You can set the following in your FDF for a single point energy calculation.
MD.TypeofRun CG MD.NumCGsteps 0 Daniel J. Backlund Texas Tech University - Physics [email protected] ________________________________________ From: Jonas Baltrusaitis [[email protected]] Sent: Monday, April 19, 2010 10:48 AM To: [email protected] Subject: RE: [SIESTA-L] dipole moment in symmetric supercell Daniel, I want to calculate a single point energy with PBE functional. Later on I want to do CG optimization. While MD.TypeofRun CG for optimization, how do I get single point energy? No molecular dynamics! This MD prefix just confuses me a lot Jonas --- On Mon, 4/19/10, 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: Monday, April 19, 2010, 6:52 AM > > I am glad that helped. I will let you know that there is a > performance trade-off > when increasing the MeshCutoff. You could perform a series > of calculations with different > MeshCutoff values and find the value that gives you a > "satisfactory" dipole moment. I > would guess 200Ry. should be enough for your system, but I > just don't know for sure. > > As for your MD selection, did you intend to do a conjugate > gradient (CG) calculation? If so, > you could add the following to your FDF file. > > MD.TypeofRun > CG > MD.NumCGsteps 100 > MD.MaxForceTol 0.01 eV/Ang > > Daniel J. Backlund > Texas Tech University - Physics > [email protected] > ________________________________________ > From: Jonas Baltrusaitis [[email protected]] > Sent: Monday, April 19, 2010 8:45 AM > To: [email protected] > Subject: RE: [SIESTA-L] dipole moment in symmetric > supercell > > 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 > > > > > > > > > > > > > > > > > >
