An automatic search method for highly symmetric adsorption sites on material surfaces based on crystal symmetry

Abstract

The present invention discloses an automatic search method for high-symmetry adsorption sites on the surface of a material based on crystal symmetry, which belongs to the field of material surface catalytic calculation. First, according to the different material types given by the user, the minimum surface repetition period of the two-dimensional material is searched as a reference lattice, or the crystal surface structure is restored as a reference lattice. Then the reference lattice is retrieved and converted into a standard unit cell lattice, and the high-symmetry sites in the standard unit cell lattice are obtained. The repeatability and wyckoff symbol of the corresponding sites of the reference lattice are obtained, and the site symmetry is evaluated by the two. The high-symmetry sites in the standard unit cell lattice are mapped back to the surface model, and the coordinates corresponding to each high-symmetry site on the surface are obtained. Finally, the small molecules and the high-symmetry sites are replaced to obtain the surface structure of the adsorbed small molecules. The present invention facilitates users to build a large number of models to analyze the catalytic reaction mechanism of materials and provide predictions and guidance for the design of new materials.

Description

Technical Field

[0001] The present invention belongs to the field of material surface catalytic calculation, and in particular relates to an automatic search method for highly symmetric adsorption sites on a material surface based on crystal symmetry. Background Art

[0002] Electrocatalysis plays a key role in clean energy conversion, converting atmospheric gases (such as H2O, CO2, and N2) into high-value products with renewable energy, such as H2, CH4, C2H4, and NH3. To study electrocatalytic reactions, computational materials researchers often use atomic structure models of small molecules added to surfaces to investigate the catalytic reaction mechanisms of various materials and improve the limitations of catalyst electrocatalytic activity and stability. For example, the hydrogen and oxygen evolution reactions on two-dimensional material surfaces and platinum surfaces have been hot topics in first-principles simulations in recent years.

[0003] However, conventional surface adsorption models generated based on visualization software and empirical methods only support limited surface structures and can only find common top, bridge and acupuncture sites such as triply symmetric surface structures. They are also cumbersome to operate and difficult to learn, and cannot be used for automated batch modeling. They have narrow applicability and are difficult to adapt to non-triply symmetric structures and complex crystal structures.

[0004] The application number is CN202110801093.8, "A high-throughput calculation method for the step-by-step adsorption of Li atoms on surfaces". However, this application uses a semi-empirical method suitable for triply symmetric surfaces in modeling, which cannot achieve automated retrieval and is also not applicable to non-triply symmetric structures and complex crystal structures. Summary of the Invention

[0005] To address the above issues, the present invention proposes an automatic search method for highly symmetric adsorption sites on material surfaces based on crystal symmetry. By querying the highly symmetric Wyckoff sites of the surface corresponding to the reference lattice generated by the algorithm, potential surface small molecule adsorption sites are given to realize the calculation of the material's adsorption catalytic performance, which facilitates users to build a large number of models to analyze the catalytic reaction mechanism of the material and provide predictions and guidance for the design of new materials.

[0006] The method for automatically searching for highly symmetric adsorption sites on a material surface based on crystal symmetry comprises the following specific steps:

[0007] Step 1: Read the material surface model file given by the user and generate the corresponding reference lattice according to the user's needs;

[0008] The material surface model file includes: 3×3 unit cell basis vector matrix L, each atom type, each atom Cartesian coordinate (x i ,y i ,z i), i represents the atomic number; take the first atom in the model, record its coordinates as the initial coordinates (x0, y0, z0), and record its atomic number as the initial number i0.

[0009] The 3×3 unit cell basis vector matrix L is:

[0010]

[0011] Each element represents the component of the basis vector a, b, c on the x, y, and z axes respectively, and the c-axis is the surface normal direction by default.

[0012] The fractional coordinates of each atom are:

[0013] (a i ,b i ,c i )=L -1 (x i ,y i ,z i ) (2)

[0014] Determine whether the material required by the user is a two-dimensional material or a three-dimensional material, and obtain the corresponding reference lattice, specifically:

[0015] (1) If it is a two-dimensional material, search for the minimum surface repetition period as the reference lattice:

[0016] Set the initial basis vector fractional coordinate v r1 =(1,0,0), v r2 =(0,1,0), v r3 =(0,0,1), read the upper limit of error Δ set by the user, the default is 0.0001. Traverse all two types of the same and the fractional coordinate difference c in the c-axis direction d For different atoms whose absolute values ​​are less than the upper limit of the error, assume that their numbers are j and k, and obtain their coordinate differences:

[0017] v d =(a d ,b d ,c d )=(a j -a k ,b j -b k ,c j -c k ) (3)

[0018] to a d ,b d ,c d Perform rollback processing, specifically: when a d ,b d ,c dWhen any item is greater than 0.5, subtract 1 from it; when any item is less than -0.5, add 0.5 to it, so that all items are between -0.5 and 0.5.

[0019] Traverse all atoms, assuming that the serial number of a certain atom is m, if there is no n that satisfies:

[0020] (a p ,b p ,c p )=(a m -a n +a d ,b m -b n +b d ,c m -c n +c d ) (4)

[0021] In the formula (a p ,b p ,c p ) After the rollback process, its length is less than the upper limit of the error, then directly judge the next group of two types with the same type and the fractional coordinate difference c in the c-axis direction d Different atoms less than the upper error limit.

[0022] If all atoms are traversed and there are corresponding atoms that satisfy formula (4), then the judgment condition is calculated:

[0023] |v d |<|v r1 | (5)

[0024]

[0025] If the judgment conditions (5) and (6) are both met, then use v d Replace v r1 Otherwise, calculate the judgment condition:

[0026] |v d |<|v r2 | (7)

[0027]

[0028] If the judgment conditions (7) and (8) are both met, then use v d Replace v r2 Otherwise, determine the next group of two types with the same c-axis fractional coordinate difference c d The number of different atoms is smaller than the upper limit of the error until no new atom pairs can be found.

[0029] Then calculate the new basis vector L′

[0030]

[0031] Recalculate the atomic fraction coordinates (a′) according to the new basis vectors i ,b′ i ,c′ i ), if the length of the coordinate difference between two atoms in the model after the modified basis vector is less than the upper limit of the error, the atom with the larger serial number in the corresponding atom pair is deleted to ensure that the atomic serial number of the initial serial number remains unchanged and is not deleted; if the atomic fractional coordinate component is greater than 1 after processing, it is subtracted by 1, and if the coordinate component is less than 0, it is added by 1. After processing, the remaining atoms are converted back to Cartesian coordinates.

[0032] (x′ i ,y′ i ,z′ i )=L′(a′ i ,b′ i ,c′ i ) (10)

[0033] 3×3 unit cell basis vector matrix L′, each atom type, the Cartesian coordinates of the remaining atoms (x′ i ,y′ i ,z′ i ) is collectively referred to as the reference lattice.

[0034] (2) Three-dimensional materials, reducing the crystal structure as a reference lattice:

[0035] Set the initial basis vector fractional coordinate v r1 =(1,0,0), v r2 =(0,1,0), v r3 =(a r3 ,b r3 ,c r3 )=(0,0,1), read the upper limit of error Δ set by the user, the default is 0.0001. Traverse the atoms to obtain the maximum value of their fractional coordinates c in the c direction max With the minimum value c min , and traverse all two of the same type and with the fractional coordinate difference c in the c-axis direction d Different atoms whose absolute values ​​are greater than the upper limit of the error are assumed to be numbered j and k, and their coordinate differences are obtained and then reconvolved;

[0036] The coordinate difference is:

[0037] v d =(a d ,b d ,c d )=(a j -a k ,b j -b k ,cj -c k ) (11)

[0038] Traverse all atoms and assume that the atomic number is m. If there is no n that satisfies:

[0039] (a p ,b p ,c p )=(a m -a n +a d ,b m -b n +b d ,c m -c n +c d ) (12)

[0040] In the formula (a p ,b p ,c p ) After the rewinding process, its length is less than the upper limit of the error, or meets the

[0041] c m +c d <c min (13)

[0042] or

[0043] c m +c d >c max (14)

[0044] Then directly judge the next group of two types with the same c-axis fractional coordinate difference c d Different atoms with a value less than the upper limit of the error. If all atoms are traversed and there are corresponding atoms, the judgment condition is calculated:

[0045] |c d |<|c r3 | (15)

[0046] If the judgment condition (15) is met, then use v d Replace v r3 Otherwise, determine the next group of two types with the same c-axis fractional coordinate difference c d The number of different atoms is smaller than the upper limit of the error until no new atom pairs can be found.

[0047] Then subtract the initial position coordinates from all atomic coordinates in the system, add atoms, and traverse all atoms. If there is no n that satisfies:

[0048] (a p ,b p ,c p)=(a m -a n +a r3 ,b m -b n +b r3 ,c m -c n +c r3 ) (16)

[0049] Add atom o, whose fractional coordinates are

[0050] (a o ,b o ,c o )=(a m +a r3 ,b m +b r3 ,c m +c r3 ) (17)

[0051] Calculate the new basis vector L′

[0052]

[0053] Recalculate the atomic fraction coordinates (a′) according to the new basis vectors i ,b′ i ,c′ i ) If the length of the coordinate difference between any two atoms in the model after the modified basis vector is less than the upper error limit, the atom with the larger sequence number is deleted to ensure that the original sequence number of the atom remains unchanged and is not deleted. If the atomic fractional coordinate component is greater than 1 after the processing, it is subtracted by 1; if the coordinate component is less than 0, it is added by 1. After the processing, the remaining atoms are converted back to Cartesian coordinates.

[0054] 3×3 unit cell basis vector matrix L′, each atom type, the Cartesian coordinates of the remaining atoms (x′ i ,y′ i ,z′ i ) is collectively referred to as the reference lattice.

[0055] Step 2: Retrieve high symmetry sites in the reference lattice;

[0056] Specifically:

[0057] Step 201: bring the integrated reference lattice information into the third-party crystal symmetry analysis function library spglib to query the crystal symmetry information;

[0058] Crystal symmetry information includes: space group number, standard primitive cell mapping table, standard unit cell mapping table, atomic fraction coordinates in standard unit cell, standard unit cell basis vector matrix L", standard unit cell rotation matrix R", a series of symmetry rotation matrices Ri , and the corresponding displacement vector t i .

[0059] Step 202, based on the crystal symmetry information, query the atom i′0 corresponding to the initial serial number atom i0 in the standard unit cell mapping table, traverse the standard unit cell mapping table to query the atomic fraction coordinates corresponding to i′0 in the standard unit cell, and record them as anchor point coordinates (a″0, b″0, c″0).

[0060] Step 203, adding sites to be tested in the test area according to the difference between the two-dimensional material and the three-dimensional material;

[0061] (1) Two-dimensional material: add 256 test sites to the test area, with coordinates p i =(a″ i ,b″ i ,c″ i ), where a″ i ,b″ i It can be 0, Any number in c i "Limited to 0.

[0062] (2) Three-dimensional material: add 4096 test sites to the test area, with coordinates p i =(a″ i ,b″ i ,c″ i ), where a″ i ,b″ i ,c″ i It can be 0, Any number in .

[0063] Step 204: Analyze the sites to be tested:

[0064] Take any test site p j ,calculate

[0065] p k =R i p j +t i (19)

[0066] If p k In the test area, the p k Move into the testing area.

[0067] If p k It is neither in the test area nor in the test area. Add p to the test area. k , the area to be tested remains unchanged.

[0068] Traverse all symmetry rotation matrices R i, and the corresponding displacement vector t i After that, the number of sites remaining in the current test area is recorded, and this number is recorded as the site repeatability;

[0069] Step 205: transform the space group number, a series of symmetry rotation matrices R i , and the corresponding displacement vector t i The site repetition degree is brought into spglib to query the wyckoff symbol corresponding to the site. The smaller the repetition degree, the closer the wyckoff symbol is to the front, which proves that the symmetry of the site is better.

[0070] Step 206: After the calculation is completed, p j and its corresponding p k Move into the surveyed area;

[0071] Step 207, return to step 204, and analyze the next site to be tested until all sites have been calculated.

[0072] Step 3: Map the high symmetry sites back to the surface model;

[0073] The mapping formula is:

[0074]

[0075] Where (x i ″,y i ″,z i ″) is the corresponding site (a i ″,b i ″,c i ″) is the Cartesian coordinate on the surface model, (x0, y0, z0) is the initial coordinate, (n a ,n b ,n c ) are integers whose absolute values ​​are less than the quotient of the radius of the circumscribed sphere of the given surface model and the radius of the inscribed sphere of the standard unit cell, (a″0″, b″0″, c″0″) are the anchor point coordinates, L″ is the standard unit cell basis vector matrix, and R″ is the standard unit cell rotation matrix. (x Δ ,y Δ ,z Δ ) is a correction vector used to correct the distance between small molecules and the surface in the two-dimensional material plane search mode. The value is related to the bond length and is generally taken from the highest point on the surface extending along the c-axis. arrive The 3D material search mode correction vector can be set to zero.

[0076] Step 4: Replace the user-specified high-symmetry site with a specified small molecule to obtain the surface structure adsorbing the small molecule;

[0077] Read the material surface model file given by the user. The file should include: each atom type, each atom Cartesian coordinate (x mi ,y mi ,z mi ), the user needs to specify the coordinates of the contact position between the small molecule and the surface (x m0 ,y m0 ,z m0 ), and the atomic coordinates after adsorption are obtained according to the following formula:

[0078]

[0079] where R m It is the rotation matrix for adjusting the molecular orientation. It is assigned only when the orientation relationship between small molecules and the interface needs to be adjusted. The default is the unit matrix.

[0080] The present invention has the following beneficial effects:

[0081] This paper proposes an automatic search method for highly symmetric adsorption sites on material surfaces based on crystal symmetry. By querying the highly symmetric Wyckoff sites of the surface corresponding to the reference lattice generated by the query algorithm, potential surface small molecule adsorption sites are given to realize the calculation of the material's adsorption catalytic performance, which facilitates users to build a large number of models to analyze the material's catalytic reaction mechanism and provide predictions and guidance for the design of new materials. BRIEF DESCRIPTION OF THE DRAWINGS

[0082] Figure 1 This is a schematic diagram of a method for automatically searching for highly symmetric adsorption sites on a material surface based on crystal symmetry according to the present invention;

[0083] Figure 2 Searching for all adsorption sites with the wyckoff symbol 1a obtained by the user on the graphene surface in the embodiment of the present invention;

[0084] Figure 3 For the embodiment of the present invention, the user searches for all adsorption sites with a wyckoff symbol of 8c on the platinum surface;

[0085] Figure 4 The graphene surface model of water molecules adsorbed by the user of the embodiment of the present invention is constructed by the method;

[0086] Figure 5 This is a platinum surface model of hydrogen atoms adsorbed by the user of the embodiment of the present invention constructed by this method. DETAILED DESCRIPTION

[0087] The present invention is described in detail below with reference to the embodiments and accompanying drawings.

[0088] The present invention discloses an automatic search method for high symmetric adsorption sites on the surface of a material based on crystal symmetry, which consists of four parts: generating a reference lattice corresponding to a user-given surface model, retrieving high symmetric sites in the reference lattice, mapping the high symmetric sites back to the surface model, and replacing the specified high symmetric sites with specified small molecules; Figure 1 As shown, first, based on the material type specified by the user, a search is performed for the minimum surface repetition period of the two-dimensional material as a reference lattice, or the crystal surface structure is restored as a reference lattice. The reference lattice is then retrieved and converted to a standard unit cell lattice, and the high-symmetry sites in the standard unit cell lattice are obtained. The repetition degree and Wyckoff symbol of the corresponding sites in the reference lattice are obtained. The site symmetry is evaluated using these two methods, and the high-symmetry sites in the standard unit cell lattice are mapped back to the surface model to obtain the corresponding coordinates of each high-symmetry site on the surface. Finally, the small molecule is replaced with the high-symmetry site to obtain the surface structure of the adsorbed small molecule.

[0089] An automatic search method for highly symmetric adsorption sites on a material surface based on crystal symmetry, the specific steps are as follows:

[0090] Step 1: Read the material surface model file given by the user and generate the corresponding reference lattice according to the user's needs;

[0091] First, the material surface model file provided by the user should include: 3×3 unit cell basis vector matrix L, each atom type, each atom Cartesian coordinate (x i ,y i ,z i ), i represents the atomic number; take the first atom in the model, record its coordinates as the initial coordinates (x0, y0, z0), and record its atomic number as the initial number i0.

[0092]

[0093] Each element represents the component of the basis vector a, b, c on the x, y, and z axes respectively, and the c-axis is the surface normal direction by default.

[0094] Calculate the fractional coordinates of each atom:

[0095] (a i ,b i ,c i )=L -1 (x i ,y i ,z i ) (2)

[0096] Then, according to user needs, proceed to step 1a to search for the minimum surface repetition period or step 1b to restore the crystal structure as a reference lattice to obtain a material reference lattice. Step 1a is suitable for thinner materials such as two-dimensional materials, and step 1b is suitable for materials that are periodically arranged in the thickness direction such as the crystal surface.

[0097] Step 1a, search for the minimum surface repetition period as the reference lattice: set the initial basis vector fractional coordinate v r1 =(1,0,0),v r2 =(0,1,0), v r3 =(0,0,1), read the upper limit of error Δ set by the user, the default is 0.0001. Traverse all two types of the same and the fractional coordinate difference c in the c-axis direction d For different atoms whose absolute values ​​are less than the upper limit of the error, assume that their numbers are j and k, and obtain their coordinate differences:

[0098] v d =(a d ,b d ,c d )=(a j -a k ,b j -b k ,c j -c k ) (3)

[0099] when a d ,b d ,c d When any item is greater than 0.5, 1 is subtracted from the item. When any item is less than -0.5, 0.5 is added to the item so that all items are ultimately between -0.5 and 0.5. This step is hereinafter referred to as rollback processing.

[0100] Traverse all atoms, assuming that the serial number of a certain atom is m, if there is no n that satisfies:

[0101] (a p ,b p ,c p )=(a m -a n +a d ,b m -b n +b d ,c m -c n +c d ) (4)

[0102] In the formula (a p ,b p ,c p) After the rollback process, its length is less than the upper limit of the error, then directly judge the next group of two types with the same type and the fractional coordinate difference c in the c-axis direction d Different atoms less than the upper error limit.

[0103] If all atoms are traversed and there are corresponding atoms that satisfy formula (4), then the judgment condition is calculated:

[0104] |v d |<|v r1 | (5)

[0105]

[0106] If the judgment conditions (5) and (6) are both met, then use v d Replace v r1 Otherwise, calculate the judgment condition:

[0107] |v d |<|v r2 | (7)

[0108]

[0109] If the judgment conditions (7) and (8) are both met, then use v d Replace v r2 Otherwise, determine the next group of two types with the same c-axis fractional coordinate difference c d The number of different atoms is smaller than the upper limit of the error until no new atom pairs can be found.

[0110] Then calculate the new basis vector L′

[0111]

[0112] Recalculate the atomic fraction coordinates (a′) according to the new basis vectors i ,b′ i ,c′ i ), if the length of the coordinate difference between two atoms in the model after the modified basis vector is less than the upper limit of the error, the atom with the larger serial number in the corresponding atom pair is deleted to ensure that the atomic serial number of the initial serial number remains unchanged and is not deleted; if the atomic fractional coordinate component is greater than 1 after processing, it is subtracted by 1, and if the coordinate component is less than 0, it is added by 1. After processing, the remaining atoms are converted back to Cartesian coordinates.

[0113] (x′ i ,y′ i ,z′ i )=L′(a′ i ,b′ i ,c′ i ) (10)

[0114] 3×3 unit cell basis vector matrix L′, each atom type, the Cartesian coordinates of the remaining atoms (x′ i ,y′ i ,z′ i ) is collectively referred to as the reference lattice.

[0115] Step 1b, restore the crystal structure as a reference lattice: set the initial basis vector fractional coordinates v r1 =(1,0,0),v r2 =(0,1,0), v r3 =(a r3 ,b r3 ,c r3 )=(0,0,1), read the upper limit of error Δ set by the user, the default is 0.0001. Traverse the atoms to obtain the maximum value of their fractional coordinates c in the c direction max With the minimum value c min , and traverse all two of the same type and with the fractional coordinate difference c in the c-axis direction d For different atoms whose absolute values ​​are greater than the upper limit of the error, assume that their serial numbers are j and k, obtain their coordinate differences and perform convolution processing on them:

[0116] v d =(a d ,b d ,c d )=(a j -a k ,b j -b k ,c j -c k ) (11)

[0117] Traverse all atoms and assume their serial number is m. If there is no n that satisfies:

[0118] (a p ,b p ,c p )=(a m -a n +a d ,b m -b n +b d ,c m -c n +c d ) (12)

[0119] In the formula (a p ,b p ,c p ) After the rewinding process, its length is less than the upper limit of the error, or meets the

[0120] c m +c d <cmin (13)

[0121] or

[0122] c m +c d >c max (14)

[0123] Then directly judge the next group of two types with the same c-axis fractional coordinate difference c d Different atoms with a value less than the upper limit of the error. If all atoms are traversed and there are corresponding atoms, the judgment condition is calculated:

[0124] |c d |<|c r3 | (15)

[0125] If the judgment condition (15) is met, then use v d Replace v r3 Otherwise, determine the next group of two types with the same c-axis fractional coordinate difference c d The number of different atoms is smaller than the upper limit of the error until no new atom pairs can be found.

[0126] Then, the initial position coordinates are subtracted from the coordinates of all atoms in the system, and the atoms are added, specifically:

[0127] Traverse all atoms, if there is no n that satisfies:

[0128] (a p ,b p ,c p )=(a m -a n +a r3 ,b m -b n +b r3 ,c m -c n +c r3 ) (16)

[0129] Add atom o, whose fractional coordinates are

[0130] (a o ,b o ,c o )=(a m +a r3 ,b m +b r3 ,c m +c r3 ) (17)

[0131] Calculate the new basis vector L′

[0132]

[0133] Recalculate the atomic fraction coordinates (a′) according to the new basis vectors i ,b′ i ,c′ i ) If the length of the coordinate difference between any two atoms in the model after the modified basis vector is less than the upper error limit, the atom with the larger sequence number is deleted to ensure that the original sequence number of the atom remains unchanged and is not deleted. If the atomic fractional coordinate component is greater than 1 after the processing, it is subtracted by 1; if the coordinate component is less than 0, it is added by 1. After the processing, the remaining atoms are converted back to Cartesian coordinates.

[0134] 3×3 unit cell basis vector matrix L′, each atom type, the Cartesian coordinates of the remaining atoms (x i ′,y i ′,z i ′) is collectively referred to as the reference lattice.

[0135] Step 2: Search for high symmetry sites in the reference lattice:

[0136] The integrated reference lattice information, including the basis vector matrix L′, each atom type, and the remaining atomic Cartesian coordinates (x i ′,y i ′,z i ′), bring in the third-party crystal symmetry analysis function library spglib to query crystal symmetry information, including: space group number, standard primitive cell mapping table, standard unit cell mapping table, atomic fraction coordinates in the standard unit cell, standard unit cell basis vector matrix L″, standard unit cell rotation matrix R″, a series of symmetry rotation matrices R i , and the corresponding displacement vector t i .

[0137] Query the atom i′0 corresponding to the initial sequence number i0 in the standard unit cell mapping table, traverse the standard unit cell mapping table to query the atomic fraction coordinates corresponding to i′0 in the standard unit cell, and record them as anchor point coordinates (a″0″, b″0″, c″0″).

[0138] Then, according to user needs, enter step 2a to search for in-plane high symmetry sites or step 2b to search for three-dimensional high symmetry sites to obtain high symmetry sites of the material. Step 2a is suitable for thinner materials such as two-dimensional materials, and step 2b is suitable for materials that are periodically arranged in the thickness direction such as the crystal surface.

[0139] Step 2a: Add 256 test sites to the test area with coordinates p i =(a″ i ,b″ i ,c″ i ), where a″ i ,b″i It can be 0, Any number in , and c″ i Limited to 0.

[0140] Step 2b: Add 4096 test sites to the test area, with coordinates p i =(a″ i ,b″ i ,c″ i ), where a″ i ,b″ i ,c″ i It can be 0, Any number in .

[0141] Next, we analyze the test sites and select any test site p. j ,calculate

[0142] p k =R i p j +t i (19)

[0143] If p k In the test area, the p k Move into the testing area.

[0144] If p k It is neither in the test area nor in the test area. Add p to the test area. k , the area to be tested remains unchanged.

[0145] Traverse all symmetry rotation matrices R i , and the corresponding displacement vector t i After that, the number of sites remaining in the current test area is recorded, and this number is recorded as the site repeatability;

[0146] The space group number, a series of symmetry rotation matrices R i , and the corresponding displacement vector t i The site repetitiveness is brought into spglib to query the wyckoff symbol corresponding to the site. The smaller the repetitiveness, the closer the wyckoff symbol is to the front, which proves that the site has better symmetry. j The corresponding p k Move to the measured area and repeat the analysis steps until all sites have been calculated.

[0147] Step 3: Map high symmetry sites back to the surface model:

[0148] Substitute the corresponding parameters in each step into the mapping formula:

[0149]

[0150] Where (x i ,y″ i ,z″ i ) is the corresponding site (a″ i ,b″ i ,c″ i ) is the Cartesian coordinate on the surface model, (x0, y0, z0) is the initial coordinate in step 1, (n a ,n b ,n c ) are integers whose absolute values ​​are less than the quotient of the radius of the circumscribed sphere of the given surface model and the radius of the inscribed sphere of the standard unit cell, (a″0, b″0, c″0) are the anchor point coordinates of step 2, L″ is the standard unit cell basis vector matrix, and R″ is the standard unit cell rotation matrix. (x Δ ,y Δ ,z Δ ) is a correction vector used to correct the distance between the small molecule and the surface in the plane search mode in step 2a. The value is related to the bond length and is generally taken as the highest point on the surface extending along the c-axis. arrive The three-dimensional search mode correction vector coefficients can be set to zero.

[0151] Step 4: Replace the designated high-symmetry site with a designated small molecule:

[0152] Read the material surface model file given by the user. The file should include: each atom type, each atom Cartesian coordinate (x mi ,y mi ,z mi ), the user needs to specify the coordinates of the contact position between the small molecule and the surface (x m0 ,y m0 ,z m0 ), and then the atomic coordinates after adsorption can be obtained according to the following formula:

[0153]

[0154] where R m It is the rotation matrix for adjusting the molecular orientation. It is assigned only when the orientation relationship between small molecules and the interface needs to be adjusted. The default is the unit matrix.

[0155] Example:

[0156] (1) Generate a reference lattice corresponding to the user-given surface model: Read the initial model, model 1 is the graphene model, such as Figure 2 As shown; Model 2 is the platinum surface model, as shown Figure 3As shown. Set the default value of 0.0001 for the upper error limit Δ. Use the method shown in step 1a to search for the minimum surface repetition period of model 1 as the reference lattice for model 1. Use the method shown in step 1b to search for the restored crystal structure of model 2 as the reference lattice for model 2. Bring the reference lattice into the next calculation.

[0157] (2) Retrieve high symmetry sites in the reference lattice: bring each reference lattice into the symmetry analysis function library spglib to query the crystal symmetry information and generate the standard unit cell of each structure. Use the method described in step 2a to add 256 test sites to the standard unit cell of model 1, and use the method described in step 2b to add 4096 test sites to the standard unit cell of model 2. Analyze the repetitiveness and wyckoff sign of each test site, retain the top three sites in the wyckoff ranking, and proceed to the next step.

[0158] (3) Calculate the coordinates of each site of the standard unit cell in the interface model using formula (20) and save the coordinates to a new model file, where the correction vector of model 1 takes the surface epitaxy Set the correction vector of model 2 to zero. Save the search results to a file. Use the external software SPaMD Studio to read the generated file and plot it on the same map as the original file and output it as a picture format, retaining all 1a sites of model 1 as shown in the figure. Figure 2 As shown, it includes the original surface atoms and the surface adsorption sites obtained by searching. It can be seen that the surface adsorption sites are all located in the center of the graphene six-membered ring, which is consistent with the conclusion of the model manually constructed in the literature. Figure 3 As shown in the figure, which includes the original surface atoms and the surface adsorption sites obtained by the search, it can be seen that the arrangement pattern of the surface adsorption sites is consistent with that of the crystal part, proving that the search is effective.

[0159] (4) Using formula 21, randomly replace a 1a site in model 1 with a water molecule, and select the contact position coordinates as the bottom hydrogen atom coordinates; randomly replace an 8c site in model 2 with a hydrogen atom to obtain the atomic configuration after adsorption, and save the results in a file. Use the external software SPaMD Studio to read the generated file and output it in image format, where the output of model 1 is as follows Figure 4 As shown, including the base graphene structure, oxygen atoms and hydrogen atoms, it can be seen that the bottom hydrogen atoms and the six-membered ring form a regular hexagonal pyramid structure. The results of model 2 are as follows Figure 5 As shown, the substrate platinum crystal structure and hydrogen atoms are included. It can be seen that the hydrogen atoms and the bonding metal form a regular isosceles triangle structure, which is consistent with the commonly used bridge site structure. This proves that the method of the present invention can achieve the expected effect.

Claims

1. A method for automatically searching for highly symmetric adsorption sites on a material surface based on crystal symmetry, characterized in that: The specific steps are as follows: Step 1: Read the material surface model file given by the user and generate the corresponding reference lattice according to the user's needs; The material surface model file includes: 3×3 unit cell basis vector matrix L, each atom type, and each atom Cartesian coordinate , i represents the atomic number; take the first atom in the model and record its coordinates as the initial coordinates , record its atomic number as the initial number ; The 3×3 unit cell basis vector matrix L is: （1） Each element represents the component of the basis vector a, b, c on the x, y, and z axes respectively, and the c axis is the surface normal direction by default; The fractional coordinates of each atom are: （2） Determine whether the material the user needs is a two-dimensional material or a three-dimensional material, and obtain the corresponding reference lattice. If it is a two-dimensional material, search for the minimum surface repetition period as the reference lattice; if it is a three-dimensional material, restore the crystal structure as the reference lattice; Step 2: Retrieve high symmetry sites in the reference lattice; Specifically: Step 201: bring the integrated reference lattice information into the third-party crystal symmetry analysis function library spglib to query the crystal symmetry information; Step 202: Query the initial sequence number based on the crystal symmetry information The atoms corresponding to the atoms in the standard primitive cell mapping table , traverse the standard cell mapping table to query the corresponding The standard atomic fraction coordinates in the unit cell are recorded as anchor point coordinates ; Step 203, adding sites to be tested in the test area according to the difference between the two-dimensional material and the three-dimensional material; Step 204: Analyze the sites to be tested: Take any site to be tested ,calculate (3) if In the test area, Move into the test area; like It is neither in the test area nor in the waiting area. , the area to be tested does not change; Traverse all symmetry rotation matrices , and the corresponding displacement vector After that, the number of sites remaining in the current test area is recorded, and this number is recorded as the site repeatability; Step 205: transform the space group number, a series of symmetry rotation matrices , and the corresponding displacement vector The site repetitiveness is brought into spglib to query the wyckoff symbol corresponding to the site. The smaller the repetitiveness, the closer the wyckoff symbol is to the front, which proves that the symmetry of the site is better. Step 206: After the calculation is completed, and its corresponding Move into the surveyed area; Step 207, returning to step 204, and analyzing the next site to be measured, until all sites have been calculated; Step 3: Map the high symmetry sites back to the surface model; The mapping formula is: + (4) in The corresponding site Cartesian coordinates on the surface model, are the initial coordinates, are integers whose absolute values ​​are smaller than the quotient of the radius of the circumscribed sphere of the given surface model and the radius of the inscribed sphere of the standard unit cell, is the anchor point coordinate, is the standard unit cell basis matrix, is the standard unit cell rotation matrix; is the correction vector used to correct the distance between small molecules and the surface in the two-dimensional material plane search mode; in the three-dimensional material search mode, the correction vector can be set to zero; Step 4: Replace the user-specified high-symmetry site with a specified small molecule: Read the material surface model file given by the user. The file should include: each atom type, each atom Cartesian coordinate , the user needs to specify the coordinates of the contact position between the small molecule and the surface , the atomic coordinates after adsorption are obtained according to the following formula: (5) in It is the rotation matrix for adjusting the molecular orientation. It is assigned only when the orientation relationship between small molecules and the interface needs to be adjusted. The default is the unit matrix.

2. The method for automatically searching for highly symmetric adsorption sites on a material surface based on crystal symmetry according to claim 1, characterized in that: The search for the minimum surface repetition period as a reference lattice is specifically as follows: Set the initial basis vector fractional coordinates , , , read the upper limit of error set by the user , the default value is 0.0001; iterates over all two objects of the same type with the difference in fractional coordinates along the c-axis. For different atoms whose absolute values ​​are less than the upper limit of the error, assume that their numbers are j and k, and obtain their coordinate differences: (6) right Perform rewind processing, specifically: When any item is greater than 0.5, subtract 1 from it; when any item is less than -0.5, add 0.5 to it so that all items are between -0.5 and 0.

5. Traverse all atoms, assuming that the serial number of a certain atom is m, if there is no n that satisfies: (7) In the formula After the rewinding process, if its length is less than the upper limit of the error, then the next group of two types are directly judged to be of the same type and the fractional coordinate difference in the c-axis direction is Different atoms smaller than the upper limit of error; If all atoms are traversed and there are corresponding atoms that satisfy formula (7), then the judgment condition is calculated: (8) (9) If the judgment conditions (8) and (9) are both met, then use replace ; Otherwise, calculate the judgment condition: (10) (11) If the judgment conditions (10) and (11) are both met, then use replace Otherwise, determine the next group of two types with the same type and the difference in fractional coordinates along the c-axis The number of different atoms is smaller than the upper limit of the error, until no new atom pairs are found; Then calculate the new basis vector (12) Recalculate the atomic fraction coordinates based on the new basis vectors If the length of the coordinate difference between two atoms in the model after the modified basis vector is less than the upper limit of the error, the atom with the larger serial number in the corresponding atom pair is deleted to ensure that the initial serial number of the atom remains unchanged and is not deleted; if the atomic fractional coordinate component is greater than 1 after processing, it is subtracted by 1, and if the coordinate component is less than 0, it is added by 1. After processing, the remaining atoms are converted back to Cartesian coordinates. (13) 3×3 unit cell basis vector matrix , each atom type, the Cartesian coordinates of the remaining atoms General term for reference lattice.

3. The method for automatically searching for highly symmetric adsorption sites on a material surface based on crystal symmetry according to claim 1, characterized in that: The reduced crystal structure is used as a reference lattice, specifically: Set the initial basis vector fractional coordinates , , , read the user-set error limit , the default value is 0.0001; traverse the atoms to obtain the maximum value of their fractional coordinates c in the c direction max With the minimum value c min , and traverse all two types of the same and c-axis fractional coordinate difference Different atoms whose absolute values ​​are greater than the upper limit of the error are assumed to be numbered j and k, and their coordinate differences are obtained and then reconvolved; The coordinate difference is: (14) Traverse all atoms and assume that the atomic number is m. If there is no n that satisfies: (15) In the formula After the rewinding process, its length is less than the upper limit of the error, or meets the (16) or (17) Then directly judge the next group of two types with the same type and the difference in fractional coordinates along the c-axis Different atoms with a value smaller than the upper limit of the error; if the corresponding atoms exist in all atoms, the judgment condition is calculated: (18) If the judgment condition (18) is met, then use replace Otherwise, determine the next group of two types with the same type and the difference in fractional coordinates along the c-axis The number of different atoms is smaller than the upper limit of the error, until no new atom pairs are found; Then subtract the initial position coordinates from all atomic coordinates in the system and add atoms: Traverse all atoms, if there is no n that satisfies: (19) Add atom o, whose fractional coordinates are = (20) Calculate new basis vectors (21) Recalculate the atomic fraction coordinates based on the new basis vectors If the length of the coordinate difference between two atoms in the model after the modified basis vector is less than the upper limit of the error, the atom with the larger serial number is deleted to ensure that the atomic serial number of the initial serial number remains unchanged and is not deleted; if the atomic fractional coordinate component is greater than 1 after the processing, it is subtracted by 1, and if the coordinate component is less than 0, it is added by 1; after the processing, the remaining atoms are converted back to Cartesian coordinates; 3×3 unit cell basis vector matrix , each atom type, the Cartesian coordinates of the remaining atoms General term for reference lattice.

4. The method for automatically searching for highly symmetric adsorption sites on a material surface based on crystal symmetry according to claim 1, characterized in that: The crystal symmetry information in step 201 includes: space group number, standard primitive cell mapping table, standard unit cell mapping table, atomic fraction coordinates in standard unit cell, standard unit cell basis vector matrix , the standard unit cell rotation matrix , a series of symmetry rotation matrices , and the corresponding displacement vector .

5. The method for automatically searching for highly symmetric adsorption sites on a material surface based on crystal symmetry according to claim 1, characterized in that: In step 203, the two-dimensional material or the three-dimensional material adds a test site in the test area, specifically: (1) Two-dimensional material: add 256 test sites to the test area, with coordinates of ,in is 0, , , , , , , , , , , , , , Any number in Limited to 0; (2) Three-dimensional material: add 4096 test sites to the test area, with coordinates of ,in is 0, , , , , , , , , , , , , , Any number in .

6. The method for automatically searching for highly symmetric adsorption sites on a material surface based on crystal symmetry according to claim 1, characterized in that: The value of the correction vector of the two-dimensional material described in step 3 is related to the bond length, and the highest point on the surface is extended 1Å to 2Å along the c-axis.

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