Further info: from the pwscf input descriptions:
celldm(i), i=1,6REAL Specify either these OR A,B,C,cosAB,cosBC,cosAC NOT both. Only needed values (depending on "ibrav") must be specified alat = celldm(1) is the lattice parameter "a" (in BOHR) If ibrav=0, only celldm(1) is used if present; cell vectors are read from card CELL_PARAMETERS It also says: 'bohr'/'angstrom': lattice vectors in bohr radii / angstrom. In this case the lattice parameter alat = sqrt(v1*v1). which doesn't make any sense. Ron --- Ronald Cohen Geophysical Laboratory Carnegie Institution 5251 Broad Branch Rd., N.W. Washington, D.C. 20015 rco...@carnegiescience.edu office: 202-478-8937 skype: ronaldcohen https://twitter.com/recohen3 https://www.linkedin.com/profile/view?id=163327727 On Wed, Jul 29, 2015 at 4:50 PM, Cohen, Ronald <rco...@carnegiescience.edu> wrote: > OK, I sorted out what is happening although the symptoms were no not so > obvious! > Pwscf now reduces the cell paremeters and computes a length to multiply them > by, so xtalopt is finding the wrong volume. Thus the result would be out of > range. So for example: > PWSCF output now shows: > > celldm(1)= 3.498840 celldm(2)= 0.000000 celldm(3)= 0.000000 > celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 > > crystal axes: (cart. coord. in units of alat) > a(1) = ( 1.276521 -0.167053 -0.156289 ) > a(2) = ( -0.172203 2.690797 -0.058968 ) > a(3) = ( 0.068258 -0.097907 2.161361 ) > > reciprocal axes: (cart. coord. in units 2 pi/alat) > b(1) = ( 0.787140 0.049879 -0.022599 ) > b(2) = ( 0.050990 0.375237 0.015387 ) > b(3) = ( 0.058310 0.013844 0.461457 ) > > and there is no way now to set celldm(1)=1 like before. Now pwscf crashes > with an error if you try to set celldm=1 as well as 3x3 cell axes. > > so structure.state now shows: > > history\cells\1\00=0.675505553217 > history\cells\1\01=-0.088400605381 > history\cells\1\02=-0.082704544153 > history\cells\1\10=-0.091125866931 > history\cells\1\11=1.423907884069 > history\cells\1\12=-0.031204509336 > history\cells\1\20=0.036120563666 > history\cells\1\21=-0.051810132539 > history\cells\1\22=1.143742529897 > > alat is fixed by pwscf at the beginning of the run: > > lattice parameter (alat) = 3.4988 a.u. > > > I do not know how these relate to the cell parameters shown in xtal.out . > Very messed up! > > Ron > > > > --- > Ronald Cohen > Geophysical Laboratory > Carnegie Institution > 5251 Broad Branch Rd., N.W. > Washington, D.C. 20015 > rco...@carnegiescience.edu > office: 202-478-8937 > skype: ronaldcohen > https://twitter.com/recohen3 > https://www.linkedin.com/profile/view?id=163327727 > > On Tue, Jul 28, 2015 at 8:40 AM, David Lonie <david.lo...@kitware.com> > wrote: >> >> I replied from my other account, but it didn't seem to go to the list? >> Here's my reply for the archives: >> >> On Mon, Jul 27, 2015 at 5:28 PM, Cohen, Ronald >> <rco...@carnegiescience.edu> wrote: >>> >>> Actually, still having problems. The attached example shows what seems to >>> me an OK run, and obabel digests it fine, but for some reason xtalopt >>> doesn't take it and generates a new random structure instead. It doesn't >>> show up as a failure (in fact none of the runs do--even the obvious >>> failures. xtalopt just keeps going generating new structures like the >>> attached snapshot shows. Maybe something is wrong with my build, though >>> everything seemed OK. I am running on a new machine. Thanks for any help! >> >> >> It looks like the parsers should still work for that file (at least for >> the energy terms that XtalOpt needs). >> >> I suspect that the candidate structures are being read in correctly, but >> are then failing some constraint set in XtalOpt (cell length, volume, >> angles, minimum interatomic distance, etc), getting kicked out, and replaced >> with new random structures, as seen in the screenshot. Do these rejected >> structures violate any of the configured cell constraints? >> >> Also, are you running on mac/linux or windows? XtalOpt will print a lot of >> information to stdout about these failed structures. On linux/mac, try >> starting avogadro from a terminal and watch the output for messages about >> rejected structures. On windows, just run avogadro normally, but run >> DebugView[1] at the same time to see the output. This should give a clearer >> idea of why the structures are being replaced. >> >> Hope this helps, >> Dave >> >> [1] https://technet.microsoft.com/en-us/Library/bb896647.aspx >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> Avogadro-Discuss mailing list >> Avogadro-Discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/avogadro-discuss >> > ------------------------------------------------------------------------------ _______________________________________________ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
