ChemWiki - User contributions [en]

Building structure with Pymatgen

2023-05-30T13:43:38Z

Fg1020: /* Building within Pymatgen */

This tutorial aims to provide a hands-on tutorial of building crystal structures and cutting surfaces with Pymatgen.

Pymatgen (Python Materials Genomics) is an open-source Python library for materials analysis.

=Pre Set-up=

Getting Pymatgen

(method 1)

<code> conda install --channel conda-forge pymatgen </code>

(method 2)

<code> pip install pymatgen </code>

=Import Structure=

==From Material Project==

<code> from mp_api.client import MPRester </code>

Please check you API code here:
https://materialsproject.org/api

==Read from local file==

<code> from pymatgen.core.structure import Structure </code>

<code> # import structure from local cif file </code>

<code> primitive = Structure.from_file("./primitive.cif") </code>

<code> from pymatgen.symmetry.analyzer import SpacegroupAnalyzer </code>

<code> SGA = SpacegroupAnalyzer(primitive) </code>

<code> conventional = SGA.get_conventional_standard_structure() </code>

==Building within Pymatgen==

statements

<code> from pymatgen import * </code>

create primitive cell from space group

<code> from pymatgen.core import Structure, Lattice </code>

<code> from pymatgen.core.surface import SlabGenerator, Slab </code>

<code> latt_length = number_1 #lattice length, here a=b=c, in A </code>

<code> latt_angle = number_2 #lattice angle, here alpha=beta=gamma, in degree </code>

<code> latt = Lattice.from_parameters(a=latt_length,b=latt_length,c=latt_length,alpha=latt_angle,beta=latt_angle,gamma=latt_angle) </code>

<code> print(latt) </code>

fractional coordinates

<code> coord = [[x1,y1,z1], </code>

<code> [x2,y2,z2], </code>

<code> [x3,y3,z3], </code>

<code> [x4,y4,z4], </code>

<code> [x5,y5,z5], </code>

<code> [x6,y6,z6]] </code>

<code> cell_name = Structure.from_spacegroup("P1", latt, ["ATOM1","ATOM2","ATOM3","ATOM4","ATOM5","ATOM6"], coord,coords_are_cartesian=False) </code>

<code> print(cell_name) </code>

==Visulising Structure==

=Generate slab from bulk system=

==Build slab model==

Generate slab using slab generator

<code> slabgen = SlabGenerator(conventional, </code>

<code> miller_index=(0,0,1), </code>

<code> min_slab_size=10, </code>

<code> min_vacuum_size=10, </code>

<code> center_slab=False) </code>

==Search for all possible terminations==

<code> slabs = slabgen.get_slabs() </code>

<code> print("The number of distinct terminations is: {}".format(len(slabs))) </code>

save these slabs in .cif files

<code> for n,slab in enumerate(slabs): </code>

<code> print(n, "writing slab{}.cif".format(n)) </code>

<code> slab.to(fmt="cif", filename="slab{}.cif".format(n)) </code>

<code> print("Slabs terminated at shift = {}".format(slab.shift)) </code>

==Search for possible adsorption sites==

statements

<code> from pymatgen.analysis.adsorption import AdsorbateSiteFinder, plot_slab </code>

<code> from matplotlib import pyplot as plt </code>

<code> fig = plt.figure() </code>

<code> ax = fig.add_subplot(111) </code>

find adsorbate sites of slab 0 generated in Step 1
will write a for loop to include all slabs

<code> ASF = AdsorbateSiteFinder(slabs[0]).find_adsorption_sites(distance=2.0, </code>

<code> put_inside=True, </code>

<code> symm_reduce=0.01, </code>

<code> near_reduce=0.01, </code>

<code> positions=('ontop','hollow','bridge'), </code>

<code> no_obtuse_hollow=True) </code>

Plot slab with adsorption sites

<code> plot_slab(slabs[0],ax,adsorption_sites=True) </code>

save as png

<code> fig.savefig("./slab0.png", dpi=200) </code>

print a list of sites coordinate

<code> sites_dict = AdsorbateSiteFinder(slabs[0]).find_adsorption_sites(distance=2.0, </code>

<code> put_inside=True, </code>

<code> symm_reduce=0.01, </code>

<code> near_reduce=0.01, </code>

<code> positions=('ontop','hollow','bridge'), </code>

<code> no_obtuse_hollow=True) </code>

<code> print(sites_dict) </code>

=Export Data=

statements

<code> from pymatgen.io.cif import CifWriter </code>

<code> from pymatgen.io.xyz import XYZ </code>

Write cif files

<code> wcif = CifWriter(structure) </code>

<code> wcif.write_file("test.cif") </code>

Write xyz files

<code> wxyz = XYZ() </code>

<code> wxyz.write_file("test.xyz") </code>

Building structure with Pymatgen

2023-05-30T13:29:04Z

Fg1020: /* Build slab model */

This tutorial aims to provide a hands-on tutorial of building crystal structures and cutting surfaces with Pymatgen.

Pymatgen (Python Materials Genomics) is an open-source Python library for materials analysis.

=Pre Set-up=

Getting Pymatgen

(method 1)

<code> conda install --channel conda-forge pymatgen </code>

(method 2)

<code> pip install pymatgen </code>

=Import Structure=

==From Material Project==

<code> from mp_api.client import MPRester </code>

Please check you API code here:
https://materialsproject.org/api

==Read from local file==

<code> from pymatgen.core.structure import Structure </code>

<code> # import structure from local cif file </code>

<code> primitive = Structure.from_file("./primitive.cif") </code>

<code> from pymatgen.symmetry.analyzer import SpacegroupAnalyzer </code>

<code> SGA = SpacegroupAnalyzer(primitive) </code>

<code> conventional = SGA.get_conventional_standard_structure() </code>

==Building within Pymatgen==

==Visulising Structure==

=Generate slab from bulk system=

==Build slab model==

Generate slab using slab generator

<code> slabgen = SlabGenerator(conventional, </code>

<code> miller_index=(0,0,1), </code>

<code> min_slab_size=10, </code>

<code> min_vacuum_size=10, </code>

<code> center_slab=False) </code>

==Search for all possible terminations==

<code> slabs = slabgen.get_slabs() </code>

<code> print("The number of distinct terminations is: {}".format(len(slabs))) </code>

save these slabs in .cif files

<code> for n,slab in enumerate(slabs): </code>

<code> print(n, "writing slab{}.cif".format(n)) </code>

<code> slab.to(fmt="cif", filename="slab{}.cif".format(n)) </code>

<code> print("Slabs terminated at shift = {}".format(slab.shift)) </code>

==Search for possible adsorption sites==

statements

<code> from pymatgen.analysis.adsorption import AdsorbateSiteFinder, plot_slab </code>

<code> from matplotlib import pyplot as plt </code>

<code> fig = plt.figure() </code>

<code> ax = fig.add_subplot(111) </code>

find adsorbate sites of slab 0 generated in Step 1
will write a for loop to include all slabs

<code> ASF = AdsorbateSiteFinder(slabs[0]).find_adsorption_sites(distance=2.0, </code>

<code> put_inside=True, </code>

<code> symm_reduce=0.01, </code>

<code> near_reduce=0.01, </code>

<code> positions=('ontop','hollow','bridge'), </code>

<code> no_obtuse_hollow=True) </code>

Plot slab with adsorption sites

<code> plot_slab(slabs[0],ax,adsorption_sites=True) </code>

save as png

<code> fig.savefig("./slab0.png", dpi=200) </code>

print a list of sites coordinate

<code> sites_dict = AdsorbateSiteFinder(slabs[0]).find_adsorption_sites(distance=2.0, </code>

<code> put_inside=True, </code>

<code> symm_reduce=0.01, </code>

<code> near_reduce=0.01, </code>

<code> positions=('ontop','hollow','bridge'), </code>

<code> no_obtuse_hollow=True) </code>

<code> print(sites_dict) </code>

=Export Data=

statements

<code> from pymatgen.io.cif import CifWriter </code>

<code> from pymatgen.io.xyz import XYZ </code>

Write cif files

<code> wcif = CifWriter(structure) </code>

<code> wcif.write_file("test.cif") </code>

Write xyz files

<code> wxyz = XYZ() </code>

<code> wxyz.write_file("test.xyz") </code>

Building structure with Pymatgen

2023-05-30T13:28:39Z

Fg1020: /* == */

This tutorial aims to provide a hands-on tutorial of building crystal structures and cutting surfaces with Pymatgen.

Pymatgen (Python Materials Genomics) is an open-source Python library for materials analysis.

=Pre Set-up=

Getting Pymatgen

(method 1)

<code> conda install --channel conda-forge pymatgen </code>

(method 2)

<code> pip install pymatgen </code>

=Import Structure=

==From Material Project==

<code> from mp_api.client import MPRester </code>

Please check you API code here:
https://materialsproject.org/api

==Read from local file==

<code> from pymatgen.core.structure import Structure </code>

<code> # import structure from local cif file </code>

<code> primitive = Structure.from_file("./primitive.cif") </code>

<code> from pymatgen.symmetry.analyzer import SpacegroupAnalyzer </code>

<code> SGA = SpacegroupAnalyzer(primitive) </code>

<code> conventional = SGA.get_conventional_standard_structure() </code>

==Building within Pymatgen==

==Visulising Structure==

=Generate slab from bulk system=

==Build slab model==

Generate slab using slab generator

<code> slabgen = SlabGenerator(af1_conventional, </code>

<code> miller_index=(0,0,1), </code>

<code> min_slab_size=10, </code>

<code> min_vacuum_size=10, </code>

<code> center_slab=False) </code>

==Search for all possible terminations==

<code> slabs = slabgen.get_slabs() </code>

<code> print("The number of distinct terminations is: {}".format(len(slabs))) </code>

save these slabs in .cif files

<code> for n,slab in enumerate(slabs): </code>

<code> print(n, "writing slab{}.cif".format(n)) </code>

<code> slab.to(fmt="cif", filename="slab{}.cif".format(n)) </code>

<code> print("Slabs terminated at shift = {}".format(slab.shift)) </code>

==Search for possible adsorption sites==

statements

<code> from pymatgen.analysis.adsorption import AdsorbateSiteFinder, plot_slab </code>

<code> from matplotlib import pyplot as plt </code>

<code> fig = plt.figure() </code>

<code> ax = fig.add_subplot(111) </code>

find adsorbate sites of slab 0 generated in Step 1
will write a for loop to include all slabs

<code> ASF = AdsorbateSiteFinder(slabs[0]).find_adsorption_sites(distance=2.0, </code>

<code> put_inside=True, </code>

<code> symm_reduce=0.01, </code>

<code> near_reduce=0.01, </code>

<code> positions=('ontop','hollow','bridge'), </code>

<code> no_obtuse_hollow=True) </code>

Plot slab with adsorption sites

<code> plot_slab(slabs[0],ax,adsorption_sites=True) </code>

save as png

<code> fig.savefig("./slab0.png", dpi=200) </code>

print a list of sites coordinate

<code> sites_dict = AdsorbateSiteFinder(slabs[0]).find_adsorption_sites(distance=2.0, </code>

<code> put_inside=True, </code>

<code> symm_reduce=0.01, </code>

<code> near_reduce=0.01, </code>

<code> positions=('ontop','hollow','bridge'), </code>

<code> no_obtuse_hollow=True) </code>

<code> print(sites_dict) </code>

=Export Data=

statements

<code> from pymatgen.io.cif import CifWriter </code>

<code> from pymatgen.io.xyz import XYZ </code>

Write cif files

<code> wcif = CifWriter(structure) </code>

<code> wcif.write_file("test.cif") </code>

Write xyz files

<code> wxyz = XYZ() </code>

<code> wxyz.write_file("test.xyz") </code>

Building structure with Pymatgen

2023-05-30T13:28:07Z

Fg1020: /* Export Data */

This tutorial aims to provide a hands-on tutorial of building crystal structures and cutting surfaces with Pymatgen.

Pymatgen (Python Materials Genomics) is an open-source Python library for materials analysis.

=Pre Set-up=

Getting Pymatgen

(method 1)

<code> conda install --channel conda-forge pymatgen </code>

(method 2)

<code> pip install pymatgen </code>

=Import Structure=

==From Material Project==

<code> from mp_api.client import MPRester </code>

Please check you API code here:
https://materialsproject.org/api

==Read from local file==

<code> from pymatgen.core.structure import Structure </code>

<code> # import structure from local cif file </code>

<code> primitive = Structure.from_file("./primitive.cif") </code>

<code> from pymatgen.symmetry.analyzer import SpacegroupAnalyzer </code>

<code> SGA = SpacegroupAnalyzer(primitive) </code>

<code> conventional = SGA.get_conventional_standard_structure() </code>

==Building within Pymatgen==

==Visulising Structure==

=Generate slab from bulk system=

==Build slab model==

Generate slab using slab generator

<code> slabgen = SlabGenerator(af1_conventional, </code>

<code> miller_index=(0,0,1), </code>

<code> min_slab_size=10, </code>

<code> min_vacuum_size=10, </code>

<code> center_slab=False) </code>

==Search for all possible terminations==

<code> slabs = slabgen.get_slabs() </code>

<code> print("The number of distinct terminations is: {}".format(len(slabs))) </code>

save these slabs in .cif files

<code> for n,slab in enumerate(slabs): </code>

<code> print(n, "writing slab{}.cif".format(n)) </code>

<code> slab.to(fmt="cif", filename="slab{}.cif".format(n)) </code>

<code> print("Slabs terminated at shift = {}".format(slab.shift)) </code>

==Search for possible adsorption sites==

statements

<code> from pymatgen.analysis.adsorption import AdsorbateSiteFinder, plot_slab </code>

<code> from matplotlib import pyplot as plt </code>

<code> fig = plt.figure() </code>

<code> ax = fig.add_subplot(111) </code>

find adsorbate sites of slab 0 generated in Step 1
will write a for loop to include all slabs

<code> ASF = AdsorbateSiteFinder(slabs[0]).find_adsorption_sites(distance=2.0, </code>

<code> put_inside=True, </code>

<code> symm_reduce=0.01, </code>

<code> near_reduce=0.01, </code>

<code> positions=('ontop','hollow','bridge'), </code>

<code> no_obtuse_hollow=True) </code>

Plot slab with adsorption sites

<code> plot_slab(slabs[0],ax,adsorption_sites=True) </code>

save as png

<code> fig.savefig("./slab0.png", dpi=200) </code>

print a list of sites coordinate

<code> sites_dict = AdsorbateSiteFinder(slabs[0]).find_adsorption_sites(distance=2.0, </code>

<code> put_inside=True, </code>

<code> symm_reduce=0.01, </code>

<code> near_reduce=0.01, </code>

<code> positions=('ontop','hollow','bridge'), </code>

<code> no_obtuse_hollow=True) </code>

<code> print(sites_dict) </code>

=Export Data=

statements

<code> from pymatgen.io.cif import CifWriter </code>

<code> from pymatgen.io.xyz import XYZ </code>

Write cif files

<code> wcif = CifWriter(structure) </code>

<code> wcif.write_file("test.cif") </code>

Write xyz files

<code> wxyz = XYZ() </code>

<code> wxyz.write_file("test.xyz") </code>

====

Building structure with Pymatgen

2023-05-30T13:24:08Z

Fg1020: /* Search for possible adsorption sites */

This tutorial aims to provide a hands-on tutorial of building crystal structures and cutting surfaces with Pymatgen.

Pymatgen (Python Materials Genomics) is an open-source Python library for materials analysis.

=Pre Set-up=

Getting Pymatgen

(method 1)

<code> conda install --channel conda-forge pymatgen </code>

(method 2)

<code> pip install pymatgen </code>

=Import Structure=

==From Material Project==

<code> from mp_api.client import MPRester </code>

Please check you API code here:
https://materialsproject.org/api

==Read from local file==

<code> from pymatgen.core.structure import Structure </code>

<code> # import structure from local cif file </code>

<code> primitive = Structure.from_file("./primitive.cif") </code>

<code> from pymatgen.symmetry.analyzer import SpacegroupAnalyzer </code>

<code> SGA = SpacegroupAnalyzer(primitive) </code>

<code> conventional = SGA.get_conventional_standard_structure() </code>

==Building within Pymatgen==

==Visulising Structure==

=Generate slab from bulk system=

==Build slab model==

Generate slab using slab generator

<code> slabgen = SlabGenerator(af1_conventional, </code>

<code> miller_index=(0,0,1), </code>

<code> min_slab_size=10, </code>

<code> min_vacuum_size=10, </code>

<code> center_slab=False) </code>

==Search for all possible terminations==

<code> slabs = slabgen.get_slabs() </code>

<code> print("The number of distinct terminations is: {}".format(len(slabs))) </code>

save these slabs in .cif files

<code> for n,slab in enumerate(slabs): </code>

<code> print(n, "writing slab{}.cif".format(n)) </code>

<code> slab.to(fmt="cif", filename="slab{}.cif".format(n)) </code>

<code> print("Slabs terminated at shift = {}".format(slab.shift)) </code>

==Search for possible adsorption sites==

statements

<code> from pymatgen.analysis.adsorption import AdsorbateSiteFinder, plot_slab </code>

<code> from matplotlib import pyplot as plt </code>

<code> fig = plt.figure() </code>

<code> ax = fig.add_subplot(111) </code>

find adsorbate sites of slab 0 generated in Step 1
will write a for loop to include all slabs

<code> ASF = AdsorbateSiteFinder(slabs[0]).find_adsorption_sites(distance=2.0, </code>

<code> put_inside=True, </code>

<code> symm_reduce=0.01, </code>

<code> near_reduce=0.01, </code>

<code> positions=('ontop','hollow','bridge'), </code>

<code> no_obtuse_hollow=True) </code>

Plot slab with adsorption sites

<code> plot_slab(slabs[0],ax,adsorption_sites=True) </code>

save as png

<code> fig.savefig("./slab0.png", dpi=200) </code>

print a list of sites coordinate

<code> sites_dict = AdsorbateSiteFinder(slabs[0]).find_adsorption_sites(distance=2.0, </code>

<code> put_inside=True, </code>

<code> symm_reduce=0.01, </code>

<code> near_reduce=0.01, </code>

<code> positions=('ontop','hollow','bridge'), </code>

<code> no_obtuse_hollow=True) </code>

<code> print(sites_dict) </code>

=Export Data=

====

Building structure with Pymatgen

2023-05-30T13:12:17Z

Fg1020: /* Search for all possible terminations */

Building structure with Pymatgen

2023-05-30T13:12:01Z

Fg1020: /* Build slab model */

Building structure with Pymatgen

2023-05-30T13:08:21Z

Fg1020: /* Build slab model */

Contributors

2023-05-26T15:26:27Z

Fg1020: /* Fei Gao */

<div style="border:0px solid #90C0FF; background:#ffffff; width:90%; padding:40px">
=Nano Electrochemistry Group=

==Clotilde Cucinotta (PI)==

==Chris Ahart==
[[File:ChrisAhartProfile.png|frameless|bottom|200px|Chris Ahart]]

Postdoc August 2022 - present.
==Frederik==

==Songyuan==

==Margherita Buraschi==
[[File:Margherita Buraschi photo.jpg|frameless|bottom|200px|Margherita Buraschi]]

PhD July 2020-present. In her PhD, Margherita is investigating the charge transfer properties of electrochemical nanojunctions (ECNJs) by means of computational studies. ECNJs are three-terminal functional devices of interest for the field of molecular electronics <ref> Huang et al., Chem. Soc. Rev., '''44''', 889-901 (2015) </ref> as they present the same functionality of common electronic units but at the molecular scale. Many factors define the conductance of ECNJs; amongst these factors are the structure of the functional unit, the type of metal as well as the EC transformations occurring in solutions. In order to obtain an atomistic understanding of all these factors and their effects on the overall conductance of the junction, ab initio molecular dynamics under bias and an explicit open‐boundary description of the electrons are performed during this project. To this end, the hair-probes formalism <ref> Horsfield, Boleininger, D'Agosta, Iyer, Thong, Todorov and White, Phys. Rev. B, '''94''', 075118 (2016) </ref><ref>Zauchner, Horsfield and Todorov, Physical Review B, '''97''', 045116 (2018) </ref>, an open‐boundary formalism suitable to describe multi-terminal EC systems, is being interfaced within the DFT scheme implemented in the CP2K computational package <ref>Kühne et al., The Journal of Chemical Physics, '''152'''(19), 194103 (2020) </ref>.
==Rashid Al-Heidous==
[[File:Rashid Personal Photo.jpeg|frameless|bottom|200px|Rashid Al-Heidous]]

==Zehui Duan==
[[File:Zehui Duan photo.jpg|frameless|bottom|200px|Zehui Duan]]

MRes Oct 2020-present. Using density functional theory (DFT) as implemented in CP2K code, Zehui is investigating the thermodynamics of the CO<sub>2</sub> reduction reaction (CO2RR), to guide the rational design for dual-atom catalysts (DAC) with both high efficiency and good selectivity.

==Lorraine Wang==
[[File:Lorraine Wang photo.jpg|frameless|bottom|200px|Lorraine Wang]]

MRes Oct 2020-presnt. In her MRes project, Lorraine is studying dual-metal-atom catalysts (DAC) by means of density functional theory (DFT) as implemented in CP2K code. Dual-metal-atom catalysts with synergistic effect <ref>X. Zhu, J. Yan, M. Gu, T. Liu, Y. Dai, Y. Gu and Y. Li, J. Phys. Chem. Lett., '''10''', [tel:7760–7766 7760–7766] (2019) </ref> between the two metal atoms can enhance the catalytic oxygen reduction reaction (ORR). They usually consist of a substrate (doped graphene layers) and anchored metal atoms. Using DFT simulations implemented within the CP2K code can help to build a fundamental understanding of the structure. By studying the thermodynamics of various patterns, we can propose a thermodynamically favourable pathway of DAC synthesis. In the future, the project can further extend to study catalysts phase stability, catalytic performance and kinetics with more complexed models.

==Kalman==

==Felix==

==Luke==

==Anthony==

</div>
<div style="border:0px solid #90C0FF; background:#ffffff; width:90%; padding:40px">

=Computational Materials Science Group (CMSG)=

CMSG is a group of scientiests under Prof. Nicholas Harrison's supervison at Imperial College London.

==Nicholas Harrison (PI)==

==Paolo Restuccia==

==Huanyu Zhou==
PhD in Chemistry 2021-present; MRes Nanomaterials 2020-2021

Huanyu's PhD research project is about the multi-scale modelling of thermodynamics of molecular crystals using ab initio methods. It involves accurate polymorphism prediction and modelling the solvation effects at solid-liquid interfaces of pharmaceutical crystals, which is a joint endeavour with Prof. Jerry Heng's group at the Department of Chemical Engineering.

During his master project co-supervised by Dr. Giuseppe Mallia, Huanyu investigated the monovacancy defect on compressed graphene by DFT. The correlation between magnetic moment and local geometry of monovacacies was identified, which lead to novel electronic and spintronic properties.

Huanyu is also one of the main authors of [https://crystal-code-tools.github.io/CRYSTALpytools/ CRYSTALpytools], the object-oriented python package for CRYSTAL, co-developed by CMSG Imperial and the Theoretical Chemistry Group (TEO) UniTo.

==Fei Gao==
[[File:Fei.jpeg|frameless|bottom|200px|Lorraine Wang]]

PhD in Chemistry 2021-present; MRes IMSE 2020-2021
</div>

Contributors

2023-05-26T15:25:33Z

Fg1020:

File:Fei.jpeg

2023-05-26T15:24:32Z

Fg1020:

Building structure with Pymatgen

2023-05-26T09:43:47Z

Fg1020: /* Build slab model */

Building structure with Pymatgen

2023-05-26T09:33:18Z

Fg1020: /* Read from local file */

Building structure with Pymatgen

2023-05-26T09:31:51Z

Fg1020: /* Read from local file */

Building structure with Pymatgen

2023-05-26T09:30:48Z

Fg1020: /* Import Structure */

Building structure with Pymatgen

2023-05-26T09:06:42Z

Fg1020: /* Pre Set-up */

Building structure with Pymatgen

2022-12-02T15:17:26Z

Fg1020: Created page with "This tutorial aims to provide a hands-on tutorial of building crystal structures and cutting surfaces with Pymatgen. Pymatgen (Python Materials Genomics) is an open-source Py..."

This tutorial aims to provide a hands-on tutorial of building crystal structures and cutting surfaces with Pymatgen.

Pymatgen (Python Materials Genomics) is an open-source Python library for materials analysis.

=Pre Set-up=

=Import Structure=

==From Material Project==

==Read from local file==

==Building within Pymatgen==

==Visulising Structure==

=Generate slab from bulk system=

==Build slab model==

==Search for all possible terminations==

==Search for possible adsorption sites==

=Export Data=

====

Nano Electrochemistry Group

2022-12-02T15:16:26Z

Fg1020:

<div style="padding: 10px; background: #87adde; border: 1px solid #FFAA99; font-family: Trebuchet MS, sans-serif; font-size: 95%;">

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
This page provides a series of tutorials designed to help with the computational modelling of electrochemical system; their aim is to provide general workflows and useful tip to model fundamental components and properties of electrochemical systems. The tutorials have been designed by the researchers of the Computational NanoElectrochemistry Group led by Dr Clotilde Cucinotta [link to group page] and collaborators.
Several simulation packages (CP2K, LAMMPS, QuantumEspresso, etc.), as well as other tools, such as molecular visualisers or programming languages, are described in these tutorials; links to the relevant manuals are provided at the bottom of the page.
Script and programs written by the components of the research group are also described in each tutorial; these tools have been devised to help with running calculations and with data analysis and can be found in the linked GitLub repository [https://gitlab.doc.ic.ac.uk/rgc].

==Running in a Cluster Tutorials==

===[[How to run on ARCHER 2]]===
Written by:[[Contributors#Songyuan| Songyuan]]

===[[Imperial CX1: Instructions and basic concepts of parallel computing|Imperial CX1: Instructions and basic concepts of parallel computing]]===
Written by:[[Contributors| Huanyu]]

A collection of useful resources and brief introductions to the basic concepts of parallel computing for beginners to use the high-performance computing service at Imperial.

==[[Reaction Dynamics]]==
===[[Lammps and plumed|Lammps and plumed]]===
Written by:[[Contributors| Frederik]]

Tutorial on how to use the PLUMED software package to perform biased molecular dynamics simulations in LAMMPS.

===[[Converging magnetic systems in CP2K]]===
Written by:[[Contributors| Chris]]

* Contents:
** MULTIPLICITY keyword to calculate magnetic systems
** &BS section and MAGNETIZATION keyword to improve convergence
* Computational package: CP2K.

===[[Optimization of metallic surfaces parameters|Optimizing parameters for metallic surfaces]]===
Written by:[[Contributors| Margherita]]

* Contents:
** Tutorials on how to define the appropriate set of parameters needed to model a metallic system: Basis set, CUTOFF and '''k'''-points grid;
** Tutorials on how to calculate relevant quantities of metallic surfaces: work function, equilibrium lattice parameter and electronic structure;
* System: metallic surfaces (Platinum slab used as example);
* Computational package: CP2K.

===Surface analysis===
Written by:[[Contributors| Songyuan]]

===[[Dimers in gas phase|Dimers in gas phase]]===
Written by:[[Contributors| Fredrik]]

Tutorial for optimising dimers in the gas phase using gaussian.

===[[Calculation of radial average|Calculation of radial average]]===
Written by:[[Contributors| Kalman]]

Tutorial for calculating the radial average ?.

===[[Adsorption of molecule on surfaces|Adsorption of molecule on surfaces]]===
Written by:[[Contributors| Paolo]]

Tutorial for calculating the adsorption energy of a molecule (or, more in general, any particle) over a specific surface.

===[[Memristors|Simulation of Memristors]]===
Written by:[[Contributors| Felix]]

Tutorial for optimising parameters for memristors using QuantumEspresso.

===[[Hard_carbon|Simulation of Hard Carbons]]===
Written by:[[Contributors| Luke]]

Tutorial for the simulation of hard carbon?

===[[Solving 1D Poisson equation |Solving 1D Poisson equation]]===
Written by:[[Contributors| Remi Khatib ]]

Tutorial for the solution of the 1D Poisson equations given a distribution of point charges

===[[TrendsCatalyticActivity|Trends in catalytic Activity]]===
Tutorial for a computational experiment about trends in catalytic activity for hydrogen evolution. This experiment is part of the third year computational chemistry lab.

===[[Convergence test of critical parameters by CRYSTAL]]===
Written by:[[Contributors| Huanyu ]]

A tutorial for performing convergence tests with LCAO-GTO DFT code, CRYSTAL.

===[[Building structure with Pymatgen]]===
Written by:[[Contributors| Fei ]]

Tutorial for generating crystal structure and surface with Python.

</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Computational Tools==

===[https://www.cp2k.org/about CP2K]===
*[[CP2K_Tutorial|CP2K TUTORIAL]];
*[https://github.com/cp2k/cp2k/blob/master/INSTALL.md Download and install CP2K ];
*[https://manual.cp2k.org/#gsc.tab=0 Manual];
*[https://www.cp2k.org/howto Useful HOWTOs];
*Reading inputs and outputs (commented files and examples);

===[https://www.quantum-espresso.org/ QUANTUM ESPRESSO]===
*[https://www.quantum-espresso.org/download Download and install QUANTUM ESPRESSO];
*[https://www.quantum-espresso.org/resources/tutorials Useful Tutorials];
*Reading inputs and outputs (commented files and examples);

===[https://www.lammps.org/ LAMMPS]===
*[https://www.lammps.org/download.html Download LAMMPS];
*[https://docs.lammps.org/Manual.html Manual];
*[https://www.lammps.org/tutorials.html Tutorials];

===[https://www.crystal.unito.it/index.php CRYSTAL]===
* [https://tutorials.crystalsolutions.eu/ CRYSTAL Tutorial Project]
* [https://www.crystal.unito.it/basis-sets.php CRYSTAL basis set database for solid state calculations]
* [http://crysplot.crystalsolutions.eu/ CRYSPLOT: A web-based visualisation tool]
* [https://github.com/crystal-code-tools/crystal_functions crystal_functions: A python-based toolbox]

===[https://www.tcd.ie/Physics/Smeagol/SmeagolAbout.htm Smeagol]===

===others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Molecular visualizers==
*[http://www.ks.uiuc.edu/Research/vmd/ VMD]
*[http://www.xcrysden.org/ Xcrysden]
*[https://jp-minerals.org/vesta/en/ VESTA]

===Others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Useful programming languages and environments==

*[http://www-eio.upc.edu/lceio/manuals/Fortran95-manual.pdf Fortran]
*[https://docs.python.org/3/ Python]
*[https://wiki.fysik.dtu.dk/ase/ ASE]
*[https://pymatgen.org/ Pymatgen]

===others===

</div>

[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page info]

</div>

Nano Electrochemistry Group

2022-12-02T15:14:16Z

Fg1020:

<div style="padding: 10px; background: #87adde; border: 1px solid #FFAA99; font-family: Trebuchet MS, sans-serif; font-size: 95%;">

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
This page provides a series of tutorials designed to help with the computational modelling of electrochemical system; their aim is to provide general workflows and useful tip to model fundamental components and properties of electrochemical systems. The tutorials have been designed by the researchers of the Computational NanoElectrochemistry Group led by Dr Clotilde Cucinotta [link to group page] and collaborators.
Several simulation packages (CP2K, LAMMPS, QuantumEspresso, etc.), as well as other tools, such as molecular visualisers or programming languages, are described in these tutorials; links to the relevant manuals are provided at the bottom of the page.
Script and programs written by the components of the research group are also described in each tutorial; these tools have been devised to help with running calculations and with data analysis and can be found in the linked GitLub repository [https://gitlab.doc.ic.ac.uk/rgc].

==Running in a Cluster Tutorials==

===[[How to run on ARCHER 2]]===
Written by:[[Contributors#Songyuan| Songyuan]]

===[[Imperial CX1: Instructions and basic concepts of parallel computing|Imperial CX1: Instructions and basic concepts of parallel computing]]===
Written by:[[Contributors| Huanyu]]

A collection of useful resources and brief introductions to the basic concepts of parallel computing for beginners to use the high-performance computing service at Imperial.

==[[Reaction Dynamics]]==
===[[Lammps and plumed|Lammps and plumed]]===
Written by:[[Contributors| Frederik]]

Tutorial on how to use the PLUMED software package to perform biased molecular dynamics simulations in LAMMPS.

===[[Converging magnetic systems in CP2K]]===
Written by:[[Contributors| Chris]]

* Contents:
** MULTIPLICITY keyword to calculate magnetic systems
** &BS section and MAGNETIZATION keyword to improve convergence
* Computational package: CP2K.

===[[Optimization of metallic surfaces parameters|Optimizing parameters for metallic surfaces]]===
Written by:[[Contributors| Margherita]]

* Contents:
** Tutorials on how to define the appropriate set of parameters needed to model a metallic system: Basis set, CUTOFF and '''k'''-points grid;
** Tutorials on how to calculate relevant quantities of metallic surfaces: work function, equilibrium lattice parameter and electronic structure;
* System: metallic surfaces (Platinum slab used as example);
* Computational package: CP2K.

===Surface analysis===
Written by:[[Contributors| Songyuan]]

===[[Dimers in gas phase|Dimers in gas phase]]===
Written by:[[Contributors| Fredrik]]

Tutorial for optimising dimers in the gas phase using gaussian.

===[[Calculation of radial average|Calculation of radial average]]===
Written by:[[Contributors| Kalman]]

Tutorial for calculating the radial average ?.

===[[Adsorption of molecule on surfaces|Adsorption of molecule on surfaces]]===
Written by:[[Contributors| Paolo]]

Tutorial for calculating the adsorption energy of a molecule (or, more in general, any particle) over a specific surface.

===[[Memristors|Simulation of Memristors]]===
Written by:[[Contributors| Felix]]

Tutorial for optimising parameters for memristors using QuantumEspresso.

===[[Hard_carbon|Simulation of Hard Carbons]]===
Written by:[[Contributors| Luke]]

Tutorial for the simulation of hard carbon?

===[[Solving 1D Poisson equation |Solving 1D Poisson equation]]===
Written by:[[Contributors| Remi Khatib ]]

Tutorial for the solution of the 1D Poisson equations given a distribution of point charges

===[[TrendsCatalyticActivity|Trends in catalytic Activity]]===
Tutorial for a computational experiment about trends in catalytic activity for hydrogen evolution. This experiment is part of the third year computational chemistry lab.

===[[Convergence test of critical parameters by CRYSTAL]]===
Written by:[[Contributors| Huanyu ]]

A tutorial for performing convergence tests with LCAO-GTO DFT code, CRYSTAL.

</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Computational Tools==

===[https://www.cp2k.org/about CP2K]===
*[[CP2K_Tutorial|CP2K TUTORIAL]];
*[https://github.com/cp2k/cp2k/blob/master/INSTALL.md Download and install CP2K ];
*[https://manual.cp2k.org/#gsc.tab=0 Manual];
*[https://www.cp2k.org/howto Useful HOWTOs];
*Reading inputs and outputs (commented files and examples);

===[https://www.quantum-espresso.org/ QUANTUM ESPRESSO]===
*[https://www.quantum-espresso.org/download Download and install QUANTUM ESPRESSO];
*[https://www.quantum-espresso.org/resources/tutorials Useful Tutorials];
*Reading inputs and outputs (commented files and examples);

===[https://www.lammps.org/ LAMMPS]===
*[https://www.lammps.org/download.html Download LAMMPS];
*[https://docs.lammps.org/Manual.html Manual];
*[https://www.lammps.org/tutorials.html Tutorials];

===[https://www.crystal.unito.it/index.php CRYSTAL]===
* [https://tutorials.crystalsolutions.eu/ CRYSTAL Tutorial Project]
* [https://www.crystal.unito.it/basis-sets.php CRYSTAL basis set database for solid state calculations]
* [http://crysplot.crystalsolutions.eu/ CRYSPLOT: A web-based visualisation tool]
* [https://github.com/crystal-code-tools/crystal_functions crystal_functions: A python-based toolbox]

===[https://www.tcd.ie/Physics/Smeagol/SmeagolAbout.htm Smeagol]===

===others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Molecular visualizers==
*[http://www.ks.uiuc.edu/Research/vmd/ VMD]
*[http://www.xcrysden.org/ Xcrysden]
*[https://jp-minerals.org/vesta/en/ VESTA]

===Others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Useful programming languages and environments==

*[http://www-eio.upc.edu/lceio/manuals/Fortran95-manual.pdf Fortran]
*[https://docs.python.org/3/ Python]
*[https://wiki.fysik.dtu.dk/ase/ ASE]
*[https://pymatgen.org/ Pymatgen]

===others===

</div>

[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page info]

</div>

Nano Electrochemistry Group

2022-12-02T15:12:35Z

Fg1020: /* Building Structure and Surface with Pymatgen */

<div style="padding: 10px; background: #87adde; border: 1px solid #FFAA99; font-family: Trebuchet MS, sans-serif; font-size: 95%;">

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
This page provides a series of tutorials designed to help with the computational modelling of electrochemical system; their aim is to provide general workflows and useful tip to model fundamental components and properties of electrochemical systems. The tutorials have been designed by the researchers of the Computational NanoElectrochemistry Group led by Dr Clotilde Cucinotta [link to group page] and collaborators.
Several simulation packages (CP2K, LAMMPS, QuantumEspresso, etc.), as well as other tools, such as molecular visualisers or programming languages, are described in these tutorials; links to the relevant manuals are provided at the bottom of the page.
Script and programs written by the components of the research group are also described in each tutorial; these tools have been devised to help with running calculations and with data analysis and can be found in the linked GitLub repository [https://gitlab.doc.ic.ac.uk/rgc].

==Running in a Cluster Tutorials==

===[[How to run on ARCHER 2]]===
Written by:[[Contributors#Songyuan| Songyuan]]

===[[Imperial CX1: Instructions and basic concepts of parallel computing|Imperial CX1: Instructions and basic concepts of parallel computing]]===
Written by:[[Contributors| Huanyu]]

A collection of useful resources and brief introductions to the basic concepts of parallel computing for beginners to use the high-performance computing service at Imperial.

==[[Reaction Dynamics]]==
===[[Lammps and plumed|Lammps and plumed]]===
Written by:[[Contributors| Frederik]]

Tutorial on how to use the PLUMED software package to perform biased molecular dynamics simulations in LAMMPS.

===[[Converging magnetic systems in CP2K]]===
Written by:[[Contributors| Chris]]

* Contents:
** MULTIPLICITY keyword to calculate magnetic systems
** &BS section and MAGNETIZATION keyword to improve convergence
* Computational package: CP2K.

===[[Optimization of metallic surfaces parameters|Optimizing parameters for metallic surfaces]]===
Written by:[[Contributors| Margherita]]

* Contents:
** Tutorials on how to define the appropriate set of parameters needed to model a metallic system: Basis set, CUTOFF and '''k'''-points grid;
** Tutorials on how to calculate relevant quantities of metallic surfaces: work function, equilibrium lattice parameter and electronic structure;
* System: metallic surfaces (Platinum slab used as example);
* Computational package: CP2K.

===Surface analysis===
Written by:[[Contributors| Songyuan]]

===[[Dimers in gas phase|Dimers in gas phase]]===
Written by:[[Contributors| Fredrik]]

Tutorial for optimising dimers in the gas phase using gaussian.

===[[Calculation of radial average|Calculation of radial average]]===
Written by:[[Contributors| Kalman]]

Tutorial for calculating the radial average ?.

===[[Adsorption of molecule on surfaces|Adsorption of molecule on surfaces]]===
Written by:[[Contributors| Paolo]]

Tutorial for calculating the adsorption energy of a molecule (or, more in general, any particle) over a specific surface.

===[[Memristors|Simulation of Memristors]]===
Written by:[[Contributors| Felix]]

Tutorial for optimising parameters for memristors using QuantumEspresso.

===[[Hard_carbon|Simulation of Hard Carbons]]===
Written by:[[Contributors| Luke]]

Tutorial for the simulation of hard carbon?

===[[Solving 1D Poisson equation |Solving 1D Poisson equation]]===
Written by:[[Contributors| Remi Khatib ]]

Tutorial for the solution of the 1D Poisson equations given a distribution of point charges

===[[TrendsCatalyticActivity|Trends in catalytic Activity]]===
Tutorial for a computational experiment about trends in catalytic activity for hydrogen evolution. This experiment is part of the third year computational chemistry lab.

===[[Convergence test of critical parameters by CRYSTAL]]===
Written by:[[Contributors| Huanyu ]]

A tutorial for performing convergence tests with LCAO-GTO DFT code, CRYSTAL.

</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

This tutorial aims to provide a hands-on tutorial of building crystal structures and cutting surfaces with Pymatgen.

Pymatgen (Python Materials Genomics) is an open-source Python library for materials analysis.

=Pre Set-up=

=Import Structure=

==From Material Project==

==Read from local file==

==Building within Pymatgen==

==Visulising Structure==

=Generate slab from bulk system=

==Build slab model==

==Search for all possible terminations==

==Search for possible adsorption sites==

=Export Data=

====

==Computational Tools==

===[https://www.cp2k.org/about CP2K]===
*[[CP2K_Tutorial|CP2K TUTORIAL]];
*[https://github.com/cp2k/cp2k/blob/master/INSTALL.md Download and install CP2K ];
*[https://manual.cp2k.org/#gsc.tab=0 Manual];
*[https://www.cp2k.org/howto Useful HOWTOs];
*Reading inputs and outputs (commented files and examples);

===[https://www.quantum-espresso.org/ QUANTUM ESPRESSO]===
*[https://www.quantum-espresso.org/download Download and install QUANTUM ESPRESSO];
*[https://www.quantum-espresso.org/resources/tutorials Useful Tutorials];
*Reading inputs and outputs (commented files and examples);

===[https://www.lammps.org/ LAMMPS]===
*[https://www.lammps.org/download.html Download LAMMPS];
*[https://docs.lammps.org/Manual.html Manual];
*[https://www.lammps.org/tutorials.html Tutorials];

===[https://www.crystal.unito.it/index.php CRYSTAL]===
* [https://tutorials.crystalsolutions.eu/ CRYSTAL Tutorial Project]
* [https://www.crystal.unito.it/basis-sets.php CRYSTAL basis set database for solid state calculations]
* [http://crysplot.crystalsolutions.eu/ CRYSPLOT: A web-based visualisation tool]
* [https://github.com/crystal-code-tools/crystal_functions crystal_functions: A python-based toolbox]

===[https://www.tcd.ie/Physics/Smeagol/SmeagolAbout.htm Smeagol]===

===others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Molecular visualizers==
*[http://www.ks.uiuc.edu/Research/vmd/ VMD]
*[http://www.xcrysden.org/ Xcrysden]
*[https://jp-minerals.org/vesta/en/ VESTA]

===Others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Useful programming languages and environments==

*[http://www-eio.upc.edu/lceio/manuals/Fortran95-manual.pdf Fortran]
*[https://docs.python.org/3/ Python]
*[https://wiki.fysik.dtu.dk/ase/ ASE]
*[https://pymatgen.org/ Pymatgen]

===others===

</div>

[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page info]

</div>

Nano Electrochemistry Group

2022-12-02T14:06:16Z

Fg1020: /* Building Structure and Surface with Pymatgen */

<div style="padding: 10px; background: #87adde; border: 1px solid #FFAA99; font-family: Trebuchet MS, sans-serif; font-size: 95%;">

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
This page provides a series of tutorials designed to help with the computational modelling of electrochemical system; their aim is to provide general workflows and useful tip to model fundamental components and properties of electrochemical systems. The tutorials have been designed by the researchers of the Computational NanoElectrochemistry Group led by Dr Clotilde Cucinotta [link to group page] and collaborators.
Several simulation packages (CP2K, LAMMPS, QuantumEspresso, etc.), as well as other tools, such as molecular visualisers or programming languages, are described in these tutorials; links to the relevant manuals are provided at the bottom of the page.
Script and programs written by the components of the research group are also described in each tutorial; these tools have been devised to help with running calculations and with data analysis and can be found in the linked GitLub repository [https://gitlab.doc.ic.ac.uk/rgc].

==Running in a Cluster Tutorials==

===[[How to run on ARCHER 2]]===
Written by:[[Contributors#Songyuan| Songyuan]]

===[[Imperial CX1: Instructions and basic concepts of parallel computing|Imperial CX1: Instructions and basic concepts of parallel computing]]===
Written by:[[Contributors| Huanyu]]

A collection of useful resources and brief introductions to the basic concepts of parallel computing for beginners to use the high-performance computing service at Imperial.

==[[Reaction Dynamics]]==
===[[Lammps and plumed|Lammps and plumed]]===
Written by:[[Contributors| Frederik]]

Tutorial on how to use the PLUMED software package to perform biased molecular dynamics simulations in LAMMPS.

===[[Converging magnetic systems in CP2K]]===
Written by:[[Contributors| Chris]]

* Contents:
** MULTIPLICITY keyword to calculate magnetic systems
** &BS section and MAGNETIZATION keyword to improve convergence
* Computational package: CP2K.

===[[Optimization of metallic surfaces parameters|Optimizing parameters for metallic surfaces]]===
Written by:[[Contributors| Margherita]]

* Contents:
** Tutorials on how to define the appropriate set of parameters needed to model a metallic system: Basis set, CUTOFF and '''k'''-points grid;
** Tutorials on how to calculate relevant quantities of metallic surfaces: work function, equilibrium lattice parameter and electronic structure;
* System: metallic surfaces (Platinum slab used as example);
* Computational package: CP2K.

===Surface analysis===
Written by:[[Contributors| Songyuan]]

===[[Dimers in gas phase|Dimers in gas phase]]===
Written by:[[Contributors| Fredrik]]

Tutorial for optimising dimers in the gas phase using gaussian.

===[[Calculation of radial average|Calculation of radial average]]===
Written by:[[Contributors| Kalman]]

Tutorial for calculating the radial average ?.

===[[Adsorption of molecule on surfaces|Adsorption of molecule on surfaces]]===
Written by:[[Contributors| Paolo]]

Tutorial for calculating the adsorption energy of a molecule (or, more in general, any particle) over a specific surface.

===[[Memristors|Simulation of Memristors]]===
Written by:[[Contributors| Felix]]

Tutorial for optimising parameters for memristors using QuantumEspresso.

===[[Hard_carbon|Simulation of Hard Carbons]]===
Written by:[[Contributors| Luke]]

Tutorial for the simulation of hard carbon?

===[[Solving 1D Poisson equation |Solving 1D Poisson equation]]===
Written by:[[Contributors| Remi Khatib ]]

Tutorial for the solution of the 1D Poisson equations given a distribution of point charges

===[[TrendsCatalyticActivity|Trends in catalytic Activity]]===
Tutorial for a computational experiment about trends in catalytic activity for hydrogen evolution. This experiment is part of the third year computational chemistry lab.

===[[Convergence test of critical parameters by CRYSTAL]]===
Written by:[[Contributors| Huanyu ]]

A tutorial for performing convergence tests with LCAO-GTO DFT code, CRYSTAL.
===[[Building Structure and Surface with Pymatgen]]===
Written by:[[Contributors| Fei ]]

Tutorial for obtaining input structure with python.

</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Computational Tools==

===[https://www.cp2k.org/about CP2K]===
*[[CP2K_Tutorial|CP2K TUTORIAL]];
*[https://github.com/cp2k/cp2k/blob/master/INSTALL.md Download and install CP2K ];
*[https://manual.cp2k.org/#gsc.tab=0 Manual];
*[https://www.cp2k.org/howto Useful HOWTOs];
*Reading inputs and outputs (commented files and examples);

===[https://www.quantum-espresso.org/ QUANTUM ESPRESSO]===
*[https://www.quantum-espresso.org/download Download and install QUANTUM ESPRESSO];
*[https://www.quantum-espresso.org/resources/tutorials Useful Tutorials];
*Reading inputs and outputs (commented files and examples);

===[https://www.lammps.org/ LAMMPS]===
*[https://www.lammps.org/download.html Download LAMMPS];
*[https://docs.lammps.org/Manual.html Manual];
*[https://www.lammps.org/tutorials.html Tutorials];

===[https://www.crystal.unito.it/index.php CRYSTAL]===
* [https://tutorials.crystalsolutions.eu/ CRYSTAL Tutorial Project]
* [https://www.crystal.unito.it/basis-sets.php CRYSTAL basis set database for solid state calculations]
* [http://crysplot.crystalsolutions.eu/ CRYSPLOT: A web-based visualisation tool]
* [https://github.com/crystal-code-tools/crystal_functions crystal_functions: A python-based toolbox]

===[https://www.tcd.ie/Physics/Smeagol/SmeagolAbout.htm Smeagol]===

===others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Molecular visualizers==
*[http://www.ks.uiuc.edu/Research/vmd/ VMD]
*[http://www.xcrysden.org/ Xcrysden]
*[https://jp-minerals.org/vesta/en/ VESTA]

===Others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Useful programming languages and environments==

*[http://www-eio.upc.edu/lceio/manuals/Fortran95-manual.pdf Fortran]
*[https://docs.python.org/3/ Python]
*[https://wiki.fysik.dtu.dk/ase/ ASE]
*[https://pymatgen.org/ Pymatgen]

===others===

</div>

[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page info]

</div>

Nano Electrochemistry Group

2022-12-02T11:05:40Z

Fg1020:

<div style="padding: 10px; background: #87adde; border: 1px solid #FFAA99; font-family: Trebuchet MS, sans-serif; font-size: 95%;">

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
This page provides a series of tutorials designed to help with the computational modelling of electrochemical system; their aim is to provide general workflows and useful tip to model fundamental components and properties of electrochemical systems. The tutorials have been designed by the researchers of the Computational NanoElectrochemistry Group led by Dr Clotilde Cucinotta [link to group page] and collaborators.
Several simulation packages (CP2K, LAMMPS, QuantumEspresso, etc.), as well as other tools, such as molecular visualisers or programming languages, are described in these tutorials; links to the relevant manuals are provided at the bottom of the page.
Script and programs written by the components of the research group are also described in each tutorial; these tools have been devised to help with running calculations and with data analysis and can be found in the linked GitLub repository [https://gitlab.doc.ic.ac.uk/rgc].

==Running in a Cluster Tutorials==

===[[How to run on ARCHER 2]]===
Written by:[[Contributors#Songyuan| Songyuan]]

===[[Imperial CX1: Instructions and basic concepts of parallel computing|Imperial CX1: Instructions and basic concepts of parallel computing]]===
Written by:[[Contributors| Huanyu]]

A collection of useful resources and brief introductions to the basic concepts of parallel computing for beginners to use the high-performance computing service at Imperial.

==[[Reaction Dynamics]]==
===[[Lammps and plumed|Lammps and plumed]]===
Written by:[[Contributors| Frederik]]

Tutorial on how to use the PLUMED software package to perform biased molecular dynamics simulations in LAMMPS.

===[[Converging magnetic systems in CP2K]]===
Written by:[[Contributors| Chris]]

* Contents:
** MULTIPLICITY keyword to calculate magnetic systems
** &BS section and MAGNETIZATION keyword to improve convergence
* Computational package: CP2K.

===[[Optimization of metallic surfaces parameters|Optimizing parameters for metallic surfaces]]===
Written by:[[Contributors| Margherita]]

* Contents:
** Tutorials on how to define the appropriate set of parameters needed to model a metallic system: Basis set, CUTOFF and '''k'''-points grid;
** Tutorials on how to calculate relevant quantities of metallic surfaces: work function, equilibrium lattice parameter and electronic structure;
* System: metallic surfaces (Platinum slab used as example);
* Computational package: CP2K.

===Surface analysis===
Written by:[[Contributors| Songyuan]]

===[[Dimers in gas phase|Dimers in gas phase]]===
Written by:[[Contributors| Fredrik]]

Tutorial for optimising dimers in the gas phase using gaussian.

===[[Calculation of radial average|Calculation of radial average]]===
Written by:[[Contributors| Kalman]]

Tutorial for calculating the radial average ?.

===[[Adsorption of molecule on surfaces|Adsorption of molecule on surfaces]]===
Written by:[[Contributors| Paolo]]

Tutorial for calculating the adsorption energy of a molecule (or, more in general, any particle) over a specific surface.

===[[Memristors|Simulation of Memristors]]===
Written by:[[Contributors| Felix]]

Tutorial for optimising parameters for memristors using QuantumEspresso.

===[[Hard_carbon|Simulation of Hard Carbons]]===
Written by:[[Contributors| Luke]]

Tutorial for the simulation of hard carbon?

===[[Solving 1D Poisson equation |Solving 1D Poisson equation]]===
Written by:[[Contributors| Remi Khatib ]]

Tutorial for the solution of the 1D Poisson equations given a distribution of point charges

===[[TrendsCatalyticActivity|Trends in catalytic Activity]]===
Tutorial for a computational experiment about trends in catalytic activity for hydrogen evolution. This experiment is part of the third year computational chemistry lab.

===[[Convergence test of critical parameters by CRYSTAL]]===
Written by:[[Contributors| Huanyu ]]

A tutorial for performing convergence tests with LCAO-GTO DFT code, CRYSTAL.

===[[Building Structure and Surface with Pymatgen]]===
Written by:[[Contributors| Fei ]]

Tutorial for obtaining input structure with python.

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==Computational Tools==

===[https://www.cp2k.org/about CP2K]===
*[[CP2K_Tutorial|CP2K TUTORIAL]];
*[https://github.com/cp2k/cp2k/blob/master/INSTALL.md Download and install CP2K ];
*[https://manual.cp2k.org/#gsc.tab=0 Manual];
*[https://www.cp2k.org/howto Useful HOWTOs];
*Reading inputs and outputs (commented files and examples);

===[https://www.quantum-espresso.org/ QUANTUM ESPRESSO]===
*[https://www.quantum-espresso.org/download Download and install QUANTUM ESPRESSO];
*[https://www.quantum-espresso.org/resources/tutorials Useful Tutorials];
*Reading inputs and outputs (commented files and examples);

===[https://www.lammps.org/ LAMMPS]===
*[https://www.lammps.org/download.html Download LAMMPS];
*[https://docs.lammps.org/Manual.html Manual];
*[https://www.lammps.org/tutorials.html Tutorials];

===[https://www.crystal.unito.it/index.php CRYSTAL]===
* [https://tutorials.crystalsolutions.eu/ CRYSTAL Tutorial Project]
* [https://www.crystal.unito.it/basis-sets.php CRYSTAL basis set database for solid state calculations]
* [http://crysplot.crystalsolutions.eu/ CRYSPLOT: A web-based visualisation tool]
* [https://github.com/crystal-code-tools/crystal_functions crystal_functions: A python-based toolbox]

===[https://www.tcd.ie/Physics/Smeagol/SmeagolAbout.htm Smeagol]===

===others===
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==Molecular visualizers==
*[http://www.ks.uiuc.edu/Research/vmd/ VMD]
*[http://www.xcrysden.org/ Xcrysden]
*[https://jp-minerals.org/vesta/en/ VESTA]

===Others===
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==Useful programming languages and environments==

*[http://www-eio.upc.edu/lceio/manuals/Fortran95-manual.pdf Fortran]
*[https://docs.python.org/3/ Python]
*[https://wiki.fysik.dtu.dk/ase/ ASE]
*[https://pymatgen.org/ Pymatgen]

===others===

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[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page info]

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