basis set etc is almost extraneous to the amount of work needed to setup input in fractional coordinates. if user can import cif, cut it to the right plane, make it 2-D slab, add some adsorbed molecules and export it to output that would be best. xyz for simple calcs is not as important, as manipulating crystal structure. 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.The killer feature will be allowing user to get rid of tedious coordinate operation manually. 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. 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.
#MATERIALS STUDIO XYZ SOFTWARE#
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. The software is freeware and it come without any (as in nothing, nada, niente, rien) WARRANTY. Using the software and the scripts in this repository is at your own risk. Gamma Radiation Chemistry of Polydimethylsiloxane Foam in Radiation-Thermal Environments: Experiments and Simulations. Atomic-scale insight into the pyrolysis of polycarbonate by ReaxFF-based reactive molecular dynamics simulation. Much work will be carried out in the furture.ģ Please cite the following papers and RMD_digging ToolKit accordingly: (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. More desired functions like orientation analysis will be added in the furture. (6)chemi_mechanism toolkit can export the products in specific trajectories and analysis the reaction path/channel. (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. (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. Moreover, the evolution of number-average molecular weight and weight-average molecular weight can be calculated. It sorts out the formed products with time sequence and can further refine them by molecular weight, elements and so on. (3)species toolkit can process the simulation generated species files. (2)loglammps toolkit is mainly used to extract and process data with statistic average method. (1)ReaxFF_Gen toolkit is used to generate standard file with ReaxFF force field parameters from literatures. Let's make it more versatile, powerful and robust together!Ģ A brief introduction to the RMD_Digging toolkit: The following softwares are used to realize these goals, including Materials studio, VMD and Gaussian. Besides, extra modelling by other softwares can be performed by preparing corresponding input files. Its functions involve formatting the reactive force field parameters, statistic anasysis of structures, trajectories and mechanisms and output of the visualization files. It is aimed to provide pre-processing and post-processing tools for the reactive molecular dynamics (ReaxFF) simulations performed on the LAMMPS platform. RMD_Digging: A Toolkit to Remove the Barriers in the Way of Scientific Calculations and Analysisġ RMD_digging is developed by the MATLAB language.