self.dims[0], self.dims[1], self.dims[2], 3))
         for i in range(self.dims[0]):
             for j in range(self.dims[1]):
-
                 xx = self.coords[i, j, :, :]
                 c = Curve(X=xx, localInterp=True)
                 # First get the distance off-wall:
@@ -2318,7 +2303,6 @@ def randomize(self, keepRHS):
         # So that filps the order of the axis. We can also perform
         # axis swapping.
         if np.random.random() > 0.5:
-
             # Swap X and Y axis
             newCoords = np.zeros((self.dims[1], self.dims[0], self.dims[2], 3))
             for k in range(self.dims[2]):
@@ -2365,7 +2349,6 @@ def symmZero(self, idir):
                 self.coords[r[0, 0] - 1 : r[0, 1], r[1, 0] - 1 : r[1, 1], r[2, 0] - 1 : r[2, 1], idir] = 0.0
 
     def symmZeroNoBC(self, idir, tol):
-
         # Find which nodes are closer than the tolerance from the symmetry plane
         nodeIDs = np.where(self.coords[:, :, :, idir] < tol)
 
@@ -2418,10 +2401,8 @@ def coarsen(self):
         """Coarsen the range of the BC"""
 
         for idim in range(3):
-
             self.ptRange[idim, 0] = int(np.floor((self.ptRange[idim, 0]) / 2)) + 1
             if self.ptRange[idim, 1] > 2:
-
                 # coarsen the data set if it is an array
                 if self.dataSets:
                     for data_set in self.dataSets:
@@ -2524,11 +2505,9 @@ def __init__(self, connectName, donorName, ptRange, donorRange, transform):
     def coarsen(self):
         """Coarsen the range of the B2B along the specified direction"""
         for idim in range(3):
-
             donorDir = abs(self.transform[idim]) - 1
 
             for j in range(2):
-
                 if self.ptRange[idim, j] > 2:
                     self.ptRange[idim, j] = (self.ptRange[idim, j] - 1) // 2 + 1
 
@@ -2811,6 +2790,7 @@ def simpleCart(xMin, xMax, dh, hExtra, nExtra, sym, mgcycle, outFile):
 #     # otherwise:
 #     return 1
 
+
 # -----------------------------------------------------------------
 # These functions perform operations that return new 'Grid' objects
 # -----------------------------------------------------------------
@@ -2848,7 +2828,6 @@ def readGrid(fileName):
             if nDataSets != 0:
                 # Loop over all the datasets for this BC
                 for iBocoDataSet in range(1, nDataSets + 1):
-
                     (
                         bocoDatasetName,
                         bocoDataSetType,
@@ -2886,7 +2865,6 @@ def getBocoDataSetArray(flagDirNeu, iDir):
                     if nDirichletArrays > 0:
                         # Loop over Dirichlet data and get the actual data
                         for iDir in range(1, nDirichletArrays + 1):
-
                             # Get the data set
                             bcDSetArr = getBocoDataSetArray(BCDATATYPE["Dirichlet"], iDir)
 
@@ -2899,7 +2877,6 @@ def getBocoDataSetArray(flagDirNeu, iDir):
                     if nNeumannArrays > 0:
                         # Loop over Neumann data sets
                         for iDir in range(1, nNeumannArrays + 1):
-
                             # Get the data set
                             bcDSetArr = getBocoDataSetArray(BCDATATYPE["Neumann"], iDir)
 
@@ -3067,7 +3044,6 @@ def mergeGrid(grid):
     blocks in the mesh"""
 
     def fullFace(blk, ptRange):
-
         # Face size of the patch:
         fSize = abs(ptRange[:, 1] - ptRange[:, 0])
 
@@ -3101,7 +3077,6 @@ def faceID(ptRange, blk):
     cont = True
     iteration = 0
     while cont:
-
         # First create a mapping of the blocks from the name to the index
         zoneMap = {}
 
@@ -3117,7 +3092,6 @@ def faceID(ptRange, blk):
 
             # We haven't used this block yet:
             if blockUsed[i] == 0:
-
                 # Loop over the B2B of this block:
                 for b2b in blk.B2Bs:
                     otherIndex = zoneMap[b2b.donorName]
@@ -3131,7 +3105,6 @@ def faceID(ptRange, blk):
                         and blockUsed[otherIndex] == 0
                         and i != otherIndex
                     ):
-
                         print("Merging:", i + 1, otherIndex + 1)
 
                         # Great! These block match. Let's make the new
@@ -3253,7 +3226,6 @@ def faceID(ptRange, blk):
                         # block. This is tricky since we need to
                         # offset and potentially reorient them .
                         for boco in otherBlk.bocos:
-
                             tmp = boco.ptRange.copy()
                             if face > 0:
                                 # blk then otherBlk. BCs need to be increemented by offset.
@@ -3331,7 +3303,6 @@ def faceID(ptRange, blk):
 
 
 def combineGrids(grids, useOldNames=False):
-
     """Method that takes in a list of grids and returns a new grid object
     containing all zones from each grid. The blocks are renamed as
     there could (almost most certainly) be conflicts between the zone
@@ -3346,7 +3317,6 @@ def combineGrids(grids, useOldNames=False):
     # as the corresponding keys
     gridDict = {}
     for grid in grids:
-
         # Create a dictionary of copies so the original grids are not modified
         gridDict[grid.name] = copy.deepcopy(grid)
 
@@ -3360,7 +3330,6 @@ def combineGrids(grids, useOldNames=False):
     # to the newGrid object
 
     for name in nameList:
-
         # Get the grid object corresponding to this name
         grid = gridDict[name]
 
@@ -3457,7 +3426,6 @@ def explodeByZoneName(grid):
 
     # Loop over all keys and add the grid to the output list
     for name in nameList:
-
         # Now rename the blocks, bcs and redo-connectivity, only if we have full mesh
         gridDict[name].renameBlocks(useOldNames=True)
         gridDict[name].renameBCs()
@@ -3471,7 +3439,6 @@ def explodeByZoneName(grid):
 
 
 def write_tecplot_file(filename, title, variable_names, data_points):
-
     """
     Auxiliary function that writes tecplot files
     """

diff --git a/config/defaults/config.LINUX_GFORTRAN.mk b/config/defaults/config.LINUX_GFORTRAN.mk
@@ -5,7 +5,7 @@
 CGNS_INCLUDE_FLAGS=-I$(CGNS_HOME)/include
 CGNS_LINKER_FLAGS=-L$(CGNS_HOME)/lib -lcgns
 
-# Gfortran compiler
+# GCC
 CC = gcc
 CFLAGS = -O2 -fPIC
 FC = gfortran

diff --git a/config/defaults/config.LINUX_INTEL.mk b/config/defaults/config.LINUX_INTEL.mk
@@ -5,8 +5,8 @@
 CGNS_INCLUDE_FLAGS=-I$(CGNS_HOME)/include
 CGNS_LINKER_FLAGS=-L$(CGNS_HOME)/lib -lcgns
 
-# Intel Fortran Compiler
-CC = gcc
+# Intel compilers
+CC = icc
 CFLAGS = -O2 -fPIC
 FC = ifort
 FFLAGS = -O2 -r8 -g -fPIC -stand f08

diff --git a/tests/test_cgnsutilities.py b/tests/test_cgnsutilities.py
@@ -157,7 +157,6 @@ def setUp(self):
         self.grid = readGrid(os.path.abspath(os.path.join(baseDir, "../examples/block_4x2x3.cgns")))
 
     def test_coarsen(self):
-
         self.grid.coarsen()
         for iDim in range(3):
             self.assertEqual(2, self.grid.blocks[0].dims[iDim])
@@ -249,7 +248,6 @@ def setUp(self):
         self.grids = [self.grid1, self.grid2]
 
     def test_combineGrids(self, train=False):
-
         combinedNewNames = combineGrids(self.grids)
         combinedOldNames = combineGrids(self.grids, useOldNames=True)
 
@@ -291,7 +289,6 @@ def test_combineGrids(self, train=False):
         )
 
     def test_mirror(self):
-
         # Test mirroring function with useOldNames=True option
         newNameList = [
             "domain.00001",
@@ -334,7 +331,6 @@ def test_mirror(self):
 
 
 class TestExamples(unittest.TestCase):
-
     # Get all example scripts in the example folder and its subfolders
     exampleDir = os.path.abspath(os.path.join(baseDir, "../examples"))
     examples = []