Wow, that has helped considerably. Now I am getting a very small dipole moment. I will increase cutoff even more and see what happens
Electric dipole (a.u.) = 0.000000 0.000000 0.002556 The other very stupid question I have: why do I feel like I am running molecular dynamics instead of quantum at GGA? In my output I am getting things like: Begin MD step and Dynamics option = Verlet MD run I tried finding an answer in the manual but failed. Could anybody elaborate? Jonas --- On Sun, 4/18/10, Backlund, Daniel <[email protected]> wrote: > From: Backlund, Daniel <[email protected]> > Subject: RE: [SIESTA-L] dipole moment in symmetric supercell > To: "[email protected]" <[email protected]> > Date: Sunday, April 18, 2010, 7:59 PM > First thing to try is increasing your > MeshCutoff, 10 Ry. is quite small. Try increasing to > at least 150 Ry. or even 200 Ry. > > Daniel J. Backlund > Texas Tech University - Physics > [email protected] > ________________________________________ > From: Jonas Baltrusaitis [[email protected]] > Sent: Sunday, April 18, 2010 9:54 PM > To: [email protected] > Subject: [SIESTA-L] dipole moment in symmetric supercell > > Hi all, > > I am trying to calculate change in dipole moment with > organic molecule adsorption. To begin I construct a neutral > hydroxylated slab of SiO2 (100) trying to maintain z axis > symmetry, e.g. so I do not introduce any dipole moment in z > direction on my initial surface. However, there is a > sizeable dipole moment (for the reason I can't quite > understand). Is it related with the supercell itself, atom > configuration or there is always going to be some initial > dipole moment no matter what? > > Below is the input, I would appreciate suggestions > > Jonas > > # SiO2(100)-2x2 supercell 7 Si layers (OH-saturated) > > ##### GENERAL SYSTEM DESCRIPTORS > ############################################### > > SystemName > SiO2(100)-2x2 supercell 7 Si layers (OH-saturated) > > SystemLabel > si001_7Si_layers > > NumberOfAtoms > 108 > > NumberOfSpecies 3 > > %block ChemicalSpeciesLabel > 1 > 1 H.pbe > 2 > 8 O.pbe > 3 14 Si.pbe > %endblock ChemicalSpeciesLabel > > ##### BASIS DEFINITION > ######################################################### > > > PAO.BasisSize > SZ > > > ##### LATTICE, COORDINATES, k-SAMPLING > ######################################### > > LatticeConstant 1 Ang > > %block LatticeParameters > 9.825999999999999 > 10.810400000000000 43.018784438344653 > 90. 90. 90. > %endblock LatticeParameters > > > AtomicCoordinatesFormat Fractional > > %block AtomicCoordinatesAndAtomicSpecies > > 0.1324750000000002 0.1666666666666667 > -0.0000000000000000 1 > > 0.3824750000000002 0.0000000000000000 0.0059145328090448 > 1 > > 0.1324749999999999 0.0000000000000000 0.3026302255704930 > 1 > > 0.3824750000000000 0.1666666666666667 0.2967156927614482 > 1 > > 0.6324750000000003 0.1666666666666667 > -0.0000000000000000 1 > > 0.8824750000000003 0.0000000000000000 0.0059145328090448 > 1 > > 0.6324750000000000 0.0000000000000000 0.3026302255704930 > 1 > > 0.8824750000000001 0.1666666666666667 0.2967156927614482 > 1 > > 0.1324750000000002 0.6666666666666667 > -0.0000000000000000 1 > > 0.3824750000000002 0.5000000000000000 0.0059145328090448 > 1 > > 0.1324749999999999 0.5000000000000000 0.3026302255704930 > 1 > > 0.3824750000000000 0.6666666666666667 0.2967156927614482 > 1 > > 0.6324750000000003 0.6666666666666667 > -0.0000000000000000 1 > > 0.8824750000000003 0.5000000000000000 0.0059145328090448 > 1 > > 0.6324750000000000 0.5000000000000000 0.3026302255704930 > 1 > > 0.8824750000000001 0.6666666666666667 0.2967156927614482 > 1 > > 0.0304000000000001 0.1070500000000000 0.0933170853734754 > 2 > > 0.2804000000000000 0.1070500000000000 0.1922223162939582 > 2 > > 0.1399000000000004 0.2737166666666666 0.0259428420704426 > 2 > > 0.3899000000000003 0.2737166666666666 0.1248480729909253 > 2 > > 0.1399000000000002 0.2737166666666666 0.2237533039114080 > 2 > > 0.3297000000000001 0.4403833333333332 0.0379697181503732 > 2 > > 0.0797000000000001 0.4403833333333332 0.1368749490708560 > 2 > > 0.3296999999999999 0.4403833333333332 0.2357801799913387 > 2 > > 0.1399000000000003 0.3929499999999999 0.0788769216590850 > 2 > > 0.3899000000000003 0.3929499999999999 0.1777821525795676 > 2 > > 0.1399000000000001 0.3929499999999999 0.2766873835000504 > 2 > > 0.3297000000000001 0.2262833333333333 0.0668500455791542 > 2 > > 0.0797000000000000 0.2262833333333333 0.1657552764996370 > 2 > > 0.3296999999999999 0.2262833333333333 0.2646605074201197 > 2 > > 0.2804000000000003 0.0596166666666666 0.1104079092765348 > 2 > > 0.0304000000000000 0.0596166666666666 0.2093131401970175 > 2 > > 0.5304000000000002 0.1070500000000000 0.0933170853734754 > 2 > > 0.7804000000000001 0.1070500000000000 0.1922223162939582 > 2 > > 0.6399000000000004 0.2737166666666666 0.0259428420704426 > 2 > > 0.8899000000000004 0.2737166666666666 0.1248480729909253 > 2 > > 0.6399000000000004 0.2737166666666666 0.2237533039114080 > 2 > > 0.8297000000000002 0.4403833333333332 0.0379697181503732 > 2 > > 0.5797000000000002 0.4403833333333332 0.1368749490708560 > 2 > > 0.8297000000000000 0.4403833333333332 0.2357801799913387 > 2 > > 0.6399000000000004 0.3929499999999999 0.0788769216590850 > 2 > > 0.8899000000000004 0.3929499999999999 0.1777821525795676 > 2 > > 0.6399000000000003 0.3929499999999999 0.2766873835000504 > 2 > > 0.8297000000000002 0.2262833333333333 0.0668500455791542 > 2 > > 0.5797000000000001 0.2262833333333333 0.1657552764996370 > 2 > > 0.8297000000000000 0.2262833333333333 0.2646605074201197 > 2 > > 0.7804000000000003 0.0596166666666666 0.1104079092765348 > 2 > > 0.5303999999999999 0.0596166666666666 0.2093131401970175 > 2 > > 0.0304000000000001 0.6070500000000001 0.0933170853734754 > 2 > > 0.2804000000000000 0.6070500000000001 0.1922223162939582 > 2 > > 0.1399000000000004 0.7737166666666666 0.0259428420704426 > 2 > > 0.3899000000000003 0.7737166666666666 0.1248480729909253 > 2 > > 0.1399000000000002 0.7737166666666666 0.2237533039114080 > 2 > > 0.3297000000000001 0.9403833333333332 0.0379697181503732 > 2 > > 0.0797000000000001 0.9403833333333332 0.1368749490708560 > 2 > > 0.3296999999999999 0.9403833333333332 0.2357801799913387 > 2 > > 0.1399000000000003 0.8929499999999999 0.0788769216590850 > 2 > > 0.3899000000000003 0.8929499999999999 0.1777821525795676 > 2 > > 0.1399000000000001 0.8929499999999999 0.2766873835000504 > 2 > > 0.3297000000000001 0.7262833333333333 0.0668500455791542 > 2 > > 0.0797000000000000 0.7262833333333333 0.1657552764996370 > 2 > > 0.3296999999999999 0.7262833333333333 0.2646605074201197 > 2 > > 0.2804000000000003 0.5596166666666667 0.1104079092765348 > 2 > > 0.0304000000000000 0.5596166666666667 0.2093131401970175 > 2 > > 0.5304000000000002 0.6070500000000001 0.0933170853734754 > 2 > > 0.7804000000000001 0.6070500000000001 0.1922223162939582 > 2 > > 0.6399000000000004 0.7737166666666666 0.0259428420704426 > 2 > > 0.8899000000000004 0.7737166666666666 0.1248480729909253 > 2 > > 0.6399000000000004 0.7737166666666666 0.2237533039114080 > 2 > > 0.8297000000000002 0.9403833333333332 0.0379697181503732 > 2 > > 0.5797000000000002 0.9403833333333332 0.1368749490708560 > 2 > > 0.8297000000000000 0.9403833333333332 0.2357801799913387 > 2 > > 0.6399000000000004 0.8929499999999999 0.0788769216590850 > 2 > > 0.8899000000000004 0.8929499999999999 0.1777821525795676 > 2 > > 0.6399000000000003 0.8929499999999999 0.2766873835000504 > 2 > > 0.8297000000000002 0.7262833333333333 0.0668500455791542 > 2 > > 0.5797000000000001 0.7262833333333333 0.1657552764996370 > 2 > > 0.8297000000000000 0.7262833333333333 0.2646605074201197 > 2 > > 0.7804000000000003 0.5596166666666667 0.1104079092765348 > 2 > > 0.5303999999999999 0.5596166666666667 0.2093131401970175 > 2 > > 0.3824750000000002 0.1666666666666667 0.0989052309204827 > 3 > > 0.1324750000000000 0.1666666666666667 0.1978104618409654 > 3 > > 0.2350500000000003 0.3333333333333333 0.0524098818647638 > 3 > > 0.4850500000000003 0.3333333333333333 0.1513151127852465 > 3 > > 0.2350500000000002 0.3333333333333333 0.2502203437057292 > 3 > 0.1324750000000002 > -0.0000000000000000 0.1048197637295275 3 > 0.3824750000000000 > -0.0000000000000000 0.2037249946500103 3 > > 0.8824750000000003 0.1666666666666667 0.0989052309204827 > 3 > > 0.6324750000000001 0.1666666666666667 0.1978104618409654 > 3 > > 0.7350500000000003 0.3333333333333333 0.0524098818647638 > 3 > > 0.9850500000000004 0.3333333333333333 0.1513151127852465 > 3 > > 0.7350500000000003 0.3333333333333333 0.2502203437057292 > 3 > 0.6324750000000003 > -0.0000000000000000 0.1048197637295275 3 > 0.8824750000000001 > -0.0000000000000000 0.2037249946500103 3 > > 0.3824750000000002 0.6666666666666667 0.0989052309204827 > 3 > > 0.1324750000000000 0.6666666666666667 0.1978104618409654 > 3 > > 0.2350500000000003 0.8333333333333334 0.0524098818647638 > 3 > > 0.4850500000000003 0.8333333333333334 0.1513151127852465 > 3 > > 0.2350500000000002 0.8333333333333334 0.2502203437057292 > 3 > > 0.1324750000000002 0.5000000000000000 0.1048197637295275 > 3 > > 0.3824750000000000 0.5000000000000000 0.2037249946500103 > 3 > > 0.8824750000000003 0.6666666666666667 0.0989052309204827 > 3 > > 0.6324750000000001 0.6666666666666667 0.1978104618409654 > 3 > > 0.7350500000000003 0.8333333333333334 0.0524098818647638 > 3 > > 0.9850500000000004 0.8333333333333334 0.1513151127852465 > 3 > > 0.7350500000000003 0.8333333333333334 0.2502203437057292 > 3 > > 0.6324750000000003 0.5000000000000000 0.1048197637295275 > 3 > > 0.8824750000000001 0.5000000000000000 0.2037249946500103 > 3 > %endblock AtomicCoordinatesAndAtomicSpecies > > kgrid_cutoff 5.0 > Ang > > %block kgrid_Monkhorst_Pack > 2 0 0 0.5 > 0 2 0 0.5 > 0 0 1 0.5 > %endblock Kgrid_Monkhorst_Pack > > > ##### DFT, GRID, SCF > ########################################################### > > SolutionMethod = diagon > XC.functional > GGA > XC.authors > PBE > MeshCutoff > 10. Ry > MaxSCFIterations 200 > DM.MixingWeight 0.1 > DM.NumberPulay 3 > > #MD.TypeOfRun CG > #MD.Num-CG-steps > 100 > > > > > > >
