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Merge pull request #3134 from pordyna/topic-saxsPlugin
SAXS plugin implementation using electron density
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| .. _usage-plugins-xrayScattering: | ||
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| xrayScattering | ||
| -------------- | ||
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| This plugin calculates Small Angle X-ray Scattering (SAXS) patterns from electron density. | ||
| ( Using a density `FieldTmp` as an intermediate step and not directly the macro particle distribution. ) | ||
| This is a species specific plugin and it has to be run separately for each scattering species. | ||
| Since the plugin output is the scattered complex amplitude, contributions from different species can be coherently summed later on. | ||
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| .. math:: | ||
| \Phi({\vec q}) &= \frac{r_e}{d} \int_{t} \mathrm{d}t \int_{V} \mathrm{d}V \phi({\vec r}, t) n({\vec r}, t) \\ | ||
| I &= \left| \Phi \right|^2 | ||
| ============================== ================================================================================ | ||
| Variable Meaning | ||
| ============================== ================================================================================ | ||
| :math:`\Phi` Scattered amplitude | ||
| :math:`\vec q` Scattering vector with :math:`|{\vec q}| = \frac{4 \pi \sin \theta}{\lambda}` | ||
| :math:`\theta` Scattering angle. :math:`2\theta` is the angle between the incoming and the scattered k-vectors. | ||
| :math:`\lambda` Probing beam wavelength | ||
| :math:`n` Electron density | ||
| :math:`\phi` Incoming wave amplitude | ||
| :math:`I` Scattering intensity | ||
| :math:`d` Screen distance | ||
| :math:`r_e` Classical electron radius | ||
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| ============================== ================================================================================ | ||
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| For the free electrons, the density :math:`n` is just their number density, for ions it is the bound electrons density of the species. | ||
| This plugin will automatically switch to bound electrons density for species having the `boundElectrons` property. | ||
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| The volume integral is realized by a discrete sum over the simulation cells and the temporal integration reduces to accumulating the amplitude over simulation time steps. | ||
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| .. note:: | ||
| This calculation is based on the kinematic model of scattering. Multiple scattering CAN NOT be handled in this model. | ||
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| .param file | ||
| ^^^^^^^^^^^ | ||
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| The `xrayScattering.param` file sets the x-ray beam alignment as well as its temporal and transverse envelope. | ||
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| .. note:: | ||
| At the moment the translation (to the side center + offset) is not working correctly. | ||
| For that reason, the envelopes and the offset can't be set in the ``.param`` file yet. | ||
| The probe is always a plane wave. | ||
| Beam rotation works. | ||
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| The alignment settings define a beam coordinate system with :math:`\hat{z} = \hat{k}` and :math:`\hat{x}`, :math:`\hat{y}` perpendicular to the x-ray propagation direction. | ||
| It is always a right-hand system. It is oriented in such way that for propagation parallel to the PIC x- or y-axis (`Side`: `X`, `XR`, `Y` or `YR`) :math:`\hat{x}_{\text{beam}} = - \hat{z}_{\text{PIC}}` holds and if :math:`{\vec k }` is parallel to the PIC z-axis (`Side`: `Z` or `ZR`), :math:`\hat{x}_{\text{beam}} = - \hat{y}_{\text{PIC}}` holds. | ||
| The orientation can be then fine adjusted with the `RotationParam` setting. | ||
| .. TODO: Figures showing the beam coordinate system orientation in the PIC system. | ||
| .. TODO: Add other parameters after the coordinate transform has been fixed and the settings have been moved back to the .param file. | ||
| ================= =============================================================================================================================== | ||
| Setting Description | ||
| ================= =============================================================================================================================== | ||
| ``ProbingSide`` The side from which the x-ray is propagated. | ||
| Set `X`, `Y` or `Z` for propagation along one of the PIC coordinate system axes; | ||
| `XR`, `YR` or `ZR` for propagation in an opposite direction. | ||
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| ``RotationParam`` Rotation of the beam axis, :math:`z_{\text{beam}}`, from the default orientation ( perpendicular the the simulation box side ). | ||
| Set the beam yaw and pitch angles in radians. | ||
| ================= =============================================================================================================================== | ||
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| .. TODO: Add BEAM_OFFSET in between after the coordinate transform has been fixed. | ||
| The coordinate transfer from the PIC system to the beam system is performed in the following order: | ||
| rotation to one of the default orientations (``ProbingSide`` setting), additional rotation (``RotationParam`` ). This has to be taken into account when defining the experimental setup. | ||
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| .cfg file | ||
| ^^^^^^^^^ | ||
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| For a specific (charged) species ``<species>`` e.g. ``e``, the scattering can be computed by the following commands. | ||
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| ============================================ ============================================================================================================================================ | ||
| Command line option Description | ||
| ============================================ ============================================================================================================================================ | ||
| ``--<species>_xrayScattering.period`` Period at which the plugin is enabled (PIC period syntax). Only the intensity from this steps is accumulated. | ||
| Default is `0`, which means that the scattering intensity in never calculated and therefor off | ||
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| ``--<species>_xrayScattering.outputPeriod`` Period at which the accumulated amplitude is written to the output file (PIC period syntax). Usually set close to the x-ray coherence time. | ||
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| ``--<species>_xrayScattering.qx_max`` Upper bound of reciprocal space range in qx direction. The unit is :math:`Å^{-1}`. Default is `5`. | ||
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| ``--<species>_xrayScattering.qy_max`` Upper bound of reciprocal space range in qy direction. The unit is :math:`Å^{-1}` Default is `5`. | ||
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| ``--<species>_xrayScattering.qx_min`` Lower bound of reciprocal space range in qx direction. The unit is :math:`Å^{-1}` Default is `-5`. | ||
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| ``--<species>_xrayScattering.qy_min`` Lower bound of reciprocal space range in qy direction. The unit is :math:`Å^{-1}` Default is `-5`. | ||
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| ``--<species>_xrayScattering.n_qx`` Number of scattering vectors needed to be calculated in qx direction. Default is `100`, | ||
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| ``--<species>_xrayScattering.n_qy`` Number of scattering vectors needed to be calculated in qy direction. Default is '100'. | ||
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| ``--<species>_xrayScattering.file`` Output file name. Default is `<species>_xrayScatteringOutput`. | ||
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| ``--<species>_xrayScattering.ext`` `openPMD` filename extension. This controls the backend picked by the `openPMD` API. Default is `bp` for adios backend. | ||
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| ``--<species>_xrayScattering.compression`` Backend-specific `openPMD` compression method (e.g.) zlib. | ||
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| ``--<species>_xrayScattering.memoryLayout`` Possible values: `mirror` and `split`. Output can be mirrored on all Host+Device pairs or uniformly split, in chunks, over all nodes. | ||
| Use split when the output array is too big to store the complete computed q-space on one device. | ||
| For small output grids the `mirror` setting could turn out to be more efficient. | ||
| ============================================ ============================================================================================================================================ | ||
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| Output | ||
| ^^^^^^ | ||
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| ``<species>_xrayScatteringOutput.<backend-specific extension>`` | ||
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| Output file in the `openPMD` standard. An example on how to access your data with the python reader: | ||
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| .. code-block:: python | ||
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| from picongpu.plugins.data import XrayScatteringData | ||
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| simulation_path = '...' # dir containing simOutput, input, .., | ||
| # Read output from the 0th step, for electrons, hdf5 backend. | ||
| data = XrayScatteringData( simulation_path, 'e', 'h5' ) | ||
| amplitude = saxsData.get(iteration=0) * saxsData.get_unit() | ||
| del XrayScatteringData | ||
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| When you don't want to use the python reader keep in mind that: | ||
| * All iterations are saved in a single file | ||
| * The mesh containing the output is called `'amplitude'` | ||
| * This mesh has 2 components, `'x'` is the real part and `'y'` is the imaginary part. | ||
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| .. note:: | ||
| The amplitude is not zeroed on ``outputPeriod`` so one has to subtract the output from the iteration one period before and then calculate :math:`\left|\Phi\right|^2` and sum it with the intensities from other coherence periods. | ||
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| References | ||
| ^^^^^^^^^^ | ||
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| - [1] Kluge, T., Rödel, C., Rödel, M., Pelka, A., McBride, E. E., Fletcher, L. B., … Cowan, T. E. (2017). Nanometer-scale characterization of laser-driven compression, shocks, and phase transitions, by x-ray scattering using free electron lasers. Physics of Plasmas, 24(10). https://doi.org/10.1063/1.5008289 |
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| Original file line number | Diff line number | Diff line change |
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| /* Copyright 2020 Pawel Ordyna | ||
| * | ||
| * This file is part of PIConGPU. | ||
| * | ||
| * PIConGPU is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU General Public License as published by | ||
| * the Free Software Foundation, either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * PIConGPU is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU General Public License | ||
| * along with PIConGPU. | ||
| * If not, see <http://www.gnu.org/licenses/>. | ||
| */ | ||
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| #pragma once | ||
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| #include "picongpu/simulation_defines.hpp" | ||
| #include "picongpu/plugins/xrayScattering/beam/Side.hpp" | ||
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| /* preprocessor struct generator */ | ||
| #include <pmacc/preprocessor/struct.hpp> | ||
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| namespace picongpu | ||
| { | ||
| namespace plugins | ||
| { | ||
| namespace xrayScattering | ||
| { | ||
| namespace beam | ||
| { | ||
| using namespace picongpu::plugins::xrayScattering::beam; | ||
| /* Choose from: | ||
| * - ZSide | ||
| * - YSide | ||
| * - XSide | ||
| * - ZRSide | ||
| * - YRSide | ||
| * - XRSide | ||
| */ | ||
| using ProbingSide = ZSide; | ||
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| PMACC_STRUCT( RotationParam, | ||
| ( PMACC_C_VALUE ( float_X, yawAngle, 0 ) ) | ||
| ( PMACC_C_VALUE ( float_X, pitchAngle, 0 ) ) | ||
| ); | ||
| }// namespace beam | ||
| }// namespace xrayScattering | ||
| }// namespace plugins | ||
| }// namespace picongpu |
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74 changes: 74 additions & 0 deletions
74
include/picongpu/plugins/xrayScattering/DetermineElectronDensitySolver.hpp
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| /* Copyright 2020 Pawel Ordyna | ||
| * | ||
| * This file is part of PIConGPU. | ||
| * | ||
| * PIConGPU is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU General Public License as published by | ||
| * the Free Software Foundation, either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * PIConGPU is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU General Public License | ||
| * along with PIConGPU. | ||
| * If not, see <http://www.gnu.org/licenses/>. | ||
| */ | ||
| #pragma once | ||
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| #include "picongpu/simulation_defines.hpp" | ||
| #include <pmacc/traits/HasFlag.hpp> | ||
| #include "picongpu/particles/particleToGrid/derivedAttributes/DerivedAttributes.def" | ||
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| namespace picongpu | ||
| { | ||
| namespace plugins | ||
| { | ||
| namespace xrayScattering | ||
| { | ||
| using namespace particles::particleToGrid; | ||
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| template< typename T_ParticleType > | ||
| struct IsIon | ||
| { | ||
| using FrameType = typename T_ParticleType::FrameType; | ||
| using type = typename pmacc::traits::HasFlag< | ||
| FrameType, | ||
| boundElectrons | ||
| >::type; | ||
| }; | ||
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| /** Chose an electron density solver for a given particle type. | ||
| * | ||
| * Switches between a bound electron number density solver for particles | ||
| * with the boundElectrons attribute (ions) and a particle number density | ||
| * solver for other particle types (electrons). | ||
| * | ||
| * @tparam T_ParticleType Scattering particles | ||
| * @return ::type TmpField solver to be used | ||
| */ | ||
| template< typename T_ParticlesType > | ||
| struct DetermineElectronDensitySolver | ||
| { | ||
| using IonSolver = typename CreateFieldTmpOperation_t< | ||
| T_ParticlesType, | ||
| derivedAttributes::BoundElectronDensity | ||
| >::Solver; | ||
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| using ElectronSolver = typename CreateFieldTmpOperation_t< | ||
| T_ParticlesType, | ||
| derivedAttributes::Density | ||
| >::Solver; | ||
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| using type = typename boost::mpl::if_< | ||
| typename IsIon< T_ParticlesType >::type, | ||
| IonSolver, | ||
| ElectronSolver | ||
| >::type; | ||
| }; | ||
| } // namespace xrayScattering | ||
| } // namespace plugins | ||
| } // namespace picongpu |
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