Method for screening local vibration mode of atomic system
By generating visualized data files and spectra of atomic structure vibrations, the problem of the inability to intuitively display atomic vibration phenomena in existing technologies has been solved, enabling more efficient data processing and experimental control analysis.
Patent Information
- Application Number
- CN202511039601.8
- Authority / Receiving Office
- CN · China
- Patent Type
- Applications(China)
- Current Assignee / Owner
- Filing Date
- 2025-07-28
- Publication Date
- 2025-11-14
AI Technical Summary
Existing first-principles calculation techniques cannot intuitively display the vibrational phenomena of atomic structures, and lack Raman activity parameter conversion and visualization analysis functions, making it difficult to compare and analyze with experimental data.
By acquiring atomic structure files, target atom coordinate files, and feature vector files, the system analyzes and generates visualization data files of atomic structure vibrations. It then combines these with the incident light direction to generate Raman and infrared spectrum data files, and performs Gaussian broadening optimization.
It enables intuitive visualization of atomic vibration modes, improves data processing efficiency, enhances the ability to compare and analyze experimental and computational data, and generates more accurate and aesthetically pleasing spectra.
Smart Images
Figure CN120954578A_ABST
Abstract
Description
Technical Field
[0001] This invention relates to the field of physical information processing technology, and in particular to a method for screening local vibrational modes of atomic systems. Background Technology
[0002] In today's highly information-driven era, with the continuous improvement of computing power, first-principles calculations have gradually become one of the important means in physics and materials engineering to study the unique physical phenomena of material properties and atomic structures. By visualizing the local vibrational modes of atomic systems, the unique vibrational characteristics of different atomic structures can be observed intuitively. Vibrational modes describe the vibrational phenomena of atoms at corresponding frequencies in different types of atomic structures. Different structures exhibit significantly different vibrational phenomena. However, existing first-principles calculation techniques rely on high-performance computing technology and output data in the form of readable data files on servers, which cannot intuitively show the vibrational phenomena of atomic structures.
[0003] The results of first-principles calculations used in existing materials projects are presented only in the form of data, which is relatively simple. The data file results are not intuitive enough, which is not conducive to researchers’ in-depth understanding and lacks user-friendliness. In addition, the phonon data output by existing calculation functions lacks Raman activity parameter conversion and visualization analysis functions, making it difficult to compare and analyze with experimental Raman spectra and to make it difficult to compare experimental and calculated data. Summary of the Invention
[0004] To address the shortcomings of existing technologies, this invention provides a method for screening local vibrational modes of atomic systems, thereby solving the problems of visualization of local vibrational modes of atoms and the lack of processing functions for Raman and infrared spectra in existing technologies.
[0005] This invention provides a method for screening local vibrational modes of an atomic system, comprising the following steps:
[0006] Step 1: Obtain the atomic structure file, the target atom coordinate file, and the feature vector file. The feature vector file contains the real and imaginary parts of the vibrational displacement of each atom at each frequency.
[0007] Step 2: Parse the target atomic coordinate file to extract lattice basis vectors, atomic coordinates, element types, and the number of atoms of each element;
[0008] Step 3: Extract the real part from the feature vector file and perform vector fusion to obtain the total vibration vector file of each atom at each frequency;
[0009] Step 4: Using visualization methods, generate a visualization data file of atomic structure vibrations based on the atomic structure file and the total vibration vector file;
[0010] Step 5: Set the incident light direction. Based on the set incident light direction, extract the vibration components in the incident light direction from the total vibration vector file, and generate a transitional vibration vector file by combining it with the target atom coordinate file.
[0011] Step 6: Select the desired frequency from the visualization data file, and combine it with the transition vibration vector file to generate Raman spectrum data file and infrared spectrum data file;
[0012] Step 7: Optimize the Raman spectrum data file and the infrared spectrum data file by Gaussian broadening to complete the screening process.
[0013] Furthermore, in step 1, the method for obtaining each file is as follows:
[0014] The data files of the first-principles calculation software and the parameter files of the target calculation structure are obtained. The atomic structure file, atomic coordinate file and eigenvector file are obtained through calculation. The atomic coordinate file is then standardized to obtain the target atomic coordinate file.
[0015] Furthermore, in step 2, the target atomic coordinate file is traversed and parsed using Python code to extract lattice basis vectors, atomic coordinates, element types, and the number of atoms of each element.
[0016] Furthermore, in step 3, the vector fusion method is as follows:
[0017] Based on the lattice basis vectors and atomic coordinates, the real displacement components of each atom in three directions are synthesized into a total vibration vector in real space.
[0018] Furthermore, in step 4, the specific process of generating a visualization data file of atomic structure vibrations is as follows:
[0019] Step 41: Construct the lattice frame of the three-dimensional crystal structure using lattice basis vectors;
[0020] Step 42: Obtain the element type of the atom and its corresponding elemental properties;
[0021] Step 43: Construct a multi-element atomic structure model based on various atomic coordinates and elemental properties of atoms;
[0022] Step 44: Embed the multi-element atomic structure model into the lattice frame to construct a complete three-dimensional crystal structure model;
[0023] Step 45: Obtain view control commands, including: elevation control commands and / or azimuth control commands;
[0024] Step 46: Render and output the corresponding visualization data file of atomic structure vibration according to the view control instructions.
[0025] Furthermore, in step 5, the generated transitional vibration vector file includes: atomic frequency, incident light direction, frequency, and vibration vector of each atom in three-dimensional space.
[0026] Furthermore, in step 6, the specific method for generating the Raman spectrum data file is as follows:
[0027] Construct a bond polarization model corresponding to the Raman tensor, calculate the Raman intensity at each frequency based on the vibration vectors of atoms in the transition vibration vector file and the direction of incident light, and output a Raman spectrum data file including frequency-Raman intensity pairs.
[0028] Furthermore, in step 6, the specific method for generating the infrared spectrum data file is as follows:
[0029] The infrared intensity is calculated by modulating the vibration vectors of atoms in the transition vibration vector file, and the output includes an infrared spectrum data file containing the frequency, infrared intensity, and vibration vector components.
[0030] The beneficial effects of this invention are:
[0031] This invention can vector synthesize and visualize the displacement of each atom in each direction at different frequencies, allowing for a more intuitive observation of atomic vibrations. By combining atomic coordinate files and transitional files that represent vibration vectors, Raman and infrared spectrum data files can be obtained, providing a more accurate representation of atomic structure-related properties.
[0032] This invention automatically recognizes file content using Python code, laying the groundwork for subsequent atomic vibration visualization, Raman spectroscopy, and infrared spectroscopy processing, thus improving data processing efficiency. This invention retains the real parts of the feature vector file, keeping only the "instantaneous amplitude" while discarding phase information. This significantly reduces the data volume and subsequent computational complexity while still accurately characterizing local atomic vibrational modes, making visualization more intuitive and spectral calculations more efficient. This invention constructs a complete three-dimensional crystal structure model based on the lattice basis vectors, lattice constants, and atomic fractional coordinates of the three-dimensional atomic structure. It then renders and outputs the corresponding atomic structure vibration visualization data file according to the user's view control commands, improving the efficiency of target user selection of the target atomic structure. This invention combines the user-selected incident light direction to generate a transitional vibration vector file, improving the normalization of the data file and significantly reducing the dimensionality and computational load of subsequent Raman / infrared calculations, facilitating further post-processing. This invention utilizes atomic coordinate files and transitional vibration vector files. This invention optimizes the Raman and infrared spectral data files by adding Gaussian broadening, making the images more aesthetically pleasing and distortion-free. Attached Figure Description
[0033] The features and advantages of the invention will be more clearly understood by referring to the accompanying drawings, which are schematic and should not be construed as limiting the invention in any way. In the drawings:
[0034] Figure 1 This is a flowchart of a specific embodiment of the present invention;
[0035] Figure 2 This is a schematic diagram of the visualization output of the target atomic structure in a specific embodiment of the present invention;
[0036] Figure 3 This is a flowchart illustrating the generation of a transitional vibration vector file in a specific embodiment of the present invention;
[0037] Figure 4 This is a schematic diagram of the Raman spectrum and infrared spectrum in a specific embodiment of the present invention;
[0038] Figure 5 This is a flowchart of Gaussian broadening processing of Raman and infrared spectra in a specific embodiment of the present invention. Detailed Implementation
[0039] To make the objectives, technical solutions, and advantages of the embodiments of the present invention clearer, the technical solutions of the embodiments of the present invention will be clearly and completely described below with reference to the accompanying drawings. Obviously, the described embodiments are only some embodiments of the present invention, not all embodiments. Based on the embodiments of the present invention, all other embodiments obtained by those skilled in the art without creative effort are within the scope of protection of the present invention.
[0040] The present invention will be further illustrated below with reference to specific embodiments. Those skilled in the art should understand that these embodiments are for illustrative purposes only and are not intended to limit the scope of the invention. Modifications to the present invention in various equivalent forms all fall within the scope defined by the appended claims.
[0041] like Figure 1 As shown, the present invention provides a method for screening local vibrational modes of an atomic system, comprising the following steps:
[0042] Step 1: Obtain the atomic structure file, the target atom coordinate file, and the feature vector file. The feature vector file contains the real and imaginary parts of the vibrational displacement of each atom at each frequency.
[0043] The first-principles calculation software used is PWmat, and all files are data files obtained after performing phonon calculations on the target structure using the first-principles calculation software.
[0044] Among them, the atomic structure file is: in the post-processing stage after the phonon calculation is completed, the target atomic structure file needs to be converted into the .vesta format using the image processing software Vesta.
[0045] The atomic coordinate file is: the target atomic structure file is converted into a .vasp format file in the current path, and the format of element types, number of elements, lattice constants and atomic coordinates in the target atomic structure file are modified to adapt to the system's recognition of the file content. After the format is modified, it is named "CONTCAR" to match the system.
[0046] The feature vector file is as follows: the target user can adjust the incident light direction, qpoints parameter, cell expansion size and other parameters according to their own needs, and use the Phononpy command to generate a feature vector data file containing the feature vectors of each atom at different frequencies - qpoints.yaml. The file includes the data of real and imaginary feature vectors. The Phononpy command is introduced. After loading the appropriate runtime environment, only one command is needed to output the relevant phonon data file required by the target user, which improves the efficiency of atomic vibration data post-processing.
[0047] Step 2: Use Python code to traverse and parse the target atomic coordinate file to extract lattice basis vectors, atomic coordinates, element types, and the number of atoms of each element;
[0048] Among them, the lattice basis vectors are three non-coplanar vectors that define the boundary of the unit cell. These vectors determine the periodic repeating pattern of the lattice and are the basis for constructing the entire lattice; the atomic coordinates are the fractional coordinates of each atom in the target atomic structure in three-dimensional space.
[0049] Step 3: Extract the real part from the feature vector file and perform vector fusion to obtain the total vibration vector file of each atom at each frequency;
[0050] The specific method for extracting the real part from the feature vector file is as follows:
[0051] First, create an array that does not contain data; this array serves as storage. Then, find the required array through the feature vector file. The required array includes the real and imaginary parts, which are the vibration vectors of each atom in three dimensions at different frequencies.
[0052] If the search is successful, the first frequency information is stored in a new array, where the first frequency information is the real part, which is the vibration vector in the three-dimensional direction of the first column; the second frequency information is stored in another array, where the second frequency information is the imaginary part, which is the vibration vector in the three-dimensional direction of the second column.
[0053] Repeat the search process until all frequencies are stored in the corresponding arrays.
[0054] The real part represents the instantaneous displacement amplitude of the atomic vibration at that frequency. It is symmetrically distributed. The real part can have two frequencies: positive and negative. When the real part is positive, it means that the atom deviates from the equilibrium position in a certain direction during vibration at a certain frequency. If the real part is large, the displacement from the equilibrium position is larger. When the real part is negative, it means that the atom deviates from the equilibrium position in the opposite direction during vibration. It is usually used to describe the symmetry of complex signals.
[0055] The imaginary part represents the phase difference between atoms in the same mode. When the phases of the imaginary parts of two atoms differ, their vibrations may be asynchronous. This so-called phase difference reflects the propagation characteristics of vibrational waves in the crystal.
[0056] The eigenvector data file contains real and imaginary parts, which together determine the shape and behavior of the vibrational modes. However, the imaginary part data is mainly reflected in the time dimension and has no reference value relative to reflecting the local vibrational modes of atoms. Therefore, the generated real part data is the main consideration.
[0057] The vector fusion process specifically involves: reconstructing the atomic structure based on the lattice basis vectors and atomic coordinates, and vector synthesizing the total vibration vector in real space based on the real displacement components of each atom in three directions.
[0058] Step 4: Using visualization methods, generate a visualization data file of atomic structure vibrations based on the atomic structure file and the total vibration vector file;
[0059] By combining the total vibration vector file obtained in step 3 with the atomic structure file, the displacement of atoms from their equilibrium positions is reflected. A three-dimensional atomic model is then used to analyze the target atomic structure and the vibration displacement vector of each atom. Figure 2 The visualization shown.
[0060] The specific process is as follows:
[0061] Step 41: Construct the lattice frame of the three-dimensional crystal structure using lattice basis vectors. The three-dimensional crystal is a crystal structure with three spatial dimensions and periodicity.
[0062] Step 42: Obtain the element type of the atom and its corresponding elemental properties. The element name is the atom type, for example, gallium. The elemental properties include color and radius.
[0063] Step 43: Construct a multi-element atomic structure model based on various atomic coordinates and elemental properties of atoms;
[0064] Step 44: Embed the multi-element atomic structure model into the lattice frame to construct a complete three-dimensional crystal structure model;
[0065] Step 45: Obtain view control commands, including: elevation control commands and / or azimuth control commands;
[0066] Step 46: Render and output the corresponding visualization data file of atomic structure vibration according to the view control instructions.
[0067] Step 5: In the data post-processing stage, use the Phononpy command to set the parameters of qpoints to determine the incident light and polarization direction. Users can customize different incident light directions according to their needs, such as... Different incident light directions have relatively different effects on the vibration vectors of atomic structures. The process of generating a transitional vibration vector file is as follows: Figure 3 As shown;
[0068] Based on the set incident light direction, the vibration components in the incident light direction are extracted from the total vibration vector file, and a transitional vibration vector file is generated by combining it with the target atom coordinate file. The format of the transitional vibration vector file is: incident and polarization directions, frequency, and vibration vectors in the three-dimensional directions of each atom, i.e., displacement.
[0069] Step 6: Select the desired frequency from the visualization data file, and combine it with the transition vibration vector file to generate Raman spectrum data files and infrared spectrum data files. The resulting Raman and infrared spectra are shown below. Figure 4 As shown;
[0070] The specific method for generating Raman spectrum data files is as follows:
[0071] Construct a bond polarization model corresponding to the Raman tensor, calculate the Raman intensity at each frequency based on the vibration vectors of atoms in the transition vibration vector file and the direction of incident light, and output a Raman spectrum data file including frequency-Raman intensity pairs.
[0072] Raman intensity is related to changes in molecular polarizability, and the bond polarization tensor can be used to describe these changes. The bond polarization tensor is a mathematical tool that describes the variation of chemical bond polarizability with bond length and bond angle. It first decomposes the overall molecular polarizability into the independent contributions of each chemical bond, then obtains molecular vibrational information, uses DFT calculations to obtain the normal modes of vibration and their frequencies, determines the symmetry of each vibrational mode, and analyzes the Raman activity of the vibrational modes. Simultaneously, it constructs the bond polarization tensor, decomposing each vibrational mode into the local displacements of each bond, i.e., through normal coordinate transformation, calculates the contribution of each bond polarization tensor to the derivative of the overall polarizability. Since Raman intensity is proportional to the square of the polarizability derivative, the Raman intensity at different frequencies can ultimately be output using calculation formulas, resulting in a Raman spectrum data file.
[0073] The specific method for generating infrared spectrum data files is as follows:
[0074] The infrared intensity is calculated by modulating the vibration vectors of atoms in the transition vibration vector file, and the output includes an infrared spectrum data file containing the frequency, infrared intensity, and vibration vector components.
[0075] Infrared spectroscopy is primarily based on changes in dipole moments caused by atomic vibrations. Point defects, including vacancies, dopants, or interstitial defects, each affect the original structure, resulting in changes in the dipole moment. This leads to changes in infrared intensity, which can be reflected in the atomic vibration vectors. Therefore, by considering the rate of change of the dipole moment of each atom at different frequencies, the infrared activity intensity can be calculated. The infrared activity intensity can be obtained by taking the modulus of the three-dimensional spatial vibration vector of each atom at different frequencies, and the calculated infrared spectral data file can be output.
[0076] Step 7: Optimize the Raman intensity in the Raman spectrum data file and the infrared intensity in the infrared spectrum data file using Gaussian broadening to complete the screening process. The process is as follows: Figure 5 As shown.
[0077] Gaussian broadening uses Gaussian convolution to weighted average neighboring data points, suppressing high-frequency noise and improving the signal-to-noise ratio (SNR) while preserving the main peak characteristics. Broadening can reduce the dynamic range of high-intensity main peaks and highlight the details of weak peaks. Users can set the Gaussian broadening according to their actual needs.
[0078] Although embodiments of the invention have been described in conjunction with the accompanying drawings, those skilled in the art can make various modifications and variations without departing from the spirit and scope of the invention, and such modifications and variations all fall within the scope defined by the appended claims.
Claims
1. A method for screening local vibrational modes of an atomic system, characterized in that, Includes the following steps: Step 1: Obtain the atomic structure file, the target atom coordinate file, and the feature vector file. The feature vector file contains the real and imaginary parts of the vibrational displacement of each atom at each frequency. Step 2: Parse the target atomic coordinate file to extract lattice basis vectors, atomic coordinates, element types, and the number of atoms of each element; Step 3: Extract the real part from the feature vector file and perform vector fusion to obtain the total vibration vector file of each atom at each frequency; Step 4: Using visualization methods, generate a visualization data file of atomic structure vibrations based on the atomic structure file and the total vibration vector file; Step 5: Set the incident light direction. Based on the set incident light direction, extract the vibration components in the incident light direction from the total vibration vector file, and generate a transitional vibration vector file by combining it with the target atom coordinate file. Step 6: Select the desired frequency from the visualization data file, and combine it with the transition vibration vector file to generate Raman spectrum data file and infrared spectrum data file; Step 7: Optimize the Raman spectrum data file and the infrared spectrum data file by Gaussian broadening to complete the screening process.
2. The method for screening local vibrational modes of an atomic system as described in claim 1, characterized in that, In step 1, the method for obtaining each file is as follows: The data files of the first-principles calculation software and the parameter files of the target calculation structure are obtained. The atomic structure file, atomic coordinate file and eigenvector file are obtained through calculation. The atomic coordinate file is then standardized to obtain the target atomic coordinate file.
3. The method for screening local vibrational modes of an atomic system as described in claim 1, characterized in that, In step 2, the target atomic coordinate file is traversed and parsed using Python code to extract lattice basis vectors, atomic coordinates, element types, and the number of atoms of each element.
4. The method for screening local vibrational modes of an atomic system as described in claim 1, characterized in that, In step 3, the vector fusion method is as follows: Based on the lattice basis vectors and atomic coordinates, the real displacement components of each atom in three directions are synthesized into a total vibration vector in real space.
5. The method for screening local vibrational modes of an atomic system as described in claim 1, characterized in that, In step 4, the specific process of generating a visualization data file of atomic structure vibrations is as follows: Step 41: Construct the lattice frame of the three-dimensional crystal structure using lattice basis vectors; Step 42: Obtain the element type of the atom and its corresponding elemental properties; Step 43: Construct a multi-element atomic structure model based on various atomic coordinates and elemental properties of atoms; Step 44: Embed the multi-element atomic structure model into the lattice frame to construct a complete three-dimensional crystal structure model; Step 45: Obtain view control commands, including: elevation control commands and / or azimuth control commands; Step 46: Render and output the corresponding visualization data file of atomic structure vibration according to the view control instructions.
6. The method for screening local vibrational modes of an atomic system as described in claim 1, characterized in that, In step 5, the generated transitional vibration vector file includes: atomic frequency, incident light direction, frequency, and vibration vector of each atom in three-dimensional space.
7. The method for screening local vibrational modes of an atomic system as described in claim 1, characterized in that, In step 6, the specific method for generating the Raman spectrum data file is as follows: Construct a bond polarization model corresponding to the Raman tensor, calculate the Raman intensity at each frequency based on the vibration vectors of atoms in the transition vibration vector file and the direction of incident light, and output a Raman spectrum data file including frequency-Raman intensity pairs.
8. The method for screening local vibrational modes of an atomic system as described in claim 1 or 7, characterized in that, In step 6, the specific method for generating the infrared spectrum data file is as follows: The infrared intensity is calculated by modulating the vibration vectors of atoms in the transition vibration vector file, and the output includes an infrared spectrum data file containing the frequency, infrared intensity, and vibration vector components.