DDD-XRD Manual - Revision history

Nbertin at 00:20, 15 June 2018

2018-06-15T00:20:17Z

← Older revision		Revision as of 00:20, 15 June 2018
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	<HR>		<HR>

	This page details how to use the DDD-XRD calculation tool (see Bertin and Cai, CMS, 2018 [~~http~~://~~micro~~.~~stanford~~.~~edu~~/~~~caiwei/papers/Bertin_Cai_CMS_2018_XRD_DDD~~.~~pdf~~ PDF]) to compute virtual diffraction patterns (micro-Laue patterns and Stokes-Wilson line profiles) associated with discrete dislocation structures generated from ParaDiS.		This page details how to use the DDD-XRD calculation tool (see Bertin and Cai, CMS, 2018 [https://doi.org/10.1016/j.commatsci.2018.01.037 PDF]) to compute virtual diffraction patterns (micro-Laue patterns and Stokes-Wilson line profiles) associated with discrete dislocation structures generated from ParaDiS.


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	\| <tt>writePeaks</tt>		\| <tt>writePeaks</tt>
	\| 0		\| 0
	\| ~~Write~~ all reflected vectors (one per sampling point) for every selected peak (hkl) in file <tt>reflected_beam_<hkl>.out</tt> in the simulation results directory. This data can then be post-processed to generate patterns on detectors with aribrary parameters (location, orientation, size, resolution) without having to re-perform the displacement gradient calculation and ray-tracing procedure.		\| Toggle to write all reflected vectors (one per sampling point) for every selected peak (hkl) in file <tt>reflected_beam_<hkl>.out</tt> in the simulation results directory. This data can then be post-processed to generate patterns on detectors with aribrary parameters (location, orientation, size, resolution) without having to re-perform the displacement gradient calculation and ray-tracing procedure.
	\|-		\|-
	\| <tt>writeDisplacementGradient</tt>		\| <tt>writeDisplacementGradient</tt>
	\| 0		\| 0
	\| ~~Output~~ the displacement gradient at each sampling point in file <tt>G_<numGrid>.out</tt> in the simulation results directory.		\| Toggle to output the displacement gradient at each sampling point in file <tt>G_<numGrid>.out</tt> in the simulation results directory.
	\|-		\|-
	\| <tt>GPU</tt>		\| <tt>GPU</tt>
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	=== Main detector vs. selected peaks ===		=== Main detector vs. selected peaks ===

	By default, the <tt>paradisxrd</tt> tool computes the virtual micro-Laue pattern collected on a detector when shining an incoming X-ray beam <tt>s0</tt> to the dislocated microstructure (see Bertin and Cai, CMS, 2018). This detector is referred to as the main detector, and its size is typically chosen to be quite large such that several reflections fall onto the detector range. The intensity pattern collected on this main detector is outputed in file <tt>laue_pattern.out</tt> in the simulation results directory.		By default, the <tt>paradisxrd</tt> tool computes the virtual micro-Laue pattern collected on a detector when shining an incoming X-ray beam <tt>s0</tt> to the dislocated microstructure (see Bertin and Cai, CMS, 2018 [https://doi.org/10.1016/j.commatsci.2018.01.037 PDF]). This detector is referred to as the main detector, and its size is typically chosen to be quite large such that several reflections fall onto the detector range. The intensity pattern collected on this main detector is outputed in file <tt>laue_pattern.out</tt> in the simulation results directory.

	In many situations, it is also of interest to examine diffraction patterns associated with specific (hkl) reflections. In the current implentation of the <tt>paradisxrd</tt> tool, the user can specify up to 10 peaks (referred to as selected peaks) using parameters <tt>numPeaks</tt> and <tt>listPeaks</tt>. A secondary detector will be associated to each of these selected peaks. The center of the secondary detectors are automatically located at the position of which the X-ray would be reflected off the corresponding (hkl) in a perfect crystal. Intensity patterns collected on secondary detectors are outputed in files <tt>laue_peak_<hkl>_<numGrid>_all.out</tt> in the simulation results directory. For each selected peak, the strain distribution resolved along the diffraction vector are also outputed in file <tt>Pstrain_peak_<hkl>_<numGrid>.out</tt>. This data can be used to compute the line profile intensity using the Stokes-Wilson approximation.		In many situations, it is also of interest to examine diffraction patterns associated with specific (hkl) reflections. In the current implentation of the <tt>paradisxrd</tt> tool, the user can specify up to 10 peaks (referred to as selected peaks) using parameters <tt>numPeaks</tt> and <tt>listPeaks</tt>. A secondary detector will be associated to each of these selected peaks. The center of the secondary detectors are automatically located at the position of which the X-ray would be reflected off the corresponding (hkl) in a perfect crystal. Intensity patterns collected on secondary detectors are outputed in files <tt>laue_peak_<hkl>_<numGrid>_all.out</tt> in the simulation results directory. For each selected peak, the strain distribution resolved along the diffraction vector are also outputed in file <tt>Pstrain_peak_<hkl>_<numGrid>.out</tt>. This data can be used to compute the line profile intensity using the Stokes-Wilson approximation.
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	\|-		\|-
	\| <tt>reflected_beam_<hkl>.out</tt>		\| <tt>reflected_beam_<hkl>.out</tt>
	\| File ~~containing~~ the direction of the outcoming ray associated with the selected (hkl) reflection at each sampling point. This file can be post-processed to create the diffraction pattern associated with the selected (hkl) reflection on any new detector. Warning: this file may become big when the resolution <tt>numGrid</tt> is large.		\| File generated when option <tt>writePeaks = 1</tt>, that contains the direction of the outcoming ray associated with the selected (hkl) reflection at each sampling point. This file can be post-processed to create the diffraction pattern associated with the selected (hkl) reflection on any new detector. Warning: this file may become big when the resolution <tt>numGrid</tt> is large.
	\|-		\|-
	\| <tt>Pstrain_peak_<hkl>_<numGrid>.out</tt>		\| <tt>Pstrain_peak_<hkl>_<numGrid>.out</tt>
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	\|-		\|-
	\| <tt>G_<numGrid>.out</tt>		\| <tt>G_<numGrid>.out</tt>
	\| File ~~containing~~ the value of the displacement gradient tensor at each sampling point. Warning: this file may become big when the resolution <tt>numGrid</tt> is large.		\| File generated when option <tt>writeDisplacementGradient = 1</tt>, that contains the value of the displacement gradient tensor at each sampling point. Warning: this file may become big when the resolution <tt>numGrid</tt> is large.
	\|}		\|}

Nbertin at 00:03, 15 June 2018

2018-06-15T00:03:24Z

← Older revision		Revision as of 00:03, 15 June 2018
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	make		make

	Make sure that the compilation mode is set to <tt>SERIAL</tt> in the global makefile.setup file before compiling. Use flag <tt>-D_XRD_GPU</tt> to enable GPU computations. Use flag <tt>-D_SPECTRAL</tt> to enable calculations using the spectral method. Successful compilation will create executable <tt>paradisxrd</tt> in the global <tt>bin/</tt> folder.		Make sure that the compilation mode is set to <tt>SERIAL</tt> in the global makefile.setup file before compiling. Use flag <tt>-D_XRD_GPU</tt> to enable GPU computations. Use flag <tt>-D_SPECTRAL</tt> to enable calculations using the spectral method (see Bertin, arXiv, 2018 [https://arxiv.org/pdf/1804.00803.pdf PDF]). The spectral method requires the FFTW library to be installed (see instructions to install FFTW [[Install_FFTW3 \| here]]). Compile without flag <tt>-D_SPECTRAL</tt> if FFTW is not installed. Successful compilation will create executable <tt>paradisxrd</tt> in the global <tt>bin/</tt> folder.

	== Usage ==		== Usage ==
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	\| <tt>spectral</tt>		\| <tt>spectral</tt>
	\| 0		\| 0
	\| Toogle to use the spectral approach (see Bertin, arXiv, 2018) to compute the displacement gradient field (very efficient). When the spectral method is used, the number of periodic images (<tt>numPBCimg</tt>) is ignored. The spectral method is not compatible with GPU calculation as of now.		\| Toogle to use the spectral approach (see Bertin, arXiv, 2018 [https://arxiv.org/pdf/1804.00803.pdf PDF]) to compute the displacement gradient field (very efficient). When the spectral method is used, the number of periodic images (<tt>numPBCimg</tt>) is ignored. The spectral method is not compatible with GPU calculation as of now. The spectral method requires the FFTW library.
	\|-		\|-
	\| <tt>material</tt>		\| <tt>material</tt>

Nbertin: /* Input files */

2018-05-30T01:04:03Z

Input files

← Older revision		Revision as of 01:04, 30 May 2018
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	\| <tt>D</tt>		\| <tt>D</tt>
	\| [1 0 0]		\| [1 0 0]
	\| Vector linking the center of the sample to the center of the main detector (i.e. specifying the position/orientation of the detector).		\| Vector linking the center of the sample to the center of the main detector (i.e. specifying the position/orientation of the detector). The detector plane will be orthogonal to <math>\vec{D}</math>.
	\|-		\|-
	\| <tt>Ddist</tt>		\| <tt>Ddist</tt>

Nbertin at 00:59, 30 May 2018

2018-05-30T00:59:39Z

← Older revision		Revision as of 00:59, 30 May 2018
Line 11:		Line 11:
	<HR>		<HR>

	This page details how to use the DDD-XRD calculation tool (see Bertin and Cai, CMS, 2018) to compute virtual diffraction patterns (micro-Laue patterns and Stokes-Wilson line profiles) associated with discrete dislocation structures generated from ParaDiS.		This page details how to use the DDD-XRD calculation tool (see Bertin and Cai, CMS, 2018 [http://micro.stanford.edu/~caiwei/papers/Bertin_Cai_CMS_2018_XRD_DDD.pdf PDF]) to compute virtual diffraction patterns (micro-Laue patterns and Stokes-Wilson line profiles) associated with discrete dislocation structures generated from ParaDiS.

Nbertin: /* Input files */

2018-05-25T17:34:32Z

Input files

← Older revision		Revision as of 17:34, 25 May 2018
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	\| <tt>Ddist</tt>		\| <tt>Ddist</tt>
	\| 70e-3		\| 70e-3
	\| Distance between the center of the sample and the detector.		\| Distance between the center of the sample and the detector (m).
	\|-		\|-
	\| <tt>numPixels</tt>		\| <tt>numPixels</tt>

Nbertin: /* Input files */

2018-05-25T17:34:01Z

Input files

← Older revision		Revision as of 17:34, 25 May 2018
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	\| [1 0 0]		\| [1 0 0]
	\| Direction of the incoming X-ray beam.		\| Direction of the incoming X-ray beam.
		⚫	\|-
		⚫	\| <tt>Emin</tt>
		⚫	\| 5e3
		⚫	\| Minimum energy of the incoming X-ray (eV).
		⚫	\|-
		⚫	\| <tt>Emax</tt>
		⚫	\| 25e3
		⚫	\| Maximum energy of the incoming X-ray (eV).
	\|-		\|-
	\| <tt>D</tt>		\| <tt>D</tt>
	\| [1 0 0]		\| [1 0 0]
	\| Vector linking the center of the ~~main~~ ~~detector~~ ~~with~~ ~~respect~~ to the ~~sample~~ ~~center~~ (i.e. specifying the position of the detector).		\| Vector linking the center of the sample to the center of the main detector (i.e. specifying the position/orientation of the detector).
	\|-		\|-
	\| <tt>Ddist</tt>		\| <tt>Ddist</tt>
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	\| 10e-5		\| 10e-5
	\| Size of the secondary detectors (m).		\| Size of the secondary detectors (m).
⚫	\|-
⚫	\| <tt>Emin</tt>
⚫	\| 5e3
⚫	\| Minimum energy of the incoming X-ray (eV).
⚫	\|-
⚫	\| <tt>Emax</tt>
⚫	\| 25e3
⚫	\| Maximum energy of the incoming X-ray (eV).
	\|}		\|}

Nbertin: /* Input files */

2018-05-25T17:32:01Z

Input files

← Older revision		Revision as of 17:32, 25 May 2018
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	\| <tt>material</tt>		\| <tt>material</tt>
	\| Cu		\| Cu
	\| ~~Material~~ (used for atomic and structural factors).		\| Symbol of the material (used for atomic and structural factors).
	\|-		\|-
	\| <tt>s0</tt>		\| <tt>s0</tt>

Nbertin: /* Input files */

2018-05-25T17:30:10Z

Input files

← Older revision		Revision as of 17:30, 25 May 2018
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	./paradisxrd -d file.data file.ctrl		./paradisxrd -d file.data file.ctrl

	The control file for the ~~energy~~ tool <tt>paradisxrd</tt> requires some additional parameters compared to the original control files used for ParaDiS simulations. Below is a list of additional parameters specific to XRD calculations that can be specified in the control file:		The control file for the XRD tool <tt>paradisxrd</tt> requires some additional parameters compared to the original control files used for ParaDiS simulations. Below is a list of additional parameters specific to XRD calculations that can be specified in the control file:

	{\| class="wikitable" cellpadding="2"		{\| class="wikitable" cellpadding="2"

Nbertin at 17:28, 25 May 2018

2018-05-25T17:28:59Z

@@ Line 21: / Line 21: @@
   make
-Make sure that the compilation mode is set to <tt>SERIAL</tt> in the global makefile.setup file before compiling. Use flag <tt>-D_XRD_GPU</tt> to enable GPU computations. Successful compilation will create executable <tt>paradisxrd</tt> in the global <tt>bin/</tt> folder.
+Make sure that the compilation mode is set to <tt>SERIAL</tt> in the global makefile.setup file before compiling. Use flag <tt>-D_XRD_GPU</tt> to enable GPU computations. Use flag <tt>-D_SPECTRAL</tt> to enable calculations using the spectral method. Successful compilation will create executable <tt>paradisxrd</tt> in the global <tt>bin/</tt> folder.
 == Usage ==
@@ Line 158: / Line 158: @@
 The DDD-XRD tool produces several outputs located in the simulation results directory.
@@ Line 176: / Line 191: @@
   cd utilities/xrd/examples
-  ../../../bin/paradisxrd -d taylor_edge_20.data taylor_edge_20.ctrl
+  ../../../bin/paradisxrd tilt_GB_10.ctrl
-  ../../../bin/paradisxrd -d rs0001.data rs0001.ctrl
+  ../../../bin/paradisxrd cu_15um_105rel_ESM_3_init.ctrl
 === Visualizing micro-Laue patterns ===

Nbertin: Created page with "
DDD-XRD profiles calculation

DDD-XRD Manual

2018-05-25T02:10:37Z

Created page with "<P ALIGN="CENTER">DDD-XRD profiles calculation</P> <P ALIGN="CENTER"><FONT SIZE="+2" color="darkred"><STRONG> DDD-XRD Manual</STRONG></font></P> <DIV> <P ALIGN="CENTER"><STRON..."

New page
<P ALIGN="CENTER">DDD-XRD profiles calculation</P>
<P ALIGN="CENTER"><FONT SIZE="+2" color="darkred"><STRONG>
DDD-XRD Manual</STRONG></font></P>
<DIV>
<P ALIGN="CENTER"><STRONG>Nicolas Bertin</STRONG></P>
</DIV>
<DIV>
<P ALIGN="CENTER">May 2018</P>
</DIV>

<HR>

This page details how to use the DDD-XRD calculation tool (see Bertin and Cai, CMS, 2018) to compute virtual diffraction patterns (micro-Laue patterns and Stokes-Wilson line profiles) associated with discrete dislocation structures generated from ParaDiS.

== Compilation ==

The DDD-XRD tool is located in directory <tt>utilities/xrd</tt> of the ParaDiS code. The compilation of the code is performed with

cd utilities/xrd
make

Make sure that the compilation mode is set to <tt>SERIAL</tt> in the global makefile.setup file before compiling. Use flag <tt>-D_XRD_GPU</tt> to enable GPU computations. Successful compilation will create executable <tt>paradisxrd</tt> in the global <tt>bin/</tt> folder.

== Usage ==

=== Input files ===

The DDD-XRD tool requires the same input files as the ParaDiS code, i.e. a control file and a data file. The calculation of the diffraction patterns is performed using the following command:

./paradisxrd -d file.data file.ctrl

The control file for the energy tool <tt>paradisxrd</tt> requires some additional parameters compared to the original control files used for ParaDiS simulations. Below is a list of additional parameters specific to XRD calculations that can be specified in the control file:

{| class="wikitable" cellpadding="2"
|-
| '''Parameter'''
| '''Default'''
| '''Description'''
|-
| <tt>numPBCimg</tt>
| 3
| Number of periodic images (in each direction) to be considered in the calculation.
|-
| <tt>numGrid</tt>
| 64
| Resolution of the sampling grid (in each direction) used to evaluate the displacement gradient field.
|-
| <tt>hklOrder</tt>
| 6
| Maximum order of the (hkl) reflections to be considered in the ray-tracing procedure.
|-
| <tt>numPeaks</tt>
| 0
| Number of selected peaks to be considered. The selected peaks allow to focus on specific reflections, by associating a secondary detector with each of them. The (hkl) indices of the selected peaks must be specified in parameter <tt>listPeaks</tt>. A maximum of 10 peaks can be selected.
|-
| <tt>listPeaks</tt>
| none
| List of (hkl) indices for the selected peaks. Secondary detectors will be associated to each selected peak.
|-
| <tt>peaksOnly</tt>
| 0
| Toggle to only consider the (hkl) peaks provided in <tt>listPeaks</tt>. When enabled, the <tt>hklOrder</tt> parameter will be ignored, and only peaks provided in <tt>listPeaks</tt> will be ray-traced.
|-
| <tt>writePeaks</tt>
| 0
| Write all reflected vectors (one per sampling point) for every selected peak (hkl) in file <tt>reflected_beam_<hkl>.out</tt> in the simulation results directory. This data can then be post-processed to generate patterns on detectors with aribrary parameters (location, orientation, size, resolution) without having to re-perform the displacement gradient calculation and ray-tracing procedure.
|-
| <tt>writeDisplacementGradient</tt>
| 0
| Output the displacement gradient at each sampling point in file <tt>G_<numGrid>.out</tt> in the simulation results directory.
|-
| <tt>GPU</tt>
| 0
| Toogle to enable GPU-accelerated calculations of the displacement gradient field.
|-
| <tt>spectral</tt>
| 0
| Toogle to use the spectral approach (see Bertin, arXiv, 2018) to compute the displacement gradient field (very efficient). When the spectral method is used, the number of periodic images (<tt>numPBCimg</tt>) is ignored. The spectral method is not compatible with GPU calculation as of now.
|-
| <tt>material</tt>
| Cu
| Material (used for atomic and structural factors).
|-
| <tt>s0</tt>
| [1 0 0]
| Direction of the incoming X-ray beam.
|-
| <tt>D</tt>
| [1 0 0]
| Vector linking the center of the main detector with respect to the sample center (i.e. specifying the position of the detector).
|-
| <tt>Ddist</tt>
| 70e-3
| Distance between the center of the sample and the detector.
|-
| <tt>numPixels</tt>
| 256
| Resolution (in each direction) of the main detector.
|-
| <tt>Dsize</tt>
| 280e-3
| Size of the main detector (m).
|-
| <tt>numPixels2</tt>
| 128
| Resolution (in each direction) of the secondary detectors.
|-
| <tt>Dsize2</tt>
| 10e-5
| Size of the secondary detectors (m).
|-
| <tt>Emin</tt>
| 5e3
| Minimum energy of the incoming X-ray (eV).
|-
| <tt>Emax</tt>
| 25e3
| Maximum energy of the incoming X-ray (eV).
|}

As an example, the following lines can be added at the end of any existing control file in order to use it with tool <tt>paradisxrd</tt>:

##----------------------------------
## DIFFRACTION
##----------------------------------
numGrid = 64
numPBCimg = 3
hklOrder = 4
numPeaks = 5
listPeaks = [1 1 3 2 0 4 2 2 4 1 3 1 1 3 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
peaksOnly = 0
writePeaks = 0
GPU = 1
spectral = 0
material = "Cu"
s0 = [1 0 0]
D = [1 0 0]
Ddist = 70e-3
numPixels = 256
Dsize = 280e-3
numPixels2 = 128
Dsize2 = 10e-5
Emin = 5e3
Emax = 25e3

Note that in this example, 5 selected peaks are specified and provided in <tt>listPeaks</tt>, namely the <math>(1 1 3), (2 0 4), (2 2 4), (1 3 1), (1 3 \overline{1})</math> reflections.

=== Main detector vs. selected peaks ===

By default, the <tt>paradisxrd</tt> tool computes the virtual micro-Laue pattern collected on a detector when shining an incoming X-ray beam <tt>s0</tt> to the dislocated microstructure (see Bertin and Cai, CMS, 2018). This detector is referred to as the main detector, and its size is typically chosen to be quite large such that several reflections fall onto the detector range. The intensity pattern collected on this main detector is outputed in file <tt>laue_pattern.out</tt> in the simulation results directory.

In many situations, it is also of interest to examine diffraction patterns associated with specific (hkl) reflections. In the current implentation of the <tt>paradisxrd</tt> tool, the user can specify up to 10 peaks (referred to as selected peaks) using parameters <tt>numPeaks</tt> and <tt>listPeaks</tt>. A secondary detector will be associated to each of these selected peaks. The center of the secondary detectors are automatically located at the position of which the X-ray would be reflected off the corresponding (hkl) in a perfect crystal. Intensity patterns collected on secondary detectors are outputed in files <tt>laue_peak_<hkl>_<numGrid>_all.out</tt> in the simulation results directory. For each selected peak, the strain distribution resolved along the diffraction vector are also outputed in file <tt>Pstrain_peak_<hkl>_<numGrid>.out</tt>. This data can be used to compute the line profile intensity using the Stokes-Wilson approximation.

=== Output files ===

The DDD-XRD tool produces several outputs located in the simulation results directory.

* <tt>laue_pattern.out</tt>: File containing the total intensity of reflected rays as collected at each pixel of the main detector.
* <tt>laue_peak_<hkl>_<numGrid>_all.out</tt>: File containing the intensity of the (hkl) reflection as collected at each pixel of the secondary detector associated with the slected (hkl) peak.
* <tt>reflected_beam_<hkl>.out</tt>: File containing the direction of the selected (hkl) reflection at each sampling point. This file can be post-processed to create the diffraction pattern associated with the selected (hkl) reflection on any new detector. Warning: this file may become huge when the resolution <tt>numGrid</tt> is large.
* <tt>Pstrain_peak_<hkl>_<numGrid>.out</tt>: File containing the value of the resolved strain in the direction of the diffracted vector of the (hkl) reflection at each sampling point. The distribution of this apparent strain can be used to calculate the line intensity profile under the Stokes-Wilson approximation.
* <tt>G_<numGrid>.out</tt> File containing the value of the displacement gradient tensor at each sampling point. Warning: this file may become big when the resolution <tt>numGrid</tt> is large.

== Examples ==

=== Generating diffraction patterns ===

Examples of input files to compute the XRD patterns asscociated with DDD configurations are provided in

utilities/xrd/examples

The examples can be run using the following commands:

cd utilities/xrd/examples
../../../bin/paradisxrd -d taylor_edge_20.data taylor_edge_20.ctrl
../../../bin/paradisxrd -d rs0001.data rs0001.ctrl

=== Visualizing micro-Laue patterns ===

=== Stokes-Wilson line profile ===