Re: [Avogadro-Discuss] xtalopt not digesting pwscf (quantum espresso) output
On Thu, Jul 30, 2015 at 8:46 AM, Ronald Cohen rco...@carnegiescience.edu wrote: I can try to fix myself. Will let you know. Thanks! Ron That's be awesome! I'm away from my main development computer at the moment, so you can probably get to it faster than me :) The parsing code is in the OpenBabel project, at src/formats/pwscfformat.cpp, if I remember correctly. Thanks, Dave -- ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
Re: [Avogadro-Discuss] xtalopt not digesting pwscf (quantum espresso) output
Yes, thank you. There is no problem coding--maybe I have already done it But nevertheless I am very confused. in xtal.out it says CELL_PARAMETERS (bohr) 4.466341244 -0.584492262 -0.546831634 -0.602509427 9.414669354 -0.206320172 0.238825493 -0.342559833 7.562254654 Yet structure state is picking up crystal axes: (cart. coord. in units of alat) a(1) = ( 0.733079 0.047228 -0.003184 ) a(2) = ( 0.368736 1.155686 0.136997 ) a(3) = ( 0.341320 0.680731 1.6875 ) even though it seems that the PWscfFormat should be looking for CELL_PARAMETERS. I need to look closer but hard to on my macair. Will have to check later, unless you understand what is happening. 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 Thu, Jul 30, 2015 at 9:55 AM, David Lonie david.lo...@kitware.com wrote: On Thu, Jul 30, 2015 at 8:46 AM, Ronald Cohen rco...@carnegiescience.edu wrote: I can try to fix myself. Will let you know. Thanks! Ron That's be awesome! I'm away from my main development computer at the moment, so you can probably get to it faster than me :) The parsing code is in the OpenBabel project, at src/formats/pwscfformat.cpp, if I remember correctly. Thanks, Dave -- ___ 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
Re: [Avogadro-Discuss] xtalopt not digesting pwscf (quantum espresso) output
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)= 0.00 celldm(3)= 0.00 celldm(4)= 0.00 celldm(5)= 0.00 celldm(6)= 0.00 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
Re: [Avogadro-Discuss] xtalopt not digesting pwscf (quantum espresso) output
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)= 0.00 celldm(3)= 0.00 celldm(4)= 0.00 celldm(5)= 0.00 celldm(6)= 0.00 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
