Re: [Wien] constrain some atoms to minimize the forces
Dear Stefan, Resending with a couple of typos corrected: You will in fact gain very little by artificially constraining the center. Let me expand upon my first response, with a simplified "toy-model" explanation. Suppose we transform the complex Pt (111) problem "somehow" to a simpler one by a transformation of the positions such that the energy is now a simple quadratic E= E_0 + a*p + b*p*p along some direction p which is a combination of movements of all the atoms. In such a case it would take at most two optimization cycles to move to the minimum. The transformation has reduced the problem to having only one eigenvalue. Now suppose that instead of one p, there were two eigenvectors -- it would take twice as long if their eigenvalues were very different, but about the same time if they were similar. Extending this to the general case gives the result I mentioned. Furthermore if you apply the same thinking to the electronic problem you will see that the number of iterations to convergence of the SCF iterations (with fixed atoms) does not scale as the number of density variables. If it did DFT would be useless! In most cases there are only a smaller number of eigenvectors of the electronic problem, much less than the number of density variables, often only 10-30. Some cases such a systems with d or f electrons have more eigenvectors so are harder to converge, and they may also have soft modes. The same thinking explains why MSR1a is often faster. Does fixing the center of a slab reduce the number of eigenvectors? It is not obvious to me that it does. I would prefer to not fix the center. If the atoms move far from flat that will tell me that the slab is too thin. Fixing the center does not make the slab thicker. On Thu, Jul 14, 2016 at 7:51 AM, Stefaan Cottenier wrote: >> Your question is based upon a common misunderstanding of minimizing >> forces. You are thinking that the time to optimize depends upon the >> number of positions (3*Number of Pt atoms that move) which is wrong. >> With PORT it scales as the number of clusters of phonon frequencies and >> weakly with the width of the clusters; with MSR1a it scales as the >> number of clusters of eigenvalues of the joint electron-phonon problem >> and their width. >> >> You will gain far more by generating a proper symmetric model with P-3m1 >> (maybe P-31m) symmetry rather than what you appear to have, a P1 >> structure. This will reduce the number of uniques phonon etc modes by >> something like 6-12, and will be much faster and converge better. > > Dear Laurence Marks, > > When having created the most symmetric slab model that is relevant for > the case at hand, wouldn't you agree that it still makes sense to fix > the positions of the middle few layers to their bulk positions? One > cannot make slabs as thick as to find spontaneously bulk behaviour in > the center, and therefore imposing the bulk geometry in the slab center > could be preferred over getting unphysical lattice spacings. Can you > comment? > > Thanks, > Stefaan > > > -- > Stefaan Cottenier > Center for Molecular Modeling (CMM) & > Department of Materials Science and Engineering (DMSE) > Ghent University > Tech Lane Ghent Science Park – Campus A > building 903 > BE-9052 Zwijnaarde > Belgium > -- Professor Laurence Marks "Research is to see what everybody else has seen, and to think what nobody else has thought", Albert Szent-Gyorgi www.numis.northwestern.edu ; Corrosion in 4D: MURI4D.numis.northwestern.edu Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent Co-Editor, Acta Cryst A ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] constrain some atoms to minimize the forces
Dear Stefan, You will in fact gain very little by artificially constraining the center. Let me expand upon my first response, with a simplified "toy-model" explanation. Suppose we transform the complex Pt (111) problem "somehow" to a simpler one by a transformation of the positions such that the energy is now a simple quadratic E= E_0 + a*p + b*p*p along some direction p which is a combination of movements of all the atoms. In such a case it would take at most to optimization cycles to move to the minimum. The transformation has reduced the problem to having only one eigenvalue. Now suppose that instead of one p, there were two eigenvectors -- it would take twice as long if their eigenvalues were very different, but about the same time if they were similar. Extending this to the general case gives the result I mentioned. Furthermore if you apply the same thinking to the electronic problem you will see that convergence of the SCF iterations (with fixed atoms) does not scale as the number of density variables. If it did DFT would be useless! In most cases there are only a smaller number of eigenvectors of the electronic problem tmuch less than the number of density variables, often only 10-30. Some cases such a systems with d or f electrons have more eigenvectors so are harder to converge, and they may also have soft modes. Does fixing the center of a slab reduce the number of eigenvectors? It is not obvious to me that it does. I would prefer to not fix the center. If the atoms move far from flat that will tell me that the slab is too thin. Fixing the center does not make the slab thicker. On Thu, Jul 14, 2016 at 7:51 AM, Stefaan Cottenier wrote: >> Your question is based upon a common misunderstanding of minimizing >> forces. You are thinking that the time to optimize depends upon the >> number of positions (3*Number of Pt atoms that move) which is wrong. >> With PORT it scales as the number of clusters of phonon frequencies and >> weakly with the width of the clusters; with MSR1a it scales as the >> number of clusters of eigenvalues of the joint electron-phonon problem >> and their width. >> >> You will gain far more by generating a proper symmetric model with P-3m1 >> (maybe P-31m) symmetry rather than what you appear to have, a P1 >> structure. This will reduce the number of uniques phonon etc modes by >> something like 6-12, and will be much faster and converge better. > > Dear Laurence Marks, > > When having created the most symmetric slab model that is relevant for > the case at hand, wouldn't you agree that it still makes sense to fix > the positions of the middle few layers to their bulk positions? One > cannot make slabs as thick as to find spontaneously bulk behaviour in > the center, and therefore imposing the bulk geometry in the slab center > could be preferred over getting unphysical lattice spacings. Can you > comment? > > Thanks, > Stefaan > > > -- > Stefaan Cottenier > Center for Molecular Modeling (CMM) & > Department of Materials Science and Engineering (DMSE) > Ghent University > Tech Lane Ghent Science Park – Campus A > building 903 > BE-9052 Zwijnaarde > Belgium > -- Professor Laurence Marks "Research is to see what everybody else has seen, and to think what nobody else has thought", Albert Szent-Gyorgi www.numis.northwestern.edu ; Corrosion in 4D: MURI4D.numis.northwestern.edu Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent Co-Editor, Acta Cryst A ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] constrain some atoms to minimize the forces
Your question is based upon a common misunderstanding of minimizing forces. You are thinking that the time to optimize depends upon the number of positions (3*Number of Pt atoms that move) which is wrong. With PORT it scales as the number of clusters of phonon frequencies and weakly with the width of the clusters; with MSR1a it scales as the number of clusters of eigenvalues of the joint electron-phonon problem and their width. You will gain far more by generating a proper symmetric model with P-3m1 (maybe P-31m) symmetry rather than what you appear to have, a P1 structure. This will reduce the number of uniques phonon etc modes by something like 6-12, and will be much faster and converge better. Dear Laurence Marks, When having created the most symmetric slab model that is relevant for the case at hand, wouldn't you agree that it still makes sense to fix the positions of the middle few layers to their bulk positions? One cannot make slabs as thick as to find spontaneously bulk behaviour in the center, and therefore imposing the bulk geometry in the slab center could be preferred over getting unphysical lattice spacings. Can you comment? Thanks, Stefaan -- Stefaan Cottenier Center for Molecular Modeling (CMM) & Department of Materials Science and Engineering (DMSE) Ghent University Tech Lane Ghent Science Park – Campus A building 903 BE-9052 Zwijnaarde Belgium http://molmod.ugent.be http://www.ugent.be/ea/dmse/en email: stefaan.cotten...@ugent.be my conference talks on Youtube: http://goo.gl/P2b1Hs for China: http://i.youku.com/cottenierlectures ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] constrain some atoms to minimize the forces
Your question is based upon a common misunderstanding of minimizing forces. You are thinking that the time to optimize depends upon the number of positions (3*Number of Pt atoms that move) which is wrong. With PORT it scales as the number of clusters of phonon frequencies and weakly with the width of the clusters; with MSR1a it scales as the number of clusters of eigenvalues of the joint electron-phonon problem and their width. You will gain far more by generating a proper symmetric model with P-3m1 (maybe P-31m) symmetry rather than what you appear to have, a P1 structure. This will reduce the number of uniques phonon etc modes by something like 6-12, and will be much faster and converge better. --- Professor Laurence Marks "Research is to see what everybody else has seen, and to think what nobody else has thought", Albert Szent-Gyorgi http://www.numis.northwestern.edu Corrosion in 4D http://MURI4D.numis.northwestern.edu Partner of the CFW 100% gender equity project, www.cfw.org/100-percent Co-Editor, Acta Cryst A On Jul 14, 2016 06:25, "Saleem Ayaz" wrote: Dear users I want to minimize the forces for Pt111 surface. I want to restrict the structure by minimizing the forces for first two layers and keeping the other layers bulk-like. Please some one can help me how to change case.inM file. Should I make some numbers equal to zero? Looking forward regards Saleem PORT 2.00 0.35 # PORT/NEWT; tolf, Initial Trust Radius 1.0 1.0 1.0 1.0 #Atom1 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom2 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom3 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom4 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom5 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom6 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom7 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom8 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom9 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 10 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 11 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 12 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 13 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 14 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 15 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 16 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 17 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 18 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 19 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 20 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 21 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 22 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 23 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 24 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 25 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 26 Generated by pairhess 1.0 1.0 1.0 1.0 #Atom 27 Generated by pairhess ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
