JPH07296045A - Molecule design support method - Google Patents

Abstract

PURPOSE:To reduce the number of repetitive times and to calculate a molecule structure optimizing problem at high speed by deciding an optimum prediction solution among the plural prediction solutions calculated by using plural previously prepared prediction procedure. CONSTITUTION:The initial coordinates of respective atoms and an interatom potential parameter in a molecule are inputted. In concrete terms, the input of an initial value by the operator of a computer 2 or an initial value previously stored in a storage device 5 provided in the computer 2 is read into an arithmetic part 2a installed in the computer 2. Then, the coordinates in the respective times of repetitive calculation are set, interatomic potential at that time is decided and the decided interatomic potential is differentiated to obtain interatomic force. The previously prepared prediction procedure is executed based on the obtained interatomic force, and prediction solutions are decided based on the respective prediction procedures to select an optimum solution among the plural obtained prediction solutions. When it is judged that the optimum solution, is convesget, the molecular characteristic of molecular structure in the optimum solution is evaluated.

Description

Detailed Description of the Invention

[0001]

BACKGROUND OF THE INVENTION 1. Field of the Invention The present invention relates to a method for supporting molecular design, that is, a method for solving a structure optimization problem of a molecule, and particularly in iterative calculation of molecular structure calculation, high-speed processing by predicting a solution and determining an optimum solution. The present invention relates to a molecular design support method that enables the above.

[0002]

2. Description of the Related Art With the progress of computers, numerical analysis such as large-scale molecular structure optimization has become possible. This allows
A molecular design support device using a molecular structure optimization technique has been put into practical use. Here, the molecular structure optimization means to determine a stable molecular structure. In such a stable molecular structure, the force acting between all the atoms in the molecule is sufficiently small, and the atoms do not move any further. Since the force acting between atoms is proportional to the distance between atoms, molecular structure optimization repeatedly calculates whether the interatomic force has become sufficiently small while changing the coordinates of each atom in the molecule. Iterative calculation is required. The total number of formulas for this atomic force is proportional to the total number of atoms in the molecule. Therefore, in order to reduce the calculation time, speeding up by reducing the number of iterative calculations affects the performance of the design support device. In the conventional molecular design support device, for the high speed calculation of the molecular structure optimization problem, for example, the force acting between each atom in the molecule is calculated as described in "Numerical simulation in engineering" (Maruzen). In doing so, the number of iterations of iterative calculation is reduced by preparing a method for predicting the interatomic force acting on each atom.

[0003]

However, in the molecular structure optimization problem, there is no effective atomic force prediction method for all atomic forces. In addition, the convergence of the atomic force in the molecular structure optimization problem often depends on the number of iterations of the iterative calculation.In the worst case, the atomic force repeatedly oscillates or diverges with the number of iterations. By doing so, the molecular structure optimization may be stopped and the atomic force may not be obtained. Therefore, high speed calculation of the molecular structure optimization problem in the design support device cannot be realized only by preparing a specific prediction method for the atomic force. The present invention has been made in view of the above circumstances, and an object of the present invention is to solve the problems as described above in the prior art and to solve a plurality of prediction methods for a solution of a molecular structure optimization problem such as atomic force. Provide a molecular design support method that prepares and executes all prediction methods at the same time, reduces the number of iterations by the procedure of selecting the optimal solution from the predicted solutions, and enables high-speed calculation of molecular structure optimization problems Especially.

[0004]

The above object of the present invention is to provide a molecular design support method for inputting an initial structure of a molecule to be designed and carrying out a structure optimization calculation. A method for supporting molecular design, comprising: a calculation step using a plurality of prepared prediction methods for calculation; and a step of determining an optimum one from a plurality of prediction solutions obtained by the calculation step. Achieved by

[0005]

The molecular design support method according to the present invention is characterized in that the interatomic force is predicted by the following procedure. In particular, it is obtained in the fourth step and the fifth step, that is, the third step. Executes a plurality of prepared solution prediction methods based on the atomic force, determines the predicted solution based on each prediction method, and selects the optimal solution from the plurality of predicted solutions obtained here. As a result, it is possible to realize a molecular design support method that reduces the number of iterations and enables calculation of a molecular structure optimization problem within a practical time. (1) First step: a step of inputting initial coordinates of each atom in a molecule and interatomic potential parameters. Specifically, it means a process of inputting an initial value by an operator of the computer, or a process of reading out the initial value stored in advance in a storage device installed in the computer to an arithmetic unit installed in the computer. (2) Second step: a step of setting the coordinates of each iteration of the iterative calculation and determining the interatomic potential at that time. (3) Third step: a step of obtaining an interatomic force by differentiating the interatomic potential determined in the previous step. (4) Fourth step: a step of executing a prediction method for a plurality of solutions prepared in advance based on the interatomic force obtained in the previous step, and determining a prediction solution based on each prediction method. (5) Fifth step: a step of selecting an optimal solution from the plurality of predicted solutions obtained in the previous step. (6) Sixth step: It is judged whether or not the optimum solution obtained in the previous step has converged, and if converged, the process is terminated, and if not converged, the optimum solution is used as an initial value and repeated until the solution converges. The step that causes the calculation to continue. In other words, the optimal interatomic force obtained in the previous step is used to determine the potential between each atom in the molecule (second step), and the interatomic potential is differentiated to obtain the interatomic force (third step). A step of executing a plurality of prepared solution prediction methods, determining a predicted solution based on each prediction method (fourth step), and selecting an optimal solution (fifth step). (7) Seventh step: a step of evaluating the molecular characteristics of the molecular structure in the optimum solution when it is determined that the convergence has occurred in the previous step.

[0006]

Embodiments of the present invention will now be described in detail with reference to the drawings. The molecular design support device is a device for designing a molecule by inputting an initial structure and an interatomic potential of the molecule and evaluating chemical properties and the like in the input optimum structure of the molecule. The interatomic force between each atom, which is necessary to obtain the optimum structure of a molecule, which is a basic physical quantity for evaluating chemical properties, is obtained by differentiating the interatomic potential. The method of differentiating the interatomic potential and calculating the interatomic force between each atom to obtain the optimum structure is called molecular structure optimization calculation, and is numerically expressed as a motion equation expressing the interaction between atoms. Be reduced.
FIG. 2 shows the configuration of the molecular design support apparatus according to one embodiment of the present invention. In the figure, 1 is a display device, 2 is an arithmetic processing device, and the arithmetic processing device 2 includes an arithmetic unit 2a, a processing procedure storage unit 2b, an intermediate data storage unit 2c, and a data output unit 2d.
And a data input unit 2e. The data created by the arithmetic processing device 2 is displayed on the display unit of the output device 4. Reference numeral 3 is an input device, and 5 is a storage device.

FIG. 1 shows a processing procedure using the molecular design support apparatus according to this embodiment. The processing procedure shown in FIG. 1 is stored in the above-described processing procedure storage unit 2b, and necessary data is read from the storage device 5 via the intermediate data storage unit 2c according to this processing procedure and executed by the calculation unit 2a. To be done. The result of the calculation executed by the calculation unit 2a is stored in the storage device 5 via the intermediate data storage unit 2c. Further, the calculation result executed by the calculation unit 2a is output to the output device 4 via the display device 1 by the data generated by the data output unit 2d according to the instruction input from the input device 3 via the data input unit 2e. Is output. Hereinafter, the procedure of the molecular design support according to this embodiment will be sequentially described. As shown in FIG. 1, step 10 is input of initial parameters,
The operator uses the input device 3 to input the total number of atoms K, X coordinates X (1) to X (K) of each atom, Y coordinates Y (1) to Y (K), and Z coordinates Z (1) to Z (K). , Mass M (1) to M (K), potential parameter, time width T, convergence determination condition GMIN of atomic force
Or a procedure for reading out the above parameters stored in the storage device 5 in advance to the calculation unit 2a.

By using each of these parameters, the interatomic potential V (r) is given by the following equation (Equation 1) when the potential parameters are ε and σ according to "Computational Material Chemistry" (Kaibundou Publishing). To be

[Equation 1] In the description here, the coordinate system is an example in which the coordinate system is rectangular. However, it is obvious that the same effect can be obtained by using another coordinate system. Step 11 to Step 15
Determines the molecular structure by iterative calculations, as described below. First, in step 11, the coordinates of each atom in each iteration are calculated. For example, the coordinates of the I-th atom in the molecule are given by the formula (Equation 2).

[Equation 2]

Specifically, the operator inputs the coordinates of atoms at each iteration using the input device 3 or calculates the coordinates of atoms at each iteration stored in the storage device 5 in advance. It means a procedure for reading to the section 2a. However, DX (I), DY (I), and DZ (I) are increment values in the X, Y, and Z directions of the I-th atom in each iteration, and are set to 0 in the first iteration. Also, the formula (Equation 1)
In the potential V (r) at, r is the distance between atoms, and for example, the distance r between the first and second atoms is
It is given by (Equation 3).

[Equation 3]

Step 12 is a potential equation (Equation 1)
Is the procedure to obtain the interatomic force by differentiating. Step 12
Then calculate each atomic force at each iteration. For example,
The force acting on the I-th atom in the molecule is given by the formula (Equation 4). The derivative is the value at each atom position.

[Equation 4] Step 13 is a procedure of executing all of the plurality of prediction methods at the same time and storing the obtained prediction solutions in the storage device 5. Here, the predicted solution refers to the predicted value of the interatomic force obtained by the prediction method. In FIG. 1, an example in which two types of prediction methods are executed is described. The total number of prediction methods may be at least two. In the following description, the prediction method in step 13 will be described using the relaxation method and the least squares method, which are typical prediction methods as the prediction method 1 and the prediction method 2.

In the iterative calculation, when the number of iterations is N, the components in the X, Y and Z directions of the simple solution obtained in step 12 are FX (I), FY (I) and FZ according to the equation (4). (I). The prediction method is simple solution FX (I), FY (I),
FZ (I) and the number of repetitions N− stored in the storage device 5
Optimal solution GX (I, N-1), GY (I, N-1), G
Prediction solution PX at the number of iterations N by Z (I, N-1)
This is a method of predicting (I), PY (I), and PZ (I). Here, GX (I, N-1), GY (I, N-1), GZ (I,
N-1) is the component of the optimal solution of the I-th atom in the X, Y, and Z directions. Also, PX (I), PY (I), PZ (I)
Are components of the predicted solution of the I-th atom in the X, Y, and Z directions. In the relaxation method as an example, the predicted solutions PX (I), PY
(I) and PZ (I) are defined by the formula (Equation 5).

[Equation 5]

Here, α is a relaxation parameter, and GX (I, N-1), which is the optimal solution when the number of iterations is (N-1),
It is a quantity indicating the weight of GY (I, N-1), GZ (I, N-1) and FX (I), FY (I), FZ (I) which are simple solutions in N times. In the least squares method, which is another example of the prediction method, for example, the optimal solution GX with the number of iterations from 1 to N is
(I, 1), GY (I, 1), GZ (I, 1) to GX (I,
A predicted solution is calculated by approximating N), GY (I, N), and GZ (I, N) by a quadratic equation. Specifically, QX, which is the component of the predicted solution of the I-th atom in the X, Y, and Z directions
(I), QY (I) and QZ (I) are given by the formula (Equation 6).

[Equation 6]

Coefficients AX, BX and CX are quadratic parameters defining QX (I), and AY, BY and CY are Q.
It is a quadratic parameter that defines Y (I).
Z and CZ are parameters of a quadratic equation that defines QZ (I), and are respectively obtained by the determinant shown in equation (7).

[Equation 7] The plurality of predicted solutions PX (I), PY (I), PZ (I) and Q obtained
X (I), QY (I), QZ (I) are stored in the storage device 5. The above procedure of step 13 is called an optimal solution prediction procedure. There are no restrictions on the atomic force prediction method used in the optimal solution prediction procedure. The same effect as in this embodiment can be obtained by using a prediction method of atomic force other than the prediction method used in this embodiment.

When the processing for all the prediction methods is completed in step 13, the process proceeds to step 14. In step 14, the optimum solution is determined by the equation (Equation 8) from the plurality of predicted solutions obtained in step 13.

[Equation 8] The obtained optimum solution is saved for use as a new initial value used in the next iteration of the iterative calculation. The increment values DX (I), DY (I), DZ (I) in the next iteration are
It is given by the formula (Equation 9).

[Equation 9] The above procedure of step 14 is called an optimal solution selection procedure.
In step 15, it is determined whether or not the optimum solution obtained in step 14 has converged using the equation (Equation 10).

[Equation 10]

If not converged, steps 11 to 14 are repeated. If it is determined in step 15 that the convergence has occurred, in step 16,
Evaluate the molecular properties of the converged optimal solution. The effect of the present invention is shown in FIG. FIG. 3 is an example in which two types of prediction methods are prepared in the optimum solution prediction procedure (step 13),
The atomic force is plotted on the vertical axis and the number of iterations is plotted on the horizontal axis, showing the behavior of convergence of the predicted solution. In the prediction method 1 in FIG. 3, the atomic force is small but the convergence is slow when the number of iterations is small. On the other hand, in Prediction Method 2, the atomic force is large but the convergence is fast when the number of iterations is small. Therefore, in this example, the combination of the prediction method 2 and the prediction method 1 indicated by the broken line is selected as the optimum solution.

According to the optimum solution predicting procedure and the optimum solution selecting procedure according to the above-described embodiment, the conventional molecular structure optimization is performed by always selecting a predictive solution having a small atomic force as the optimum solution shown in FIG. The number of iterations of the iterative calculation can be reduced as compared with the solution method of the problem. Therefore, since the structure optimization problem can be solved at high speed, there is an advantage that it becomes possible to support high-speed molecular design. It is needless to say that the above embodiment shows one example of the present invention, and the present invention should not be limited to this.
For example, the processing procedure of the molecular design support has been described in the above embodiment, but the configuration of the apparatus is the same as that shown in FIG. Therefore, if the processing procedure described in the above embodiment is stored in a recording medium such as a floppy disk, it is apparent that the molecular design support can be realized on any computer having the configuration shown in FIG.

[0017]

As described above in detail, according to the present invention, a plurality of prediction methods are prepared for the solution of a molecular structure optimization problem such as interatomic force, and all the prediction methods are executed at the same time to perform prediction. The remarkable effect that the number of iterations is reduced by the procedure of selecting an optimal solution from among the solutions and a molecular design support method that enables high-speed calculation of a molecular structure optimization problem can be realized. Further, by using a recording medium in which the procedure of the molecular design support method according to the present invention is recorded, the number of iterations in the calculation of the force acting between each atom in the molecule is reduced, and the molecular structure optimization problem can be processed in a short time. it can.

[Brief description of drawings]

FIG. 1 is a flowchart of a molecular design support procedure according to an embodiment of the present invention.

FIG. 2 is a configuration diagram of a molecular design support apparatus according to an embodiment.

FIG. 3 is a diagram showing an effect of the invention.

[Explanation of symbols]

 DESCRIPTION OF SYMBOLS 1 display device 2 arithmetic processing device 2a arithmetic unit 2b processing procedure storage unit 2c intermediate data storage unit 2d data output unit 2e data input unit 3 input device 4 output device 5 storage device

Claims (1)

[Claims] 1. A plurality of preliminarily prepared prediction methods for calculating an optimal structure of a molecule based on a force acting between atoms in a molecular design support method for inputting an initial structure of a molecule to be designed and performing a structure optimization calculation. And a step of determining an optimum one from a plurality of prediction solutions obtained by the calculation step.