diff --git a/2021-09-03_pl-0.1_cyl10_core5_sp60/Material0.txt b/2021-09-03_pl-0.1_cyl10_core5_sp60/Material0.txt
new file mode 100644
index 00000000..217393be
--- /dev/null
+++ b/2021-09-03_pl-0.1_cyl10_core5_sp60/Material0.txt
@@ -0,0 +1,2400 @@
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diff --git a/2021-09-03_pl-0.1_cyl10_core5_sp60/Material1.txt b/2021-09-03_pl-0.1_cyl10_core5_sp60/Material1.txt
new file mode 100644
index 00000000..861dafa9
--- /dev/null
+++ b/2021-09-03_pl-0.1_cyl10_core5_sp60/Material1.txt
@@ -0,0 +1,2400 @@
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diff --git a/2021-09-03_pl-0.1_cyl10_core5_sp60/Material2.txt b/2021-09-03_pl-0.1_cyl10_core5_sp60/Material2.txt
new file mode 100644
index 00000000..3e9581f2
--- /dev/null
+++ b/2021-09-03_pl-0.1_cyl10_core5_sp60/Material2.txt
@@ -0,0 +1,2400 @@
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+}
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+}
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+}
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+}
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+}
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+}
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+}
+EnergyData298:
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+Energy = 299.80;
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+}
+EnergyData299:
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diff --git a/2021-09-03_pl-0.1_cyl10_core5_sp60/check.txt b/2021-09-03_pl-0.1_cyl10_core5_sp60/check.txt
new file mode 100644
index 00000000..bb712dbe
--- /dev/null
+++ b/2021-09-03_pl-0.1_cyl10_core5_sp60/check.txt
@@ -0,0 +1,19 @@
+Model has 3 materials
+Dataset dimensions: 1 x 1024 x 1024
+Material 1 Unaligned. Min:0.0 Max:1.0
+Material 1 Aligned. Min:0.0 Max:0.0
+Material 1 Total. Min:0.0 Max:1.0
+Material 1 minimum in-plane rotation:0.0 max:0.0
+Material 1 minimum out-of-plane rotation:0.0 max:0.0
+Material 2 Unaligned. Min:0.0 Max:1.0
+Material 2 Aligned. Min:0.0 Max:0.0
+Material 2 Total. Min:0.0 Max:1.0
+Material 2 minimum in-plane rotation:0.0 max:0.0
+Material 2 minimum out-of-plane rotation:0.0 max:0.0
+Material 3 Unaligned. Min:0.0 Max:0.0662616640329361
+Material 3 Aligned. Min:0.0 Max:0.9970908145231228
+Material 3 Total. Min:0.0 Max:1.0000000661985524
+Material 3 minimum in-plane rotation:0.0 max:179.90870138657237
+Material 3 minimum out-of-plane rotation:0.0 max:89.89209350958103
+All materials Total. Min:0.9999999327831404 Max:1.0000000661985524
+0:00:01.815826
diff --git a/2021-09-03_pl-0.1_cyl10_core5_sp60/config.txt b/2021-09-03_pl-0.1_cyl10_core5_sp60/config.txt
new file mode 100644
index 00000000..681d208a
--- /dev/null
+++ b/2021-09-03_pl-0.1_cyl10_core5_sp60/config.txt
@@ -0,0 +1,15 @@
+Energies=[270.0,280.0,285.0,290.0,299.9];
+EAngleRotation=[0.0,2.0,180.0];
+NumThreads = 4;
+NumX = 1024;
+NumY = 1024;
+NumZ = 1;
+PhysSize = 8.0;
+RotMask = False;
+EwaldsInterpolation= 1;
+WriteVTI = False;
+WindowingType = 0;
+MorphologyType = 1;
+ScatterApproach = 0;
+KRotationType = 0;
+KAngleRotation=[0.0,2.0,180.0];
diff --git a/2021-09-03_pl-0.1_cyl10_core5_sp60/cyrsoxs.4897.out b/2021-09-03_pl-0.1_cyl10_core5_sp60/cyrsoxs.4897.out
new file mode 100644
index 00000000..82aeceb4
--- /dev/null
+++ b/2021-09-03_pl-0.1_cyl10_core5_sp60/cyrsoxs.4897.out
@@ -0,0 +1,394 @@
+--> No loaded packages!
+--> Adding package cyrsoxs version 0.9.0 to ['PATH', 'PYTHONPATH']
+/home/tbm/software/anaconda/lib/python3.8/site-packages/matplotlib/image.py:446: UserWarning: Warning: converting a masked element to nan.
+  dv = np.float64(self.norm.vmax) - np.float64(self.norm.vmin)
+/home/tbm/software/anaconda/lib/python3.8/site-packages/matplotlib/image.py:453: UserWarning: Warning: converting a masked element to nan.
+  a_min = np.float64(newmin)
+/home/tbm/software/anaconda/lib/python3.8/site-packages/matplotlib/image.py:458: UserWarning: Warning: converting a masked element to nan.
+  a_max = np.float64(newmax)
+/home/tbm/software/anaconda/lib/python3.8/site-packages/matplotlib/image.py:477: UserWarning: Warning: converting a masked element to nan.
+  vrange = np.array([self.norm.vmin, self.norm.vmax],
+directory: .
+file: 2021-09-03_pl-0.1_cyl10_core5_sp60.h5
+Model has 3 materials
+Dataset dimensions: 1 x 1024 x 1024
+Material 1 Unaligned. Min:0.0 Max:1.0
+Material 1 Aligned. Min:0.0 Max:0.0
+Material 1 Total. Min:0.0 Max:1.0
+Material 1 minimum in-plane rotation:0.0 max:0.0
+Material 1 minimum out-of-plane rotation:0.0 max:0.0
+Material 2 Unaligned. Min:0.0 Max:1.0
+Material 2 Aligned. Min:0.0 Max:0.0
+Material 2 Total. Min:0.0 Max:1.0
+Material 2 minimum in-plane rotation:0.0 max:0.0
+Material 2 minimum out-of-plane rotation:0.0 max:0.0
+Material 3 Unaligned. Min:0.0 Max:0.0662616640329361
+Material 3 Aligned. Min:0.0 Max:0.9970908145231228
+Material 3 Total. Min:0.0 Max:1.0000000661985524
+Material 3 minimum in-plane rotation:0.0 max:179.90870138657237
+Material 3 minimum out-of-plane rotation:0.0 max:89.89209350958103
+All materials Total. Min:0.9999999327831404 Max:1.0000000661985524
+0:00:01.815826
+~~MORPHOLOGY CHECK RESULTS~~
+~~~~~~~see images too~~~~~~~
+Model has 3 materials
+Dataset dimensions: 1 x 1024 x 1024
+Material 1 Unaligned. Min:0.0 Max:1.0
+Material 1 Aligned. Min:0.0 Max:0.0
+Material 1 Total. Min:0.0 Max:1.0
+Material 1 minimum in-plane rotation:0.0 max:0.0
+Material 1 minimum out-of-plane rotation:0.0 max:0.0
+Material 2 Unaligned. Min:0.0 Max:1.0
+Material 2 Aligned. Min:0.0 Max:0.0
+Material 2 Total. Min:0.0 Max:1.0
+Material 2 minimum in-plane rotation:0.0 max:0.0
+Material 2 minimum out-of-plane rotation:0.0 max:0.0
+Material 3 Unaligned. Min:0.0 Max:0.0662616640329361
+Material 3 Aligned. Min:0.0 Max:0.9970908145231228
+Material 3 Total. Min:0.0 Max:1.0000000661985524
+Material 3 minimum in-plane rotation:0.0 max:179.90870138657237
+Material 3 minimum out-of-plane rotation:0.0 max:89.89209350958103
+All materials Total. Min:0.9999999327831404 Max:1.0000000661985524
+0:00:01.815826
+~~WITH MATERIALS~~
+lrwxrwxrwx 1 pab2 users 31 Sep  2 14:32 Material0.txt -> ../optical-constants/vacuum.txt
+lrwxrwxrwx 1 pab2 users 27 Sep  2 14:32 Material1.txt -> ../optical-constants/Si.txt
+lrwxrwxrwx 1 pab2 users 39 Sep  2 14:32 Material2.txt -> ../optical-constants/PA_extrap_1cyc.txt
+RUNNING ON GPU1
+[WARNING] : No value corresponding to VTIDirName found. Setting to default
+[WARNING] : No value corresponding to HDF5DirName found. Setting to default
+[INFO] 2D computation enabled
+Input Data : [OK] 
+Dimensions           : [1024 1024 1]
+PhysSize             : 8 nm 
+E Rotation Angle     : 0 : 2 : 180
+K RotationType       : No Rotation : (k = 0,0,1)
+MorphologyType       : VectorMorphology
+Energies simulated   : [270 270.1 270.2 270.3 270.4 270.5 270.6 270.7 270.8 270.9 271 271.1 271.2 271.3 271.4 271.5 271.6 271.7 271.8 271.9 272 272.1 272.2 272.3 272.4 272.5 272.6 272.7 272.8 272.9 273 273.1 273.2 273.3 273.4 273.5 273.6 273.7 273.8 273.9 274 274.1 274.2 274.3 274.4 274.5 274.6 274.7 274.8 274.9 275 275.1 275.2 275.3 275.4 275.5 275.6 275.7 275.8 275.9 276 276.1 276.2 276.3 276.4 276.5 276.6 276.7 276.8 276.9 277 277.1 277.2 277.3 277.4 277.5 277.6 277.7 277.8 277.9 278 278.1 278.2 278.3 278.4 278.5 278.6 278.7 278.8 278.9 279 279.1 279.2 279.3 279.4 279.5 279.6 279.7 279.8 279.9 280 280.1 280.2 280.3 280.4 280.5 280.6 280.7 280.8 280.9 281 281.1 281.2 281.3 281.4 281.5 281.6 281.7 281.8 281.9 282 282.1 282.2 282.3 282.4 282.5 282.6 282.7 282.8 282.9 283 283.1 283.2 283.3 283.4 283.5 283.6 283.7 283.8 283.9 284 284.1 284.2 284.3 284.4 284.5 284.6 284.7 284.8 284.9 285 285.1 285.2 285.3 285.4 285.5 285.6 285.7 285.8 285.9 286 286.1 286.2 286.3 286.4 286.5 286.6 286.7 286.8 286.9 287 287.1 287.2 287.3 287.4 287.5 287.6 287.7 287.8 287.9 288 288.1 288.2 288.3 288.4 288.5 288.6 288.7 288.8 288.9 289 289.1 289.2 289.3 289.4 289.5 289.6 289.7 289.8 289.9 290 290.1 290.2 290.3 290.4 290.5 290.6 290.7 290.8 290.9 291 291.1 291.2 291.3 291.4 291.5 291.6 291.7 291.8 291.9 292 292.1 292.2 292.3 292.4 292.5 292.6 292.7 292.8 292.9 293 293.1 293.2 293.3 293.4 293.5 293.6 293.7 293.8 293.9 294 294.1 294.2 294.3 294.4 294.5 294.6 294.7 294.8 294.9 295 295.1 295.2 295.3 295.4 295.5 295.6 295.7 295.8 295.9 296 296.1 296.2 296.3 296.4 296.5 296.6 296.7 296.8 296.9 297 297.1 297.2 297.3 297.4 297.5 297.6 297.7 297.8 297.9 298 298.1 298.2 298.3 298.4 298.5 298.6 298.7 298.8 298.9 299 299.1 299.2 299.3 299.4 299.5 299.6 299.7 299.8 299.9 ]
+Windowing Type       : NONE
+Rotation Mask        : 0
+Interpolation Type   : Trilinear interpolation
+HDF Output Directory : HDF5
+Scatter Approach     : Partial
+ __________________________________________________________________________________________________
+|                                 Thanks for using Cy-RSoXS                                        |
+|--------------------------------------------------------------------------------------------------|
+|  Copyright          : Iowa State University                                                      |
+|  License            : MIT                                                                        |
+|  Acknowledgement    : ONR MURI                                                                   |
+|  Developed at Iowa State University in collaboration with NIST                                   |
+|  Please cite the following publication :                                                         |
+|  Comments/Questions :                                                                            |
+|          1. Dr. Baskar GanapathySubramanian (baskarg@iastate.edu)                                |
+|          2. Dr. Adrash Krishnamurthy        (adarsh@iastate.edu)                                 |
+ -------------------------------------------------------------------------------------------------- 
+
+Number of CUDA devices:1
+[INFO] [GPU = NVIDIA Quadro RTX 8000] : 270eV -> 299.9eV
+ [STAT] Energy = 270 starting 
+ [STAT] Energy = 270.1 starting 
+ [STAT] Energy = 270.2 starting 
+ [STAT] Energy = 270.3 starting 
+ [STAT] Energy = 270.4 starting 
+ [STAT] Energy = 270.5 starting 
+ [STAT] Energy = 270.6 starting 
+ [STAT] Energy = 270.7 starting 
+ [STAT] Energy = 270.8 starting 
+ [STAT] Energy = 270.9 starting 
+ [STAT] Energy = 271 starting 
+ [STAT] Energy = 271.1 starting 
+ [STAT] Energy = 271.2 starting 
+ [STAT] Energy = 271.3 starting 
+ [STAT] Energy = 271.4 starting 
+ [STAT] Energy = 271.5 starting 
+ [STAT] Energy = 271.6 starting 
+ [STAT] Energy = 271.7 starting 
+ [STAT] Energy = 271.8 starting 
+ [STAT] Energy = 271.9 starting 
+ [STAT] Energy = 272 starting 
+ [STAT] Energy = 272.1 starting 
+ [STAT] Energy = 272.2 starting 
+ [STAT] Energy = 272.3 starting 
+ [STAT] Energy = 272.4 starting 
+ [STAT] Energy = 272.5 starting 
+ [STAT] Energy = 272.6 starting 
+ [STAT] Energy = 272.7 starting 
+ [STAT] Energy = 272.8 starting 
+ [STAT] Energy = 272.9 starting 
+ [STAT] Energy = 273 starting 
+ [STAT] Energy = 273.1 starting 
+ [STAT] Energy = 273.2 starting 
+ [STAT] Energy = 273.3 starting 
+ [STAT] Energy = 273.4 starting 
+ [STAT] Energy = 273.5 starting 
+ [STAT] Energy = 273.6 starting 
+ [STAT] Energy = 273.7 starting 
+ [STAT] Energy = 273.8 starting 
+ [STAT] Energy = 273.9 starting 
+ [STAT] Energy = 274 starting 
+ [STAT] Energy = 274.1 starting 
+ [STAT] Energy = 274.2 starting 
+ [STAT] Energy = 274.3 starting 
+ [STAT] Energy = 274.4 starting 
+ [STAT] Energy = 274.5 starting 
+ [STAT] Energy = 274.6 starting 
+ [STAT] Energy = 274.7 starting 
+ [STAT] Energy = 274.8 starting 
+ [STAT] Energy = 274.9 starting 
+ [STAT] Energy = 275 starting 
+ [STAT] Energy = 275.1 starting 
+ [STAT] Energy = 275.2 starting 
+ [STAT] Energy = 275.3 starting 
+ [STAT] Energy = 275.4 starting 
+ [STAT] Energy = 275.5 starting 
+ [STAT] Energy = 275.6 starting 
+ [STAT] Energy = 275.7 starting 
+ [STAT] Energy = 275.8 starting 
+ [STAT] Energy = 275.9 starting 
+ [STAT] Energy = 276 starting 
+ [STAT] Energy = 276.1 starting 
+ [STAT] Energy = 276.2 starting 
+ [STAT] Energy = 276.3 starting 
+ [STAT] Energy = 276.4 starting 
+ [STAT] Energy = 276.5 starting 
+ [STAT] Energy = 276.6 starting 
+ [STAT] Energy = 276.7 starting 
+ [STAT] Energy = 276.8 starting 
+ [STAT] Energy = 276.9 starting 
+ [STAT] Energy = 277 starting 
+ [STAT] Energy = 277.1 starting 
+ [STAT] Energy = 277.2 starting 
+ [STAT] Energy = 277.3 starting 
+ [STAT] Energy = 277.4 starting 
+ [STAT] Energy = 277.5 starting 
+ [STAT] Energy = 277.6 starting 
+ [STAT] Energy = 277.7 starting 
+ [STAT] Energy = 277.8 starting 
+ [STAT] Energy = 277.9 starting 
+ [STAT] Energy = 278 starting 
+ [STAT] Energy = 278.1 starting 
+ [STAT] Energy = 278.2 starting 
+ [STAT] Energy = 278.3 starting 
+ [STAT] Energy = 278.4 starting 
+ [STAT] Energy = 278.5 starting 
+ [STAT] Energy = 278.6 starting 
+ [STAT] Energy = 278.7 starting 
+ [STAT] Energy = 278.8 starting 
+ [STAT] Energy = 278.9 starting 
+ [STAT] Energy = 279 starting 
+ [STAT] Energy = 279.1 starting 
+ [STAT] Energy = 279.2 starting 
+ [STAT] Energy = 279.3 starting 
+ [STAT] Energy = 279.4 starting 
+ [STAT] Energy = 279.5 starting 
+ [STAT] Energy = 279.6 starting 
+ [STAT] Energy = 279.7 starting 
+ [STAT] Energy = 279.8 starting 
+ [STAT] Energy = 279.9 starting 
+ [STAT] Energy = 280 starting 
+ [STAT] Energy = 280.1 starting 
+ [STAT] Energy = 280.2 starting 
+ [STAT] Energy = 280.3 starting 
+ [STAT] Energy = 280.4 starting 
+ [STAT] Energy = 280.5 starting 
+ [STAT] Energy = 280.6 starting 
+ [STAT] Energy = 280.7 starting 
+ [STAT] Energy = 280.8 starting 
+ [STAT] Energy = 280.9 starting 
+ [STAT] Energy = 281 starting 
+ [STAT] Energy = 281.1 starting 
+ [STAT] Energy = 281.2 starting 
+ [STAT] Energy = 281.3 starting 
+ [STAT] Energy = 281.4 starting 
+ [STAT] Energy = 281.5 starting 
+ [STAT] Energy = 281.6 starting 
+ [STAT] Energy = 281.7 starting 
+ [STAT] Energy = 281.8 starting 
+ [STAT] Energy = 281.9 starting 
+ [STAT] Energy = 282 starting 
+ [STAT] Energy = 282.1 starting 
+ [STAT] Energy = 282.2 starting 
+ [STAT] Energy = 282.3 starting 
+ [STAT] Energy = 282.4 starting 
+ [STAT] Energy = 282.5 starting 
+ [STAT] Energy = 282.6 starting 
+ [STAT] Energy = 282.7 starting 
+ [STAT] Energy = 282.8 starting 
+ [STAT] Energy = 282.9 starting 
+ [STAT] Energy = 283 starting 
+ [STAT] Energy = 283.1 starting 
+ [STAT] Energy = 283.2 starting 
+ [STAT] Energy = 283.3 starting 
+ [STAT] Energy = 283.4 starting 
+ [STAT] Energy = 283.5 starting 
+ [STAT] Energy = 283.6 starting 
+ [STAT] Energy = 283.7 starting 
+ [STAT] Energy = 283.8 starting 
+ [STAT] Energy = 283.9 starting 
+ [STAT] Energy = 284 starting 
+ [STAT] Energy = 284.1 starting 
+ [STAT] Energy = 284.2 starting 
+ [STAT] Energy = 284.3 starting 
+ [STAT] Energy = 284.4 starting 
+ [STAT] Energy = 284.5 starting 
+ [STAT] Energy = 284.6 starting 
+ [STAT] Energy = 284.7 starting 
+ [STAT] Energy = 284.8 starting 
+ [STAT] Energy = 284.9 starting 
+ [STAT] Energy = 285 starting 
+ [STAT] Energy = 285.1 starting 
+ [STAT] Energy = 285.2 starting 
+ [STAT] Energy = 285.3 starting 
+ [STAT] Energy = 285.4 starting 
+ [STAT] Energy = 285.5 starting 
+ [STAT] Energy = 285.6 starting 
+ [STAT] Energy = 285.7 starting 
+ [STAT] Energy = 285.8 starting 
+ [STAT] Energy = 285.9 starting 
+ [STAT] Energy = 286 starting 
+ [STAT] Energy = 286.1 starting 
+ [STAT] Energy = 286.2 starting 
+ [STAT] Energy = 286.3 starting 
+ [STAT] Energy = 286.4 starting 
+ [STAT] Energy = 286.5 starting 
+ [STAT] Energy = 286.6 starting 
+ [STAT] Energy = 286.7 starting 
+ [STAT] Energy = 286.8 starting 
+ [STAT] Energy = 286.9 starting 
+ [STAT] Energy = 287 starting 
+ [STAT] Energy = 287.1 starting 
+ [STAT] Energy = 287.2 starting 
+ [STAT] Energy = 287.3 starting 
+ [STAT] Energy = 287.4 starting 
+ [STAT] Energy = 287.5 starting 
+ [STAT] Energy = 287.6 starting 
+ [STAT] Energy = 287.7 starting 
+ [STAT] Energy = 287.8 starting 
+ [STAT] Energy = 287.9 starting 
+ [STAT] Energy = 288 starting 
+ [STAT] Energy = 288.1 starting 
+ [STAT] Energy = 288.2 starting 
+ [STAT] Energy = 288.3 starting 
+ [STAT] Energy = 288.4 starting 
+ [STAT] Energy = 288.5 starting 
+ [STAT] Energy = 288.6 starting 
+ [STAT] Energy = 288.7 starting 
+ [STAT] Energy = 288.8 starting 
+ [STAT] Energy = 288.9 starting 
+ [STAT] Energy = 289 starting 
+ [STAT] Energy = 289.1 starting 
+ [STAT] Energy = 289.2 starting 
+ [STAT] Energy = 289.3 starting 
+ [STAT] Energy = 289.4 starting 
+ [STAT] Energy = 289.5 starting 
+ [STAT] Energy = 289.6 starting 
+ [STAT] Energy = 289.7 starting 
+ [STAT] Energy = 289.8 starting 
+ [STAT] Energy = 289.9 starting 
+ [STAT] Energy = 290 starting 
+ [STAT] Energy = 290.1 starting 
+ [STAT] Energy = 290.2 starting 
+ [STAT] Energy = 290.3 starting 
+ [STAT] Energy = 290.4 starting 
+ [STAT] Energy = 290.5 starting 
+ [STAT] Energy = 290.6 starting 
+ [STAT] Energy = 290.7 starting 
+ [STAT] Energy = 290.8 starting 
+ [STAT] Energy = 290.9 starting 
+ [STAT] Energy = 291 starting 
+ [STAT] Energy = 291.1 starting 
+ [STAT] Energy = 291.2 starting 
+ [STAT] Energy = 291.3 starting 
+ [STAT] Energy = 291.4 starting 
+ [STAT] Energy = 291.5 starting 
+ [STAT] Energy = 291.6 starting 
+ [STAT] Energy = 291.7 starting 
+ [STAT] Energy = 291.8 starting 
+ [STAT] Energy = 291.9 starting 
+ [STAT] Energy = 292 starting 
+ [STAT] Energy = 292.1 starting 
+ [STAT] Energy = 292.2 starting 
+ [STAT] Energy = 292.3 starting 
+ [STAT] Energy = 292.4 starting 
+ [STAT] Energy = 292.5 starting 
+ [STAT] Energy = 292.6 starting 
+ [STAT] Energy = 292.7 starting 
+ [STAT] Energy = 292.8 starting 
+ [STAT] Energy = 292.9 starting 
+ [STAT] Energy = 293 starting 
+ [STAT] Energy = 293.1 starting 
+ [STAT] Energy = 293.2 starting 
+ [STAT] Energy = 293.3 starting 
+ [STAT] Energy = 293.4 starting 
+ [STAT] Energy = 293.5 starting 
+ [STAT] Energy = 293.6 starting 
+ [STAT] Energy = 293.7 starting 
+ [STAT] Energy = 293.8 starting 
+ [STAT] Energy = 293.9 starting 
+ [STAT] Energy = 294 starting 
+ [STAT] Energy = 294.1 starting 
+ [STAT] Energy = 294.2 starting 
+ [STAT] Energy = 294.3 starting 
+ [STAT] Energy = 294.4 starting 
+ [STAT] Energy = 294.5 starting 
+ [STAT] Energy = 294.6 starting 
+ [STAT] Energy = 294.7 starting 
+ [STAT] Energy = 294.8 starting 
+ [STAT] Energy = 294.9 starting 
+ [STAT] Energy = 295 starting 
+ [STAT] Energy = 295.1 starting 
+ [STAT] Energy = 295.2 starting 
+ [STAT] Energy = 295.3 starting 
+ [STAT] Energy = 295.4 starting 
+ [STAT] Energy = 295.5 starting 
+ [STAT] Energy = 295.6 starting 
+ [STAT] Energy = 295.7 starting 
+ [STAT] Energy = 295.8 starting 
+ [STAT] Energy = 295.9 starting 
+ [STAT] Energy = 296 starting 
+ [STAT] Energy = 296.1 starting 
+ [STAT] Energy = 296.2 starting 
+ [STAT] Energy = 296.3 starting 
+ [STAT] Energy = 296.4 starting 
+ [STAT] Energy = 296.5 starting 
+ [STAT] Energy = 296.6 starting 
+ [STAT] Energy = 296.7 starting 
+ [STAT] Energy = 296.8 starting 
+ [STAT] Energy = 296.9 starting 
+ [STAT] Energy = 297 starting 
+ [STAT] Energy = 297.1 starting 
+ [STAT] Energy = 297.2 starting 
+ [STAT] Energy = 297.3 starting 
+ [STAT] Energy = 297.4 starting 
+ [STAT] Energy = 297.5 starting 
+ [STAT] Energy = 297.6 starting 
+ [STAT] Energy = 297.7 starting 
+ [STAT] Energy = 297.8 starting 
+ [STAT] Energy = 297.9 starting 
+ [STAT] Energy = 298 starting 
+ [STAT] Energy = 298.1 starting 
+ [STAT] Energy = 298.2 starting 
+ [STAT] Energy = 298.3 starting 
+ [STAT] Energy = 298.4 starting 
+ [STAT] Energy = 298.5 starting 
+ [STAT] Energy = 298.6 starting 
+ [STAT] Energy = 298.7 starting 
+ [STAT] Energy = 298.8 starting 
+ [STAT] Energy = 298.9 starting 
+ [STAT] Energy = 299 starting 
+ [STAT] Energy = 299.1 starting 
+ [STAT] Energy = 299.2 starting 
+ [STAT] Energy = 299.3 starting 
+ [STAT] Energy = 299.4 starting 
+ [STAT] Energy = 299.5 starting 
+ [STAT] Energy = 299.6 starting 
+ [STAT] Energy = 299.7 starting 
+ [STAT] Energy = 299.8 starting 
+ [STAT] Energy = 299.9 starting 
+Complete. Exiting 
+/home/pab2/pyhyper-dev/PyHyperScattering/src/PyHyperScattering/IntegrationUtils.py:12: UserWarning: Could not import package for interactive integration utils.  Install holoviews and scikit-image.
+  warnings.warn('Could not import package for interactive integration utils.  Install holoviews and scikit-image.')
+Imports failed.  Are you running on a machine with proper libraries for databroker, tiled, etc.?
+directory: .
+file: 2021-09-03_pl-0.1_cyl10_core5_sp60.h5
+Finished reading 300 energies. Time required: 0:00:01.322912
diff --git a/2021-09-03_pl-0.1_cyl10_core5_sp60/job.slurm b/2021-09-03_pl-0.1_cyl10_core5_sp60/job.slurm
new file mode 100644
index 00000000..bdc73b10
--- /dev/null
+++ b/2021-09-03_pl-0.1_cyl10_core5_sp60/job.slurm
@@ -0,0 +1,54 @@
+#!/bin/bash -l
+#SBATCH --job-name=CYRSOXS      # Job name
+#SBATCH --output=cyrsoxs.%j.out # Stdout (%j expands to jobId)
+#SBATCH --error=cyrsoxs.%j.out  # Stderr (%j expands to jobId)
+#SBATCH --time=04:00:00         # walltime
+#SBATCH --nodes=1               # Number of nodes requested (only one node on glados)
+#SBATCH --ntasks=1              # Number of tasks(processes) (tasks distributed across nodes)
+#SBATCH --ntasks-per-node=1     # Tasks per node
+#SBATCH --cpus-per-task=1       # Threads per task (all cpus will be on same node)
+#SBATCH --gres=gpu:turing:1     # number and type of GPUS to use (glados only has turing)
+#SBATCH --gres-flags=enforce-binding
+
+set -e
+
+if [ x$SLURM_CPUS_PER_TASK == x ]; then
+  export OMP_NUM_THREADS=1
+else
+  export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
+fi
+
+# load necessary modules
+source ~/.typyEnv CLEAN
+typyEnv --add cyrsoxs/0.9.0
+
+# Check the morphology
+
+python /home/pab2/membrane-model/checkH5.py *.h5
+
+cat check.txt
+
+echo "~~MORPHOLOGY CHECK RESULTS~~"
+echo "~~~~~~~see images too~~~~~~~"
+cat check.txt
+
+echo "~~WITH MATERIALS~~"
+#Store morphology data
+ls -al Material*
+
+## RUN YOUR PROGRAM ##
+echo "RUNNING ON GPU"${CUDA_VISIBLE_DEVICES}
+CyRSoXS_N3 *.h5
+
+# Reduce the data
+
+python /home/pab2/membrane-model/reduce.py *.h5
+
+# assemble the artifacts
+
+cp *_ISI.png /home/pab2/membrane-model/artifacts/ISI/
+cp *raw280.png /home/pab2/membrane-model/artifacts/raw280/
+cp *red280.png /home/pab2/membrane-model/artifacts/red280/
+cp *IqE.png /home/pab2/membrane-model/artifacts/IqE/
+cp *AR.png /home/pab2/membrane-model/artifacts/AR/
+cp *.redp /home/pab2/membrane-model/artifacts/redp/
diff --git a/2021-09-03_pl-0.1_cyl10_core5_sp60/metadata.txt b/2021-09-03_pl-0.1_cyl10_core5_sp60/metadata.txt
new file mode 100644
index 00000000..7994229c
--- /dev/null
+++ b/2021-09-03_pl-0.1_cyl10_core5_sp60/metadata.txt
@@ -0,0 +1,41 @@
+ __________________________________________________________________________________________________
+|                                 Thanks for using Cy-RSoXS                                        |
+|--------------------------------------------------------------------------------------------------|
+|  Copyright          : Iowa State University                                                      |
+|  License            : MIT                                                                        |
+|  Acknowledgement    : ONR MURI                                                                   |
+|  Developed at Iowa State University in collaboration with NIST                                   |
+|  Please cite the following publication :                                                         |
+|  Comments/Questions :                                                                            |
+|          1. Dr. Baskar GanapathySubramanian (baskarg@iastate.edu)                                |
+|          2. Dr. Adrash Krishnamurthy        (adarsh@iastate.edu)                                 |
+ -------------------------------------------------------------------------------------------------- 
+
+
+
+CyRSoXS: 
+=========================================================================================
+Version              : 0.9.0
+Git patch            : 7cde310
+Size of Real         : 4
+Number of material   : 3
+
+Scaling Information:
+=========================================================================================
+Number of pixel      :[1024,1024]
+Q range              :[-0.392699,0.392699]
+
+
+
+InputData : 
+=========================================================================================
+Dimensions           : [1024 1024 1]
+PhysSize             : 8nm 
+E Rotation Angle     : 0 : 2 : 180
+K RotationType       : No Rotation : (k = 0,0,1)
+Energies simulated   : [270 270.1 270.2 270.3 270.4 270.5 270.6 270.7 270.8 270.9 271 271.1 271.2 271.3 271.4 271.5 271.6 271.7 271.8 271.9 272 272.1 272.2 272.3 272.4 272.5 272.6 272.7 272.8 272.9 273 273.1 273.2 273.3 273.4 273.5 273.6 273.7 273.8 273.9 274 274.1 274.2 274.3 274.4 274.5 274.6 274.7 274.8 274.9 275 275.1 275.2 275.3 275.4 275.5 275.6 275.7 275.8 275.9 276 276.1 276.2 276.3 276.4 276.5 276.6 276.7 276.8 276.9 277 277.1 277.2 277.3 277.4 277.5 277.6 277.7 277.8 277.9 278 278.1 278.2 278.3 278.4 278.5 278.6 278.7 278.8 278.9 279 279.1 279.2 279.3 279.4 279.5 279.6 279.7 279.8 279.9 280 280.1 280.2 280.3 280.4 280.5 280.6 280.7 280.8 280.9 281 281.1 281.2 281.3 281.4 281.5 281.6 281.7 281.8 281.9 282 282.1 282.2 282.3 282.4 282.5 282.6 282.7 282.8 282.9 283 283.1 283.2 283.3 283.4 283.5 283.6 283.7 283.8 283.9 284 284.1 284.2 284.3 284.4 284.5 284.6 284.7 284.8 284.9 285 285.1 285.2 285.3 285.4 285.5 285.6 285.7 285.8 285.9 286 286.1 286.2 286.3 286.4 286.5 286.6 286.7 286.8 286.9 287 287.1 287.2 287.3 287.4 287.5 287.6 287.7 287.8 287.9 288 288.1 288.2 288.3 288.4 288.5 288.6 288.7 288.8 288.9 289 289.1 289.2 289.3 289.4 289.5 289.6 289.7 289.8 289.9 290 290.1 290.2 290.3 290.4 290.5 290.6 290.7 290.8 290.9 291 291.1 291.2 291.3 291.4 291.5 291.6 291.7 291.8 291.9 292 292.1 292.2 292.3 292.4 292.5 292.6 292.7 292.8 292.9 293 293.1 293.2 293.3 293.4 293.5 293.6 293.7 293.8 293.9 294 294.1 294.2 294.3 294.4 294.5 294.6 294.7 294.8 294.9 295 295.1 295.2 295.3 295.4 295.5 295.6 295.7 295.8 295.9 296 296.1 296.2 296.3 296.4 296.5 296.6 296.7 296.8 296.9 297 297.1 297.2 297.3 297.4 297.5 297.6 297.7 297.8 297.9 298 298.1 298.2 298.3 298.4 298.5 298.6 298.7 298.8 298.9 299 299.1 299.2 299.3 299.4 299.5 299.6 299.7 299.8 299.9 ]
+Windowing Type       : NONE
+Rotation Mask        : 0
+Interpolation Type   : Trilinear interpolation
+HDF Output Directory : HDF5
+Scatter Approach     : Partial
diff --git a/2021-09-03_pl-0.1_cyl10_core5_sp60/morphology_gen.txt b/2021-09-03_pl-0.1_cyl10_core5_sp60/morphology_gen.txt
new file mode 100644
index 00000000..a796f70e
--- /dev/null
+++ b/2021-09-03_pl-0.1_cyl10_core5_sp60/morphology_gen.txt
@@ -0,0 +1,19 @@
+
+Lattice Information
+
+cylinder radius = 80 nm
+center-center spacing = 480 nm
+(100) d-spacing = 415.692 nm
+q* = 0.015 nm^-1
+
+~~orientation~~
+decay model: powerlaw
+if linear: decay width 5 from 1 to 0
+if powerlaw: exponent -0.1 starting at 1 at shell wall
+2021-09-03_pl-0.1_cyl10_core5_sp60.h5
+tiled_morphology shape: (1768, 2040)
+Tiled_directors shape: (1768, 2040, 3)
+tiled_distance shape: (1768, 2040)
+Morphology shape: (1024, 1024)
+Director shape: (1024, 1024, 3)
+Distance shape: (1024, 1024)
diff --git a/mask-test-pack/37738-CB_TPD314K1_mask.tif b/mask-test-pack/37738-CB_TPD314K1_mask.tif
new file mode 100644
index 00000000..aaf24eea
Binary files /dev/null and b/mask-test-pack/37738-CB_TPD314K1_mask.tif differ
diff --git a/mask-test-pack/liquidMask.json b/mask-test-pack/liquidMask.json
new file mode 100644
index 00000000..af695c2c
--- /dev/null
+++ b/mask-test-pack/liquidMask.json
@@ -0,0 +1 @@
+["{\"x\":{\"0\":492.1705617978,\"1\":494.9319101124,\"2\":515.6420224719,\"3\":581.9143820225,\"4\":605.3858426966,\"5\":602.624494382,\"6\":1029.2528089888,\"7\":1037.5368539326,\"8\":-13.1561797753,\"9\":-22.8208988764,\"10\":494.9319101124,\"11\":492.1705617978,\"12\":492.1705617978},\"y\":{\"0\":335.1684732361,\"1\":478.9096807415,\"2\":496.6555097837,\"3\":491.5852729145,\"4\":463.6989701339,\"5\":2.307415036,\"6\":-2.7628218332,\"7\":1038.1568132175,\"8\":1036.8892540002,\"9\":-12.1427523046,\"10\":-21.0156668257,\"11\":335.1684732361,\"12\":335.1684732361}}", "{\"x\":{\"0\":471.4604494382,\"1\":539.1134831461,\"2\":539.1134831461,\"3\":550.1588764045,\"4\":568.1076404494,\"5\":601.2438202247,\"6\":595.7211235955,\"7\":570.868988764,\"8\":554.3008988764,\"9\":546.0168539326,\"10\":536.3521348315,\"11\":485.2671910112,\"12\":463.1764044944,\"13\":471.4604494382},\"y\":{\"0\":412.2360581749,\"1\":364.0688079174,\"2\":329.8447090503,\"3\":365.3363671347,\"4\":397.0253475672,\"5\":397.0253475672,\"6\":407.1658213057,\"7\":407.1658213057,\"8\":421.108972696,\"9\":465.4735453015,\"10\":431.2494464344,\"11\":470.5437821707,\"12\":431.2494464344,\"13\":412.2360581749}}"]
\ No newline at end of file
diff --git a/src/PyHyperScattering/SST1RSoXSDB.py b/src/PyHyperScattering/SST1RSoXSDB.py
index d9be19ea..d802814b 100644
--- a/src/PyHyperScattering/SST1RSoXSDB.py
+++ b/src/PyHyperScattering/SST1RSoXSDB.py
@@ -557,6 +557,7 @@ def loadRun(
         coords={},
         return_dataset=False,
         useMonitorShutterThinning=True,
+        average_repeats=True
     ):
         """
         Loads a run entry from a catalog result into a raw xarray.
@@ -699,120 +700,135 @@ def loadRun(
             data = run["primary"]["data"].read()[md["detector"] + "_image"]
         
         # Handle extra dimensions (non-pixel and non-intended dimensions from repeat exposures) by averaging them along the dim_0 axis
-        if len(data.shape) > 3:
-            data = data.mean("dim_0")
-
-
-        data = data.astype(int)  # convert from uint to handle dark subtraction
-
-        if self.dark_subtract:
-            dark = run["dark"]["data"][md["detector"] + "_image"]
-            if (
-                type(dark) == tiled.client.array.ArrayClient
-                or type(dark) == tiled.client.array.DaskArrayClient
-            ):
-                dark = run["dark"]["data"].read()[md["detector"] + "_image"]
-            darkframe = np.copy(data.time)
-            for n, time in enumerate(dark.time):
-                darkframe[(data.time - time) > 0] = int(n)
-            data = data.assign_coords(dark_id=("time", darkframe))
-
-            def subtract_dark(img, pedestal=100, darks=None):
-                return img + pedestal - darks[int(img.dark_id.values)]
-
-            data = data.groupby("time",squeeze=False).map(subtract_dark, darks=dark, pedestal=self.dark_pedestal)
-
-        dims_to_join = []
-        dim_names_to_join = []
-
-        for dim in dims:
-            try:
-                test = len(md[dim])  # this will throw a typeerror if single value
-                if type(md[dim]) == dask.array.core.Array:
-                    dims_to_join.append(md[dim].compute())
-                else:
-                    dims_to_join.append(md[dim])
-                dim_names_to_join.append(dim)
-            except TypeError:
-                dims_to_join.append([md[dim]] * run.start["num_points"])
-                dim_names_to_join.append(dim)
-
-        for key, val in coords.items():
-            dims_to_join.append(val)
-            dim_names_to_join.append(key)
-
-        index = pd.MultiIndex.from_arrays(dims_to_join, names=dim_names_to_join)
-        # handle the edge case of a partly-finished scan
-        if len(index) != len(data["time"]):
-            index = index[: len(data["time"])]
-        actual_exposure = md["exposure"] * len(data.dim_0)
-        mindex_coords = xr.Coordinates.from_pandas_multiindex(index, 'system')
-        retxr = (
-            data.sum("dim_0")
-            .rename({"dim_1": "pix_y", "dim_2": "pix_x"})
-            .rename({"time": "system"})
-            .assign_coords(mindex_coords)
-        )  # ,md['detector']+'_image':'intensity'})
-
-        # this is needed for holoviews compatibility, hopefully does not break other features.
-        retxr = retxr.assign_coords(
-            {
-                "pix_x": np.arange(0, len(retxr.pix_x)),
-                "pix_y": np.arange(0, len(retxr.pix_y)),
-            }
-        )
-        try:
-            monitors = (
-                monitors.rename({"time": "system"})
-                .reset_index("system")
-                .assign_coords(system=index)
-            )
-
-            if "system_" in monitors.indexes.keys():
-                monitors = monitors.drop("system_")
-
-        except Exception as e:
-            warnings.warn(
-                (
-                    "Monitor streams loaded successfully, but could not be correlated to images. "
-                    " Check monitor stream for issues, probable metadata change."
-                ),
-                stacklevel=2,
-            )
-        retxr.attrs.update(md)
-
-        retxr.attrs["exposure"] = (
-            len(data.dim_0) * retxr.attrs["exposure"]
-        )  # patch for multi exposures
-        # now do corrections:
-        frozen_attrs = retxr.attrs
-        if self.corr_mode == "i0":
-            retxr = retxr / monitors["RSoXS Au Mesh Current"]
-        elif self.corr_mode != "none":
-            warnings.warn(
-                "corrections other than none or i0 are not supported at the moment",
-                stacklevel=2,
+        def do_all(d1=data): # turned into a function to allow repeated executions for scans with repeat exposures
+            d1 = d1.astype(int)  # convert from uint to handle dark subtraction
+    
+            if self.dark_subtract:
+                dark = run["dark"]["data"][md["detector"] + "_image"]
+                if (
+                    type(dark) == tiled.client.array.ArrayClient
+                    or type(dark) == tiled.client.array.DaskArrayClient
+                ):
+                    dark = run["dark"]["data"].read()[md["detector"] + "_image"]
+                darkframe = np.copy(d1.time)
+                for n, time in enumerate(dark.time):
+                    darkframe[(d1.time - time) > 0] = int(n)
+                d1 = d1.assign_coords(dark_id=("time", darkframe))
+    
+                def subtract_dark(img, pedestal=100, darks=None):
+                    return img + pedestal - darks[int(img.dark_id.values)]
+    
+                d1 = d1.groupby("time",squeeze=False).map(subtract_dark, darks=dark, pedestal=self.dark_pedestal)
+    
+            dims_to_join = []
+            dim_names_to_join = []
+    
+            for dim in dims:
+                try:
+                    test = len(md[dim])  # this will throw a typeerror if single value
+                    if type(md[dim]) == dask.array.core.Array:
+                        dims_to_join.append(md[dim].compute())
+                    else:
+                        dims_to_join.append(md[dim])
+                    dim_names_to_join.append(dim)
+                except TypeError:
+                    dims_to_join.append([md[dim]] * run.start["num_points"])
+                    dim_names_to_join.append(dim)
+    
+            for key, val in coords.items():
+                dims_to_join.append(val)
+                dim_names_to_join.append(key)
+    
+            index = pd.MultiIndex.from_arrays(dims_to_join, names=dim_names_to_join)
+            # handle the edge case of a partly-finished scan
+            if len(index) != len(data["time"]):
+                index = index[: len(data["time"])]
+            actual_exposure = md["exposure"] * len(d1.dim_0)
+            mindex_coords = xr.Coordinates.from_pandas_multiindex(index, 'system')
+            retxr = (
+                d1.sum("dim_0")
+                .rename({"dim_1": "pix_y", "dim_2": "pix_x"})
+                .rename({"time": "system"})
+                .assign_coords(mindex_coords)
+            )  # ,md['detector']+'_image':'intensity'})
+    
+            # this is needed for holoviews compatibility, hopefully does not break other features.
+            retxr = retxr.assign_coords(
+                {
+                    "pix_x": np.arange(0, len(retxr.pix_x)),
+                    "pix_y": np.arange(0, len(retxr.pix_y)),
+                }
             )
+            try:
+                monitors = (
+                    monitors.rename({"time": "system"})
+                    .reset_index("system")
+                    .assign_coords(system=index)
+                )
+    
+                if "system_" in monitors.indexes.keys():
+                    monitors = monitors.drop("system_")
+    
+            except Exception as e:
+                warnings.warn(
+                    (
+                        "Monitor streams loaded successfully, but could not be correlated to images. "
+                        " Check monitor stream for issues, probable metadata change."
+                    ),
+                    stacklevel=2,
+                )
+            retxr.attrs.update(md)
+    
+            retxr.attrs["exposure"] = (
+                len(d1.dim_0) * retxr.attrs["exposure"]
+            )  # patch for multi exposures
+            # now do corrections:
+            frozen_attrs = retxr.attrs
+            if self.corr_mode == "i0":
+                retxr = retxr / monitors["RSoXS Au Mesh Current"]
+            elif self.corr_mode != "none":
+                warnings.warn(
+                    "corrections other than none or i0 are not supported at the moment",
+                    stacklevel=2,
+                )
+    
+            retxr.attrs.update(frozen_attrs)
+    
+            # deal with the edge case where the LAST energy of a run is repeated... this may need modification to make it correct (did the energies shift when this happened??)
+            try:
+                if retxr.system[-1] == retxr.system[-2]:
+                    retxr = retxr[:-1]
+            except IndexError:
+                pass
+    
+            if return_dataset:
+                # retxr = (index,monitors,retxr)
+                monitors.attrs.update(retxr.attrs)
+                retxr = monitors.merge(retxr)
+    
+            if self.use_chunked_loading:
+                # dask and multiindexes are like PEO and PPO.  They're kinda the same thing and they don't like each other.
+                retxr = retxr.unstack("system")
+            return retxr
+        
+        
+        
+        if len(data.shape) > 3: # this will occur if there are repeats in the sample
+            if average_repeats==True: # default
+                data = data.mean("dim_0")
+                all_xr = do_all(d1=data)
+                
+            elif average_repeats==False:
+                all_xr = xr.Dataset()
+                for r in data.dim_0:
+                    da = data.sel(dim_0=r)
+                    temp_da = do_all(d1=da)
+                    all_xr[f'r{int(r)+1}'] = temp_da
 
-        retxr.attrs.update(frozen_attrs)
-
-        # deal with the edge case where the LAST energy of a run is repeated... this may need modification to make it correct (did the energies shift when this happened??)
-        try:
-            if retxr.system[-1] == retxr.system[-2]:
-                retxr = retxr[:-1]
-        except IndexError:
-            pass
-
-        if return_dataset:
-            # retxr = (index,monitors,retxr)
-            monitors.attrs.update(retxr.attrs)
-            retxr = monitors.merge(retxr)
-
-        if self.use_chunked_loading:
-            # dask and multiindexes are like PEO and PPO.  They're kinda the same thing and they don't like each other.
-            retxr = retxr.unstack("system")
+        else:
+            all_xr = do_all(d1=data)
 
-        return retxr
+        return all_xr
 
     def peekAtMd(self, run):
         return self.loadMd(run)
diff --git a/src/PyHyperScattering/Untitled.ipynb b/src/PyHyperScattering/Untitled.ipynb
new file mode 100644
index 00000000..41ca3638
--- /dev/null
+++ b/src/PyHyperScattering/Untitled.ipynb
@@ -0,0 +1,53 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "63125f8c-1574-49f9-999a-f0fda4aac330",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "import xarray as xr"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a8773180-2716-4d4d-a58a-3cace6564a41",
+   "metadata": {},
+   "source": [
+    "# Combining simple xarrays"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9b5211d5-92e6-4077-97b9-7cf48787697d",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}