Generating structuress of carbon nanobelts (CNBs)
This program generates structures of carbon nanobelts (CNBs), including both the standard and nonstandard CNBs. All constructed molecular structures are exported in Cartesian coordinates in *.xyz files.
If you have used the GenCNB program in your research papers or presentations, it is obligatory to cite the following paper:
- Yang Wang, Yi Zhou, Ke Du. Enumeration, Nomenclature and Stability Rules of Carbon Nanobelts. ChemRxiv 2023, DOI:10.26434/chemrxiv-2023-85ww5
The Author of the GenCNB software is Yang Wang (yangwang@yzu.edu.cn; orcid.org/0000-0003-2540-2199). The GenCNB program is released under GNU General Public License v3 (GPLv3).
The GenCNB software is provided as it is, with no warranties. The Author shall not be liable for any use derived from it. Feedbacks and bug reports are always welcome (yangwang@yzu.edu.cn). However, it is kindly reminded that the Author does not take on the responsibility of providing technical support.
No installation is required as this program is composed of MATLAB scripts, which have been tested with MATLAB version R2023a/b.
To enumerate and generate the structures of all possible isomers of the standardCNBs (n,m), simply call the function:
gen_belts( n, m, true )
which first generates a path file named PATH_{n}_{m}_R{NR} and then a folder named R{NR}-{n}_{m} that stores the xyz files. Note that {NR} represent the number of rings for the CNB. The path code file lists the canonical path codes of all enumerated isomers. Each xyz file in folder R{NR}-{n}_{m} contains the following information of the corresponding CNB isomer:
- Number of atoms
- Stoichiometry, Isomer No.: [path code] Hueckel total energy, Hueckel HOMO-LUMO gap
- Atomic numbers/symbols + Cartesian coordinates
*NOTE: If the last argument of gen_belts() is false, then only the path code file is generated without producing any Cartesian coordinates.
Upon execution of
gen_belts( 7, 3, true )
we enumerate and obtain all isomers of the standard [10]CNBs (7,3). The onscreen output is as follows:
Enumerating all nonequivalent (7,3) nanobelt isomers ...
File PATH_7_3_R10 written
Generating 3D coordinates in xyz files ...
Folder R10-07_03 created
8 isomers read from PATH_7_3_R10
C40H20 Isomer 1: [ 3 1 2 1 2 1 ] -57.12321180 0.49143180
Coordinates written to file R10-07_03/R10-7_3-1.xyz
C40H20 Isomer 2: [ 3 1 3 1 1 1 ] -57.08934344 0.46822321
Coordinates written to file R10-07_03/R10-7_3-2.xyz
C40H20 Isomer 3: [ 4 1 2 1 1 1 ] -57.07766625 0.42782322
Coordinates written to file R10-07_03/R10-7_3-3.xyz
C40H20 Isomer 4: [ 5 1 1 1 1 1 ] -57.02514860 0.35638249
Coordinates written to file R10-07_03/R10-7_3-4.xyz
C40H20 Isomer 5: [ 4 2 3 1 ] -56.91984845 0.41115384
Coordinates written to file R10-07_03/R10-7_3-5.xyz
C40H20 Isomer 6: [ 5 2 2 1 ] -56.90061329 0.35551010
Coordinates written to file R10-07_03/R10-7_3-6.xyz
C40H20 Isomer 7: [ 6 2 1 1 ] -56.83596861 0.29433540
Coordinates written to file R10-07_03/R10-7_3-7.xyz
C40H20 Isomer 8: [ 7 3 ] -56.61671443 0.24447759
Coordinates written to file R10-07_03/R10-7_3-8.xyz
We call the function:
gen_belts_ext( n, m, l, true )
to enumerate and generate all possible isomers of the nonstandard CNBs
(n,m,l). The corresponding path code file is generated as XPATH_{n}_{m}_{l}_R{NR} and, if the last argument of gen_belts_ext() is true, the folder is created as XR{NR}-{n}_{m}_{l} containing the xyz files for all isomers.
We want to construct all possible isomers of the nonstandard CNBs (6,2,3). Simply call
gen_belts_ext( 6, 2, 3, true )
We obtain the path code file XPATH_6_2_3_R11 and the folder XR11-06_02_03 where there are four xyz files, XR11-6_2_3-1.xyz, ..., XR11-6_2_3-4.xyz for the four possible isomers. The output on screen is collected in the following:
Enumerating all nonequivalent (6,2,3) nanobelt isomers ...
n1 = 3, m1 = 5
File XPATH_6_2_3_R11 written
Generating 3D coordinates in xyz files ...
Folder XR11-06_02_03 created
4 isomers read from XPATH_6_2_3_R11
H atoms 47--66 too close to each other
H47--H66 distance converged to 1.577 Angstrom after 3 iterations
H atoms 60--63 too close to each other
H60--H63 distance converged to 1.577 Angstrom after 3 iterations
C44H22 Isomer 1: [ 1 3 1 2 1 -3 ] -62.75076792 0.56607072
Coordinates written to file XR11-06_02_03/XR11-6_2_3-1.xyz
H atoms 47--66 too close to each other
H47--H66 distance converged to 1.577 Angstrom after 3 iterations
H atoms 60--63 too close to each other
H60--H63 distance converged to 1.577 Angstrom after 3 iterations
C44H22 Isomer 2: [ 1 4 1 1 1 -3 ] -62.70769145 0.47883420
Coordinates written to file XR11-06_02_03/XR11-6_2_3-2.xyz
H atoms 47--66 too close to each other
H47--H66 distance converged to 1.577 Angstrom after 3 iterations
H atoms 58--61 too close to each other
H58--H61 distance converged to 1.577 Angstrom after 3 iterations
C44H22 Isomer 3: [ 1 5 1 -1 1 -2 ] -62.69242729 0.39166782
Coordinates written to file XR11-06_02_03/XR11-6_2_3-3.xyz
H atoms 60--63 too close to each other
H60--H63 distance converged to 1.577 Angstrom after 3 iterations
C44H22 Isomer 4: [ 2 5 1 -3 ] -62.54187725 0.40476208
Coordinates written to file XR11-06_02_03/XR11-6_2_3-4.xyz