CN109920486B

CN109920486B - Method for improving molecular dynamics batch modeling efficiency based on Shell language

Info

Publication number: CN109920486B
Application number: CN201910021513.3A
Authority: CN
Inventors: 杨亮
Original assignee: Jiangsu University of Technology
Current assignee: Jiangsu University of Technology
Priority date: 2019-01-10
Filing date: 2019-01-10
Publication date: 2021-03-16
Anticipated expiration: 2039-01-10
Also published as: CN109920486A

Abstract

The invention relates to an improvement of a modeling method, in particular to a method for improving molecular dynamics batch modeling efficiency based on Shell language, which comprises the following steps: step one, establishing a basic model for molecular dynamics calculation; modifying main parameters in the basic model into undetermined parameters, and modifying the basic model into an undetermined model; copying and renaming the undetermined model through the Shell language to obtain a target model containing undetermined parameters; setting undetermined parameters as target parameters through Shell language to obtain a target model; and step five, the target models are generated in batches under the control of Shell language circulation, so that the batch modeling efficiency is greatly improved, the working intensity of scientific research personnel is reduced, and the possibility of manual operation errors is avoided.

Description

Method for improving molecular dynamics batch modeling efficiency based on Shell language

Technical Field

The invention relates to improvement of a modeling method, in particular to a method for improving molecular dynamics batch modeling efficiency based on Shell language.

Background

The molecular dynamics method is a computer simulation experiment method and is an important tool for researching the science of the nano materials. The technology can obtain the motion trail of atoms, can observe various microscopic details in the deformation process of the material, and is a powerful supplement to theoretical analysis and experimental tests. The wide application of the molecular dynamics simulation method has important significance for promoting the development of the nanometer material science.

After the material enters the nanometer scale, the material shows different physical and chemical characteristics from the material in the macroscopic scale, wherein one effect is a size effect, which means that the property of the nanometer material is related to the size of the nanometer material. Therefore, regardless of micro-nano scale experiments or molecular dynamics simulation, the size of the nano material is considered, and a series of nano materials with the sizes can be tested.

For example, the tensile properties of nanowires are studied by molecular dynamics simulation, and a series of nanowire models with different three-dimensional sizes need to be established, wherein the number of nanowire models is dozens, and the number of nanowire models is hundreds. The establishment of a geometric model of a cuboid nanowire requires three geometric dimensions of length, width and height, if each geometric model is manually operated, the basic model needs to be continuously copied, the model is opened, and the three-dimensional dimensions in the model need to be modified, so that the workload is huge, the time and the labor are consumed, and errors are easy to occur.

Disclosure of Invention

Aiming at the defects in the prior art, the invention provides the method for improving the molecular dynamics batch modeling efficiency based on the Shell language, which not only greatly improves the batch modeling efficiency and lightens the working intensity of scientific research personnel, but also avoids the possibility of manual operation errors.

In order to achieve the technical purpose, the technical scheme of the invention is that the method for improving the molecular dynamics batch modeling efficiency based on the Shell language comprises the following steps:

step one, establishing a basic model for molecular dynamics calculation;

modifying main parameters in the basic model into undetermined parameters, and modifying the basic model into an undetermined model;

copying and renaming the undetermined model through the Shell language to obtain a target model containing undetermined parameters;

setting undetermined parameters as target parameters through Shell language to obtain a target model;

and fifthly, generating the target models in batch through Shell language circulation control.

Preferably, in the second step, the main parameters in the basic model are modified into undetermined parameters, and the basic model is modified into an undetermined model, namely, the geometric dimension parameters in the basic model setting file are modified into the undetermined parameters, and the basic model is modified into the undetermined model with the geometric dimension being undetermined.

Preferably, in the third step, the objective model containing the undetermined parameters is obtained by copying and renaming the undetermined model through the Shell language, which means that the undetermined model with undetermined geometric dimension is copied through a cp command of the Shell language, and is renamed by taking the objective parameters as characteristics to obtain the objective model containing the undetermined parameters.

Preferably, in the fourth step, the undetermined parameter is set by the Shell language as the target parameter to obtain the target model, which means that the undetermined parameter in the target model setting file is set as the target parameter by the sed command of the Shell language to obtain the required target model.

Preferably, the step five of generating the target models in batch through the Shell language loop control means that the target models are generated in batch by repeating the step three and the step four through the Shell language loop control.

As can be seen from the above description, the present invention has the following advantages: the method for improving the molecular dynamics batch modeling efficiency based on the Shell language not only greatly improves the batch modeling efficiency, lightens the working intensity of scientific research personnel, but also avoids the possibility of manual operation errors.

Drawings

FIG. 1 is a method for improving the molecular dynamics batch modeling efficiency based on Shell language.

Detailed Description

The invention is further illustrated in the following description with reference to the given figures and specific examples, which are to be understood as merely illustrative of the invention and not as limiting its scope, based on which all other embodiments can be obtained by the person skilled in the art without inventive step. All fall within the scope of the invention.

In specific implementation, with reference to fig. 1, a basic model of molecular dynamics calculation is established in step one:

the basic geometric model established was a cuboid nanowire with three dimensions of 10a 2a 3a, where a is the lattice constant of the material, described in the LAMMPS programming language as

region nanowire block 0 10 0 2 0 3

The geometric model is stored in a setting file in. All the setting files are placed in a folder nanowire, which is a basic model and can be run by using molecular dynamics software LAMMPS to obtain reasonable results.

Step two, modifying the main parameters in the basic model into undetermined parameters, and modifying the basic model into an undetermined model:

modifying the main geometric parameters in the basic model setting file established in the step one, namely the three-dimensional size of the cuboid into undetermined parameters, such as TBDX, TBDY and TBDZ, which are described as undetermined parameters by using LAMMPS program language

region nanowire block 0TBDX 0TBDY 0TBDZ

And meanwhile, the positioned folder nanowire is modified into TBD _ nanowire, namely the undetermined model with undetermined geometric dimension.

Thirdly, copying the undetermined model through the Shell language and renaming to obtain a target model containing undetermined parameters:

copying and renaming the pending model TBD _ nanowire through a cp command of the Shell language, wherein the name of the pending model TBD _ nanowire comprises target three-dimensional size parameters of $ X, $ Y, $ Z and is described as the model in the Shell language

cp-r TBD_nanowire $X_$Y_$Z_nanowire

Step four, setting undetermined parameters as target parameters through Shell language to obtain a target model:

setting undetermined parameters TBDX, TBDY and TBDZ in the target model as target three-dimensional size parameters through sed commands of Shell language, and describing the parameters as target three-dimensional size parameters by the Shell language

sed-i“s/TBDX/$X/g”in.nanowire

sed-i“s/TBDY/$Y/g”in.nanowire

sed-i“s/TBDZ/$Z/g”in.nanowire

Step five, generating target models in batches through Shell language circulation control:

and repeating the third step and the fourth step through the loop control of the Shell language, and generating the target model in batches, wherein for example, the length X is selected to be three sizes of 10a, 20a and 30a, the width Y is selected to be four sizes of 2a, 3a, 4a and 5a, the height Z is selected to be two sizes of 3a and 6a, and the target model is described as being in the Shell language

for X in 'seq 101030' # (cycle one, X is 10a, 20a, 30a in sequence)

do

for Y in 'seq 215' # (cycle two, Y is 2a, 3a, 4a, 5a in sequence)

do

for Z in 'seq 336' # (cycle three, Z is 3a, 6a in sequence)

do

cp-r TBD _ nanowire $ X _ $ Y _ $ Z _ nanowire # (step three)

cd $ X _ $ Y _ $ Z _ nanowire # (entering the pending model whose geometry is pending)

sed-i "s/TBDX/$ X/g" in. nanowire # (step four)

sed-i“s/TBDY/$Y/g”in.nanowire

sed-i“s/TBDZ/$Z/g”in.nanowire

cd.. # (exit target model)

done

This embodiment can quickly generate 24 target models with lengths X of 10a, 20a, and 30a, widths Y of 2a, 3a, 4a, and 5a, and heights Z of 3a and 6a, respectively, for a total of 3 × 4 × 2.

The present invention and its embodiments have been described above, and the description is not intended to be limiting, and the drawings are only one embodiment of the present invention, and the actual configuration is not limited thereto. In summary, those skilled in the art should appreciate that they can readily use the disclosed conception and specific embodiments as a basis for designing or modifying other structures for carrying out the same purposes of the present invention without departing from the spirit and scope of the invention as defined by the appended claims.

Claims

1. A method for improving molecular dynamics batch modeling efficiency based on Shell language is characterized in that: the method comprises the following steps:

step one, establishing a basic model for molecular dynamics calculation;

step five, generating target models in batches through Shell language circulation control;

modifying the main parameters in the basic model into undetermined parameters, modifying the basic model into an undetermined model, namely modifying the geometric dimension parameters in the basic model setting file into undetermined parameters, and modifying the basic model into the undetermined model with the geometric dimension to be determined;

in the third step, the undetermined model is copied and renamed through the Shell language to obtain a target model containing undetermined parameters, namely, the undetermined model with undetermined geometric dimension is copied through a cp command of the Shell language and renamed by taking the target parameters as characteristics to obtain the target model containing undetermined parameters;

setting the undetermined parameters as target parameters through the Shell language to obtain a target model, namely setting the undetermined parameters in a target model setting file as the target parameters through a sed command of the Shell language to obtain a required target model;

and in the fifth step, the target models are generated in batch through the Shell language circulation control, namely, the target models are generated in batch through the Shell language circulation control by repeating the third step and the fourth step.