Execution method and device of molecular dynamics constraint algorithm, chip and medium
By pre-determining and storing atomic position association parameters and PV values in the GPU chip, the problem of redundant calculations in the execution of molecular dynamics constraint algorithms by the GPU chip is solved, thus improving the execution efficiency.
Patent Information
- Application Number
- CN202511059182.4
- Authority / Receiving Office
- CN · China
- Patent Type
- Applications(China)
- Current Assignee / Owner
- Filing Date
- 2025-07-30
- Publication Date
- 2025-11-07
AI Technical Summary
In the prior art, graphics processing unit (GPU) chips perform redundant calculations when executing molecular dynamics constraint algorithms, resulting in low utilization and execution efficiency.
By processing multiple molecules sequentially in a GPU chip, pre-determining atomic position association parameters and PV values, and storing them in a cache, redundant computations are reduced and execution efficiency is improved.
This reduces redundant computational processes in molecular dynamics constraint algorithms and improves the execution efficiency of GPU chips.
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Figure CN120913672A_ABST
Abstract
Description
TECHNICAL FIELD
[0001] The present application relates to the technical field of computer technology, and in particular to a molecular dynamics constraint algorithm execution method and device, a chip and a medium. BACKGROUND
[0002] At present, in molecular dynamics simulation, constraint algorithms are used to maintain specific structural characteristics (such as bond length, bond angle) of the molecular system, so as to reduce the amount of calculation and improve the stability of simulation. Common constraint algorithms include mrattle algorithms, which achieve the fixation of molecular structure through mathematical transformation or physical constraints, and are suitable for different systems and scenarios.
[0003] In the prior art, when a Graphics Processing Unit (GPU) chip executes a molecular dynamics constraint algorithm, a large amount of repetitive calculations are usually required, wasting 30%-50% of iterative computing power, and the communication delay is amplified due to redundant calculations, resulting in low GPU chip utilization and algorithm execution efficiency. SUMMARY
[0004] The present application provides a molecular dynamics constraint algorithm execution method, device, chip and medium, which can reduce the redundant calculation process of the molecular dynamics constraint algorithm operation and improve the execution efficiency of the GPU chip for the molecular dynamics constraint algorithm.
[0005] According to an aspect of the present application, a molecular dynamics constraint algorithm execution method is provided, which is applied in a GPU chip, and the method comprises:
[0006] A molecule is sequentially determined as a current molecule in a plurality of substance molecules to be processed;
[0007] The atomic coordinates and atomic velocities corresponding to the current molecule are obtained, and a molecular dynamics constraint algorithm operation is performed on the current molecule according to the atomic coordinates, atomic velocities and a plurality of target parameters determined in advance;
[0008] Among them, the plurality of target parameters includes atomic position correlation parameters and atomic pressure-volume product PV value;
[0009] It is judged whether the operation on all molecules is completed;
[0010] If not, the operation of sequentially determining a molecule as a current molecule in a plurality of substance molecules to be processed is returned to be executed until the operation on all molecules is completed.
[0011] Optionally, before sequentially determining a molecule as a current molecule in a plurality of substance molecules to be processed, it further comprises:
[0012] The atomic position correlation parameters and the PV values are determined in advance according to different atomic coordinates, atomic velocities and atomic masses.
[0013] The atomic position correlation parameters include an interatomic distance vector, a tolerance parameter corresponding to a constraint matrix and a mass inverse matrix.
[0014] Optionally, after the atomic position correlation parameters and the PV values are determined in advance according to different atomic coordinates, atomic velocities and atomic masses, the method further includes:
[0015] The atomic position correlation parameters and the PV values are stored in a cache.
[0016] Optionally, the molecular dynamics constraint algorithm operation is performed on the current molecule according to the atomic coordinates, the atomic velocities and the plurality of target parameters determined in advance, including:
[0017] A current PV value corresponding to the current molecule is obtained according to the atomic coordinates and the atomic velocities of the current molecule;
[0018] The atomic position correlation parameters are obtained according to the atomic coordinates of the current molecule;
[0019] It is determined whether the current PV value is qualified for constraint according to the atomic masses and the atomic position correlation parameters;
[0020] If yes, it is determined that the molecular dynamics constraint algorithm operation corresponding to the current molecule is completed;
[0021] If no, the atomic velocities are updated, and the current PV value is determined again according to the atomic coordinates and the updated atomic velocities;
[0022] The operation of determining whether the current PV value is qualified for constraint is returned to be performed until the molecular dynamics constraint algorithm operation corresponding to the current molecule is completed.
[0023] Optionally, it is determined whether the current PV value is qualified for constraint according to the atomic masses and the atomic position correlation parameters, including:
[0024] A constraint matrix corresponding to the current molecule is determined according to the atomic masses and an interatomic distance vector determined in advance;
[0025] A tolerance parameter and a mass inverse matrix determined in advance are obtained according to the constraint matrix;
[0026] It is determined whether the current PV value is qualified for constraint according to the tolerance parameter.
[0027] Optionally, the atomic velocities are updated, including:
[0028] determine a Lagrange multiplier according to the current PV value and the mass inverse matrix;
[0029] determine a velocity increment according to the Lagrange multiplier and the atomic mass, and update the atomic velocity using the velocity increment.
[0030] According to another aspect of the present application, there is provided an execution device of a molecular dynamics constraint algorithm, applied in a GPU chip, comprising:
[0031] a molecule determination module configured to determine a molecule as a current molecule in turn from a plurality of substance molecules to be processed;
[0032] an algorithm execution module configured to acquire atomic coordinates and atomic velocity corresponding to the current molecule, and execute a molecular dynamics constraint algorithm operation on the current molecule according to the atomic coordinates, the atomic velocity, and a plurality of target parameters determined in advance;
[0033] wherein the plurality of target parameters comprise an atomic position correlation parameter and an atomic pressure-volume product PV value;
[0034] a judgment module configured to judge whether the operation on all molecules is completed; if not, return to execute the operation of determining a molecule as a current molecule in turn from a plurality of substance molecules to be processed until the operation on all molecules is completed.
[0035] According to another aspect of the present application, there is provided a chip, comprising:
[0036] at least one processor; and
[0037] a memory in communication connection with the at least one processor; wherein,
[0038] the memory stores a computer program executable by the at least one processor, and the computer program is executed by the at least one processor to enable the at least one processor to execute the execution method of the molecular dynamics constraint algorithm according to any one of the embodiments of the present application.
[0039] According to another aspect of the present application, there is provided a computer readable storage medium storing computer instructions for enabling a processor to execute the execution method of the molecular dynamics constraint algorithm according to any one of the embodiments of the present application when executed by the processor.
[0040] According to another aspect of the present application, there is provided a computer program product comprising a computer program for enabling a processor to execute the execution method of the molecular dynamics constraint algorithm according to any one of the embodiments of the present application when executed by the processor.
[0041] The technical scheme provided by the embodiment of the present application, by means of the GPU chip, sequentially determines one molecule as a current molecule among the plurality of substance molecules to be processed, acquires the atomic coordinates and atomic velocities corresponding to the current molecule, performs a molecular dynamics constraint algorithm operation on the current molecule according to the atomic coordinates, the atomic velocities, and a plurality of target parameters determined in advance, judges whether the operation on all molecules is completed, if yes, determines that the method execution is completed, and if not, returns to perform the operation of sequentially determining one molecule as a current molecule among the plurality of substance molecules to be processed, until the operation on all molecules is completed, thereby reducing the redundant calculation process of the molecular dynamics constraint algorithm operation, and improving the execution efficiency of the GPU chip on the molecular dynamics constraint algorithm.
[0042] It should be understood that the content described in this part is not intended to identify the key or important features of the embodiments of the present application, nor is it used to limit the scope of the present application. Other features of the present application will become apparent from the following description. BRIEF DESCRIPTION OF DRAWINGS
[0043] In order to more clearly illustrate the technical solutions in the embodiments of the present application, the drawings needed in the embodiment description will be briefly introduced below. Obviously, the drawings in the following description are only some embodiments of the present application, and other drawings can also be obtained by those skilled in the art without creative labor.
[0044] Figure 1 is a flow chart of a molecular dynamics constraint algorithm execution method according to an embodiment of the present application;
[0045] Figure 2a is a flow chart of another molecular dynamics constraint algorithm execution method according to an embodiment of the present application;
[0046] Figure 2b is a scene diagram applicable to a molecular dynamics constraint algorithm according to an embodiment of the present application;
[0047] Figure 3 is a structural diagram of a molecular dynamics constraint algorithm execution device according to an embodiment of the present application;
[0048] Figure 4 is a structural diagram of a chip for implementing a molecular dynamics constraint algorithm execution method according to an embodiment of the present application. DETAILED DESCRIPTION
[0049] In the following, the technical solutions in the embodiments of the present application will be described clearly and completely with reference to the drawings in the embodiments of the present application. Obviously, the described embodiments are only a part of the embodiments of the present application, rather than all the embodiments of the present application. Based on the embodiments in the present application, all the other embodiments obtained by a person of ordinary skill in the art without creative effort should fall within the protection scope of the present application.
[0050] It should be noted that the terms "first", "second", and the like in the specification and claims of the present application and the above-described drawings are used to distinguish similar objects, and do not necessarily indicate a specific order or a chronological sequence. It should be understood that the data thus used can be interchanged under appropriate circumstances, so that the embodiments of the present application described herein can be implemented in an order other than that illustrated or described herein. In addition, the terms "include" and "have" and any variations thereof are intended to cover non-exclusive inclusion, for example, a process, method, system, product, or device including a series of steps or units does not necessarily have to be limited to the clearly listed steps or units, but can include other steps or units not clearly listed or inherent to the process, method, product, or device.
[0051] Figure 1 A flowchart of an execution method of a molecular dynamics constraint algorithm is provided for an embodiment of the present application. The embodiment can be applicable to a case where a GPU chip performs a dynamics constraint algorithm on a substance molecule to perform a pre-play simulation on a structure of the substance molecule. The method can be executed by an execution device of the molecular dynamics constraint algorithm, which can be realized in the form of hardware and / or software and configured in the GPU chip. As shown in the figure, the method comprises: Figure 1
[0052] Step 110: sequentially determining one molecule as a current molecule in a plurality of substance molecules to be processed.
[0053] In the embodiment, specifically, the substance molecule can be a drug molecule in the field of new drug research and development. In the process of molecular dynamics simulation of the drug by the GPU chip, one molecule can be sequentially determined as a current molecule in a plurality of drug molecules.
[0054] Step 120: acquiring atomic coordinates and atomic velocities corresponding to the current molecule, and performing a molecular dynamics constraint algorithm operation on the current molecule according to the atomic coordinates, the atomic velocities, and a plurality of target parameters determined in advance.
[0055] The plurality of target parameters include an atomic position correlation parameter and a Pressure Volume (PV) value.
[0056] In this step, the atomic coordinates and the atomic speed derived parameters corresponding to the current molecule can be constrained and qualified according to a plurality of predetermined target parameters. If qualified, it is determined that the molecular dynamics constraint algorithm operation corresponding to the current molecule is executed. If not qualified, the velocity increment is determined to obtain new atomic speed, and then the next round of judgment process is performed according to the atomic coordinates and the new atomic speed.
[0057] In one embodiment of the present embodiment, before a molecule is determined as the current molecule in the plurality of molecules to be processed, the different atomic position correlation parameters and PV values are determined in advance according to different atomic coordinates, atomic speeds and atomic masses. The atomic position correlation parameters include atomic distance vector, tolerance parameters corresponding to the constraint matrix and mass inverse matrix.
[0058] In the prior art, the judgment process of each round of the algorithm operation on the molecule is long, and a large amount of repeated calculation is required. In order to improve the execution efficiency of the GPU chip, the present embodiment proposes a pre-processing method to determine the target parameters. Since the atomic coordinates do not change in each iteration process, the subsequent parameters (i.e. atomic position correlation parameters) calculated by the atomic coordinates are also fixed values. Therefore, the atomic position correlation parameters can be obtained by processing each molecule once in the pre-processing process. In the actual iteration process, the atomic position correlation parameters can be directly obtained, thereby avoiding a large amount of repeated calculation and reducing the redundant calculation process.
[0059] Secondly, in the iteration process, once a molecule is qualified, it is immediately replaced by the next molecule to be processed for calculation. The new molecule still corresponds to the original speed and coordinates of the previous molecule. Therefore, the PV value can be calculated in advance in the pre-processing to ensure that the new molecule can be directly calculated when it enters the operation system in the iteration process, thereby saving the time length of each iteration.
[0060] In one specific embodiment, after the different atomic position correlation parameters and PV values are determined according to different atomic coordinates, atomic speeds and atomic masses, the atomic position correlation parameters and PV values are stored in the cache.
[0061] The advantage of such setting is that by storing the target parameters obtained by pre-processing in the cache, the access frequency of the atomic coordinates can be reduced by 80%. Compared with the real-time calculation of parameters in the prior art, the atomic coordinate and mass data need to be frequently read, which can avoid high-concurrency memory conflicts and release the memory bandwidth.
[0062] Step 130: Determine whether the operation on all molecules has been completed. If yes, the method is considered to have ended. If no, return to step 110 to sequentially determine one molecule as the current molecule from among the multiple molecules to be processed, until the operation on all molecules is completed.
[0063] The technical solution provided by this invention involves using a GPU chip to sequentially determine one molecule from a plurality of molecules to be processed as the current molecule, obtaining the atomic coordinates and atomic velocities corresponding to the current molecule, and performing a molecular dynamics constraint algorithm operation on the current molecule based on the atomic coordinates, atomic velocities, and a plurality of pre-determined target parameters. The solution then determines whether the operation on all molecules has been completed. If yes, the method is considered complete; otherwise, the process returns to the previous steps of sequentially determining one molecule from the plurality of molecules to be processed as the current molecule until the operation on all molecules is completed. This approach reduces redundant computational processes in the molecular dynamics constraint algorithm and improves the execution efficiency of the GPU chip for the molecular dynamics constraint algorithm.
[0064] Figure 2a A flowchart of another molecular dynamics constraint algorithm execution method provided in an embodiment of the present invention is shown below. Figure 2a As shown, the method includes:
[0065] Step 210: Select one molecule from the multiple substances to be processed as the current molecule.
[0066] Step 220: Obtain the atomic coordinates and atomic velocity corresponding to the current molecule, and obtain the predetermined current PV value corresponding to the current molecule based on the atomic coordinates and atomic velocity corresponding to the current molecule.
[0067] Step 230: Obtain the pre-determined atomic position association parameters based on the atomic coordinates corresponding to the current molecule.
[0068] In this embodiment, Figure 2b This can be a schematic diagram illustrating a scenario where a molecular dynamics constraint algorithm is applicable. Figure 2b The interatomic distance vector, PV value, tolerance parameter tolvel, and inverse mass matrix invmatr can all be obtained through preprocessing calculations.
[0069] The constraint matrix `matr` describes the mathematical relationship between atomic coordinates and constraints, while the tolerance parameter `tolvel` controls the convergence of constraint iterations. The two are linked through residual analysis of the constraint equations. The core logic is to dynamically or empirically set the tolerance parameter based on the condition number or residual norm of the constraint matrix to balance constraint accuracy and computational efficiency. The inverse of the constraint matrix `matr` yields the inverse mass matrix `invmatr`.
[0070] Step 240, judging whether the current PV value is qualified according to the atomic mass and the atomic position correlation parameter, if yes, executing step 250, if no, executing step 260.
[0071] In the embodiment, if the current PV value is qualified, it is determined that the operation of the molecular dynamics constraint algorithm corresponding to the current molecule is completed.
[0072] In one embodiment of the embodiment, as shown in the figure, Figure 2b judging whether the current PV value is qualified according to the atomic mass and the atomic position correlation parameter includes: determining a constraint matrix matr corresponding to the current molecule according to the atomic mass and a predetermined interatomic distance vector; obtaining a predetermined tolerance parameter tolvel and a mass reciprocal matrix invmat according to the constraint matrix matr; and judging whether the current PV value is qualified according to the tolerance parameter.
[0073] The core physical meaning of the constraint matrix matr is a measure of the effective inertia or generalized mass of the system in the constraint direction.
[0074] Step 250, judging whether the operation on all molecules is completed, if yes, it is determined that the method is executed to end, if no, returning to execute the operation of determining a molecule in the plurality of substance molecules to be processed as the current molecule in step 210 until the operation on all molecules is completed.
[0075] Step 260, updating the atomic velocity, and re-determining the current PV value according to the atomic coordinates and the updated atomic velocity, and then returning to execute the operation of judging whether the current PV value is qualified in step 240 until the operation of the molecular dynamics constraint algorithm corresponding to the current molecule is completed.
[0076] In one embodiment of the embodiment, as shown in the figure, Figure 2b updating the atomic velocity includes: determining a Lagrange multiplier according to the current PV value and the mass reciprocal matrix; determining a velocity increment according to the Lagrange multiplier and the atomic mass, and updating the atomic velocity using the velocity increment.
[0077] The technical solution provided by this invention involves using a GPU chip to sequentially determine one molecule from a plurality of molecules to be processed as the current molecule, obtaining the atomic coordinates and atomic velocity corresponding to the current molecule, obtaining a predetermined current PV value based on the atomic coordinates and atomic velocity, determining whether the current PV value is constrained based on the atomic mass and predetermined atomic position association parameters, and if not, updating the atomic velocity and re-determining the current PV value based on the atomic coordinates and the updated atomic velocity, until the molecular dynamics constraint algorithm operation corresponding to the current molecule is completed, and determining whether the operation on all molecules is completed, and if not, returning to the operation of sequentially determining one molecule from a plurality of molecules to be processed as the current molecule until the operation on all molecules is completed. This technical means can reduce the redundant calculation process of the molecular dynamics constraint algorithm operation and improve the execution efficiency of the GPU chip for the molecular dynamics constraint algorithm.
[0078] Figure 3 This is a schematic diagram of the structure of an execution device for a molecular dynamics constraint algorithm provided in an embodiment of the present invention. The device is applied in a GPU chip, such as... Figure 3 As shown, the device includes: a molecule determination module 310, an algorithm execution module 320, and a judgment module 330.
[0079] The molecule determination module 310 is used to sequentially determine one molecule as the current molecule from among multiple substance molecules to be processed.
[0080] The algorithm execution module 320 is used to obtain the atomic coordinates and atomic velocities corresponding to the current molecule, and to perform molecular dynamics constraint algorithm operations on the current molecule based on the atomic coordinates, atomic velocities and multiple predetermined target parameters.
[0081] The multiple target parameters include atomic position correlation parameters and PV values;
[0082] The judgment module 330 is used to determine whether the operation on all molecules has been completed; if not, it returns to the operation of sequentially determining one molecule as the current molecule among the multiple substances to be processed, until the operation on all molecules has been completed.
[0083] The technical scheme provided by the embodiment of the present application can reduce the redundant calculation process of the molecular dynamics constraint algorithm operation and improve the execution efficiency of the GPU chip for the molecular dynamics constraint algorithm by sequentially determining one molecule as a current molecule from the plurality of substance molecules to be processed, obtaining the atomic coordinates and atomic velocities corresponding to the current molecule, performing a molecular dynamics constraint algorithm operation on the current molecule according to the atomic coordinates, the atomic velocities and a plurality of target parameters determined in advance, determining whether the operation on all molecules is completed, and if so, determining that the method execution is completed, and if not, returning to perform the operation of sequentially determining one molecule as a current molecule from the plurality of substance molecules to be processed until the operation on all molecules is completed.
[0084] On the basis of the above-mentioned embodiment, the device further comprises:
[0085] The preprocessing module is configured to determine different atomic position correlation parameters and PV values in advance according to different atomic coordinates, atomic velocities and atomic masses, wherein the atomic position correlation parameters include an interatomic distance vector, a tolerance parameter corresponding to a constraint matrix and a mass inverse matrix.
[0086] The parameter storage module is configured to store the atomic position correlation parameters and the PV values in the cache.
[0087] The algorithm execution module 320 comprises:
[0088] The parameter acquisition unit is configured to acquire a current PV value corresponding to the current molecule in advance according to the atomic coordinates and the atomic velocities corresponding to the current molecule, and acquire atomic position correlation parameters in advance according to the atomic coordinates corresponding to the current molecule.
[0089] The constraint judgment unit is configured to determine whether the current PV value is qualified for constraint according to the atomic masses and the atomic position correlation parameters, and if so, determine that the molecular dynamics constraint algorithm operation corresponding to the current molecule is completed.
[0090] The iterative execution unit is configured to update the atomic velocities when the current PV value is unqualified, re-determine the current PV value according to the atomic coordinates and the updated atomic velocities, and return to perform the operation of determining whether the current PV value is qualified for constraint until the molecular dynamics constraint algorithm operation corresponding to the current molecule is completed.
[0091] The constraint matrix determination unit is configured to determine a constraint matrix corresponding to the current molecule according to the atomic masses and an interatomic distance vector determined in advance, acquire a tolerance parameter and a mass inverse matrix determined in advance according to the constraint matrix, and determine whether the current PV value is qualified for constraint according to the tolerance parameter.
[0092] The velocity increment determination unit is used to determine the Lagrange multiplier based on the current PV value and the reciprocal mass matrix; determine the velocity increment based on the Lagrange multiplier and the atomic mass; and update the atomic velocity using the velocity increment.
[0093] The above-described apparatus can execute the methods provided in all the foregoing embodiments of the present invention, and has the corresponding functional modules and beneficial effects for executing the above methods. Technical details not described in detail in the embodiments of the present invention can be found in the methods provided in all the foregoing embodiments of the present invention.
[0094] Figure 4 A schematic diagram of the structure of a chip 10 that can be used to implement an embodiment of the present invention is shown. For example... Figure 4 As shown, chip 10 includes at least one processor 11 and a memory, such as read-only memory (ROM) 12 and random access memory (RAM) 13, communicatively connected to at least one processor 11. The memory stores computer programs executable by at least one processor. The processor 11 can perform various appropriate actions and processes based on the computer program stored in the ROM 12 or loaded from storage unit 18 into the RAM 13. The RAM 13 can also store various programs and data required for the operation of chip 10. The processor 11, ROM 12, and RAM 13 are interconnected via bus 14. Input / output (I / O) interface 15 is also connected to bus 14.
[0095] Multiple components in chip 10 are connected to I / O interface 15, including: input unit 16, such as keyboard, mouse, etc.; output unit 17, such as various types of displays, speakers, etc.; storage unit 18, such as disk, optical disk, etc.; and communication unit 19, such as network card, modem, wireless transceiver, etc. Communication unit 19 allows chip 10 to exchange information / data with other devices through computer networks such as the Internet and / or various telecommunications networks.
[0096] Processor 11 can be a variety of general-purpose and / or special-purpose processing components with processing and computing capabilities. Some examples of processor 11 include, but are not limited to, a central processing unit (CPU), a graphics processing unit (GPU), various special-purpose artificial intelligence (AI) computing chips, various processors running machine learning model algorithms, a digital signal processor (DSP), and any suitable processor, controller, microcontroller, etc. Processor 11 performs the various methods and processes described above, such as the execution method of molecular dynamics constraint algorithms.
[0097] In some embodiments, the execution method of the molecular dynamics constraint algorithm can be implemented as a computer program tangibly embodied in a computer readable storage medium, e.g., storage unit 18. In some embodiments, some or all of the computer program can be loaded and / or installed onto chip 10 via ROM 12 and / or communication unit 19. When the computer program is loaded onto RAM 13 and executed by processor 11, one or more of the steps of the execution method of the molecular dynamics constraint algorithm described above can be performed. Alternatively, in other embodiments, processor 11 can be configured to perform the execution method of the molecular dynamics constraint algorithm by other means, e.g., with the aid of firmware.
[0098] Various implementations of the systems and techniques described above can be realized in digital electronic circuitry, integrated circuitry, a field programmable gate array (FPGA), an application specific integrated circuit (ASIC), a system on a chip (SOC), a complex programmable logic device (CPLD), computer hardware, firmware, software, and / or combinations thereof. These various implementations can include implementation in one or more computer programs that are executable and / or interpretable on a programmable system including at least one programmable processor, which can be special or general purpose, coupled to receive data and instructions from, and to transmit data and instructions to, a storage system, at least one input device, and at least one output device.
[0099] Computer programs used to implement the processes of the present application can be written in any combination of one or more programming languages. These computer programs can be provided to a processor of a general purpose computer, special purpose computer, or other programmable data processing apparatus to produce a machine, such that the computer program, when executed, implements the functions / acts specified in the flowcharts and / or block diagrams. The computer program can be executed entirely on a machine, partially on a machine, partially on a machine and partially on a remote machine or entirely on a remote machine or server.
[0100] In the context of the present application, a computer-readable storage medium can be a tangible medium that can contain or store computer programs for use by or in connection with an instruction execution system, apparatus, or device. Computer-readable storage media can include, but are not limited to, electronic, magnetic, optical, electromagnetic, infrared, or semiconductor systems, apparatus, or devices, or any suitable combination of the foregoing. Alternatively, a computer-readable storage medium can be a machine-readable signal medium. More specific examples of a machine-readable storage medium will include one or more lines of a program of instructions in a transitory signal, a portable computer diskette, a hard disk, a random access memory (RAM), a read-only memory (ROM), an erasable programmable read-only memory (EPROM or Flash memory), an optical fiber, a portable compact disc read-only memory (CD-ROM), an optical storage device, a magnetic storage device, or any suitable combination of the foregoing.
[0101] To provide for interaction with a user, the systems and techniques described here can be implemented on a chip having a display device (e.g., a CRT (cathode ray tube) or LCD (liquid crystal display) monitor) for displaying information to the user and a keyboard and a pointing device (e.g., a mouse or a trackball) by which the user can provide input to the chip. Other kinds of devices can be used to provide for interaction with a user as well; for example, feedback provided to the user can be any form of sensory feedback (e.g., visual feedback, auditory feedback, or tactile feedback); and input from the user can be received in any form, including acoustic, speech, or tactile input.
[0102] The systems and techniques described here can be implemented in a computing system that includes a back end component (e.g., as a data server), or that includes a middleware component (e.g., an application server), or that includes a front end component (e.g., a user computer having a graphical user interface or a Web browser through which a user can interact with an implementation of the systems and techniques described here), or any combination of such back end, middleware, or front end components. The components of the system can be interconnected by any form or medium of digital data communication (e.g., a communication network). Examples of communication networks include a local area network (LAN), a wide area network (WAN), blockchain network, and the Internet.
[0103] The computing system can include clients and servers. A client and server are generally remote from each other and typically interact through a communication network. The relationship of client and server arises by virtue of computer programs running on the respective computers and having a client-server relationship to each other. The server can be a cloud server, also known as a cloud computing server or cloud host, which is a host product in the cloud computing service system, to solve the defects of large management difficulty and weak business scalability in traditional physical host and VPS service.
[0104] It should be understood that the various forms of flow shown above can be used to reorder, add or delete steps. For example, each step described in the present application can be executed in parallel, sequentially or in a different order, as long as the desired results of the technical solutions of the present application can be achieved, which is not limited herein.
[0105] The above detailed description does not constitute a limitation on the protection scope of the present application. Those skilled in the art should understand that various modifications, combinations, sub-combinations and substitutions can be made according to design requirements and other factors. Any modifications, equivalent replacements and improvements made within the spirit and principles of the present application shall be included in the protection scope of the present application.
Claims
1. A method of performing a molecular dynamics constraint algorithm, the method comprising: Applied to a graphics processing unit chip, the method comprises: sequentially determining one molecule as a current molecule in a plurality of substance molecules to be processed; obtaining atomic coordinates and atomic velocities corresponding to the current molecule, and performing a molecular dynamics constraint algorithm operation on the current molecule according to the atomic coordinates, the atomic velocities, and a plurality of target parameters determined in advance; wherein the plurality of target parameters comprises an atomic position correlation parameter and an atomic pressure-volume product (PV) value; determining whether the operation on all molecules is completed; if not, returning to perform the operation of sequentially determining one molecule as a current molecule in a plurality of substance molecules to be processed until the operation on all molecules is completed.
2. The method of claim 1, wherein, Before sequentially determining one molecule as a current molecule in a plurality of substance molecules to be processed, the method further comprises: determining different atomic position correlation parameters and PV values in advance according to different atomic coordinates, atomic velocities, and atomic masses; wherein the atomic position correlation parameter comprises an interatomic distance vector, a tolerance parameter corresponding to a constraint matrix, and a mass inverse matrix.
3. The method of claim 2, wherein, After determining different atomic position correlation parameters and PV values according to different atomic coordinates, atomic velocities, and atomic masses, the method further comprises: storing the atomic position correlation parameters and the PV values in a cache.
4. The method of claim 1, wherein, Performing a molecular dynamics constraint algorithm operation on the current molecule according to the atomic coordinates, the atomic velocities, and the plurality of target parameters determined in advance comprises: obtaining a current PV value corresponding to the current molecule determined in advance according to the atomic coordinates and the atomic velocities corresponding to the current molecule; obtaining the atomic position correlation parameters determined in advance according to the atomic coordinates corresponding to the current molecule; determining whether the current PV value is qualified for constraint according to the atomic mass and the atomic position correlation parameters; if yes, determining that the molecular dynamics constraint algorithm operation corresponding to the current molecule is completed; if not, updating the atomic velocities and re-determining the current PV value according to the atomic coordinates and the updated atomic velocities; returning to perform the operation of determining whether the current PV value is qualified for constraint until the molecular dynamics constraint algorithm operation corresponding to the current molecule is completed.
5. The method of claim 4, wherein, Determining whether the current PV value is qualified for constraint according to the atomic mass and the atomic position correlation parameters comprises: determining a constraint matrix corresponding to the current molecule according to the atomic mass and the interatomic distance vector determined in advance; obtaining a tolerance parameter and a mass inverse matrix determined in advance according to the constraint matrix; determining whether the current PV value is qualified for constraint according to the tolerance parameter.
6. The method of claim 5, wherein, Updating the atomic velocities comprises: determining a Lagrange multiplier according to the current PV value and the mass inverse matrix; determining a velocity increment according to the Lagrange multiplier and the atomic mass, and updating the atomic velocities using the velocity increment.
7. An execution device of a molecular dynamics constraint algorithm, characterized by, Applied to a graphics processing unit chip, the device comprises: a molecule determination module configured to sequentially determine one molecule as a current molecule in a plurality of substance molecules to be processed; An algorithm execution module is configured to acquire atomic coordinates and atomic velocities corresponding to the current molecule, and perform a molecular dynamics constraint algorithm operation on the current molecule according to the atomic coordinates, the atomic velocities, and a plurality of target parameters determined in advance. The plurality of target parameters include an atomic position correlation parameter and an atomic pressure-volume product (PV) value. A judgment module is configured to judge whether the operation on all molecules is completed. If not, the operation of sequentially determining one molecule as the current molecule from the plurality of substance molecules to be processed is returned until the operation on all molecules is completed.
8. A chip, characterized by The chip comprises: at least one processor; and a memory connected in communication with the at least one processor; wherein The memory stores a computer program executable by the at least one processor, and the computer program is executed by the at least one processor to enable the at least one processor to execute the execution method of the molecular dynamics constraint algorithm according to any one of claims 1-6.
9. A computer-readable storage medium, characterized in that, The computer readable storage medium stores computer instructions for enabling the processor to implement the execution method of the molecular dynamics constraint algorithm according to any one of claims 1-6 when executed.
10. A computer program product, characterised in that, The computer program product comprises a computer program, and the computer program implements the execution method of the molecular dynamics constraint algorithm according to any one of claims 1-6 when executed by the processor.