CN113012764B - Bioactive glass structure based on molecular dynamics and simulation method of XRD calculation - Google Patents
Bioactive glass structure based on molecular dynamics and simulation method of XRD calculation Download PDFInfo
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Abstract
The invention discloses a bioactive glass structure based on molecular dynamics and an XRD calculation simulation method. The method comprises the following steps: compiling a script to construct a data file of molecular dynamics simulation software, and establishing an initial model of the amorphous structure of the bioactive glass; selecting a potential function of interaction force among atoms of the bioactive glass; calculating by running molecular dynamics simulation software, and outputting an atomic coordinate file and XRD data of the bioactive glass model; and obtaining the microstructure information of the bioactive glass by combining visualization and data analysis software. Based on the molecular dynamics theory, the invention obtains the structural information of the glass atomic layer by a molecular dynamics simulation method and calculates to obtain XRD, makes up the defect that the experimental research can not realize the analysis of the atomic structure, deeply analyzes the relation among the structure, ion diffusion, surface characteristics and biological activity of the bioactive glass, and can predict the performance of bioactive glass structures with different components.
Description
Technical Field
The invention belongs to the field of biomedical materials, and particularly relates to a bioactive glass structure based on molecular dynamics and an XRD calculation simulation method.
Background
In the field of biomedical materials, Bioactive Glasses (BG) have been widely used in clinical treatments such as tissue repair and regeneration due to its excellent biocompatibility and bioactivity, and therefore, the search for the mechanism of bioactivity becomes an inevitable problem for researchers. At present, researchers have studied the action mechanism of BG in organisms through various biological methods, but in terms of material structure, computer simulation has become a powerful tool for studying amorphous material structure and performance due to the limitations of current detection techniques for amorphous materials.
It is important to understand the structure of bioactive glasses for better interpretation and optimization of the experiments. Furthermore, molecular dynamics simulation (MD) by computer can give details of the glass structure, as well as important information about the structure and performance relationships of complex glasses. Since the biological activity strongly depends on the release of ionic species in the physiological environment, a prerequisite for a direct prediction of the bioactive response of the glass is a correct understanding of the structure of the components constituting the glass at the atomic level, as well as the changes that occur on a (sub-) nanometer scale when changing the glass composition. By utilizing the molecular dynamics simulation technology, BG structure and surface characteristics can be deeply explained and characterized in a microscopic level from an atomic layer surface, and a novel glass compound for biological materials can be reasonably designed and the reaction process of BG and biomacromolecules can be realized so as to more accurately guide experimental research and reduce research and development cost.
The existing BG atomic layer structure can be researched by using neutron diffraction, magic angle rotation solid-state nuclear magnetic resonance technology, high-energy X-ray synchrotron radiation and other detection technologies to test the bond length, coordination, network connectivity and the like among atoms, but the tests are expensive, difficult to reserve and long in period, and only single properties of the structure can be obtained finally. However, the molecular dynamics simulation technology can not only obtain a reliable BG structure in the same time, but also analyze various properties and structures such as thermodynamics, kinetics and the like.
Disclosure of Invention
In order to overcome the defects in the prior art, the invention aims to provide a bioactive glass structure based on molecular dynamics and an XRD calculation simulation method.
The invention provides a simulation method of bioactive glass sintering and XRD calculation based on molecular dynamics. The method adopts molecular dynamics simulation, selects a proper potential function, sets reasonable simulation parameters and method steps, directly obtains a coordinate file and XRD data of the bioactive glass structure, compares the coordinate file and the XRD data with experiments, and carries out short-range and medium-range structural analysis on the bioactive glass.
Firstly, the invention can provide a method for reasonably explaining and characterizing experiments by deeply researching the microstructure and surface characteristics of a certain bioactive glass; secondly, bioactive glass with different components can be constructed according to the method to carry out structure and performance prediction to directly carry out experiments, so that a large amount of experiment expenses are avoided; in addition, the structure and ion diffusion performance of the bioactive glass can be studied intensively by this method, and the relation between the bioactivity and the like can be studied.
The purpose of the invention is realized by at least one of the following technical solutions.
The invention provides a molecular dynamics-based bioactive glass sintering and XRD calculation simulation method, which comprises the following steps: selecting a potential function capable of reflecting interaction force among atoms contained in a bioactive glass system; constructing an initial amorphous structure model of the bioactive glass and generating a data file which can be identified by molecular dynamics simulation software; determining parameters and conditions of a molecular dynamics simulation calculation process and writing the parameters and conditions into molecular dynamics simulation software; calculating and outputting a bioactive glass structure model coordinate file and XRD data through molecular dynamics simulation software; the reliability of the structure is proved by comparing XRD data with experiments, and the microstructure information of the bioactive glass is obtained by combining visualization and data analysis software short-range and medium-range structural analysis.
The invention provides a molecular dynamics-based bioactive glass structure and an XRD calculation simulation method, which specifically comprises the following steps:
(1) selecting bioactive glass to be tested, testing the density, defining the total number of atoms of the bioactive glass, obtaining the side length of a simulated cubic box according to the density and the total number of atoms, and generating a data file containing the initial coordinates of each atom of the bioactive glass to be tested by using a Python script, namely the data file of the initial structure of the bioactive glass to be tested;
(2) importing the data file and the potential function of the initial structure of the bioactive glass to be detected in the step (1) into an in file executing a Lammps software operation command, minimizing energy of the initial structure of the bioactive glass to be detected in the Lammps software, heating the initial structure of the bioactive glass to be detected in the Lammps software for simulated heating treatment, then cooling to normal temperature, collecting data of a balance structure after simulated heating and cooling, and performing XRD calculation to obtain an XRD (X-ray diffraction) diagram;
(3) and (3) inputting the balance structure data in the step (2) into visual software VMD to obtain a network structure diagram and an atom structure diagram of the bioactive glass to be detected, and performing structural analysis to complete the simulation of the bioactive glass structure and XRD calculation.
Further, the initial structure of the bioactive glass in the step (1) is built in a simulation cubic box, each atom initial coordinate is located in the simulation cubic box, the density of the bioactive glass is obtained according to experimental tests, Python scripts are compiled according to the requirements of the box side length and Lammps on the input model format, the initial amorphous structure of the bioactive glass is built, and model input data which can be identified by Lammps are generated. The initial structure of the bioactive glass is limited in a cubic box, and the side length of the box is calculated according to the density of the bioactive glass tested by experiments.
Further, the data file containing the initial coordinates of each atom of the bioactive glass to be detected in the step (1) also contains information of boundary conditions, simulation ensemble, a temperature control method, a cooling rate, a summation method and XRD calculation parameters. The data file is a Lammps input file. The simulation process calculation conditions also need to be written into a Lammps input in file. The data file is a Python script written according to the requirements of the box side length and Lammps on the input model format, establishes an initial amorphous structure of the bioactive glass, and generates model input data recognizable by Lammps.
Further, the boundary condition adopts a periodic boundary condition, a normal ensemble (NVT) and an EWald summation method are selected, the time step is set to be 2fs, a Nose-Hoover hot bath method is adopted to regulate and control the temperature of the NVT normal ensemble, and after 5000-6000k relaxation, the optimal cooling rate is selected to be reduced to 300k between 1-5 k/ps. The system was fully relaxed at high temperature for 100ps to equilibrate, run under NVT ensemble after cooling to 300k, then fully relaxed under micro-canonical ensemble (NVE) to eliminate residual stress to energy minimization and data was collected for results analysis.
Further, the temperature of the simulated heating treatment in the step (2) is 5000-.
Further, the potential function in the step (2) is a Morse potential function, and the expression of the potential function is
Wherein, UijIs a distance rijThe total potential energy of all atoms i and j; i and j represent any two atoms in the system; z is a radical ofiAnd zjRepresents an effective charge; e represents a primary charge (e ═ 1.6 × 10)-19C)；rijRepresents the distance between two atoms i and j; dijIs the bond dissociation energy of atoms i and j; a isijIs a function of the slope of the potential energy well; r is0Is the bond balance distance; cijIs the elastic constant.
Further, the potential function in the step (2) is composed of coulomb potential describing long-range interaction force, Morse potential function (Morse term) describing short-range interaction force on the silicon-based glass and mutual exclusion term for preventing atomic fusion at high temperature
Further, during the XRD calculation in step (3), a 2Theta range is set as required to calculate XRD, and a computer XRD command is run after the structure is balanced to complete the XRD calculation.
Further, in step (3), the xyz-format file of the balanced structure data is input into the visualization software VMD, the structure is observed, and the radial distribution function and Q are usednApproach to one anotherThe relation between the structure and the performance is judged by the process and the intermediate process structure analysis method. QnIs the connection ratio of Si or P and the bridge oxygen in the glass, and n is 0 to 4.
According to the invention, through Lammps operation molecular dynamics simulation calculation, a coordinate data file and XRD data of a balanced structure model after a bioactive glass simulation structure are obtained. XRD data plots were compared to experiments by data processing software to verify the reliability of the structure. And opening the simulated coordinate data observation structure through VMD visualization software, and analyzing the relation between the structure and the performance of the structure through a short-range structure and a medium-range structure.
The method constructs a data file which can be identified by molecular dynamics simulation software by compiling scripts so as to establish an initial model of the amorphous structure of the bioactive glass; selecting a potential function for calculating interaction force among atoms contained in the bioactive glass; setting calculation parameters of a molecular dynamics simulation structure, and running and calculating through molecular dynamics simulation software, wherein the calculation parameters comprise 1) high-temperature structure relaxation, 2) continuous cooling according to a specified rate, 3) low-temperature structure balance, and 4) XRD of a balance structure; outputting an atomic coordinate file and XRD data of the bioactive glass model; the reliability of the structure is proved by comparing XRD data with experiments, and short-range and middle-range structural analysis is carried out by combining visualization and data analysis software to obtain the microstructure information of the bioactive glass.
In the method provided by the invention, the molecular dynamics simulation result can be calculated to obtain a structural factor; calculation of x-ray diffraction (XRD) intensities as described in the calculation simulating radiation using specific wavelength rays on a grid of reciprocal lattice points defined by the entire simulation domain, the x-ray diffraction intensities at each reciprocal lattice point being calculable by the structural factor, thereby obtaining XRD data of the simulated structure; comparing XRD data with experiments, the feasibility of the method of the invention can be further verified.
Compared with the prior art, the invention has the following advantages and beneficial effects:
(1) the invention provides a bioactive glass structure based on molecular dynamics and a simulation method of XRD calculation, which can simulate the bioactive glass structure and XRD data by molecular dynamics through Lammps and verify the reliability of the structure through XRD and experiment comparison.
(2) Compared with the traditional experimental characterization, the structural characterization method of the bioactive glass can analyze the relationship between the short-range and intermediate-range structural characteristics and the bioactivity of the bioactive glass in detail from the atomic scale so as to further explain and optimize the experiment and carry out related theoretical guidance on the batch production of the bioactive glass.
(3) The bioactive glass with different components can be constructed according to the method provided by the invention to carry out structural performance prediction to carry out a targeted experiment, so that expensive experiment expenses are avoided.
(4) The structural model constructed by the method provided by the invention can be used for researching the ion diffusion performance and the surface structure of the bioactive glass and reasonably explaining the experimental result.
Drawings
FIG. 1 is a flow chart of a simulation method of molecular dynamics based bioactive glass structure and XRD calculations in an exemplary embodiment of the invention;
FIG. 2 is a graph comparing XRD (58S-MD) versus experimental XRD (58S-EXP) for a simulated bioactive glass structure in an exemplary embodiment of the invention;
FIG. 3 is a schematic representation of the amorphous network structure of a relaxed-equilibrated 58S bioactive glass in an exemplary embodiment of the present invention;
FIG. 4 is a schematic diagram of the atomic structure of a relaxationally equilibrated 58S bioactive glass in an exemplary embodiment of the invention.
Detailed Description
The following examples are presented to further illustrate the practice of the invention, but the practice and protection of the invention is not limited thereto. It is noted that the processes described below, if not specifically described in detail, are all realizable or understandable by those skilled in the art with reference to the prior art. The reagents or apparatus used are not indicated to the manufacturer, and are considered to be conventional products available by commercial purchase.
One aspect of the embodiments of the present invention provides a simulation method of bioactive glass structure and XRD calculation based on molecular dynamics, the flow chart of the method is shown in fig. 1, which includes:
the method comprises the following steps: selecting a potential function capable of reflecting interaction force among atoms contained in a bioactive glass system;
step two: constructing an initial amorphous structure model of the bioactive glass and generating a data file which can be identified by molecular dynamics simulation software;
step three: determining parameters and conditions of a molecular dynamics simulation calculation process and writing the parameters and conditions into molecular dynamics simulation software;
step four: and calculating and outputting a bioactive glass structure model coordinate file and XRD data through molecular dynamics simulation software.
Step five: the reliability of the structure is proved by comparing XRD data with experiments, and the microstructure information of the bioactive glass is obtained by combining visualization and data analysis software short-range and medium-range structural analysis.
In the first step, the selected potential function consists of a Coulomb potential for describing the long-range interaction force, a Morse potential function well describing the short-range interaction force of the silicon-based glass and a mutual exclusion term for preventing atom fusion at high temperature.
Therefore, the potential function describing the interatomic interaction is:
wherein, UijIs a distance rijThe total potential energy of all atoms i and j; i and j represent any two atoms in the system; z is a radical ofiAnd zjRepresents an effective charge; e represents a primary charge (e ═ 1.6 × 10)-19C)；rijRepresents the distance between two atoms i and j; dijIs the bond dissociation energy of atoms i and j; a isijIs a function of the slope of the potential energy well; r is0Is the bond balance distance; cijIs the elastic constant.
And in the second step, the initial structure model of the bioactive glass is placed in a cubic box, and the side length of the box is calculated according to the density of the bioactive glass tested by experiments.
And compiling a Python script, establishing an initial amorphous structure of the bioactive glass according to the side length of the box, enabling each atom initial coordinate to be located in the box, and generating data format data which can be identified by Lammps.
In the third step, the conditions and parameters of the simulation process are input by compiling the Lammps simulation control file in file, which mainly comprises: boundary conditions, simulation ensemble, a temperature control method, a cooling rate, a summation method and XRD calculation parameters.
In some examples, the boundary conditions are periodic boundary conditions, a normal ensemble (NVT) and an EWald summation method are selected, the time step is set to be 2fs, a Nose-over hot bath method is used for regulating the temperature of the NVT, and after 6000k relaxation, the temperature is reduced to 300k at a cooling rate of 5 k/ps.
In some examples, 100ps was fully relaxed at 6000k to balance the system, 50ps was run under NVT ensemble after cooling to 300k, followed by 50ps run under micro-canonical ensemble (NVE) for full relaxation to eliminate residual stress to energy minimization, and data was collected for results analysis.
In some examples, the XRD calculation parameters were set to 2Theta range of 10-70 degrees, and the XRD calculation was done by running 1000 steps after balancing the structure, using the Lammps statement computer XRD command.
In the fourth step, molecular dynamics simulation calculation is carried out by adopting a Lammps operation in file to obtain an xyz-format coordinate file of the bioactive glass simulated equilibrium structure model and an XRD file containing XRD data.
And fifthly, analyzing and processing XRD data through data processing software, comparing the XRD data with an experiment, verifying the reliability of a basic structure, considering that simulation is carried out under a vacuum condition, and ensuring that XRD does not have any impurity peak and accords with a main peak related to a structural component.
And step five, opening a simulated structure coordinate data observation structure through VMD visualization software, and processing and analyzing the short-range and medium-range structures of the bioactive glass through data processing software ISAACS, thereby analyzing the relationship between the structures and the performance by combining experiments.
Example 1
The experiment is carried out by using a simulation method of a bioactive glass structure based on molecular dynamics and XRD calculation, and the simulation method mainly comprises the following steps:
(1) firstly, a component of 60 percent SiO is determined2-36％CaO-4％P2O5(mol%) bioactive glass, 58S for short, 7560 atoms is adopted in design simulation, and the experimental density is 2.67g/cm3The side length of the cubic box simulating 7560 atoms is calculated
Generating a 58S structure model data file by using a Python script according to the format requirement of Lammps on an input structure data file;
(2) writing the determined Morse potential function parameters and related calculation conditions into an in file for executing a Lammps operation command, introducing a linear table in Lammps for a high-temperature mutual exclusion item, then minimizing energy of an initial structure, setting a periodic boundary condition in an XYZ direction of a cubic box under an NVT (noise vibration and harshness) ensemble, heating the initial 58S structure to 5000k with the time step of 2fs, operating the structure at a constant temperature of 100ps under 5000k to ensure that the structure is fully relaxed, cooling to 300k at the rate of 5k/ps, relaxing by 50ps, operating 50ps under an NVE ensemble, collecting balanced structure data for data analysis, and finally using a computer XRD command and setting a scanning angle of 10-70 degrees to perform XRD (X-ray diffraction) calculation.
(3) As shown in figure 2, when the XRD is plotted after being treated, compared with the experimental test, the main peak of the glass amorphous structure 21-30 degrees is consistent with the experiment, and the experimental test shows that the crystallization peak about 32 degrees is due to the strong reaction activity of the sample and the CO in the air2React with water to form Hydroxyapatite (HAP) crystals, independent of sample composition, so that the simulated 58S structure is reliable and can be further subjected to structural analysis.
(4) 58S structure data files in an xyz format are opened through visual software VMD, a 58S network structure diagram shown in figure 3 and an atom structure diagram shown in figure 4 can be seen, the xyz format files are led into ISAACS software to carry out short-range and medium-range structure analysis such as radial distribution function, bond length, bond angle distribution, ring distribution statistics and the like, so that structural analysis which cannot be realized by experimental tests is obtained, a biological activity mechanism is further deeply explained, and the experimental design of the biological activity glass is guided.
Example 2
The experiment of the embodiment uses a simulation method of a bioactive glass structure and XRD calculation based on molecular dynamics, and mainly comprises the following steps (as shown in figure 1):
(1) firstly, a component of 46.1SiO is determined2,-24.4Na2O-26.9CaO-2.6P2O5(mol%) bioactive glass, abbreviated to 45S5, is designed and simulated by adopting 4992 atoms according to the experimental density of 2.72g/cm3The side length of the cubic box simulating the box containing 4992 atoms is calculated
Generating a 45S5 structure model data file by using a Python script according to the format requirement of Lammps on the input structure data file;
(2) writing the determined Morse potential function parameters and related calculation conditions into an in file for executing a Lammps operation command, introducing a linear table in Lammps for a high-temperature mutual exclusion item, then minimizing energy of an initial structure, setting periodic boundary conditions in an XYZ direction of a cubic box under an NVT (noise vibration and harshness) ensemble, heating the initial 45S5 structure to 6000k at a time step of 2fs, operating 100ps at 6000k at a constant temperature to ensure that the structure is fully relaxed, cooling to 300k at a rate of 5k/ps, relaxing 50ps, operating 50ps under an NVE ensemble, collecting balanced structure data for data analysis, and finally using a compute XRD command and setting a scanning angle of 10-70 degrees to perform XRD calculation.
(3) Comparing the XRD with the experimental test, the main peak of the glass structure is consistent with the experiment, so that the 45S5 structure generated by simulation is reliable, and the structural analysis can be further carried out.
(4) The 45S5 structure data file in xyz format is opened through the visual software VMD, and the xyz format file is imported into the ISAACS software to carry out short-range and medium-range structure analysis such as radial distribution function, bond length, bond angle distribution, ring distribution statistics and the like, further deeply explain the bioactivity mechanism, and guide the experiment result and prediction of bioactive glass.
Example 3
The experiment of the embodiment uses a simulation method of a bioactive glass structure and XRD calculation based on molecular dynamics, and mainly comprises the following steps (as shown in figure 1):
(1) firstly, a component of 75% SiO is determined2-15％CaO-10％Na2O (mol%) inactive bioglass, designed to simulate 114 atoms, according to an experimental density of 2.5g/cm3The side length of the cubic box simulating 114 atoms is calculated
Generating a structure model data file by using a Python script according to the format requirement of Lammps on the input structure data file;
(2) writing the determined Morse potential function parameters and related calculation conditions into an in file for executing a Lammps operation command, introducing a linear table in Lammps for a high-temperature mutual exclusion item, then minimizing energy of an initial structure, setting a periodic boundary condition in an XYZ direction of a cubic box under an NVT (noise, vibration and harshness) ensemble, heating the initial structure to 6000k with the time step of 2fs, operating 100ps at 6000k at constant temperature to ensure that the structure is fully relaxed, cooling to 300k at the speed of 2.5k/ps, relaxing 50ps, operating 50ps under an NVE ensemble, collecting balanced structure data for data analysis, and finally using a computer XRD command and setting a scanning angle of 10-70 degrees to perform XRD calculation.
(3) Comparing XRD with experimental test, the main peak of glass structure is consistent with that of experiment, so that the structure generated by simulation is reliable, and further structural analysis can be carried out to judge the structural difference between inactive glass and active glass.
(4) The method is characterized in that a structural data file in an xyz format is opened through a visual software VMD, and the structural data file in the xyz format is imported into ISAACS software to perform short-range and medium-range structural analysis such as radial distribution function, key length, key angle distribution, ring distribution statistics and the like, and is used as a partial reference basis of an experiment.
Example 4
The experiment of the embodiment uses a simulation method of a bioactive glass structure and XRD calculation based on molecular dynamics, and mainly comprises the following steps (as shown in figure 1):
(1) firstly, a component of 70% SiO is determined2Bioactive glass with 30% CaO (mol%), designed to simulate 2798 atoms, according to an experimental density of 2.58g/cm3Calculating to obtain the side length of the cubic box simulating the contained atoms
Generating a structure model data file by using a Python script according to the format requirement of Lammps on an input structure data file;
(2) writing the determined Morse potential function parameters and related calculation conditions into an in file for executing a Lammps operation command, introducing a linear table in Lammps for a high-temperature mutual exclusion item, then minimizing energy of an initial structure, setting a periodic boundary condition in an XYZ direction of a cubic box under an NVT (noise, vibration and harshness) ensemble, heating the initial structure to 6000k with the time step of 2fs, operating 100ps at 6000k at constant temperature to ensure that the structure is fully relaxed, cooling to 300k at the rate of 1k/ps, performing 50ps relaxation, operating 50ps under an NVE ensemble, collecting balanced structure data for data analysis, and finally using a computer XRD command and setting a scanning angle of 10-70 degrees to perform XRD (X-ray diffraction) calculation.
(3) Comparing XRD with experimental test, neglecting error brought by real experimental environment, the main peak of glass structure is basically consistent with experimental result, so that the glass structure generated by simulation is reliable, and further structure analysis can be carried out.
(4) The structural data file in the xyz format is opened through the visual software VMD, and the structural analysis in the short-range and medium-range ranges such as radial distribution function, key length, key angle distribution, ring distribution statistics and the like can be carried out by importing the file in the xyz format into the ISAACS software, so that the biological activity mechanism of the binary system BG is further deeply explained, and the experiment is guided to carry out component improvement.
The above examples are only preferred embodiments of the present invention, which are intended to be illustrative and not limiting, and those skilled in the art should understand that they can make various changes, substitutions and alterations without departing from the spirit and scope of the invention.
Claims (10)
1. A simulation method of a bioactive glass structure based on molecular dynamics and XRD calculation is characterized by comprising the following steps:
(1) selecting bioactive glass to be tested, testing the density, defining the total number of atoms of the bioactive glass, obtaining the side length of a simulated cubic box according to the density and the total number of atoms, and generating a data file containing the initial coordinates of each atom of the bioactive glass to be tested by using a Python script, namely the data file of the initial structure of the bioactive glass to be tested;
(2) importing the data file and the potential function of the initial structure of the bioactive glass to be detected in the step (1) into an in file executing a Lammps software operation command, minimizing energy of the initial structure of the bioactive glass to be detected in the Lammps software, heating the initial structure of the bioactive glass to be detected in the Lammps software for simulated heating treatment, then cooling to normal temperature, collecting data of a balance structure after simulated heating and cooling, and performing XRD calculation to obtain an XRD (X-ray diffraction) diagram;
(3) and (3) inputting the balance structure data in the step (2) into visual software VMD to obtain a network structure diagram and an atom structure diagram of the bioactive glass to be detected, and performing structural analysis to complete the simulation of the bioactive glass structure and XRD calculation.
2. The molecular dynamics-based bioactive glass structure and XRD calculation simulation method according to claim 1, wherein the bioactive glass initial structure of step (1) is built in a simulation cubic box, each atomic initial coordinate is located in the simulation cubic box, the density of the bioactive glass is obtained according to experimental tests, Python script is compiled according to the requirements of box side length and Lammps on input model format, the initial amorphous structure of the bioactive glass is built, and a model input data file recognizable by Lammps is generated.
3. The molecular dynamics-based bioactive glass structure and XRD calculation simulation method according to claim 1 wherein the in file for executing the Lammps software operation command in step (2) further comprises information of boundary conditions, simulation ensemble, temperature control method, cooling rate, summation method and XRD calculation parameters.
4. The molecular dynamics-based bioactive glass structure and XRD calculation simulation method according to claim 3, wherein the boundary conditions are periodic boundary conditions, the simulation ensemble selects NVT regular ensemble and the summation method selects EWald summation method, time step is set as 2fs, and the temperature control method adopts Nose-Hoover hot bath method to regulate and control temperature of NVT regular ensemble.
5. The molecular dynamics-based bioactive glass structure and XRD calculation simulation method as claimed in claim 1, wherein the temperature of the simulated heating treatment in step (2) is 5000-.
6. The molecular dynamics-based bioactive glass structure and XRD calculation simulation method of claim 5 wherein the simulated heat treatment temperature is 6000k and the cooling rate is 5 k/ps.
7. The molecular dynamics-based bioactive glass structure and XRD calculation simulation method according to claim 1, wherein the potential function in step (2) is composed of coulomb potential describing long-range interaction force, Morse potential function describing short-range interaction force on silica-based glass, and mutual exclusion term for preventing atomic fusion at high temperature.
8. The molecular dynamics-based bioactive glass structure and XRD calculation simulation method of claim 1, wherein the potential function of step (2) is expressed as
Wherein, UijIs a distance rijThe total potential energy of all atoms i and j; i and j represent any two atoms in the system; z is a radical ofiAnd zjRepresents an effective charge; e represents a elementary charge; r isijRepresents the distance between two atoms i and j; dijIs the bond dissociation energy of atoms i and j; a isijIs a function of the slope of the potential energy well; r is0Is the bond balance distance; cijIs the elastic constant.
9. The method for simulating a bioactive glass structure and XRD calculation based on molecular dynamics as claimed in claim 1, wherein during the XRD calculation in step (2), 2Theta range is set, and after collecting the equilibrium structure data, computer XRD command is run to complete XRD calculation.
10. A simulation method of bioactive glass structure and XRD calculation based on molecular dynamics according to any one of claims 1-9, wherein in step (3), the xyz-format file of equilibrium structure data is inputted into the visualization software VMD to observe the structure; and the relation between the structure and the performance is judged by a radial distribution function and a short-range and medium-range structure analysis method.
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