A simulation method and electronic device for chemical reaction process after ionizing radiation

Abstract

The present invention belongs to the technical field of radiation chemistry and radiation biology, and specifically relates to a simulation method and electronic device for a chemical reaction process after ionizing radiation. The central processing unit calculates the data that each processing unit of the graphics processing unit needs to process, and then copies the data to the graphics processing unit. The central processing unit immediately starts to prepare new data after the transmission is completed. At this time, the graphics processing unit immediately starts to calculate the reaction time, and after completion, copies it to the central processing unit. The central processing unit transmits the new data to the graphics processing unit, and the graphics processing unit waits until the data transmission is completed to continue the calculation. The method of the present invention utilizes the coupling acceleration of the central processing unit and the graphics processing unit. Through the design of this timing diagram, the central processing unit and the graphics processing unit can work at the same time, thereby greatly improving the calculation speed. The simulation speed of ionizing radiation chemical groups is greatly improved, and the development of radiation biology and radiation chemistry applications is promoted.

Description

Technical Field

[0001] The invention belongs to the technical field of radiation chemistry and radiation biology, and specifically relates to a simulation method and electronic equipment for a chemical reaction process after ionizing radiation. Background Art

[0002] Ionizing radiation can generate a large number of radicals such as ions and free radicals, which can cause damage to organisms. In the field of radiation chemistry, the radicals generated by ionizing radiation can be used for radiation processing, radiation disinfection, and the production of chemical dosimeters. The spatial distribution of radicals generated by ionizing radiation is extremely uneven, and the Monte Carlo method is usually used to simulate and calculate their diffusion and reaction processes, so as to evaluate the radiobiological effects, radiation processing, disinfection effects, and the response of chemical dosimeters. However, due to the large number of chemical groups, the simulation calculation requires a lot of computing resources, and needs to be accelerated from both hardware and software aspects.

[0003] In terms of hardware, the special structure of the graphics processing unit (hereinafter referred to as GPU) enables it to greatly accelerate certain numerical calculations, so the use of GPU can greatly improve the speed of radiation chemistry simulation. However, the simulation of chemical reactions contains some codes that need to be executed serially, which are extremely inefficient when running on a graphics processor. When only using the image processor for simulation calculations, the calculation speed is limited by the above serial execution code, and the efficiency is not high enough.

[0004] The simulation speed of the chemical simulation program run by the central processing unit (hereinafter referred to as CPU) is not fast enough, and the simulation time is too long when a large number of chemical groups need to be simulated.

[0005] In terms of software, the independent reaction time algorithm is a method used in Monte Carlo simulation of chemical reactions. This method has a great advantage in calculation speed over the step-by-step simulation method. However, the independent reaction time calculation method contains a considerable proportion of serial calculation tasks, and it is difficult to achieve a good acceleration effect using only GPU acceleration. Summary of the invention

[0006] In view of this, the embodiments of the present invention provide a simulation method and electronic device for the chemical reaction process after ionizing radiation. To address the problems of large amount of calculation and slow calculation speed in the prior art of ionizing radiation chemical simulation, the CPU and GPU coupling acceleration are used to greatly improve the simulation speed of ionizing radiation chemical groups, thereby promoting the development of radiobiology and radiation chemistry applications.

[0007] A method for simulating a chemical reaction process after ionizing radiation according to an embodiment of the present invention includes:

[0008] (1) obtaining reactant information and storing the reactant information in a memory of a central processing unit;

[0009] (2) copying the reactant information in the memory of the central processing unit and transmitting the reactant information to the video memory of the graphics processing unit;

[0010] (3) determining the data processed by each processing unit in the graphics processor;

[0011] (4) according to the serial number of the reactant, the m processing units in the graphics processor calculate the reaction time of the p copied to the graphics processor memory to the reactant;

[0012] (5) copying the reaction time of p to the reactant in the video memory of the image processor to the memory of the central processor;

[0013] (6) The central processing unit traverses the serial numbers of all R reactants in the reactant information, repeats steps (3) to (5), and obtains the reaction times of all R reactants;

[0014] (7) sorting the reaction times of all reactants in step (6) from small to large, and obtaining a product according to the sorting;

[0015] (8) Using the product as a reactant, repeat steps (3) to (7) to simulate the chemical reaction process after ionizing radiation.

[0016] Optionally, the reactant information includes the serial number of the reactant, the type of the reactant, the three-dimensional coordinates of the reactant and the generation time of the reactant.

[0017] Optionally, in step (3), determining the data processed by each processing unit in the graphics processor comprises the following steps:

[0018] (1) Assume that there are m processing units in the graphics processor, and each processing unit processes p data.

[0019] (2) The CPU sets up a buffer array in the memory, and the size of the buffer array is p×m;

[0020] (3) The central processing unit traverses the reactant information and writes the reactant serial number in the reactant information into the buffer array. The writing method is:

[0021] There are R reactants in total. Starting from the reactant numbered 1, any reactant R among the R reactants i and any reactant R j As a pair written into the buffer array, i = 1, 2, 3 ... R, j = 1, 2, 3 ... R, i ≠ j;

[0022] (4) The CPU uses the asynchronous data transmission function of the GPU to copy the buffer array to the video memory of the GPU and obtain the data processed by each processing unit in the GPU.

[0023] Optionally, in step (4), the m processing units in the graphics processor calculate the reaction time of the p copied to the graphics processor video memory to the reactant according to the reactant sequence number, including the following steps:

[0024] (1) The processing unit of the graphics processor calculates the time difference Δt of the generation time according to the generation time of two reactants in any pair of the p pairs of reactants, records the reactant with an earlier generation time as the first reactant, records the first diffusion constant of the first reactant as D1, records the reactant with a later generation time as the second reactant, and records the second diffusion constant of the second reactant as D2;

[0025] (2) According to the time difference Δt and the first diffusion constant D1, the Gaussian distribution standard deviation is obtained:

[0026] (3) taking the Gaussian distribution as the probability distribution, randomly sampling to obtain three numbers Δx, Δy and Δz, and adding the Δx, Δy and Δz to the original three-dimensional coordinates of the first reactant to obtain new coordinates of the first reactant;

[0027] (4) calculating the distance r between the new coordinates of the first reactant and the original three-dimensional coordinates of the second reactant;

[0028] (5) Calculate the probability distribution function of reaction time P(t) using the following formula:

[0029]

[0030] Wherein, σ is the reaction radius between the first reactant and the second reactant, Erfc is the complementary error function (the complementary error function is a well-known technology, and the function expression is: D is the sum of the first diffusion constant D1 and the second diffusion constant D2;

[0031] (6) Solve the probability distribution function of the above reaction time to obtain the reaction time t of the first reactant and the second reactant:

[0032] (7) Traverse p pairs of reactants and repeat steps (1) to (6) to obtain the reaction time of p pairs of reactants processed by m processing units in the graphics processor.

[0033] Optionally, in step (7), the reaction times of all reactants are sorted in ascending order, and a product is obtained according to the sorting, comprising the following steps:

[0034] (1) Assume that there are R reactants. From any reactant R i and any reactant R j Among the reaction times, the reactant i corresponding to the shortest reaction time is selected to react with the reactant j to obtain a product;

[0035] (2) Mark reactants i and j that have reacted as inactive, and delete reactants i and j from the R reactants;

[0036] (3) Traverse R reactants and repeat steps (1) and (2) to obtain all products;

[0037] (4) Record the generation time and type of all generated products;

[0038] (5) Store the obtained products in the product array.

[0039] To achieve the above objective, according to another aspect of an embodiment of the present invention, an electronic device is provided.

[0040] An electronic device according to an embodiment of the present invention includes:

[0041] Memory, used to store computer executable programs;

[0042] The processor, when the program is executed by the processor, enables the processor to execute the simulation method of the chemical reaction process after ionizing radiation according to the embodiment of the present invention.

[0043] To achieve the above objective, according to another aspect of an embodiment of the present invention, a computer-readable storage medium is provided.

[0044] The computer-readable storage medium of the embodiment of the present invention stores a computer program, which is used to enable the computer to execute the simulation method of the chemical reaction process after ionizing radiation of the embodiment of the present invention.

[0045] The above embodiments of the present invention have the following advantages or beneficial effects:

[0046] The embodiment of the present invention can make full use of the advantages of the central processing unit and the graphics processing unit, and process the parts suitable for serial calculation and parallel calculation in the chemical reaction simulation separately, and make the central processing unit and the graphics processing unit run at the same time by designing a timing diagram. The simulation method of the present invention greatly improves the speed of chemical reaction simulation after ionizing radiation irradiation, and greatly improves the simulation ability of radiation chemical process and intracellular chemical reaction and damage process after ionizing radiation irradiation.

[0047] Additional aspects and advantages of the present disclosure will be given in part in the following description and in part will be obvious from the following description or will be learned through practice of the present invention. BRIEF DESCRIPTION OF THE DRAWINGS

[0048] In order to more clearly illustrate the embodiments of the present invention, the drawings required for use in the embodiments are briefly introduced below. Obviously, the drawings described below are only some embodiments of the present invention, and a person of ordinary skill in the art can obtain other drawings based on the drawings without creative work.

[0049] Figure 1 It is a timing diagram of the simulation program of the chemical reaction process after ionizing radiation. DETAILED DESCRIPTION

[0050] The following will be combined with the drawings in the embodiments of the present invention to clearly and completely describe the technical solutions in the embodiments of the present invention. Obviously, the described embodiments are only part of the embodiments of the present invention, not all of the embodiments. Based on the embodiments of the present invention, all other embodiments obtained by ordinary technicians in this field without making creative work are within the scope of protection of the present invention.

[0051] The method for simulating a chemical reaction process after ionizing radiation provided in an embodiment of the present invention comprises the following steps:

[0052] In step 1, the reactant information is obtained and stored in the memory of the central processing unit, wherein the reactant information includes the serial number of the reactant, the type of the reactant, the three-dimensional coordinates of the reactant and the generation time of the reactant. The reactant information can be obtained from the hard disk or the results of other simulation software, such as Geant4-DNA software.

[0053] In step 2, the reactant information is copied in the memory of the central processing unit, and the reactant information is transmitted to the video memory of the graphics processing unit.

[0054] In step 3, data processed by each processing unit in the graphics processor is determined.

[0055] In the embodiment of the present invention, determining the data processed by each processing unit in the graphics processor includes the following steps:

[0056] (1) Assume that there are m processing units in a graphics processor. The graphics processor used in the embodiment of the present invention is produced by NVIDIA and is called CUDA core or SP. It is a hardware with computing and processing functions. Different processing units can perform parallel computing. Each processing unit processes p data.

[0057] (2) The CPU sets up a buffer array in the memory, and the size of the buffer array is p×m;

[0058] (3) The central processing unit traverses the reactant information and writes the reactant serial number in the reactant information into the buffer array. The writing method is:

[0059] There are R reactants in total. Starting from the reactant numbered 1, any reactant R among the R reactants i and any reactant R j As a pair written into the buffer array, i=1, 2, 3...R, j=1, 2, 3...R, i≠j, for example, write (1, 2), (1, 3), (1, 4)..., (1, R), (2, 3), (2, 4)... until the amount of data written into the buffer array is equal to the size of the buffer array.

[0060] (4) The CPU uses the asynchronous data transmission function of the GPU to copy the buffer array to the video memory of the GPU and obtain the data processed by each processing unit in the GPU.

[0061] In step 4, according to the sequence number of the reactant, the m processing units in the graphics processor calculate the reaction time of the p copied to the graphics processor memory to the reactant.

[0062] In the embodiment of the present invention, the m processing units in the graphics processor calculate the reaction time of the p to the reactant copied to the graphics processor memory according to the reactant sequence number, including the following steps:

[0063] (1) The processing unit of the graphics processor calculates the time difference Δt of the generation time according to the generation time of two reactants in any pair of the p pairs of reactants, records the reactant with an earlier generation time as the first reactant, records the first diffusion constant of the first reactant as D1, records the reactant with a later generation time as the second reactant, records the second diffusion constant of the second reactant as D2, and the reactant diffusion constant is determined by the type of reactant;

[0064] (2) According to the time difference Δt and the first diffusion constant D1, the Gaussian distribution standard deviation is obtained:

[0065] (3) taking the Gaussian distribution as the probability distribution, randomly sampling to obtain three numbers Δx, Δy and Δz, and adding the Δx, Δy and Δz to the original three-dimensional coordinates of the first reactant to obtain new coordinates of the first reactant;

[0066] (4) Calculate the distance r between the new coordinates of the first reactant and the original three-dimensional coordinates of the second reactant; the calculation formula is: Assume that the original three-dimensional coordinates of the first reactant and the second reactant are (x1 ,y 1 ,z 1 ) and (x 2 ,y 2 ,z 2 ), the distance r is calculated as:

[0067] (5) Calculate the probability distribution function of reaction time P(t) using the following formula:

[0068]

[0069] Wherein, σ is the reaction radius between the first reactant and the second reactant (the reaction radius is determined by the type of reactants), Erfc is the complementary error function (the complementary error function is a well-known technology, and the function expression is: D is the sum of the first diffusion constant D1 and the second diffusion constant D2;

[0070] (6) Solve the probability distribution function of the above reaction time to obtain the reaction time t of the first reactant and the second reactant:

[0071] (7) Traverse p pairs of reactants and repeat steps (1) to (6) to obtain the reaction time of p pairs of reactants processed by m processing units in the graphics processor.

[0072] In step 5, the reaction time of p to the reactant in the video memory of the image processor is copied to the memory of the central processor.

[0073] In step 6, the central processing unit traverses the serial numbers of all R reactants in the reactant information, repeats steps 3 to (5), and obtains the reaction times of all R reactants.

[0074] In the embodiment of the present invention, the timing diagram of the above steps (3) to (6) is as follows: Figure 1 As shown: In step (3), the CPU calculates the data that each processing unit of the GPU needs to process, and then copies the data to the GPU. The GPU immediately starts step (4) after the transmission is completed. At this time, the CPU immediately starts step (3) to prepare new data, and copies it to the GPU after completion (at this time, it can be transmitted regardless of whether step (4) in the GPU is completed). After the GPU completes step (4), it transmits the result to the CPU, and the CPU waits until the data transmission is completed before continuing with step (3). Through the design of this timing diagram, the CPU and the GPU can work simultaneously, thereby greatly improving the calculation speed.

[0075] In step 7, the reaction times of all reactants in step (6) are sorted from small to large, and the product is obtained according to the sorting.

[0076] In an embodiment of the present invention, the reaction times of all reactants are sorted in ascending order, and a product is obtained according to the sorting, comprising the following steps:

[0077] (1) Assume that there are R reactants. From any reactant R i and any reactant R j Among the reaction times, the reactant i corresponding to the shortest reaction time is selected to react with the reactant j to obtain a product;

[0078] (2) Mark reactants i and j that have reacted as inactive, and delete reactants i and j from the R reactants;

[0079] (3) Traverse R reactants and repeat steps (1) and (2) to obtain all products;

[0080] (4) Record the generation time and type of all generated products;

[0081] (5) Store the obtained products in the product array.

[0082] In step 8, the product is used as a reactant, and steps 3 to 7 are repeated until there is no new product after step 7, thereby completing the simulation of the chemical reaction process after ionizing radiation.

[0083] In the following examples of the present invention, the simulation method of the chemical reaction process after ionizing radiation proposed by the present invention is applied to the simulation of oxygen consumption in an aqueous solution after ultra-high dose rate irradiation, so as to study the chemical reaction and biological effect mechanism of ultra-high dose rate radiotherapy.

[0084] Example: Calculate the change in oxygen content of an aqueous solution after ionizing radiation irradiation. Dose 10 Gy, oxygen content in water 3%. Compare the calculation time with Geant4-DNA (chemical reaction simulation run by the CPU) and gMicroMC (chemical reaction simulation accelerated by the graphics processor) in the reference: Lai Y, Jia X, Chi Y. Modeling the effect of oxygen on the chemical stage of water radiolysis using GPU-based microscopic Monte Carlo simulations, with an application in FLASH radiotherapy [J]. Physics in Medicine and Biology, 2020, 66 (2). The comparison results are shown in the following table:

[0085] The present invention Geant4-DNA gMicroMC 1.5s 70000s 57s

[0086] As can be seen from the above table, the simulation method of the present invention greatly improves the speed of simulating chemical reactions after ionizing radiation irradiation, and greatly improves the simulation capabilities of radiation chemical processes and intracellular chemical reactions and damage processes after ionizing radiation irradiation.

[0087] The simulation method of the chemical reaction process after ionizing radiation in the embodiment of the present invention involves the coordinated acceleration of the CPU and GPU, and the CPU and GPU memories are separated, and the data storage location needs to be explained. The storage locations involved are: computer hard disk, referred to as hard disk; memory that can be directly read by the CPU, that is, the computer's memory, hereinafter referred to as memory; memory that can be directly read by the GPU, referred to as video memory. Three arrays are set in the memory, one for storing reactants, one for storing products, and one for storing reaction pair information. The reactant and product information records the type, position, and generation time of the chemical group, and the reaction pair information records the reactant number and reaction occurrence time of a certain reaction. An array is set in the video memory for storing reactant information, and two buffer arrays are set for sending reaction pair information to the memory.

[0088] During the alternating calculation process, the CPU first stores the reaction pair information in the memory buffer array 1. When the number of reaction pair information reaches the processing capacity of the GPU user preset, that is, p data, the CPU asynchronously calls the function of copying and transferring from the memory to the video memory, and transfers the reaction pair information in the memory buffer array to the video memory buffer array. The GPU calculates the reaction time of the reaction pair. At this time, the calculation result is stored in the video memory buffer array. After the calculation is completed, the data is sent to the memory buffer array 1. During the process of the GPU calculating the reaction time, the CPU continues to traverse the reactants, stores the reaction pair information in the memory buffer array 2, and after the calculation is completed, the reaction pair information in the cache array 2 is transmitted to the video memory buffer array. The GPU calculates the reaction time of the reaction pair, and after completion, the calculation result is sent to the memory buffer array 2. The process is alternating until the reactant traversal is completed.

[0089] An electronic device according to an embodiment of the present invention includes:

[0090] Memory, used to store computer executable programs;

[0091] The processor, when the program is executed by the processor, enables the processor to execute the simulation method of the chemical reaction process after ionizing radiation according to the embodiment of the present invention.

[0092] To achieve the above objective, according to another aspect of an embodiment of the present invention, a computer-readable storage medium is provided.

[0093] The computer-readable storage medium of the embodiment of the present invention stores a computer program, which is used to enable the computer to execute the simulation method of the chemical reaction process after ionizing radiation of the embodiment of the present invention.

[0094] It should be noted that in the embodiments of the present invention, the processor may be a central processing unit (CPU), or other general-purpose processors, digital signal processors (DSP), application-specific integrated circuits (ASIC), field programmable gate arrays (FPGA) or other programmable logic devices, discrete gates or transistor logic devices, discrete hardware components, etc. The general-purpose processor may be a microprocessor, or the processor may be any conventional processor, etc. The memory may be used to store the computer program and / or module, and the processor implements various functions of the simulation method of the chemical reaction process after ionizing radiation by running or executing the computer program and / or module stored in the memory, and calling the data stored in the memory. The memory may mainly include a program storage area and a data storage area, wherein the program storage area may store an operating system, an application required for at least one function (such as a sound playback function, an image playback function, etc.), etc.; the data storage area may store data (such as audio data, graphic data, etc.) created by the operating system during the operation of the application, etc. In addition, the memory may include a high-speed random access memory and may also include a non-volatile memory, such as a hard disk, a memory, a plug-in hard disk, a smart media card (SMC), a secure digital (SD) card, a flash card (Flash Card), a storage device of at least one disk or a flash memory device.

[0095] Based on such understanding, the present invention implements all or part of the processes in the above-mentioned embodiment method, and can also be completed by instructing related hardware through a computer program, and the computer program can be stored in a computer-readable storage medium, and the computer program can implement the steps of each of the above-mentioned method embodiments when executed by a processor. Among them, the computer program includes computer program code, and the computer program code can be in source code form, object code form, executable file or some intermediate form. The computer-readable medium may include: any entity or device capable of carrying the computer program code, recording medium, U disk, mobile hard disk, magnetic disk, optical disk, computer memory, read-only memory (ROM, ReadOnly Memory), random access memory (RAM, Random Access Memory), electrical carrier signal, telecommunication signal and software distribution medium, etc.

[0096] The above is an implementation method of the present invention, which can be understood and implemented by ordinary technicians in this field without creative work. It should be pointed out that ordinary technicians in this technical field can make several improvements and modifications without departing from the principle of the present invention, and these improvements and modifications are also considered to be within the protection scope of the present invention.

Claims

1. A method for simulating chemical reaction processes after ionizing radiation, It is characterized in that include: (1) Obtaining reactant information and storing the reactant information in the memory of the central processing unit; (2) copying the reactant information in the memory of the central processing unit and transmitting the reactant information to the video memory of the graphics processing unit; (3) determining data processed by each processing unit in the graphics processor; and comprising the following steps: (3.1) Assume that there are m processing units in the graphics processor, and each processing unit processes p data. (3.2) The CPU sets up a buffer array in the memory, and the size of the buffer array is p×m; (3.3) The central processing unit traverses the reactant information and writes the reactant serial number in the reactant information into the buffer array. The writing method is: There are R reactants in total, starting from the reactant numbered 1, any reactant Ri and any reactant Rj among the R reactants are written into the buffer array as a pair, i=1, 2, 3...R, j=1, 2, 3...R, i≠j; (3.4) The CPU uses the asynchronous data transfer function of the GPU to copy the buffer array to the GPU's video memory, and obtains the data processed by each processing unit in the GPU; (4) Based on the reactant sequence number, the m processing units in the graphics processor calculate the reaction time of the p copied to the graphics processor memory to the reactant; (5) copy the reaction time of p to the reactant in the image processor video memory to the central processor memory; (6) The central processing unit traverses the serial numbers of all R reactants in the reactant information, repeats steps (3) to (5), and obtains the reaction times of all R reactants; (7) sorting the reaction times of all reactants in step (6) from small to large, and obtaining a product according to the sorting; (8) Using the product as a reactant, repeat steps (3) to (7) to simulate the chemical reaction process after ionizing radiation.

2. The simulation method according to claim 1, It is characterized in that In the step (1), the reactant information includes the serial number of the reactant, the type of the reactant, the three-dimensional coordinates of the reactant and the generation time of the reactant.

3. The simulation method according to claim 1 or 2, It is characterized in that In step (4), the m processing units in the graphics processor calculate the reaction time of the p copied to the graphics processor memory to the reactant according to the reactant sequence number, including the following steps: (1) The processing unit of the graphics processor calculates the time difference Δt of the generation time according to the generation time of two reactants in any pair of the p pairs of reactants, records the reactant with an earlier generation time as the first reactant, records the first diffusion constant of the first reactant as D1, records the reactant with a later generation time as the second reactant, and records the second diffusion constant of the second reactant as D2; (2) According to the time difference Δt and the first diffusion constant D1, the Gaussian distribution standard deviation is obtained ; (3) taking the Gaussian distribution as the probability distribution, randomly sampling to obtain three numbers Δx, Δy and Δz, and adding the Δx, Δy and Δz to the original three-dimensional coordinates of the first reactant to obtain new coordinates of the first reactant; (4) calculating the distance r between the new coordinates of the first reactant and the original three-dimensional coordinates of the second reactant; (5) Calculate the probability distribution function of reaction time P(t) using the following formula: Wherein, σ is the reaction radius between the first reactant and the second reactant, Erfc is the complementary error function, and D is the sum of the first diffusion constant D1 and the second diffusion constant D2; (6) Solve the probability distribution function of the above reaction time and obtain the reaction time t of the first reactant and the second reactant: (7) Traverse p pairs of reactants and repeat steps (1) to (6) to obtain the reaction time of p pairs of reactants processed by m processing units in the graphics processor.

4. The simulation method according to claim 1 or 2, It is characterized in that In step (7), the reaction times of all reactants in step (6) are sorted in ascending order, and a product is obtained according to the sorting, including the following steps: (1) Assume that there are R reactants. From any reactant R i and any reactant R j Among the reaction times, the reactant i corresponding to the shortest reaction time is selected to react with the reactant j to obtain a product; (2) Mark reactants i and j that have reacted as inactive, and delete reactants i and j from the R reactants; (3) Traverse R reactants and repeat steps (1) and (2) to obtain all products; (4) Record the generation time and type of all generated products; (5) Store the obtained products in the product array.

5. An electronic device, It is characterized in that include: Memory, used to store computer executable programs; A processor, when the program is executed by the processor, causes the processor to execute the method for simulating a chemical reaction process after ionizing radiation according to any one of claims 1 to 4.

6. A computer-readable storage medium, It is characterized in that A computer program is stored thereon, and the computer program is used to enable the computer to execute the method for simulating a chemical reaction process after ionizing radiation according to any one of claims 1 to 4.

Images