I have got problem with pseudohydrogen declaration in newest ASE working with siesta.
I declare my h-075 as H_075.GGA in pseudopotentials and everywhere, but when I want to turn NEB calculation, .fdf siesta file prepared by ASE is wrong.
here are my include options
NumberOfSpecies 5
%block ChemicalSpecieslabel
1 201 H_075.GGA.1
2 7 N.GGA.2
3 31 Ga.GGA.3
4 49 In.GGA.4
5 14 Si.GGA.5
%endblock ChemicalSpecieslabel
below is my declaration
from ase import Atom
from ase.data import *
atomic_numbers[‘H_075’] = 201
atomic_numbers[‘H_125’] = 301
import array
tmp1 =
#atomic masses
for i in range(len(atomic_masses)):
tmp1.append(atomic_masses[i])
start = len(atomic_masses)
for i in range(start, 302):
tmp1.append(0.)
tmp1[201] = tmp1[1]
tmp1[301] = tmp1[1]
import numpy as np
atomic_masses = np.array(tmp1)
#atomic names
start = len(atomic_names)
for i in range(start, 302):
atomic_names.append(‘’)
atomic_names[201] = ‘H_075’
atomic_names[301] = ‘H_125’
#chemical_symbols
start = len(chemical_symbols)
for i in range(start, 302):
chemical_symbols.append(‘’)
chemical_symbols[201] = ‘H_075’
chemical_symbols[301] = ‘H_125’
here are coordinates by siesta
%block AtomicCoordinatesAndAtomicSpecies
6.49399856 -4.8210435 16.59533805 0 <-there should be 1 instead 0
3.71030311 0.0004507 16.59531386 0
9.27769872 0.00046536 16.59532909 0
6.49399672 4.82214203 16.5952319 0
3.71025772 -6.42831439 16.59529544 0
0.92636869 -1.60670723 16.5953032 0
6.49399327 -1.60670071 16.59542365 0
3.71025283 3.21489119 16.59529283 0
6.49399433 -8.0355778 16.59523524 0
3.71029553 -3.21387894 16.59533201 0
9.27769047 -3.21386892 16.59534081 0
6.4940194 1.60762509 16.5953037 0
6.49405438 -4.821136 17.64580428 2
3.71029472 0.00046134 17.64579074 2
9.27780528 0.00046754 17.64580275 2
6.49405106 4.82212127 17.64569947 2
3.71028597 -6.42836899 17.64576852 2
(…)
and here is error
rcut: Wrong species 0. Have 5
Stopping Program from Node: 3
rcut: Wrong species 0. Have 5
Stopping Program from Node: 2
rcut: Wrong species 0. Have 5
Stopping Program from Node: 1
rcut: Wrong species 0. Have 5
Stopping Program from Node: 0
if i change to normal hydrogen it works.
it works in previous verion of ASE
so - to conclude - how can I change that importing pseudohydrogen in ASE for 1 instead 0? In (xsf) file I declare pseudohydrogen as 201.