[CPMD-list] Metadynamics
Axel Kohlmeyer
akohlmey at cmm.chem.upenn.edu
Mon Feb 18 02:34:27 CET 2008
On Sun, 17 Feb 2008, Nora Mohamed wrote:
NM> Dr. Kohlmeyer,
nora,
NM> Thank you very much for your very quick and extremely clarifying
NM> response, I did not expect you to reply to my questions that fast. I
well, you basically have the choice between fast or not at all.
NM> managed to get the two books you recommended for me and started
NM> reading the first one besides the one I am already reading
NM> "Essentials of Computational Chemistry". I also noticed that neither
NM> of the books mention metadynamics, is there any textbook you know of
NM> that explains the concept and algorithm of metadynamics, the way the
NM> algorithm of Monte Carlo and MD were explained in the first
NM> textbook?
none that i know of. MD is around for over 40 years, car-parrinello
for over 25 years. i guess it takes a while until method get
transformed into textbooks. for the time beingm, you'll have to live
with the available papers and tutorials.
i won't worry too much, since it takes a while to master
regular cp dynamics well enough.
NM> Also, your answered my second question as follows:
NM>
[...]
NM>
NM> I don't think I understand this part fully. In your tutorial you
NM> wrote an input file to calculate the electronic structure of an
NM> isolated hydrogen molecule and set the symmetry to one. if it is
NM> isolated hydrogen molecule, then what does it mean that we set the
NM> symmetry to simple cubic? also, you said that we do single molecule
NM> calculations if we were interested in gas phase properties. If I am
NM> interested in gas phase properties, shouldn't I set the symmetry to
NM> zero and it would be meaningless to set the symmetry value to any
NM> other value except zero. Am I getting it right?
in CPMD you _never_ do a real isolated system calculation. the
difference between symmetry 0 and symmetry 1 (actually 8 for which
ibrav=1 is a special case) is that with symmetry 0 you run an
additional step to "electrostatically decouple" periodic images
by solving the poisson equation. for a (non-polar) hydrogen molecule
this has essentially no effect other than requiring more memory,
more time and imposing additional constraints on the unit cell size.
for non-polar molecules it is freuqently better to do a periodic
calculation, since the long range interactions are negligible (as
you already have heard, dispersion is very underrepresented in
current DFT implementations.
hope that helps,
axel.
NM>
NM> Thank you very much Dr. Kohlmeyer.
NM> Best Regards,
NM> Nora M. Hassan
NM>
NM>
NM>
NM>
NM>
NM>
NM> Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu> wrote: On Sun, 10 Feb 2008, Nora Mohamed wrote:
NM>
NM> NM> Hi CPMD users.
NM>
NM> hi nora,
NM>
NM> NM> This is my first encounter with molecular dynamics and so I have few
NM> NM> elementary question.
NM>
NM> this is fine, but it would be _much_ easier to answer your
NM> question if you gave us a little bit of information about
NM> what your background is and what you want to do.
NM>
NM> one more thing that is important to note. CPMD stands for
NM> a software package and a method.the CPMD code implements
NM> this CP-MD method, but a lot of other types of calculations
NM> on top of that. the common denominator is that it you do
NM> quantum chemical calculations from first priciples with
NM> density functional theory and use plane waves as basis set
NM> and pseudopotentials.
NM>
NM> since you have elementary questions, i think it is also in
NM> place to recommend a couple of textbooks which should cover
NM> a lot of what you want to know (and then some).
NM>
NM> on molecular dynamics (and monte carlo):
NM> d. frenkel, b. smit, understanding molecular simulation
NM>
NM> on electronic structure:
NM> j. kohanoff, electronic structure calculations for solids and molecules
NM>
NM> NM> 1. I am confused when to do bulk systems simulations and one
NM> NM> molecule simulations. in the tutorials I read, I found examples
NM> NM> that simulate only one water molecule and others that simulate
NM> NM> many water molecules in the simulation cell. when I use either?
NM>
NM> please note, that many examples in the tutorials and on the web are
NM> designed to be fast and simple and help understanding the method, but
NM> do not necessarily show best practices or overly useful applications.
NM> with that in mind, the answer to your question is very simple:
NM> you do single molecule calculations if you are interested in gas
NM> phase properties, you simulate clusters when you want to learn
NM> about clusters and bulks systems if you are interested in the bulk.
NM> each of those systems have their own set of challenges to get them
NM> right and produce meaningful results.
NM>
NM> NM> 2. also, what does it mean when I have only one molecule in the
NM> NM> simulation cell and have the SYMMETRY keyword is set to fcc or
NM> NM> bcc. As I said this is my first encounter with simulation and so
NM> NM> have a difficulty in imagining the supercell that is simulated.
NM>
NM> as far as the CPMD program (or any electronic structure code) is
NM> concerned, there are no molecules. just electrons and the potential
NM> they are in. molecules is something that is defined by analysis
NM> of the result of the electronis structure calculation (or sometimes
NM> common sense). however, if inputs specify fcc or bcc symmetry they
NM> usually are meant for cystals. please check the dimensions of the
NM> unit cell. it could just be that the two atoms in that input define
NM> the crystal structure (cf. diamond, silicon).
NM>
NM> NM> 3. If I wanted to enter the primitive cell vectors instead of the
NM> NM> SYMMETRY keyword, do I still have to enter the atoms coordinates?
NM> NM> wouldn't that be redundant since primitive vectors define the
NM> NM> lattice completely?
NM>
NM> the symmetry keyword only defines the bravais lattice, _not_
NM> the positions of the atoms in the primitive cell. this only
NM> seems redundant, if you have a simple lattice with just one
NM> atom in the primitive cell.
NM>
NM> NM> 4. I want to make sure of an information I read, is it right that in
NM> NM> the &SYSTEM section, I define the symmetry and cell section
NM> NM> according to the conventional cell and in the ATOMS section I put
NM> NM> the atoms coordinates according to the primitive cell?
NM>
NM> yes. there is a simple way to confirm this "experimentally".
NM> do a wavefunction optimization calculation with a small cutoff
NM> and MAXSTEP set to 1 and add the RHOOUT keyword. the resulting
NM> output (DENSITY) has to be converted to a .cube file and can
NM> then be visualized (e.g. VMD, xcrysden) and when looking at
NM> the electron density you'll see the initial guess and how CPMD
NM> understands the cell that you entered.
NM>
NM> NM> 5. in the examples I read, I got confused by the way the atoms
NM> NM> coordinates were defined. in some examples I find negative
NM> NM> numbers like in the example below from Dr. Axel's website and
NM>
NM> CPMD _always_ wraps atom coordinates back into the principal
NM> unit cell for the electronic structure calculation. so if they
NM> are "outside" they are just periodic replica of the corresponding
NM> atom "inside". please check in the MD literature about periodic
NM> boundary conditions.
NM>
NM> NM> from another tutorial I find the coordinates are defined from 0
NM> NM> to 1 or to the value of "scale". Are there any rules to use
NM> NM> either or I have complete freedom in my choice.
NM>
NM> you are free to use whatever you want. output will (almost) always
NM> be in cartesian coordiantes though.
NM>
NM> [...]
NM>
NM> NM> 6. In the example below ( from the Institute of Physical Chemistry
NM> NM> (Group of Prof. Dr. Jürg Hutter), I found the information given
NM> NM> in the SYSTEM section inconsistent with that given in the ATOMS
NM> NM> sections which shows that there must be some information that I
NM> NM> am missing. In the SYSTEM section I have the symmetry set to fcc
NM> NM> and the cell size to 20.53 au and scale to 2 which is consistent
NM> NM> with the information given in kittel (5th edition). according to
NM> NM> Kittel p25 the silicon crystallizes in (diamond structure) an fcc
NM> NM> lattice with two silicon atoms for the basis with conventional
NM> NM> cell lattice constant a= 5.43 A = 10.263102 au half the value
NM> NM> given under the CELL keyword. however, according to kittel p16
NM> NM> and p17 the primitive cell as shown takes up only one fourth of
NM> NM> the volume of the conventional cell, and in the ATOMS section the
NM> NM> primitive cell takes up the whole volume of the conventional
NM> NM> cell. there must be something I am missing but I don't know what
NM> NM> it is. Any help?
NM>
NM> have you considered that the input is representing a supercell
NM> built from 8 primitive cells? this input is the primitive cell
NM> doubled into each direction. there is a good reason to do this:
NM> if you compare the resulting total energy per atom with a
NM> similar calculation that has only the primitive cell and two
NM> atoms and second calculation with a 2x2x2 k-point grid (and
NM> larger k-point grids). you can see that enlarging the cell is
NM> equivalent to using k-points and that doing a gamma point
NM> calculation of the minimal primitive cell is not sufficient.
NM> for more details, please see the kohanoff textbook.
NM>
NM> [...]
NM>
NM> NM> 7. How to choose my pseudopotential? I know I have to test each
NM>
NM> pseudopotentials are a bit of a black art (same as force fields
NM> in classical molecular dynamics). you can trust the person that
NM> provides you with a potential (dangerous), you can check in the
NM> literature for publications that list pseudopotential parameters
NM> (which is rarely done these days), you can run your own tests.
NM>
NM> NM> pseudopotential for each atom in my simulation. for example if I
NM> NM> am simulating ch4, then I have to test the pseudopotential for
NM> NM> hydrogen alone and the pseudopotential for carbon alone. however,
NM>
NM> you can tests against whatever is relevant for your project.
NM> you do not need to test each single pseudopotential seperately,
NM> but this way it is sometimes easier to determine its adequacy.
NM> if a pseudopotential cannot reproduce a lattice constant of the
NM> element (eg. diamond or graphite) in the case of carbon) within
NM> the limits of the functional used, it has to be discarded. but
NM> that does not guarantee transferability, i.e. applicability
NM> where its oxidation state is different. so you'll have to test
NM> that as well. there are some tests, that can also be run on
NM> the pseudopotential directly with an atomic code, e.g. check
NM> the eigenvalue spectrum of the psp against all-electron calculations
NM> for different occupationa and oxidation patterns. finally one
NM> has to check for "ghosts" (i.e. unphysical bound states) and
NM> the required basis set size (= cutoff).
NM>
NM> NM> should I test the pseudopotential with bulk carbon or with one
NM> NM> carbon molecule. I also want to know what the pseudopotential
NM> NM> accuracy depends on. does it depend on my system (i.e my
NM> NM> computer, operating system and the set up in general? I got that
NM> NM> impression since I read everywhere that I must test the
NM> NM> pseudopotential first)
NM>
NM> some of the pseudopotential libraries available come with a list
NM> of references that document the use of those pseudopotentials
NM> (e.g. mauro boero's collection). if you trust (see above) the
NM> publications to be correct and applicable for your purposes,
NM> then you can get away with some minimal testing. please note,
NM> however, that what is adequate accuracy has changed from the
NM> time CPMD was conceived to now. some calculations that were a
NM> big achievment 20 years ago, would now ne considered sloppy.
NM> the advances in high-performance computing have made it
NM> possible that calculations which once took months on
NM> supercomputers now complete in hours on a laptop.
NM>
NM> NM> 8. I got warned that cf4 is a molecular crystal, bonded by Van der
NM> NM> Waals forces between the molecules and so not well given by
NM> NM> present Density Functional Theory calculations.Does this mean
NM> NM> that I can't use cpmd to simulate cf4 or ch4 since my results
NM> NM> would be wrong or inaccurate at best.
NM>
NM> the warnings that plain DFT with current functionals does not
NM> represent vdW interactions well is correct. there are several
NM> ways how people try to cope with this. improving functionals,
NM> using hybrid functionals with hartree-fock exchanged mixed in
NM> (very costly with plane waves), using empirical corrections.
NM> whether CPMD is the right tool for your needs depends a lot
NM> on what you want to do and cannot be answered a priori.
NM>
NM> NM> 9. I also read that when I do calculations under high pressure, I
NM> NM> must also watch that I do not have too much overlap between the
NM> NM> pseudising spheres of neighboring atoms and that 10 percent maybe
NM> NM> OK.Does anybody know how do I know that my pseudising spheres
NM> NM> overlapped or even how to calculate that ten percent? I need more
NM> NM> details on that matter please.
NM>
NM> if you want to do high pressure systems, you will most likely need
NM> custom pseudopotentials with lower pseudization cutoff radii.
NM> so it is probably advisable that you read up on pseudopotential
NM> generation first. the fhi98pp code (see CPMD manual) comes with
NM> a nice tutorial on that, so you can gain practice.
NM> the cutoff radii for many CPMD pseudopotentials are listed
NM> in their respective &INFO section.
NM>
NM> NM> 10. I am really worried about the results I get. I know I have to
NM> NM> optimize my wavefunction at first and then do whatever molecular
NM> NM> dynamics I need. the problem is how to know that my results are
NM> NM> right; I mean is there any convention or procedure I should
NM> NM> follow to make sure that the results I got, either from
NM> NM> wavefunction optimization or molecular dynamics, are accurate?
NM> NM> what values I should keep an eye on to validate my results or
NM> NM> know that there is something wrong?
NM>
NM> before doing CP dynamics, you should practice and understand
NM> classical molecular dynamics. the CP hamiltonian puts an extra
NM> complication on that, namely the fictitious dynamics of the
NM> electronic system. please read through the two textbooks suggested
NM> above and you most of your uncertainties will be gone, after
NM> you had a little practice with actual examples where the results
NM> are known.
NM>
NM> NM> 11. concerning Metadynamics, I don't know how to set the necessary
NM> NM> parameters. Mainly I want to study how a material undergoes
NM> NM> phase change under high pressure, I studied the example about
NM> NM> silicon and read the section about metadynamics in the cpmd
NM> NM> manual, but I think I should read more about this part. does
NM> NM> anybody know any paper or material to read concerning this part
NM> NM> or its theoretical background?
NM>
NM> it is completely pointless to try using metadynamics in CPMD without
NM> being confident in doing regular CPMD calculations. meta-dynamics
NM> is essentially a completely independent technique from CPMD (it
NM> has been implemented into various other codes and used with other
NM> MD methods), and thus there is no need to complicate your life
NM> by looking into this right now. so please ask about this again,
NM> when you have caught up on the previous 10 questions.
NM> this will be a _lot_ of work. CPMD is a very powerful tool, but
NM> that also means that one needs to learn it with care (which you
NM> obvious have, as is evident from your questions) to not shoot
NM> yourself in the foot.
NM>
NM> with best regards,
NM> axel.
NM>
NM>
NM> NM>
NM> NM> Thank you.
NM> NM>
NM> NM> ---------------------------------
NM>
NM>
--
=======================================================================
Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
Center for Molecular Modeling -- University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
=======================================================================
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