CN-121999890-A - Molecular dynamics modeling method and system for porous medium

CN121999890ACN 121999890 ACN121999890 ACN 121999890ACN-121999890-A

Abstract

The invention discloses a molecular dynamics modeling method and a molecular dynamics modeling system for a porous medium, which relate to the technical field of molecular dynamics modeling and comprise the following steps of identifying a pore voxel region and a non-pore voxel region based on a three-dimensional matrix, conducting boundary division on a plurality of non-pore voxel regions to obtain a boundary layer anchor point pool and a non-boundary layer anchor point pool, dividing the boundary layer anchor point pool and the non-boundary layer anchor point pool into a plurality of grid units, filling anchor points in the grid units through molecules to be filled based on target filling quantity and target mask values, conducting random rotation on the current molecules to be filled, giving up the current placement if the distance between the current molecules to be filled and the placed atoms is smaller than a corresponding minimum distance threshold value, counting spatial absolute coordinates of all atoms after all the molecules are filled, and outputting a coordinate file. The invention realizes the accurate and non-overlapping placement of molecules in the complex pore structure, and can realize the establishment of a micro molecular dynamics model of the complex random pore of the porous medium.

Inventors

CHEN WENBIN
SONG HONGJIE
LIU FENGBIN
DOU ZHAOLIANG

Assignees

北方工业大学

Dates

Publication Date: 20260508
Application Date: 20260129

Claims (9)

1. A method for modeling molecular dynamics of a porous medium, comprising the steps of: Converting the pore structure three-dimensional voxel data into a three-dimensional matrix corresponding to the three-dimensional pore structure space, wherein the value in the three-dimensional matrix is assigned to be a mask value of 0 or 1, wherein 1 represents a pore voxel region, and 0 represents a non-pore voxel region; Setting the size of a simulation box for modeling the molecular dynamics of a target porous medium, setting the types of molecules to be filled in the simulation box, wherein the types of the molecules to be filled comprise the filling number of the molecules, the relative coordinates of atoms in the molecules and corresponding target mask values; Dividing boundary division is carried out on a plurality of non-pore voxel areas based on a three-dimensional matrix to obtain a boundary layer anchor point pool and a non-boundary layer anchor point pool, dividing the boundary layer anchor point pool and the non-boundary layer anchor point pool into a plurality of grid units, distributing target filling quantity of the grid units based on molecule filling quantity, filling anchor points in the grid units through molecules to be filled based on the target filling quantity and a target mask value, carrying out random rotation on the current molecules to be filled in the filling process, and giving up the current placement if the distance between the current molecules to be filled and the placed atoms is smaller than a corresponding minimum distance threshold value; And after all the molecules are filled, counting the space absolute coordinates of all the atoms, outputting a coordinate file, and completing the molecular dynamics modeling of the target porous medium.
2. A method of modeling molecular dynamics of a porous media according to claim 1, wherein the boundary layer anchor pool is a plurality of non-pore voxel regions immediately adjacent to the pore voxel regions, and the anchor pool for the plurality of pore voxel regions is not partitioned.
3. The method for modeling molecular dynamics of a porous medium according to claim 1, wherein the filling of anchor points in a grid cell by molecules to be filled is based on a target filling quantity and a target mask value, specifically comprising the steps of: randomly traversing a plurality of grid cells; for the current grid unit, randomly selecting anchor points in the current grid unit to fill; And after filling all the grid cells, acquiring the number of the placed molecules, and if the number of the placed molecules is smaller than the set number of the molecules, performing the complementary placement of the remaining molecules.
4. A method of molecular dynamics modeling a porous media according to claim 1, wherein said converting the three-dimensional voxel data of the pore structure into a three-dimensional matrix corresponding to the three-dimensional pore structure space comprises the steps of: Reading uint8 data matched with the size of the simulated box in the pore structure three-dimensional voxel data through a fread function; The uint8 data is stored as one-dimensional vectors, and the one-dimensional vectors are remodeled into a three-dimensional matrix through reshape functions.
5. The method for modeling molecular dynamics of a porous medium according to claim 1, wherein after the filling of all the molecules is completed, the spatial absolute coordinates of all the atoms are counted, and the method specifically comprises the following steps: Respectively obtaining extremum for the relative coordinates of atoms in each molecule, and averaging the extremum corresponding to each molecule to obtain the geometric center coordinate of each molecule; Subtracting the corresponding geometric center coordinates from the relative coordinates of all atoms in each molecule to obtain coordinate differences corresponding to the atoms in each molecule; And adding the geometrical center coordinates of the newly placed molecules and the coordinate difference values corresponding to the atoms to obtain the spatial absolute coordinates of all atoms in the newly placed molecules.
6. The method for modeling molecular dynamics of a porous medium according to claim 1, wherein the method for obtaining three-dimensional voxel data of a pore structure of a target porous medium based on a four-parameter growth method specifically comprises the following steps: establishing an initial model of the target porous medium based on a four-parameter growth method, and performing pore modification on the initial model to obtain a pore structure numerical model; The method for establishing the initial model of the target porous medium based on the four-parameter growth method comprises the following steps: Defining a growth domain, setting porosity, the number of solid-phase particles and the generation probability of the solid-phase particles, completing random layout of the solid-phase particles in the growth domain according to the number of the solid-phase particles and the generation probability of the solid-phase particles, traversing grids in the growth domain, and obtaining three-dimensional space coordinates of all the solid-phase particles; Setting anisotropic growth parameters of solid-phase particles, wherein the anisotropic growth parameters comprise main axis direction growth probability, surface diagonal direction growth probability and body diagonal direction growth probability; Randomly generating 0-1 random numbers uniformly distributed in adjacent grid cells in all directions around a reference node by taking three-dimensional space coordinates of solid-phase particles as the reference node, changing the particle states of the adjacent grid cells in the current direction into pore particles if the random numbers in the current direction are smaller than the growth probability set in the direction, and storing newly generated particle coordinates; All solid phase particles were traversed to obtain the initial model.
7. The method for modeling molecular dynamics of a porous medium according to claim 6, wherein the pore modification is performed on the initial model to obtain a numerical model of pore structure, and the method specifically comprises the following steps: the method comprises the steps of carrying out space connectivity analysis on a plurality of pores of an initial model to obtain an analysis result, detecting the position and the number of openings of each pore on the surface of a material, and obtaining the volume of each pore; Setting a minimum pore volume threshold, and if the volume of the current pore is smaller than the minimum pore volume threshold, removing the pore of the opening at the edge of the material; Dividing a plurality of pores into a plurality of open communication pores, a single open pore and a blind pore according to the analysis result and the surface opening number, and removing the blind pore to obtain a pore structure numerical model.
8. The method for modeling molecular dynamics of a porous medium according to claim 6, wherein the establishing an initial model of a target porous medium based on a four-parameter growth method further comprises: Setting edge suppression parameters, including edge suppression distance and edge suppression factors, and restraining the positions of the holes through the edge suppression parameters.
9. A molecular dynamics modeling system for a porous medium, comprising: The acquisition module is used for acquiring the pore structure three-dimensional voxel data of the target porous medium based on a four-parameter growth method, converting the pore structure three-dimensional voxel data into a three-dimensional matrix corresponding to the three-dimensional pore structure space, wherein the value in the three-dimensional matrix is assigned to be a mask value of 0 or 1, wherein 1 represents a pore voxel region, and 0 represents a non-pore voxel region; The setting module is used for setting the size of a simulation box for modeling the molecular dynamics of the target porous medium; setting the types of molecules to be filled in a simulation box, wherein the types of the molecules to be filled comprise the filling quantity of the molecules, the relative coordinates of atoms in the molecules and corresponding target mask values, setting the minimum distance between the atoms and an anchor point of a single effective space position for placing the molecules, and acquiring a minimum distance threshold value between the molecules based on the minimum distance between the atoms; The filling module is used for identifying a pore voxel region and a non-pore voxel region based on a three-dimensional matrix, carrying out boundary division on a plurality of non-pore voxel regions to obtain a boundary layer anchor point pool and a non-boundary layer anchor point pool, dividing the boundary layer anchor point pool and the non-boundary layer anchor point pool into a plurality of grid units, distributing the target filling quantity of the grid units based on the molecular filling quantity, and filling anchor points in the grid units through molecules to be filled based on the target filling quantity and a target mask value; and the output module is used for counting the space absolute coordinates of all atoms after filling all molecules, outputting a coordinate file and completing the molecular dynamics modeling of the target porous medium.

Description

Molecular dynamics modeling method and system for porous medium Technical Field The invention relates to the technical field of molecular dynamics modeling, in particular to a molecular dynamics modeling method and a molecular dynamics modeling system for a porous medium. Background The porous medium is a substance composed of a skeleton composed of a solid substance and a plurality of minute voids partitioned by the skeleton into a plurality of densely packed groups. The micro voids may be interconnected, or may be partially interconnected or partially non-interconnected. The porous medium has extremely wide application, realizes the functions of substance separation, adsorption, fluid transportation and the like by virtue of the complex pore structure, and is applied to a plurality of key fields of energy sources, environment, biology, chemical industry and the like. By establishing quantitative association between complex micro pore structures and macroscopic physical phenomena, an important foundation is provided for predicting the distribution condition and flow behavior of fluid in complex pores such as rock, soil, biological tissues and the like, so as to solve a series of serious engineering, science and environmental problems. The porous medium modeling can analyze the influence of a pore structure on material transmission and energy conversion from a microscopic scale, reveal a microscopic mechanism which cannot be involved in a macroscopic experiment, and define macroscopic performance control factors to guide the optimization of practical application. By modeling the porous medium, setting boundary conditions to simulate extreme scenes, predicting potential risks and providing a coping scheme basis, potential safety hazards in practical application are avoided. Along with development of a pore structure model and improvement of calculation efficiency, an internal relation and a quantitative relation between a microscopic mechanism and macroscopic features are established, and further predictive analysis of macroscopic seepage and substance transfer behaviors based on porous medium material features is an important research direction in the future. Molecular dynamics technology has been widely applied to research on microfluidic flow behavior and law, and molecular dynamics simulation can track and analyze atomic motion behavior at nano-scale and micro-scale, so that the method is an effective means for researching fluid flow behavior inside micropores of porous media. The current microscopic molecular dynamics modeling method establishes a pore structure with regular shape through molecular arrangement, extracts microscopic molecular properties to serve as research factors, but the established microscopic model is mainly a regular model, and lacks an effective molecular filling method for an irregular model, so that a complex shape can not be broken through all the time, and the molecular dynamics research on a porous medium stays at a simplified model level for a long time, so that a molecular model which accords with the microscopic pore structure of an actual porous material can not be established. Disclosure of Invention Based on the defects existing in the prior art, the invention provides a molecular dynamics modeling method and a molecular dynamics modeling system for a porous medium, which solve the problems that the molecular dynamics research of the existing porous medium stays on the simplified model level for a long time, an effective molecular filling method is lacking for a complex model, and the microscopic behaviors of complex pore molecules of a real material are difficult to reflect. The invention adopts the following technical scheme: In a first aspect, the present invention provides a method for modeling molecular dynamics of a porous medium, comprising the steps of: Converting the pore structure three-dimensional voxel data into a three-dimensional matrix corresponding to the three-dimensional pore structure space, wherein the value in the three-dimensional matrix is assigned to be a mask value of 0 or 1, wherein 1 represents a pore voxel region, and 0 represents a non-pore voxel region; Setting the size of a simulation box for modeling the molecular dynamics of a target porous medium, setting the types of molecules to be filled in the simulation box, wherein the types of the molecules to be filled comprise the filling number of the molecules, the relative coordinates of atoms in the molecules and corresponding target mask values; Dividing boundary division is carried out on a plurality of non-pore voxel areas based on a three-dimensional matrix to obtain a boundary layer anchor point pool and a non-boundary layer anchor point pool, dividing the boundary layer anchor point pool and the non-boundary layer anchor point pool into a plurality of grid units, distributing target filling quantity of the grid units based on molecule filling quantity, filling anchor points in the gri