# RMD_Digging: A Toolkit to Remove the Barriers in the Way of Scientific Calculations and Analysis
# <span style="color: red"> Notice: An upgrade version RMD_Digging_v3.1_dev has been released! This version is more fast and robust, with more practical functions and little bugs. It is also aimed to alleviate the memory consumption in many tasks. Both versions with respective English and Chinese language will be provided. Enjoy it. </span>
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## Development Target
RMD_Digging is developed by the MATLAB language. It is aimed to provide pre-processing and post-processing tools for the reactive molecular dynamics (ReaxFF) simulations performed on the LAMMPS platform. Its functions involve formatting the reactive force field parameters, statistic anasysis of structures, trajectories and mechanisms and output of the visualization files. Besides, extra modelling by other softwares can be performed by preparing corresponding input files. The following softwares are used to realize these goals, including Materials studio, VMD and Gaussian. Let's make it more versatile, powerful and robust together!
## A Brief Introduction to the RMD_Digging Toolkit
(1)**ReaxFF_Gen toolkit** is used to generate standard file with ReaxFF force field parameters from literatures.<br>
(2)**loglammps toolkit** is mainly used to extract and process data with statistic average method.<br>
(3)**species toolkit** can process the simulation generated species files. It sorts out the formed products with time sequence and can further refine them by molecular weight, elements and so on. Moreover, the evolution of number-average molecular weight and weight-average molecular weight can be calculated.<br>
(4)**bonds_analysis toolkit** can read and handle the bond order (BO) information, further mainly cope with the BO information with the following purpose: a)obtain the BO information of the specific molecule or fragment; b)give the chemical composition of all the molecules and fragments (molecular formula); c)rearrange molecular formula and trace the BO information of the interested species.<br>
(5)**lammpstrj2xyz_arc_pdb toolkit** can output the *.xyz, *.arc and *.pdb file, which can be be used for visualization by virture of Materials studio and VMD software, both in the form of static image and dynamic trajectory. <br>
(6)**chemi_mechanism** toolkit can export the products in specific trajectories and analysis the reaction path/channel. More desired functions like orientation analysis will be added in the furture.<br>
(7)structure_analysis toolkit is aimed to analysis the complex molecular structure, such as benzene ring, phenolic hydroxylic group and other specific chemical bonds or groups. However, its function is incomplete. Much work will be carried out in the furture.
## Please Cite the Following Papers and RMD_Digging ToolKit Accordingly:
(1) **Liu, Q.**, RMD_Digging ToolKit, 2020, https://github.com/dadaoqiuzhi/RMD_Digging, accessed date.<br>
(2) **Liu, Q.**; Liu, S.; Lv, Y.; Hu, P.; Huang, Y.; Kong, M.; Li, G. Atomic-scale insight into the pyrolysis of polycarbonate by ReaxFF-based reactive molecular dynamics simulation. Fuel 2021, 287, 119484, DOI: https://doi.org/10.1016/j.fuel.2020.119484.<br>
(3) **Liu, Q.**; Huang, W.; Liu, B.; Wang, P.-C.; Chen, H.-B. Gamma Radiation Chemistry of Polydimethylsiloxane Foam in Radiation-Thermal Environments: Experiments and Simulations. ACS Appl. Mat. Interfaces 2021, 13 (34), 41287-41302, DOI: https://doi.org/10.1021/acsami.1c10765.<br>
(4) C. Li, **Q. Liu**, W. Gong, Z. Zhou, Z. Yao, X. Meng, Study on the atomic scale of thermal and thermo-oxidative degradation of polylactic acid via reactive molecular dynamics simulation, Thermochim. Acta 709 (2022) 179144, DOI: https://doi.org/10.1016/j.tca.2021.179144<br>
(5) **Liu, Q.**; Huang, W.; Chen, H. Paving the Way to Simulate and Understand the Radiochemical Damage of Porous Polymer Foam. ACS Materials Letters 2023, 2174-2188. DOI: 10.1021/acsmaterialslett.3c00307.<br>
## Disclaimer:
***Using the software and the scripts in this repository is at your own risk***. The software is freeware and it come without any (as in nothing, nada, niente, rien) WARRANTY. Therefore, Neither me nor the Institute of Nuclear Physics and Chemistry is responsible for the loss of data, time, bad results or anything else deriving by the use of my software or this repository. We do not make any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any software, scipts, information, apparatus, product, disclosed process, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial software, product, process, or service by trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the People's Republic of China. The views and opinions of authors expressed herein do not necessarily state or reflect those of the People's Republic of China or the Institute of Nuclear Physics and Chemistry, and shall not be used for advertising or product endorsement purposes.
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毕业设计&课设-RMD_diging旨在为基于…的反应分子动力学(ReaxFF)模拟提供预处理和后处理工具….zip
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matlab算法,工具源码,适合毕业设计、课程设计作业,所有源码均经过严格测试,可以直接运行,可以放心下载使用。有任何使用问题欢迎随时与博主沟通,第一时间进行解答! matlab算法,工具源码,适合毕业设计、课程设计作业,所有源码均经过严格测试,可以直接运行,可以放心下载使用。有任何使用问题欢迎随时与博主沟通,第一时间进行解答! matlab算法,工具源码,适合毕业设计、课程设计作业,所有源码均经过严格测试,可以直接运行,可以放心下载使用。有任何使用问题欢迎随时与博主沟通,第一时间进行解答! matlab算法,工具源码,适合毕业设计、课程设计作业,所有源码均经过严格测试,可以直接运行,可以放心下载使用。有任何使用问题欢迎随时与博主沟通,第一时间进行解答! matlab算法,工具源码,适合毕业设计、课程设计作业,所有源码均经过严格测试,可以直接运行,可以放心下载使用。有任何使用问题欢迎随时与博主沟通,第一时间进行解答! matlab算法,工具源码,适合毕业设计、课程设计作业,所有源码均经过严格测试,可以直接运行,可以放心下载使用。有任何使用问题欢迎随
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毕业设计&课设-RMD_diging旨在为基于…的反应分子动力学(ReaxFF)模拟提供预处理和后处理工具….zip (105个子文件)
log.lammps 676KB
chemi_mechanism.m 47KB
xyz_arc_pdb_filemaker.m 32KB
xyz_arc_filemaker_speedupMOLE.m 22KB
MWevolution_new.m 15KB
chainend.m 14KB
orient_entangle.m 12KB
PBC_Unwrap.m 12KB
species_bonds_lammpstrj_framecheck.m 10KB
bonds_analysis.m 10KB
species_classfy.m 8KB
xyz_car_pdb_filemaker.m 7KB
lammpstrj_analysis.m 6KB
bonds_lammpstrj_framecheck.m 6KB
species_capture.m 6KB
lammpstrj_analysis.m 6KB
delnonbackbone.m 6KB
bondorder_deepmining.m 6KB
ReaxFF_Gen.m 6KB
bonds_analysis_speedup.m 5KB
bonds_analysis_speedup.m 5KB
bondorder_capture.m 5KB
bondorder_deepmining.m 5KB
bondorder_deepmining.m 5KB
bondorder_deepmining.m 5KB
speciesbond_classify.m 5KB
bonds_analysis_speedup.m 4KB
bonds_analysis_speedup.m 4KB
react_blocklocate.m 4KB
car_mdf_filemaker.m 3KB
loglammps.m 3KB
species_analysis_capture.m 3KB
species_analysis.m 3KB
statistics_cell.m 3KB
lammpstrj_analysis.m 3KB
species_analysis.m 3KB
order_idtag.m 2KB
anaoptlogic.m 2KB
BondForm.m 2KB
bondanamain.m 2KB
bondedatom_tracking.m 2KB
logicinspect.m 2KB
species_capture.m 2KB
Posi_map.m 2KB
statisave_matrix.m 2KB
speanamain.m 2KB
statisave.m 2KB
BOentity.m 1KB
BondLink.m 1KB
seekBOinform.m 1KB
BOele_rank.m 1KB
atomnummolecule_strcat.m 1KB
molecuweight.m 1KB
entanglement_cal.m 1KB
inspectBOinform.m 956B
orient_cal.m 947B
atomnummolecule_strcat.m 892B
SysConvert.m 891B
SysConvert.m 889B
atom_num_autoread.m 825B
atom_num_autoread.m 825B
char26cor.m 778B
num_obtain.m 730B
cellrowcol_del.m 678B
cellrowcol_del.m 678B
cellrowcol_del.m 678B
cellrowcol_del.m 678B
charnum_match.m 643B
charnum_match.m 634B
MW_fileread.m 621B
molecuweight.m 598B
membercheck.m 535B
membercheck.m 534B
Deconvolu_SysConvert.m 533B
charnum_match.m 498B
delzero.m 491B
BOidentify.m 482B
charnum_match.m 476B
bondnumfind.m 414B
BO_match.m 397B
atomtypefind.m 391B
eleme_molecule.m 387B
eleme_molecule.m 387B
eleme_molecule.m 387B
eleme_molecule.m 387B
lpnumfind.m 365B
atomidfind.m 349B
BOid_element.m 310B
forcefield.m 309B
forcefield.m 309B
del_repeat.m 225B
delnull.m 209B
coord_position_get.m 145B
coord_position_get.m 145B
unrap_data.mat 179KB
BondRadii.mat 1KB
README.md 6KB
RMD_Digging manual V3.pdf 3.99MB
output.txt 17KB
input-example.txt 13KB
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