XANSONS for COD
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About XANSONS for COD

XANSONS for COD is a research project aimed to create an open access database of simulated x-ray and neutron powder diffraction patterns for nanocrystalline phase of the materials presented in the Crystallography Open Database (COD). You can participate by downloading and running a free program on your computer.

This project is in beta-testing stage. If no critical errors are found, all the results obtained during this stage will be included in the final database.

This project uses original open source (GPLv3 license) software XaNSoNS (X-ray and Neutron Scattering on Nanoscale Structures) to simulate the diffraction patterns on CPU and GPU. Download the source code of the client app here.

XANSONS for COD is a privately managed BOINC project supported by the Russian Foundation for Basic Research (project RFBR #15-07-07901-a).

Scientific Problem

The conventional technique used to recover the structural properties of the crystalline samples by their powder diffraction pattern is the Rietveld refinement method. In this method, the theoretical powder diffraction pattern is refined until it fits the experimental one. The computation of the angles and intensities of the Bragg peaks can be made almost instantaneously in the approximation of the infinite size of the crystallite. To adjust for the finite size of the crystallites in the samples or finite resolution of the measurement device, these peaks are broadened artificially with the broadening function (usually Gaussian). This artificial broadening works great until the size of the crystallite in the sample is something below few tens of nanometers. For the such small crystallites, it is very hard to get the right broadening function which works fine for all Bragg peaks. Fortunately, for the such small crystallites, it is not a problem to calculate the powder diffraction patterns using the Debye equation (with the distance-histogram approximation, such as that proposed by Marcin Wojdyr and implemented in his Debyer code). This project is aimed to calculate the x-ray and neutron powder diffraction patterns for the nanocrystallites with the size varying from 6 nm to 30 nm for the most of the entries of the Crystallography Open Database. The two different types of materials are considered: (a) isolated spherical crystalline nanoparticle of a given size (diameter), (b) crystalline material with long-range order broken on the distances greater than a given value. The obtained database may simplify the diagnostics of the nanocrystalline samples and complement the Full Profile Search Match method in the crystallite size analysis of the nanocrystalline samples.

In addition to the above, the calculation of the powder diffraction pattern using the Debye equation allows to account the lattice defects such as site vacancies, atom replacements and displacements. So, if the Crystallography Information File (CIF) for the given structure provides the site occupancy numbers and atomic displacement parameters, the application will use them to calculate the diffraction pattern.

System Requirements

Supported operating systems: Supported GPUs:
  • Nvidia GPU with CUDA Compute Capability 1.3 and above (Windows, Linux) or 2.0 and above (OS X/macOS) with at least 1GB of memory (GDDR5 memory is recommended). Driver version 340.21 and above (Windows, Linux) or CUDA Driver for MAC version 7.0.29 and above (OS X/macOS).
  • AMD GPU with OpenCL 1.2+ support with at least 1GB of memory (integrated AMD GPUs, a.k.a. APUs, are not recomended, see Important Notes below).
  • Intel GPU of 8-th generation and above with OpenCL 1.2+ support (older Intel GPUs are not recommended, see Important Notes below).

Important Notes

  • The apps of this project do not make checkpoints. If stopped, the task will be restarted from the beginning. The task execution time should not exceed 10 minutes for moderate PCs. However, some tasks may take longer to complete on low-end PCs. This is particularly true for low-end GPUs. If the execution time of tasks is unacceptably high for your GPU, consider disabling it in the 'Preferences for this project' in your profile page.

  • Some antivirus software may place the executables into quarantine as unknown (and therefore suspicious) files. To prevent this from happening, disable blocking of unknown files in the antivirus preferences (e.g. in Avast disable CyberCapture feature). When BOINC client will download the executables, you can manually scan the BOINC data directory (C:\ProgramData\BOINC\ by default) for viruses. After that, the disabled antivirus functionality may be re-enabled again.

  • The algorithm which solves the problem on GPU uses 64-bit integer atomic functions on Nvidia and AMD GPUs and emulates them on Intel GPUs. All tested integrated AMD GPUs (APU) and all tested Intel GPUs below 8-th generation showed very poor performance for the tasks of this project probably caused by specific hardware architectures of these GPUs. If your GPU is affected, you can disable it in the 'Preferences for this project' in your profile page.

  • GPU apps do not require dedicated CPU core by default anymore. If you notice any performance issues caused by this, consider using custom app configuration. Place this file in the project’s folder.

  • The progress bar for GPU tasks may freeze on 0% for a few seconds. This is OK and does not mean that the app is hanging (at that time CPU computes the atomic ensemble and does not report a progress).

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News

Active phase of the project is completed by 20% in the first 24 days
Only about 0.2% of the obtained results should be recalculated due to bugs in the early versions of the apps (the results obtained with the version 1.04 mostly). All other results are included in the final database. 12 Jul 2017, 20:28:27 UTC · Comment

Crystallography Open Database server is temporarily down
We get the input data for the WUs from the http://crystallography.net. So, while this server is down we can't generate new WUs.

Update
Added a mirror.

Update 2
It seems that http://crystallography.net/ is up again. But if the problem recurs in the future, the requests will be redirected to the mirror server, http://qiserver.ugr.es/cod/. 12 Jul 2017, 16:20:55 UTC · Comment

Source code of the client app is released
You can download it here. 28 Jun 2017, 21:18:48 UTC · Comment

CPU usage in GPU apps
The new CUDA app 1.03 does not use the CPU core anymore except for the computation of the atomic ensemble in the beginning.
The new OpenCL app 1.03 has a command line option --nowait which when specified reduces the CPU load to zero but at the same time makes the system almost unusable due to lagging. If you do not use the system while crunching, you may add this to your app_config.xml:

<app_version> <app_name>xansons_gpu</app_name> <plan_class>opencl_ati_102_windows</plan_class> <cmdline>--nowait</cmdline> </app_version>

Replace 'opencl_ati_102_windows' with the appropriate plan class: opencl_ati_102_mac, opencl_ati_102_linux, opencl_intel_gpu_102_windows, opencl_intel_gpu_102_linux, opencl_intel_gpu_102_mac or opencl_nvidia_102_linux.

Update
All OpenCL 1.03 versions are marked as beta due to potential memory leak problem.


Update 2
The 1.03 app uses exactly the same amount of memory as 1.02 does, so there is no memory leak. The memory consumption depends on the WU. Those tasks which have 'solid_material' in their names may consume up to 1.5 GB of memory depending on the initial data. Please take this into consideration when launching multiple WUs in parallel.
I'll try to reduce memory consumption in the next version. 25 Jun 2017, 23:13:15 UTC · Comment

Maintenance is over!
The project is restarted with new native BOINC apps and additional computational scenario.

Now the large WUs can be assigned only to the GPU and the small ones only to the CPU.

GPU apps do not require dedicated CPU core by default anymore. If you notice any performance issues caused by this, consider using custom app configuration. Place this file in the project's folder.

The apps of this project do not make checkpoints. If stopped, the task will be restarted from the beginning. The task execution time should not exceed 10 minutes for moderate PCs. However, some tasks may take longer to complete on low-end PCs. This is particularly true for low-end GPUs. If the execution time of tasks is unacceptably high for your GPU, consider disabling it in the "Preferences for this project" in your profile page.

The project is in beta-testing stage. Bugs are more than likely. However, all the results obtained during this stage will be included in the final database If no critical errors are found.

Thank you for participating! 18 Jun 2017, 18:09:05 UTC · Comment

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