Updates for running Windows executables from Linux side with WSL, plu…

…s other updates:

 * add note to README about code availability
 * update openpmd_beamphysics requirement
 * interpolate.py: run_cmd include optional t35 filename (needed for WSL)
 * superfish.py: if self.use_container is False, run windows cmd (don't check platform again)
 * writers.py: update deprecated np.complex
 * some comments added to examples about running on WSL or using custom container

README.md

@@ -3,12 +3,18 @@ Python tools for Poisson Superfish calculations
 
 https://laacg.lanl.gov
 
+> :warning: As of April 2024, and since at least May 2023, the download site for
+Poisson/Superfish is unavailable. Unfortunately, we do not have any information
+about when or if it will be made available again. (see https://github.com/ChristopherMayes/PySuperfish/issues/2)
+
 ## Native Windows
 
 Download and install Poisson Supefish from:
 
 https://laacg.lanl.gov
 
+*see note above about availability of Poisson/Superfish files.
+
 ## Docker 
 
 Public (you must provide the executables)

examples/T7_fieldmaps.ipynb

@@ -341,11 +341,18 @@
    "source": [
     "os.remove('TEST.T7')"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -359,7 +366,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.1"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,

requirements.txt

@@ -1,3 +1,3 @@
 numpy
 matplotlib
-pmd_beamphysics
+openpmd_beamphysics

superfish/interpolate.py

@@ -76,9 +76,13 @@ def interpolate2d(sf,
     with open(inifile, 'w') as f:
         f.write("""[global]
 Force1MVperMeter=No""")
+
+    # Needed on WSL, otherwise optional
+    t35file = sf.basename+'.T35'
 
+
     # Run
-    sf.run_cmd('sf7', ifile)
+    sf.run_cmd('sf7', ifile, t35file)
 
     # Get the filename
     t7file = get_t7(sf.path)
@@ -112,4 +116,4 @@ def interpolate2d(sf,
             type = 'magnetic'
         d =  parse_poisson_t7(t7file, type=type)
 
-    return d
+    return d

superfish/superfish.py

@@ -243,17 +243,17 @@ def windows_run_cmd(self, *args):
         return cmd
 
     def run_cmd(self, *cmds, **kwargs):
-        """
-        Runs a command in in self.
+        r"""
+        Runs a command in self.
         
         Example:
             .run_cmd(['C:\LANL\AUTOMESH.EXE', 'TEST.AM'], timeout=1)
         
         """
-        if platform.system() == 'Windows':
-            cmds = self.windows_run_cmd(*cmds)
-        else:
+        if self.use_container:
             cmds = self.container_run_cmd(*cmds)
+        else:
+            cmds = self.windows_run_cmd(*cmds)
 
         self.vprint(f'Running: {cmds}')
 

superfish/writers.py

@@ -82,8 +82,8 @@ def fish_externalfield_data(t7data,
         Ez0_max = 1
 
     components = {}
-    components['electricField/r'] = t7data['Er'].reshape(nr, 1, nz).astype(np.complex) * 1e6/Ez0_max
-    components['electricField/z'] = t7data['Ez'].reshape(nr, 1, nz).astype(np.complex) * 1e6/Ez0_max
+    components['electricField/r'] = t7data['Er'].reshape(nr, 1, nz).astype(complex) * 1e6/Ez0_max
+    components['electricField/z'] = t7data['Ez'].reshape(nr, 1, nz).astype(complex) * 1e6/Ez0_max
     components['magneticField/theta'] = t7data['Hphi'].reshape(nr, 1, nz) * -1j*mu_0/Ez0_max # -i * mu_0
 
 
@@ -246,4 +246,4 @@ def write_poisson_t7(filename, t7data,  fmt='%10.8e'):
 
     np.savetxt(filename, dat, header=header, comments='',  fmt = fmt)
 
-    return filename
+    return filename