added repeat loader

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

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];

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/

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

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)

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}}"]