[Pw_forum] phonon errors

[vtmtr...@caltech.edu]

Thanks, Paolo.

I'll chack on this too.

MyTrinh

> Try to find out if the problem you have is related to the
> usage of local disks as scratch directories. It is quite
> tricky, because you have no control on which filesystem
> the various pieces are written to.
>
> Paolo
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

[Pw_forum] phonon errors

[Paolo Giannozzi]

Try to find out if the problem you have is related to the
usage of local disks as scratch directories. It is quite
tricky, because you have no control on which filesystem
the various pieces are written to.

Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

[Pw_forum] Tips for vc-relax when far from equilibrium

[Paolo Giannozzi]

On Oct 7, 2009, at 3:08 , Brad Malone wrote:

>  extrapolated charge6.83616, renormalised to8.0

do not use either wavefunction or potential extrapolation other than
the default together with bfgs. You might also try damped dynamics
with a relatively small time step in extreme cases

Paolo
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

[Pw_forum] How to consider more valence electrons in Pseudopotentials?

[Jiayu Dai]

Dear Users,

I have a question about the generation of pseudopotential(PP): how to consider
more electrons as valence electrons? For example, the configurations of Al is 
1s2
2s2 2p6 3s2 3p1, and we usually consider 3s2 3p1 as valence electrons. Now, i 
want
consider 2s2 and 2p6 as valence electrons also. Then, i should generate new PP. 
I
used the configuration in inputfile of ld1.x

[He] 2s2 sp6 3s2 3p1 3d-2
5
2S 1 0  2.00 0.00 1.60 1.60
2P 2 1  6.00 0.00 1.60 1.60
3S 3 0  2.00 0.00 2.40 2.40
3P 4 1  1.00 0.05 2.60 2.60
3D 5 2 -2.00 0.25 2.30 2.30

And the errors tell me ps-label wrong. I knew if i treat the 2s and 2p electrons
as semicore states, this propblem can be considered partly. But the question is
how to consider them as semicore states? Can they be like this?

[He] 2s2 2p6 3s0 3p0 3d0
3
2S  1  0  2.00 0.00 1.60  1.60
2P  2  1  6.00 0.00 1.60  1.60
3D  3  2  0.00 0.05 2.30  2.30  

Here, the cutoff energy will be tested after the generation of PPs.

Thanks in advance.

Jiayu





--
---
Jiayu Dai
Department of Physics
National University of Defense Technology, 
Changsha, 410073, P R China
-

[Pw_forum] Relaxation of low symmetry lattices

[Manoj Srivastava]

Dear PWSCF users, 
 I have a question regarding relaxation of low symmetry lattices. I did
relaxation of 5 atoms FCC unit cell of copper. This is pure copper, no
interface, no defect or anything. The unit cell is just not conventional,
but a different way of choosing bulk FCC. For the default value of
convergence the calculation finishes at the end of 1st scf cycle, but I
see different forces when I describe nosym=.TRUE. or cell_parameters
{cubic}. Following is the input file.


calculation='relax'
pseudo_dir = '/home/manoj/espresso-4.0.4/pseudo',
outdir='./',
prefix='lcu',
wf_collect=.TRUE.
 /
 
ibrav =0,
celldm(1)=6.81650937063832
nat= 5,
ntyp= 1,
ecutwfc =50.0,
occupations='smearing',
smearing='gaussian',
degauss=0.02,
ecutrho=500
 /

conv_thr = 1.0e-8
mixing_beta=0.7
/

ion_dynamics='bfgs'
pot_extrapolation='second_order'
wfc_extrapolation='second_order'
/
ATOMIC_SPECIES
 Cu 63.55  Cu.pz-d-rrkjus.UPF
ATOMIC_POSITIONS
  Cu  0.0   0.0   0.0
  Cu  0.5   0.5   0.0
  Cu  0.0   1.0   0.0
  Cu  1.0   1.0   0.0
  Cu  0.5   1.5   0.0

K_POINTS (automatic)
8 8 8 0 0 0
CELL_PARAMETERS {cubic}
 1.5   0.5  0.0
-0.5   1.5  0.0
 0.0   0.5  0.5
 
Result of relaxation : The covergence is achieved with follwing forces on
the atoms. 
Forces acting on atoms (Ry/au):

   Forces acting on atoms (Ry/au):

 atom   1 type  1   force = 0.0.0.
 atom   2 type  1   force = 0.05670.0185   -0.0172
 atom   3 type  1   force = 0.11550.0377   -0.0372
 atom   4 type  1   force =-0.1155   -0.03770.0372
 atom   5 type  1   force =-0.0567   -0.01850.0172


I realized that I should not have chosen cubic symmetry group, as my unit
cell is not cubic. So, as described in the input file parameters, for the
low symmetry lattices, I specifed nosym=.TRUE., and again the relaxation
stopped after 1 scf cycle, acheiving convergence. But the forces on the
atoms are -  

Forces acting on atoms (Ry/au):

 atom   1 type  1   force = 0.13550.0524   -0.0516
 atom   2 type  1   force =-0.1493   -0.03950.0395
 atom   3 type  1   force = 0.0253   -0.00430.0045
 atom   4 type  1   force = 0.08200.0230   -0.0239
 atom   5 type  1   force =-0.0935   -0.03160.0315

So, still forces are .001 ev/a.u, which i think is higher for a perfect
FCC lattice. I can specify stricter convergence of force, but that would
move atoms around and break symmetry. So, as long as the lattice parameter
is correct, I think for perfect FCC lattice, forces on atoms should be
smaller than what they are presently. I have checked the lattice constant
for bulk FCC with a different calculation, so lattice constant is not an
issue. Another possibility is symmetry group, as you can see with the same
input variables, changing symmetry group changes results.I was wondering
if there is a way i can choose correct symmetry group for this low
symmetry lattice which might give me smaller forces? Are there any other
parameters I need to specify? On a broad view I am curious to know how to
do relaxation of low symmetry lattices.

Regards, 
Manoj Srivastava
University of Florida
Gainesville, USA

[Pw_forum] phonon errors (vtmtr...@caltech.edu)

[vtmtr...@caltech.edu]

Dear Prof. Isaev,

Thank you very much for your detailed answer.  It is clear for me now.

MyTrinh


>
> Hi,
>
> --- On Thu, 10/8/09, vtmtrinh at caltech.edu  wrote:
>
>> My main purpose is to calculate the phonon dispersion curve from Gamma
>> to X  for Si. I'd like to reproduce the Si phonon dispersion curve from
>> > Gamma  to X.?
>
> In order to do this one correctly first you should calculate dynamical
> matrices for a given q-mesh, then perform FFT by q2r.x, then apply
> matdyn.x to calculate phonons along  given directions (specifying a list
> of q-points). In this way you apply ASR for both q2r.x and matdyn.x
> calculations.
>
> If you have only \Gamma-point phonons you can use dynmat.x to apply ASR.
>
>> I thought that after the scf calculation for 10x10x10, I can
>> run phonon calculation directly for a series of q points from Gamma to
>> X (let say 5 points).? Then from there, I use q2r.x and then
>> dynmat.x to calculate  intermediate points in order to fix the non-zero
>> > frequency  at Gamma point  (applying ASR) and to get a smooth
>> dispersion > curve  curve.?
>
> This is a wrong way to calculate phonons. Of course, you can calculate
> phonons for any q-point you like, but they are not oblidged to form a
> proper mesh for Fast-Fourier-Transformation. In this way you always  will
> meet troubles with q2r.x (FFT).
>
>> However, the phonon calculation (the first crash) crashed all the
>> >times.? Now I am  testing by running phonon calculation for a mesh of
>> >4x4x4  to see if it  still crashes. If it works, this means that direct
>> calculation of phonon  by specifying directly q points along G-X does
>> not
>> work.? However, this  will be expensive calculation if to get phonon
>> dispersion a long one  direction, I have to do the 3D-messh phonon
>> calculation  first.
>>
>> If I did only a single q-point calculation one at a time,
>> which would be  much faster than does the approach above,
>
> Sorry, I  am not sure I exactly understand what you mean, but calculations
> performed in the right way (see above) give you Interatomic Force
> Constants (IFC) matrix which allows you to evaluate many thermodynamical
> properties, besides  phonons along high symmetry directions.
>
>>how could I  specify q-grid in  q2r.x?
>
> You should not specify q-grid in q2r.x's input file. It (q2r.x) reads
> Sysname.dyn0 file generated by ph.x which contains info about the q-grid
> (divisions along each basis vectors, total number of q-points and q-points
> itself.
>
> Of course, you could calculate dynamical matrices in the old manner,
> specifying a list of q-points (but they have to be a result of KxLxM mesh,
> and calculated before you start phonon calculations). In this case you can
> follow your example given below.
>
>>
>> Also, I have another question, if I would like to apply ASR
>> to fix the phonon freq. at Gamma point, is it correct to just specify
>> the q-grid in  the input files for q2r.x and matdyn.x as follows:
>>
>> 
>> ? ? fildyn='si.dyn', zasr='crystal',
>> flfrc='si.fc'
>> ? /
>>  1 1 1
>>  1
>>  si.dyn1? ? !this the *.dyn file at gamma
>
> I do not think so, as q2r.x calculates IFC Matrix, not phonon modes as
> matdyn.x does this job.
> How to apply ASR for Gamma-point phonons  see above.
>
> Bests,
> Eyvaz.
>
> ---
> Prof. Eyvaz Isaev,
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
> Russia,
> Department of Physics, Chemistry, and Biology (IFM), Linkoping University,
> Sweden
> Condensed Matter Theory Group, Uppsala University, Sweden
> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com
>
> __
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[Pw_forum] phonon errors (vtmtr...@caltech.edu)

[Eyvaz Isaev]

Hi,

--- On Thu, 10/8/09, vtmtrinh at caltech.edu  wrote:

> My main purpose is to calculate the phonon dispersion curve from Gamma 
> to X  for Si. I'd like to reproduce the Si phonon dispersion curve from > 
> Gamma  to X.? 

In order to do this one correctly first you should calculate dynamical matrices 
for a given q-mesh, then perform FFT by q2r.x, then apply matdyn.x to calculate 
phonons along  given directions (specifying a list of q-points). In this way 
you apply ASR for both q2r.x and matdyn.x calculations.

If you have only \Gamma-point phonons you can use dynmat.x to apply ASR. 

> I thought that after the scf calculation for 10x10x10, I can
> run phonon calculation directly for a series of q points from Gamma to
> X (let say 5 points).? Then from there, I use q2r.x and then
> dynmat.x to calculate  intermediate points in order to fix the non-zero > 
> frequency  at Gamma point  (applying ASR) and to get a smooth dispersion > 
> curve  curve.? 

This is a wrong way to calculate phonons. Of course, you can calculate phonons 
for any q-point you like, but they are not oblidged to form a proper mesh for 
Fast-Fourier-Transformation. In this way you always  will meet troubles with 
q2r.x (FFT).

> However, the phonon calculation (the first crash) crashed all the >times.? 
> Now I am  testing by running phonon calculation for a mesh of >4x4x4  to see 
> if it  still crashes. If it works, this means that direct
> calculation of phonon  by specifying directly q points along G-X does not
> work.? However, this  will be expensive calculation if to get phonon 
> dispersion a long one  direction, I have to do the 3D-messh phonon 
> calculation  first.
> 
> If I did only a single q-point calculation one at a time,
> which would be  much faster than does the approach above, 

Sorry, I  am not sure I exactly understand what you mean, but calculations 
performed in the right way (see above) give you Interatomic Force Constants 
(IFC) matrix which allows you to evaluate many thermodynamical properties, 
besides  phonons along high symmetry directions.

>how could I  specify q-grid in  q2r.x?

You should not specify q-grid in q2r.x's input file. It (q2r.x) reads 
Sysname.dyn0 file generated by ph.x which contains info about the q-grid 
(divisions along each basis vectors, total number of q-points and q-points 
itself.

Of course, you could calculate dynamical matrices in the old manner, specifying 
a list of q-points (but they have to be a result of KxLxM mesh, and calculated 
before you start phonon calculations). In this case you can 
follow your example given below.

> 
> Also, I have another question, if I would like to apply ASR
> to fix the phonon freq. at Gamma point, is it correct to just specify
> the q-grid in  the input files for q2r.x and matdyn.x as follows:
> 
> 
> ? ? fildyn='si.dyn', zasr='crystal',
> flfrc='si.fc'
> ? /
>  1 1 1
>  1
>  si.dyn1? ? !this the *.dyn file at gamma

I do not think so, as q2r.x calculates IFC Matrix, not phonon modes as matdyn.x 
does this job. 
How to apply ASR for Gamma-point phonons  see above. 

Bests,
Eyvaz.

---
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, 
Russia, 
Department of Physics, Chemistry, and Biology (IFM), Linkoping University, 
Sweden 
Condensed Matter Theory Group, Uppsala University, Sweden 
Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com

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[Pw_forum] worth recompiling ?

[Carlo Nervi]

Hello,
when i was able to compile everything and all was working, I recompiled 
with intel 11.0 and especially with MKL 10 libraries.
There is a switch in intel 11 compiler (-xHost) that choose the best 
code for the CPU you have. This switch improved (at least for me) the 
speed. From my point of view I would give to it a try.

However, there others in this forum that could properly answer (as you 
have probably read, now I'm in still trouble and cannot compile anymore 
QE...)

Carlo

Boris Skegin ha scritto:
> Hallo.
> 
> I managed to compile espresso-4.1 on our Linux PC cluster using
>  intel/9.1
>  mkl/9.1
> vltmpi/mvapich_0.9.4
> 
> as it is said in
> http://www.pwscf.org/user_guide/node13.html#SECTION00036600 :
> 
> "The latest (July 2006) 32-bit version of ifort 9.1 works flawlessy."
> 
> And espresso-4.1 does work in the parallel version on our cluster, at
> least, if checked with simple examples.
> 
> 
> Besides intel/9.1 and mkl/9.1 we have also
> 
> intel/11.0
> intel/10.0   
> intel/10.1  
> 
> mkl/10.0 
> mkl/10.1 
> mkl/9.1 
> 
> As I have some free time now, I'd like to ask you if it is worth to
> recompile, say, with intel/11.0 and mkl/10.0  in order  to  achieve even
> better performance for complicated jobs?  
> 
> Regards,
> Boris Skegin  
> 
>  
> 
> 


-- 
--
Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8
Fax: +39 011 6707855   -   Dipartimento di Chimica IFM
via P. Giuria 7, 10125 Torino, Italy
http://lem.ch.unito.it/

[Pw_forum] phonon errors (vtmtr...@caltech.edu)

[vtmtr...@caltech.edu]

Dear Miguel and Mikiyas,

Thanks for your help.

Yes, I am sure that the outdirs are in the same directory. My main purpose
is to calculate the phonon dispersion curve from Gamma to X for Si. I'd
like to reproduce the Si phonon dispersion curve from Gamma to X.  I
thought that after the scf calculation for 10x10x10, I can run phonon
calculation directly for a series of q points from Gamma to X (let say 5
points).  Then from there, I use q2r.x and then dynmat.x to calculate
intermediate points in order to fix the non-zero frequency at Gamma point
(applying ASR) and to get a smooth dispersion curve curve.  However, the
phonon calculation (the first crash) crashed all the times.  Now I am
testing by running phonon calculation for a mesh of 4x4x4 to see if it
still crashes. If it works, this means that direct calculation of phonon
by specifying directly q points along G-X does not work.  However, this
will be expensive calculation if to get phonon dispersion a long one
direction, I have to do the 3D-messh phonon calculation first.

If I did only a single q-point calculation one at a time, which would be
much faster than does the approach above, how could I specify q-grid in
q2r.x?

Also, I have another question, if I would like to apply ASR to fix the
phonon freq. at Gamma point, is it correct to just specify the q-grid in
the input files for q2r.x and matdyn.x as follows:


fildyn='si.dyn', zasr='crystal', flfrc='si.fc'
  /
 1 1 1
 1
 si.dyn1!this the *.dyn file at gamma

Best,

MyTrinh



>
> On Oct 7, 2009, at 3:24 AM, pw_forum-request at pwscf.org wrote:
>
>>
>> Message: 7
>> Date: Wed, 7 Oct 2009 00:07:18 -0700 (PDT)
>> From: vtmtrinh at caltech.edu
>> Subject: [Pw_forum] phonon errors
>> To: pw_forum at pwscf.org
>> Message-ID:
>>  <2940.137.78.73.28.1254899238.squirrel at webmail.caltech.edu>
>> Content-Type: text/plain;charset=iso-8859-1
>>
>> Dear PWSCF Users,
>>
>> I have 2 questions:
>>
>> 1. I did a test phonon calculation for Si bulk, 2atom-cell, following
>> example_06.  I first did an scf calculation with k-point mesh
>> 10x10x10 Si.
>> Next, I wanted to do a phonon calculation along [001] direction (i.e
>> q=0,
>> q=0.1, 0.2,...).  If I specified 'ldisp=.true.', it was supposed to do
>> nscf calculation and then phonon calculation in a series.  However, it
>> stopped with errors.  When I checked the output file, after it had
>> finished calculation at Gamma point and nscf calculations, when it
>> entered
>> the phonon calculations for q !=0, it stopped with the error:
>> task # 8
>> from openfilq : error # 1
>> file si.wfc not found
>> The run is supposed to run continously as I specified ldisp=.true.
>> Now
>> suddenly, it stopped with that error, so I could not understand
>> why.  When
>> I tried with different q-point mesh, e.g. 4x4x4.  I ahd the same
>> problem.
>>
>> Here is my input for the phonon calculation:
>>
>> phonons of Si bulk
>> 
>>  tr2_ph=1.0d-14,
>>  prefix='si',
>>  ldisp=.true.,
>>  nq1=1, nq2=1, nq3=10   !(or nq1=4, nq2=4, nq3=4 for second test)
>>  amass(1)=28.086,
>>  outdir='./',
>>  fildyn='si.dyn',
>> /
>>
>> 2. If I run each single q-point,i.e. did scf, then Gamma
>> calculation, then
>> nscf and phonon calculation for each single q-point, it was fine. I
>> obtained 6 dyn files for 6 q-points from 0 to 0.5. However, I had
>> problem
>> when I used q2r.x.  In the input file, q2r.in, if I specified the q-
>> point
>> mesh: 1 1 10, and below it I provided a list of 6 dyn files that I
>> calculated above, I got an error:
>>
>>  task # 0
>> from init : error # 1
>> q not allowed
>>
>> I am not sure what is the correct input for the q-point mesh in q2r.in
>> that I should use in this case.
>>
>> Below is my q2r.in:
>>
>> 
>>   fildyn='si.dyn', zasr='crystal', flfrc='si.fc'
>> /
>> 1 1 10
>> 6
>> si.dyn1
>> si.dyn2
>> si.dyn3
>> si.dyn4
>> si.dyn5
>> si.dyn5
>>
>> I am using QE version 4.0.3.
>>
>> Thank you very much,
>>
>> MyTrinh
>> JPL/CakTech
>>
>>
>>
>
> Dear,
>
> It is essentially complaining that the data from your first pw.x run
> is not found in the outdir under that prefix ("si"). Have you checked
> that the outdir matches in both input files? Also, you can manually
> make sure that Si.wfc does exist in the outdir. Another helpful thing
> to do is to clear the outdir before you do these runs.
>
> - Mikiyas Tsegaye
> University of Virginia
> Charlottesville, VA, USA
> mastermik at gmail.com
>
>
>
>
> ___
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> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

[Pw_forum] worth recompiling ?

[Boris Skegin]

Hallo.

I managed to compile espresso-4.1 on our Linux PC cluster using
 intel/9.1
 mkl/9.1
vltmpi/mvapich_0.9.4

as it is said in
http://www.pwscf.org/user_guide/node13.html#SECTION00036600 :

"The latest (July 2006) 32-bit version of ifort 9.1 works flawlessy."

And espresso-4.1 does work in the parallel version on our cluster, at
least, if checked with simple examples.


Besides intel/9.1 and mkl/9.1 we have also

intel/11.0
intel/10.0   
intel/10.1  

mkl/10.0 
mkl/10.1 
mkl/9.1 

As I have some free time now, I'd like to ask you if it is worth to
recompile, say, with intel/11.0 and mkl/10.0  in order  to  achieve even
better performance for complicated jobs?  

Regards,
Boris Skegin  

 


-- 
Telefon: +49-(0)221-470-6392
Universit?t zu K?ln
II. Physikalisches Institut
Z?lpicher Str. 77
50937 K?ln
Deutschland

[Pw_forum] again on OpenMPI 1.3.3

[Carlo Nervi]

Hi again,
I am sorry to bother all the community with my compiling problems, that 
a little OT, but they are quite unusual. Certainly something is wrong in 
my machine (Linux Gentoo on dual Xeon 5345), but I cannot guess what.

After many tests and compiling I found that pw.x run perfectly using 
"mpirun -np 2", but fail with "mpirun -np 8". The error is
"MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with 
errorcode 0".

This really I cannot understand.
Is there anyone that could give me a hint?

I succesfully compiled the "pingpong" code below with mpif90 (wrapper to 
ifort). Also in this case mpirun -np 2 works, but if I put -np 4, 6 or 8 
the program crash with the following message:

*** Process received signal ***
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: (nil)
[ 0] /lib/libpthread.so.0 [0x2b48da46b400]
[ 1] /lib/libc.so.6(fputs+0x1e) [0x2b48da6d9d0e]
[ 2] ./pingpong(main+0x206) [0x402536]
[ 3] /lib/libc.so.6(__libc_start_main+0xf4) [0x2b48da6965e4]
[ 4] ./pingpong [0x4022b9]
*** End of error message ***

I was thinking that ssh does not propagate the environment variables (so 
the libraries cannot be found), but it runs on 2 cpus!

Any helps would be greatly appreciated.
Carlo



/* pingpong - measure effective bandwidth and latency */

#include "mpi.h"

#include 
#include 
#include 
#include 
#include 

#define MAXSIZE (1024*1024)
#define MINSIZE (0)
#define REPEAT  50

#define INCSIZE (2)
#define INCOP   *=

#define CALIBRATION_LOOPS 100

#define TAG_PING 1
#define TAG_PONG 2

/* define DETAIL if you want to create histogramms by measuring
the latency of each single ping-pong transfer */
#if 0
#define DETAIL
#include "getus.h"
#endif

#ifdef linux
#define longlong_t long long
#endif

char *buffer;
char *exename;
int min_size, max_size, inc_size, repeats;
int myrank, mysize;
static FILE* fpGlobal = NULL;
static FILE* fpDetail = NULL;


void ping (int to, int from);
void pong (int to);

int main(int argc, char **argv) {
 MPI_Status status;
 int first;
 char fname[128];
 MPI_Init(, );
 MPI_Comm_rank(MPI_COMM_WORLD, );
 MPI_Comm_size(MPI_COMM_WORLD, );

 if (myrank == 0) {
 strcpy(fname, argv[0]);
 strcat(fname,".dat");
 fpGlobal = fopen(fname,"w");
 }
 exename = argv[0];

 if(mysize % 2 != 0) {
 printf ("pingpong must be used with an even number of 
processes.\n");
 MPI_Finalize();
 exit (1);
 }

 /* set run parameters */
 if (argc != 4) {
 printf ("usage: pingpong min_size max_size repeats\n");
 printf ("using default values for this run\n");

 min_size = MINSIZE;
 max_size = MAXSIZE;
 inc_size = INCSIZE;
 repeats  = REPEAT;
 } else {
 min_size = atoi( argv[1] );
 max_size = atoi( argv[2] );
 inc_size = INCSIZE;
 repeats  = atoi( argv[3] );
 }
 buffer = (char *)malloc (max_size);

 /* find ping and pong processes */
 if ( myrank < mysize/2 ) {
 if (myrank % 2 == 0)
 ping(  myrank + mysize/2, myrank);
 else
 pong( myrank + mysize/2 );
 } else {
 first = (mysize/2) % 2;
 if (myrank % 2 == first)
 pong( myrank - mysize/2 );
 else
 ping( myrank - mysize/2, myrank );
 }

 if (myrank == 0) {
 fclose(fpGlobal);
 }

 free (buffer);
 MPI_Finalize();
}


void ping( int to, int from ) {
 MPI_Status status;

 double starttime, totaltime;
 double getticks_overhead;

#ifdef DETAIL
 longlong_t hr_start, hr_end;
 longlong_t calibration = 0;
 longlong_t *timings;
#endif

 char fname[128];
 char bytes[128];
 int i, j;
 int firstrun = 1;


#ifdef DETAIL
 fprintf (stderr, "Calibrating...");
 for (i = 0; i < CALIBRATION_LOOPS; i++) {
 GETTICKS(_start);
 GETTICKS(_end);
 calibration += hr_end - hr_start;
 }
 getticks_overhead = ((double)calibration)/(CALIBRATION_LOOPS);
 fprintf (stderr, "gethrtime() overhead is %6.3f\n", getticks_overhead);

 timings = (longlong_t *)malloc (repeats*sizeof(longlong_t));
#endif

 printf("pingpong from %d to %d\n\n", from, to);
 fprintf(fpGlobal, "# msgsize[byte]  repeats  bandwidth[MB/s] 
latency[us]\n");
 fflush(stdout);

 for( i = min_size; i <= max_size; i INCOP inc_size) {
 if ((!firstrun) && (i == 0)) {
 i++;
 if (i > max_size)
 break;
 }


-- 
--
Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8
Fax: +39 011 6707855   -   Dipartimento di Chimica IFM
via P. Giuria 7, 10125 Torino, Italy
http://lem.ch.unito.it/

[Pw_forum] How to consider more valence electrons in Pseudopotentials?

[Lorenzo Paulatto]

In data 07 ottobre 2009 alle ore 13:47:35, Jiayu Dai  
 ha scritto:
> [He] 2s2 sp6 3s2 3p1 3d-2
> 5
> 2S 1 0  2.00 0.00 1.60 1.60
> 2P 2 1  6.00 0.00 1.60 1.60
> 3S 3 0  2.00 0.00 2.40 2.40
> 3P 4 1  1.00 0.05 2.60 2.60
> 3D 5 2 -2.00 0.25 2.30 2.30
>
> And the errors tell me ps-label wrong.

It is not very clear to me what's your problem, please remember to ALWAYS  
attach the full output of the calculation. Anyway, you are requesting the  
2S pseudo-wavefunction to have zero node and the 3S one to have 2 nodes,  
which is at least awkward. The situation is even worst for the 3P, as for  
no apparent reason you have set their principal quantum number to 4.

Finally, you have put electrons in the 3P norm-conserving orbital and also  
specified a positive energy for it, that will make it unbound. It is not  
necessarily wrong, but I would not do it before having explored any other  
possibility.

Change the input as following and it may work:
5
2S 1 0  2.00 0.00 1.60 1.60
2P 2 1  6.00 0.00 1.60 1.60
3S 2 0  2.00 0.00 2.40 2.40
3P 3 1  1.00 0.00 2.60 2.60
3D 5 2 -2.00 0.25 2.30 2.30


-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

 *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

[Pw_forum] occupations fixed

[udayagiri sai babu]

Dear Lorenzo thanks for the answer. My problem is simple it is to find out
the cohesive energy of Cr,V,Ti. I posted this question earlier also. I was
told to try out with occupations=from_input instead of degauss value to get
the accurate value of the ground state energy because i am getting an error
of around 10% in Ec (i was wondering if that can be acceptable) meanwhile i
came across the post which says to use ocuupations=fixed.

On Wed, Oct 7, 2009 at 1:09 PM, Lorenzo Paulatto  wrote:

> In data 07 ottobre 2009 alle ore 09:24:28, udayagiri sai babu
>  ha scritto:
>
> > In the archive I have seen a discussion suggesting use of
> > occupations=fixed to find out the ground state energy of isolated oxygen
> > atom accurately. Can I use the same (occupations=fixed) for metal also.
> > Because in the pw
> > document it is told to use only for insulators.
>
>
> Dear U,
> for isolated atoms you can always use fixed occupations: as you use only
> use the Gamma point, bands are actually flat. Nevertheless it may be
> difficult to reach the ground state in some cases, I suggest using a small
> smearing which should give exactly the same result but makes convergence
> faster.
>
> I see you have already asked how to compute the ground state for a Ti atom
> (e.g.
> <http://www.democritos.it/pipermail/pw_forum/2009-September/014246.html>),
> which actually is a metal... why don't you tell us your problem, instead
> of your guess for a solution?
>
> best regards
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/<http://people.sissa.it/%7Epaulatto/>
>
> *** save italian brains ***
>  http://saveitalianbrains.wordpress.com/
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
U.Saibabu
PhD student,
Deformation mechanisms modeling group,
Materials engineering department,
IISc Bangalore,
India.
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[Pw_forum] occupations fixed

[udayagiri sai babu]

In the archive I have seen a discussion suggesting use of occupations=fixed
to find out the ground state energy of isolated oxygen atom accurately. Can
I use the same (occupations=fixed) for metal also. Because in the pw
document it is told to use only for insulators.

-- 
U.Saibabu
PhD student,
Deformation mechanisms modeling group,
Materials engineering department,
IISc Bangalore,
India.
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[Pw_forum] scf calculation of isolated atom

[udayagiri sai babu]

Thank you for the answer GS and Lorenzo. I am using 10 occupations per line
in the occupations card as you suggested and It is not giving any error now.


On Tue, Oct 6, 2009 at 6:18 PM, Lorenzo Paulatto  wrote:

> In data 06 ottobre 2009 alle ore 11:34:33, udayagiri sai babu
>  ha scritto:
> > I got an error saying *"strange occupations:number of electrons from
> > occupations is wrong"*. I undestood like my occupation card is not
> > matching with my "nbnd" value but i could not correct it can somebody
> > give me some
> > suggestion.
>
> In QE versions 4.0.x and before the occupations you had to specify at most
> ten occupations per line, you input would work this way:
>
> OCCUPATIONS
> 1  1 1 1  1  1 1 1 1 1
> 0 0 0
> 1  1 1 1  0  0 0 0 0 0
> 0 0 0
>
> QE 4.1 and newer do not have this limitation.
>
> best regards
>
>
>
> --
> Lorenzo Paulatto
> SISSA  &  DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www:   http://people.sissa.it/~paulatto/<http://people.sissa.it/%7Epaulatto/>
>
> *** save italian brains ***
>  http://saveitalianbrains.wordpress.com/
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
U.Saibabu
PhD student,
Deformation mechanisms modeling group,
Materials engineering department,
IISc Bangalore,
India.
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[Pw_forum] GIPAW pseudopotentials

[Pallister, Peter]

Hi all,

I am attempting to generate a gipaw pseudopotentials, in this case for
Mg, but I am having tremendous difficulty. The wavefunctions produced
with the input below (or minute variations thereof) continuously show
discontinuities, specifically at a radius of 15bohrs. I have looked at
the previous entries in the forum on this topic as well as looked at the
tutorials available on Dr. Seitsonen's webpage and the QE summer school
media but I still cannot successfully generate one of these
pseudopotentials. Any help is greatly appreciated.

 

Below is a typical input I use for the ld1.x module:

 



title = 'Mg-oct09'

prefix = 'Mg-oct09'

zed = 12.0

rel = 0

nld = 3

rlderiv = 5.0

eminld = -6.0

emaxld = -1.0

deld = 0.01

config = '1s2 2s2 2p6 3s2 3p-1 3d-1'

iswitch = 3

dft = 'PBE'

/



pseudotype = 1

lloc = 2

file_pseudopw = 'Mg.pbe-gipaw-oct09.UPF'

file_recon = 'Mg.pbe-gipaw-oct09.recon'

lgipaw_reconstruction = .true.

tm = .true.

/

3

2S 1 0  2.00  0.00 1.600 1.600

2P 2 1  6.00  0.00 1.600 1.600

3D 3 2 -1.00 -0.30 1.600 1.600

 



/

4

2S 1 0  2.00  0.00 1.600 1.600

3S 2 0  2.00  0.00 1.600 1.600

2P 2 1  6.00  0.00 1.600 1.600

3P 3 1 -1.00 -0.10 1.600 1.600

 

Thanks,

 

Peter Pallister

Steacie Institute for Molecular Sciences

National Research Council

Ottawa, Ontario

Canada

 

 

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[Pw_forum] occupations fixed

[Lorenzo Paulatto]

In data 07 ottobre 2009 alle ore 10:32:28, udayagiri sai babu  
 ha scritto:

> Dear Lorenzo thanks for the answer. My problem is simple it is to find  
> out the cohesive energy of Cr,V,Ti. I posted this question earlier also.  
> I was told to try out with occupations=from_input instead of degauss  
> value to get the accurate value of the ground state energy because i am  
> getting an error of around 10% in Ec (i was wondering if that can be  
> acceptable) meanwhile i came across the post which says to use  
> ocuupations=fixed.

Isolated Cr, V and Ti all have magnetic ground state, you have to take  
care in making the calculation for the isolated atom with spin and with  
some initial magnetization. It would be even better to compute it with and  
without spin, so you can see the difference.

V and Ti have a ground state which is NOT spherical, you absolutely must  
use *nosym=.true.*, and break the symmetry somehow, e.g. by specifying  
occupations from input, or tot_magnetization or multiplicity; or taking a  
slightly non-cubic unit cell.

Best regards.


-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

 *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

[Pw_forum] PDOS on different Oxygen atoms

[Gabriele Sclauzero]

Huolin Xin wrote:
> Hi all,
> 
> I have a layered structure ...,AO,AO,BO,BO, Does projwfc.x gives
> seperate PDOS for the Oxygen in AO layers and BO layers automatically?

projwfc.x gives you separate PDOS for each atom in your system, numbering the 
corresponding files according to the order which is shown in the list of atoms 
at the 
beginning of the output of the preceding pw.x calculation.
After identifying the number of the atom(s) of interest (e.g. by looking at the 
coordinates reported in the list), you can easily match the file containing the 
PDOS of 
that atom.
I think it is more difficult to explain than to try it directly. Simply run 
projwfc.x and 
I think you will see clearly (also give a look at Doc/INPUT_PROJWFC.txt, if you 
haven't 
already).

HTH

GS


> 
> H. Xin
> Cornell University
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 

-- 


o  o
| Gabriele Sclauzero, PhD Student  |
| c/o:   SISSA & CNR-INFM Democritos,  |
|via Beirut 2-4, 34014 Trieste (Italy) |
| email: sclauzer at sissa.it |
| phone: +39 040 3787 511  |
| skype: gurlonotturno |
o  o

[Pw_forum] occupations fixed

[Lorenzo Paulatto]

In data 07 ottobre 2009 alle ore 09:24:28, udayagiri sai babu  
 ha scritto:

> In the archive I have seen a discussion suggesting use of  
> occupations=fixed to find out the ground state energy of isolated oxygen  
> atom accurately. Can I use the same (occupations=fixed) for metal also.  
> Because in the pw
> document it is told to use only for insulators.


Dear U,
for isolated atoms you can always use fixed occupations: as you use only  
use the Gamma point, bands are actually flat. Nevertheless it may be  
difficult to reach the ground state in some cases, I suggest using a small  
smearing which should give exactly the same result but makes convergence  
faster.

I see you have already asked how to compute the ground state for a Ti atom  
(e.g.  
),  
which actually is a metal... why don't you tell us your problem, instead  
of your guess for a solution?

best regards

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/

 *** save italian brains ***
  http://saveitalianbrains.wordpress.com/

[Pw_forum] phonon errors

[Miguel Martínez]

Dear Mytrinh,

As far as I know, q2r.x requires a regular mesh (i.e. 4 4 4), and that
would explain why it's crashing in your second question. Regarding your
first crash, I'd make sure outdirs are identical in both the pw.x and
ph.x inputs and then check why ph.x can't read the files in the outdir
specified to pw.x.



On Wed, 7 Oct 2009 00:07:18 -0700 (PDT) vtmtrinh at caltech.edu wrote:
> Dear PWSCF Users,
> 
> I have 2 questions:
> 
> 1. I did a test phonon calculation for Si bulk, 2atom-cell, following
> example_06.  I first did an scf calculation with k-point mesh
> 10x10x10 Si. Next, I wanted to do a phonon calculation along [001]
> direction (i.e q=0, q=0.1, 0.2,...).  If I specified 'ldisp=.true.',
> it was supposed to do nscf calculation and then phonon calculation in
> a series.  However, it stopped with errors.  When I checked the
> output file, after it had finished calculation at Gamma point and
> nscf calculations, when it entered the phonon calculations for q !=0,
> it stopped with the error: task # 8
>  from openfilq : error # 1
>  file si.wfc not found
> The run is supposed to run continously as I specified ldisp=.true.
> Now suddenly, it stopped with that error, so I could not understand
> why.  When I tried with different q-point mesh, e.g. 4x4x4.  I ahd
> the same problem.
> 
> Here is my input for the phonon calculation:
> 
> phonons of Si bulk
>  
>   tr2_ph=1.0d-14,
>   prefix='si',
>   ldisp=.true.,
>   nq1=1, nq2=1, nq3=10   !(or nq1=4, nq2=4, nq3=4 for second test)
>   amass(1)=28.086,
>   outdir='./',
>   fildyn='si.dyn',
>  /
> 
> 2. If I run each single q-point,i.e. did scf, then Gamma calculation,
> then nscf and phonon calculation for each single q-point, it was
> fine. I obtained 6 dyn files for 6 q-points from 0 to 0.5. However, I
> had problem when I used q2r.x.  In the input file, q2r.in, if I
> specified the q-point mesh: 1 1 10, and below it I provided a list of
> 6 dyn files that I calculated above, I got an error:
> 
>   task # 0
>  from init : error # 1
>  q not allowed
> 
> I am not sure what is the correct input for the q-point mesh in q2r.in
> that I should use in this case.
> 
> Below is my q2r.in:
> 
>  
>fildyn='si.dyn', zasr='crystal', flfrc='si.fc'
>  /
> 1 1 10
> 6
> si.dyn1
> si.dyn2
> si.dyn3
> si.dyn4
> si.dyn5
> si.dyn5
> 
> I am using QE version 4.0.3.
> 
> Thank you very much,
> 
> MyTrinh
> JPL/CakTech
> 
> 
> 
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 

Miguel Mart?nez Canales
   Condensed Matter Physics Dpt.
   UPV/EHU
   Faculty of Science and Technology
   Apdo. 644
   48080 Bilbao (Spain)
Fax:  +34 94 601 3500
Tlf:  +34 94 601 5326


 "If you have an apple and I have an apple and
 we exchange these apples then you and I will
 still each have one apple. But if you have an
 idea and I have an idea and we exchange these
 ideas, then each of us will have two ideas."

 George Bernard Shaw 

[Pw_forum] phonon errors (vtmtr...@caltech.edu)

[Mikiyas Tsegaye]

On Oct 7, 2009, at 3:24 AM, pw_forum-request at pwscf.org wrote:

>
> Message: 7
> Date: Wed, 7 Oct 2009 00:07:18 -0700 (PDT)
> From: vtmtrinh at caltech.edu
> Subject: [Pw_forum] phonon errors
> To: pw_forum at pwscf.org
> Message-ID:
>   <2940.137.78.73.28.1254899238.squirrel at webmail.caltech.edu>
> Content-Type: text/plain;charset=iso-8859-1
>
> Dear PWSCF Users,
>
> I have 2 questions:
>
> 1. I did a test phonon calculation for Si bulk, 2atom-cell, following
> example_06.  I first did an scf calculation with k-point mesh  
> 10x10x10 Si.
> Next, I wanted to do a phonon calculation along [001] direction (i.e  
> q=0,
> q=0.1, 0.2,...).  If I specified 'ldisp=.true.', it was supposed to do
> nscf calculation and then phonon calculation in a series.  However, it
> stopped with errors.  When I checked the output file, after it had
> finished calculation at Gamma point and nscf calculations, when it  
> entered
> the phonon calculations for q !=0, it stopped with the error:
> task # 8
> from openfilq : error # 1
> file si.wfc not found
> The run is supposed to run continously as I specified ldisp=.true.   
> Now
> suddenly, it stopped with that error, so I could not understand  
> why.  When
> I tried with different q-point mesh, e.g. 4x4x4.  I ahd the same  
> problem.
>
> Here is my input for the phonon calculation:
>
> phonons of Si bulk
> 
>  tr2_ph=1.0d-14,
>  prefix='si',
>  ldisp=.true.,
>  nq1=1, nq2=1, nq3=10   !(or nq1=4, nq2=4, nq3=4 for second test)
>  amass(1)=28.086,
>  outdir='./',
>  fildyn='si.dyn',
> /
>
> 2. If I run each single q-point,i.e. did scf, then Gamma  
> calculation, then
> nscf and phonon calculation for each single q-point, it was fine. I
> obtained 6 dyn files for 6 q-points from 0 to 0.5. However, I had  
> problem
> when I used q2r.x.  In the input file, q2r.in, if I specified the q- 
> point
> mesh: 1 1 10, and below it I provided a list of 6 dyn files that I
> calculated above, I got an error:
>
>  task # 0
> from init : error # 1
> q not allowed
>
> I am not sure what is the correct input for the q-point mesh in q2r.in
> that I should use in this case.
>
> Below is my q2r.in:
>
> 
>   fildyn='si.dyn', zasr='crystal', flfrc='si.fc'
> /
> 1 1 10
> 6
> si.dyn1
> si.dyn2
> si.dyn3
> si.dyn4
> si.dyn5
> si.dyn5
>
> I am using QE version 4.0.3.
>
> Thank you very much,
>
> MyTrinh
> JPL/CakTech
>
>
>

Dear,

It is essentially complaining that the data from your first pw.x run  
is not found in the outdir under that prefix ("si"). Have you checked  
that the outdir matches in both input files? Also, you can manually  
make sure that Si.wfc does exist in the outdir. Another helpful thing  
to do is to clear the outdir before you do these runs.

- Mikiyas Tsegaye
University of Virginia
Charlottesville, VA, USA
mastermik at gmail.com

[Pw_forum] PDOS on different Oxygen atoms

[Huolin Xin]

Hi all,

I have a layered structure ...,AO,AO,BO,BO, Does projwfc.x gives
seperate PDOS for the Oxygen in AO layers and BO layers automatically?

H. Xin
Cornell University

[Pw_forum] Tips for vc-relax when far from equilibrium

[xirainbow]

Dear Brad Malone:
You can opitmize structure using empirical or semi-empirical method(for
example: tight-binding method) with other software??
After that, the pre-optimized structure will be more suitable for DFT
calculation??


-- 

Hui Wang
School of physics, Nankai University, Tianjin, China
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[Pw_forum] phonon errors

[vtmtr...@caltech.edu]

Dear PWSCF Users,

I have 2 questions:

1. I did a test phonon calculation for Si bulk, 2atom-cell, following
example_06.  I first did an scf calculation with k-point mesh 10x10x10 Si.
 Next, I wanted to do a phonon calculation along [001] direction (i.e q=0,
q=0.1, 0.2,...).  If I specified 'ldisp=.true.', it was supposed to do
nscf calculation and then phonon calculation in a series.  However, it
stopped with errors.  When I checked the output file, after it had
finished calculation at Gamma point and nscf calculations, when it entered
the phonon calculations for q !=0, it stopped with the error:
 task # 8
 from openfilq : error # 1
 file si.wfc not found
The run is supposed to run continously as I specified ldisp=.true.  Now
suddenly, it stopped with that error, so I could not understand why.  When
I tried with different q-point mesh, e.g. 4x4x4.  I ahd the same problem.

Here is my input for the phonon calculation:

phonons of Si bulk
 
  tr2_ph=1.0d-14,
  prefix='si',
  ldisp=.true.,
  nq1=1, nq2=1, nq3=10   !(or nq1=4, nq2=4, nq3=4 for second test)
  amass(1)=28.086,
  outdir='./',
  fildyn='si.dyn',
 /

2. If I run each single q-point,i.e. did scf, then Gamma calculation, then
nscf and phonon calculation for each single q-point, it was fine. I
obtained 6 dyn files for 6 q-points from 0 to 0.5. However, I had problem
when I used q2r.x.  In the input file, q2r.in, if I specified the q-point
mesh: 1 1 10, and below it I provided a list of 6 dyn files that I
calculated above, I got an error:

  task # 0
 from init : error # 1
 q not allowed

I am not sure what is the correct input for the q-point mesh in q2r.in
that I should use in this case.

Below is my q2r.in:

 
   fildyn='si.dyn', zasr='crystal', flfrc='si.fc'
 /
1 1 10
6
si.dyn1
si.dyn2
si.dyn3
si.dyn4
si.dyn5
si.dyn5

I am using QE version 4.0.3.

Thank you very much,

MyTrinh
JPL/CakTech

[Pw_forum] write on local disk

[Lorenzo Paulatto]

On Tue, October 6, 2009 23:00, vtmtrinh at caltech.edu wrote:
>  If I would like to write wavefunction files on local disk (to avoid
>  network file system daemon), besides creating scratch directory in each
>  node, do I need to do additional configuration.

Dear MyTrinh,
the outdir variable, or at least the wfcdir variable, must point to the
local scratch directory: their default value is $HOME/tmp.

You can also use disk_io='none' to completely prevent the output of
wavefunctions to disk. It may see a drastic solution, but if you don't
have the possibility to restart an interrupted job on the same nodes it
does not really make much difference.

best regards

-- 
Lorenzo Paulatto
SISSA  &  DEMOCRITOS (Trieste)
phone: +39 040 3787 511
skype: paulatz
www:   http://people.sissa.it/~paulatto/




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