Dear Siesta Users, i had try to perform a geometry optimization of some
atoms only, using geometry constrains in Siesta3
I havd try diferent set of parameters to do it, in the GeometryConstraints
section with position -1 to -68 and 1 to 68, but always the geometry
optimization is perform to all the atoms.( The atoms i want to fix are from
1 to 68)
Can anyone help me with this, PLEASE!!!
This is the input file (*.fdf)
Thanks in Advance
Walter
Here is the file:
# General system descriptors
SystemName fosfitos-optgeom-h18-3
SystemLabel fosfitos-optgeom-h18-3
Number_of_species 4
NumberOfAtoms 86
NetCharge +3
%block ChemicalSpeciesLabel
1 26 Fe
2 8 O
3 15 P
4 1 H
%endblock ChemicalSpeciesLabel
# Spin defintion
SpinPolarized T
FixSpin T
TotalSpin 15.0
%block DM.InitSpin
1 +5.0
2 +5.0
3 +5.0
%endblock DM.InitSpin
# Basis definition
PAO.BasisSize DZP
PAO.EnergyShift 50.0 meV
%block PAO.Basis
Fe 5 2.25014
n=3 0 1 E 0.64399 2.65247
3.03150
1.00000
n=4 0 2 E 18.52214 3.13305
4.15184 3.42190
1.00000 1.00000
n=3 1 1 E 8.12894 2.27894
3.02759
1.00000
n=4 1 1 E 16.26911 2.00889
4.26349
1.00000
n=3 2 2 E 14.23042 3.38062
3.78964 2.62819
1.00000 1.00000
%endblock PAO.Basis
# DFT, Grid, SCF
xc.functional GGA
xc.authors PBE
MeshCutoff 200.0 Ry # def 100 Ry
MaxSCFIterations 400
DM.MixingWeight 0.10 # def 0.250
DM.NumberPulay 8 # def 0
DM.Tolerance 0.1E-04 # def 0.1E-4
# Eigenvalue problem
SolutionMethod diagon # diagon or OrderN
ElectronicTemperature 300 K # Def 300 K, 1meV=11.6K
# Molecular dynamics and relaxations
MD.TypeOfRun cg
MD.NumCGsteps 100 # geometry optimization
# Efficiency options
DirectPhi T
SaveMemory T
# Output options
WriteCoorInitial F
WriteMullikenPop 2
WriteCoorXmol T
WriteDenchar F
# options for saving reading
DM.UseSaveDM T # T = restart if DM
# Lattices, coordinates
AtomicCoordinatesFormat
NotScaledCartesianAng
%block AtomicCoordinatesAndAtomicSpecies
0.000300 3.078600 10.498600 1 -2.665700 7.696200 10.498600 1 2.666300
7.696200 10.498600 1 -0.000300 6.156700 7.555200 4 -2.666300 1.539100
7.555200 4 5.331700 6.156700 7.555200 4 0.000000 0.000000 9.860000 4
-5.332300 6.156700 7.555200 4 -2.666000 4.617700 9.860000 4 0.000000
9.235300 9.860000 4 -5.332000 9.235300 9.860000 4 -2.666300 10.774400
7.555200 4 2.666000 4.617700 9.860000 4 5.332000 9.235300 9.860000 4
2.665700 10.774400 7.555200 4 2.665700 1.539100 7.555200 4 -1.407100
3.890800 11.681600 2 0.000000 1.453600 11.681600 2 2.666000 0.064600
9.312800 2 3.943000 2.276500 9.312800 2 1.389000 2.276500 9.312800 2
-1.258900 -0.726800 11.681600 2 1.258900 -0.726800 11.681600 2 -3.924900
3.890800 11.681600 2 -2.666000 6.071300 11.681600 2 3.924900 3.890800
11.681600 2 2.666000 6.071300 11.681600 2 0.000000 4.682300 9.312800 2
-1.389000 2.276500 9.312800 2 1.277000 6.894100 9.312800 2 -1.277000
6.894100 9.312800 2 -2.666000 0.064600 9.312800 2 -3.943000 2.276500
9.312800 2 5.332000 4.682300 9.312800 2 6.609000 6.894100 9.312800 2
4.055000 6.894100 9.312800 2 -5.332000 4.682300 9.312800 2 -4.055000
6.894100 9.312800 2 -6.609000 6.894100 9.312800 2 -1.258900 8.508500
11.681600 2 -4.073100 8.508500 11.681600 2 -2.666000 9.299900 9.312800 2
1.258900 8.508500 11.681600 2 0.000000 10.688900 11.681600 2 -6.590900
8.508500 11.681600 2 -5.332000 10.688900 11.681600 2 -1.389000 11.511800
9.312800 2 -3.943000 11.511800 9.312800 2 4.073100 8.508500 11.681600 2
2.666000 9.299900 9.312800 2 6.590900 8.508500 11.681600 2 5.332000
10.688900 11.681600 2 3.943000 11.511800 9.312800 2 1.389000 11.511800
9.312800 2 1.407100 3.890800 11.681600 2 0.000000 0.000000 11.199700 3
-2.666000 4.617700 11.199700 3 -0.000300 6.156700 8.929500 3 -2.666300
1.539100 8.929500 3 2.666000 4.617700 11.199700 3 5.331700 6.156700
8.929500 3 -5.332300 6.156700 8.929500 3 0.000000 9.235300 11.199700 3
-5.332000 9.235300 11.199700 3 -2.666300 10.774400 8.929500 3 5.332000
9.235300 11.199700 3 2.665700 10.774400 8.929500 3 2.665700 1.539100
8.929500 3 -4.326171 2.184353 10.121928 4 -3.164426 -0.135204 8.590547 4
-1.436524 -0.616472 10.806227 4 1.180805 -0.622751 10.791053 4 2.591226
-0.026408 8.420541 4 4.296581 2.452158 8.504020 4 5.248833 4.347074
8.481712 4 7.452485 7.124382 9.099483 4 6.607276 8.672537 10.796827 4
5.386294 11.121510 10.894262 4 4.280096 11.467893 10.146130 4 1.383872
11.494575 10.212621 4 -1.129565 11.495814 10.174448 4 -5.462202 4.365031
10.144898 4 -6.694968 6.633470 10.169936 4 -7.455458 8.312509 11.526273 4
-5.679234 11.371473 12.154381 4 -3.916203 11.509169 10.212397 4 %endblock
AtomicCoordinatesAndAtomicSpecies
%block GeometryConstraints
position 1 to 68
%endblock GeometryConstraints
--
Walter Alberto Cañón Mancisidor
Químico, Licenciado en Química
Candidato a Doctor en Química
Laboratorio de Magnetismo Molecular
Facultad de Ciencias Químicas y Farmacéutica
Universidad de Chile
Tel: 56 (2) 978-2987
[email protected]
