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The following figure is generated with the data obtained by post-processing tools those written under the framework 'md_tools'. The main intention for presenting the figure is to show the visual capabilities rather than for discussing the scientific findings. Therefore, please excuse for any missing details in the figure. The list of tools along their short description are presented following the figure.
Figure description:
a) CMAS glass (11096 atoms) with the assignment of various colors to various atom types
b) Diffusion path of Na in NAP glass
c) Distribution of Li and K in Vanadium containing glasses
d) Brding Oxygen (BO) rich network region of NAPS glass
e) Non-Bridging Oxygen (NBO) rich Channel region of NAPS glass
f) Demonstrating the role of Na in the presence of Si
g) Separating the channel and network regions based on BO and NBO for NAPS glass
h) Identification of clusters in CMAS glass
i) Computing the presence of Na at various oxgen sites (NAPS glasses)
j) Percentage of Al-O-Al bonds in CAS glasses
k) Pair distribution functions of CMAS glass
l) Distribution of O at various sites in NAPS glasses
m) Percentages of O in Al-O-V and V-O-V in Vanadium containing glasses
n) Extraction of triclusters (CMAS glass)
o) Influence of F on the network structure of Bio-glasses
(The figures are generated with ovito and gnuplot software packages)
The following tools are very useful for analysing various properties of amorphous materials (glasses) with given atomic positions and chemical atom types. The main intension of these programs is to post-process the output files obtained by the atomistic simulations (LAMMPS and IMD programs).
- 001_ganisetti_tools_module : a module with a lot of classes and functions for computing various properties
- 002_compute_glass_density : computes the density of a glass
- 003_CMAS_glass_structural_properties : computes the structural properties of CMAS glass
- 004_NAPS_glass_structural_properties : computes the structural properties of NAPS glass
- 005_SiO2_Al2O3_RO_TernaryPhaseDiagram : plots the ternary phase diagram of SiO2, Al2O3 and RO
- 006_Compute_MeanSquareDisplacement : computes the mean square displacement of each atom type
- 007_StructureGeneration : generate the structure of desired composition by placing the atoms randomly
- 008_structural_properties_for_all_glasses : a generalized programm for computing structural properties of any kind of glass
- 009_compute_pair_distribution : computes pair distribution function of any glass composition (still need to normalize)
- 010_IMD_projection_of_pair_distribution : computes projection of pair distribution function on x,y, and z-axis
- 011_IMD_projection_of_angle_distribution : computes azimuthal and polar angles from the angle distributions
- 012_compute_broken_bonds : computes broken bonds when given two files contains same number of atoms
- 013_change_atom_type_of_selected_atoms : changes the atom type of selected atoms
- 014_ReadingAtomNumbersFromAFileAndCollectingThem : three different codes exist for reading atoms from a file and collect only these atoms from: (1) imd chkpt file (2) lammps dump file (3) nnl file
- 015_compute_common_atoms_of_two_data_files : get the common atoms of two data files (for example two ring data files)
- 016_separating_each_tetrahedron : separate each tetrahedron
- 017_extracting_atoms_of_a_ring_and_its_neighbours : extract the atoms of a given ring and also their neighbors from a given chkpt file
- 018_script_to_extract_edge_corner_tets_info : extract the edge and corner sharing tetrahedra information from a rings_code output file
- 019_making_SLICES_compute_Guttman_rings : make the sample into slices and compute the ring statistics with Gutman rings criterion using rings_code
- 020_mean_square_displacement : compute mean square displacement
- 021_bond_orientations_alpha_beta : compute orientation of each bond in terms of alpha and beta in spherical coordinates
- 022_compute_local_atomic_density_based_on_voxels : the local atomic density has been calculated for the given atoms from a lammps dum file which can be useful to analyze the channel regions formed by the given atoms
- 023_compute_the_diffusion_path_of_each_given_atom_during_MSD: Computes the diffusion path of each given atom during MSD
- 024_extract_given_list_of_atoms_from_the_given_chkpt_file : Extract the list of atoms provided by the atom numbers in a text file from the given chkpt file
- 025_checking_for_network_glitches_using_ping : A small code to report the network glitches
- 026_compute_channels_clustering_based_on_voxels: Computes the channel regions provided by the type of atoms that the channel contains. For example, extract the channels containing the network modifier atoms
- 027_compute_bond_statistics : Computes broken bonds, switched bonds and new bonds during the MSD
- 028_ContourPlot_of_ModifierCation_Connected_to_BO_and_NBO: Generates a nice illustration (contour plot) of percentage of Na atoms accommodated at various sites based on the bridging oxygen (BO) and non-bridging oxygen (NBO).
NOTE: IMD input or output file formats will not work for all the programs, however, this can be solved in near future.