JP2008065556A - Molecule formation simulation method and program - Google Patents

Abstract

<P>PROBLEM TO BE SOLVED: To provide a molecule formation simulation method and program that automatically simulate the formation of a molecule having a layer structure involving van der Waals potential. <P>SOLUTION: The computerized molecule formation simulation method calculates bonding potentials of covalent bonds of target element atoms at each time point of a molecular dynamics simulation by means of a processor, determines and clusters the bonds of the target element atoms while removing catalytic atoms growing the target element atoms and the target element atoms in contact with the catalytic atoms, calculates van der Waals potentials only among different clusters resulting from the clustering, which are assumed to be single layers, and automatically simulates and displays the formation of a molecule having a layer structure involving van der Waals potential according to the calculated bonding potentials and van der Waals potentials. <P>COPYRIGHT: (C)2008,JPO&INPIT

Description

  The present invention relates to a molecular formation simulation method and program, and in particular, simulates the formation of a molecule having a layer structure in which van der Waals potential is interposed, such as a multi-layered multi-walled nanotube or a bundled nanotube composed of a plurality of nanotubes. The present invention relates to a molecule formation simulation method to be performed, and a program for causing a computer to perform such a molecule formation simulation.

  The formation mechanism of carbon nanotubes is not yet well understood. Elucidating the formation mechanism of carbon nanotubes through simulation and proposing structure control methods is indispensable for device application of carbon nanotubes. Until now, several simulations of the formation of single-walled carbon nanotubes as shown in FIG. 1 have been performed by the first principle molecular dynamics method (for example, Non-Patent Document 1). However, conventionally, a formation simulation of a multi-layer nanotube composed of a plurality of layers as shown in FIG. 2 or a bundle nanotube composed of a plurality of nanotubes as shown in FIG. 3 has not been performed. 2 and 3, vdW indicates Van der Waals force.

  Conventionally, for example, the simulation of the formation of a carbon nanotube having a layer structure in which a van der Waals potential intervenes has not been performed because of a strong bonding potential of a short distance (˜2 （) between carbon atoms and a long distance (˜3Å). This is because it is difficult to coexist with the weak van der Waals potential. FIG. 4 is a diagram for explaining a bond potential by a covalent bond, and FIG. 5 is a diagram for explaining a van der Waals potential by a van der Waals binding. 4 and 5, the vertical axis represents potential energy, and the horizontal axis represents interatomic distance. The solid line indicates the bond potential due to the covalent bond, and the broken line indicates the van der Waals potential due to the van der Waals bond.

In a special structure in which the form of atomic bonds is predetermined, the operator of the simulation system can classify the cases by manually setting the bond form. Since recombination of the binding occurs, the binding form cannot be determined in advance. In this case, as can be seen from FIGS. 4 and 5 showing the potential energy, when the potential energy of the covalent bond and the van der Waals bond is coexisted, it is always controlled by the van der Waals potential. In addition, although it is conceivable to divide the bond form according to the interatomic distance, it is affected by the potential at a position depending on the initial value, and the potential cannot be changed. Furthermore, it is conceivable to divide the bond form according to the number of bond bonds, but the bond angle and the state of bonding of surrounding atoms must be taken into consideration, which makes the simulation procedure very complicated. End up.
Y. Shibuta, S. Maruyama, Chemical Physics Letter 382, 381 (2003)

  Conventionally, it has been difficult to coexist the bond potential and the van der Waals potential, so there has been a problem that no molecular formation simulation method has been proposed for simulating the formation of molecules having a layer structure with the van der Waals potential. .

  Therefore, an object of the present invention is to provide a molecule formation simulation method and program capable of automatically performing the formation simulation of a molecule having a layer structure in which van der Waals potential is interposed.

  The above-described problem is a molecular formation simulation method in which a molecule formation simulation is performed by a computer system having a processor, a storage unit, and a display unit. The target element is calculated by the processor in a state in which the first calculation step calculated by the processor and stored in the storage unit, the catalyst atoms for growing the target element atoms, and the target element atoms in contact with the catalyst atoms are removed. A clustering step in which the bonding state between atoms is examined to perform clustering, and the clustering result is stored in the storage unit, and the clustering result is read from the storage unit, and each cluster obtained from the clustering result is stored in one layer. Only between different clusters A second calculation step of calculating a Ndelwals potential by the processor and storing it in the storage unit; reading out a coupling potential and a van der Waals potential from the storage unit; Achieved by a molecular formation simulation method characterized in that the computer system automatically performs a simulation step of simulating the formation of a molecule having a layer structure with potential intervening and displaying the simulation result on the display unit. it can.

  The above-described problem is a program for causing a computer that can be connected to the storage unit and the display unit to perform a simulation of molecule formation, and to the computer by a covalent bond of target element atoms at each time of molecular dynamics simulation A first calculation procedure for calculating the potential and storing the potential element in the storage unit; and the target element in a state in which the catalyst atom for growing the target element atom and the target element atom in contact with the catalyst atom are removed from the computer A clustering procedure for checking the bonding state between atoms and performing clustering, and storing the clustering result in the storage unit, and causing the computer to read the clustering result stored in the clustering procedure from the storage unit. Each cluster obtained by this clustering result is regarded as one layer. A second calculation procedure for calculating the van der Waals potential only between different clusters and storing it in the storage unit; and a coupling potential and a van der Waals potential stored in the computer by the first and second calculation procedures Simulation procedure for causing the display unit to display a simulation result by automatically performing a simulation of the formation of a molecule having a layer structure with a van der Waals potential intervening based on these potentials It can be achieved by a program characterized by including.

  ADVANTAGE OF THE INVENTION According to this invention, the molecular formation simulation method and program which can perform automatically the simulation of the formation of the molecule | numerator which has the layer structure which Van der Waals potential interposes are realizable.

  The present invention simulates the formation of molecules having a layered structure with a van der Waals potential, such as multi-layer nanotubes composed of a plurality of layers and bundle nanotubes composed of a plurality of nanotubes.

  Taking the case of carbon nanotubes with a layer structure as an example, in the simulation process that you want to draw, for example, a gas containing carbon that has come in as a gas dissolves in the catalyst metal and decomposes, creating a carbon network, If the layers are formed separately, van der Waals force acts between them, and the interlayer distance is maintained. On the other hand, when carbon atoms fly near the already formed layer, when the layer is formed in the carbon network or near the already formed layer, the layer moves to maintain the interlayer distance. Or

  Therefore, at each time of molecular dynamics simulation, first, the bond potential by the covalent bond of the target element atom, for example, a carbon atom is calculated, and the catalyst atom for growing the carbon atom and the carbon atom in contact with it are removed. Clustering is performed by examining the bonding state between carbon atoms. Each cluster obtained by this clustering is regarded as one layer, and the van der Waals potential between different clusters is calculated. Thus, based on the calculated bond potential and the van der Waals potential calculated according to the recombination of the bonds that occurs from time to time, it has a layer structure in which van der Waals potentials such as multi-wall nanotubes and band nanotubes intervene Realize molecular formation simulation to form molecules.

  Thereby, the interlayer distance by the van der Waals force of different layers is maintained, and carbon atoms can also be incorporated into the network of already formed layers. Further, when a layer is formed in the vicinity of the already formed layer, the bond potential is weakened, and the distance between the layers is slightly increased, so that the van der Waals force can be automatically changed. Therefore, when a new layer of carbon atoms is formed from a network of carbon atoms as shown in FIG. 6A, for example, carbon nanotubes having a layer structure can be formed as shown in FIG. 6B. FIG. 6 is a diagram illustrating the formation of a carbon nanotube having a layer structure.

  As described above, in the present invention, both potentials can be handled by coexisting the binding potential and the van der Waals potential corresponding to the recombination of the coupling that occurs every moment without determining the coupling form in advance. For this reason, it is possible to automatically perform the formation process of various molecules having a layer structure in which a multi-wall nanotube formation process, a bundle nanotube formation process, a van der Waals potential intervene, and the like.

  Hereinafter, each embodiment of the molecular formation simulation method and the program of the present invention will be described with reference to FIG.

  One embodiment of the molecule formation simulation method of the present invention uses one embodiment of the program of the present invention. In this embodiment, the present invention is applied to a computer system. FIG. 7 is a perspective view showing a computer system to which the present invention is applied in this embodiment.

  A computer system 100 shown in FIG. 7 displays an image of a molecule or the like formed by a molecule formation simulation on a display screen 102a in accordance with an instruction from the main body 101 including a CPU (processor) and a disk drive. Another computer by accessing a display (display unit) 102, a keyboard 103 for inputting various information to the computer system 100, a mouse 104 for designating an arbitrary position on the display screen 102a of the display 102, an external database, etc. A modem 105 for downloading a program or the like stored in the system is included.

  A program that causes the computer system 100 to have at least a molecular formation simulation function, which is stored in a portable recording medium such as the disk 110 or downloaded from the recording medium 106 of another computer system using a communication device such as the modem 105 ( This embodiment of the molecular formation software is input to the computer system 100 and compiled. In this embodiment of the program, the computer system 100 (that is, a CPU 201 described later) is operated as a simulator (or simulation system) having a molecule formation simulation function. This embodiment of the program may be stored in a computer-readable recording medium such as the disk 110, for example. The computer-readable recording medium is not limited to a portable recording medium such as a disk 110, an IC card memory, a magnetic disk such as a floppy (registered trademark) disk, a magneto-optical disk, or a CD-ROM. Various recording media accessible by a computer system connected via a communication device such as a LAN or communication means are included.

  FIG. 8 is a block diagram illustrating a configuration of a main part in the main body 101 of the computer system 100. In FIG. 1, the main unit 101 includes a CPU 201 connected by a bus 200, a memory unit 202 including a RAM and a ROM, a disk drive 203 for the disk 110, and a hard disk drive (HDD) 204. In this embodiment, the display 102, the keyboard 103, and the mouse 104 are also connected to the CPU 201 via the bus 200, but these may be directly connected to the CPU 201. The display 102 may be connected to the CPU 201 via a known graphic interface (not shown) that processes input / output image data.

  The configuration of the computer system 100 is not limited to the configuration shown in FIGS. 7 and 8, and various known configurations may be used instead.

  Next, the operation of this embodiment will be described with reference to FIGS. FIG. 9 is a flowchart for explaining the process of obtaining the number and atomic number of carbon-carbon bonds (hereinafter simply referred to as carbon-carbon bonds), and FIG. 10 is a carbon-metal bond (hereinafter simply referred to as carbon-metal bonds). ) And an atomic number acquisition process. FIG. 11 is a flowchart illustrating a process for calculating the number of bonds of each carbon atom. FIG. 12 is a flowchart for explaining a process for determining whether or not a metal is in contact, FIG. 13 is a flowchart for explaining a process for calculating van der Waals forces between clusters, and FIG. 14 is a van der Waals for a single carbon atom. It is a flowchart explaining the process which calculates force. The processing shown in FIGS. 9 to 14 is executed by the CPU 201 shown in FIG. Specifically, in the processing of the CPU 201, intermediate data and the like are temporarily stored in the storage unit based on programs and data (parameters) stored in the storage unit such as the memory unit 202, the disk drive 203, and the HDD 204. This is done by using it as a work area.

  In FIG. 9, natom1 is the number of carbon atoms, t1 is the position coordinate of the carbon atom, rc11 is a bond determination condition of the carbon-carbon bond, and rc11 is 2Å, for example. In step S1, ia is set to 1, and it is determined whether or not ia ≦ natom1. If the decision result in the step S1 is YES, a step S2 sets ja to 1, and decides whether or not ja ≦ natom1. If the decision result in the step S2 is YES, the step S3 calculates the difference dr of the carbon atom coordinates based on dr (i) = t1 (i, ja) -t1 (i, ia), i = 1, 3. Calculate and store in storage. In step S4, the inter-carbon atom distance r is calculated based on r = sqrt (dr (1) ** 2 + dr (2) ** 2 + dr (3) ** 2) and stored in the storage unit. Here, sqrt is a square root, and ** 2 is a power of 2. Step S5 determines whether r <rc11 using the inter-carbon distance r stored in the storage unit. If the determination result is YES, step S6 is based on nr11 = nr11 + 1. The number of carbon-carbon bonds is calculated and stored in the storage unit. In step S7, atomic numbers iar11 (nr) and Jar11 (nr) for the bonds are obtained based on iar11 (nr) = ia, Jar11 (nr) = ja, and stored in the storage unit.

  If the decision result in the step S1 is NO, the process advances to a step S11 in FIG.

  If the determination result in step S2 is NO, ia is incremented by 1, and then the process returns to step S1 to determine whether or not ia ≦ natom1.

  If the determination result in step S5 is NO, or after step S7, ja is incremented by 1, and then the process returns to step S2 to determine whether ja ≦ natom1.

  In this way, the number of carbon-carbon bonds and the atomic number are acquired and stored in the storage unit.

  In FIG. 10, natom2 is the number of metal atoms, t2 is the position coordinate of the metal atom, rc12 is a bond determination condition for the carbon-metal bond, and rc12 is 3Å, for example. A step S11 sets ia to 1 and determines whether or not ia ≦ natom1. If the decision result in the step S11 is YES, a step S12 decides whether ja is set to 1 and whether ja ≦ natom2. If the decision result in the step S12 is YES, the step S13 calculates the difference dr of the carbon atom coordinates based on dr (i) = t2 (i, ja) -t1 (i, ia), i = 1, 3. Calculate and store in storage. In step S14, the inter-carbon atom distance r is calculated based on r = sqrt (dr (1) ** 2 + dr (2) ** 2 + dr (3) ** 2) and stored in the storage unit. Step S15 determines whether r <rc12 using the inter-carbon atom distance r stored in the storage unit. If the determination result is YES, step S16 is based on indvdw (ia) = 1. Set the van der Waals force index indvdw to the carbon atom. The index indvdw of a single carbon atom is set to 0 at the beginning of the calculation, and the index indvdw of the carbon atom in contact with the metal is changed to 1. In step S17, the number nr12 of carbon-metal bonds is calculated based on nr12 = nr12 + 1 and stored in the storage unit. In step S18, the atom numbers iar12 (nr) and Jar12 (nr) for the bonds are obtained based on iar12 (nr) = ia, Jar12 (nr) = ja, and stored in the storage unit.

  If the decision result in the step S11 is NO, the process advances to a step S21 in FIG.

  If the determination result in step S12 is NO, ia is incremented by 1, and then the process returns to step S11 to determine whether or not ia ≦ natom1.

  The determination result of step S15 is NO, or after step S18, ja is incremented by 1, and then the process returns to step S12 to determine whether ja ≦ natom2.

  In this way, the number and atomic number of carbon-metal bonds are acquired and stored in the storage unit.

  In FIG. 11, step S21 sets ia to 1 and determines whether or not ia ≦ natom1. If the decision result in the step S21 is YES, the step S22 sets the bond number by setting the number nb1 (a) of carbon bonds of each carbon atom and the number nb2 (ia) of metal bonds of each carbon atom to 0, respectively. Initialize the number. After step S22, ia is incremented by 1, and then the process returns to step S21 to determine whether or not ia ≦ natom1. If the decision result in the step S21 is NO, the process advances to a step S23.

  A step S23 sets ir to 1, and determines whether or not ir ≦ nr11. If the decision result in the step S23 is YES, a step S24 is nb1 (iar11 (ir)) = nb1 (iar11 (ir)) + 1, nb1 (jar11 (ir)) = nb1 (jar11 (ir)) + 1 The number of carbon bonds of carbon atoms is calculated from the above and stored in the storage unit. After step 24, ir is incremented by 1, and then the process returns to step S23 to determine whether or not ir ≦ nr11. If the decision result in the step S23 is NO, the process advances to a step S25.

  A step S25 sets ir to 1, and determines whether or not ir ≦ nr12. If the decision result in the step S25 is YES, a step S26 calculates the number of metal bonds of carbon atoms from nb2 (iar12 (ir)) = nb2 (iar12 (ir)) + 1 and stores it in the storage unit. After step 26, ir is incremented by 1, and then the process returns to step S25 to determine whether or not ir ≦ nr12. If the decision result in the step S25 is NO, the process advances to a step S31 in FIG.

  In this way, the number of bonds of each carbon atom is calculated and stored in the storage unit.

  In FIG. 12, nc represents the number of clusters, and indc represents the number of the cluster to which the carbon atom belongs. indc is -1 when there is a metal bond and 0 when there is no metal bond. A step S31 sets ia to 1 and determines whether or not ia ≦ natom1. If the decision result in the step S31 is YES, a step S32 decides whether or not indvdw (ia) = 1, nb1 (ia) = 0, and nb2 (ia) = 0. If the decision result in the step S32 is YES, a step S33 sets the index indvdw (ia) to 0, and returns the index indvdw of the carbon atom that has jumped out after contacting the metal to 0. In step S34, it is determined whether nb2 (ia)> 0. If the determination result is YES, the process proceeds to step S35, and if the determination result is NO, the process proceeds to step S36. In step S35, the cluster number indc (ia) is set to -1, and the cluster number indc of the carbon atom in contact with the metal is set to -1. A step S36 sets the cluster number indc (1) to 0. After step S35 or step S36, ia is incremented by 1, and then the process returns to step S31 to determine whether or not ia ≦ natom1.

  On the other hand, if the decision result in the step S31 is NO, the step S37 performs clustering only with carbon atoms that are not in contact with the metal. Specifically, clustering is performed using only the atoms with the cluster number indc (ia) = 0, the cluster number nc and the cluster number indc (ia) are acquired and stored in the storage unit. A step S38 sets ic to 0 and determines whether or not ic ≦ nc. If the decision result in the step S38 is YES, a step S39 initializes the atomic number nac of the cluster by setting nac (ic) to 0. After step S39, ic is incremented by 1, and the process returns to step S38 to determine whether or not ic ≦ nc.

  If the decision result in the step S38 is NO, a step S40 sets ia to 1 and decides whether or not ia ≦ natom1. If the decision result in the step S40 is YES, a step S41 decides whether or not indc (ia)> 0. If the decision result in the step S41 is YES, the step S42 sets nac (indc (ia)) = nac (indc (ia)) + 1, inda (nac (indc (ia), indc (ia))) = ia Based on the number of atoms and the atomic number of the cluster based on the result, the result is stored in the storage unit, the determination result of step S41 is NO, or after step S42, ia is incremented by 1, and the process returns to step S40. It is determined whether or not ≦ natom 1. If the determination result in step S40 is NO, the process proceeds to step S51 in FIG.

  In this way, clustering is performed only with carbon atoms that are not in contact with the metal, and the clustering result is stored in the storage unit.

  In FIG. 13, rcvdw is, for example, 6cm. In step S51, ic is set to 0, and it is determined whether or not ic ≦ nc. If the decision result in the step S51 is YES, a step S52 decides whether or not nac (ic)> 0. If the decision result in the step S52 is YES, a step S53 sets ia to 1 and decides whether or not ia ≦ nac (ic). If the decision result in the step S53 is YES, a step S54 decides whether or not indvdw (inda (ia, ic)) = 1. Indvdw = 0 is calculated as a single carbon atom by the process shown in FIG. If the decision result in the step S54 is YES, a step S55 sets jc to ic + 1 and decides whether jc ≦ nc. If the decision result in the step S55 is YES, a step S56 sets ja to 1, and determines whether or not ja ≦ nac (jc).

  If the decision result in the step S56 is YES, a step S57 sets dr (i) = t1 (i, inda (ja, ic))-t1 (i, inda (ia, ic)), i = 1, 3 Based on this, a cluster coordinate difference dr is calculated and stored in the storage unit. In step S58, a distance r between clusters is calculated based on r = sqrt (dr (1) ** 2 + dr (2) ** 2 + dr (3) ** 2) and stored in the storage unit. Step S59 determines whether r <rcvdw using the distance r between clusters stored in the storage unit. If the determination result is YES, step S60 determines s = (3.37 / r) *. * 6, The potential energy e between clusters is calculated based on e = e + 0.0096 * (s * ss) and stored in the storage unit. In addition, step S61 includes dr (i) = dr (i) / (r * r), f = 0.0096 * (-s * s * 12.0 + s * 6.0) * dr (i), hf (i, inda ( ia, ic)) = hf (i, inda (ia, ic)) + f, hf (i, inda (ja, jc)) = hf (i, inda (ja, jc))-f The van der Waals force f is calculated and stored in the storage unit.

  If the decision result in the step S51 is NO, the process advances to a step S71 in FIG.

  If the determination result in step S52 or step S53 is NO, ic is incremented by 1, and then the process returns to step S41 to determine whether ic ≦ nc.

  If the determination result in step S54 or step S55 is NO, ia is incremented by 1, and then the process returns to step S53 to determine whether or not ia ≦ nac (ic).

  If the decision result in the step S56 is NO, the jc is incremented by 1, and then the process returns to the step S55 to judge whether or not jc ≦ nc.

  If the determination result in step S59 is NO, or after step S61, ja is incremented by 1, and then the process returns to step S56 to determine whether ja ≦ nac (jc).

  In this way, van der Waals forces between the clusters are calculated and stored in the storage unit.

  In FIG. 14, rcmol is, for example, from 2 to 6 for the assumed molecule. When rcmol is large, carbon is unlikely to contact the metal near the carbon on the metal. Step S71 determines whether or not nac (0)> 0. If the determination result in Step S71 is YES, Step S72 sets ia to 1 and whether or not ia ≦ nac (0). Determine whether. If the decision result in the step S72 is YES, a step S73 decides whether or not indvdw (inda (ia, 0) = 0. If the decision result in the step S73 is YES, a step S74 is changed to ja. Is set to 1, and it is determined whether or not ja ≦ natom 1. If the determination result in the step S74 is YES, a step S75 determines whether or not ja = inda (ia, 0).

  If the decision result in the step S75 is YES, the step S76 determines that a single carbon atom is based on dr (i) = tau (i, ja) -tau (i, inda (ia, 0)), i = 1, 3. Is calculated and stored in the storage unit. Step S77 calculates the distance r between the single carbon atom and the cluster based on r = sqrt (dr (1) ** 2 + dr (2) ** 2 + dr (3) ** 2), and the storage unit To store. In step S78, it is determined whether r <rcmol using the distance r between the clusters stored in the storage unit. If the determination result is YES, step S79 determines s = (3.37 / r) * * 6, Calculate the potential energy e between the single carbon atom and the cluster based on e = e + 0.0096 * (s * ss) and store it in the storage unit. Also, step S80 is dr (i) = dr (i) / (r * r), f = 0.0096 * (-s * s * 12.0 + s * 6.0) * dr (i), hd (i, inda ( ia, 0) = hf (i, inda (ia, 0)) + f, hf (i, ja) = hf (i, ja) -f based on van der Waals force f between a single carbon atom and a cluster Calculate and store in storage.

  The process ends if the decision result in the step S71 or the step S72 is NO.

  If the determination result in step S73 or step S74 is NO, ia is incremented by 1, and then the process returns to step S72 to determine whether or not ia ≦ nac (0).

  The determination result of step S75 or step S78 is NO, or after step S80, ja is incremented by 1, and then the process returns to step S74 to determine whether ja ≦ natom1.

  In this way, the van der Waals force between the single carbon atom and the cluster is calculated and stored in the storage unit.

  Therefore, at each time of molecular dynamics simulation, the bond potential due to the covalent bond of the carbon atom that is the target element atom is calculated and stored, and the catalyst atom for growing the carbon atom and the carbon atom in contact with the catalyst atom are removed. Clustering is performed by checking the bonding state between carbon atoms in the state, storing the clustering result, reading the stored clustering result, and considering each cluster obtained from the clustering result as one layer between different clusters Just calculate and store the van der Waals potential, read out the stored binding potential and van der Waals potential, and based on these potentials, simulate the formation of a molecule with a layered structure mediated by the van der Waals potential On the computer Ri can be performed automatically display the results of the simulation. In this case, the molecule having a layer structure in which the van der Waals potential intervenes is a multi-layer (carbon) nanotube or a bundle (carbon) nanotube, and has a layer structure as shown in FIG. Carbon nanotubes are formed and displayed on the display screen 102 a of the display 102.

  The procedure or means for calculating the binding potential itself is well known. Conventionally, in a special structure in which the form of atomic bonds is determined in advance, the operator of the simulation system manually sets the bond form, that is, the van der Waals potential. Procedures or means for forming molecules based on a manually set fixed van der Waals potential are also well known. Therefore, in the present embodiment, by using a well-known procedure or means, in addition to the calculated and stored binding potential, the vandel that is automatically calculated and stored according to the recombination of the bond that occurs every moment is stored. It is possible to display a simulation result by performing a molecular formation simulation in which molecules are formed in consideration of the Waals potential.

  The present inventor conducted a molecular dynamics simulation for 1 ns at 1000 K from a structure in which an amorphous is attached to a single-walled nanotube to obtain a bond potential, obtains a van der Waals potential using the above calculation routine, and obtains a bond potential and a van der A simulation of molecule formation based on the Waals potential confirmed that a new layer structure was formed at the interlayer distance inside the nanotube.

  In addition, the present inventor supplies 100 atomic atoms to catalytic metal fine particles consisting of 108 atoms, performs molecular dynamics simulation at 1000 K for 100 ns to obtain a binding potential, and uses the above calculation routine to obtain the van der Waals potential. As a result, a simulation of the formation of molecules was performed based on the bond potential and van der Waals potential. As a result, it was confirmed that multi-walled carbon nanotube nuclei composed of two layers separated from each other were formed.

In addition, this invention also includes the invention attached to the following.
(Supplementary Note 1) A molecule formation simulation method for performing a simulation of molecule formation by a computer system having a processor, a storage unit, and a display unit,
A first calculation step of calculating a bond potential due to a covalent bond of a target element atom at each time of molecular dynamics simulation by the processor and storing it in the storage unit;
Clustering is performed by examining the bonding state between the target element atoms by the processor in a state where the catalyst atoms for growing the target element atoms and the target element atoms in contact with the catalyst atoms are removed, and the clustering result is stored in the storage unit A clustering step to store in
A clustering result is read from the storage unit, each cluster obtained by the clustering result is regarded as one layer, and the van der Waals potential between different clusters is calculated by the processor and stored in the storage unit. 2 calculation steps;
The binding potential and van der Waals potential are read out from the storage unit, and based on these potentials, the processor simulates the formation of molecules having a layer structure in which the van der Waals potential is interposed, and the simulation result is displayed on the display unit. A molecular formation simulation method, wherein the computer system automatically performs a simulation step to be displayed on the screen.
(Supplementary Note 2) The clustering step is based on the number of bonds between the target element atoms, the number of bonds between the target element atoms and the catalyst atoms, and whether each target element atom is in contact with the catalyst atoms. The molecule formation simulation method according to appendix 1, wherein the clustering is performed by the processor.
(Supplementary Note 3) The second calculation step includes a step of calculating van der Waals potential between each cluster by the processor and storing it in the storage unit, and calculating a van der Waals potential of a single target element atom by the processor. And storing the data in the storage unit. 3. The molecular formation simulation method according to appendix 1 or 2, characterized by comprising:
(Appendix 4) The target element is carbon,
The catalytic atom is a metal atom;
The molecule formation simulation method according to any one of appendices 1 to 3, wherein the molecule having a layer structure in which the van der Waals potential is interposed is a multi-wall carbon nanotube or a bundle carbon nanotube.
(Supplementary note 5) The simulation step is characterized in that molecules having a layer structure with the van der Waals potential formed by the processor as a result of the simulation are displayed on the display unit. The molecule formation simulation method according to claim 1.
(Supplementary Note 6) A program for causing a computer connectable to a storage unit and a display unit to perform a simulation of molecule formation,
A first calculation procedure for causing the computer to calculate a bond potential due to a covalent bond of a target element atom at each time of molecular dynamics simulation and to store it in the storage unit;
The computer is caused to perform clustering by examining the bonding state between the target element atoms in a state in which the catalyst atoms for growing the target element atoms and the target element atoms in contact with the catalyst atoms are removed. A clustering procedure to be stored in the storage unit;
The computer reads the clustering result stored in the clustering procedure from the storage unit, and regards each cluster obtained by the clustering result as one layer, and calculates the van der Waals potential only between different clusters. A second calculation procedure for calculating and storing in the storage unit;
The computer has a layer structure in which the coupling potential and van der Waals potential stored in the first and second calculation procedures are read from the storage unit and the van der Waals potential is interposed based on these potentials. And a simulation procedure for automatically performing a simulation of molecule formation and displaying a result of the simulation on the display unit.
(Supplementary note 7) The clustering procedure is performed by the computer to determine the number of bonds between the target element atoms, the number of bonds between the target element atoms and the catalyst atoms, and whether each target element atom is in contact with the catalyst atoms. The program according to appendix 6, wherein the clustering is performed based on whether or not.
(Supplementary Note 8) The second calculation procedure includes a procedure for causing the computer to calculate a van der Waals potential between each cluster and storing it in the storage unit, and for causing the computer to have a van der Waals potential of a single target element atom. The program according to appendix 6 or 7, characterized by comprising the steps of calculating and storing in the storage unit.
(Supplementary note 9) The target element is carbon,
The catalytic atom is a metal atom;
The program according to any one of appendices 6 to 8, wherein the molecule having a layer structure in which the van der Waals potential is interposed is a multi-walled carbon nanotube or a bundled carbon nanotube.
(Supplementary Note 10) The simulation procedure causes the computer to display on the display unit molecules having a layer structure intervening the van der Waals potential formed as a result of the simulation performed in the simulation procedure. The program according to any one of appendices 6 to 9.

  While the present invention has been described with reference to the embodiments, it is needless to say that the present invention is not limited to the above-described embodiments, and various modifications and improvements can be made within the scope of the present invention.

It is sectional drawing which shows a single-walled carbon nanotube. It is sectional drawing which shows a multi-walled nanotube. It is sectional drawing which shows a bundle nanotube. It is a figure explaining the coupling potential by a covalent bond. It is a figure explaining the van der Waals potential by van der Waals coupling. It is a figure explaining formation of the carbon nanotube which has a layered structure. 1 is a perspective view showing a computer system to which the present invention is applied. It is a block diagram explaining the structure of the principal part in the main-body part of a computer system. It is a flowchart explaining the acquisition process of the number of carbon-carbon bonds, and an atomic number. It is a flowchart explaining the acquisition process of the number of carbon-metal bonds, and an atomic number. It is a flowchart explaining the process which calculates the number of bonds of each carbon atom. It is a flowchart explaining the process which determines whether it is contacting the metal. It is a flowchart explaining the process which calculates the van der Waals force between each cluster. It is a flowchart explaining the process which calculates the van der Waals force of a single carbon atom.

Explanation of symbols

100 Computer System 101 Main Body 102 Display 102a Display Screen 103 Keyboard 104 Mouse 105 Modem 106 Recording Medium 110 Disk 200 Bus 201 CPU
202 Memory unit 203 Disk drive 204 Hard disk drive

Claims (5)

A molecule formation simulation method for performing a molecule formation simulation by a computer system having a processor, a storage unit, and a display unit,
A first calculation step of calculating a bond potential due to a covalent bond of a target element atom at each time of molecular dynamics simulation by the processor and storing it in the storage unit;
Clustering is performed by examining the bonding state between the target element atoms by the processor in a state where the catalyst atoms for growing the target element atoms and the target element atoms in contact with the catalyst atoms are removed, and the clustering result is stored in the storage unit A clustering step to store in
A clustering result is read from the storage unit, each cluster obtained by the clustering result is regarded as one layer, and the van der Waals potential between different clusters is calculated by the processor and stored in the storage unit. 2 calculation steps;
The binding potential and van der Waals potential are read out from the storage unit, and based on these potentials, the processor simulates the formation of molecules having a layer structure in which the van der Waals potential is interposed, and the simulation result is displayed on the display unit. A molecular formation simulation method, wherein the computer system automatically performs a simulation step to be displayed on the screen. A program for causing a computer connectable to a storage unit and a display unit to perform a simulation of molecule formation,
A first calculation procedure for causing the computer to calculate a bond potential due to a covalent bond of a target element atom at each time of molecular dynamics simulation and to store it in the storage unit;
The computer is caused to perform clustering by examining the bonding state between the target element atoms in a state in which the catalyst atoms for growing the target element atoms and the target element atoms in contact with the catalyst atoms are removed. A clustering procedure to be stored in the storage unit;
The computer reads the clustering result stored in the clustering procedure from the storage unit, and regards each cluster obtained by the clustering result as one layer, and calculates the van der Waals potential only between different clusters. A second calculation procedure for calculating and storing in the storage unit;
The computer has a layer structure in which the coupling potential and van der Waals potential stored in the first and second calculation procedures are read from the storage unit and the van der Waals potential is interposed based on these potentials. And a simulation procedure for automatically performing a simulation of molecule formation and displaying a result of the simulation on the display unit.   The clustering procedure is based on the number of bonds between the target element atoms, the number of bonds between the target element atoms and the catalyst atoms, and whether each target element atom is in contact with the catalyst atoms. The program according to claim 2, wherein the clustering is performed.   The second calculation procedure includes causing the computer to calculate a van der Waals potential between each cluster and storing it in the storage unit, and causing the computer to calculate a van der Waals potential of a single target element atom. The program according to claim 2 or 3, comprising a procedure for storing in the storage unit. The target element is carbon,
The catalytic atom is a metal atom;
The program according to any one of claims 2 to 4, wherein the molecule having a layer structure in which the van der Waals potential is interposed is a multi-walled carbon nanotube or a bundled carbon nanotube.

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