CN109920486A - A method of molecular dynamics batch modeling efficiency is improved based on Shell language - Google Patents
A method of molecular dynamics batch modeling efficiency is improved based on Shell language Download PDFInfo
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Abstract
The present invention relates to a kind of improvement of modeling method, in particular to a kind of methods for improving molecular dynamics batch modeling efficiency based on Shell language, comprising the following steps: Step 1: establishing Molecular Dynamics Calculation basic model；Step 2: the major parameter in modification basic model is undetermined parameter, basic model is revised as model undetermined；The object module containing undetermined parameter is obtained Step 3: passing through Shell speech reproduction model undetermined and renaming；Step 4: it is that target component obtains object module that undetermined parameter, which is arranged, by Shell language；Step 5: not only significantly improving batch modeling efficiency by Shell language loop control Mass production object module, alleviating the working strength of scientific research personnel, and avoid a possibility that manual operation malfunctions.
Description
Technical field
The present invention relates to a kind of improvement of modeling method, in particular to a kind of Shell language that is based on to improve molecular dynamics
The method of batch modeling efficiency.
Background technique
Molecular Dynamics method is a kind of method of Computer Simulation Experiment, is the important tool for studying nanometer material science.
The motion profile of the technology not only available atom, it can also be observed that various micro details in material deformation process, it is
To the strong supplement of theory analysis and experiment test.The extensive utilization of molecular dynamics simulation, for pushing nano material
The reach of science is significant.
After material enters nanoscale, the physicochemical characteristics different from macro-scale material is shown, one of effect
It should be dimensional effect, refer to that the property of nano material is related with the size of nano material size.Therefore whether micro-nano-scale
Experiment or molecular dynamics simulation, will consider the size of nano material, a series of nano material of sizes can be tested.
Such as the tensile property with molecular dynamics simulation research nano wire, it is different to need to establish a series of three-dimensional dimensions
Nanometer line model, it is few then tens, it is how then several hundred a.The geometrical model for establishing a cuboid nano wire needs length three
A geometric dimension needs constantly to replicate basic model, opens model, repairs if each geometrical model is manual operation
Change the three-dimensional dimension in model, workload is huge, time and effort consuming, and is easy to appear mistake.
Summary of the invention
For above-mentioned deficiency in the prior art, the present invention provides a kind of based on Shell language raising molecular dynamics batch
The method for measuring modeling efficiency, not only significantly improves batch modeling efficiency, alleviates the working strength of scientific research personnel, and keep away
A possibility that having exempted from manual operation error.
To realize the above technical purpose, the technical scheme is that a kind of improve molecular dynamics based on Shell language
The method of batch modeling efficiency, comprising the following steps:
Step 1: establishing Molecular Dynamics Calculation basic model；
Step 2: the major parameter in modification basic model is undetermined parameter, basic model is revised as model undetermined；
The object module containing undetermined parameter is obtained Step 3: passing through Shell speech reproduction model undetermined and renaming；
Step 4: it is that target component obtains object module that undetermined parameter, which is arranged, by Shell language；
Step 5: passing through Shell language loop control Mass production object module.
Preferably, the major parameter modified in basic model is undetermined parameter in step 2, basic model is revised as
Model undetermined refers to that the geometric dimension parameter that basic model is arranged in file is revised as undetermined parameter, basic model is modified
For geometric dimension model undetermined undetermined.
Preferably, passing through Shell speech reproduction model undetermined in step 3 and renaming being obtained containing undetermined parameter
Object module refers to the cp order by Shell language, geometric dimension model undetermined undetermined is replicated, and with target
Parameter, which is characterized, to be renamed, and the object module containing undetermined parameter is obtained.
Preferably, it is that target component obtains object module that undetermined parameter, which is arranged, by Shell language in step 4, it is
Refer to the sed order for passing through Shell language, sets target component for the undetermined parameter that object module is arranged in file, obtain institute
The object module needed.
Preferably, by Shell language loop control Mass production object module, referring in step 5 and passing through Shell
The loop control of language repeats step 3 and step 4, Mass production object module.
Above description can be seen that the present invention and have following advantages: improve molecule based on Shell language using of the invention
The method of dynamics batch modeling efficiency not only significantly improves batch modeling efficiency, and the work for alleviating scientific research personnel is strong
Degree, and avoid a possibility that manual operation malfunctions.
Detailed description of the invention
Fig. 1 is the method for the invention for improving molecular dynamics batch modeling efficiency based on Shell language.
Specific embodiment
Below with reference to the given attached drawing of the present invention and specific example, the present invention is further explained, it should be understood that these embodiments
It is only illustrative of the invention and is not intended to limit the scope of the invention, based on the embodiment of the present invention, ordinary skill people
Member's every other embodiment obtained under the premise of no creative work.Belong to protection scope of the present invention.
In the specific implementation, in conjunction with shown in attached drawing 1, Step 1: establishing Molecular Dynamics Calculation basic model:
The basic geometrical model established is the cuboid nano wire that three-dimensional dimension is 10a*2a*3a, and wherein a is material
Lattice constant is described as with LAMMPS program language
region nanowire block 0 10 0 2 0 3
The geometrical model is stored in setting file in.nanowire, since other settings are not the weights that the present invention is implemented
Point, therefore without repeating.All setting files are placed in file nanowire, this document folder is basic model, Ke Yiyong
Molecular dynamics software LAMMPS runs to obtain reasonable result.
Step 2: the major parameter in modification basic model is undetermined parameter, basic model is revised as model undetermined:
The main geometric parameters in file, the i.e. three-dimensional dimension of cuboid are arranged in the basic model established in step 1
It is revised as undetermined parameter, such as TBDX, TBDY, TBDZ, is described as with LAMMPS program language
region nanowire block 0TBDX 0TBDY 0TBDZ
Meanwhile the file nanowire at place is revised as TBD_nanowire, as geometric dimension is undetermined to cover half
Type.
The object module containing undetermined parameter is obtained Step 3: passing through Shell speech reproduction model undetermined and renaming:
By the cp order of Shell language, model TBD_nanowire undetermined is replicated, and is renamed, title
Comprising target three-dimensional dimension parameter $ X, $ Y, $ Z, it is with Shell language description
cp-r TBD_nanowire $X_$Y_$Z_nanowire
Step 4: it is that target component obtains object module that undetermined parameter, which is arranged, by Shell language:
By the sed order of Shell language, target is set by the undetermined parameter TBDX, TBDY, TBDZ in object module
Three-dimensional dimension parameter is with Shell language description
sed-i“s/TBDX/$X/g”in.nanowire
sed-i“s/TBDY/$Y/g”in.nanowire
sed-i“s/TBDZ/$Z/g”in.nanowire
Step 5: passing through Shell language loop control Mass production object module:
By the loop control of Shell language, step 3 and step 4, Mass production object module, such as length X are repeated
Selection three having a size of 10a, 20a, 30a, width Y select four having a size of 2a, 3a, 4a, 5a, height Z select two having a size of
3a, 6a are with Shell language description
10 10 30`# of for X in`seq (one, X of circulation is followed successively by 10a, 20a, 30a)
do
21 5`# of for Y in`seq (two, Y of circulation is followed successively by 2a, 3a, 4a, 5a)
do
33 6`# of for Z in`seq (three, Z of circulation is followed successively by 3a, 6a)
do
Cp-r TBD_nanowire $ X_ $ Y_ $ Z_nanowire# (step 3)
Cd $ X_ $ Y_ $ Z_nanowire# (the undetermined model undetermined into geometric dimension)
Sed-i " s/TBDX/ $ X/g " in.nanowire# (step 4)
sed-i“s/TBDY/$Y/g”in.nanowire
sed-i“s/TBDZ/$Z/g”in.nanowire
Cd..# (exits object module)
done
done
done
It is respectively 10a, 20a, 30a that the present embodiment, which can quickly generate length X, and width Y is respectively 2a, 3a, 4a, 5a, height
Degree Z is respectively 3a, 6a, amounts to 3*4*2=24 object module.
The present invention and its embodiments have been described above, description is not limiting, it is shown in the drawings also only
It is one of embodiments of the present invention, actual structure is not limited to this.All in all if the ordinary skill people of this field
Member is enlightened by it, without departing from the spirit of the invention, is not inventively designed similar to the technical solution
Frame mode and embodiment, be within the scope of protection of the invention.
Claims (5)
1. a kind of method for improving molecular dynamics batch modeling efficiency based on Shell language, it is characterised in that: including following step
It is rapid:
Step 1: establishing Molecular Dynamics Calculation basic model；
Step 2: the major parameter in modification basic model is undetermined parameter, basic model is revised as model undetermined；
The object module containing undetermined parameter is obtained Step 3: passing through Shell speech reproduction model undetermined and renaming；
Step 4: it is that target component obtains object module that undetermined parameter, which is arranged, by Shell language；
Step 5: passing through Shell language loop control Mass production object module.
2. the method according to claim 1 for improving molecular dynamics batch modeling efficiency based on Shell language, feature
Be: in step 2, the major parameter modified in basic model is undetermined parameter, and basic model is revised as model undetermined, is
Refer to that the geometric dimension parameter that basic model is arranged in file is revised as undetermined parameter, basic model is revised as geometric dimension and is waited for
Fixed model undetermined.
3. the method according to claim 1 for improving molecular dynamics batch modeling efficiency based on Shell language, feature
It is: in step 3, passes through Shell speech reproduction model undetermined and renaming obtains the object module containing undetermined parameter, be
Refer to the cp order for passing through Shell language, geometric dimension model undetermined undetermined is replicated, and the weight characterized by target component
New name, obtains the object module containing undetermined parameter.
4. the method according to claim 1 for improving molecular dynamics batch modeling efficiency based on Shell language, feature
Be: in step 4, it is that target component obtains object module that undetermined parameter, which is arranged, by Shell language, is referred to through Shell language
The sed order of speech sets target component for the undetermined parameter that object module is arranged in file, obtains required object module.
5. the method according to claim 1 for improving molecular dynamics batch modeling efficiency based on Shell language, feature
It is: in step 5, by Shell language loop control Mass production object module, refers to the circulation control by Shell language
System repeats step 3 and step 4, Mass production object module.
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