updated notebooks to phiflow 3.1

fixed cleanup script
SoL training updated for phiflow3.1 and new data loader
2024-10-09 12:17:46 +08:00 · 2024-10-09 10:36:24 +08:00 · 2024-10-08 13:30:33 +08:00 · 2024-09-25 14:52:34 +08:00 · 2024-09-17 11:07:01 +08:00 · 2024-09-12 17:20:19 +08:00
9 changed files with 1946 additions and 2129 deletions
--- a/diffphys-code-burgers.ipynb
+++ b/diffphys-code-burgers.ipynb
@@ -32,7 +32,7 @@
   },
   "outputs": [],
   "source": [
-    "!pip install --upgrade --quiet phiflow==2.2\n",
+    "!pip install --upgrade --quiet phiflow==3.1\n",
    "from phi.tf.flow import *\n",
    "\n",
    "N = 128\n",
--- a/diffphys-code-ns.ipynb
+++ b/diffphys-code-ns.ipynb
@@ -86,7 +86,7 @@
   },
   "outputs": [],
   "source": [
-    "!pip install --upgrade --quiet phiflow==2.2\n",
+    "!pip install --upgrade --quiet phiflow==3.1\n",
    "from phi.torch.flow import *  \n",
    "import pylab # for visualizations later on"
   ]
--- a/diffphys-code-sol.ipynb
+++ b/diffphys-code-sol.ipynb
--- a/json-cleanup-for-pdf.py
+++ b/json-cleanup-for-pdf.py
@@ -8,152 +8,154 @@ pdfMode = True

 print(format(sys.argv))
 if len(sys.argv)>1:
-	if int(sys.argv[1])>0:
-		print("WWW mode on")
-		pdfMode = False
+    if int(sys.argv[1])>0:
+        print("WWW mode on")
+        pdfMode = False

 fileList = [ 
-	"diffphys-code-burgers.ipynb", "diffphys-code-ns.ipynb", "diffphys-code-sol.ipynb", "physicalloss-code.ipynb", # TF
-	"bayesian-code.ipynb", "supervised-airfoils.ipynb", # pytorch
-	"reinflearn-code.ipynb", # phiflow
-	"physgrad-comparison.ipynb", # jax
-	"physgrad-code.ipynb", # pip
-	]
+    "diffphys-code-burgers.ipynb", "diffphys-code-ns.ipynb", "diffphys-code-sol.ipynb", "physicalloss-code.ipynb", # TF
+    "bayesian-code.ipynb", "supervised-airfoils.ipynb", # pytorch
+    "reinflearn-code.ipynb", # phiflow
+    "physgrad-comparison.ipynb", # jax
+    "physgrad-code.ipynb", # pip
+    ]

 #fileList = [ "physgrad-code.ipynb"] # debug, only 1 file
-#fileList = [ "t1.ipynb" ] # debug
+#fileList = [ "diffphys-code-sol.ipynb" ] # debug


 # main

 for fnOut in fileList:
-	if not os.path.isfile(fnOut):
-		print("Error: "+fnOut+" not found!"); exit(1)
+    if not os.path.isfile(fnOut):
+        print("Error: "+fnOut+" not found!"); exit(1)

-	# create backups
-	fn0 = fnOut[:-5] + "bak"
-	fn = fn0 + "0"; cnt = 0
-	while os.path.isfile(fn):
-		#print("Error: "+fn+" already exists!"); exit(1)
-		print("Warning: "+fn+" already exists!")
-		fn = fn0 + format(cnt); cnt=cnt+1
+    # create backups
+    fn0 = fnOut[:-5] + "bak"
+    fn = fn0 + "0"; cnt = 0
+    while os.path.isfile(fn):
+        #print("Error: "+fn+" already exists!"); exit(1)
+        print("Warning: "+fn+" already exists!")
+        fn = fn0 + format(cnt); cnt=cnt+1

-	print("renaming "+fnOut+ " to "+fn )
-	if os.path.isfile(fnOut):
-		os.rename(fnOut, fn)
-	if not os.path.isfile(fn):
-		print("Error: "+fn+" missing!")
-		exit(1)
+    print("renaming "+fnOut+ " to "+fn )
+    if os.path.isfile(fnOut):
+        os.rename(fnOut, fn)
+    if not os.path.isfile(fn):
+        print("Error: "+fn+" missing!")
+        exit(1)

-	with open(fn) as file:
-		d = json.load(file)
+    with open(fn) as file:
+        d = json.load(file)

-	#print(d.keys()) #print(d["cells"][0].keys())
+    #print(d.keys()) #print(d["cells"][0].keys())

-	# remove TF / pytorch warnings, build list of regular expressions to search for
-	# double check, redundant with removing stderr cells (cf delE)
-	res = []
-	res.append( re.compile(r"WARNING:tensorflow:") )
-	res.append( re.compile(r"UserWarning:") )
-	res.append( re.compile(r"DeprecationWarning:") )
-	res.append( re.compile(r"InsecureRequestWarning") ) # for https download
-	res.append( re.compile(r"Building wheel") ) # phiflow install, also gives weird unicode characters
-	res.append( re.compile(r"warnings.warn") )  # phiflow warnings
-	res.append( re.compile(r"WARNING:absl") )  # jax warnings
+    # remove TF / pytorch warnings, build list of regular expressions to search for
+    # double check, redundant with removing stderr cells (cf delE)
+    res = []
+    res.append( re.compile(r"WARNING:tensorflow:") )
+    res.append( re.compile(r"UserWarning:") )
+    res.append( re.compile(r"DeprecationWarning:") )
+    res.append( re.compile(r"InsecureRequestWarning") ) # for https download
+    res.append( re.compile(r"Building wheel") ) # phiflow install, also gives weird unicode characters
+    res.append( re.compile(r"warnings.warn") )  # phiflow warnings
+    res.append( re.compile(r"WARNING:absl") )  # jax warnings

-	res.append( re.compile(r"ERROR: pip") )  # pip dependencies
-	res.append( re.compile(r"requires imgaug") )  # pip dependencies
-	res.append( re.compile(r"See the documentation of nn.Upsample") )  # pip dependencies
+    res.append( re.compile(r"ERROR: pip") )  # pip dependencies
+    res.append( re.compile(r"requires imgaug") )  # pip dependencies
+    res.append( re.compile(r"See the documentation of nn.Upsample") )  # pip dependencies

-	# remove all "warnings.warn" from phiflow?
+    # remove all "warnings.warn" from phiflow?

-	# shorten data line: "0.008612174447657694, 0.02584669669548606, 0.043136357266407785"
-	reD = re.compile(r"\[0.008612174447657694, 0.02584669669548606, 0.043136357266407785.+\]" )
-	reDt = "[0.008612174447657694, 0.02584669669548606, 0.043136357266407785 ... ]"
+    # shorten data line: "0.008612174447657694, 0.02584669669548606, 0.043136357266407785"
+    reD = re.compile(r"\[0.008612174447657694, 0.02584669669548606, 0.043136357266407785.+\]" )
+    reDt = "[0.008612174447657694, 0.02584669669548606, 0.043136357266407785 ... ]"

-	t="cells"
-	okay = 0
-	deletes = 0
-	for i in range(len(d[t])):
-		#for i in range(len(d[t])):
-			#print(d[t][0]["cell_type"])
-		#print(d[t][i]["cell_type"])
+    t="cells"
+    okay = 0
+    deletes = 0
+    for i in range(len(d[t])):
+        #for i in range(len(d[t])):
+            #print(d[t][0]["cell_type"])
+        #print(d[t][i]["cell_type"])

-		# remove images after code
+        # remove images after code

-		if d[t][i]["cell_type"]=="code":
-			#print(d[t][i].keys())
-			#d[t][i]["outputs"] = ""
-			#print(d[t][i]["outputs"])
+        if d[t][i]["cell_type"]=="code":
+            #print(d[t][i].keys())
+            #d[t][i]["outputs"] = ""
+            #print(d[t][i]["outputs"])

-			if pdfMode:
-				for j in range(len( d[t][i]["source"] )):
-					#print( d[t][i]["source"][j] )
-					#print( type(d[t][i]["source"][j] ))
-					dsOut = reD.sub( reDt, d[t][i]["source"][j] )  # replace long number string (only for burgers)
-					d[t][i]["source"][j] = dsOut
-					deletes = deletes+1
-					#print( d[t][i]["source"][j] +"\n >>> \n" +d2 )
+            if pdfMode:
+                for j in range(len( d[t][i]["source"] )):
+                    #print( d[t][i]["source"][j] )
+                    #print( type(d[t][i]["source"][j] ))
+                    dsOut = reD.sub( reDt, d[t][i]["source"][j] )  # replace long number string (only for burgers)
+                    d[t][i]["source"][j] = dsOut
+                    deletes = deletes+1
+                    #print( d[t][i]["source"][j] +"\n >>> \n" +d2 )

-			delE = [] # collect whole entries (sections) to delete
+            delE = [] # collect whole entries (sections) to delete

-			#print(len( d[t][i]["outputs"] ))
-			for j in range(len( d[t][i]["outputs"] )):
-				#print(type( d[t][i]["outputs"][j] ))
-				#print( d[t][i]["outputs"][j].keys() )
+            #print(len( d[t][i]["outputs"] ))
+            for j in range(len( d[t][i]["outputs"] )):
+                #print(type( d[t][i]["outputs"][j] ))
+                #print( d[t][i]["outputs"][j].keys() )

-				# search for error stderr cells
-				if d[t][i]["outputs"][j]["output_type"]=="stream":
-					#print("output j name: "+ format( d[t][i]["outputs"][j]["name"] ) )
-					#print("output j: "+ format( d[t][i]["outputs"][j] ) )
-					if d[t][i]["outputs"][j]["name"]=="stderr":
-						print("stderr found! len text "+ format(len( d[t][i]["outputs"][j]["text"]) ) +", removing entry "+format(j) )
-						delE.append(j) # remove the whole stderr entry
+                # search for error stderr cells
+                if d[t][i]["outputs"][j]["output_type"]=="stream":
+                    #print("output j name: "+ format( d[t][i]["outputs"][j]["name"] ) )
+                    #print("output j: "+ format( d[t][i]["outputs"][j] ) )
+                    if d[t][i]["outputs"][j]["name"]=="stderr":
+                        print("stderr found! len text "+ format(len( d[t][i]["outputs"][j]["text"]) ) +", removing entry "+format(j) )
+                        delE.append(j) # remove the whole stderr entry

-				# images
-				if d[t][i]["outputs"][j]["output_type"]=="stream":
-					#print("len "+  format(len( d[t][i]["outputs"][j]["text"] )) )
+                # images
+                if d[t][i]["outputs"][j]["output_type"]=="stream":
+                    #print("len "+  format(len( d[t][i]["outputs"][j]["text"] )) )

-					dell = [] # collect lines to delete
-					for k in range(  len( d[t][i]["outputs"][j]["text"] )  ):
-						#print(" tout "+   d[t][i]["outputs"][j]["text"][k] ) # debug , print all lines
-						nums = []; all_good = True
-						for rr in range(len(res)):
-							nums.append( res[rr].search( d[t][i]["outputs"][j]["text"][k] ) )
-							if nums[-1] is not None:
-								all_good = False # skip!
+                    dell = [] # collect lines to delete
+                    for k in range(  len( d[t][i]["outputs"][j]["text"] )  ):
+                        #print(" tout "+   d[t][i]["outputs"][j]["text"][k] ) # debug , print all lines - ACTIVATE to LOCATE errors
+                        nums = []; all_good = True
+                        for rr in range(len(res)):
+                            nums.append( res[rr].search( d[t][i]["outputs"][j]["text"][k] ) )
+                            if nums[-1] is not None:
+                                all_good = False # skip!

-						if all_good:
-							okay = okay+1
-						else: # delete line "dell"
-							deletes = deletes+1
-							dell.append(d[t][i]["outputs"][j]["text"][k])
-							#print( format(nums) +"  " + d[t][i]["outputs"][j]["text"][k] ) # len( d[t][i]["outputs"][j]["text"][k] ) )
+                        if all_good:
+                            okay = okay+1
+                        else: # delete line "dell"
+                            deletes = deletes+1
+                            dell.append(d[t][i]["outputs"][j]["text"][k])
+                            #print( format(nums) +"  " + d[t][i]["outputs"][j]["text"][k] ) # len( d[t][i]["outputs"][j]["text"][k] ) )

-					for dl in dell:
-						d[t][i]["outputs"][j]["text"].remove(dl)
-				#print("len after "+format( len( d[t][i]["outputs"][j]["text"] )) + " A") # debug
+                    for dl in dell:
+                        d[t][i]["outputs"][j]["text"].remove(dl)
+                #print("len after "+format( len( d[t][i]["outputs"][j]["text"] )) + " A") # debug

-			# afterwards (potentially remove whole entries)
-			# if len(delE)>0:
-			# 	print("len bef "+format( len( d[t][i]["outputs"] )) + " A " + format(delE)) # debug
-			for de in delE:
-				#print(type(d[t][i]["outputs"])); print(de)
-				d[t][i]["outputs"].pop(de) # remove array element
-				deletes+=1
-			# if len(delE)>0:
-			# 	print("len after "+format( len( d[t][i]["outputs"] )) + " A") # debug
+            # afterwards (potentially remove whole entries)
+            if len(delE)>0:
+                delE.sort(reverse=True)
+                #print("len bef "+format( len( d[t][i]["outputs"] )) + " A " + format(delE)) # debug
+            
+            for de in delE: 
+                #print(type(d[t][i]["outputs"])); print(de)
+                d[t][i]["outputs"].pop(de) # remove array element
+                deletes+=1
+            # if len(delE)>0:
+            # 	print("len after "+format( len( d[t][i]["outputs"] )) + " A") # debug

-	if deletes==0:
-		print("Warning: Nothing found in "+fn+"!")
-		if not os.path.isfile(fnOut):
-			os.rename(fn, fnOut)
-		else:
-			print("Error, both files exist!?")
-			exit(1)
+    if deletes==0:
+        print("Warning: Nothing found in "+fn+"!")
+        if not os.path.isfile(fnOut):
+            os.rename(fn, fnOut)
+        else:
+            print("Error, both files exist!?")
+            exit(1)

-	else:
-		print(" ... writing "+fnOut )
-		with open(fnOut,'w') as fileOut:
-			json.dump(d,fileOut, indent=1, sort_keys=True)
+    else:
+        print(" ... writing "+fnOut )
+        with open(fnOut,'w') as fileOut:
+            json.dump(d,fileOut, indent=1, sort_keys=True)

--- a/make-pdf.sh
+++ b/make-pdf.sh
@@ -10,7 +10,6 @@ echo
 echo WARNING - still requires one manual quit of first pdf/latex pass, use shift-x to quit
 echo

-PYT=python3.7
 PYT=python3

 # warning - modifies notebooks!
@@ -18,9 +17,21 @@ ${PYT} json-cleanup-for-pdf.py

 # clean / remove _build dir ?

-# GEN!
+/Users/thuerey/Library/Python/3.9/bin/jupyter-book build . 
+xelatex book
+
+exit # sufficient for newer jupyter book versions
+
+
+
+
+
+
+# old "pre" GEN
 #/Users/thuerey/Library/Python/3.7/bin/jupyter-book build . --builder pdflatex
-/Users/thuerey/Library/Python/3.9/bin/jupyter-book build . --builder pdflatex
+#/Users/thuerey/Library/Python/3.9/bin/jupyter-book build . --builder pdflatex
+
+# old cleanup

 cd _build/latex
 #mv book.pdf book-xetex.pdf # not necessary, failed anyway
--- a/overview-burgers-forw.ipynb
+++ b/overview-burgers-forw.ipynb
@@ -45,12 +45,12 @@
     "name": "stdout",
     "output_type": "stream",
     "text": [
-      "Using phiflow version: 2.2.0\n"
+      "Using phiflow version: 3.1.0\n"
     ]
    }
   ],
   "source": [
-    "!pip install --upgrade --quiet phiflow==2.2\n",
+    "!pip install --upgrade --quiet phiflow==3.1\n",
    "from phi.flow import *\n",
    "\n",
    "from phi import __version__\n",
--- a/overview-ns-forw.ipynb
+++ b/overview-ns-forw.ipynb
--- a/physgrad-code.ipynb
+++ b/physgrad-code.ipynb
--- a/references.bib
+++ b/references.bib
@@ -25,7 +25,7 @@
@inproceedings{liu2024airfoils,
 	  title={Uncertainty-aware Surrogate Models for Airfoil Flow Simulations with Denoising Diffusion Probabilistic Models},
 	  author={Liu, Qiang and Thuerey, Nils},
-	  booktitle={Journal of the American Institute of Aeronautics and Astronautics},
+	  booktitle={Journal of the American Institute of Aeronautics and Astronautics, 62(8)},
 	  year={2024},
 }

@@ -72,7 +72,7 @@
  title={Learning Similarity Metrics for Volumetric Simulations with Multiscale CNNs},
  author={Kohl, Georg and Chen, Li-Wei and Thuerey, Nils},
  booktitle={AAAI Conference on Artificial Intelligence},
-  year={2022}
+  year={2022}, 
  url={https://github.com/tum-pbs/VOLSIM},
 }
Author	SHA1	Message	Date
N_T	245a81bfa5	updated notebooks to phiflow 3.1	2024-10-09 12:17:46 +08:00
N_T	1548db1731	fixed cleanup script	2024-10-09 10:36:24 +08:00
N_T	2db1f59d24	SoL training updated for phiflow3.1 and new data loader	2024-10-08 13:30:33 +08:00
N_T	4afc1c816e	Updated SOL code	2024-09-25 14:52:34 +08:00
N_T	85c12f7d52	updated SOL	2024-09-17 11:07:01 +08:00
N_T	3d1819c1eb	Updated references	2024-09-12 17:20:19 +08:00