From 0abc2afe7c62706f8949f7e39ed576882688eaf1 Mon Sep 17 00:00:00 2001
From: Gerhard Holzinger <gerhard.holzinger@k1-met.com>
Date: Thu, 12 Feb 2026 17:00:25 +0100
Subject: [PATCH 1/3] Adjust some of thg Python code for modern numpy, remove
 use of old Numeric Python module

The Numeric module of SciPy has been deprecated for quite a while.
In fact, we find a commit changing from Numeric to numpy from 2006
https://github.com/scipy/scipy/commit/574897ffbff8cac6f13e2974f5221c9e150d7378

numpy, under its current name numpy, is around since 2006.
https://en.wikipedia.org/wiki/NumPy

With Python-3 being release in 2008, we feel there is no need, let alone
justification, to support a pre-2008 numerics module in the Python-3 branch of LPP.

The code was adjusted such that numpy module is loaded, and if this fails an exception is raised
instead of falling back to the older Numeric module.

--------------------------------------------------------------------------------------------------

We furthermore made some adjustments, which relate to recent versions of numpy specifically.

* do not use the type np.float; use float

With release of numpy-1.20, the use of the type np.float as an alias for the build-in float type
has been deprecated. With the release of numpy-1.24, this has been finally removed.

https://numpy.org/devdocs/release/1.20.0-notes.html
https://numpy.org/devdocs/release/1.24.0-notes.html

The time between a feature being considered deprecated and being finally removed is not
fixed. However, there is an official policy document discussing this.

https://numpy.org/neps/nep-0023-backwards-compatibility.html

* do not use atoms != [] to test for atoms being empty; use atoms.size > 0

We have not been able to find the reason why this poses no problem using numpy-1.21.5 on
Python-3.10.12; however with numpy-2.2.6 under Python-3.10.12 this comparison does not work anymore.

The release notes of numpy-1.25 discuss the use of == and != operators on arrays in the Expired Deprecations
section, i.e., these features were removed.

https://numpy.org/doc/2.0/release/1.25.0-notes.html
---
 src/__pycache__/DEFAULTS.cpython-310.pyc | Bin 0 -> 205 bytes
 src/__pycache__/dump.cpython-310.pyc     | Bin 0 -> 29272 bytes
 src/__pycache__/vtk.cpython-310.pyc      | Bin 0 -> 9118 bytes
 src/bdump.py                             |   9 +++------
 src/dump.py                              |  10 +++-------
 src/ldump.py                             |   9 +++------
 src/mdump.py                             |   9 +++------
 src/tdump.py                             |   9 +++------
 src/vtk.py                               |   6 ++++--
 9 files changed, 19 insertions(+), 33 deletions(-)
 create mode 100644 src/__pycache__/DEFAULTS.cpython-310.pyc
 create mode 100644 src/__pycache__/dump.cpython-310.pyc
 create mode 100644 src/__pycache__/vtk.cpython-310.pyc

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diff --git a/src/bdump.py b/src/bdump.py
index ac75c04..2a67860 100644
--- a/src/bdump.py
+++ b/src/bdump.py
@@ -68,11 +68,9 @@
 #     atoms[i][j] = 2d array of floats, i = 0 to natoms-1, j = 0 to ncols-1
 
 try:
-    import numpy as np
-    oldnumeric = False
+  import numpy as np
 except:
-    import Numeric as np
-    oldnumeric = True
+  raise Exception("no numpy Python module available")
 
 try: from DEFAULTS import PIZZA_GUNZIP
 except: PIZZA_GUNZIP = "gunzip"
@@ -188,8 +186,7 @@ def read_snapshot(self,f):
         for i in range(1,snap.natoms):
           words += f.readline().split()
         floats = list(map(float,words))
-        if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float)
-        else: atoms = np.zeros((snap.natoms,ncol),np.float)
+        atoms = np.zeros((snap.natoms,ncol),float)
         start = 0
         stop = ncol
         for i in range(snap.natoms):
diff --git a/src/dump.py b/src/dump.py
index 6d6280b..5e9f3f4 100644
--- a/src/dump.py
+++ b/src/dump.py
@@ -191,10 +191,8 @@
 
 try:
   import numpy as np
-  oldnumeric = False
 except:
-  import Numeric as np
-  oldnumeric = True
+  raise Exception("no numpy Python module available")
 
 try: from DEFAULTS import PIZZA_GUNZIP
 except: PIZZA_GUNZIP = "gunzip"
@@ -418,8 +416,7 @@ def read_snapshot(self,f):
         for i in range(1,snap.natoms):
           words += f.readline().split()
         floats = list(map(float,words))
-        if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float)
-        else: atoms = np.zeros((snap.natoms,ncol),np.float)
+        atoms = np.zeros((snap.natoms,ncol),float)
         start = 0
         stop = ncol
         for i in range(snap.natoms):
@@ -887,8 +884,7 @@ def newcolumn(self,str):
     self.map(ncol+1,str)
     for snap in self.snaps:
       atoms = snap.atoms
-      if oldnumeric: newatoms = np.zeros((snap.natoms,ncol+1),np.Float)
-      else: newatoms = np.zeros((snap.natoms,ncol+1),np.float)
+      newatoms = np.zeros((snap.natoms,ncol+1),float)
       newatoms[:,0:ncol] = snap.atoms
       snap.atoms = newatoms
 
diff --git a/src/ldump.py b/src/ldump.py
index 8660afe..a30d7eb 100644
--- a/src/ldump.py
+++ b/src/ldump.py
@@ -75,11 +75,9 @@
 #     atoms[i][j] = 2d array of floats, i = 0 to natoms-1, j = 0 to ncols-1
 
 try:
-    import numpy as np
-    oldnumeric = False
+  import numpy as np
 except:
-    import Numeric as np
-    oldnumeric = True
+  raise Exception("no numpy Python module available")
 
 try: from DEFAULTS import PIZZA_GUNZIP
 except: PIZZA_GUNZIP = "gunzip"
@@ -202,8 +200,7 @@ def read_snapshot(self,f):
         for i in range(1,snap.natoms):
           words += f.readline().split()
         floats = list(map(float,words))
-        if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float)
-        else: atoms = np.zeros((snap.natoms,ncol),np.float)
+        atoms = np.zeros((snap.natoms,ncol),float)
         start = 0
         stop = ncol
         for i in range(snap.natoms):
diff --git a/src/mdump.py b/src/mdump.py
index 714add5..37aa5df 100644
--- a/src/mdump.py
+++ b/src/mdump.py
@@ -133,11 +133,9 @@
 #     evalues[i][j] = 2d array of floats, i = 0 to Nel-1, j = 0 to Ncol
 
 try:
-    import numpy as np
-    oldnumeric = False
+  import numpy as np
 except:
-    import Numeric as np
-    oldnumeric = True
+  raise Exception("no numpy Python module available")
 
 try: from DEFAULTS import PIZZA_GUNZIP
 except: PIZZA_GUNZIP = "gunzip"
@@ -318,8 +316,7 @@ def read_snapshot(self,f):
         for i in range(1,n):
           words += f.readline().split()
         floats = list(map(float,words))
-        if oldnumeric: values = np.zeros((n,ncol),np.Float)
-        else: values = np.zeros((n,ncol),np.float)
+        values = np.zeros((n,ncol),float)
         start = 0
         stop = ncol
         for i in range(n):
diff --git a/src/tdump.py b/src/tdump.py
index 711551e..b151229 100644
--- a/src/tdump.py
+++ b/src/tdump.py
@@ -76,11 +76,9 @@
 #     atoms[i][j] = 2d array of floats, i = 0 to natoms-1, j = 0 to ncols-1
 
 try:
-    import numpy as np
-    oldnumeric = False
+  import numpy as np
 except:
-    import Numeric as np
-    oldnumeric = True
+  raise Exception("no numpy Python module available")
 
 try: from DEFAULTS import PIZZA_GUNZIP
 except: PIZZA_GUNZIP = "gunzip"
@@ -203,8 +201,7 @@ def read_snapshot(self,f):
         for i in range(1,snap.natoms):
           words += f.readline().split()
         floats = list(map(float,words))
-        if oldnumeric: atoms = np.zeros((snap.natoms,ncol),np.Float)
-        else: atoms = np.zeros((snap.natoms,ncol),np.float)
+        atoms = np.zeros((snap.natoms,ncol),float)
         start = 0
         stop = ncol
         for i in range(snap.natoms):
diff --git a/src/vtk.py b/src/vtk.py
index 96c2dc7..83f4590 100644
--- a/src/vtk.py
+++ b/src/vtk.py
@@ -346,7 +346,8 @@ def particleGran(file,atoms,names,n_values):
       continue
 
     vectortype = 'float'
-    if atoms != []:
+    #if atoms != []:
+    if atoms.size > 0:
       vectortype = typestr(atoms[0][vectors[key]])
       if 'float' in vectortype: vectortype = 'float'
       elif 'int' in vectortype: vectortype = 'int'
@@ -361,7 +362,8 @@ def particleGran(file,atoms,names,n_values):
   # print SCALARS
   for key in scalars.keys():
     scalartype =''
-    if atoms != []:
+    #if atoms != []:
+    if atoms.size > 0:
       scalartype = typestr(atoms[0][scalars[key]])
       if 'float' in scalartype: scalartype = 'float'
       elif 'int' in scalartype: scalartype = 'int'

From 6116d93e093d7f30b87b76373261c5f11ee443f2 Mon Sep 17 00:00:00 2001
From: Gerhard Holzinger <gerhard.holzinger@k1-met.com>
Date: Thu, 12 Feb 2026 17:39:14 +0100
Subject: [PATCH 2/3] remove __pycache__ files

---
 src/__pycache__/DEFAULTS.cpython-310.pyc | Bin 205 -> 0 bytes
 src/__pycache__/dump.cpython-310.pyc     | Bin 29272 -> 0 bytes
 src/__pycache__/vtk.cpython-310.pyc      | Bin 9118 -> 0 bytes
 3 files changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 src/__pycache__/DEFAULTS.cpython-310.pyc
 delete mode 100644 src/__pycache__/dump.cpython-310.pyc
 delete mode 100644 src/__pycache__/vtk.cpython-310.pyc

diff --git a/src/__pycache__/DEFAULTS.cpython-310.pyc b/src/__pycache__/DEFAULTS.cpython-310.pyc
deleted file mode 100644
index 965e46f798779cd57428bfd44c32a55ec520219b..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 205
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diff --git a/src/__pycache__/dump.cpython-310.pyc b/src/__pycache__/dump.cpython-310.pyc
deleted file mode 100644
index bc0faa037e5b7a52e89eb27ab71adee9b30a4b6d..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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From 6b949a7fc7fb48937cc16acafb9c679c2b04f38d Mon Sep 17 00:00:00 2001
From: Gerhard Holzinger <gerhard.holzinger@k1-met.com>
Date: Thu, 12 Feb 2026 17:39:27 +0100
Subject: [PATCH 3/3] added .gitignore

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..bee8a64
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+__pycache__