A method and device for initial path insertion of transition state based on homogeneous coordinate transformation matrix

Abstract

A method and device for inserting points in the initial path of a transition state based on a homogeneous coordinate change matrix, the method comprising: S1. Structural optimization of the initial state and final state of a chemical reaction, obtaining reasonable structural files of the initial state and final state of the reaction and placing them under the current path of the script; S2. Identifying the structural files of the initial and final states of the reaction, the reaction atom serial numbers, the total number of insertion points in the transition state, and the number of steps in the activation stage; S3. Reading and dividing the atomic coordinate data in the structural file, and storing the atomic coordinates in the form of a two-dimensional array, namely an IS coordinate matrix and a FS coordinate matrix; S4. Calculating the atomic coordinate data of each step of the reaction in the activation stage; S5. Calculating the atomic coordinate data of each step of the reaction in the reaction stage; S6. Linearly interpolating all atoms to obtain the original atomic coordinate data of the transition state; S7. Overwriting the original transition state coordinate data with the atomic coordinate data of the activation stage and the atomic coordinate data of the reaction stage to generate the final initial path of the transition state.

Description

Technical Field

[0001] The present invention relates to a method and device for inserting points of an initial path of a transition state based on a homogeneous coordinate transformation matrix, and in particular to a method and device for generating an initial path for calculating a transition state by using a homogeneous transformation matrix when calculating a chemical reaction transition state using a VASP program package (Vienna Ab-initio Simulation Package). Background Art

[0002] The transition state is the highest energy state experienced during a chemical reaction. It is the state in which the old chemical bonds have not yet been completely broken and the new chemical bonds have not yet been completely formed during the process of reactants being transformed into products. The transition state plays an important role in understanding the reaction mechanism of chemical processes.

[0003] The Nudged Elastic Band (NEB) method built into the VASP package (Vienna Ab-initio Simulation Package) is one of the most commonly used methods for calculating transition states of periodic reaction systems. This method requires the initial intermediate states of several reaction paths to be provided as input files for the package. During the iterative calculation process, the intermediate states are connected by virtual springs. When the spring force of the virtual springs along the reaction path converges, all intermediate states stop moving, and their position is the lowest energy reaction path. The position with the highest energy is the transition state of the reaction.

[0004] In the NEB method, the input of the initial state has a great influence on the result of the final reaction path. The initial reaction path formed by the initial state will affect the direction of the entire chemical reaction mechanism. The most commonly used method to generate the initial reaction path is to provide the initial state and the final state of the reaction path, and use the linear interpolation method to generate several intermediate states. The linear interpolation method is to connect the atoms of the initial state and the final state into a straight line one by one, divide the straight line into several equal parts, and place the corresponding atoms at the positions of the equal divisions of the straight line to complete the interpolation.

[0005] However, linear interpolation is a relatively simple interpolation method. This method only considers the absolute position of atoms in space. It is a better solution for solving the translation transformation of reactant molecules in space. For the rotation and distortion transformation of reactant molecules in space, the interpolation result is not ideal and often causes atomic overlap. In this case, directly using the result of linear interpolation will cause the initial state atoms to be subjected to excessive force, program calculation errors, deviation from the correct reaction path, and other problems. It takes a lot of manpower to manually adjust and correct the initial path.

[0006] The interpolation method for transition state calculation based on homogeneous coordinate transformation matrix utilizes the concept of homogeneous transformation matrix. Homogeneous transformation matrix is ​​a method of using matrix to transform coordinates in three-dimensional space, which allows operations such as translation, rotation and scaling of atomic coordinates. By calculating the homogeneous transformation matrix of the initial state and the final state, the homogeneous transformation matrix is ​​used to interpolate the intermediate state of the reaction. Ultimately, we can obtain the intermediate state that has undergone both translation and rotation transformations, effectively solving problems such as atomic overlap caused by linear interpolation, and improving the efficiency and accuracy of transition state calculations. Summary of the invention

[0007] The purpose of the present invention is to provide a transition state initial path interpolation method and device based on a homogeneous coordinate change matrix, which can solve the problem of unreasonable transition state initial path such as atomic overlap caused by linear interpolation.

[0008] To achieve the above object, the present invention provides a transition state initial path point insertion method based on a homogeneous coordinate change matrix, comprising the following steps:

[0009] S1. Use VASP software to optimize the structure of the initial and final states of the chemical reaction, and obtain reasonable initial and final state structure files of the reaction and place them in the current path of the script.

[0010] S2. Start the data reading module of the Python script to identify the initial and final state structure files of the reaction, the reaction atom numbers, the total number of transition state insertion points, and the number of activation stage steps.

[0011] S3. Start the text reading module of the Python script, read and segment the atomic coordinate data in the structure file, and store the atomic coordinates in the form of two-dimensional arrays, namely the IS (Initial State) coordinate matrix and the FS (Final State) coordinate matrix.

[0012] S4. Start the activation stage insertion module and calculate the coordinate data of the reaction atoms in each step of the activation stage according to the number of steps in the activation stage.

[0013] S5. Start the reaction stage insertion module and calculate the coordinate data of the reaction atoms in each step of the reaction stage according to the total number of insertion points in the transition state.

[0014] S6. Start the atomic coordinate linear interpolation module, perform linear interpolation on all atoms according to the IS coordinate matrix and the FS coordinate matrix and the total number of transition state interpolation points to obtain the original transition state atomic coordinate data.

[0015] S7. Overwrite the original transition state coordinate data with the atomic coordinate data of the activation stage and the atomic coordinate data of the reaction stage to generate the final transition state initial path.

[0016] Furthermore, the specific steps of step S1 are as follows:

[0017] S11. Use VASP software to rationally optimize the initial and final states of chemical reactions;

[0018] S12. Name the initial state and final state structure files IS (Initial State) File and FS (Final State) File respectively, and place them under the current path of the script.

[0019] Furthermore, the specific steps of step S2 are as follows:

[0020] S21. Identify the initial state and final state structure files of the reaction and store them in the form of strings;

[0021] S22. Identify the atomic numbers involved in the reaction, the total number of transition state insertion points, and the number of activation stage steps, and store them in the form of integers.

[0022] Furthermore, the specific steps of step S3 are as follows:

[0023] S31. Start the data reading module of the Python script to store the text content of the IS file and the FS file;

[0024] S32. Cut all the atomic coordinate information in the structure file content and split it into a two-dimensional array and store it, denoted as IS Coord and FS Coord ;

[0025] S33. According to the reaction atom number, the coordinate information of the atoms participating in the reaction is cut out from all the atomic coordinate information and stored as a two-dimensional array in the form of a 1×3 row vector, denoted as IS ReacCoord and FS ReacCoord ;

[0026] S34. Transpose the 1×3 row vector into a 3×1 column vector, and add a dimension in the column vector direction to form a 4×1 homogeneous coordinate two-dimensional array, denoted as IS ReacCoord_homo and FS ReacCoord_homo .

[0027] Furthermore, the specific steps of step S4 are as follows:

[0028] S41. According to the coordinate information of the atoms involved in the reaction, calculate the geometric center IS of the coordinates of the reaction atoms center and FS center ;

[0029] S42. Initialize the homogeneous coordinate transformation matrix M and the geometric center IS center and FS centerConstruct the matrix equation, call the "L-BFGS-B" algorithm, and solve the geometric center transformation matrix M center ;

[0030] S43. Calculate the geometric center transformation matrix M center The eigenvalues ​​and eigenvectors of the geometric center are transformed into the matrix M using the eigenvalues ​​and eigenvectors. center Diagonalize.

[0031] S44. Root the diagonal elements according to the number of steps in the activation stage to obtain the geometric center transformation matrix M after the square root center_root ;

[0032] S45. Use the geometric center transformation matrix M after square root center_root , calculate the atomic coordinate data Coord of each step of the activation stage ActStep .

[0033] Furthermore, the specific steps of step S5 are as follows:

[0034] S51. Geometric center IS using the coordinates of the reaction atoms center and FS center As the initialization condition of the homogeneous coordinate transformation matrix M;

[0035] S52. Initialize the homogeneous coordinate transformation matrix M and the homogeneous coordinate two-dimensional array IS ReacCoord_homo and FS homogeneous coordinate 2D array FS ReacCoord_homo Construct the matrix equation, call the "L-BFGS-B" algorithm, and solve the homogeneous coordinate transformation matrix M;

[0036] S53. Calculate the eigenvalues ​​and eigenvectors of the homogeneous coordinate transformation matrix M, and use the eigenvalues ​​and eigenvectors to diagonalize the homogeneous coordinate transformation matrix M;

[0037] S54. Take the square root of the diagonal elements according to the total number of transition state insertion points to obtain the homogeneous coordinate transformation matrix M after the square root root ;

[0038] S55. Using the homogeneous coordinate transformation matrix M after square root root , calculate the atomic coordinate data Coord of each step of the reaction stage ReacStep .

[0039] Furthermore, the specific steps of step S6 are as follows:

[0040] S61. According to the IS coordinate matrix IS Coord and FS coordinate matrix FS Coord Calculate the difference of coordinate matrices;

[0041] S62. According to the difference of the coordinate matrix and the total number of transition state interpolation points, linear interpolation is performed on all atoms to obtain the original transition state atomic coordinate data of each step.

[0042] Furthermore, the specific steps of step S7 are as follows:

[0043] S71. Coord the atomic coordinate data of each step of the activation stage ActStep Overwrite the original transition state coordinate data;

[0044] S72. Coord the atomic coordinate data of each step of the reaction stage ReacStep Overwrite the original transition state coordinate data to generate the final transition state initial path.

[0045] The second aspect of the present invention relates to a transition state initial path point insertion device based on a homogeneous coordinate change matrix, comprising a memory and one or more processors, wherein the memory stores executable code, and when the one or more processors execute the executable code, they are used to implement a transition state initial path point insertion method based on a homogeneous coordinate change matrix of the present invention.

[0046] The third aspect of the present invention relates to a computer-readable storage medium having a program stored thereon, which, when executed by a processor, implements a transition state initial path insertion method based on a homogeneous coordinate change matrix of the present invention.

[0047] The beneficial effects of the present invention are:

[0048] The transition state initial path interpolation method based on the homogeneous coordinate transformation matrix provided by the present invention divides the transition state interpolation into an activation stage in which the chemical bonds are fixed and a reaction stage in which the chemical bonds change. A homogeneous coordinate transformation matrix that can control the rotation and translation operations of the reactant molecules is introduced. Compared with the ordinary linear interpolation method, more accurate interpolation of the initial state of the transition state reaction path can be achieved when the reactant molecules need to rotate. BRIEF DESCRIPTION OF THE DRAWINGS

[0049] In order to more clearly illustrate the embodiments of the present invention or the technical solutions in the prior art, the drawings required for use in the embodiments or the description of the prior art will be briefly introduced below. Obviously, for ordinary technicians in this field, other drawings can be obtained based on these drawings without paying any creative work.

[0050] Figure 1 Flow chart of the method for interpolating points of the transition state initial path of the homogeneous coordinate transformation matrix in an embodiment of the present invention.

[0051] Figure 2The actual insertion effect of the transition state initial path insertion method using the homogeneous coordinate transformation matrix in the embodiment of the present invention, wherein 00 is the optimized initial state IS of the chemical reaction, 01, 02, ..., 08 are the transition state initial paths obtained by the insertion method, and 09 is the optimized final state FS of the chemical reaction.

[0052] Figure 3 In the embodiment of the present invention, the initial path of the transition state is obtained by interpolation of the transition state initial path interpolation method using the homogeneous coordinate transformation matrix, and the final path of the transition state is obtained after optimization by the VASP software package, wherein 00 is the optimized initial state IS of the chemical reaction, 01, 02, ..., 08 are respectively the optimized transition state paths, and 09 is the optimized final state FS of the chemical reaction. DETAILED DESCRIPTION

[0053] In order to make the technical method understood by the persons skilled in the art, the technical solution will be clearly described below in conjunction with the embodiments. Unless otherwise defined, the technical terms or scientific terms used in the present invention should be the common meanings understood by persons with ordinary skills in the field to which the present invention belongs. Obviously, the embodiments described here are only some embodiments of the present invention, not all embodiments. Based on the embodiments in the present invention, all other embodiments obtained by ordinary technicians in the field without making creative work should fall within the scope of protection of the present invention.

[0054] Example 1

[0055] like Figure 1 As shown, a transition state initial path interpolation method based on a homogeneous coordinate transformation matrix according to an embodiment of the present invention comprises the following steps:

[0056] S1. Use VASP software to optimize the structure of the initial and final states of the chemical reaction, and obtain reasonable initial and final state structure files of the reaction and place them in the current path of the script.

[0057] S2. Start the data reading module of the Python script to identify the initial and final state structure files of the reaction, the reaction atom numbers, the total number of transition state insertion points, and the number of activation stage steps.

[0058] S3. Start the text reading module of the Python script, read and segment the atomic coordinate data in the structure file, and store the atomic coordinates in the form of two-dimensional arrays, namely the IS (Initial State) coordinate matrix and the FS (Final State) coordinate matrix.

[0059] S4. Start the activation stage insertion module and calculate the coordinate data of the reaction atoms in each step of the activation stage according to the number of steps in the activation stage.

[0060] S5. Start the reaction stage insertion module and calculate the coordinate data of the reaction atoms in each step of the reaction stage according to the total number of insertion points in the transition state.

[0061] S6. Start the atomic coordinate linear interpolation module, perform linear interpolation on all atoms according to the IS coordinate matrix and the FS coordinate matrix and the total number of transition state interpolation points to obtain the original transition state atomic coordinate data.

[0062] S7. Overwrite the original transition state coordinate data with the atomic coordinate data of the activation stage and the atomic coordinate data of the reaction stage to generate the final transition state initial path.

[0063] Furthermore, the specific steps of step S1 are as follows:

[0064] S11. Use VASP software to rationally optimize the initial and final states of chemical reactions;

[0065] S12. Name the initial state and final state structure files IS (Initial State) File and FS (Final State) File respectively, and place them in the current path of the script;

[0066] Furthermore, the specific steps of step S2 are as follows:

[0067] S21. Identify the initial state and final state structure files of the reaction and store them in the form of strings;

[0068] S22. Specify the atomic numbers of participating reactions, the total number of transition state insertion points, and the number of activation stage steps, which are stored in integer form;

[0069] Furthermore, the specific steps of step S3 are as follows:

[0070] S31. Start the data reading module of the Python script to store the text content of the IS file and the FS file;

[0071] S32. Cut all the atomic coordinate information in the structure file content and split it into a two-dimensional array and store it, denoted as IS Coord and FS Coord ;

[0072] S33. According to the reaction atom number, the coordinate information of the atoms participating in the reaction is cut out from all the atomic coordinate information and stored as a two-dimensional array in the form of a 1×3 row vector, denoted as IS ReacCoord and FS ReacCoord ;

[0073] S34. Transpose the 1×3 row vector into a 3×1 column vector, and add a dimension in the column vector direction to form a 4×1 homogeneous coordinate two-dimensional array, denoted as ISReacCoord_homo and FS ReacCoord_homo ;

[0074] Furthermore, the specific steps of step S4 are as follows:

[0075] S41. According to the coordinate information of the atoms involved in the reaction, calculate the geometric center IS of the coordinates of the reaction atoms center and FS center ;

[0076] S42. Initialize the homogeneous coordinate transformation matrix M and the geometric center IS center and FS center Construct the matrix equation, call the "L-BFGS-B" algorithm, and solve the geometric center transformation matrix M center ;

[0077] S43. Calculate the geometric center transformation matrix M center The eigenvalues ​​and eigenvectors of the geometric center are transformed into the matrix M using the eigenvalues ​​and eigenvectors. center Diagonalize.

[0078] S44. Root the diagonal elements according to the number of steps in the activation stage to obtain the geometric center transformation matrix M after the square root center_root ;

[0079] S45. Use the geometric center transformation matrix M after square root center_root , calculate the atomic coordinate data Coord of each step of the activation stage ActStep .

[0080] Furthermore, the specific steps of step S5 are as follows:

[0081] S51. Geometric center IS using the coordinates of the reaction atoms center and FS center As the initialization condition of the homogeneous coordinate transformation matrix M;

[0082] S52. Initialize the homogeneous coordinate transformation matrix M and the homogeneous coordinate two-dimensional array IS ReacCoord_homo and FS homogeneous coordinate 2D array FS ReacCoord_homo Construct the matrix equation, call the "L-BFGS-B" algorithm, and solve the homogeneous coordinate transformation matrix M;

[0083] S53. Calculate the eigenvalues ​​and eigenvectors of the homogeneous coordinate transformation matrix M, and use the eigenvalues ​​and eigenvectors to diagonalize the homogeneous coordinate transformation matrix M;

[0084] S54. Take the square root of the diagonal elements according to the total number of transition state insertion points to obtain the homogeneous coordinate transformation matrix M after the square root root ;

[0085] S55. Using the homogeneous coordinate transformation matrix M after square root root , calculate the atomic coordinate data Coord of each step of the reaction stage ReacStep .

[0086] Furthermore, the specific steps of step S6 are as follows:

[0087] S61. According to the IS coordinate matrix IS Coord and FS coordinate matrix FS Coord Calculate the difference of coordinate matrices;

[0088] S62. According to the difference of the coordinate matrix and the total number of transition state interpolation points, linear interpolation is performed on all atoms to obtain the original transition state atomic coordinate data of each step.

[0089] Furthermore, the specific steps of step S7 are as follows:

[0090] S71. Coord the atomic coordinate data of each step of the activation stage ActStep Overwrite the original transition state coordinate data;

[0091] S72. Coord the atomic coordinate data of each step of the reaction stage ReacStep Overwrite the original transition state coordinate data to generate the final transition state initial path;

[0092] In this example, the dissociation reaction of formic acid on activated carbon-supported Pt cluster catalyst was selected. According to the present invention, the VASP software was first used to perform structural optimization on the initial state (chemical adsorption state) and final state (dissociated state) of formic acid on activated carbon-supported Pt cluster catalyst. The structural optimization parameters used were 450 eV plane wave cutoff energy, 3x3x3 K-point grid, and 10 convergence criteria. -6 eV / atom.

[0093] The initial and final states of the optimization completed CONTCAR are renamed IS and FS respectively and placed in the current path of the script.

[0094] Start the script, designate the initial state file of the reaction as "IS" and the final state file as "FS", and store them in the form of strings.

[0095] Specify the reaction atom number. For the formic acid dissociation reaction, the reactant is formic acid, and there are a total of 5 atoms H, C, O, O, H participating in the reaction, and the numbers are [56, 64, 65, 66, 67]. Specify the total number of transition state insertion points to be 8, and the number of activation stage steps to be 4.

[0096] The script data reading module reads the IS and FS file contents.

[0097] And cut the structure file content, split it into two-dimensional array form storage, recorded as IS Coord and FS Coord .

[0098] According to the specified reaction atom number, its three-dimensional coordinates are stored as a two-dimensional array in the form of a 1×3 row vector, denoted as IS ReacCoord and FS ReacCoord , there are 5 atoms here, so a 5×3 two-dimensional array is finally generated.

[0099] Transpose the matrix, convert all row vectors into column vector representation, and transpose the 5×3 matrix into a 3×5 matrix. Expand the transposed matrix into a homogeneous coordinate form, becoming a 4×5 matrix. The newly added 4th row defaults to all integers "1", denoted as IS ReacCoord_homo and FS ReacCoord_homo .

[0100] According to the coordinate information of the IS coordinate matrix and the FS coordinate matrix, calculate the geometric center IS of the two center and FS center .

[0101] Start the activation phase insertion module, call the "L-BFGS-B" algorithm, set the number of algorithm iterations to 1000, the convergence limit to 1e-10, and solve the homogeneous coordinate transformation matrix M center .

[0102] Start the reaction phase insertion module, call the "L-BFGS-B" algorithm, set the number of algorithm iterations to 1000, the convergence limit to 1e-10, and solve the homogeneous coordinate transformation matrix M.

[0103] Start the atomic coordinate linear interpolation module, according to the atomic coordinate IS Coord and FS Coord , and the total number of transition state interpolation points is 8, linear interpolation is performed on all atoms to obtain the original transition state atomic coordinate data.

[0104] According to the requirements of the VASP transition state input file, a series of folders are created. At this time, the number of transition state insertion points is 8. Create a series of folders 01, 02, ..., 08 and fill in the original transition state atomic coordinate data.

[0105] The atomic coordinate data of the activation stage and the atomic coordinate data of the reaction stage are overwritten with the original transition state coordinate data to generate the final transition state initial path.

[0106] The homogeneous coordinate transformation matrix interpolation method was used to interpolate the dissociation reaction of formic acid on activated carbon-supported Pt single atom catalyst. The results showed that:

[0107] First, the transition state initial path interpolation method based on the homogeneous coordinate transformation matrix of the present invention can successfully complete the preparation of the structure file of the transition state initial path, such as Figure 2 As shown, the format of the structure file meets the requirements of VASP software for transition state calculation using the NEB method.

[0108] Second, the insertion point method of the present invention introduces a homogeneous coordinate transformation matrix, which is composed of a rotation matrix and a displacement matrix. It transforms the translation and rotation of atoms at the same time and can better handle the situation where chemical bond rotation occurs in the reactant molecules during the reaction process.

[0109] Third, the transition state initial path interpolation method based on homogeneous coordinate transformation matrix of the present invention is compared with the common nebmake interpolation method and idpp interpolation method, and the results are shown in Table 1. HC (homogeneous coordinates) is the transition state initial path interpolation method based on homogeneous coordinate transformation matrix of the present invention, nebmake is the classic linear interpolation method, and idpp is based on linear interpolation.

[0110] The insertion point method considering atomic forces can solve the problem of atomic overlap. The optimized transition state path is used as the standard path reference, and the displacement deviation values ​​of the atomic paths of the three paths are compared. It can be seen that the displacement deviation value of HC is smaller and closer to the actual transition state path.

[0111] Table 1

[0112]

[0113] Example 2

[0114] This embodiment relates to a method for generating a transition state initial path by applying a transition state initial path insertion method based on a homogeneous coordinate transformation matrix of the present invention and completing transition state structure optimization by VASP to finally draw a schematic diagram of an actual transition state reaction path, comprising the following steps:

[0115] S1. Use VASP software to optimize the structure of the initial and final states of the chemical reaction, and obtain reasonable initial and final state structure files of the reaction and place them in the current path of the script.

[0116] S2. Start the data reading module of the Python script to identify the initial and final state structure files of the reaction, the reaction atom numbers, the total number of transition state insertion points, and the number of activation stage steps.

[0117] S3. Start the text reading module of the Python script, read and segment the atomic coordinate data in the structure file, and store the atomic coordinates in the form of two-dimensional arrays, namely the IS (Initial State) coordinate matrix and the FS (Final State) coordinate matrix.

[0118] S4. Start the activation stage insertion module and calculate the coordinate data of the reaction atoms in each step of the activation stage according to the number of steps in the activation stage.

[0119] S5. Start the reaction stage insertion module and calculate the coordinate data of the reaction atoms in each step of the reaction stage according to the total number of insertion points in the transition state.

[0120] S6. Start the atomic coordinate linear interpolation module, perform linear interpolation on all atoms according to the IS coordinate matrix and the FS coordinate matrix and the total number of transition state interpolation points to obtain the original transition state atomic coordinate data.

[0121] S7. Overwrite the original transition state coordinate data with the atomic coordinate data of the activation stage and the atomic coordinate data of the reaction stage to generate the final transition state initial path.

[0122] S8. According to the structure file of the initial path of the transition state, configure the VASP transition state calculation related input files, including KPOINT, POTCAR, and INCAR files.

[0123] S9. Submit the transition state optimization task to the server. The initial transition state path is structurally optimized using the NEB method to finally obtain the optimized transition state path, which is the transition state path of the actual chemical reaction. The final transition state reaction path is exported and drawn into a schematic diagram of the transition state reaction molecular structure.

[0124] Furthermore, the specific steps of step S1 are as follows:

[0125] S11. Use VASP software to rationally optimize the initial and final states of chemical reactions;

[0126] S12. Name the initial state and final state structure files IS (Initial State) File and FS (Final State) File respectively, and place them in the current path of the script;

[0127] Furthermore, the specific steps of step S2 are as follows:

[0128] S21. Identify the initial state and final state structure files of the reaction and store them in the form of strings;

[0129] S22. Specify the atomic numbers of participating reactions, the total number of transition state insertion points, and the number of activation stage steps, which are stored in integer form;

[0130] Furthermore, the specific steps of step S3 are as follows:

[0131] S31. Start the data reading module of the Python script to store the text content of the IS file and the FS file;

[0132] S32. Cut all the atomic coordinate information in the structure file content and split it into a two-dimensional array and store it, denoted as IS Coord and FS Coord ;

[0133] S33. According to the reaction atom number, the coordinate information of the atoms participating in the reaction is cut out from all the atomic coordinate information and stored as a two-dimensional array in the form of a 1×3 row vector, denoted as IS ReacCoord and FS ReacCoord ;

[0134] S34. Transpose the 1×3 row vector into a 3×1 column vector, and add a dimension in the column vector direction to form a 4×1 homogeneous coordinate two-dimensional array, denoted as IS ReacCoord_homo and FS ReacCoord_homo ;

[0135] Furthermore, the specific steps of step S4 are as follows:

[0136] S41. According to the coordinate information of the atoms involved in the reaction, calculate the geometric center IS of the coordinates of the reaction atoms center and FS center ;

[0137] S42. Initialize the homogeneous coordinate transformation matrix M and the geometric center IS center and FS center Construct the matrix equation, call the "L-BFGS-B" algorithm, and solve the geometric center transformation matrix M center ;

[0138] S43. Calculate the geometric center transformation matrix M center The eigenvalues ​​and eigenvectors of the geometric center are transformed into the matrix M using the eigenvalues ​​and eigenvectors. center Diagonalize.

[0139] S44. Root the diagonal elements according to the number of steps in the activation stage to obtain the geometric center transformation matrix M after the square root center_root ;

[0140] S45. Use the geometric center transformation matrix M after square root center_root , calculate the atomic coordinate data Coord of each step of the activation stage ActStep .

[0141] Furthermore, the specific steps of step S5 are as follows:

[0142] S51. Geometric center IS using the coordinates of the reaction atoms center and FS center As the initialization condition of the homogeneous coordinate transformation matrix M;

[0143] S52. Initialize the homogeneous coordinate transformation matrix M and the homogeneous coordinate two-dimensional array IS ReacCoord_homo and FS homogeneous coordinate 2D array FS ReacCoord_homo Construct the matrix equation, call the "L-BFGS-B" algorithm, and solve the homogeneous coordinate transformation matrix M;

[0144] S53. Calculate the eigenvalues ​​and eigenvectors of the homogeneous coordinate transformation matrix M, and use the eigenvalues ​​and eigenvectors to diagonalize the homogeneous coordinate transformation matrix M;

[0145] S54. Take the square root of the diagonal elements according to the total number of transition state insertion points to obtain the homogeneous coordinate transformation matrix M after the square root root ;

[0146] S55. Using the homogeneous coordinate transformation matrix M after square root root , calculate the atomic coordinate data Coord of each step of the reaction stage ReacStep .

[0147] Furthermore, the specific steps of step S6 are as follows:

[0148] S61. According to IS coordinate matrix IS Coord and FS coordinate matrix FS Coord Calculate the difference of coordinate matrices;

[0149] S62. According to the difference of the coordinate matrix and the total number of transition state interpolation points, linear interpolation is performed on all atoms to obtain the original transition state atomic coordinate data of each step.

[0150] Furthermore, the specific steps of step S7 are as follows:

[0151] S71. Coord the atomic coordinate data of each step of the activation stage ActStep Overwrite the original transition state coordinate data;

[0152] S72. Coord the atomic coordinate data of each step of the reaction stage ReacStep Overwrite the original transition state coordinate data to generate the final transition state initial path;

[0153] Furthermore, the specific steps of step S8 are as follows:

[0154] S81. Place the folders 00, 01, ..., 09 containing the initial path of the transition state in the specified directory;

[0155] S82. According to the unit cell size of the structure file of the initial path of the transition state, set the KPOINT file with reasonable k-point density;

[0156] S83. According to the chemical element types contained in the structure file of the initial path of the transition state, select the corresponding pseudopotential data and splice them into a POTCAR file;

[0157] S84. According to the optimization requirements of the initial path of the transition state, set the INCAR file with reasonable parameters, the main contents of which include the electron step convergence limit, the ion step convergence limit, the number of transition state insertion points, and the transition state optimization algorithm.

[0158] Furthermore, the specific steps of step S9 are as follows:

[0159] S91. Submit the input file to VASP, VASP reads the transition state initial path, KPOINT, POTCAR, INCAR, and starts the transition state path optimization task;

[0160] S92. The path of each step of the transition state has reached the convergence limit of the ion step and the electronic step, and the transition state optimization task is completed. Export the CONTCAR files in the 01, 02, ..., 08 directories, which are the transition state paths of the optimized target chemical reactions;

[0161] S93. cutting out the molecular coordinates from the CONTCAR files in the 01, 02, ..., 08 directories and the POSCAR files in the 00, 09 directories, and splicing them into a movie.xyz file;

[0162] S94. Import the movie.xyz file into the Jmol software;

[0163] S95. Adjust the atom color, atom size, bonding distance, and bonding method in Jmol software to complete the drawing of the final transition state reaction path diagram.

[0164] In this example, the acetylene hydrochlorination reaction of acetylene and hydrogen chloride molecules on a Ru-ligand catalyst is selected. According to the present invention, the VASP software is first used to optimize the co-adsorption state of acetylene and hydrogen chloride molecules on the catalyst (initial state) and the final generation of vinyl chloride molecules (final state). The structural optimization parameters use a 450eV plane wave cutoff energy, a 3x3x3 K-point grid, and a convergence criterion of 10 -6 eV / atom.

[0165] The initial and final states of the optimization completed CONTCAR are renamed IS and FS respectively and placed in the current path of the script.

[0166] Start the script, designate the initial state file of the reaction as "IS" and the final state file as "FS", and store them in the form of strings.

[0167] Specify the reaction atom number. For the acetylene hydrochlorination reaction, the reactants are acetylene and hydrogen chloride molecules. There are a total of 6 atoms H, Cl, C, C, H, H involved in the reaction, and the numbers are [4, 5, 22, 23, 33, 37]. Specify the total number of transition state insertion points as 8 and the number of activation stage steps as 4.

[0168] The script data reading module reads the IS and FS file contents.

[0169] And cut the structure file content, split it into two-dimensional array form storage, recorded as IS Coord and FS Coord .

[0170] According to the specified reaction atom number, its three-dimensional coordinates are stored as a two-dimensional array in the form of a 1×3 row vector, denoted as IS ReacCoord and FS ReacCoord , there are 6 atoms here, so a 6×3 two-dimensional array is finally generated.

[0171] Transpose the matrix, convert all row vectors into column vector representation, and transpose the 6×3 matrix into a 3×6 matrix. Expand the transposed matrix into a homogeneous coordinate form, becoming a 4×6 matrix. The newly added 4th row defaults to all integers "1", denoted as IS ReacCoord_homo and FS ReacCoord_homo .

[0172] According to the coordinate information of the IS coordinate matrix and the FS coordinate matrix, calculate the geometric center IS of the two center and FS center .

[0173] Start the activation phase insertion module, call the "L-BFGS-B" algorithm, set the number of algorithm iterations to 1000, the convergence limit to 1e-10, and solve the homogeneous coordinate transformation matrix M center .

[0174] Start the reaction phase insertion module, call the "L-BFGS-B" algorithm, set the number of algorithm iterations to 1000, the convergence limit to 1e-10, and solve the homogeneous coordinate transformation matrix M.

[0175] Start the atomic coordinate linear interpolation module, according to the atomic coordinate IS Coord and FS Coord , and the total number of transition state interpolation points is 8, linear interpolation is performed on all atoms to obtain the original transition state atomic coordinate data.

[0176] Create a series of folders according to the VASP transition state input file requirements. At this time, the number of transition state insertion points is 8. Create a series of folders 01, 02, ..., 08, and fill the original transition state atomic coordinate data in. Create folders 00 and 09, and fill the IS and FS files respectively.

[0177] The atomic coordinate data of the activation stage and the atomic coordinate data of the reaction stage are overwritten with the original transition state coordinate data to generate the initial structure of the transition state.

[0178] Place the folders 00, 01, ..., 09 containing the initial path of the transition state in the specified directory. Set the k-point density to 3x3x1, select the pseudopotential data of C, O, N, H, Ru, and Cl elements, and splice them into a POTCAR file. Set the electronic step convergence limit to 10 -6 eV / atom, the ion step convergence limit was set to 0.05 eV / atom, the number of transition state insertion points was 8, and the transition state optimization algorithm was set to the NEB algorithm.

[0179] Submit the input file to VASP, VASP reads the initial transition state path, KPOINT, POTCAR, INCAR, and starts the transition state path optimization task. After completing the task, the CONTCAR files in the 01, 02, ..., 08 directories are obtained. Export the CONTCAR files in the 01, 02, ..., 08 directories, cut the molecular coordinates of the CONTCAR files in the 01, 02, ..., 08 directories and the POSCAR files in the 00, 09 directories, and splice them into a movie.xyz file. Import the movie.xyz file into the Jmol software. Adjust the atomic color (using the default atomic color), atomic size (the atomic radius of the 6 reactants is increased by 0.2 angstroms, and the rest of the system uses the default atomic radius), bonding distance (using the default bonding distance), bonding mode (acetylene molecules are double bonds, and the rest of the system is single bonds), and complete the drawing of the final transition state reaction path schematic diagram.

[0180] like Figure 3 Shown is a schematic diagram of the transition state pathway of the optimized acetylene hydrochlorination reaction of acetylene and hydrogen chloride molecules on a Ru-ligand catalyst.

[0181] Example 3

[0182] The present embodiment relates to a transition state initial path point insertion device based on a homogeneous coordinate change matrix, comprising a memory and one or more processors, wherein the memory stores executable code, and when the one or more processors execute the executable code, they are used to implement a transition state initial path point insertion method based on a homogeneous coordinate change matrix of embodiment 1.

[0183] Example 4

[0184] This embodiment relates to a computer-readable storage medium having a program stored thereon. When the program is executed by a processor, a transition state initial path insertion method based on a homogeneous coordinate change matrix of embodiment 1 is implemented.

Claims

1. A transition state initial path interpolation method based on homogeneous coordinate change matrix, characterized in that: The following steps are involved: S1. Use VASP software to optimize the structure of the initial and final states of the chemical reaction, and obtain reasonable initial and final state structure files of the reaction and place them in the current path of the script; S2. Start the data reading module of the Python script to identify the initial and final state structure files of the reaction, the atomic number of the reaction, the total number of insertion points in the transition state, and the number of steps in the activation stage; S3. Start the text reading module of the Python script, read and segment the atomic coordinate data in the structure file, and store the atomic coordinates in the form of two-dimensional arrays, namely the IS (Initial State) coordinate matrix and the FS (Final State) coordinate matrix; the specific steps are as follows: S31. Start the data reading module of the Python script to store the text content of the IS file and the FS file; S32. Cut all the atomic coordinate information in the structure file content and split it into a two-dimensional array and store it, denoted as IS Coord and FS Coord ; S33. According to the reaction atom number, the coordinate information of the atoms participating in the reaction is cut out from all the atomic coordinate information and stored as a two-dimensional array in the form of a 1×3 row vector, denoted as IS ReacCoord and FS ReacCoord ; S34. Transpose the 1×3 row vector into a 3×1 column vector, and add a dimension in the column vector direction to form a 4×1 homogeneous coordinate two-dimensional array, denoted as IS ReacCoord_homo and FS ReacCoord_homo ; S4. Start the activation stage insertion module, and calculate the atomic coordinate data of each step of the activation stage according to the number of steps in the activation stage; the specific steps are as follows: S41. According to the coordinate information of the atoms involved in the reaction, calculate the geometric center IS of the coordinates of the reaction atoms center and FS center ; S42. Initialize the homogeneous coordinate transformation matrix M and the geometric center IS center and FS center Construct the matrix equation and call the "L-BFGS-B" algorithm to solve the geometric center transformation matrix M center ; S43. Calculate the geometric center transformation matrix M center The eigenvalues ​​and eigenvectors of the geometric center are transformed into the matrix M using the eigenvalues ​​and eigenvectors. center Diagonalize. S44. Root the diagonal elements according to the number of steps in the activation stage to obtain the geometric center transformation matrix M after the square root center_root ; S45. Use the geometric center transformation matrix M after square root center_root , calculate the atomic coordinate data Coord of each step of the activation stage ActStep ; S5. Start the reaction stage insertion module, and calculate the coordinate data of the reaction atoms in each step of the reaction stage according to the total number of transition state insertion points; the specific steps are as follows: S51. Geometric center IS using the coordinates of the reaction atoms center and FS center As the initialization condition of the homogeneous coordinate transformation matrix M; S52. Initialize the homogeneous coordinate transformation matrix M and the homogeneous coordinate two-dimensional array IS ReacCoord_homo and FS homogeneous coordinate 2D array FS ReacCoord_homo Construct the matrix equation and call the "L-BFGS-B" algorithm to solve the homogeneous coordinate transformation matrix M; S53. Calculate the eigenvalues ​​and eigenvectors of the homogeneous coordinate transformation matrix M, and use the eigenvalues ​​and eigenvectors to diagonalize the homogeneous coordinate transformation matrix M; S54. Take the square root of the diagonal elements according to the total number of transition state insertion points to obtain the homogeneous coordinate transformation matrix M after the square root root ; S55. Using the homogeneous coordinate transformation matrix M after square root root , calculate the atomic coordinate data Coord of each step of the reaction stage ReacStep ; S6. Start the atomic coordinate linear interpolation module, perform linear interpolation on all atoms according to the IS coordinate matrix and the FS coordinate matrix, and the total number of transition state interpolation points, and obtain the original transition state atomic coordinate data; the specific steps are as follows: S61. According to IS coordinate matrix IS Coord and FS coordinate matrix FS Coord Calculate the difference of coordinate matrices; S62. According to the difference of the coordinate matrix and the total number of transition state interpolation points, linear interpolation is performed on all atoms to obtain the original transition state atomic coordinate data of each step; S7. Overwrite the original transition state coordinate data with the atomic coordinate data of the activation stage and the atomic coordinate data of the reaction stage to generate the final transition state initial path.

2. A transition state initial path interpolation method based on a homogeneous coordinate change matrix as claimed in claim 1, characterized in that: The specific steps of step S1 are as follows: S11. Use VASP software to rationally optimize the initial and final states of chemical reactions; S12. Name the initial state and final state structure files IS (Initial State) File and FS (Final State) File respectively, and place them under the current path of the script.

3. A transition state initial path interpolation method based on homogeneous coordinate change matrix as claimed in claim 1, characterized in that: The specific steps of step S2 are as follows: S21. Identify the initial state and final state structure files of the reaction and store them in the form of strings; S22. Identify the atomic numbers involved in the reaction, the total number of transition state insertion points, and the number of activation stage steps, and store them in the form of integers.

4. A transition state initial path interpolation method based on homogeneous coordinate change matrix as claimed in claim 1, characterized in that: The specific steps of step S7 are as follows: S71. Coord the atomic coordinate data of each step of the activation stage ActStep Overwrite the original transition state coordinate data; S72. Coord the atomic coordinate data of each step of the reaction stage ReacStep Overwrite the original transition state coordinate data to generate the final transition state initial path.

5. A transition state initial path insertion device based on a homogeneous coordinate change matrix, characterized in that: It comprises a memory and one or more processors, wherein the memory stores executable code, and when the one or more processors execute the executable code, it is used to implement a transition state initial path insertion method based on a homogeneous coordinate change matrix as described in any one of claims 1-4.

6. A computer-readable storage medium, characterized in that: A program is stored thereon, and when the program is executed by a processor, a transition state initial path interpolation method based on a homogeneous coordinate change matrix as described in any one of claims 1 to 4 is implemented.

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