CN111599421A - Full-automatic phonon spectrum calculation method and system based on high-flux material calculation - Google Patents
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Abstract
The invention discloses a full-automatic phonon spectrum calculation method and a system thereof based on high-flux material calculation, wherein the method comprises the following steps: A. creating a phonon spectrum calculation workflow by using a workflow design module, loading a crystal structure to be calculated and setting parameters; B. utilizing a workflow execution engine module to call an analysis and execution module to analyze and execute the phononic spectrum calculation workflow; C. putting a crystal structure to be calculated into a crystal structure set module to be calculated; D. constructing a supercell through a perturbation structure module, and generating perturbation structures in batches; E. performing static calculation and energy calculation on the supercell and the perturbation structure by using a first principle static calculation module to obtain atom stress data; F. and calculating to obtain a phonogram spectrum and obtain related thermodynamic data through a phonogram calculation module. By adopting the invention, multi-step connection and automatic flow of the calculation of the phononic spectrum can be realized in a one-key, networked and graphical mode, so that the calculation of the phononic spectrum is simple and easy.
Description
Technical Field
The invention relates to a material genetic engineering and solid physical material calculation technology, in particular to a full-automatic phonon spectrum calculation method and a full-automatic phonon spectrum calculation system based on high-throughput material calculation.
Background
Phonons (Phonon), the normal mode energy quanta of lattice vibrations. In the concept of solid physics, atoms or molecules in a crystalline solid are arranged in a certain order on a crystal lattice. In the crystal, there are interactions between atoms, which are not static, and on the one hand they always vibrate continuously around their equilibrium position; on the other hand, these atoms are in turn linked together by the interaction forces between them, i.e. their respective vibrations are not independent of each other. The interaction forces between atoms can generally be well approximated as elastic forces.
The phonon spectrum is an important index for judging whether a system can exist stably, and thermodynamic properties such as phonon dispersion spectrum, phonon state density, free energy, heat capacity and enthalpy can be obtained by utilizing phonon spectrum calculation, and the phonon spectrum is a commonly used calculation amount in material calculation.
However, the most popular commercial software in the scientific research of material Simulation and computational materials, such as VASP (Vienna Ab-initio Simulation Package), does not support the function of directly calculating the phonon spectrum, and the phonon spectrum can be obtained through a plurality of processing steps by combining with software specially performing phonon calculation and drawing software. The VASP is complex in calculation, and the difficulty is increased by adding special calculation of the phonon spectrum.
For example: in the traditional phononic spectrum calculation, the phononic spectrum calculation is carried out based on VASP, and mainly through the combination of VASP + Phonopy (a crystal phonon analysis program), at present, two methods are mainly adopted:
the method comprises the following steps: VASP & Phonopy method. Atom stress is calculated through VASP for each perturbation structure by generating a batch of perturbation structures, a phonon spectrum file is obtained by calling a Phonopy tool, and a phonon spectrum is obtained by calling drawing software.
The second method comprises the following steps: VASP-DFPT method. Constructing a supercell, generating a batch of perturbation structures, carrying out VASP calculation (IBRION 8and NSW 1) on the SPOSCAR, obtaining a Hessian matrix, thereby obtaining a mechanical constant and a phonon spectrum file, and finally calling drawing software to obtain a phonon spectrum.
In addition, some academic websites in China, such as computational materials science, hundred-degree experience, small wood worms, direct physical workers, scientific networks and the like, also disclose some introduction for carrying out phononic spectrum calculation based on VASP, and are basically developed around the method.
The following takes a simpler VASP-DFTP method as an example to illustrate a specific procedure of calculating the phonon spectrum as follows:
1) download install Phonopy (if there is no VASP, also download, install and compile VASP).
2) Constructing the supercell. A POSCAR file was prepared and phonopy-d-dim was run as "113" to generate a supercell. Many POSCAR001, POSCAR002, POSCAR003,. and sposscar are generated after the command is completed.
3) The file is renamed (SPOSCAR is renamed to POSCAR, POSCAR is changed to POSCAR-unit cell).
4) VASP calculations were performed to obtain vasrun. IBRION ═ 8and NSW ═ 1).
5) And processing by a Phonopy program and calling drawing software to obtain a final phonon spectrum.
The method comprises the following specific steps:
a) run phonopy-fc vasprun. xml, generate the mechanical constants file:
ORCE_CONSTANTS。
b) connf file is added with a line of FORCE _ configurations ═ READ.
c) Run phonopy-dim ═ m n l "-c POSCAR-unit cell band.
d) And acquiring a phononic spectrum file. bandplot-gnuplot > phono.
e) And (6) drawing a phonon spectrum. Dat is processed by data processing software (e.g. Origin).
From the above analysis, it can be seen that even in the simplest way, performing a phononic spectrum calculation involves many links including: preprocessing, VASP calculation, post-processing, drawing and the like; involving the integrated use of multiple software, such as VASP, Phonopy, drawing software, etc.; the method needs to be used in a Linux command line mode, and needs to be familiar with Linux if a circulating program is written; the conversion and processing of data among different software are extremely easy to make mistakes; the problem of machine time needs to be solved; the physical properties such as phonon spectrum data, phonon dispersion spectrum, phonon state density, free energy, heat capacity, enthalpy and the like obtained by data post-processing also relate to the problem of how to store permanently. Particularly, if the first method is adopted, a batch of perturbation structures are generated, and the VASP calculation is performed on each perturbation structure to obtain a force constant (force constant).
Therefore, developing a technology capable of effectively reducing the difficulty in calculating the phonon spectrum is an important problem to be solved in material calculation.
Disclosure of Invention
In view of the above, the main objective of the present invention is to provide a full-automatic phononic spectrum calculation method based on high-throughput material calculation and a system thereof, which can perform phononic spectrum calculation in a one-click, networked, graphical, flow-based and automated manner by using a high-throughput material calculation technology, automatically store the obtained thermodynamic property data in a database, implement linkage and flow of multiple steps such as pre-processing, VASP calculation, post-processing and drawing of the phononic spectrum calculation, and implement parallel calculation and reduction processing of large-scale VASPs.
In order to achieve the purpose, the technical scheme of the invention is as follows:
a method for fully automated phononic spectrum calculation based on high-throughput material calculation, the method comprising:
A. logging in a high-throughput material computing system, creating a phononic spectrum computing workflow based on a preset phononic spectrum computing template by utilizing a workflow design module, loading a crystal structure to be computed, and setting parameters;
B. a workflow execution engine module is utilized to call an analysis and execution module of the high-throughput material computing system, and the phononic spectrum computing workflow is analyzed and executed;
C. putting the crystal structure to be calculated into a crystal structure set module to be calculated;
D. constructing supercells through the perturbation structure module, and generating perturbation structures in batches;
E. performing static calculation on the supercell by using a first principle static calculation module to obtain a wave function file; performing first principle static energy calculation on the perturbation structures generated in batch by using the wave function file through the first principle static calculation module to obtain atom stress data;
F. and processing the calculation result of the perturbation structures generated in batches through a phonon spectrum calculation module to obtain the atomic stress value of the perturbation structures, constructing a second-order force constant matrix, calculating phonon frequency and characteristic values to obtain a phonon spectrogram and obtain related thermodynamic data.
Preferably, the method further comprises:
G. and storing the intermediate data of the phononic spectrum calculation and the result data of the phononic spectrum calculation into a database.
Step C, putting the crystal structure to be calculated into a crystal structure set module to be calculated, which specifically comprises the following steps: putting a crystal structure to be calculated of a high-flux material into a crystal container, wherein the crystal container provides data base building uploading, hard disk uploading and structure on-line design, and putting the crystal structure to be calculated into the crystal container to be centralized.
D, generating a plurality of perturbation structures in batches, specifically: a finite bit shift operation module is used for generating a plurality of perturbation structures.
Step E, the step of performing static energy calculation on the perturbation structure by using the first principle static calculation module further includes: a step of setting parameters, wherein the parameters comprise: high-performance calculation parameter setting, first-principle calculation parameter setting and personalized parameter setting.
The parameters can be modified online through a parameter setting table of the first principle static calculation module.
Before performing the phonon calculation in steps B to E, the K-point grid needs to be set.
The first principle static calculation module is a VASP static calculation module.
A fully automated phononic spectrum calculation system based on high-throughput material calculation, comprising:
the workflow design module is used for creating a phonon spectrum calculation workflow, loading a crystal structure to be calculated and setting parameters;
the workflow execution engine module is used for calling an analysis and execution module of the high-flux material computing system;
the analysis and execution module is used for analyzing and executing the phononic spectrum calculation workflow;
the crystal structure set module to be calculated is used for putting the crystal structure to be calculated;
the perturbation structure module is used for constructing a plurality of supercells according to the called phonon spectrum calculation template and generating a plurality of perturbation structures in batches;
the first principle static calculation module is used for performing static calculation on the supercell to obtain a wave function file; performing first principle static energy calculation on the perturbation structures generated in batch by using the wave function file to obtain atom stress data;
and the phonon spectrum calculation module is used for processing the calculation result of the perturbation structures generated in batches, acquiring the atomic stress value of the perturbation structures, constructing a second-order force constant matrix, calculating the phonon frequency and the characteristic value, acquiring a phonon spectrogram and acquiring related thermodynamic data.
Preferably, the method further comprises the following steps: and the database is used for storing the intermediate data of the phononic spectrum calculation and the result data of the phononic spectrum calculation.
The full-automatic phonon spectrum calculation method and the system thereof based on high-flux material calculation have the following beneficial effects:
1) by applying the phononic spectrum calculation method and the system thereof to high-flux material calculation under the MatCloud + material cloud platform environment, phononic spectrum calculation can be carried out in a one-key, networked, graphical, flow and automatic local mode, and the acquired thermodynamic property data is automatically stored in a database.
2) By adopting the invention, the connection and the process of a plurality of steps such as the pre-processing of the phononic spectrum calculation, the VASP calculation, the post-processing, the drawing and the like can be realized, and further, the parallel calculation and the reduction processing of a large number of VASPs are realized. Once the calculation is finished, the phonon spectrum can be directly obtained, so that the simplification of the material calculation process from the user side to the data side is realized.
Drawings
FIG. 1 is a schematic diagram of a fully automatic phononic spectrum calculation process based on high-throughput material calculation according to an embodiment of the present invention;
fig. 2 is a schematic view of a workflow for calculating a phononic spectrum according to an embodiment of the present invention (the phononic spectrum calculation template has effectively integrated various links of phononic spectrum calculation, and includes a perturbation structure module, a first-principle static calculation module, and a phononic spectrum calculation module);
FIG. 3 is a schematic diagram of a Crystal Structure set of a Crystal container (Crystal Structure) for placing R53(C12H6) to be subjected to high throughput material calculation according to an embodiment of the present invention;
FIG. 4 is a schematic diagram of a process of creating a number of supercells to generate a plurality of perturbation structures according to an embodiment of the present invention;
fig. 5 is an interface diagram illustrating parameter setting for performing VASP calculation on the perturbation structure according to the embodiment of the present invention;
FIG. 6 is a parameter setting representation of an embodiment VASP INCAR of the present invention;
FIG. 7 is a schematic diagram of an interface for setting a K-point grid;
FIG. 8 is a schematic view of a status monitoring and results viewing interface for static energy calculations;
FIG. 9 is a schematic diagram of automatic generation of a phononic spectrum after completion of a phononic spectrum calculation workflow;
FIG. 10 is a schematic diagram of automatic generation of phonon density of states after completion of a phonon spectrum calculation workflow;
FIG. 11 is a schematic diagram of the automatic acquisition of enthalpy and Gibbs free energy after completion of a phononic spectrum calculation workflow;
FIG. 12 is a schematic diagram of an automatic entropy acquisition result after completion of a phononic spectrum calculation workflow;
FIG. 13 is a schematic diagram of an automatic acquisition result of heat capacity after completion of a phononic spectrum calculation workflow;
fig. 14 is a schematic structural diagram of a fully automatic phononic spectrum calculation system based on high-throughput material calculation according to an embodiment of the present invention.
Detailed Description
The present invention will be described in further detail below with reference to the accompanying drawings and embodiments thereof.
After analyzing the traditional method for carrying out phonon spectrum calculation, the invention takes calculating the phonon spectrum of the porous graphene as an example, and details the calculation process of carrying out the phonon spectrum calculation through the high-flux material calculation cloud platform MatCloud +, and after the calculation is finished, the phonon spectrum can be directly obtained, thereby realizing the simplification of the material calculation process from a user side to a data side.
For example: in order to find a porous graphene material as a high-capacity lithium ion battery cathode material, phonon spectrums of R30(C26H6) and R53(C12H6) need to be calculated respectively, and a phonon spectrum calculation method based on high-flux material calculation is adopted to judge which of R30 and R53 systems can exist more stably through the phonon spectrums.
Fig. 1 is a schematic flow chart of phononic spectrum calculation based on high-throughput material calculation according to an embodiment of the present invention.
First, the cloud platform MatCloud + needs to be calculated by high-throughput materials to explain how to perform high-throughput calculation of phonon spectrum one-click. The user only needs one browser to log in MatCloud +, and the phononic spectrum calculation can be carried out without downloading and installing any software.
As shown in fig. 1, the procedure of calculating the phonon spectrum based on the high-flux material calculation mainly includes the following steps:
step 11: logging in a high-throughput material computing system, creating a phononic spectrum computing workflow based on a preset phononic spectrum computing template by utilizing a workflow design module, loading a crystal structure to be computed and setting parameters. The method specifically comprises the following steps:
in this embodiment, the user types in the MatCloud + web site (www.matcloudplus.com) through a web browser and then logs in. And then creating a project by utilizing the workflow design module, dragging the phononic spectrum calculation template to a design page, and designing a workflow as shown in figure 2.
Step 12: and calling an analysis and execution module of the high-throughput material computing system by using a workflow execution engine module, and analyzing and executing the phononic spectrum computing workflow. As shown in fig. 2.
Step 13: and putting the crystal structure to be calculated into a crystal structure set module to be calculated.
In this example, R53(C12H6) to be subjected to high throughput material calculation was put into a crystal container (CrystalStructure) crystal structure set, as shown in fig. 3.
Specifically, the method comprises the following steps: and the Crystal Structure provides uploading through a data base, uploading through a hard disk and online Structure design, and the Crystal Structure to be calculated is arranged in the Crystal Structure set of the Crystal Structure.
Step 14: and calling the preset phonon spectrum calculation template, creating a supercell through a perturbation structure module, and generating a plurality of perturbation structures in batches.
In the embodiment of the present invention, 1 supercell 1 × 3 is created, and 108 perturbation structures are generated in batch by using a finite Displacement (Displacement) operation module, as shown in fig. 4.
The following is a description of a process of performing first-principle static energy calculation on 108 generated perturbation structures and respectively obtaining atomic stress of the perturbation structures according to the embodiment of the present invention.
Step 15: and performing static calculation on the supercell by using a first principle static calculation module to obtain a wave function file, and performing first principle static energy calculation on the perturbation structures generated in batches by using the generated wave function file through the first principle static calculation module to obtain atom stress data.
In this embodiment, the first-principle static calculation module may be a VASP static calculation module.
The first principle static energy calculation may be performed on the perturbation structures generated in batch, specifically, a VASP static calculation module may be used to perform VASP calculation on the perturbation structures to obtain atomic stress data.
In this embodiment, before performing VASP calculation on the 108 perturbation structures, parameter setting is required, as shown in fig. 5. And acquiring the atomic stress through VASP Static Calculation (Static Calculation).
Referring to the graphical interface shown in fig. 5, the parameter setting is performed, and the content mainly includes:
high Performance Computing (HPC) parameter settings: each crystal structure calculation was assigned 1 node, 24 cores each. The MatCloud + provides an extensible computing resource pool which can be connected with a set super-computation center.
First principles calculation (Basic) parameter settings: basic settings of VASP calculations include accuracy, pseudopotential file selection, etc. Here, the accuracy is set to normal. The K point is set to 4, 4, 7.
The personalization (Custom Param) parameter is set to: LWAVE ═ false; LREAL is Auto.
The VASP INCAR parameter setting table, as shown in FIG. 6, allows parameters to be modified online.
Step 16: and processing the calculation result of the batch perturbation structure through a phonon spectrum calculation module to obtain the atomic stress values of the batch perturbation structure, constructing a second-order force constant matrix, calculating phonon frequency and characteristic values, generating a phonon spectrogram and obtaining related thermodynamic data.
In this embodiment, a phonon calculation (phonon calculation) subsystem is used to construct a second-order force constant matrix to obtain a force constant, calculate a phonon frequency and a characteristic value, and finally generate a phonon spectrogram and related thermodynamic data.
Here, the phonon calculation needs to be performed on a K-point grid, which is set to 1 × 3 in this embodiment, as shown in fig. 7.
After the parameters are set, clicking the "Start" button shown in fig. 2, and starting the phononic spectrum calculation workflow. After the process is started, supercell creation, 108 perturbation structures generation, submission and monitoring of high-flux calculation operation of 108 perturbation structures, force constant acquisition, phononic spectrum, phononic spectrogram creation, warehousing and the like can sequentially realize end-to-end automation and pipelined completion.
After the above-mentioned flow is started, there are 108 jobs which can concurrently and parallelly develop calculation. Clicking a "View Task" button in a static calculation (StaticCalculation) module can perform state monitoring and result viewing on the static energy calculation of 108 perturbation structures, as shown in fig. 8. The information viewed includes: completion status, parameter status, convergence status, etc. of 108 jobs. The entire process takes about 3500 nuclei.
The phononic spectrum calculation workflow is completed, and the phononic spectrum is automatically generated, as shown in fig. 9.
The phonon spectrum calculation workflow is completed, and the phonon state density is automatically generated, as shown in fig. 10.
The phonon spectrum calculation workflow is completed, and enthalpy and gibbs free energy are automatically obtained, as shown in fig. 11.
The phononic spectrum calculation workflow is completed, and the result is automatically obtained by the entropy, as shown in fig. 12
The phononic spectrum calculation workflow is completed, and the heat capacity automatically acquires a result, as shown in fig. 13.
Preferably, the method further comprises the following steps:
and step 17: and storing the intermediate data of the phononic spectrum calculation and the result data of the phononic spectrum calculation into a database.
Fig. 14 is a schematic structural diagram of a high-throughput material calculation-based phononic spectrum calculation system according to an embodiment of the present invention.
As shown in fig. 14, the high-flux material calculation-based phononic spectrum calculation system mainly includes:
the workflow design module is used for creating a phonon spectrum calculation workflow, loading a crystal structure to be calculated and setting parameters;
the workflow execution engine module is used for calling an analysis and execution module of the high-flux material computing system;
the analysis and execution module is used for analyzing and executing the phononic spectrum calculation workflow;
the crystal structure set module to be calculated is used for putting the crystal structure to be calculated;
the perturbation structure module is used for constructing the supercell and generating batch perturbation structures;
the first principle static calculation module is used for performing static calculation on the supercell to obtain a wave function file; performing first principle static energy calculation on the perturbation structures generated in batch by using the wave function file to obtain atom stress data;
and the phonon spectrum calculation module is used for processing the calculation result of the perturbation structures generated in batches, acquiring the atomic stress value of the perturbation structures, constructing a second-order force constant matrix, calculating the phonon frequency and the characteristic value, acquiring a phonon spectrogram and acquiring related thermodynamic data.
Preferably, the method further comprises the following steps:
and the database is used for storing the intermediate data of the phononic spectrum calculation and the result data of the phononic spectrum calculation.
Through the embodiment, it is obvious that the MatCloud + material cloud system disclosed by the invention is applied to high-flux material calculation, phononic spectrum calculation can be carried out in a one-click type, networked, graphical, flow and automatic manner, and the acquired thermodynamic property data are automatically stored in a database. The method realizes the connection and the flow of a plurality of steps of pre-processing of phonon spectrum calculation, VASP calculation, post-processing, drawing and the like, and realizes the parallel calculation and reduction processing of a large number of VASPs. After the calculation is finished, the phonon spectrum can be directly obtained, and the simplification of the material calculation process from the user side to the data side is directly realized.
The above description is only a preferred embodiment of the present invention, and is not intended to limit the scope of the present invention.
Claims (10)
1. A full-automatic phononic spectrum calculation method based on high-flux material calculation is characterized by comprising the following steps:
A. logging in a high-throughput material computing system, creating a phononic spectrum computing workflow based on a preset phononic spectrum computing template by utilizing a workflow design module, loading a crystal structure to be computed, and setting parameters;
B. a workflow execution engine module is utilized to call an analysis and execution module of the high-throughput material computing system, and the phononic spectrum computing workflow is analyzed and executed;
C. putting the crystal structure to be calculated into a crystal structure set module to be calculated;
D. constructing a supercell through a perturbation structure module, and generating a plurality of perturbation structures in batches;
E. performing static calculation on the supercell by using a first principle static calculation module to obtain a wave function file; performing first principle static energy calculation on the perturbation structures generated in batch by using the wave function file through the first principle static calculation module to obtain atom stress data;
F. and processing the calculation result of the perturbation structures generated in batches through a phonon spectrum calculation module to obtain the atomic stress value of the perturbation structures, constructing a second-order force constant matrix, calculating phonon frequency and characteristic values to obtain a phonon spectrogram and obtain related thermodynamic data.
2. The method for fully automated phononic spectrum calculation based on high throughput material calculation as claimed in claim 1, the method further comprising:
G. and storing the intermediate data of the phononic spectrum calculation and the result data of the phononic spectrum calculation into a database.
3. The method for computing full-automatic phononic spectrum based on high-throughput material computing according to claim 1, wherein the step C of putting the crystal structure to be computed into a crystal structure set module to be computed specifically comprises: putting a crystal structure to be calculated of a high-flux material into a crystal container, wherein the crystal container provides data base building uploading, hard disk uploading and structure on-line design, and putting the crystal structure to be calculated into the crystal container to be centralized.
4. The method according to claim 1 or 3, wherein the step D of batch generation of the perturbation structures comprises: a finite bit shift operation module is used for generating a plurality of perturbation structures.
5. The method according to claim 1, wherein the step E of performing static energy calculation on the perturbation structure by using the first-principle static calculation module further comprises: a step of setting parameters, wherein the parameters comprise: high-performance calculation parameter setting, first-principle calculation parameter setting and personalized parameter setting.
6. The method of claim 5, wherein the parameters can be modified on-line by a parameter setting table of the first-principle static calculation module.
7. The method for computing full-automatic phononic spectrum based on high-throughput material calculation according to claim 1, wherein a K-point grid is required to be set before performing phononic calculation in steps B to E.
8. The method for full-automatic calculation of phononic spectrum based on high-flux material calculation according to claim 1, 5 or 6, characterized in that the first-principle static calculation module is a VASP static calculation module.
9. A fully automated phononic spectrum calculation system based on high-throughput material calculation, comprising:
the workflow design module is used for creating a phonon spectrum calculation workflow, loading a crystal structure to be calculated and setting parameters;
the workflow execution engine module is used for calling an analysis and execution module of the high-flux material computing system;
the analysis and execution module is used for analyzing and executing the phononic spectrum calculation workflow;
the crystal structure set module to be calculated is used for putting the crystal structure to be calculated;
the perturbation structure module is used for constructing a plurality of supercells and generating a plurality of perturbation structures in batches;
the first principle static calculation module is used for performing static calculation on the supercell to obtain a wave function file; performing first principle static energy calculation on the perturbation structures generated in batch by using the wave function file to obtain atom stress data;
and the phonon spectrum calculation module is used for processing the calculation result of the perturbation structures generated in batches, acquiring the atomic stress value of the perturbation structures, constructing a second-order force constant matrix, calculating the phonon frequency and the characteristic value, acquiring a phonon spectrogram and acquiring related thermodynamic data.
10. The fully automated high-throughput-material-computation-based phononic spectrum calculation system of claim 9 further comprising: and the database is used for storing the intermediate data of the phononic spectrum calculation and the result data of the phononic spectrum calculation.
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| CN110954512A (en) * | 2019-10-18 | 2020-04-03 | 北京应用物理与计算数学研究所 | Analytic calculation method and device for phonon spectrum of primitive cell of alloy material |
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| CN112102887A (en) * | 2020-09-02 | 2020-12-18 | 北京航空航天大学 | Multi-scale integrated visual high-throughput automatic calculation process and data intelligent system |
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