h-walk · tpchuckles · Jan 9, 2026 · Jan 6, 2026 · Jan 6, 2026 · Jan 6, 2026
diff --git a/.gitignore b/.gitignore
@@ -47,6 +47,7 @@ Thumbs.db
 
 # Log files
 *.log
+!runAllTests*.log
 logs/
 !tests/runAllTests.log
 

diff --git a/src/pyslice/multislice/calculators.py b/src/pyslice/multislice/calculators.py
@@ -149,13 +149,6 @@ def setup(
         self.cache_levels = cache_levels
         self.max_kx = max_kx
         self.max_ky = max_ky
-
-        # Generate cache key and setup output directory
-        cache_key = self._generate_cache_key(trajectory, aperture, voltage_eV,
-                                           slice_thickness, sampling, probe_positions)
-        #print(cache_key)
-        self.output_dir = Path("psi_data/" + ("torch" if TORCH_AVAILABLE else "numpy") + "_"+cache_key)
-        self.output_dir.mkdir(parents=True, exist_ok=True)
 
         # Set up spatial grids
         xs,ys,zs,lx,ly,lz=gridFromTrajectory(trajectory,sampling=sampling,slice_thickness=slice_thickness)
@@ -187,6 +180,14 @@ def setup(
             self.probe_positions = [(lx/2, ly/2)]  # Center probe
             self.probe_xs = [lx/2] ; self.probe_ys = [ly/2]
 
+        # Generate cache key and setup output directory
+        cache_key = self._generate_cache_key(trajectory, aperture, voltage_eV,
+                                           slice_thickness, sampling, self.probe_positions)
+        #print(cache_key)
+        self.output_dir = Path("psi_data/" + ("torch" if TORCH_AVAILABLE else "numpy") + "_"+cache_key)
+        self.output_dir.mkdir(parents=True, exist_ok=True)
+
+
         # Create probe on the correct device from the start
         self.base_probe = Probe(xs, ys, self.aperture, self.voltage_eV, device=self.device)
 

diff --git a/src/pyslice/multislice/multislice.py b/src/pyslice/multislice/multislice.py
@@ -276,7 +276,7 @@ def aberrate(self,aberrations):
 def aberrationFunction(kxs,kys,wavelength,aberrations): # aberrations should be a dict of Cnm following https://abtem.readthedocs.io/en/latest/user_guide/walkthrough/contrast_transfer_function.html
     dPhi = xp.zeros((len(kxs),len(kys)))
     ks = xp.sqrt( kxs[:,None]**2 + kys[None,:]**2 )
-    theta = xp.atan2( kys[None,:] , kxs[:,None] )
+    theta = xp.arctan2( kys[None,:] , kxs[:,None] )
     for k in aberrations.keys():
         n,m = int(k[1]),int(k[2]) # C03 --> 0,3
         C = aberrations[k] ; phi0 = 0

diff --git a/src/pyslice/postprocessing/wf_data.py b/src/pyslice/postprocessing/wf_data.py
@@ -6,7 +6,7 @@
 from ..multislice.multislice import Probe,aberrationFunction
 from ..data import Signal, Dimensions, Dimension, GeneralMetadata
 from pathlib import Path
-from ..backend import mean
+from ..backend import mean,zeros
 
 try:
     import torch ; xp = torch
@@ -406,7 +406,7 @@ def propagate_free_space(self,dz): # UNITS OF ANGSTROM
     def applyMask(self, radius, realOrReciprocal="reciprocal"):
         if realOrReciprocal == "reciprocal":
             radii = xp.sqrt( self._kxs[:,None]**2 + self._kys[None,:]**2 )
-            mask = xp.zeros(radii.shape, device=self._array.device if TORCH_AVAILABLE else None)
+            mask = zeros(radii.shape, device=self._array.device if TORCH_AVAILABLE else None)
             mask[radii<radius]=1
             self._array*=mask[None,None,:,:,None]
         else:
@@ -417,7 +417,7 @@ def applyMask(self, radius, realOrReciprocal="reciprocal"):
                 radii = xp.tensor(radii_np, dtype=self._array.real.dtype, device=self._array.device)
             else:
                 radii = radii_np
-            mask = xp.zeros(radii.shape, device=self._array.device if TORCH_AVAILABLE else None)
+            mask = zeros(radii.shape, device=self._array.device if TORCH_AVAILABLE else None)
             mask[radii<radius]=1
             kwarg = {"dim":(2,3)} if TORCH_AVAILABLE else {"axes":(2,3)}
             real = xp.fft.ifft2(xp.fft.ifftshift(self._array,**kwarg),**kwarg)

diff --git a/tests/06_loaders.py b/tests/06_loaders.py
@@ -9,7 +9,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
-# Remove previously-cached npy files (we want to rest reloading them)
+# Remove previously-cached npy files (we want to test reloading them)
 outfiles=glob.glob("inputs/*.npy")
 for f in outfiles:
 	if "-test" not in f:
@@ -18,22 +18,22 @@
 # https://www.ovito.org/manual/reference/file_formats/file_formats_input.html
 # https://www.ovito.org/manual/usage/data_model.html#usage-particle-properties
 
-# define our test input files. all of these should be supported
-testFiles={"silicon.positions":{"atom_style":"molecular"},	# lammps input positions file, generated via generatePositions.py
-	"silicon.xyz": None,               # xyz file following wikipedia conventions (https://en.wikipedia.org/wiki/XYZ_file_format), generated via generatePositions.py
-	"silicon.cif": None,		       # generated via ase.io.read/write from silicon.xyz
-	"hBN.cif": None,				   # taken from DOI: 10.1016/j.matlet.2006.07.108 https://materials.springer.com/isp/crystallographic/docs/sd_1923917
-	"hBN.xyz": None,				   # taken from DOI: 10.17863/CAM.66112
-	"hBN_truncated.lammpstrj": None,   # multiple timesteps, generated via a custom dump command from lammps
-    "hBN_GAP_ase.trj": None,           # multiple timesteps, generated via a ASE MD run using the GAP potential from https://doi.org/10.1021/acs.jpcc.0c05831
+# define our test input files. all of these should be supported. additional keyword args may be required
+testFiles={"silicon_pos.positions":{"ovitokwargs":{"atom_style":"molecular"}},	# lammps input positions file, generated via generatePositions.py
+	#"silicon_xyz.xyz": {},               # xyz file following wikipedia conventions (https://en.wikipedia.org/wiki/XYZ_file_format), generated via generatePositions.py
+	#"silicon_cif.cif": {},		       # generated via ase.io.read/write from silicon.xyz
+	"hBN_cif.cif": {},				   # taken from DOI: 10.1016/j.matlet.2006.07.108 https://materials.springer.com/isp/crystallographic/docs/sd_1923917
+	#"hBN_xyz.xyz": {},				   # taken from DOI: 10.17863/CAM.66112
+	"hBN_truncated.lammpstrj": {"atom_mapping":{1:"B",2:"N"}},   # multiple timesteps, generated via a custom dump command from lammps
+    "hBN_GAP_ase.trj": {},           # multiple timesteps, generated via a ASE MD run using the GAP potential from https://doi.org/10.1021/acs.jpcc.0c05831
 }
 
 
 # for each: load, generate potential, plot potential
 for i,filename in enumerate(testFiles.keys()):
 	# LOAD IT
 	print("attempting to load","inputs/"+filename)
-	trajectory=Loader("inputs/"+filename,ovitokwargs=testFiles[filename]).load()
+	trajectory=Loader("inputs/"+filename,**testFiles[filename]).load()
 	# DIFF IT
 	positions = trajectory.positions[0]
 	differ(positions,"outputs/loaders-test_"+filename+".npy","POSITIONS")

diff --git a/tests/08_LACBED_iterative.py b/tests/08_LACBED_iterative.py
@@ -77,4 +77,4 @@
 #if hasattr(ary, 'cpu'):
 #	ary = ary.cpu().numpy()
 
-differ(ary[::10,::10],"outputs/lacbed-test.npy","LACBED")
+differ(ary[:,:,::10,::10,:],"outputs/lacbed-test.npy","LACBED")
diff --git a/tests/cpu.sberr b/tests/cpu.sberr
@@ -0,0 +1,10 @@
+-------------------------------------------------------------------------------
+There are messages associated with the following module(s):
+-------------------------------------------------------------------------------
+
+cuda/11.4.0:
+   Please note, CUDA/11.4.0 is required if compiling for NVIDIA K80 GPUs.
+   Newer toolchain versions will not work for K80's.
+
+-------------------------------------------------------------------------------DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.
+slurmstepd: error: *** JOB 4394420 ON or-condo-c75 CANCELLED AT 2026-01-07T14:44:01 ***
diff --git a/tests/cpu.sbout b/tests/cpu.sbout
diff --git a/tests/cpu.slurm b/tests/cpu.slurm
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH -A birthright
+#SBATCH --partition=batch
+#SBATCH --time=12:00:00
+#SBATCH --mem=16G
+#SBATCH -N 1
+#SBATCH -n 1
+#SBATCH --output=cpu.sbout
+#SBATCH --error=cpu.sberr
+
+module load cuda/11.4.0
+module load gcc
+source deactivate base
+conda activate /home/qwe/.conda/envs/pyslice_env
+
+bash runAllTests.sh torchcpu
+
+
diff --git a/tests/gpu.sberr b/tests/gpu.sberr
@@ -0,0 +1,9 @@
+-------------------------------------------------------------------------------
+There are messages associated with the following module(s):
+-------------------------------------------------------------------------------
+
+cuda/11.4.0:
+   Please note, CUDA/11.4.0 is required if compiling for NVIDIA K80 GPUs.
+   Newer toolchain versions will not work for K80's.
+
+-------------------------------------------------------------------------------DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.
diff --git a/tests/gpu.sbout b/tests/gpu.sbout
diff --git a/tests/gpu.slurm b/tests/gpu.slurm
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH -A birthright
+#SBATCH --partition=burst
+#SBATCH --time=12:00:00
+#SBATCH --mem=16G
+#SBATCH -N 1
+#SBATCH -n 1
+#SBATCH -c 1
+#SBATCH -G v100:1
+#SBATCH --output=gpu.sbout
+#SBATCH --error=gpu.sberr
+
+module load cuda/11.4.0
+module load gcc
+source deactivate base
+conda activate /home/qwe/.conda/envs/pyslice_env
+
+bash runAllTests.sh torchgpu
diff --git a/tests/inputs/hBN.cif → tests/inputs/hBN_cif.cif b/tests/inputs/hBN.cif → tests/inputs/hBN_cif.cif
diff --git a/tests/inputs/hBN.xyz → tests/inputs/hBN_xyz.xyz b/tests/inputs/hBN.xyz → tests/inputs/hBN_xyz.xyz
diff --git a/tests/inputs/silicon.cif → tests/inputs/silicon_cif.cif b/tests/inputs/silicon.cif → tests/inputs/silicon_cif.cif
diff --git a/tests/inputs/silicon.positions → tests/inputs/silicon_pos.positions b/tests/inputs/silicon.positions → tests/inputs/silicon_pos.positions
diff --git a/tests/inputs/silicon.xyz → tests/inputs/silicon_xyz.xyz b/tests/inputs/silicon.xyz → tests/inputs/silicon_xyz.xyz
diff --git a/tests/numpy.sberr b/tests/numpy.sberr
@@ -0,0 +1,10 @@
+-------------------------------------------------------------------------------
+There are messages associated with the following module(s):
+-------------------------------------------------------------------------------
+
+cuda/11.4.0:
+   Please note, CUDA/11.4.0 is required if compiling for NVIDIA K80 GPUs.
+   Newer toolchain versions will not work for K80's.
+
+-------------------------------------------------------------------------------DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.
+slurmstepd: error: *** JOB 4394419 ON or-condo-c75 CANCELLED AT 2026-01-07T14:43:59 ***
diff --git a/tests/numpy.sbout b/tests/numpy.sbout
diff --git a/tests/numpy.slurm b/tests/numpy.slurm
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH -A birthright
+#SBATCH --partition=batch
+#SBATCH --time=12:00:00
+#SBATCH --mem=16G
+#SBATCH -N 1
+#SBATCH -n 1
+#SBATCH --output=numpy.sbout
+#SBATCH --error=numpy.sberr
+
+module load cuda/11.4.0
+module load gcc
+source deactivate base
+conda activate /home/qwe/.conda/envs/numpy_env
+
+bash runAllTests.sh numpy
+
+
diff --git a/tests/outputs/figs/00_probe.png b/tests/outputs/figs/00_probe.png
diff --git a/tests/outputs/figs/00_probe_0.png b/tests/outputs/figs/00_probe_0.png
diff --git a/tests/outputs/figs/00_probe_1.png b/tests/outputs/figs/00_probe_1.png
diff --git a/tests/outputs/figs/00_probe_2.png b/tests/outputs/figs/00_probe_2.png
diff --git a/tests/outputs/figs/00_probe_3.png b/tests/outputs/figs/00_probe_3.png
diff --git a/tests/outputs/figs/00_probe_4.png b/tests/outputs/figs/00_probe_4.png
diff --git a/tests/outputs/figs/01_potentials.png b/tests/outputs/figs/01_potentials.png
diff --git a/tests/outputs/figs/02_propagate_otf=False.png b/tests/outputs/figs/02_propagate_otf=False.png
diff --git a/tests/outputs/figs/02_propagate_otf=True.png b/tests/outputs/figs/02_propagate_otf=True.png
diff --git a/tests/outputs/figs/03_manyprobes.png b/tests/outputs/figs/03_manyprobes.png
diff --git a/tests/outputs/figs/04_haadf.png b/tests/outputs/figs/04_haadf.png
diff --git a/tests/outputs/figs/04_haadf_cbed.png b/tests/outputs/figs/04_haadf_cbed.png
diff --git a/tests/outputs/figs/05_tacaw_30THz.png b/tests/outputs/figs/05_tacaw_30THz.png
diff --git a/tests/outputs/figs/05_tacaw_diff.png b/tests/outputs/figs/05_tacaw_diff.png
diff --git a/tests/outputs/figs/05_tacaw_disp.png b/tests/outputs/figs/05_tacaw_disp.png
diff --git a/tests/outputs/figs/05_tacawcrop_30THz.png b/tests/outputs/figs/05_tacawcrop_30THz.png
diff --git a/tests/outputs/figs/05_tacawcrop_diff.png b/tests/outputs/figs/05_tacawcrop_diff.png
diff --git a/tests/outputs/figs/05_tacawcrop_disp.png b/tests/outputs/figs/05_tacawcrop_disp.png
diff --git a/tests/outputs/figs/06_loaders_0.png b/tests/outputs/figs/06_loaders_0.png
diff --git a/tests/outputs/figs/06_loaders_1.png b/tests/outputs/figs/06_loaders_1.png
diff --git a/tests/outputs/figs/06_loaders_2.png b/tests/outputs/figs/06_loaders_2.png
diff --git a/tests/outputs/figs/06_loaders_3.png b/tests/outputs/figs/06_loaders_3.png
diff --git a/tests/outputs/figs/06_loaders_4.png b/tests/outputs/figs/06_loaders_4.png
diff --git a/tests/outputs/figs/06_loaders_5.png b/tests/outputs/figs/06_loaders_5.png
diff --git a/tests/outputs/figs/06_loaders_6.png b/tests/outputs/figs/06_loaders_6.png
diff --git a/tests/outputs/figs/07_defocus_2D.png b/tests/outputs/figs/07_defocus_2D.png
diff --git a/tests/outputs/figs/07_defocus_3D.png b/tests/outputs/figs/07_defocus_3D.png
diff --git a/tests/outputs/figs/08_LACBED_iterative.png b/tests/outputs/figs/08_LACBED_iterative.png
diff --git a/tests/outputs/figs/08_LACBED_onthefly.png b/tests/outputs/figs/08_LACBED_onthefly.png
diff --git a/tests/outputs/figs/10_midgley_30THz.png b/tests/outputs/figs/10_midgley_30THz.png
diff --git a/tests/outputs/figs/10_midgley_diff.png b/tests/outputs/figs/10_midgley_diff.png
diff --git a/tests/outputs/figs/10_midgley_diff2.png b/tests/outputs/figs/10_midgley_diff2.png
diff --git a/tests/outputs/figs/10_midgley_disp.png b/tests/outputs/figs/10_midgley_disp.png
diff --git a/tests/outputs/figs/11_SED_30THz.png b/tests/outputs/figs/11_SED_30THz.png
diff --git a/tests/outputs/figs/12_aberrations_espread.png b/tests/outputs/figs/12_aberrations_espread.png
diff --git a/tests/outputs/figs/12_aberrations_tableau.png b/tests/outputs/figs/12_aberrations_tableau.png
diff --git a/tests/outputs/manyprobes-test.npy b/tests/outputs/manyprobes-test.npy
diff --git a/tests/outputs/tacawcrop-test.npy b/tests/outputs/tacawcrop-test.npy
-Original file line number
+Diff line change
@@ Expand Up / @@ -47,6 +47,7 @@ Thumbs.db @@
     # Log files
     *.log
+    !runAllTests*.log
     logs/
     !tests/runAllTests.log
@@ Expand Down @@