Merge pull request #119 from kaschau/gDot

Using g. not gv.
kaschau · Mar 11, 2022 · 83d8435 · 83d8435
2 parents 07f8364 + 5681da2
commit 83d8435
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Showing 9 changed files with 20 additions and 24 deletions.
diff --git a/src/peregrinepy/readers/readGrid.py b/src/peregrinepy/readers/readGrid.py
@@ -21,7 +21,7 @@ def readGrid(mb, path="./"):
     """
 
     for blk in mb:
-        fileName = f"{path}/gv.{blk.nblki:06d}.h5"
+        fileName = f"{path}/g.{blk.nblki:06d}.h5"
         if blk.blockType == "solver":
             ng = blk.ng
             readS = np.s_[ng:-ng, ng:-ng, ng:-ng]

diff --git a/src/peregrinepy/writers/parallelWriter.py b/src/peregrinepy/writers/parallelWriter.py
@@ -95,13 +95,13 @@ def registerParallelXdmf(mb, blocksForProcs, path="./", gridPath="./", animate=T
             dataXElem.set("Dimensions", f"{nk} {nj} {ni}")
             dataXElem.set("Precision", "8")
             dataXElem.set("Format", "HDF")
-            dataXElem.text = f"{gridPath}/gv.{nblki:06d}.h5:/coordinates/x"
+            dataXElem.text = f"{gridPath}/g.{nblki:06d}.h5:/coordinates/x"
 
             geometryElem.append(deepcopy(dataXElem))
-            geometryElem[-1].text = f"{gridPath}/gv.{nblki:06d}.h5:/coordinates/y"
+            geometryElem[-1].text = f"{gridPath}/g.{nblki:06d}.h5:/coordinates/y"
 
             geometryElem.append(deepcopy(dataXElem))
-            geometryElem[-1].text = f"{gridPath}/gv.{nblki:06d}.h5:/coordinates/z"
+            geometryElem[-1].text = f"{gridPath}/g.{nblki:06d}.h5:/coordinates/z"
 
             # Only solvers will call this
             names = ["rho", "p", "T"] + mb[0].speciesNames

diff --git a/src/peregrinepy/writers/writeGrid.py b/src/peregrinepy/writers/writeGrid.py
@@ -50,7 +50,7 @@ def writeGrid(mb, path="./", precision="double", withHalo=False):
         else:
             writeS = np.s_[:, :, :]
 
-        with h5py.File(f"{path}/gv.{blk.nblki:06d}.h5", "w") as f:
+        with h5py.File(f"{path}/g.{blk.nblki:06d}.h5", "w") as f:
             f.create_group("coordinates")
             f.create_group("dimensions")
 
@@ -94,19 +94,19 @@ def writeGrid(mb, path="./", precision="double", withHalo=False):
         dataX1Elem.set("Dimensions", f"{blk.nk+2*ng} {blk.nj+2*ng} {blk.ni+2*ng}")
         dataX1Elem.set("Precision", "8")
         dataX1Elem.set("Format", "HDF")
-        dataX1Elem.text = f"gv.{blk.nblki:06d}.h5:/coordinates/x"
+        dataX1Elem.text = f"g.{blk.nblki:06d}.h5:/coordinates/x"
 
         geometryElem.append(deepcopy(dataX1Elem))
-        geometryElem[-1].text = f"gv.{blk.nblki:06d}.h5:/coordinates/y"
+        geometryElem[-1].text = f"g.{blk.nblki:06d}.h5:/coordinates/y"
 
         geometryElem.append(deepcopy(dataX1Elem))
-        geometryElem[-1].text = f"gv.{blk.nblki:06d}.h5:/coordinates/z"
+        geometryElem[-1].text = f"g.{blk.nblki:06d}.h5:/coordinates/z"
 
         gridElem.append(deepcopy(blockElem))
 
         if mb.mbType in ["grid", "restart"]:
             progressBar(blk.nblki + 1, len(mb), f"Writing out block {blk.nblki}")
 
     et = etree.ElementTree(xdmfElem)
-    save_file = f"{path}/gv.xmf"
+    save_file = f"{path}/g.xmf"
     et.write(save_file, pretty_print=True, encoding="UTF-8", xml_declaration=True)
diff --git a/src/peregrinepy/writers/writeRestart.py b/src/peregrinepy/writers/writeRestart.py
@@ -118,13 +118,13 @@ def writeRestart(mb, path="./", gridPath="./", animate=True, precision="double")
         dataXElem.set("Dimensions", f"{blk.nk} {blk.nj} {blk.ni}")
         dataXElem.set("Precision", "8")
         dataXElem.set("Format", "HDF")
-        dataXElem.text = f"{gridPath}/gv.{blk.nblki:06d}.h5:/coordinates/x"
+        dataXElem.text = f"{gridPath}/g.{blk.nblki:06d}.h5:/coordinates/x"
 
         geometryElem.append(deepcopy(dataXElem))
-        geometryElem[-1].text = f"{gridPath}/gv.{blk.nblki:06d}.h5:/coordinates/y"
+        geometryElem[-1].text = f"{gridPath}/g.{blk.nblki:06d}.h5:/coordinates/y"
 
         geometryElem.append(deepcopy(dataXElem))
-        geometryElem[-1].text = f"{gridPath}/gv.{blk.nblki:06d}.h5:/coordinates/z"
+        geometryElem[-1].text = f"{gridPath}/g.{blk.nblki:06d}.h5:/coordinates/z"
 
         if blk.blockType == "solver":
             names = ["rho", "p", "T"] + blk.speciesNames

diff --git a/utilities/analyzeGrid.py b/utilities/analyzeGrid.py
@@ -53,9 +53,7 @@ def analyzeGrid(mb):
     args = parser.parse_args()
     gp = args.gridDir
 
-    nblks = len(
-        [i for i in os.listdir(gp) if i.startswith("gv.") and i.endswith(".h5")]
-    )
+    nblks = len([i for i in os.listdir(gp) if i.startswith("g.") and i.endswith(".h5")])
 
     mb = mbg(nblks)
     readGrid(mb, gp)

diff --git a/utilities/cutGrid.py b/utilities/cutGrid.py
@@ -380,7 +380,7 @@ def performCutOperations(mb, cutOps):
         metavar="<fromDir>",
         dest="fromDir",
         default="./from",
-        help="Directory containing the gv.* and conn.yaml files to cut. Default is ./from",
+        help="Directory containing the g.* and conn.yaml files to cut. Default is ./from",
         type=str,
     )
     parser.add_argument(

diff --git a/utilities/interpolate.py b/utilities/interpolate.py
@@ -39,7 +39,7 @@
         metavar="<fromDir>",
         dest="fromDir",
         default="./from",
-        help="Directory containing the gv.*.h5 and q.*.h5 files to interpolate from. Default is ./from",
+        help="Directory containing the g.*.h5 and q.*.h5 files to interpolate from. Default is ./from",
         type=str,
     )
     parser.add_argument(
@@ -49,7 +49,7 @@
         metavar="<toDir>",
         dest="toDir",
         default="./to",
-        help="Directory containing the gv.*.h5 files to interpolate to. Default is ./to",
+        help="Directory containing the g.*.h5 files to interpolate to. Default is ./to",
         type=str,
     )
     parser.add_argument(
@@ -102,7 +102,7 @@
 
     # Read in from data
     nblkFrom = len(
-        [i for i in os.listdir(fromDir) if i.startswith("gv.") and i.endswith(".h5")]
+        [i for i in os.listdir(fromDir) if i.startswith("g.") and i.endswith(".h5")]
     )
     mbFrom = mbr(nblkFrom, speciesNames)
     fromNrst = int(
@@ -113,7 +113,7 @@
 
     # Read in to data
     nblkTo = len(
-        [i for i in os.listdir(toDir) if i.startswith("gv.") and i.endswith(".h5")]
+        [i for i in os.listdir(toDir) if i.startswith("g.") and i.endswith(".h5")]
     )
     mbTo = mbr(nblkTo, speciesNames)
     readGrid(mbTo, toDir)

diff --git a/utilities/loadBalancer.py b/utilities/loadBalancer.py
@@ -74,7 +74,7 @@ def allBlocksAssigned(mb, procGroups):
         metavar="<fromDir>",
         dest="fromDir",
         default="./",
-        help="Directory containing the gv.* files. Default is ./",
+        help="Directory containing the g.* files. Default is ./",
         type=str,
     )
     parser.add_argument(

diff --git a/utilities/verifyGrid.py b/utilities/verifyGrid.py
@@ -234,9 +234,7 @@ def extractFace(blk, nface):
 
     gp = args.gridPath
     cp = args.connPath
-    nblks = len(
-        [i for i in os.listdir(gp) if i.startswith("gv.") and i.endswith(".h5")]
-    )
+    nblks = len([i for i in os.listdir(gp) if i.startswith("g.") and i.endswith(".h5")])
     assert nblks > 0
     mb = pg.multiBlock.grid(nblks)