[Pw_forum] possible bug in scatter_forw.f90
Dear Alexander,
Thank you very much for your answer. I have one more question, it seems
my list of questions is never gonna end :(
this is about init_gper.f90 subroutine. where you calculate
|G+k|^2 Dear Manoj
>
> On Thursday 16 October 2008 23:15, Manoj Srivastava wrote:
> > Dear Alexandar,
> > Thank you very much. Your answers make sense and now i have better
> > understanding of the subroutine scatter_forw.f90. I have one question
> > about poten.f90 subroutine, where you calculate the V(p,gper) in each
> > slices of the slab(equation 15). I have a question about Gz, which is
> > 2*pi*q/L, with [-N/2]+1<=q>=[N/2]. Now in the code at the line at the line
> > 60, you have Gz multiplied with bg(3,3). I kind of understand this is
> > because 3rd direction is perpendicular to xy plane,
> Exactly. As it is implemented now pwcond deals with systems
> having monoclinic unit cell, i.e. such that a3 is perpendicular to both a1
> and
> a2 (a1 and a2 are not necessary orthogonal one to another) and the direction
> of transport is a3. This seems to us the most general setup for transport and
> I do not think we should consider at the moment the situation where the a3 is
> not perpendicular to the xy plane.
>
> Best regards,
> Alexander
>
> > but not totally clear
> > about it. Would you mind explaining? my other question is when reciprocal
> > space vectors b1, b2 and b3 are not orhogonal to each other, which is
> > more general case, then should not we take bg(1,3) and bg(2,3) in there
> > too?
> > Thank you once again for listening to my questions and i hope i am
> > not bothering you too much.
> >
> > Regards,
> > Manoj Srivastava
> > Physics Graduate Student
> > Department of Physics
> > Gainesville, FL, USA.
> >
> > have On Wed, 15 Oct 2008, Alexander wrote:
> > > Dear Manoj
> > >
> > > On Tuesday 14 October 2008 17:49, Manoj Srivastava wrote:
> > > > Dear Alexader,
> > > >
> > > > Thank you very much for your reply. I was out of town and could not
> > > > see the message till yesterday. I have some questions on it, it would
> > > > be great if you could answer them.
> > > >
> > > > On Fri, 10 Oct 2008, Alexander wrote:
> > > > > Dear Manoj
> > > > >
> > > > > On Friday 10 October 2008 05:20, Manoj Srivastava wrote:
> > > > > > Any follow ups on the message below? Alexander?
> > > > > >
> > > > > > Regards,
> > > > > > Manoj
> > > > > >
> > > > > > On Wed, 8 Oct 2008, Manoj Srivastava wrote:
> > > > > > > Dear All,
> > > > > > > Is any body familiar with the scatter_forw.f90 subroutine of
> > > > > > > PWCOND? I think there is a bug in this subroutine at the place
> > > > > > > where you calculate intw2, which is z integration of nonlocal
> > > > > > > wavefunction with beta function. I have looked up the necessary
> > > > > > > formulae in the Choi & Ihm's paper (PRB 59, 2267, Jan 1999). In
> > > > > > > the paper, nonlocal wavefunction has 3 terms, one of which
> > > > > > > contains beta function, say W. The other two parts dont have any
> > > > > > > W in them, rather they are just plane wave solution. (Please have
> > > > > > > a look at equation 24 and 26 of the paper ). So, when we are
> > > > > > > doing z integration of nonlocal wavefunction with beta function
> > > > > > > W, we should have three terms, one of which should contain two W,
> > > > > > > but rest should just have one W. On the other hand in the code
> > > > > > > all three terms contain two beta functions!! (please have a look
> > > > > > > at line 228 of scatter_forw.f90). I am wondering if my
> > > > > > > understanding is right?
> > > > >
> > > > > Your understanding is wrong. On the line 228 you add to the integral
> > > > > ONLY contribution with two beta functions (from the 1st term in the
> > > > > nonlocal function, see Eq. 24) but on the line 393 the contribution
> > > > > from the 2nd term is added too. There is no 3rd term since every step
> > > > > you rotate your local solutions \psi_n in such a way that b_{\lambda
> > > > > \alpha lm} vanish (see the paragraph after Eq. 37).
> > > >
> > > > I believe that the equations 40, 41 and 42 implemented in the code
> > > > are in the momentum space. In the code, intw2 has 3 terms. We can tell
> > > > this by looking at the subroutine integrals.f90, where int2d is
> > > > defined. Now, by looking at the choi& Ihm 's paper, the very first term
> > > > of psi{alpha,l,m} has f{lambda,alpha,l,m}(equation26).And, if we
> > > > substitute this in equation 40, we should just get one term. I am just
> > > > confuesd on the fact that how come this one term in paper gets
> > > > transformed into 3 terms of the code!
> > >
> > > intw2(alpha,beta) is the integral of nonlocal solution (24) with w
> > > functions, intw2(alpha,beta) = \int_{0,d} w_{alpha}(r)*psi_{beta}(r)dr,
> > > where alpha,beta={alpha,l,m} in the paper. In each slab it will have TWO
> > > contributions from the first and second terms of (24), the one from the
> > > third term vanishes as I explained
[Pw_forum] QE 4.0.2: configure error
On Mon, Oct 20, 2008 at 1:19 PM, Paolo Giannozzi wrote: > Sangamesh B wrote: > > > I don't think so. Because I set - CC= F77= > > and MPIF90= > > if you set those variables, instead of letting configure find them, > you have to set them to the correct values. It looks like MPIF90 > is not the correct location of the parallel compiler: > No. I've set it to correct location of the parallel compiler. I'll send you the output of 'make all' error tomorrow. What might be the cause? Will it work, If I upgrade the gcc version to 4.3.0? > > > configure:2052: checking for /opt/mpich2GNU/bin/mpif90 > > configure:2081: result: no > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20081020/445c9950/attachment.htm
[Pw_forum] running paw on 4.0.1
Jes?s Cruz ha scritto: > Segmentation fault while reading the potential, the problem, the two > scalars nqlc and nwfc, the vector lll, and the matrix dion were not > writen into the UPF file when generated. So I modified pwscf to fill > these values while reading the potential. I've compiled a fresh and clean 4.0.1 version, generated the Cu pseudo, run the example01 with it and everything works perfectly fine for me. Can you please provide some additional information on your platform? regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/
[Pw_forum] QE 4.0.2: configure error
Sangamesh B wrote: > No. I've set it to correct location of the parallel compiler. this is what you think. Based on the file you sent, "configure" seems to think otherwise. > I'll send you the output of 'make all' error tomorrow. if it is a "compiler internal error" or something similar, please look into the user guide. > What might be the cause? anything: there are pages and pages in the user guide describing what can go wrong. > Will it work, If I upgrade the gcc version to 4.3.0? hard to predict. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] QE 4.0.2: configure error
Hi Paolo, On Mon, Oct 20, 2008 at 12:47 PM, Paolo Giannozzi wrote: > Sangamesh B wrote: > > > I tested the installation of Quantum Espresso-4.0.2 on Rocks-5.0 > > on WHAT?!? > If you asking about Rocks-5.0, then Rocks is a clustering tool which is built on Cent OS. The cluster has two nodes, with Dual core, dual AMD64 Opteron processors. > > > But the same installation is failing on Rocks-4.2 cluster [..] > > The strange thing happened with Rocks-4.2 is, if the variables CC, F77 > > or MPIF90 did not set to either gcc or pathscale, then configure works > > fine, but fails during make. > > how does it fails? > Right now I don't have that output. In further I'll send it. > > > If set the variables it fails in configure itself. > > because they are not properly set, I guess > I don't think so. Because I set - CC= F77= and MPIF90= > > Paolo > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20081020/b5aaea30/attachment.htm
[Pw_forum] QE 4.0.2: configure error
Hi all, I tested the installation of Quantum Espresso-4.0.2 on Rocks-5.0 with GNU compilers ( gcc-4.1.2 & gfortran-4.1.2) succeessfully. But the same installation is failing on Rocks-4.2 cluster either with GNU compilers or pathscale compilers. The error is: configure:2314: WARNING: serial/parallel compiler mismatch detected configure:2316: WARNING: parallel compiler uses gfortran, but serial compiler is /usr/bin/gfortran ... configure:2983: /usr/bin/gcc4 -E conftest.c conftest.c:9:28: error: ac_nonexistent.h: No such file or directory configure:2989: $? = 1 configure:4172: --version &5 ./configure: line 4173: --version: command not found configure:4175: $? = 127 configure:4177: -v &5 ./configure: line 4178: -v: command not found configure:4180: $? = 127 configure:4182: -V &5 ./configure: line 4183: -V: command not found configure:4185: $? = 127 configure:4193: checking whether we are using the GNU Fortran 77 compiler configure:4207: -c conftest.F >&5 ./configure: line 4208: -c: command not found configure:4213: $? = 127 The GNU version of Rocks 4.2 is 4.1.0 but in Rocks 5.0 it is 4.1.2. The strange thing happened with Rocks-4.2 is, if the variables CC, F77 or MPIF90 did not set to either gcc or pathscale, then configure works fine, but fails during make. If set the variables it fails in configure itself. I'm attaching here the config.log file. Please let me know if any one has faced this problem or atleast anybody successful to install QE on Rocks 4.2. Thanks, Sangamesh -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20081020/d2b7509d/attachment-0001.htm -- next part -- A non-text attachment was scrubbed... Name: config1.log Type: application/octet-stream Size: 26547 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20081020/d2b7509d/attachment-0001.obj
[Pw_forum] Stop job/ Davidson diagonalization with overlap
Dear Paolo, At first I thought so. But at this moment I do not think so because I did calculation on 72 atoms rutile and 72 atoms anatas . the 72 atom anatas job with ecut 30 ry crash but rutile run. regards Fariba Nazari IASBS > nazari at iasbs.ac.ir wrote: > >> when I do scf or relax calculation job starts the first iteration but >> stop immedietly. with this line in output: >> >> iteration # 1 ecut=30.00 Ry beta=0.70 >> Davidson diagonalization with overlap > > as a first guess I would say "out of memory" > > Paolo > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >
[Pw_forum] QE 4.0.2: configure error
Sangamesh B wrote: > I don't think so. Because I set - CC= F77= > and MPIF90= if you set those variables, instead of letting configure find them, you have to set them to the correct values. It looks like MPIF90 is not the correct location of the parallel compiler: > configure:2052: checking for /opt/mpich2GNU/bin/mpif90 > configure:2081: result: no P. -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] QE 4.0.2: configure error
Sangamesh B wrote: > I tested the installation of Quantum Espresso-4.0.2 on Rocks-5.0 on WHAT?!? > But the same installation is failing on Rocks-4.2 cluster [..] > The strange thing happened with Rocks-4.2 is, if the variables CC, F77 > or MPIF90 did not set to either gcc or pathscale, then configure works > fine, but fails during make. how does it fails? > If set the variables it fails in configure itself. because they are not properly set, I guess Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] Stop job/ Davidson diagonalization with overlap
Dear all, when I do scf or relax calculation job starts the first iteration but stop immedietly. with this line in output: iteration # 1 ecut=30.00 Ry beta=0.70 Davidson diagonalization with overlap any suggestion? regards Fariba nazari IASBS
[Pw_forum] Stop job/ Davidson diagonalization with overlap
nazari at iasbs.ac.ir wrote: > when I do scf or relax calculation job starts the first iteration but > stop immedietly. with this line in output: > > iteration # 1 ecut=30.00 Ry beta=0.70 > Davidson diagonalization with overlap as a first guess I would say "out of memory" Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] possible bug in scatter_forw.f90
Dear Manoj
On Thursday 16 October 2008 23:15, Manoj Srivastava wrote:
> Dear Alexandar,
> Thank you very much. Your answers make sense and now i have better
> understanding of the subroutine scatter_forw.f90. I have one question
> about poten.f90 subroutine, where you calculate the V(p,gper) in each
> slices of the slab(equation 15). I have a question about Gz, which is
> 2*pi*q/L, with [-N/2]+1<=q>=[N/2]. Now in the code at the line at the line
> 60, you have Gz multiplied with bg(3,3). I kind of understand this is
> because 3rd direction is perpendicular to xy plane,
Exactly. As it is implemented now pwcond deals with systems
having monoclinic unit cell, i.e. such that a3 is perpendicular to both a1 and
a2 (a1 and a2 are not necessary orthogonal one to another) and the direction
of transport is a3. This seems to us the most general setup for transport and
I do not think we should consider at the moment the situation where the a3 is
not perpendicular to the xy plane.
Best regards,
Alexander
> but not totally clear
> about it. Would you mind explaining? my other question is when reciprocal
> space vectors b1, b2 and b3 are not orhogonal to each other, which is
> more general case, then should not we take bg(1,3) and bg(2,3) in there
> too?
> Thank you once again for listening to my questions and i hope i am
> not bothering you too much.
>
> Regards,
> Manoj Srivastava
> Physics Graduate Student
> Department of Physics
> Gainesville, FL, USA.
>
> have On Wed, 15 Oct 2008, Alexander wrote:
> > Dear Manoj
> >
> > On Tuesday 14 October 2008 17:49, Manoj Srivastava wrote:
> > > Dear Alexader,
> > >
> > > Thank you very much for your reply. I was out of town and could not
> > > see the message till yesterday. I have some questions on it, it would
> > > be great if you could answer them.
> > >
> > > On Fri, 10 Oct 2008, Alexander wrote:
> > > > Dear Manoj
> > > >
> > > > On Friday 10 October 2008 05:20, Manoj Srivastava wrote:
> > > > > Any follow ups on the message below? Alexander?
> > > > >
> > > > > Regards,
> > > > > Manoj
> > > > >
> > > > > On Wed, 8 Oct 2008, Manoj Srivastava wrote:
> > > > > > Dear All,
> > > > > > Is any body familiar with the scatter_forw.f90 subroutine of
> > > > > > PWCOND? I think there is a bug in this subroutine at the place
> > > > > > where you calculate intw2, which is z integration of nonlocal
> > > > > > wavefunction with beta function. I have looked up the necessary
> > > > > > formulae in the Choi & Ihm's paper (PRB 59, 2267, Jan 1999). In
> > > > > > the paper, nonlocal wavefunction has 3 terms, one of which
> > > > > > contains beta function, say W. The other two parts dont have any
> > > > > > W in them, rather they are just plane wave solution. (Please have
> > > > > > a look at equation 24 and 26 of the paper ). So, when we are
> > > > > > doing z integration of nonlocal wavefunction with beta function
> > > > > > W, we should have three terms, one of which should contain two W,
> > > > > > but rest should just have one W. On the other hand in the code
> > > > > > all three terms contain two beta functions!! (please have a look
> > > > > > at line 228 of scatter_forw.f90). I am wondering if my
> > > > > > understanding is right?
> > > >
> > > > Your understanding is wrong. On the line 228 you add to the integral
> > > > ONLY contribution with two beta functions (from the 1st term in the
> > > > nonlocal function, see Eq. 24) but on the line 393 the contribution
> > > > from the 2nd term is added too. There is no 3rd term since every step
> > > > you rotate your local solutions \psi_n in such a way that b_{\lambda
> > > > \alpha lm} vanish (see the paragraph after Eq. 37).
> > >
> > > I believe that the equations 40, 41 and 42 implemented in the code
> > > are in the momentum space. In the code, intw2 has 3 terms. We can tell
> > > this by looking at the subroutine integrals.f90, where int2d is
> > > defined. Now, by looking at the choi& Ihm 's paper, the very first term
> > > of psi{alpha,l,m} has f{lambda,alpha,l,m}(equation26).And, if we
> > > substitute this in equation 40, we should just get one term. I am just
> > > confuesd on the fact that how come this one term in paper gets
> > > transformed into 3 terms of the code!
> >
> > intw2(alpha,beta) is the integral of nonlocal solution (24) with w
> > functions, intw2(alpha,beta) = \int_{0,d} w_{alpha}(r)*psi_{beta}(r)dr,
> > where alpha,beta={alpha,l,m} in the paper. In each slab it will have TWO
> > contributions from the first and second terms of (24), the one from the
> > third term vanishes as I explained before. These two contributions are
> > calculated on the lines 228 and 393 of the code. The integrals intw1
> > (alpha,n)=\int_{0,d} w_{alpha}(r)*psi_{n}(r)dr are the integrals of local
> > solutions (17) with the same projector functions w.
> > The integrals intw2 and intw1 have nothing to do with boundary conditions
> > (40). They enter in (11) and are needed to construct the final
[Pw_forum] problem with convergence during SCF-procedure
Dear all I perform the calculations of surface with adsorbed cluster Ag4/TiO2 and have a problem with convergence during SCF-procedure. It does not converge. In order to eliminate it I tried the shown methods in the user_guide: to decrease mixing beta, to increase mixing ndim, to increase ecutwfc and ecutrho. But it didn't help me. Is there any other methods to solve such problem? The input file is here attached. Best regards Alex Mazheika, Research Institute for phys. and chem. problems, Minsk, Belarus -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20081020/51e58c8f/attachment.htm -- next part -- A non-text attachment was scrubbed... Name: Ag4+R2.pw.inp Type: application/octet-stream Size: 3771 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20081020/51e58c8f/attachment.obj
