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License: MIT License
AiiDA plugin for PorousMaterials package
License: MIT License
The aim is writing a calculation plugin which can create the PorousMaterials template which I was using for Voronoi Energy calculations outside the AiiDA.
The input file for Julia
calculation should like:
#Loading necessary modules
using PorousMaterials
PorousMaterials.set_path_to_data("/storage/brno9-ceitec/home/pezhman/projects/noble_gas_epfl/xe_kr/data")
path = PorousMaterials.PATH_TO_DATA
# Loading General Setting like LJForceField, Framework, and replication
ljff = LJForceField("UFF.csv", cutoffradius=12.5, mixing_rules="Lorentz-Berthelot")
framework = Framework("AMIMEP_clean.cssr")
rep_factor = replication_factors(framework.box, ljff)
framework = replicate(framework, rep_factor)
# Generating associated result file
result = open("Ev_AMIMEP_clean.csv","w")
write(result, "Ev(kJ/mol),Rv(A),x,y,z,Framework,Adsorbate,Accuracy\n")
# Iterating over Adsorbates
for i in ["Xe","Kr"]
for j in ["S50"]
posfile = open(path*"/zeopp/Voronoi/AMIMEP_clean_voro_"*i*"_acc_"*j*".xyz")
lines = readlines(posfile)
n_nodes = parse(Int, lines[1])
# Iterating over nodes, calculating the Voronoi energy, and saving results.
for k = 1:n_nodes
xyz = split(lines[2+k])[2:4]
r = split(lines[2+k])[5]
x = parse.(Float64, xyz)
molecule = Molecule(i)
set_fractional_coords!(molecule, framework.box)
translate_to!(molecule,framework.box.c_to_f * x)
energy = (vdw_energy(framework, molecule, ljff)) * 0.00831441001625545
saveresults = energy, r, x[1], x[2], x[3], "AMIMEP_clean", i, j
write(result, join(saveresults,","), "\n")
end
close(posfile)
end
end
close(result)
Therefore, the current inputs should be provided to each calculation:
Forcefield: It is provided as a
csvfile and therefore needs a
SinglefileData` object.Structure
: SinglefileData
in the format of cif
or cssr
Parameters
: The can contain cutoff
, mixing rules
, adsorbate name/symbol
, zeo++ accuracy level
Output
: The output is being written in csv
file and therefore, a SinglefileData
object should be defined for it.The output of calculation is a csv
file with the following header:
Ev(kJ/mol),Rv(A),x,y,z,Framework,Adsorbate,Accuracy
-20.922297115210764,2.310,2.04,8.432,17.478,AMIMEP_clean,Xe,S50
-13.294986262533834,3.039,1.829,8.651,16.396,AMIMEP_clean,Xe,S50
-20.795105692170782,2.333,2.037,8.441,17.444,AMIMEP_clean,Xe,S50
-18.52121794539584,2.205,1.663,7.812,16.878,AMIMEP_clean,Xe,S50
.
.
.
-22.245109724646177,1.913,2.048,2.809,2.002,AMIMEP_clean,Kr,S50
-21.513764289691064,1.867,2.116,2.813,1.929,AMIMEP_clean,Kr,S50
-21.89122001822926,1.914,3.259,1.931,3.089,AMIMEP_clean,Kr,S50
-21.281570222909348,1.877,2.818,1.73,3.231,AMIMEP_clean,Kr,S50
-22.721536697668167,1.934,2.519,2.819,2.213,AMIMEP_clean,Kr,S50
Each file contains information for a framework and at a certain zeo++ accuracy level for different adsorbates.
The parsing should be simple while it is informative by doing the following tasks:
input
like [5,10,50]
and calculates the average Voronoi energy for nodes that their Voronoi energy falls into to the required percentile.A declarative, efficient, and flexible JavaScript library for building user interfaces.
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