[Pw_forum] Cannot allocate FFT

[GAO Zhe]

Dear QE users and developers,


I am trying to compile QE 5.4.0 under MinGW-32 with MPICH2.
However, pw.x met error while allocating FFT as following:
 G-vector sticks info
 
 sticks:   dense  smooth PW G-vecs:dense   smooth  PW
 Sum   0   0  000   0
 %%
 Error in routine allocate_fft (1):
 wrong ngm
 %%
 
During compiling, the only warning information was occurred for zhpev_drv.f90 
in LAXlib as:


gfortran -O3 -static  -x f95-cpp-input  -D__WIN32 -D__FFTW3 -D__GFORTRAN 
-D__STD_F95 -D__MPI -D__PARA   -I../include -I/$(MPICH_TOP)/include 
-I/local/include  -I../ELPA/src   -c zhpev_drv.f90
mpif.h:511.11:
Included at zhpev_drv.f90:14:
   SAVE /MPIFCMB1/, /MPIFCMB2/
   1
Warning: SAVE statement at (1) follows blanket SAVE statement
mpif.h:512.11:
Included at zhpev_drv.f90:14:
   SAVE /MPIFCMB3/, /MPIFCMB4/, /MPIFCMB5/, /MPIFCMB6/
   1
Warning: SAVE statement at (1) follows blanket SAVE statement
mpif.h:513.11:
Included at zhpev_drv.f90:14:
   SAVE /MPIFCMB7/, /MPIFCMB8/
   1
Warning: SAVE statement at (1) follows blanket SAVE statement


So far, I have no idea why the strange error took place. Would you like to 
share some comments with me how to avoiding the error?
Many thanks.
Best Regards,


--
GAO Zhe, Dr.,
Research Engineer,
Gypsum Activity R - Asia,
Saint-Gobain Research Shanghai Co., Ltd.,

No. 55, Wenjing-road, Minhang-district, Shanghai, China,
Tel: +86-21-5475-7251
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[Pw_forum] NVT simulations using cp.x

[Zeeshan Ahmad]

Dear all,

I intend to use cp.x to perform constant temperature simulations. The document 
cp_user_guide.pdf, recommends adding a random displacement to ions before 
switching on the thermostat and not to increase the temperature too much. In 
order to achieve a high temperature ~ 800-1000 K, the random displacement must 
be increased in the 1st step. Based on my microcanonical simulations, I found 
out that adding a very high random displacement of ~0.9-1 a.u. gives the 
required average temperature for my system. So, my question is: is it okay to 
first run a micro canonical simulation with such a high random displacement to 
achieve a temperature close to the required (high) temperature and then turning 
on the thermostat?

Thank you,
--
Zeeshan Ahmad
PhD student, Mechanical Engineering
Carnegie Mellon University
email: azees...@andrew.cmu.edu 
http://www.andrew.cmu.edu/user/azeeshan/ 







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Re: [Pw_forum] wrong number of symmetries!

[Li Mingkai]

Actually, it's working after using ibrav=14 and  a,b,c and cosab, cosac,
cosbc. I just don't understand what happens. All vectors look good and just
some atoms' position are perturbated. Is it supposed not to check the
symmetry when I use nosym and nosym_vec?

CELL_PARAMETERS alat
6.930132 -2.310044 0.00
0.00 -6.930132 -2.310044
2.310044 0.00 -6.930132
ATOMIC_SPECIES
  O 16 o_pbe_v1.2.uspp.F.UPF
  Zn 65.38 zn_pbe_v1.uspp.F.UPF
ATOMIC_POSITIONS crystal
  O 0.214285714285714 0.928571428571429 0.357142857142857
  Zn 0.625 0.625 0.625
  O 0.642857142857143 0.785714285714286 0.071428571428571
  Zn 0.053571428571429 0.482142857142857 0.339285714285714
  O 0.500 0.500 0.500
  Zn 0.910714285714286 0.196428571428571 0.767857142857143
  O 1.000 1.000 1.000
  Zn 0.410714285714286 0.696428571428572 0.267857142857143
  O 0.428571428571429 0.857142857142857 0.714285714285714
  Zn 0.839285714285714 0.553571428571429 0.982142857142857
  O 0.857142857142857 0.714285714285715 0.428571428571428
  Zn 0.267857142857143 0.410714285714286 0.696428571428571
  O 0.285714285714286 0.571428571428572 0.142857142857143
  Zn 0.696428571428572 0.267857142857143 0.410714285714286
  O 0.714285714285714 0.428571428571429 0.857142857142857
  Zn 0.125 0.125 0.125
  O 0.142857142857143 0.285714285714286 0.571428571428572
  Zn 0.553571428571429 0.982142857142857 0.839285714285714
  O 0.571428571428571 0.142857142857143 0.285714285714286
  Zn 0.982142857142857 0.839285714285715 0.553571428571428
  O 0.071428571428571 0.642857142857142 0.785714285714286
  Zn 0.482142857142857 0.339285714285714 0.053571428571429
  O 0.928571428571429 0.357142857142857 0.214285714285714
  Zn 0.339285714285714 0.053571428571429 0.482142857142857
  O 0.357142857142857 0.214285714285714 0.928571428571429
  Zn 0.767857142857143 0.910714285714285 0.196428571428572
  O 0.794990546871463 0.068336484376179 0.615028359385610
  Zn 0.196428571428572 0.767857142857143 0.910714285714286


Mingkai Li


On Sat, Oct 15, 2016 at 5:17 PM, Paolo Giannozzi 
wrote:

> (I was referring to symmetries of the lattice alone, not symmetries of the
> crystal; if you are sure that the crystal has no symmetries, commenting out
> the check should do the job)
>
> Il 15/ott/2016 11:13 AM, "Paolo Giannozzi"  ha
> scritto:
>
>> In order to find symmetries, the code uses a threshold to decide if a
>> rotated vector is the same as the original one. It may sometimes happen
>> that some "quasi-symmetries" are recognized as symmetries, some are not,
>> leading to a "symmetry group" that is not a group. This is likely what
>> happened in your case.  Paolo
>>
>> Il 15/ott/2016 01:27 AM, "Li Mingkai"  ha scritto:
>>
>>> I tried to do the scf calculation on a perturbated cell. I used
>>> "CELL_PARAMETERS alat" to specify vector. However, I got an error.
>>>
>>>  %%%
>>> %%%
>>>  Error in routine set_sym_bl (3):
>>>  wrong number of symmetries! Use standard orientations for axis
>>>  %%%
>>> %%%
>>>
>>> Since the cell is perturbated, there is no symmetry on it and space
>>> group should be P1. But it seemed that the pw.x tried to find some symmetry
>>> and got wrong number of symmetries. I tried nosym, nosym_vec, no_inv.
>>> Nothing works. I tried old version down to 5.0, which worked. After version
>>> 5.1, the error emergied. Of course, I tried to use celldm(1)~(6). It works
>>> well for all version. Since this input file is generated by a script
>>> automatically. I don't tend to modify the script a lot and try to figure
>>> out what happened before change everything.
>>>
>>> --
>>> Mingkai Li
>>> ===
>>> School of Material Science and Engineering
>>> Hubei University
>>> Wuhan, Hubei Province
>>> P. R. China
>>> ===
>>>
>>> ___
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>>> Pw_forum@pwscf.org
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>>>
>>
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-- 
Mingkai Li
===
Quantum-functional Semiconductor Research Center(QSRC)
Dongguk Univeristy, 3-26 Pil-dong, Joong-gu,
Seoul 100-715, Korea
Tel:(+82)-2-2260-3688
Fax:(+82)-2-2260-3945
===
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Re: [Pw_forum] Question about vc-relax

[Anand Chandra]

Hi Joshua,

If you are running a vc-relax calculation, the stress after each relaxation
step will be written in the output file (see tag tstress). Is the stress
less than the default threshold (see tag press_conv_thr)?

Also, for optimizing lattice parameters of a 2D material you should use the
tag cell_dofree="2Dxy" .

Regards,
Anand Chandrasekaran
Post-doctoral researher
Materials Research Center
Indian Institute of Science

On Fri, Oct 14, 2016 at 10:44 PM, Joshua Young 
wrote:

> Hi QE community,
>
> I am attempting to relax the lattice parameters and internal atomic
> positions of monolayer MoS2 using a variable cell relaxation. However,
> although the atom positions will change over the course of the calculation,
> the lattice parameters do not even though the calculation converges. I have
> attached my input file here, as well as the atomic positions and lattice
> parameters output for five steps of the calculation. I am including van der
> Waals correction, spin-orbit coupling, and using fully relativistic
> pseudopotentials.
>
> Could this be because I have started from lattice parameters which are
> close to the equilibrium values of MoS2? Or do I simply have a tag wrong in
> the input file?
>
> Any help would be greatly appreciated.
>
> Thank you,
> Joshua Young, PhD
> Postdoctoral Research Associate
> Naval Research Laboratory
> Washington, DC
>
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Re: [Pw_forum] Problem in parallel execution

[Paolo Giannozzi]

It looks like you are running in parallel a code compiled for serial
execution.  There is a rather long section in the general user guide
describing compilation for parallel execution and what to do in case
configure does not recognize your parallel compilation environment. Paolo

Il 15/ott/2016 12:28 AM, "Afshin Arjangmehr"  ha
scritto:

> Dear QE developers and users,
>
> I have asked the authorities to install QE 5.4.0 on university cluster
> (operating system: CentOS) and now, after installation, something is wrong
> with the parallel executions.
> I perform pwscf run and in its output file, every step is repeated equal
> to the number of cpu cores (N). It is similar to performing N serial runs
> altogether, each on a single core (please see attached output file).
> I had this problem on my personal cluster (operating system: Ubuntu 16.04
> LTS) with QE 5.4.0 and QE 6.0 (not with QE 5.1 that I installed using sudo
> apt-get install ... ). I am really confused right now, since I have no idea
> whether it is related to QE or mpich2. Can you please recommend me on how
> to solve this issue? Is there any specific setting in ./configure step?
>
> Thanks for your kind response in advance.
>
>
> Bests,
> Afshin
>
>
> --
> With Best Regards
> Afshin Arjhangemehr
> PhD student in Radiation Application
> Shahid Beheshti University G.C, Tehran, IRAN
> (+98) 912 439 20 64
>
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[Pw_forum] Fwd: vdw interaction and pseudopotentials

[Zara Nosh]

Dear all,
I would like to study the interaction between 2 organic molecules (contains
O, H, and C atoms).
I calculate vdw forces with vdw-df algorithm which should be used rev-pbe
pseudopotential but it seems that my results by blyp+vdw-df is better that
revpbe+vdw-df.

Can we use blyp pseudopotentials with vdw-df?

I really appreciate your help.

Zara,
Tern uni
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Re: [Pw_forum] cp.x output with cppp.x not showing correct atom type?

[Rolly Ng]

Hi all,

Found my careless mistakes, cppp.x demands atomic_number instead of 
atomic mass.

It works okay!

On 10/15/2016 02:28 PM, Rolly Ng wrote:
> Dear cp.x users,
>
> I have completed my first cp simulation with benzene and its output 
> with cppp.x to produce an axfs file.
>
> The geometry at ground state looks okay and the starting atomic 
> position was copied from a previous pw.x run with 'relax'.
>
> My question with the cp.x output is that the axfs file seems not 
> carrying the correct atomic type info? The carbon atom was 
> miss-identified as Mg?
>
> How can I correct my problem?
>
> Best,
> Rolly
>

-- 
PhD. Research Fellow,
Dept. of Physics & Materials Science,
City University of Hong Kong
Tel: +852 3442 4000
Fax: +852 3442 0538

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Re: [Pw_forum] wrong number of symmetries!

[Paolo Giannozzi]

(I was referring to symmetries of the lattice alone, not symmetries of the
crystal; if you are sure that the crystal has no symmetries, commenting out
the check should do the job)

Il 15/ott/2016 11:13 AM, "Paolo Giannozzi"  ha
scritto:

> In order to find symmetries, the code uses a threshold to decide if a
> rotated vector is the same as the original one. It may sometimes happen
> that some "quasi-symmetries" are recognized as symmetries, some are not,
> leading to a "symmetry group" that is not a group. This is likely what
> happened in your case.  Paolo
>
> Il 15/ott/2016 01:27 AM, "Li Mingkai"  ha scritto:
>
>> I tried to do the scf calculation on a perturbated cell. I used
>> "CELL_PARAMETERS alat" to specify vector. However, I got an error.
>>
>>  %%%
>> %%%
>>  Error in routine set_sym_bl (3):
>>  wrong number of symmetries! Use standard orientations for axis
>>  %%%
>> %%%
>>
>> Since the cell is perturbated, there is no symmetry on it and space group
>> should be P1. But it seemed that the pw.x tried to find some symmetry and
>> got wrong number of symmetries. I tried nosym, nosym_vec, no_inv. Nothing
>> works. I tried old version down to 5.0, which worked. After version 5.1,
>> the error emergied. Of course, I tried to use celldm(1)~(6). It works well
>> for all version. Since this input file is generated by a script
>> automatically. I don't tend to modify the script a lot and try to figure
>> out what happened before change everything.
>>
>> --
>> Mingkai Li
>> ===
>> School of Material Science and Engineering
>> Hubei University
>> Wuhan, Hubei Province
>> P. R. China
>> ===
>>
>> ___
>> Pw_forum mailing list
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>>
>
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Re: [Pw_forum] wrong number of symmetries!

[Paolo Giannozzi]

In order to find symmetries, the code uses a threshold to decide if a
rotated vector is the same as the original one. It may sometimes happen
that some "quasi-symmetries" are recognized as symmetries, some are not,
leading to a "symmetry group" that is not a group. This is likely what
happened in your case.  Paolo

Il 15/ott/2016 01:27 AM, "Li Mingkai"  ha scritto:

> I tried to do the scf calculation on a perturbated cell. I used
> "CELL_PARAMETERS alat" to specify vector. However, I got an error.
>
>  %%%
> %%%
>  Error in routine set_sym_bl (3):
>  wrong number of symmetries! Use standard orientations for axis
>  %%%
> %%%
>
> Since the cell is perturbated, there is no symmetry on it and space group
> should be P1. But it seemed that the pw.x tried to find some symmetry and
> got wrong number of symmetries. I tried nosym, nosym_vec, no_inv. Nothing
> works. I tried old version down to 5.0, which worked. After version 5.1,
> the error emergied. Of course, I tried to use celldm(1)~(6). It works well
> for all version. Since this input file is generated by a script
> automatically. I don't tend to modify the script a lot and try to figure
> out what happened before change everything.
>
> --
> Mingkai Li
> ===
> School of Material Science and Engineering
> Hubei University
> Wuhan, Hubei Province
> P. R. China
> ===
>
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[Pw_forum] vdw interaction and pseudopotentials

[Zara Nosh]

Dear all,
I would like to study the interaction between 2 organic molecules (contains
O, H, and C atoms).
As the first step I relax
​ed​
 the structure
​

​(​
using
​ dft-input= 'vdw-df' )
.

Using vdw-df we should use rev-pbe pseudopotential but
it seems that my results from blyp+vdw-df is better that revpbe+vdw-df.

Can we use blyp pseudopotentials with vdw-df?

I really appreciate your help.

Zara,
Tern uni
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Re: [Pw_forum] wrong number of symmetries!

[Amer Hamzaoui]

Dear Li MingkaiThe practical solution for your problem is to set verbosity = 
'high' in your control card, change ibrav to "1", ignore CELL_PARAMETERS card, 
then do your calculation.look at the head of your output file, then copy and 
paste the new  CELL_PARAMETERS and atomic positions for ibrav=0 and redo your 
calculation.

===Amer Hamzaoui hamzaouiamer@yahoo.frDepartement of 
physicsUFAS Algeria===
 

Le Samedi 15 octobre 2016 0h30, Li Mingkai  a écrit :
 

 Sorry. I forgot the input file.
Mingkai Li
On Sat, Oct 15, 2016 at 7:27 AM, Li Mingkai  wrote:

I tried to do the scf calculation on a perturbated cell. I used 
"CELL_PARAMETERS alat" to specify vector. However, I got an error.
 % %% 
%%%     Error in routine set_sym_bl (3):     wrong number of 
symmetries! Use standard orientations for axis % 
%% %%%
Since the cell is perturbated, there is no symmetry on it and space group 
should be P1. But it seemed that the pw.x tried to find some symmetry and got 
wrong number of symmetries. I tried nosym, nosym_vec, no_inv. Nothing works. I 
tried old version down to 5.0, which worked. After version 5.1, the error 
emergied. Of course, I tried to use celldm(1)~(6). It works well for all 
version. Since this input file is generated by a script automatically. I don't 
tend to modify the script a lot and try to figure out what happened before 
change everything. 
-- 
Mingkai Li
== =
School of Material Science and EngineeringHubei UniversityWuhan, Hubei 
ProvinceP. R. China
== =




-- 
Mingkai Li
===
Quantum-functional Semiconductor Research Center(QSRC)
Dongguk Univeristy, 3-26 Pil-dong, Joong-gu,
Seoul 100-715, Korea
Tel:(+82)-2-2260-3688
Fax:(+82)-2-2260-3945
===

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[Pw_forum] cp.x output with cppp.x not showing correct atom type?

[Rolly Ng]

Dear cp.x users,

I have completed my first cp simulation with benzene and its output with 
cppp.x to produce an axfs file.


The geometry at ground state looks okay and the starting atomic position 
was copied from a previous pw.x run with 'relax'.


My question with the cp.x output is that the axfs file seems not 
carrying the correct atomic type info? The carbon atom was 
miss-identified as Mg?


How can I correct my problem?

Best,
Rolly

--
PhD. Research Fellow,
Dept. of Physics & Materials Science,
City University of Hong Kong
Tel: +852 3442 4000
Fax: +852 3442 0538


  prefix = 'C6H6' ,
 fileout = '/home/MS70/rolly/cpmd/C6H6/C6H6_cp3' ,
  output = 'xsf' ,
  outdir = '/home/MS70/rolly/cpmd/C6H6/' ,
   ldynamics = .TRUE. ,
 nframes = 3000 ,
atomic_number(1) = 12.010700d0 , 
atomic_number(2) = 1.007940d0 ,
 ndr = 53 ,
/
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