Authors: Geoffrey R. Weal, Caitlin A. Casey-Stevens and Dr. Anna L. Garden (University of Otago, Dunedin, New Zealand)
Group page: https://blogs.otago.ac.nz/annagarden/
Page to cite with work from: XXX; XXX;
GeoProps is a program designed to provide information about the geometric properties of individual nanoclusters, including the radial distribution function and the number of neighbours surrounding each atom within the nanocluster. This program utilises modules from the Atomic Simulation Environment (ASE) and As Soon As Possible (ASAP3) packages.
GeoProps requires the following programs before it can be used:
- Atomic Simulation Environment (ASE): https://wiki.fysik.dtu.dk/ase/
- ASAP3: https://wiki.fysik.dtu.dk/asap
- Packaging
The easiest way to install these is through pip. Type the following two lines into the terminal:
.. code-block:: bash
pip3 install --upgrade --user ase packaging
pip3 install --upgrade --user asap3==3.11.10
See https://pip.pypa.io/en/stable/installation/ if you do not have pip installed on your computer.
To install this program on your computer, pop open your terminal, cd to where you want to place this program on your computer, and clone the program to your computer by typing the following into your terminal:
git clone https://github.com/GardenGroupUO/GeoProps
If you do not have git installed on your computer, see https://www.atlassian.com/git/tutorials/install-git
Once you have done this, type pwd into the terminal and copy this path into your ~\.bashrc in the following format:
#####################################################################################
# These lines will allow python to locate this program on your computer.
export PATH_TO_GeoProps='/PATH_GIVEN_BY_THE_PWD_COMMAND/GeoProps'
export PYTHONPATH="$PATH_TO_GeoProps":$PYTHONPATH
#####################################################################################This will allow your computer to run this program through your terminal on python3.
An example of the script used to run this program is given below, called run_GeoProps.py.
from GeoProps import GeoProps_Program
rdf_max_dist = 15.0
no_of_bins = 500
colours = {'Cu': 'y', 'Pd': 'b', ('Cu','Pd'): 'm'}
r_cut = 2.9
xlim_RDF = (1.8,8.2)
xlim_CN = None
GeoProps_Program(rdf_max_dist, no_of_bins, colours, r_cut, xlim_RDF=xlim_RDF, xlim_CN=xlim_CN)When you execute this program by running python3 run_GeoProps.py in the terminal, GeoProps will look through all subdirectories from where you place the run_GeoProps.py program and create radial distribution function plots, number of neighbour plots, and text files giving information about the number of neighbours and number of bonds within your nanocluster/chemical system for each nanoclusters and chemical systems that is found as either a XYZ file (ending with .xyz) or ASE trajectory file (ending with .traj).
Geoprops will search through all the subdirectories that are contained in the same directory as the run_GeoProps.py python file and make folders of these subdirectories that contain GeoProps in the name. It will do this one for folders that contain .xyz or .traj files. GeoProps will then work on these files and give structural and geometric data on those .xyz and .traj files.
Examples of the plots that are created are shown below. These include a radial distribution function plot, and number of neighbours bar plot, a text document describing all the number of neighbours found in your cluster with the associated atoms (these can be seen by opening up the xyz file, where the tags describe the index for each atom. These can be coloured by the ASE GUI), and a text document describing all the bonds that are found in your nanocluster/chemical system.
A example radial distribution function plot of a Cu10Pd28 nanocluster:
A bar plot of the number of neighbour for each atom within a Cu10Pd28 nanocluster:
A text document describing the number of neighbour for each atom within a Cu10Pd28 nanocluster:
The following file contains information about the number of neighbours that each atom contains in the cluster, as well as the atom indices of atoms in the cluster with those number of neighbours.
To see each atom in your cluster, open the xyz file of your nanocluster/chemical system, and in View -> Colors, change the colouring of your cluster to "By tag".
The colours represent the index for each atom, which corresponce to the atom indices in this document.
No of neighbours | Atom Indices in Cluster/Chemical System
---------------------------------------------------------------
5 | 2 (Cu), 4 (Cu), 7 (Cu), 16 (Cu), 33 (Cu), 34 (Cu), 35 (Cu), 37 (Cu)
7 | 0 (Pd), 3 (Pd), 5 (Pd), 6 (Pd), 8 (Pd), 12 (Pd), 14 (Pd), 17 (Pd), 20 (Pd), 21 (Pd), 22 (Pd), 23 (Pd), 25 (Pd), 27 (Pd), 30 (Pd), 32 (Pd)
8 | 13 (Cu), 36 (Cu)
9 | 1 (Pd), 9 (Pd), 10 (Pd), 18 (Pd), 19 (Pd), 24 (Pd), 26 (Pd), 28 (Pd)
14 | 11 (Pd), 15 (Pd), 29 (Pd), 31 (Pd)
This is the same list as above, but without elements given for each atom
No of neighbours | Atom Indices in Cluster/Chemical System
---------------------------------------------------------------
5 | 2, 4, 7, 16, 33, 34, 35, 37
7 | 0, 3, 5, 6, 8, 12, 14, 17, 20, 21, 22, 23, 25, 27, 30, 32
8 | 13, 36
9 | 1, 9, 10, 18, 19, 24, 26, 28
14 | 11, 15, 29, 31
A text document describing the types of bonds that are found within a Cu10Pd28 nanocluster:
This text file contains all the information about the number of bonds in this cluster/chemical system.
Total Number of Bonds = 148
Number of ('Cu', 'Pd') Bonds = 56
Number of ('Pd', 'Pd') Bonds = 92
Bond lengths
('Cu', 'Pd'): [2.1426188343062393, 2.1427583193546424, 2.1432650445862267, 2.143300820985679, 2.1433095103614477, 2.143380473937092, 2.1433839899624885, 2.1434279554194773, 2.143507790605591, 2.1437730945180347, 2.1438763872817526, 2.1439948295534226, 2.144006910513814, 2.1440639238653416, 2.144205373937482, 2.144493576045379, 2.178961208591983, 2.179887442593907, 2.1806525368249456, 2.1810616814402115, 2.181135064498954, 2.1815224144682235, 2.1816343117860595, 2.1816578674672766, 2.182015356466698, 2.1821257243283667, 2.182864657104268, 2.1828785262204318, 2.18302277865161, 2.183386345004728, 2.1834696152952877, 2.184521453798309, 2.217582435677598, 2.218172444316745, 2.2187914425746462, 2.2191048987125654, 2.220141304533914, 2.2205328743133554, 2.221514996477335, 2.22154726929384, 2.358535891394043, 2.3592521580784362, 2.3593498449566153, 2.3602507521567317, 2.3602969850076247, 2.361987794973941, 2.362088885121336, 2.3628606855912677, 2.59450012702186, 2.59548672244819, 2.5957151669869707, 2.5963379770634623, 2.5963452624928935, 2.5966444264082984, 2.5966541916292996, 2.5969446051485834]
('Pd', 'Pd'): [2.53371554658355, 2.534070088067998, 2.5342318599496294, 2.534432572208152, 2.5346591614609326, 2.534747097401316, 2.5347748674838084, 2.534955457000947, 2.5740522808982362, 2.574164244902007, 2.5747521491283845, 2.574943804555506, 2.5752974443694345, 2.5755487995606403, 2.5763093979612304, 2.5763258504937077, 2.585286152404103, 2.5853496319609794, 2.5855440296721075, 2.5863472844610604, 2.587268362421799, 2.588225939568966, 2.5883859393806694, 2.588981455960284, 2.5994533249150997, 2.600159636544112, 2.60068668255829, 2.6012124609572282, 2.654168913395472, 2.65689031132755, 2.6576241356976653, 2.6579748494763265, 2.658025020530186, 2.6595973390046317, 2.659746674540581, 2.660005934961473, 2.660578844208819, 2.6613002992039054, 2.66184445696002, 2.662789933778821, 2.663056027294901, 2.664147560864939, 2.6647311328700805, 2.665685035213337, 2.6752655328698767, 2.6759345230031872, 2.677247048785563, 2.678104132030415, 2.680797897001479, 2.681261423810827, 2.681442991272282, 2.6821099371289026, 2.6821525108011843, 2.6821742304107947, 2.682202318865889, 2.682213923244818, 2.6822737895008983, 2.6823470477962554, 2.68253424712709, 2.6827883619378263, 2.6828303710984174, 2.683032599296767, 2.6831520137342086, 2.6840670632573294, 2.735669657462604, 2.736685619285227, 2.736900711681779, 2.7374891499595178, 2.7377133709569943, 2.738549835325026, 2.7387186235763226, 2.73957905227037, 2.7798282332909934, 2.7833749587071575, 2.7836822303565953, 2.7857944595947397, 2.8408295701934363, 2.842052785220107, 2.843253412723664, 2.8432975618208345, 2.843855460526484, 2.8445754358180295, 2.8447587971949986, 2.8454969731182698, 2.8468719651232313, 2.8474147920619752, 2.8479874357866053, 2.8481862322274885, 2.8487682483616887, 2.849951244492647, 2.8512530194249783, 2.853020129286062]
In a folder called Useful_Subsidiary_Programs are some other useful scripts that have been written when developing this program.
make_pages_of_plots.py: This script allows you to turn a number of plots into pages that contain 12 plots each on them.
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| Authors | Geoffrey R. Weal, Caitlin A. Casey-Stevens, and Dr. Anna L. Garden |
| Group Website | https://blogs.otago.ac.nz/annagarden/ |