Molecular system simulation method and system, computer equipment and storage medium

Abstract

The invention relates to the technical field of molecular dynamics, in particular to a molecular system simulation method and system, computer equipment and a storage medium. The molecular system simulation method at least comprises the steps that virtual site information of virtual sites in a molecular system is calculated in parallel based on all calculation units, and the virtual site information and charge information of the virtual sites are updated to a virtual site information table in a storage unit; calculating the atomic information of each atom in the molecular system in parallel based on each calculation unit; updating the virtual site information of each virtual site based on the obtained atomic information to obtain new virtual site information; distributing the obtained new virtual site information to each atom to obtain new atom information of each atom; and carrying out constraint processing on the boundary of the dynamic system where the molecular system is located based on the new atomic information, and outputting integrated data of the dynamic system. The invention provides a molecular system simulation method with higher efficiency for a large-scale system.

Description

Technical Field

[0001] The present application relates to the field of molecular dynamics technology, and in particular, to a molecular system simulation method, system, computer device and storage medium. Background Art

[0002] The TIP4P model is a four-point rigid water model widely used in molecular dynamics simulations. It consists of one oxygen atom, two hydrogen atoms and a virtual site. The model can accurately simulate a variety of physical and chemical properties of water by accurately describing the charge distribution and geometric structure of water molecules. As research needs grow, the scale of water system simulation continues to expand, and traditional methods are computationally inefficient when dealing with large-scale systems. Summary of the invention

[0003] The embodiments of the present application provide a molecular system simulation method, system, computer device and storage medium.

[0004] In a first aspect of an embodiment of the present application, a molecular system simulation method is provided, which is applied to a distributed three-dimensional grid system, wherein each subspace in the three-dimensional grid system includes at least one computing unit and one storage unit, and the method includes at least:

[0005] For each molecular system, virtual site information of virtual sites in the molecular system is calculated in parallel based on each of the calculation units, and the virtual site information and charge information of the virtual site are updated to the virtual site information table in the storage unit; wherein the virtual site refers to any virtual point in the molecular system used to characterize the molecular system;

[0006] For each atom in each molecular system, atomic information of each atom in the molecular system is calculated in parallel based on each of the calculation units; wherein the atomic information includes at least one of short-range forces and long-range electrostatic forces between atoms, and atomic positions and atomic velocities of each atom;

[0007] Based on the obtained atomic information, the virtual site information of each virtual site is updated to obtain new virtual site information;

[0008] Assigning the obtained new virtual site information to each atom to obtain new atomic information of each atom;

[0009] Based on the new atomic information, the boundary of the dynamic system where the molecular system is located is constrained, and the integrated data of the dynamic system is output.

[0010] In an optional embodiment of the present application, the calculating virtual site information of the virtual sites in the molecular system based on the parallel calculation of the calculation units includes:

[0011] A plurality of data structures are configured in each of the storage units, and molecular computing model parameters are configured in a global control unit in the computing unit; wherein the plurality of data structures at least include: a molecular information list, an atom information list, and the virtual site information list;

[0012] For each of the molecular systems, each of the calculation units calculates the molecular centroid position and the molecular target calculation unit of each of the molecular systems based on the molecular calculation model parameters, and stores the molecular centroid position and the molecular target calculation unit in the molecular information list corresponding to the storage unit, and stores the atomic information of each atom in the molecular system in the molecular information list corresponding to the storage unit;

[0013] For each of the molecular systems, each of the calculation units calculates the virtual site information of the virtual site based on the molecular calculation model parameters, and stores the virtual site information in the virtual site information list.

[0014] In an optional embodiment of the present application, if the molecular system is a water molecule, the molecular centroid position is calculated according to the following formula:

[0015] r_com=(r_O+r_H1+r_H2) / 3

[0016] Among them, r_com represents the position of the molecular centroid, r_O represents the calculation of the three-dimensional coordinates of the O atom, r_H1 represents the calculation of the three-dimensional coordinates of the first H atom, and r_H2 represents the calculation of the three-dimensional coordinates of the second H atom;

[0017] The molecular target calculation unit is calculated according to the following formula:

[0018] CU:(x,y,z)=floor(r_com / box_size*[X,Y,Z])

[0019] CU: (x, y, z) represents the coordinates of the molecular target calculation unit, r_com represents the position of the molecular centroid, and box_size*[X, Y, Z] represents the total length of the three directions of the simulation box.

[0020] In an optional embodiment of the present application, if the molecular system is a water molecule, the virtual site information is calculated according to the following formula:

[0021] a=b=0.5*(r_OM(cos(θ_HOM)*r_OH))

[0022] x_M=x_O+a*(x_H1–x_O)+b*(x_H2–x_O)

[0023] y_M=y_O+a*(y_H1–y_O)+b*(y_H2–y_O)

[0024] z_M=z_O+a*(z_H1–z_O)+b*(z_H2–z_O)

[0025] Among them, a and b represent the weight coefficients of the virtual site M, which are determined according to the angles between O, H, and M atoms; x_M, y_M, and z_M represent the three-dimensional coordinates of the virtual site M, respectively; x_O, y_O, and z_O represent the three-dimensional coordinates of the O atom, respectively; x_H1, y_H1, and z_H1 represent the three-dimensional coordinates of the first H atom, respectively; x_H2, y_H2, and z_H2 represent the three-dimensional coordinates of the second H atom, respectively; r_OM and r_OH represent the position vectors of OM and OH, respectively; and θ_HOM represents the angle between OM and OH.

[0026] In an optional embodiment of the present application, the calculating atomic information of each atom in the molecular system based on each of the calculating units in parallel includes:

[0027] The short-range force in the atomic information is calculated according to the following formula:

[0028] U_LJ(r)=4ε[(σ / r)^12-(σ / r)^6]

[0029] F_LJ(r)=24ε[(σ / r)^6*1 / r^2–2*(σ / r)^12*1 / r^2]*x

[0030] Among them, U_LJ(r) represents the Lanner-Jones potential between atoms, F_LJ(r) represents the Lanner-Jones force between atoms, ε and σ represent the Lanner-Jones interaction parameters, r represents the set cutoff radius, and x represents the distance between atoms;

[0031] The long range electrostatic forces are calculated according to the kgse method.

[0032] In an optional embodiment of the present application, before updating the virtual site information of each virtual site based on the obtained atomic information to obtain new virtual site information, the method further includes:

[0033] For each of the molecular systems, the force acting on the virtual site in the molecular system is distributed to each atom to obtain the virtual force acting on each atom.

[0034] In an optional embodiment of the present application, if the molecular system is a water molecule, then for each of the molecular systems, the force exerted on the virtual site in the molecular system is distributed to each atom to obtain the virtual force exerted on each atom, which is calculated according to the following formula:

[0035] F_O=F_O_direct+F_M*(1-ab)

[0036] F_H1=F_H1_direct+F_M*a

[0037] F_H2=F_H2_direct+F_M*b

[0038] Among them, F_O, F_H1, F_H2 are the virtual forces acting on the O atom, the first H atom and the second H atom respectively, F_O_direct, F_H1_direct, F_H2_direct represent the total forces of the long-range electrostatic force, short-range force and the allocated virtual force acting on the O atom, the first H atom and the second H atom respectively, F_M represents the virtual force acting on the virtual site M, a and b represent the weight coefficients of the virtual site M, which are determined according to the angles between the O, H and M atoms.

[0039] In an optional embodiment of the present application, allocating the obtained new virtual site information to each atom to obtain new atomic information of each atom includes:

[0040] After allocating the obtained new virtual site information to each atom, each of the calculation units calculates the position information and atomic velocity information of each atom in parallel.

[0041] In an optional embodiment of the present application, each of the calculation units calculates the position information and atomic velocity information of each atom in parallel based on the following formula:

[0042] r(t+Δt)=r(t)+v(t)Δt+0.5a(t)Δt^2

[0043] v(t+Δt / 2)=v(t)+0.5a(t)Δt

[0044] a(t+Δt)=F(t+Δt) / m

[0045] v(t+Δt)=v(t+Δt / 2)+0.5a(t+Δt)Δt

[0046] Among them, r represents the set cutoff radius, v represents the atomic velocity, a represents the atomic acceleration, F represents the sum of the short-range force and the long-range electrostatic force acting on the atom, m represents the atomic mass, t represents the current moment, and Δt represents the time step.

[0047] In an optional embodiment of the present application, after allocating the obtained new virtual site information to each atom to obtain new atomic information of each atom, the method further includes:

[0048] The mshake / mrattle algorithm was applied to maintain the rigid structure of each of the described molecular systems.

[0049] In an optional embodiment of the present application, the above molecular system simulation method further includes:

[0050] The virtual site information of the virtual site is recalculated according to the molecular information and atomic information of each molecule after maintaining the rigid structure of each molecular system.

[0051] In an optional embodiment of the present application, the constraining the boundary of the dynamic system where the molecular system is located based on the new atomic information and outputting the integrated data of the dynamic system includes:

[0052] Determine whether each of the molecular systems and each atom in the molecular system is beyond a preset range, and if the molecular system or each atom in the molecular system is beyond the preset range, redetermine the position of the target computing unit;

[0053] The molecular system or atom beyond the preset range is relocated, and the molecular information list, the atom information list and the virtual site information list are updated based on the molecular information and atom information after the relocation.

[0054] In an optional embodiment of the present application, for atoms beyond the boundary of the simulation box, the position information of the migrated atoms is calculated according to the following formula:

[0055] r_new=r_old-box_size*fix(r_old / box_size)

[0056] Among them, r_new represents the atomic coordinates after migration, r_old represents the atomic coordinates before migration, box_size represents the size of the simulation box, and fix represents the truncation operation.

[0057] In an optional embodiment of the present application, the above molecular system simulation method further includes:

[0058] The global control unit calculates global information of the dynamics system where all molecular systems are located and distributes it to each of the calculation units;

[0059] Each calculation unit repeatedly iteratively calculates the molecular information and atomic information of each molecular system until an iteration condition is met, and then outputs the integrated data of the dynamic system.

[0060] A second aspect of an embodiment of the present application provides a molecular system simulation system, which is applied to a distributed three-dimensional grid system, wherein each subspace in the three-dimensional grid system includes at least one computing unit and one storage unit, and the system includes at least:

[0061] A first calculation module, for calculating, for each molecular system, virtual site information of virtual sites in the molecular system in parallel based on the calculation units, and updating the virtual site information and the charge information of the virtual site to the virtual site information table in the storage unit; wherein the virtual site refers to any virtual point in the molecular system used to characterize the molecular system;

[0062] A second calculation module is used to calculate, for each atom in each molecular system, atomic information of each atom in the molecular system in parallel based on each of the calculation units; wherein the atomic information includes at least one of short-range forces and long-range electrostatic forces between atoms, and atomic positions and atomic velocities of each atom;

[0063] An updating module, used for updating the virtual site information of each virtual site based on the obtained atomic information to obtain new virtual site information;

[0064] An allocating module, used for allocating the obtained new virtual site information to each atom to obtain new atomic information of each atom;

[0065] The output module is used to constrain the boundary of the dynamic system where the molecular system is located based on the new atomic information, and output the integrated data of the dynamic system.

[0066] According to a third aspect of an embodiment of the present application, a computer device is provided, comprising: a memory and a processor, wherein the memory stores a computer program, and the processor implements the steps of any of the above methods when executing the computer program.

[0067] According to a fourth aspect of the embodiments of the present application, a computer-readable storage medium is provided, on which a computer program is stored. When the computer program is executed by a processor, the steps of any of the above methods are implemented.

[0068] On the one hand, the molecular system simulation method provided in the embodiment of the present application is based on the hardware of a distributed three-dimensional grid system. The three-dimensional grid system can divide the simulation system into multiple subspaces, each subspace includes at least one computing unit (CU) and one storage unit (SU), which can independently be responsible for the corresponding computing functions and storage functions. For each atom in each molecular system, the atomic information of each atom in the molecular system is calculated in parallel based on each computing unit, so that each computing unit and storage unit can operate independently, thereby realizing parallel processing of each unit, and realizing multi-level parallel computing from a single atom to a single molecular system to a large-scale dynamic system, maximizing hardware utilization, improving overall computing efficiency, and greatly improving overall computing efficiency; highly adaptable distributed computing architecture: can flexibly handle water systems of different scales.

[0069] On the second aspect, the embodiment of the present application calculates the position of the virtual site M based on the set global calculation unit, thereby ensuring the accuracy of the geometric structure of the molecular system calculation model, improving the calculation accuracy and the accuracy and reliability of molecular simulation.

[0070] In a third aspect, the molecular system simulation method provided in the embodiment of the present application updates the virtual site information of each virtual site based on the obtained atomic information, and after obtaining the new virtual site information, distributes the obtained new virtual site information to each atom to obtain new atomic information of each atom; and utilizes an efficient force redistribution mechanism to accurately redistribute the force on the virtual site M to the actual atom, thereby further improving the accuracy of the final simulation result;

[0071] In the fourth aspect, the embodiments of the present application calculate the atomic information of each atom in each molecular system based on each of the computing units in parallel; wherein the atomic information includes at least the short-range force between each atom, the long-range electrostatic force, and at least one of the atomic position and atomic velocity of each atom; through the constraints of the above-mentioned improved data structure and the precise geometric structure of the computational model, the stability and reliability of long-term simulation are enhanced. In the fourth aspect, the accuracy of the molecular computational model depends largely on the accurate positioning of the virtual site M and the distribution of the force. The molecular system simulation method provided in the embodiments of the present application greatly improves the overall accuracy of the simulation through precise model geometry calculation and virtual site force redistribution algorithm. BRIEF DESCRIPTION OF THE DRAWINGS

[0072] The drawings described herein are used to provide a further understanding of the present application and constitute a part of the present application. The illustrative embodiments of the present application and their descriptions are used to explain the present application and do not constitute an improper limitation on the present application. In the drawings:

[0073] Figure 1A flow chart of a molecular system simulation method provided in one embodiment of the present application;

[0074] Figure 2 A flow chart of a molecular system simulation method provided in one embodiment of the present application;

[0075] Figure 3 A flow chart of a molecular system simulation method provided in one embodiment of the present application;

[0076] Figure 4 A flow chart of a molecular system simulation method provided in one embodiment of the present application;

[0077] Figure 5 A schematic diagram of the structure of a molecular system simulation device provided in one embodiment of the present application;

[0078] Figure 6 A schematic diagram of the computer device structure provided for one embodiment of the present application. DETAILED DESCRIPTION

[0079] In the process of realizing the present application, the inventors found that the traditional methods are computationally inefficient when processing large-scale systems.

[0080] In response to the above problems, the embodiments of the present application provide a molecular system simulation method, system, computer device and storage medium to improve the simulation efficiency of large-scale systems.

[0081] The solutions in the embodiments of the present application can be implemented using various computer languages, for example, the object-oriented programming language Java and the interpreted scripting language JavaScript.

[0082] In order to make the technical solutions and advantages in the embodiments of the present application more clearly understood, the exemplary embodiments of the present application are further described in detail below in conjunction with the accompanying drawings. Obviously, the described embodiments are only part of the embodiments of the present application, rather than an exhaustive list of all the embodiments. It should be noted that the embodiments in the present application and the features in the embodiments can be combined with each other without conflict.

[0083] The following is a brief description of the application environment of the molecular system simulation method provided in the embodiment of the present application:

[0084] The molecular system simulation method provided by the embodiments of this application can be applied to any electronic device such as a server, computer, laptop, mobile terminal, wearable device, etc., which will not be enumerated here and can be flexibly configured according to the actual situation. The molecular system simulation method provided by the embodiments of this application is applied to a distributed three-dimensional grid system of X*Y*Z. Each subspace in the three-dimensional grid system, that is, each grid point, at least includes a computing unit (CU) and a storage unit (SU). The entire system is connected by a high-speed interconnect network, supporting neighbor communication and global data broadcasting. The total number of computing units N_total = X*Y*Z. Before implementing the molecular system simulation method provided by the embodiments of this application, system initialization of the distributed three-dimensional grid system can be performed first, including but not limited to: hardware configuration, data structure initialization, and global parameter setting, where:

[0085] 1) Hardware configuration:

[0086] Set up a three-dimensional grid system of X*Y*Z: Each computing unit CU(x,y,z), where 0 ≤ x < X, 0 ≤ y < Y, 0 ≤ z < Z. Each computing unit CU is directly connected to adjacent computing units CU. The edge computing unit CU is connected to the opposite edge computing unit CU to form a periodic boundary condition;

[0087] 2) Data structure initialization (taking water molecules as an example):

[0088] In each storage unit SU(x,y,z), define the following data structures:

[0089] Molecular information list water_list: used to store water molecule information {O_id, H1_id, H2_id, M_id}; where {O_id, H1_id, H2_id, M_id} respectively represent the id numbers of O, H, and virtual atom M.

[0090] Atom information list atom_list: used to store actual atom information {id, type, position[3], velocity[3], force[3], mass, charge}; where Position represents the atomic coordinate, velocity represents the atomic velocity, mass represents the atomic mass, and charge represents the atomic charge.

[0091] Virtual site M information list m_point_list: used to store virtual site M information {id, position[3], force[3], charge}; where id represents the id number of virtual site M, Position represents the atomic coordinate of virtual site M, force represents the sum of the long-range electrostatic force and short-range force exerted on the atom, and charge represents the charge of virtual site M.

[0092] 3) Global parameter setting: Set the molecular system simulation parameters in the global control unit GCU (usually select CU(0,0,0)), such as the TIP4P model parameters for calculating the water molecule system.

[0093] See also Figure 1 The following embodiments take the above electronic device as the execution subject, and apply the molecular system simulation method provided in the embodiment of the present application to the above electronic device to simulate the molecular system of water molecules (H2O, including two H atoms and one O atom) as an example for specific description. The molecular system simulation method provided in the embodiment of the present application includes the following steps 101-105:

[0094] Step 101: for each molecular system, based on each of the calculation units, calculating in parallel the virtual site information of the virtual site in the molecular system, and updating the virtual site information and the charge information of the virtual site to the virtual site information table in the storage unit;

[0095] Wherein, the virtual site M refers to any virtual point in the molecular system used to characterize the molecular system;

[0096] Step 102: for each atom in each molecular system, calculating atomic information of each atom in the molecular system in parallel based on each of the calculation units;

[0097] The atomic information includes at least one of the short-range force and long-range electrostatic force between atoms, and the atomic position and atomic velocity of each atom;

[0098] Step 103: updating the virtual site information of each virtual site based on the obtained atomic information to obtain new virtual site information;

[0099] Step 104, assigning the obtained new virtual site information to each atom to obtain new atomic information of each atom;

[0100] Step 105: Constrain the boundaries of the dynamic system in which the molecular system is located based on the new atomic information, and output integrated data of the dynamic system.

[0101] The dynamic system may include but is not limited to multiple molecular systems, for example, multiple water molecules.

[0102] On the one hand, the molecular system simulation method provided in the embodiment of the present application is based on the hardware of a distributed three-dimensional grid system. The three-dimensional grid system can divide the simulation system into multiple subspaces, each subspace includes at least one computing unit (CU) and one storage unit (SU), which can independently be responsible for the corresponding computing functions and storage functions. For each atom in each molecular system, the atomic information of each atom in the molecular system is calculated in parallel based on each computing unit, so that each computing unit and storage unit can operate independently, thereby realizing parallel processing of each unit, and realizing multi-level parallel computing from a single atom to a single molecular system to a large-scale dynamic system, maximizing hardware utilization, improving overall computing efficiency, and greatly improving overall computing efficiency; highly adaptable distributed computing architecture: can flexibly handle water systems of different scales.

[0103] On the second aspect, the embodiment of the present application calculates the position of the virtual site M based on the set global calculation unit, thereby ensuring the accuracy of the geometric structure of the molecular system calculation model, improving the calculation accuracy and the accuracy and reliability of molecular simulation.

[0104] In a third aspect, the molecular system simulation method provided in the embodiment of the present application updates the virtual site information of each virtual site based on the obtained atomic information, and after obtaining the new virtual site information, distributes the obtained new virtual site information to each atom to obtain new atomic information of each atom; and utilizes an efficient force redistribution mechanism to accurately redistribute the force on the virtual site M to the actual atom, thereby further improving the accuracy of the final simulation result;

[0105] In the fourth aspect, the embodiments of the present application calculate the atomic information of each atom in each molecular system based on each of the computing units in parallel; wherein the atomic information includes at least the short-range force between each atom, the long-range electrostatic force, and at least one of the atomic position and atomic velocity of each atom; through the constraints of the above-mentioned improved data structure and the precise geometric structure of the computational model, the stability and reliability of long-term simulation are enhanced. In the fourth aspect, the accuracy of the molecular computational model depends largely on the accurate positioning of the virtual site M and the distribution of the force. The molecular system simulation method provided in the embodiments of the present application greatly improves the overall accuracy of the simulation through precise model geometry calculation and virtual site force redistribution algorithm.

[0106] See also Figure 2 In an optional embodiment of the present application, the above step 101, the virtual site information of the virtual sites in the molecular system is calculated in parallel based on each of the calculation units, includes the following steps 201-203:

[0107] Step 201, configuring a plurality of data structures in each of the storage units, and configuring molecular computing model parameters in a global control unit in the computing unit;

[0108] Wherein, the multiple data structures at least include: a molecular information list, an atom information list and the virtual site information list;

[0109] Step 202: for each of the molecular systems, each of the calculation units respectively calculates the molecular centroid position and the molecular target calculation unit of each of the molecular systems based on the molecular calculation model parameters, and stores the molecular centroid position and the molecular target calculation unit in the molecular information list in the corresponding storage unit, and stores the atomic information of each atom in the molecular system in the molecular information list in the corresponding storage unit;

[0110] Step 203: For each of the molecular systems, each of the calculation units calculates the virtual site information of the virtual site based on the molecular calculation model parameters, and stores the virtual site information in the virtual site information list.

[0111] When allocating molecular information and atomic information, the lists after the data structure 2) is initialized may be read, for example: the molecular information list water_list, the atomic information list atom_list and the virtual site M information list m_point_list.

[0112] In an optional embodiment of the present application, if the molecular system is a water molecule, the molecular centroid position is calculated according to the following formula:

[0113] r_com=(r_O+r_H1+r_H2) / 3

[0114] Among them, r_com represents the position of the molecular centroid, r_O represents the calculation of the three-dimensional coordinates of the O atom, r_H1 represents the calculation of the three-dimensional coordinates of the first H atom, and r_H2 represents the calculation of the three-dimensional coordinates of the second H atom;

[0115] The molecular target calculation unit is calculated according to the following formula:

[0116] CU:(x,y,z)=floor(r_com / box_size*[X,Y,Z])

[0117] CU: (x, y, z) represents the coordinates of the molecular target calculation unit, r_com represents the position of the molecular centroid, and box_size*[X, Y, Z] represents the total length of the three directions of the simulation box.

[0118] In an optional embodiment of the present application, taking the molecular computing model as TIP4P as an example, the geometric structure of the TIP4P model is calculated in parallel in all computing units CU (x, y, z):

[0119] If the molecular system is a water molecule, the virtual site information is calculated according to the following formula:

[0120] a=b=0.5*(r_OM(cos(θ_HOM)*r_OH))

[0121] x_M=x_O+a*(x_H1–x_O)+b*(x_H2–x_O)

[0122] y_M=y_O+a*(y_H1–y_O)+b*(y_H2–y_O)

[0123] z_M=z_O+a*(z_H1–z_O)+b*(z_H2–z_O)

[0124] Among them, a and b represent the weight coefficients of the virtual site M, which are determined according to the angles between O, H, and M atoms; x_M, y_M, and z_M represent the three-dimensional coordinates of the virtual site M, respectively; x_O, y_O, and z_O represent the three-dimensional coordinates of the O atom, respectively; x_H1, y_H1, and z_H1 represent the three-dimensional coordinates of the first H atom, respectively; x_H2, y_H2, and z_H2 represent the three-dimensional coordinates of the second H atom, respectively; r_OM and r_OH represent the position vectors of OM and OH, respectively; and θ_HOM represents the angle between OM and OH.

[0125] After obtaining the above virtual site information, update m_point_list: add the calculated M point position and charge information to the virtual site M information list m_point_list of the storage unit SU (x, y, z).

[0126] In an optional embodiment of the present application, the above step 102, the step of calculating the atomic information of each atom in the molecular system in parallel based on each of the calculation units, includes:

[0127] The short-range force in the atomic information is calculated according to the following formula:

[0128] U_LJ(r)=4ε[(σ / r)^12-(σ / r)^6]

[0129] F_LJ(r)=24ε[(σ / r)^6*1 / r^2–2*(σ / r)^12*1 / r^2]*x

[0130] Among them, U_LJ(r) represents the Lanner-Jones potential between atoms, F_LJ(r) represents the Lanner-Jones force between atoms, ε and σ represent the Lanner-Jones interaction parameters, r represents the set cutoff radius, and x represents the distance between atoms;

[0131] For example, the LJ interactions with atoms in the neighboring 26 CUs are calculated using neighbor communication in the same way in subsequent calculations and loops.

[0132] The long-range electrostatic force is calculated according to the kgse method:

[0133] Use the kgse method (Semantic Extension Knowledge Graph, a semantic extension knowledge graph method): calculate the electrostatic interaction in each computing unit CU (x, y, z), and the global control unit GCU coordinates the execution of the 3DFFT (three-dimensional fast Fourier transform) calculation part: collect the charge grid data of all computing units CU, perform 3DFFT, perform iFFT (fast Fourier transform of each computing unit), and distribute the results back to each computing unit CU.

[0134] In an optional embodiment of the present application, before the above step 103, in which the virtual site information of each virtual site is updated based on the obtained atomic information to obtain new virtual site information, the above analysis system simulation method further includes the following steps:

[0135] For each of the molecular systems, the force acting on the virtual site in the molecular system is distributed to each atom to obtain the virtual force acting on each atom.

[0136] In an optional embodiment of the present application, if the molecular system is a water molecule, then for each molecular system, the force exerted on the virtual site in the molecular system is distributed to each atom to obtain the virtual force exerted on each atom, which is calculated according to the following formula:

[0137] F_O=F_O_direct+F_M*(1-ab)

[0138] F_H1=F_H1_direct+F_M*a

[0139] F_H2=F_H2_direct+F_M*b

[0140] Among them, F_O, F_H1, F_H2 are the virtual forces acting on the O atom, the first H atom and the second H atom respectively, F_O_direct, F_H1_direct, F_H2_direct represent the total forces of the long-range electrostatic force, short-range force and the allocated virtual force acting on the O atom, the first H atom and the second H atom respectively, F_M represents the virtual force acting on the virtual site M, a and b represent the weight coefficients of the virtual site M, which are determined according to the angles between the O, H and M atoms.

[0141] In an optional embodiment of the present application, the above step 104, assigning the obtained new virtual site information to each atom to obtain new atomic information of each atom, includes the following steps:

[0142] After allocating the obtained new virtual site information to each atom, each of the calculation units calculates the position information and atomic velocity information of each atom in parallel.

[0143] For example, the VelocityVerlet algorithm may be used to update the positions and velocities of O and H atoms. In an optional embodiment of the present application, each of the calculation units calculates the position information and atomic velocity information of each atom in parallel based on the following formula:

[0144] r(t+Δt)=r(t)+v(t)Δt+0.5a(t)Δt^2

[0145] v(t+Δt / 2)=v(t)+0.5a(t)Δt

[0146] a(t+Δt)=F(t+Δt) / m

[0147] v(t+Δt)=v(t+Δt / 2)+0.5a(t+Δt)Δt

[0148] Among them, r represents the set cutoff radius, v represents the atomic velocity, a represents the atomic acceleration, F represents the sum of the short-range force and the long-range electrostatic force acting on the atom, m represents the atomic mass, t represents the current moment, and Δt represents the time step.

[0149] In an optional embodiment of the present application, after the above step 104, in which the obtained new virtual site information is assigned to each atom to obtain new atomic information of each atom, the above molecular system simulation method further includes the following steps:

[0150] The mshake / mrattle algorithm was applied to maintain the rigid structure of each of the described molecular systems.

[0151] For example, accurate rigid constraints can be achieved through the optimized SHAKE / RATTLE algorithm to ensure the precise maintenance of the geometric structure of water molecules and improve the accuracy of the overall molecular system simulation.

[0152] The virtual site information of the virtual site is recalculated according to the molecular information and atomic information of each molecule after maintaining the rigid structure of each molecular system.

[0153] See also Figure 3 In an optional embodiment of the present application, the above step 105, the constraint processing of the boundary of the dynamic system where the molecular system is located based on the new atomic information, and the output of the integrated data of the dynamic system, includes the following steps 301-302:

[0154] Step 301, determining whether each of the molecular systems and each atom in the molecular system is beyond a preset range, if the molecular system or each atom in the molecular system is beyond the preset range, re-determining the position of the target computing unit;

[0155] Step 302: relocate the molecular system or atoms beyond the preset range, and update the molecular information list, the atomic information list and the virtual site information list based on the molecular information and atomic information after the relocation.

[0156] Boundary processing: Check in each computing unit CU (x, y, z) whether the molecular system (such as water molecules) crosses the unit boundary: for each atom in the atomic information list atom_list, check whether its position is within the spatial range of the current CU. If not, calculate the position of the target computing unit CU; then migrate the water molecules that cross the boundary: create a migration list, including: water molecule ID and target computing unit coordinates; use neighbor communication to send the migration information to the corresponding target computing unit after migration; the target computing unit CU receives the migrated molecular information, and updates the local molecular information list water_list, atomic information list atom_list and virtual site information list m_point_list.

[0157] At the same time, for atoms that cross the boundary of the simulation box, periodic mapping is applied for boundary processing: In an optional embodiment of the present application, for atoms that exceed the boundary of the simulation box, the position information of the migrated atoms is calculated according to the following formula:

[0158] r_new=r_old-box_size*fix(r_old / box_size)

[0159] Among them, r_new represents the atomic coordinates after migration, r_old represents the atomic coordinates before migration, box_size represents the size of the simulation box, and fix represents the truncation operation.

[0160] Update the atomic position information in the corresponding computing unit CU

[0161] See also Figure 4 In an optional embodiment of the present application, the molecular system simulation method further includes the following steps 401-402:

[0162] Step 401, the global control unit calculates global information of the dynamics system where all molecular systems are located and distributes it to each of the calculation units;

[0163] This embodiment synchronizes and communicates all the obtained data: adjacent CUs exchange water molecule information in the boundary area:

[0164] Define the interaction radius r_cut, each CU exchanges atomic information within the range of r_cut with other adjacent CUs, and use asynchronous communication to overlap calculation and communication;

[0165] Global data collection and distribution of dynamic systems: The global computing unit GCU initializes the global data structure (such as total energy, temperature, etc.), and can use the tree reduction algorithm to collect the local statistics of each CU. The global computing unit GCU calculates the global statistics, and then uses the broadcast algorithm to distribute the global information to all computing units CU.

[0166] Step 402: Each calculation unit repeatedly iterates and calculates the molecular information and atomic information of each molecular system until an iteration condition is met, and then outputs the integrated data of the dynamic system.

[0167] Iteration and output: Repeat the above steps to simulate through a specified number of time steps (each time step Δt is usually 1-2fs, and the total simulation time is set according to research requirements, which can reach ns or μs) or a specified periodic simulation; output simulation results regularly: each computing unit CU sends local data to the global computing unit GCU, and the global computing unit GCU integrates the data and writes it to the output file, that is, outputs the integrated data of the dynamic system.

[0168] It should be understood that, although the various steps in the flow chart are displayed in sequence according to the indication of the arrows, these steps are not necessarily executed in sequence according to the order indicated by the arrows. Unless there is a clear description in this article, the execution of these steps is not strictly limited in order, and these steps can be executed in other orders. Moreover, at least a portion of the steps in the figure may include multiple sub-steps or multiple stages, and these sub-steps or stages are not necessarily executed at the same time, but can be executed at different times, and the execution order of these sub-steps or stages is not necessarily to be carried out in sequence, but can be executed in turn or alternately with other steps or at least a portion of the sub-steps or stages of other steps.

[0169] See also Figure 5 An embodiment of the present application provides a molecular system simulation system 500, which is applied to a distributed three-dimensional grid system. Each subspace in the three-dimensional grid system includes at least one computing unit and one storage unit. The system 500 includes at least: a first computing module 510, a second computing module 520, an updating module 530, an allocating module 540 and an output module 550, wherein:

[0170] The first calculation module 510 is used to calculate the virtual site information of the virtual site in the molecular system in parallel based on each of the calculation units for each molecular system, and update the virtual site information and the charge information of the virtual site to the virtual site information table in the storage unit; wherein the virtual site refers to any virtual point in the molecular system used to characterize the molecular system;

[0171] The second calculation module 520 is used to calculate the atomic information of each atom in each molecular system in parallel based on each of the calculation units; wherein the atomic information includes at least one of the short-range force and long-range electrostatic force between each atom, and the atomic position and atomic velocity of each atom;

[0172] The updating module 530 is used to update the virtual site information of each virtual site based on the obtained atomic information to obtain new virtual site information;

[0173] The allocation module 540 is used to allocate the obtained new virtual site information to each atom to obtain new atomic information of each atom;

[0174] The output module 550 is used to constrain the boundary of the dynamic system where the molecular system is located based on the new atomic information, and output the integrated data of the dynamic system.

[0175] In an optional embodiment of the present application, the first computing module 510 is specifically used to configure multiple data structures in each of the storage units and configure molecular computing model parameters in the global control unit in the computing unit; wherein the multiple data structures include at least: a molecular information list, an atomic information list and the virtual site information list; for each of the molecular systems, each of the computing units calculates the molecular centroid position and the molecular target computing unit of each of the molecular systems based on the molecular computing model parameters, and stores the molecular centroid position and the molecular target computing unit in the molecular information list corresponding to the storage unit, and stores the atomic information of each atom in the molecular system in the molecular information list corresponding to the storage unit; for each of the molecular systems, each of the computing units calculates the virtual site information of the virtual site based on the molecular computing model parameters, and stores the virtual site information in the virtual site information list.

[0176] In an optional embodiment of the present application, if the molecular system is a water molecule, the molecular centroid position is calculated according to the following formula:

[0177] r_com=(r_O+r_H1+r_H2) / 3

[0178] Among them, r_com represents the position of the molecular centroid, r_O represents the calculation of the three-dimensional coordinates of the O atom, r_H1 represents the calculation of the three-dimensional coordinates of the first H atom, and r_H2 represents the calculation of the three-dimensional coordinates of the second H atom;

[0179] The molecular target calculation unit is calculated according to the following formula:

[0180] CU:(x,y,z)=floor(r_com / box_size*[X,Y,Z])

[0181] CU: (x, y, z) represents the coordinates of the molecular target calculation unit, r_com represents the position of the molecular centroid, and box_size*[X, Y, Z] represents the total length of the three directions of the simulation box.

[0182] In an optional embodiment of the present application, if the molecular system is a water molecule, the virtual site information is calculated according to the following formula:

[0183] a=b=0.5*(r_OM(cos(θ_HOM)*r_OH))

[0184] x_M=x_O+a*(x_H1–x_O)+b*(x_H2–x_O)

[0185] y_M=y_O+a*(y_H1–y_O)+b*(y_H2–y_O)

[0186] z_M=z_O+a*(z_H1–z_O)+b*(z_H2–z_O)

[0187] Among them, a and b represent the weight coefficients of the virtual site M, which are determined according to the angles between O, H, and M atoms; x_M, y_M, and z_M represent the three-dimensional coordinates of the virtual site M, respectively; x_O, y_O, and z_O represent the three-dimensional coordinates of the O atom, respectively; x_H1, y_H1, and z_H1 represent the three-dimensional coordinates of the first H atom, respectively; x_H2, y_H2, and z_H2 represent the three-dimensional coordinates of the second H atom, respectively; r_OM and r_OH represent the position vectors of OM and OH, respectively; and θ_HOM represents the angle between OM and OH.

[0188] In an optional embodiment of the present application, the short-range force in the atomic information is calculated according to the following formula:

[0189] U_LJ(r)=4ε[(σ / r)^12-(σ / r)^6]

[0190] F_LJ(r)=24ε[(σ / r)^6*1 / r^2–2*(σ / r)^12*1 / r^2]*x

[0191] Among them, U_LJ(r) represents the Lanner-Jones potential between atoms, F_LJ(r) represents the Lanner-Jones force between atoms, ε and σ represent the Lanner-Jones interaction parameters, r represents the set cutoff radius, and x represents the distance between atoms;

[0192] The long range electrostatic forces are calculated according to the kgse method.

[0193] In an optional embodiment of the present application, the updating module 530 is further used to distribute the force acting on the virtual site in the molecular system to each atom for each molecular system, so as to obtain the virtual force acting on each atom.

[0194] In an optional embodiment of the present application, if the molecular system is a water molecule, then for each of the molecular systems, the force exerted on the virtual site in the molecular system is distributed to each atom to obtain the virtual force exerted on each atom, which is calculated according to the following formula:

[0195] F_O=F_O_direct+F_M*(1-ab)

[0196] F_H1=F_H1_direct+F_M*a

[0197] F_H2=F_H2_direct+F_M*b

[0198] Among them, F_O, F_H1, F_H2 are the virtual forces acting on the O atom, the first H atom and the second H atom respectively, F_O_direct, F_H1_direct, F_H2_direct represent the total forces of the long-range electrostatic force, short-range force and the allocated virtual force acting on the O atom, the first H atom and the second H atom respectively, F_M represents the virtual force acting on the virtual site M, a and b represent the weight coefficients of the virtual site M, which are determined according to the angles between the O, H and M atoms.

[0199] In an optional embodiment of the present application, the allocation module 540 is specifically used to, after allocating the obtained new virtual site information to each atom, each of the calculation units calculates the position information and atomic velocity information of each atom in parallel.

[0200] In an optional embodiment of the present application, each of the calculation units calculates the position information and atomic velocity information of each atom in parallel based on the following formula:

[0201] r(t+Δt)=r(t)+v(t)Δt+0.5a(t)Δt^2

[0202] v(t+Δt / 2)=v(t)+0.5a(t)Δt

[0203] a(t+Δt)=F(t+Δt) / m

[0204] v(t+Δt)=v(t+Δt / 2)+0.5a(t+Δt)Δt

[0205] Among them, r represents the set cutoff radius, v represents the atomic velocity, a represents the atomic acceleration, F represents the sum of the short-range force and the long-range electrostatic force acting on the atom, m represents the atomic mass, t represents the current moment, and Δt represents the time step.

[0206] In an optional embodiment of the present application, the allocation module 540 is further used to apply the mshake / mrattle algorithm to maintain the rigid structure of each of the molecular systems.

[0207] In an optional embodiment of the present application, the allocation module 540 is further used to recalculate the virtual site information of the virtual site according to the molecular information and atomic information of each molecule after maintaining the rigid structure of each molecular system.

[0208] In an optional embodiment of the present application, the output module 550 is specifically used to determine whether each of the molecular systems and each atom in the molecular system is beyond a preset range. If the molecular system or each atom in the molecular system is beyond the preset range, the position of the target computing unit is re-determined; the molecular system or the atom that is beyond the preset range is migrated, and the molecular information list, the atomic information list and the virtual site information list are updated based on the molecular information and atomic information after migration.

[0209] In an optional embodiment of the present application, the atomic position information after migration is calculated according to the following formula:

[0210] r_new=r_old-box_size*fix(r_old / box_size)

[0211] Among them, r_new represents the atomic coordinates after migration, r_old represents the atomic coordinates before migration, box_size represents the size of the simulation box, and fix represents the truncation operation.

[0212] In an optional embodiment of the present application, the output module 550 is also used for the global control unit to perform global information calculation on the dynamic systems in which all molecular systems are located and distribute it to each of the calculation units; each calculation unit repeatedly iteratively calculates the molecular information and atomic information of each molecular system until the iteration conditions are met, and then outputs the integrated data of the dynamic system.

[0213] For the specific definition of the molecular system simulation system 500, please refer to the definition of the molecular system simulation method above, which will not be repeated here. Each module in the molecular system simulation system 500 can be implemented in whole or in part by software, hardware and a combination thereof. Each of the above modules can be embedded in or independent of the processor in the computer device in the form of hardware, or can be stored in the memory in the computer device in the form of software, so that the processor can call and execute the operations corresponding to each of the above modules.

[0214] In one embodiment, a computer device is provided, the internal structure diagram of which can be as follows: Figure 6As shown. The computer device includes a processor, a memory, a network interface and a database connected via a system bus. Among them, the processor of the computer device is used to provide computing and control capabilities. The memory of the computer device includes a non-volatile storage medium and an internal memory. The non-volatile storage medium stores an operating system, a computer program and a database. The internal memory provides an environment for the operation of the operating system and the computer program in the non-volatile storage medium. The database of the computer device is used to store data. The network interface of the computer device is used to communicate with an external terminal via a network connection. When the computer program is executed by the processor, a molecular system simulation method as described above is implemented. It includes: a memory and a processor, the memory stores a computer program, and when the processor executes the computer program, any step in the molecular system simulation method as described above is implemented.

[0215] In one embodiment, a computer-readable storage medium is provided, on which a computer program is stored. When the computer program is executed by a processor, any step in the above molecular system simulation method can be implemented.

[0216] Those skilled in the art will appreciate that the embodiments of the present application may be provided as methods, systems, or computer program products. Therefore, the present application may adopt the form of a complete hardware embodiment, a complete software embodiment, or an embodiment in combination with software and hardware. Moreover, the present application may adopt the form of a computer program product implemented in one or more computer-usable storage media (including but not limited to disk storage, CD-ROM, optical storage, etc.) that include computer-usable program code.

[0217] The present application is described with reference to the flowcharts and / or block diagrams of the methods, devices (systems), and computer program products according to the embodiments of the present application. It should be understood that each process and / or box in the flowchart and / or block diagram, as well as the combination of the processes and / or boxes in the flowchart and / or block diagram, can be implemented by computer program instructions. These computer program instructions can be provided to a processor of a general-purpose computer, a special-purpose computer, an embedded processor, or other programmable data processing device to generate a machine, so that the instructions executed by the processor of the computer or other programmable data processing device generate instructions for implementing the processes in the flowchart and / or block diagram. Figure 1 A process or multiple processes and / or boxes Figure 1 A device that provides the functions specified in a block or multiple blocks.

[0218] These computer program instructions may also be stored in a computer-readable memory capable of directing a computer or other programmable data processing device to operate in a specific manner, so that the instructions stored in the computer-readable memory produce an article of manufacture comprising an instruction device, which implements the process Figure 1 A process or multiple processes and / or boxes Figure 1A function specified in one or more boxes.

[0219] These computer program instructions can also be loaded onto a computer or other programmable data processing device so that a series of operating steps are executed on the computer or other programmable device to produce a computer-implemented process, thereby providing instructions for implementing the process. Figure 1 A process or multiple processes and / or boxes Figure 1 The steps for the functions specified in one or more boxes.

[0220] Although the preferred embodiments of the present application have been described, those skilled in the art may make other changes and modifications to these embodiments once they have learned the basic creative concept. Therefore, the appended claims are intended to be interpreted as including the preferred embodiments and all changes and modifications falling within the scope of the present application.

[0221] Obviously, those skilled in the art can make various changes and modifications to the present application without departing from the spirit and scope of the present application. Thus, if these modifications and variations of the present application fall within the scope of the claims of the present application and their equivalents, the present application is also intended to include these modifications and variations.

Claims

1. A molecular system simulation method, characterized in that: Applied to a distributed three-dimensional grid system, each subspace in the three-dimensional grid system includes at least one computing unit and one storage unit, and the method includes at least: For each molecular system, virtual site information of virtual sites in the molecular system is calculated in parallel based on each of the calculation units, and the virtual site information and charge information of the virtual site are updated to the virtual site information table in the storage unit; wherein the virtual site refers to any virtual point in the molecular system used to characterize the molecular system; For each atom in each molecular system, atomic information of each atom in the molecular system is calculated in parallel based on each of the calculation units; wherein the atomic information includes at least one of short-range forces and long-range electrostatic forces between atoms, and atomic positions and atomic velocities of each atom; Based on the obtained atomic information, the virtual site information of each virtual site is updated to obtain new virtual site information; Assigning the obtained new virtual site information to each atom to obtain new atomic information of each atom; Based on the new atomic information, the boundary of the dynamic system where the molecular system is located is constrained, and the integrated data of the dynamic system is output.

2. The molecular system simulation method according to claim 1, characterized in that: The step of calculating the virtual site information of the virtual sites in the molecular system based on the parallel calculation of the calculation units includes: A plurality of data structures are configured in each of the storage units, and molecular computing model parameters are configured in a global control unit in the computing unit; wherein the plurality of data structures at least include: a molecular information list, an atom information list, and the virtual site information list; For each of the molecular systems, each of the calculation units calculates the molecular centroid position and the molecular target calculation unit of each of the molecular systems based on the molecular calculation model parameters, and stores the molecular centroid position and the molecular target calculation unit in the molecular information list corresponding to the storage unit, and stores the atomic information of each atom in the molecular system in the molecular information list corresponding to the storage unit; For each of the molecular systems, each of the calculation units calculates the virtual site information of the virtual site based on the molecular calculation model parameters, and stores the virtual site information in the virtual site information list.

3. The molecular system simulation method according to claim 2, characterized in that: If the molecular system is a water molecule, the position of the molecular centroid is calculated according to the following formula: r_com=(r_O+r_H1+r_H2) / 3 Among them, r_com represents the position of the molecular centroid, r_O represents the calculation of the three-dimensional coordinates of the O atom, r_H1 represents the calculation of the three-dimensional coordinates of the first H atom, and r_H2 represents the calculation of the three-dimensional coordinates of the second H atom; The molecular target calculation unit is calculated according to the following formula: CU:(x,y,z)=floor(r_com / box_size*[X,Y,Z]) CU: (x, y, z) represents the coordinates of the molecular target calculation unit, r_com represents the position of the molecular centroid, and box_size*[X, Y, Z] represents the total length of the three directions of the simulation box.

4. The molecular system simulation method according to claim 1, characterized in that: The calculating atomic information of each atom in the molecular system in parallel based on each of the calculating units includes: The short-range force in the atomic information is calculated according to the following formula: U_LJ(r)=4ε[(σ / r)^12-(σ / r)^6] F_LJ(r)=24ε[(σ / r)^6*1 / r^2–2*(σ / r)^12*1 / r^2]*x Among them, U_LJ(r) represents the Lanner-Jones potential between atoms, F_LJ(r) represents the Lanner-Jones force between atoms, ε and σ represent the Lanner-Jones interaction parameters, r represents the set cutoff radius, and x represents the distance between atoms; The long range electrostatic forces are calculated according to the kgse method.

5. The molecular system simulation method according to claim 1, characterized in that: Before updating the virtual site information of each virtual site based on the obtained atomic information to obtain new virtual site information, the method further includes: For each of the molecular systems, the force acting on the virtual site in the molecular system is distributed to each atom to obtain the virtual force acting on each atom.

6. The molecular system simulation method according to claim 1, characterized in that: The step of allocating the obtained new virtual site information to each atom to obtain new atomic information of each atom includes: After allocating the obtained new virtual site information to each atom, each of the calculation units calculates the position information and atomic velocity information of each atom in parallel.

7. The molecular system simulation method according to claim 1, characterized in that: The method further comprises: The virtual site information of the virtual site is recalculated according to the information of each molecule and the atomic information after maintaining the rigid structure of the molecular system.

8. A molecular system simulation system, characterized in that: Applied to a distributed three-dimensional grid system, each subspace in the three-dimensional grid system includes at least one computing unit and one storage unit, and the system includes at least: A first calculation module, for calculating, for each molecular system, virtual site information of virtual sites in the molecular system in parallel based on the calculation units, and updating the virtual site information and the charge information of the virtual site to the virtual site information table in the storage unit; wherein the virtual site refers to any virtual point in the molecular system used to characterize the molecular system; A second calculation module is used to calculate, for each atom in each molecular system, atomic information of each atom in the molecular system in parallel based on each of the calculation units; wherein the atomic information includes at least one of short-range forces and long-range electrostatic forces between atoms, and atomic positions and atomic velocities of each atom; An updating module, used for updating the virtual site information of each virtual site based on the obtained atomic information to obtain new virtual site information; An allocating module, used for allocating the obtained new virtual site information to each atom to obtain new atomic information of each atom; The output module is used to constrain the boundary of the dynamic system where the molecular system is located based on the new atomic information, and output the integrated data of the dynamic system.

9. A computer device comprising: The method comprises a memory and a processor, wherein the memory stores a computer program, and wherein the processor implements the steps of the method according to any one of claims 1 to 7 when executing the computer program.

10. A computer-readable storage medium having a computer program stored thereon, characterized in that: When the computer program is executed by a processor, the steps of the method according to any one of claims 1 to 7 are implemented.

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