Re: [Pw_forum] Xcrysden and crystal_sg ATOMIC_POSITION

[Daniel Reta]

Dear Tone,

Thank you very much for this.

Best



Dr. Daniel Reta,
Post-doctoral Research Associate,
Computational Chemistry, School of Chemistry
University of Manchester

Email: daniel.r...@manchester.ac.uk




From: pw_forum-boun...@pwscf.org [pw_forum-boun...@pwscf.org] on behalf of Tone 
Kokalj [tone.kok...@ijs.si]
Sent: 11 April 2017 09:59
To: pw_forum@pwscf.org
Subject: Re: [Pw_forum] Xcrysden and crystal_sg ATOMIC_POSITION

On Tue, 2017-04-11 at 08:37 +, Daniel Reta wrote:
> Hi,
>
> I have a crystal with two molecular units in the unit cell, but they
> are related by an inversion centre (triclinic). I am indicating the
> inequivalent atomic positions only, using the appropriate space_group
> and crystal_sg.

xcrysden currently does not understand "crystal_sg" specs of
coordinates from pw.x input (there are plans to implement this
feature). Hence, the way to proceed is to visualize the structure from
the output as you did.

Best regards, Tone
--
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
(tel: +386-1-477-3523 // fax: +386-1-251-9385)

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Xcrysden and crystal_sg ATOMIC_POSITION

[Tone Kokalj]

On Tue, 2017-04-11 at 08:37 +, Daniel Reta wrote:
> Hi,
> 
> I have a crystal with two molecular units in the unit cell, but they
> are related by an inversion centre (triclinic). I am indicating the
> inequivalent atomic positions only, using the appropriate space_group
> and crystal_sg. 

xcrysden currently does not understand "crystal_sg" specs of
coordinates from pw.x input (there are plans to implement this
feature). Hence, the way to proceed is to visualize the structure from
the output as you did.

Best regards, Tone
-- 
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax: +386-1-251-9385)

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Xcrysden and crystal_sg ATOMIC_POSITION

[Daniel Reta]

Hi,

I have a crystal with two molecular units in the unit cell, but they are 
related by an inversion centre (triclinic). I am indicating the inequivalent 
atomic positions only, using the appropriate space_group and crystal_sg. When I 
submit the job, the output contains the correct number of atoms in the 
translational cell (double the ones indicated in the input) The problem is that 
when I open the input file with xcrysden, only one of the molecule appears. Am 
I doing something wrong or it is a Xcrysden issue? 

The input looks like
 
prefix='adpm416',
pseudo_dir='CurDir',
outdir='Scratch',
calculation='scf'
 /
 
ibrav=14,
celldm(1)=22.12623628,
celldm(2)=1.067214977,
celldm(3)=1.711616149,
celldm(4)=-0.120708606,
celldm(5)=-0.00120427689,
celldm(6)=-0.180913961,
nat=138, 
ntyp=5,
ecutwfc=40.0,
vdw_corr='Grimme-D2',
space_group=2
 /
 
conv_thr=1.D-7
 /
ATOMIC_SPECIES
 Y 88.90585 Y.pbe-sp-hgh.UPF 
 F 18.9984 F.pbe-hgh.UPF
 C 12.011 C.pbe-hgh.UPF
 B 10.81 B.pbe-hgh.UPF
 H 1.008 H.pbe-hgh.UPF
ATOMIC_POSITIONS crystal_sg
 Y 0.878770.31670   0.71532 
 C 0.6920 0.39090.7461  
   **
K_POINTS automatic
 4 4 2 1 1 1

Thank you very much in advance.

Best



Dr. Daniel Reta,
Post-doctoral Research Associate,
Computational Chemistry, School of Chemistry
University of Manchester

Email: daniel.r...@manchester.ac.uk



___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Xcrysden

[Uttam Paliwal]

MANY MANY THANKS
NOW IT IS WORKING



On Fri, Nov 18, 2016 at 12:37 PM, Uttam Paliwal  wrote:

> the error message is
>
> couldn't execute "xcrysden": no such file or directory
> couldn't execute "xcrysden": no such file or directory
> while executing
> "exec xcrysden --pwi $tmpFile &"
> (procedure "::pwscf::view::structByXcrysden" line 71)
> invoked from within
> "::pwscf::view::structByXcrysden ::gUI0"
> invoked from within
> ".gui0.shellchildsite.menubar.menubar.view.menu invoke active"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke active]"
> (procedure "tk::MenuInvoke" line 50)
> invoked from within
> "tk::MenuInvoke .gui0.shellchildsite.menubar.menubar.view.menu 1"
> (command bound to event)
>
>
> KINDLY HELP
>
> On Thu, Nov 17, 2016 at 5:21 PM, Tone Kokalj  wrote:
>
>> On Thu, 2016-11-17 at 15:47 +0530, Uttam Paliwal wrote:
>> > Kindly forget previous mail
>> > Now it is active but when i click
>> > " structure with xcrysden" then following error message displayed
>> > Exec couldn't find xcrysden : no such file or directory
>>
>> According to this error it seems that you do not have xcrysden on the
>> PATH and in addition that you have XCRYSDEN_TOPDIR variable defined,
>> but pointing to a wrong directory (perhaps to an old no-more-existing
>> version of xcrysden). Try this:
>>
>> unset XCRYSDEN_TOPDIR
>> pwgui
>>
>>
>> Is now the "View-->Structure with XCrySDen" menu active? If not then
>> the above is very likely the problem.
>>
>> Best regards, Tone
>> --
>> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
>> (tel: +386-1-477-3523 // fax: +386-1-251-9385)
>>
>> > Please help
>> >
>> > On Nov 17, 2016 12:44 PM, "Uttam Paliwal"  wrote:
>> > > sorry it didn't work
>> > >
>> > > On Wed, Nov 16, 2016 at 5:35 PM, Matic Poberznik > > > mail.com> wrote:
>> > > > I'm sorry I made a slight error in the previous email, the path
>> > > > should
>> > > > point to the xcrysden shell script (which is used to run
>> > > > xcrysden).
>> > > > Simply add the directory where the ./xcrysden command works to
>> > > > the $PATH
>> > > > variable and it should work.
>> > > >
>> > > > Best regards,
>> > > >
>> > > > Matic
>> > > > --
>> > > > Matic Poberznik
>> > > > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
>> > > >
>> > > > > I' assuming you have to be in the xcrysden binary directory for
>> > > > that to
>> > > > > work;
>> > > > >
>> > > > > so if you have not done so already I suggest you add the path
>> > > > to
>> > > > > xcrysden installation folder where you have to add xcrysden to
>> > > > the $PATH
>> > > > > variable in .bashrc. This file is located in your home
>> > > > directory, open
>> > > > > it with an editor and add the line:
>> > > > >
>> > > > > export PATH=/path/to/xcrysden/bin/:$PATH
>> > > > >
>> > > > > Where /path/to/xcrysden/bin/ is the full path to the folder
>> > > > where you
>> > > > > have the xcrysden binary. When you finish editing type
>> > > > >
>> > > > > source ~/.bashrc
>> > > > >
>> > > > > in the terminal to implement the changes. If it works you
>> > > > should be able
>> > > > > to run xcrysden by simply typing:
>> > > > >
>> > > > > xcrysden
>> > > > >
>> > > > > in any directory and PWgui should be able to find it.
>> > > > > I hope this helps,
>> > > > >
>> > > > > Best regards,
>> > > > >
>> > > > > Matic
>> > > > >
>> > > >
>> > > >
>> > > >
>> > > > ___
>> > > > Pw_forum mailing list
>> > > > Pw_forum@pwscf.org
>> > > > http://pwscf.org/mailman/listinfo/pw_forum
>> > > >
>> > >
>> > >
>> > >
>> > > ___
>> > > Pw_forum mailing list
>> > > Pw_forum@pwscf.org
>> > > http://pwscf.org/mailman/listinfo/pw_forum
>> > >
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
>
> --
> Uttam Paliwal
> *Assistant Professor*
> Department of Physics
> J.N.V. University
> Jodhpur (India)
> Phone- 7597908441
>



-- 
Uttam Paliwal
*Assistant Professor*
Department of Physics
J.N.V. University
Jodhpur (India)
Phone- 7597908441
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Xcrysden

[Uttam Paliwal]

the error message is

couldn't execute "xcrysden": no such file or directory
couldn't execute "xcrysden": no such file or directory
while executing
"exec xcrysden --pwi $tmpFile &"
(procedure "::pwscf::view::structByXcrysden" line 71)
invoked from within
"::pwscf::view::structByXcrysden ::gUI0"
invoked from within
".gui0.shellchildsite.menubar.menubar.view.menu invoke active"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke active]"
(procedure "tk::MenuInvoke" line 50)
invoked from within
"tk::MenuInvoke .gui0.shellchildsite.menubar.menubar.view.menu 1"
(command bound to event)


KINDLY HELP

On Thu, Nov 17, 2016 at 5:21 PM, Tone Kokalj  wrote:

> On Thu, 2016-11-17 at 15:47 +0530, Uttam Paliwal wrote:
> > Kindly forget previous mail
> > Now it is active but when i click
> > " structure with xcrysden" then following error message displayed
> > Exec couldn't find xcrysden : no such file or directory
>
> According to this error it seems that you do not have xcrysden on the
> PATH and in addition that you have XCRYSDEN_TOPDIR variable defined,
> but pointing to a wrong directory (perhaps to an old no-more-existing
> version of xcrysden). Try this:
>
> unset XCRYSDEN_TOPDIR
> pwgui
>
>
> Is now the "View-->Structure with XCrySDen" menu active? If not then
> the above is very likely the problem.
>
> Best regards, Tone
> --
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
> (tel: +386-1-477-3523 // fax: +386-1-251-9385)
>
> > Please help
> >
> > On Nov 17, 2016 12:44 PM, "Uttam Paliwal"  wrote:
> > > sorry it didn't work
> > >
> > > On Wed, Nov 16, 2016 at 5:35 PM, Matic Poberznik  > > mail.com> wrote:
> > > > I'm sorry I made a slight error in the previous email, the path
> > > > should
> > > > point to the xcrysden shell script (which is used to run
> > > > xcrysden).
> > > > Simply add the directory where the ./xcrysden command works to
> > > > the $PATH
> > > > variable and it should work.
> > > >
> > > > Best regards,
> > > >
> > > > Matic
> > > > --
> > > > Matic Poberznik
> > > > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
> > > >
> > > > > I' assuming you have to be in the xcrysden binary directory for
> > > > that to
> > > > > work;
> > > > >
> > > > > so if you have not done so already I suggest you add the path
> > > > to
> > > > > xcrysden installation folder where you have to add xcrysden to
> > > > the $PATH
> > > > > variable in .bashrc. This file is located in your home
> > > > directory, open
> > > > > it with an editor and add the line:
> > > > >
> > > > > export PATH=/path/to/xcrysden/bin/:$PATH
> > > > >
> > > > > Where /path/to/xcrysden/bin/ is the full path to the folder
> > > > where you
> > > > > have the xcrysden binary. When you finish editing type
> > > > >
> > > > > source ~/.bashrc
> > > > >
> > > > > in the terminal to implement the changes. If it works you
> > > > should be able
> > > > > to run xcrysden by simply typing:
> > > > >
> > > > > xcrysden
> > > > >
> > > > > in any directory and PWgui should be able to find it.
> > > > > I hope this helps,
> > > > >
> > > > > Best regards,
> > > > >
> > > > > Matic
> > > > >
> > > >
> > > >
> > > >
> > > > ___
> > > > Pw_forum mailing list
> > > > Pw_forum@pwscf.org
> > > > http://pwscf.org/mailman/listinfo/pw_forum
> > > >
> > >
> > >
> > >
> > > ___
> > > Pw_forum mailing list
> > > Pw_forum@pwscf.org
> > > http://pwscf.org/mailman/listinfo/pw_forum
> > >
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
Uttam Paliwal
*Assistant Professor*
Department of Physics
J.N.V. University
Jodhpur (India)
Phone- 7597908441
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Xcrysden

[Tone Kokalj]

On Thu, 2016-11-17 at 15:47 +0530, Uttam Paliwal wrote:
> Kindly forget previous mail
> Now it is active but when i click
> " structure with xcrysden" then following error message displayed
> Exec couldn't find xcrysden : no such file or directory

According to this error it seems that you do not have xcrysden on the
PATH and in addition that you have XCRYSDEN_TOPDIR variable defined,
but pointing to a wrong directory (perhaps to an old no-more-existing
version of xcrysden). Try this:

unset XCRYSDEN_TOPDIR
pwgui


Is now the "View-->Structure with XCrySDen" menu active? If not then
the above is very likely the problem.

Best regards, Tone
-- 
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax: +386-1-251-9385)

> Please help
> 
> On Nov 17, 2016 12:44 PM, "Uttam Paliwal"  wrote:
> > sorry it didn't work
> > 
> > On Wed, Nov 16, 2016 at 5:35 PM, Matic Poberznik  > mail.com> wrote:
> > > I'm sorry I made a slight error in the previous email, the path
> > > should
> > > point to the xcrysden shell script (which is used to run
> > > xcrysden).
> > > Simply add the directory where the ./xcrysden command works to
> > > the $PATH
> > > variable and it should work.
> > > 
> > > Best regards,
> > > 
> > > Matic
> > > --
> > > Matic Poberznik
> > > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
> > > 
> > > > I' assuming you have to be in the xcrysden binary directory for
> > > that to
> > > > work;
> > > >
> > > > so if you have not done so already I suggest you add the path
> > > to
> > > > xcrysden installation folder where you have to add xcrysden to
> > > the $PATH
> > > > variable in .bashrc. This file is located in your home
> > > directory, open
> > > > it with an editor and add the line:
> > > >
> > > > export PATH=/path/to/xcrysden/bin/:$PATH
> > > >
> > > > Where /path/to/xcrysden/bin/ is the full path to the folder
> > > where you
> > > > have the xcrysden binary. When you finish editing type
> > > >
> > > > source ~/.bashrc
> > > >
> > > > in the terminal to implement the changes. If it works you
> > > should be able
> > > > to run xcrysden by simply typing:
> > > >
> > > > xcrysden
> > > >
> > > > in any directory and PWgui should be able to find it.
> > > > I hope this helps,
> > > >
> > > > Best regards,
> > > >
> > > > Matic
> > > >
> > > 
> > > 
> > > 
> > > ___
> > > Pw_forum mailing list
> > > Pw_forum@pwscf.org
> > > http://pwscf.org/mailman/listinfo/pw_forum
> > > 
> > 
> > 
> > 
> > ___
> > Pw_forum mailing list
> > Pw_forum@pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
> > 
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Xcrysden

[Tone Kokalj]

On Thu, 2016-11-17 at 12:11 +0100, Matic Poberžnik wrote:
> Can you send me the output from those commands? Please make sure that
> you download the source package of PWgui5.1.1:
> 
> http://www-k3.ijs.si/kokalj/pwgui/download.html

PWgui version is irrelevant; PWgui-6.0 should be just fine: the problem
is elsewhere.

Best regards, Tone
-- 
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax: +386-1-251-9385)
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Xcrysden

[Matic Poberžnik]

I'm sorry, I don't know but it works for me. I have the $PATH variable
configured like this (line from .bashrc file):

export PATH=/home/matic/xcrysden-1.5.60/:/home/matic/src/PWgui-5.1.1/:$PATH

i.e. only the top directories are needed. Can you paste the output of the
command:

echo $PATH

Also a simple test is to try running xcrysden from terminal by typing:

xcrysden

Can you send me the output from those commands? Please make sure that you
download the source package of PWgui5.1.1:

http://www-k3.ijs.si/kokalj/pwgui/download.html

Best Regards,

Matic








2016-11-17 11:17 GMT+01:00 Uttam Paliwal :

> Kindly forget previous mail
>
> Now it is active but when i click
> " structure with xcrysden" then following error message displayed
> Exec couldn't find xcrysden : no such file or directory
>
> Please help
>
> On Nov 17, 2016 12:44 PM, "Uttam Paliwal"  wrote:
>
>> sorry it didn't work
>>
>> On Wed, Nov 16, 2016 at 5:35 PM, Matic Poberznik <
>> matic.poberz...@gmail.com> wrote:
>>
>>> I'm sorry I made a slight error in the previous email, the path should
>>> point to the xcrysden shell script (which is used to run xcrysden).
>>> Simply add the directory where the ./xcrysden command works to the $PATH
>>> variable and it should work.
>>>
>>> Best regards,
>>>
>>> Matic
>>> --
>>> Matic Poberznik
>>> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
>>>
>>> > I' assuming you have to be in the xcrysden binary directory for that to
>>> > work;
>>> >
>>> > so if you have not done so already I suggest you add the path to
>>> > xcrysden installation folder where you have to add xcrysden to the
>>> $PATH
>>> > variable in .bashrc. This file is located in your home directory, open
>>> > it with an editor and add the line:
>>> >
>>> > export PATH=/path/to/xcrysden/bin/:$PATH
>>> >
>>> > Where /path/to/xcrysden/bin/ is the full path to the folder where you
>>> > have the xcrysden binary. When you finish editing type
>>> >
>>> > source ~/.bashrc
>>> >
>>> > in the terminal to implement the changes. If it works you should be
>>> able
>>> > to run xcrysden by simply typing:
>>> >
>>> > xcrysden
>>> >
>>> > in any directory and PWgui should be able to find it.
>>> > I hope this helps,
>>> >
>>> > Best regards,
>>> >
>>> > Matic
>>> >
>>>
>>>
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum@pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
>>
>> --
>> Uttam Paliwal
>> *Assistant Professor*
>> Department of Physics
>> J.N.V. University
>> Jodhpur (India)
>> Phone- 7597908441
>>
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Xcrysden

[Uttam Paliwal]

Kindly forget previous mail

Now it is active but when i click
" structure with xcrysden" then following error message displayed
Exec couldn't find xcrysden : no such file or directory

Please help

On Nov 17, 2016 12:44 PM, "Uttam Paliwal"  wrote:

> sorry it didn't work
>
> On Wed, Nov 16, 2016 at 5:35 PM, Matic Poberznik <
> matic.poberz...@gmail.com> wrote:
>
>> I'm sorry I made a slight error in the previous email, the path should
>> point to the xcrysden shell script (which is used to run xcrysden).
>> Simply add the directory where the ./xcrysden command works to the $PATH
>> variable and it should work.
>>
>> Best regards,
>>
>> Matic
>> --
>> Matic Poberznik
>> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
>>
>> > I' assuming you have to be in the xcrysden binary directory for that to
>> > work;
>> >
>> > so if you have not done so already I suggest you add the path to
>> > xcrysden installation folder where you have to add xcrysden to the $PATH
>> > variable in .bashrc. This file is located in your home directory, open
>> > it with an editor and add the line:
>> >
>> > export PATH=/path/to/xcrysden/bin/:$PATH
>> >
>> > Where /path/to/xcrysden/bin/ is the full path to the folder where you
>> > have the xcrysden binary. When you finish editing type
>> >
>> > source ~/.bashrc
>> >
>> > in the terminal to implement the changes. If it works you should be able
>> > to run xcrysden by simply typing:
>> >
>> > xcrysden
>> >
>> > in any directory and PWgui should be able to find it.
>> > I hope this helps,
>> >
>> > Best regards,
>> >
>> > Matic
>> >
>>
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
>
> --
> Uttam Paliwal
> *Assistant Professor*
> Department of Physics
> J.N.V. University
> Jodhpur (India)
> Phone- 7597908441
>
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Xcrysden

[Uttam Paliwal]

sorry it didn't work

On Wed, Nov 16, 2016 at 5:35 PM, Matic Poberznik 
wrote:

> I'm sorry I made a slight error in the previous email, the path should
> point to the xcrysden shell script (which is used to run xcrysden).
> Simply add the directory where the ./xcrysden command works to the $PATH
> variable and it should work.
>
> Best regards,
>
> Matic
> --
> Matic Poberznik
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
>
> > I' assuming you have to be in the xcrysden binary directory for that to
> > work;
> >
> > so if you have not done so already I suggest you add the path to
> > xcrysden installation folder where you have to add xcrysden to the $PATH
> > variable in .bashrc. This file is located in your home directory, open
> > it with an editor and add the line:
> >
> > export PATH=/path/to/xcrysden/bin/:$PATH
> >
> > Where /path/to/xcrysden/bin/ is the full path to the folder where you
> > have the xcrysden binary. When you finish editing type
> >
> > source ~/.bashrc
> >
> > in the terminal to implement the changes. If it works you should be able
> > to run xcrysden by simply typing:
> >
> > xcrysden
> >
> > in any directory and PWgui should be able to find it.
> > I hope this helps,
> >
> > Best regards,
> >
> > Matic
> >
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
Uttam Paliwal
*Assistant Professor*
Department of Physics
J.N.V. University
Jodhpur (India)
Phone- 7597908441
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Xcrysden

[Matic Poberznik]

I'm sorry I made a slight error in the previous email, the path should
point to the xcrysden shell script (which is used to run xcrysden).
Simply add the directory where the ./xcrysden command works to the $PATH
variable and it should work.

Best regards,

Matic
-- 
Matic Poberznik
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia

> I' assuming you have to be in the xcrysden binary directory for that to
> work;
> 
> so if you have not done so already I suggest you add the path to
> xcrysden installation folder where you have to add xcrysden to the $PATH
> variable in .bashrc. This file is located in your home directory, open
> it with an editor and add the line:
> 
> export PATH=/path/to/xcrysden/bin/:$PATH
> 
> Where /path/to/xcrysden/bin/ is the full path to the folder where you
> have the xcrysden binary. When you finish editing type
> 
> source ~/.bashrc
> 
> in the terminal to implement the changes. If it works you should be able
> to run xcrysden by simply typing:
> 
> xcrysden
> 
> in any directory and PWgui should be able to find it.
> I hope this helps,
> 
> Best regards,
> 
> Matic
> 



___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Xcrysden

[Matic Poberznik]

> Yes it is running by terminal using
> ./xcrysden commond.
n/listinfo/pw_forum

I' assuming you have to be in the xcrysden binary directory for that to
work;

so if you have not done so already I suggest you add the path to
xcrysden installation folder where you have to add xcrysden to the $PATH
variable in .bashrc. This file is located in your home directory, open
it with an editor and add the line:

export PATH=/path/to/xcrysden/bin/:$PATH

Where /path/to/xcrysden/bin/ is the full path to the folder where you
have the xcrysden binary. When you finish editing type

source ~/.bashrc

in the terminal to implement the changes. If it works you should be able
to run xcrysden by simply typing:

xcrysden

in any directory and PWgui should be able to find it.
I hope this helps,

Best regards,

Matic
-- 
Matic Poberznik
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Xcrysden

[Uttam Paliwal]

Yes it is running by terminal using
./xcrysden commond.

On Nov 16, 2016 3:39 PM, "Matic Poberznik" 
wrote:

> Dear Uttam,
>
> > Hi
> > I have installed espresso 6.0 on cygwin (windows8.1). PWGUI6.0 is
> > working fine but not unable to  launch xcrysden through pwgui. This
> > option is inactive i.e. faded.
> > Kindly help
>
> Are you sure you have xcrysden installed and it works when you try to
> run it from the terminal?
>
> Best regards,
>
> Matic
> --
> Matic Poberznik
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Xcrysden

[Matic Poberznik]

Dear Uttam,

> Hi
> I have installed espresso 6.0 on cygwin (windows8.1). PWGUI6.0 is
> working fine but not unable to  launch xcrysden through pwgui. This
> option is inactive i.e. faded.
> Kindly help

Are you sure you have xcrysden installed and it works when you try to
run it from the terminal?

Best regards,

Matic
-- 
Matic Poberznik
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Xcrysden

[Uttam Paliwal]

Hi
I have installed espresso 6.0 on cygwin (windows8.1). PWGUI6.0 is working
fine but not unable to  launch xcrysden through pwgui. This option is
inactive i.e. faded.
Kindly help
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] xcrysden site

[pmoreira]

 Thank you very much everybody.

 I had tried www.xcrysden.org, but the server was down.

 Pedro Moreira

 Assistent professor
 UFSCar, Brazil

> try www.xcrysden.org
>
> N. A. W. Holzwarth   email:
> nata...@wfu.edu
> Department of Physics  web:
> http://www.wfu.edu/~natalie
> Wake Forest University phone:
> 1-336-758-5510
> Winston-Salem, NC 27109 USA office: Rm. 300 Olin
> Physical Lab
>
> On Tue, May 3, 2016 at 1:05 PM,  wrote:
>
>>  Dear PW users.
>>
>>  Sorry for the question is not related to QE. But I imagine the most of
>> you are xcrysden users.
>>
>>  I am trying to connect to the xcrysden.org, but it is down. Does anyone
>> konw any problem with the site? And, is there any alternative to get
>> xcrysden?
>>
>>  Thank you
>>
>>  Pedro Moreira
>>
>>  Assistent professor
>>  UFSCar, Brazil
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] xcrysden site

[Holzwarth, Natalie]

try www.xcrysden.org

N. A. W. Holzwarth   email:
nata...@wfu.edu
Department of Physics  web:
http://www.wfu.edu/~natalie
Wake Forest University phone:
1-336-758-5510
Winston-Salem, NC 27109 USA office: Rm. 300 Olin
Physical Lab

On Tue, May 3, 2016 at 1:05 PM,  wrote:

>  Dear PW users.
>
>  Sorry for the question is not related to QE. But I imagine the most of
> you are xcrysden users.
>
>  I am trying to connect to the xcrysden.org, but it is down. Does anyone
> konw any problem with the site? And, is there any alternative to get
> xcrysden?
>
>  Thank you
>
>  Pedro Moreira
>
>  Assistent professor
>  UFSCar, Brazil
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] xcrysden site

[Tone Kokalj]

On Tue, 2016-05-03 at 14:05 -0300, pmore...@ifi.unicamp.br wrote:
>  Dear PW users.
> 
>  Sorry for the question is not related to QE. But I imagine the most
> of
> you are xcrysden users.
> 
>  I am trying to connect to the xcrysden.org, but it is down. Does
> anyone
> konw any problem with the site? And, is there any alternative to get
> xcrysden?

The server was down. It is back on now. Let me know if you can access
it.

Thanks, Tone
-- 
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax: +386-1-251-9385)

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] xcrysden site

[pmoreira]

 Dear PW users.

 Sorry for the question is not related to QE. But I imagine the most of
you are xcrysden users.

 I am trying to connect to the xcrysden.org, but it is down. Does anyone
konw any problem with the site? And, is there any alternative to get
xcrysden?

 Thank you

 Pedro Moreira

 Assistent professor
 UFSCar, Brazil

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] XCRYSDEN Primitive cell: Reg

[Tone Kokalj]

On Tue, 2016-01-19 at 13:48 +0530, Suresh A wrote:
> Dear All,
>     Herewith I have included two primitive cell input filefor anatase 
> strucutre. Between them XCRYSDEN shows correct structure for file one where 
> atomic positions are in angstrom unit and for another structure it shows 
> wrong strucutre where atomic positions are  in relative crystal coordinate. 
> Will you please point out where the problem is? And I am using 
> xcrysden-1.5.60-semishared linux 


Typically such problems stem from the following reason: the user and
the program have a different idea of the unit-cell. In particular,
there are two flavors of these problems:

(i) the crystallographic vectors are chosen differently between the
user and the program (in such cases specified Cartesian coordinates do
not give correct structure)

(ii) the crystallographic coordinates refers to different set of
vectors, e.g, primitive vs. conventional (in such cases the specified
crystal coordinates do not give the correct structure)

In your case it is the second problem. You have specified the crystal
coordinates with respect to conventional vectors, but the pw.x expects
the coordinates wrt primitive vectors (and consequently also xcrysden
interprets the QE input this way).

--
Excerpt from the pw.x documentation:
--
crystal : atomic positions are in crystal coordinates, i.e.
  in relative coordinates of the primitive lattice
  vectors as defined either in card CELL_PARAMETERS
  or via the ibrav + celldm / a,b,c... variables



Best regards, Tone

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html


___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] XCRYSDEN Primitive cell: Reg

[Suresh A]

Dear All,
Herewith I have included two primitive cell input file for
anatase strucutre. Between them XCRYSDEN shows correct structure for file
one where atomic positions are in angstrom unit and for another structure
it shows wrong strucutre where atomic positions are  in relative crystal
coordinate. Will you please point out where the problem is? And I am using
xcrysden-1.5.60-semishared linux version.

input file1:

 
  title = 'TiO2' ,
calculation = 'scf',
 outdir ='$TMP_DIR/'
 prefix = 'anatase',
 pseudo_dir = '$PSEUDO_DIR/',
 /

 
  ibrav = 7,
  celldm(1) = 7.1356,
  celldm(3) = 2.51218,
nat = 6 ,
   ntyp = 2 ,
ecutwfc = 30.00 ,
ecutrho = 300,


 /

 

   conv_thr = 1.0d-09,

 /
ATOMIC_SPECIES
 O  15.999  O.pw91-van_ak.UPF
 Ti 47.867  Ti.pw91-nsp-van.UPF
 ATOMIC_POSITIONS angstrom
 Ti   0.0   0.0   0.0
 Ti   0.0   1.88800   2.37150
 O0.0   0.0  -1.983097630
 O0.0   0.0   1.983097630
 O0.0   1.88800   0.387796645
 O0.0   1.88800   4.355203355
 K_POINTS   automatic
 4 4 4  0 0 0

INPUTFILE 2

 
   title = 'anatase' ,
 calculation = 'scf' ,
restart_mode = 'from_scratch' ,
  pseudo_dir = '/home/suresh/GN2/',
  outdir ='/home/suresh/Desktop/primitivecell/tmp/',
  prefix = 'anatase' ,
 tstress = .true. ,
 tprnfor = .true. ,



 /
 
   ibrav = 7,
   celldm(1) = 7.153,
   celldm(3) = 2.513,
 nat = 6,
ntyp = 2,
 ecutwfc = 60 ,
exxdiv_treatment = 'none' ,



 /
 


 /
 


 /
 



 /
ATOMIC_SPECIES
   Ti   47.86700  Ti.pz-mt_fhi.UPF
O   15.99940  O.pz-mt_fhi.UPF
ATOMIC_POSITIONS (crystal)
Ti  0.000   0.000   0.000
Ti  0.000   0.500   0.250
O   0.000   0.000   0.208
O   0.000   0.000  -0.208000
O   0.000   0.500   0.458
O   0.000   0.500  -0.042000
K_POINTS automatic
4 4 2 1 1 1


  With Regards,
A.Suresh,
Research Scholar,
Madurai Kamaraj University,
Madurai.
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] xcrysden problem

[Giovanni Cantele]

if you read the error message, you can easily figure out that xcrysden is 
looking for an input file named “pwi” instead of
si.scf.in.

Indeed, if you look to the terminal line you included in your message, you 
specified “— pwi” instead of “—pwi”, so the blank
space left after “—“ let xcrysden think that the first argument, pwi, is the 
file to look for!

Giovanni


> On 19 Feb 2015, at 11:36, TIMOTHY UTO  wrote:
> 
> 
> please i was trying to visualize my structures from both the input and out 
> file by using 
> xcrysden --pwi si.scf.in
> it gave me this message
> 
> ERROR: file "/home /timuto/espresso-5.1.1/my examples/espresso 
> v5/silicon/pwi." does not exits !!!
> 
> it then displaced this on the terminal 
> 
> [timuto@localhost silicon]$ xcrysden -- pwi si.scf.in
> 
> ++
> ||
> |*  *|
> |*  XCrySDen - (X-Window) CRYstalline Structures and DENsities  *|
> |*  = === =  ===*|
> |*--*|
> |*  *|
> |*Anton Kokalj (tone.kok...@ijs.si) *|
> |*Jozef Stefan Institute, Ljubljana, Slovenia   *|
> |*  *|
> |*Copyright (c) 1996--2004 by Anton Kokalj  *|
> |*  *|
> ||
> ++
> 
>  Version: 1.5.17
> 
>  Please report bugs to: tone.kok...@ijs.si
> 
> 
>  TERMS OF USE:
>  -
>  XCRYSDEN is released under the GNU General Public License.
> 
>  Whenever graphics generated by XCRYSDEN are used in scientific
>  publications, it shall be greatly appreciated to include an explicit
>  reference. The preferred form is the following:
> 
>  [ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003.
>Code available from http://www.xcrysden.org/.
> 
> TCL_LIBRARY=/usr/local/XCrySDen/external/lib/tcl8.5
> XCRYSDEN_TOPDIR=/usr/local/XCrySDen
> XCRYSDEN_SCRATCH=/tmp
> 
> Running on platform: unix
> Executing: /usr/local/XCrySDen/bin/ftnunit
> /usr/local/XCrySDen/xcrysden: line 252: test: too many arguments
> 
> Uto Timothy
> UI
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
> 

-- 

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cant...@spin.cnr.it
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele



___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] xcrysden problem

[Tone Kokalj]

On Thu, 2015-02-19 at 02:36 -0800, TIMOTHY UTO wrote:
> please i was trying to visualize my structures from both the input and out 
> file by using 
> xcrysden --pwi si.scf.in
> it gave me this message
> 
> ERROR: file "/home /timuto/espresso-5.1.1/my examples/espresso 
> v5/silicon/pwi." does not exits !!!
> 
> it then displaced this on the terminal 
> 
> [timuto@localhost silicon]$ xcrysden -- pwi si.scf.in

Correct to:

xcrysden --pwi si.scf.in

Regards, Tone

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] xcrysden problem

[TIMOTHY UTO]

please i was trying to visualize my structures from both the input and out file 
by using 
xcrysden --pwi si.scf.in
it gave me this message

ERROR: file "/home /timuto/espresso-5.1.1/my examples/espresso v5/silicon/pwi." 
does not exits !!!

it then displaced this on the terminal 

[timuto@localhost silicon]$ xcrysden -- pwi si.scf.in

++
||
|*  *|
|*  XCrySDen - (X-Window) CRYstalline Structures and DENsities  *|
|*  = === =  ===*|
|*--*|
|*  *|
|*Anton Kokalj (tone.kok...@ijs.si) *|
|*Jozef Stefan Institute, Ljubljana, Slovenia   *|
|*  *|
|*Copyright (c) 1996--2004 by Anton Kokalj  *|
|*  *|
||
++

  Version: 1.5.17

  Please report bugs to: tone.kok...@ijs.si


  TERMS OF USE:
  -
  XCRYSDEN is released under the GNU General Public License.

  Whenever graphics generated by XCRYSDEN are used in scientific
  publications, it shall be greatly appreciated to include an explicit
  reference. The preferred form is the following:

  [ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003.
Code available from http://www.xcrysden.org/.

TCL_LIBRARY=/usr/local/XCrySDen/external/lib/tcl8.5
XCRYSDEN_TOPDIR=/usr/local/XCrySDen
XCRYSDEN_SCRATCH=/tmp

Running on platform: unix
Executing: /usr/local/XCrySDen/bin/ftnunit
/usr/local/XCrySDen/xcrysden: line 252: test: too many arguments

Uto Timothy
UI
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] xcrysden shows only primitive structure for output of QE

[Michael Mehl]

You might try findsym: http://stokes.byu.edu/iso/findsym.php , where you 
enter the primitive vectors and lattice coordinates, and the program 
gives you the space group, conventional cell, and Wyckoff positions. For 
Linux there is also downloadable command line version: 
http://stokes.byu.edu/iso/isolinux.php


On 11/28/14 9:11 AM, James Lee wrote:

Dear Tone, and developers of QE:

Thanks for the reply.
however, it will be interesting that the next versions of QE provide the 
conventional
cell output in conjunction with the primitive one.
In some cases (for example vc-relax command ) it is possible that the optimized 
primitive cell changes drastically.
For some users (such as me) transforming non-standard primitives to 
conventional is a hard job.



--
Michael J. Mehl
Head, Center for Materials Physics & Technology
Naval Research Laboratory Code 6390
Washington DC



smime.p7s
Description: S/MIME Cryptographic Signature
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] xcrysden shows only primitive structure for output of QE

[James Lee]

Dear Tone, and developers of QE:

Thanks for the reply. 
however, it will be interesting that the next versions of QE provide the 
conventional 
cell output in conjunction with the primitive one.
In some cases (for example vc-relax command ) it is possible that the optimized 
primitive cell changes drastically.
For some users (such as me) transforming non-standard primitives to 
conventional is a hard job.


> -Original Message-
> From: tone.kok...@ijs.si
> Sent: Thu, 27 Nov 2014 09:37:20 +0100
> To: pw_forum@pwscf.org
> Subject: Re: [Pw_forum] xcrysden shows only primitive structure for
> output of QE
> 
> On Sat, 2014-11-22 at 20:40 -0800, James Lee wrote:
>> Hi
>> When I use ibrav=0 and conventional cell coordinates, xcrysden shows
>> conventional cell for vc-relax
>> output, and everything is ok.
> 
> When ibrav=0, xcrysden shows the lattice as specified by
> CELL_PARAMETERS ...
> 
>> when I use ibrav=2, xcrysden can show both primitive and conventional
>> cell
>> for input file, but for its vc-relax output, xcrysden only shows
>> optimized primitive cell.
> 
> This is correct. For output, xcrysden relies only on the data stored in
> the output file. Because only the primitive vectors are printed in the
> output, xcrysden shows only primitive lattice.
> 
> If you want to see also the conventional lattice then transform pw.x
> output file to XSF file (using pwo2xsf.sh filter) and then supplement
> the XSF file with the corresponding convetional vectors, specified by
> the CONVVEC card (see: http://www.xcrysden.org/doc/XSF.html#__toc__4 )
> 
> Regards, Tone
> 
> --
> Anton Kokalj
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
> (tel: +386-1-477-3523 // fax:+386-1-477-3822)
> 
> Please, if possible, avoid sending me Word or PowerPoint attachments.
> See:  http://www.gnu.org/philosophy/no-word-attachments.html
> 
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum


FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
Check it out at http://www.inbox.com/earth



___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] xcrysden shows only primitive structure for output of QE

[Tone Kokalj]

On Sat, 2014-11-22 at 20:40 -0800, James Lee wrote:
> Hi 
> When I use ibrav=0 and conventional cell coordinates, xcrysden shows 
> conventional cell for vc-relax
> output, and everything is ok.

When ibrav=0, xcrysden shows the lattice as specified by
CELL_PARAMETERS ...

> when I use ibrav=2, xcrysden can show both primitive and conventional cell
> for input file, but for its vc-relax output, xcrysden only shows optimized 
> primitive cell. 

This is correct. For output, xcrysden relies only on the data stored in
the output file. Because only the primitive vectors are printed in the
output, xcrysden shows only primitive lattice.

If you want to see also the conventional lattice then transform pw.x
output file to XSF file (using pwo2xsf.sh filter) and then supplement
the XSF file with the corresponding convetional vectors, specified by
the CONVVEC card (see: http://www.xcrysden.org/doc/XSF.html#__toc__4 )

Regards, Tone

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html

___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] xcrysden shows only primitive structure for output of QE

[James Lee]

Hi 
When I use ibrav=0 and conventional cell coordinates, xcrysden shows 
conventional cell for vc-relax
output, and everything is ok.
when I use ibrav=2, xcrysden can show both primitive and conventional cell
for input file, but for its vc-relax output, xcrysden only shows optimized 
primitive cell. 
I need the optimized structure in conventional form.
I use QE5.1.1, and Xcrysden 1.5.60.

Regards
James


Can't remember your password? Do you need a strong and secure password?
Use Password manager! It stores your passwords & protects your account.
Check it out at http://mysecurelogon.com/password-manager



___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] xcrysden failure

[Winfred Mulwa]

Dear all,
I have installed xcrysden 1.5.24 in my laptop, but when i try to visualize
a cell, it gives an error in startup script: couldn't change working
directory to
"Documents/xc_6882": no such file or directory. Please advice me what might
be the problem?
Mulwa Winfred.
D Phil Student, Computational Material Science Group,
University of the Free State - QwaQwa,
South Africa.
-- next part --
An HTML attachment was scrubbed...
URL: 
http://pwscf.org/pipermail/pw_forum/attachments/20140814/d401dad2/attachment.html
 

[Pw_forum] xcrysden failure

[Tone Kokalj]

On Thu, 2014-08-14 at 14:00 +0300, Winfred Mulwa wrote:
> Dear all,
> 
> I have installed xcrysden 1.5.24 in my laptop, but when i try to
> visualize a cell, it gives an error in startup script: couldn't change
> working directory to 
> 
> "Documents/xc_6882": no such file or directory. Please advice me what
> might be the problem?

The cause is a very improper definition of XCRYSDEN_SCRATCH
environmental variable. Simplest way to fix the problem is to unset it
(then the /tmp will be used instead).

Please consider asking next time such question to xcrysden mailing list.

Regards,
-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html

[Pw_forum] Xcrysden 3D-charge plot for missing atoms-Reg

[Tone Kokalj]

On Fri, 2014-07-25 at 15:09 +0530, Suresh A wrote:
> Respected experts/Dear Friends,
> 
>I have done
> optimisation for Cu doped tio2. Then I used postprocessing code for 3D
> charge density plot. It is known that atoms having negative sign in
> its coordinates will not be shown by XCRYSDEN. So i can not saw 3D
> charge plot for some  missing atoms in xcrysden.

This is not actually the case. First, the atoms which are shifted
"outside" the reference cell box (i.e., those having negative crystal
coordinate) are cropped only in the "nicely-cut unit cell" display mode,
but not in "translational asymmetric unit" mode (notice the two small
buttons right of the "Dihedral" button in the bottom toolbox). Second,
even if the atom is cropped, its charge density will still be shown
(actually, there are some specifics here of how the region for charge
density plot is selected). Thirdly, you can always "multiply" periodic
structure by showing more cells along periodic directions. The same can
be done with the charge density plot.

Please consider asking next time such question to xcrysden mailing list.

Regards,

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html

[Pw_forum] Xcrysden 3D-charge plot for missing atoms-Reg

[Suresh A]

Respected experts/Dear Friends,
   I have done  optimisation
for Cu doped tio2. Then I used postprocessing code for 3D charge density
plot. It is known that atoms having negative sign in its coordinates will
not be shown by XCRYSDEN. So i can not saw 3D charge plot for some  missing
atoms in xcrysden.

Is there a way to visualise 3d charge plot for atoms which is not shown in
XCRYSDEN.
If this thing is already discussed in the forum please let me know about it.

  With Regards,
A.Suresh,
Project Fellow,
Madurai Kamaraj University,
Madurai.
-- next part --
An HTML attachment was scrubbed...
URL: 
http://pwscf.org/pipermail/pw_forum/attachments/20140725/ab3d9864/attachment.html
 

[Pw_forum] xcrysden

[Tone Kokalj]

On Fri, 2014-06-06 at 11:34 +0200, Tommaso Francese wrote:
> Dear all, 
> i  built a monoclinic structure with ibrav = -12, but Xcrysden is not able to 
> show me the structure, and so, i don?t know if it might be correct or not. Do 
> you know how to overcome the problem? 

Recompile the new files for pwi2xsf filter that I posted this Monday to
the pw_forum and it will work; for instructions see:
http://qe-forge.org/pipermail/pw_forum/2014-June/104369.html 

Regards,
-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html

[Pw_forum] xcrysden

[Tommaso Francese]

Dear all, 
i  built a monoclinic structure with ibrav = -12, but Xcrysden is not able to 
show me the structure, and so, i don?t know if it might be correct or not. Do 
you know how to overcome the problem? 
Thanks in advance.
Tommaso Francese,
Universit? C? Foscari of Venice

[Pw_forum] Xcrysden display incorrect structure (when using angstrom units)

[Surender]

>
> gfortran pwi2xsf.f pwLatgen.f pwError.f -o pwi2xsf
>
> and then put the so created "pwi2xsf" binary to a proper place,
> which should be either $XCRYSDEN_TOPDIR/bin/ (if you installed one of
> the xcrysden's tarballs from www.xcrysden.org) or the /usr/lib/xcrysden/
> if you are using the Ubuntu/Debian provided xcrysden.
>
> Regards,
> --
> Anton Kokalj
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
> (tel: +386-1-477-3523 // fax:+386-1-477-3822)
>

Thank you very much, now it works as expected. The command line issue is
also solved, actually the problem was in my script which I used to call
XCrysDen.

I have one more problem, if I right click on 'black' background then
XCrysDen exit with the following error.

+-+

  Version: 1.5.53

  Please report bugs to: tone.kokalj at ijs.si


  TERMS OF USE:
  -
  XCRYSDEN is released under the GNU General Public License.

  Whenever graphics generated by XCRYSDEN are used in scientific
  publications, it shall be greatly appreciated to include an explicit
  reference. The preferred form is the following:

  [ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003.
Code available from http://www.xcrysden.org/.

TCL_LIBRARY=/home/surender/src/xcrysden-1.5.53-bin-semishared/external/lib/tcl8.5
XCRYSDEN_TOPDIR=/home/surender/src/xcrysden-1.5.53-bin-semishared
XCRYSDEN_SCRATCH=/home/surender/xcrys_tmp

Running on platform : unix
   Operating system : Linux
Package ImageMagick's convert: /usr/bin/convert
Package ImageMagick's import: /usr/bin/import
Package Mencoder: /usr/bin/mencoder
Package Ppmtompeg: /usr/bin/ppmtompeg
Package Babel: /usr/bin/babel
Package Xwd: /usr/bin/xwd
Executing: /home/surender/src/xcrysden-1.5.53-bin-semishared/bin/ftnunit
TEXT-WIDGET: .a1.f1.t
Executing: sh
/home/surender/src/xcrysden-1.5.53-bin-semishared/scripts/pwi2xsf.sh
/home/surender/src/xcrysden-1.5.53-bin-semishared/cu.scf.in
reading PRIMCOORD
Number of Atoms:  0
Number of Frames: 0
Estimated number of bonds = 0
sInfo(dim) = 3; periodic(dim) = 3
Executing: /home/surender/src/xcrysden-1.5.53-bin-semishared/bin/gengeom 0
1 11 1 1 1 1 xc_gengeom.4033
/home/surender/xcrys_tmp/xc_4033/pwi2xsf.xsf_out.raw
Executing: /home/surender/src/xcrysden-1.5.53-bin-semishared/bin/gengeom 2
1 11 1 1 1 1 /home/surender/xcrys_tmp/xc_4033/xc_struc.4033
/home/surender/xcrys_tmp/xc_4033/pwi2xsf.xsf_out.raw
reading PRIMCOORD
reading CONVCOORD
Number of Atoms:  14
Number of Frames: 12
natoms: 14 , ndel: 0
Filtered number of atoms: 14
Estimated number of bonds = 72
sInfo(dim) = 3; periodic(dim) = 3
X Error of failed request:  BadValue (integer parameter out of range for
operation)
  Major opcode of failed request:  91 (X_QueryColors)
  Value in failed request:  0xff00
  Serial number of failed request:  8079
  Current serial number in output stream:  8079
+-+

I am using pre-compiled semi-shared version downloaded from
http://www.xcrysden.org/download/xcrysden-1.5.53-linux_x86_64-semishared.tar.gz
The input file is also attached.

Regards,
Surender
-- next part --
A non-text attachment was scrubbed...
Name: cu.scf.in
Type: application/octet-stream
Size: 631 bytes
Desc: not available
Url : 
http://pwscf.org/pipermail/pw_forum/attachments/20140602/bfcac260/attachment.obj
 

[Pw_forum] Xcrysden display incorrect structure (when using angstrom units)

[Surender]

Thank you Giovanni, may I ask one more question. Earlier version (I don't
remember exactly which one) of XCrysDen  used to work from command line
using  xcrysden --pwi pwscf.in but XCrysDen-1.5.53 simply ignores all the
command line options and just show the main window, then I have to use the
file menu to load the file. It's not a very big issue but sometime it's
annoying especially when you need to visualize the structures quite
frequently.

Regards,
Surender

>
> On 1 Jun 2014, at 17:41, Paolo Giannozzi wrote:
>
>> I am not sure that xcrysden can understand the
>> "CELL_PARAMETERS {angstrom}" card, since option
>> "angstrom" was added quite recently
>>
>> P.
>
> Indeed, I also noticed that Xcrysden does not properly cope with
> "CELL_PARAMETERS angstrom" (at least the version that I have installed).
>
> As a workaround, run the calculation just for a few seconds (e.g.,
> creating a prefix.EXIT file in the same folder as the input file - where
> you have to substitute 'prefix' with the prefix you chose - that will
> automatically stop the code after the initialization part) and then open
> instead the output file with xcrysden. This should work properly in both
> cases (i.e., input file in angstrom or bohr).
>
> Best,
> Giovanni
>
>
>
> --
> Giovanni Pizzi
> Post-doctoral Research Scientist
> EPFL STI IMX THEOS
> MXC 340 (B?timent MXC)
> Station 12
> CH-1015 Lausanne (Switzerland)
> Phone: +41 21 69 31124
>
>
>
>> On Sun, 2014-06-01 at 14:41 +0530, Surender wrote:
>>> Dear QE Users,
>>> I don't know whether it's an issue related to XCrysDen or something is
>>> wrong wih my QE input file. Following is the first input file
>>>
>>> 
>>> cu.scf_bohr.in
>>> 
>>> 
>>>calculation='scf'
>>>prefix='cu',
>>>pseudo_dir='./pseudo',
>>>outdir='./tmp'
>>> /
>>> 
>>>ibrav=0
>>>ntyp= 1,
>>>nat= 4,
>>>ecutwfc= 50.0,
>>>occupations='smearing',
>>>smearing='methfessel-paxton',
>>>degauss=0.005
>>> /
>>> 
>>>conv_thr = 1.0D-10
>>>mixing_beta = 0.7
>>> /
>>> ATOMIC_SPECIES
>>> Cu 63.55 Cu.pz-d-rrkjus.UPF
>>> ATOMIC_POSITIONS {bohr}
>>> Cu 0. 0. 0.
>>> Cu 3.4155 3.4155 0.
>>> Cu 0. 3.4155 3.4155
>>> Cu 3.4155 0. 3.4155
>>> K_POINTS automatic
>>>   12 12 12 0 0 0
>>> CELL_PARAMETERS {bohr}
>>>   6.831 0.000 0.000
>>>   0.000 6.831 0.000
>>>   0.000 0.000 6.83
>>> ==
>>>
>>> I can visualize cu.scf_bohr.in using XCrysDen and everything is ok (I
>>> mean
>>> no overlapping atoms). But if I specify the ATOMIC_POSITIONS and CELL
>>> PARAMETERS in ANGSTROM (see cu.scf_angstrom.in) and visualize the
>>> structure then atoms start overlapping. Following is the second input
>>> file
>>>
>>> 
>>> cu.scf_angstrom.in
>>> 
>>> 
>>>calculation='scf'
>>>prefix='cu',
>>>pseudo_dir='./pseudo',
>>>outdir='./tmp'
>>> /
>>> 
>>>ibrav=0
>>>ntyp= 1,
>>>nat= 4,
>>>ecutwfc= 50.0,
>>>occupations='smearing',
>>>smearing='methfessel-paxton',
>>>degauss=0.005
>>> /
>>> 
>>>conv_thr = 1.0D-10
>>>mixing_beta = 0.7
>>> /
>>> ATOMIC_SPECIES
>>> Cu 63.55 Cu.pz-d-rrkjus.UPF
>>> ATOMIC_POSITIONS {angstrom}
>>> Cu 0. 0. 0.
>>> Cu 1.8074 1.8074 0.
>>> Cu 0. 1.8074 1.8074
>>> Cu 1.8074 0. 1.8074
>>> K_POINTS automatic
>>>   12 12 12 0 0 0
>>> CELL_PARAMETERS {angstrom}
>>>   3.6148 0. 0.
>>>   0. 3.6148 0.
>>>   0. 0. 3.6148
>>> 
>>>
>>> I don't know what's going on or did I miss something. I am using
>>> XCrysDen
>>> Version: 1.5.53 on Ubuntu-12.04 LTS. Any help would be appreciated.
>>>
>>> Thanks,
>>> Surender
>>> IIT Bombay, India
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>

[Pw_forum] Xcrysden display incorrect structure (when using angstrom units)

[Tone Kokalj]

On Mon, 2014-06-02 at 14:38 +0530, Surender wrote:
> Thank you Giovanni, may I ask one more question. Earlier version (I don't
> remember exactly which one) of XCrysDen  used to work from command line
> using  xcrysden --pwi pwscf.in but XCrysDen-1.5.53 simply ignores all the
> command line options and just show the main window, 

This shouldn't happen (the handling of command line options didn't
change). It is the first time somebody reported this. Which version do
you use: your compiled source, precompiled package from
www.xcrysden.org , or the Ubuntu/Debian provided package?

As for the parsing of CELL_PARAMETERS {unit} syntax, Paolo was right.
XCrysden does not yet "speak" the new "dialect" of QE. If you find this
annoying, consider compiling the attached corrected source files.
Compile them as:

gfortran pwi2xsf.f pwLatgen.f pwError.f -o pwi2xsf

and then put the so created "pwi2xsf" binary to a proper place,
which should be either $XCRYSDEN_TOPDIR/bin/ (if you installed one of
the xcrysden's tarballs from www.xcrysden.org) or the /usr/lib/xcrysden/
if you are using the Ubuntu/Debian provided xcrysden.

Regards,
-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html
-- next part --
A non-text attachment was scrubbed...
Name: pwi2xsf.f
Type: text/x-fortran
Size: 15121 bytes
Desc: not available
Url : 
http://pwscf.org/pipermail/pw_forum/attachments/20140602/822499a0/attachment.bin
 
-- next part --
A non-text attachment was scrubbed...
Name: pwLatgen.f
Type: text/x-fortran
Size: 12860 bytes
Desc: not available
Url : 
http://pwscf.org/pipermail/pw_forum/attachments/20140602/822499a0/attachment-0001.bin
 
-- next part --
A non-text attachment was scrubbed...
Name: pwError.f
Type: text/x-fortran
Size: 1246 bytes
Desc: not available
Url : 
http://pwscf.org/pipermail/pw_forum/attachments/20140602/822499a0/attachment-0002.bin
 

[Pw_forum] Xcrysden display incorrect structure (when using angstrom units)

[Giovanni Pizzi]

On 1 Jun 2014, at 17:41, Paolo Giannozzi wrote:

> I am not sure that xcrysden can understand the 
> "CELL_PARAMETERS {angstrom}" card, since option
> "angstrom" was added quite recently
> 
> P.

Indeed, I also noticed that Xcrysden does not properly cope with 
"CELL_PARAMETERS angstrom" (at least the version that I have installed).

As a workaround, run the calculation just for a few seconds (e.g., creating a 
prefix.EXIT file in the same folder as the input file - where you have to 
substitute 'prefix' with the prefix you chose - that will automatically stop 
the code after the initialization part) and then open instead the output file 
with xcrysden. This should work properly in both cases (i.e., input file in 
angstrom or bohr).

Best,
Giovanni



-- 
Giovanni Pizzi
Post-doctoral Research Scientist
EPFL STI IMX THEOS
MXC 340 (B?timent MXC)
Station 12
CH-1015 Lausanne (Switzerland)
Phone: +41 21 69 31124



> On Sun, 2014-06-01 at 14:41 +0530, Surender wrote:
>> Dear QE Users,
>> I don't know whether it's an issue related to XCrysDen or something is
>> wrong wih my QE input file. Following is the first input file
>> 
>> 
>> cu.scf_bohr.in
>> 
>> 
>>calculation='scf'
>>prefix='cu',
>>pseudo_dir='./pseudo',
>>outdir='./tmp'
>> /
>> 
>>ibrav=0
>>ntyp= 1,
>>nat= 4,
>>ecutwfc= 50.0,
>>occupations='smearing',
>>smearing='methfessel-paxton',
>>degauss=0.005
>> /
>> 
>>conv_thr = 1.0D-10
>>mixing_beta = 0.7
>> /
>> ATOMIC_SPECIES
>> Cu 63.55 Cu.pz-d-rrkjus.UPF
>> ATOMIC_POSITIONS {bohr}
>> Cu 0. 0. 0.
>> Cu 3.4155 3.4155 0.
>> Cu 0. 3.4155 3.4155
>> Cu 3.4155 0. 3.4155
>> K_POINTS automatic
>>   12 12 12 0 0 0
>> CELL_PARAMETERS {bohr}
>>   6.831 0.000 0.000
>>   0.000 6.831 0.000
>>   0.000 0.000 6.83
>> ==
>> 
>> I can visualize cu.scf_bohr.in using XCrysDen and everything is ok (I mean
>> no overlapping atoms). But if I specify the ATOMIC_POSITIONS and CELL
>> PARAMETERS in ANGSTROM (see cu.scf_angstrom.in) and visualize the
>> structure then atoms start overlapping. Following is the second input file
>> 
>> 
>> cu.scf_angstrom.in
>> 
>> 
>>calculation='scf'
>>prefix='cu',
>>pseudo_dir='./pseudo',
>>outdir='./tmp'
>> /
>> 
>>ibrav=0
>>ntyp= 1,
>>nat= 4,
>>ecutwfc= 50.0,
>>occupations='smearing',
>>smearing='methfessel-paxton',
>>degauss=0.005
>> /
>> 
>>conv_thr = 1.0D-10
>>mixing_beta = 0.7
>> /
>> ATOMIC_SPECIES
>> Cu 63.55 Cu.pz-d-rrkjus.UPF
>> ATOMIC_POSITIONS {angstrom}
>> Cu 0. 0. 0.
>> Cu 1.8074 1.8074 0.
>> Cu 0. 1.8074 1.8074
>> Cu 1.8074 0. 1.8074
>> K_POINTS automatic
>>   12 12 12 0 0 0
>> CELL_PARAMETERS {angstrom}
>>   3.6148 0. 0.
>>   0. 3.6148 0.
>>   0. 0. 3.6148
>> 
>> 
>> I don't know what's going on or did I miss something. I am using XCrysDen
>> Version: 1.5.53 on Ubuntu-12.04 LTS. Any help would be appreciated.
>> 
>> Thanks,
>> Surender
>> IIT Bombay, India
>> 
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
> 
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Xcrysden display incorrect structure (when using angstrom units)

[Paolo Giannozzi]

I am not sure that xcrysden can understand the 
"CELL_PARAMETERS {angstrom}" card, since option
"angstrom" was added quite recently

P.
On Sun, 2014-06-01 at 14:41 +0530, Surender wrote:
> Dear QE Users,
> I don't know whether it's an issue related to XCrysDen or something is
> wrong wih my QE input file. Following is the first input file
> 
> 
>  cu.scf_bohr.in
> 
>  
> calculation='scf'
> prefix='cu',
> pseudo_dir='./pseudo',
> outdir='./tmp'
>  /
>  
> ibrav=0
> ntyp= 1,
> nat= 4,
> ecutwfc= 50.0,
> occupations='smearing',
> smearing='methfessel-paxton',
> degauss=0.005
>  /
>  
> conv_thr = 1.0D-10
> mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
>  Cu 63.55 Cu.pz-d-rrkjus.UPF
> ATOMIC_POSITIONS {bohr}
>  Cu 0. 0. 0.
>  Cu 3.4155 3.4155 0.
>  Cu 0. 3.4155 3.4155
>  Cu 3.4155 0. 3.4155
> K_POINTS automatic
>12 12 12 0 0 0
> CELL_PARAMETERS {bohr}
>6.831 0.000 0.000
>0.000 6.831 0.000
>0.000 0.000 6.83
> ==
> 
> I can visualize cu.scf_bohr.in using XCrysDen and everything is ok (I mean
> no overlapping atoms). But if I specify the ATOMIC_POSITIONS and CELL
> PARAMETERS in ANGSTROM (see cu.scf_angstrom.in) and visualize the
> structure then atoms start overlapping. Following is the second input file
> 
> 
>  cu.scf_angstrom.in
> 
>  
> calculation='scf'
> prefix='cu',
> pseudo_dir='./pseudo',
> outdir='./tmp'
>  /
>  
> ibrav=0
> ntyp= 1,
> nat= 4,
> ecutwfc= 50.0,
> occupations='smearing',
> smearing='methfessel-paxton',
> degauss=0.005
>  /
>  
> conv_thr = 1.0D-10
> mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
>  Cu 63.55 Cu.pz-d-rrkjus.UPF
> ATOMIC_POSITIONS {angstrom}
>  Cu 0. 0. 0.
>  Cu 1.8074 1.8074 0.
>  Cu 0. 1.8074 1.8074
>  Cu 1.8074 0. 1.8074
> K_POINTS automatic
>12 12 12 0 0 0
> CELL_PARAMETERS {angstrom}
>3.6148 0. 0.
>0. 3.6148 0.
>0. 0. 3.6148
> 
> 
> I don't know what's going on or did I miss something. I am using XCrysDen
> Version: 1.5.53 on Ubuntu-12.04 LTS. Any help would be appreciated.
> 
> Thanks,
> Surender
> IIT Bombay, India
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Xcrysden display incorrect structure (when using angstrom units)

[Surender]

Dear QE Users,
I don't know whether it's an issue related to XCrysDen or something is
wrong wih my QE input file. Following is the first input file


 cu.scf_bohr.in

 
calculation='scf'
prefix='cu',
pseudo_dir='./pseudo',
outdir='./tmp'
 /
 
ibrav=0
ntyp= 1,
nat= 4,
ecutwfc= 50.0,
occupations='smearing',
smearing='methfessel-paxton',
degauss=0.005
 /
 
conv_thr = 1.0D-10
mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Cu 63.55 Cu.pz-d-rrkjus.UPF
ATOMIC_POSITIONS {bohr}
 Cu 0. 0. 0.
 Cu 3.4155 3.4155 0.
 Cu 0. 3.4155 3.4155
 Cu 3.4155 0. 3.4155
K_POINTS automatic
   12 12 12 0 0 0
CELL_PARAMETERS {bohr}
   6.831 0.000 0.000
   0.000 6.831 0.000
   0.000 0.000 6.83
==

I can visualize cu.scf_bohr.in using XCrysDen and everything is ok (I mean
no overlapping atoms). But if I specify the ATOMIC_POSITIONS and CELL
PARAMETERS in ANGSTROM (see cu.scf_angstrom.in) and visualize the
structure then atoms start overlapping. Following is the second input file


 cu.scf_angstrom.in

 
calculation='scf'
prefix='cu',
pseudo_dir='./pseudo',
outdir='./tmp'
 /
 
ibrav=0
ntyp= 1,
nat= 4,
ecutwfc= 50.0,
occupations='smearing',
smearing='methfessel-paxton',
degauss=0.005
 /
 
conv_thr = 1.0D-10
mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Cu 63.55 Cu.pz-d-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
 Cu 0. 0. 0.
 Cu 1.8074 1.8074 0.
 Cu 0. 1.8074 1.8074
 Cu 1.8074 0. 1.8074
K_POINTS automatic
   12 12 12 0 0 0
CELL_PARAMETERS {angstrom}
   3.6148 0. 0.
   0. 3.6148 0.
   0. 0. 3.6148


I don't know what's going on or did I miss something. I am using XCrysDen
Version: 1.5.53 on Ubuntu-12.04 LTS. Any help would be appreciated.

Thanks,
Surender
IIT Bombay, India

[Pw_forum] xcrysden

[Tone Kokalj]

On Thu, 2014-04-24 at 08:27 -0700, mohammad moaddeli wrote:
> Dear all,
> 
> 
> I usually install Xcrysden on Fedora 64 bit operating systems, but I
> have a few problems with installing it on 32 bit OS. Is there any
> libraries I should install?


Please provide more information or nobody will be able to help!
You should search for help at xcrysden mailing list for this specific
question.

Regards,

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html

[Pw_forum] xcrysden

[mohammad moaddeli]

Thanks for your help

regards,

mm


On Friday, April 25, 2014 6:22 PM, Tone Kokalj  wrote:
 
On Thu, 2014-04-24 at 08:27 -0700, mohammad moaddeli wrote:

> Dear all,
> 
> 
> I usually install Xcrysden on Fedora 64 bit operating systems, but I
> have a few problems with installing it on 32 bit OS. Is there any
> libraries I should install?


Please provide more information or nobody will be able to help!
You should search for help at xcrysden mailing list for this specific
question.

Regards,

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:? http://www.gnu.org/philosophy/no-word-attachments.html

___
Pw_forum mailing list
Pw_forum at pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
-- next part --
An HTML attachment was scrubbed...
URL: 
http://pwscf.org/pipermail/pw_forum/attachments/20140425/d817e769/attachment.html
 

[Pw_forum] xcrysden

[mohammad moaddeli]

Dear all,

I usually install Xcrysden on Fedora 64 bit operating systems, but I have a few 
problems with installing it on 32 bit OS. Is there any libraries I should 
install?

Any help will be appreciated,
Mohammad
-- next part --
An HTML attachment was scrubbed...
URL: 
http://pwscf.org/pipermail/pw_forum/attachments/20140424/b4a0be93/attachment.html
 

[Pw_forum] xcrysden visualization

[mayank gupta]

Dear users

I am not able to visualize the crystal structure with ibrav=-12 flag.
Please suggest the possible alternatives.


Thanks

-- 
--with regard's
Mayank

 BARC
MUMBAI, INDIA
-- next part --
An HTML attachment was scrubbed...
URL: 
http://pwscf.org/pipermail/pw_forum/attachments/20140317/4bfa95eb/attachment.html
 

[Pw_forum] xcrysden visualization

[Carlo Nervi]

Regarding this question, is there any differences in calculating 
structures having the ibrav=-12 or ibrav=0 (and setting the 
corresponding CELL_PARAMETERS)?
In other words the calculations should be equivalent. Is it?
Also, do the calculations in both cases make use of symmetry?

In this case one can use the cif2qe.sh utility to generate the ibrav=0 
input file starting from the corresponding cif file.

As far as I know xcrysgen can handle ibrav=0

Correct?
thanks,
Carlo

Il 17/03/2014 13.16, Tone Kokalj ha scritto:
> On Mon, 2014-03-17 at 17:23 +0530, mayank gupta wrote:
>> Dear users
>>
>> I am not able to visualize the crystal structure with ibrav=-12 flag.
>
> This is correct; ibrav=-12 is not yet supported by xcrysden.
>
>>   Please suggest the possible alternatives.
>
> Here is the trick how you can still see the pertinent structure with
> xcrysden:
>
> 1. generate your input file
>
> 2. run pw.x on this input file for, say, only a few seconds, so that the
> initial coordinates are written to output file, i.e.:
>
> pw.x < file.in > file.out
> (press Control-C after a few seconds)
>
> 3. visualize the "Initial Coordinates" from this input file, i.e.:
>
> xcrysden --pwo file.out
>
> Regards,
>


-- 

Prof. Carlo Nervi carlo.nervi at unito.it  Tel:+39 0116707507/8
Fax: +39 0116707855  -  Dipartimento di Chimica, via
P. Giuria 7, 10125 Torino, Italy.http://lem.ch.unito.it/

[Pw_forum] xcrysden visualization

[Tone Kokalj]

On Mon, 2014-03-17 at 17:23 +0530, mayank gupta wrote:
> Dear users
> 
> I am not able to visualize the crystal structure with ibrav=-12 flag.

This is correct; ibrav=-12 is not yet supported by xcrysden.

>  Please suggest the possible alternatives. 

Here is the trick how you can still see the pertinent structure with
xcrysden:

1. generate your input file

2. run pw.x on this input file for, say, only a few seconds, so that the
initial coordinates are written to output file, i.e.:

pw.x < file.in > file.out
(press Control-C after a few seconds)

3. visualize the "Initial Coordinates" from this input file, i.e.:

xcrysden --pwo file.out

Regards,

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html

[Pw_forum] Xcrysden charge plot - reg.,

[Muthu V]

Dear QE'ians

i drawn charge density plot using .xsf (for charge density)  file. i have
two questions  regarding plotting with xcrysden

1.   xcrysden do well. but i want to display atom only at the interested
point in crystal not all atoms in whole crystal. i do not have crystal.xx
package and i
  want to delete unwanted atom. can i do this in xcrysden (without
crystal package) ? ( since with out this package of the options in xcrysden
are inactive
  for e.g *"AdvGeom,Properties"*

2.   at starting window if i load .xsf (charge density file)file , xcrysden
shows opening with which gives details of the file along with multiplying
factor. if
  change this value nothing happens except changes in lower and higher
rendering value of charge. what is the use of multiplying factor?

3.   i want to plot for specific bands in that in band structure. QE gives
me options for this. but by changing the  lowest and highest rendered value
i can get
  different plot. what they mean?  is this correspond to charge plot
for different bands?

dear qe users your help will be appreciated

thank you



*_*
*Muthu.V*
*Project Fellow*
*School of Physics*
*Madurai Kamaraj University*
*Mandurai, Tamil Nadu*
*India*

*__*
-- next part --
An HTML attachment was scrubbed...
URL: 
http://pwscf.org/pipermail/pw_forum/attachments/20140131/9d7c1a36/attachment.html
 

[Pw_forum] Xcrysden charge plot - reg.,

[Tone Kokalj]

On Fri, 2014-01-31 at 12:28 +0530, Muthu V wrote:
> Dear QE'ians
> 
> 
> i drawn charge density plot using .xsf (for charge density)  file. i
> have two questions  regarding plotting with xcrysden
> 
> 
> 1.   xcrysden do well. but i want to display atom only at the
> interested point in crystal not all atoms in whole crystal...

The easiest way is to edit the XSF file and delete the unwanted atoms.
For the description of XSF file, see:
http://www.xcrysden.org/doc/XSF.html

> 
> 
> 2.   ... xcrysden shows opening with which gives details of the file
> along with multiplying factor. if change this value nothing happens
> except changes in lower and higher rendering value of charge. what is
> the use of multiplying factor?

http://www.xcrysden.org/doc/density.html


> 3.   i want to plot for specific bands in that in band structure. QE
> gives me options for this. but by changing the  lowest and highest
> rendered value i can get different plot. what they mean?  is this
> correspond to charge plot for different bands? 

It is not clear what you mean  elaborate!

Regards,

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html

[Pw_forum] xcrysden

[Abolore Musari]

Dear ramzi
You can view this structure using xcrysden by using the following command
xcrysden --pwi filename

On 3/28/12, Tone Kokalj  wrote:
> On Tue, 2012-03-27 at 11:38 +0100, ramzi alaya wrote:
>> Dear all,
>>
>>
>> I have a file input structure Zinc blenbe relaxed, do I draw this
>> structure with xcrysden?
>> Can you help me out?
>
> You would like to visualize the structure from your pw.x input file or
> what?
>
> If so you may try with: xcrysden --pwi filename
>
> Regards, Tone
>
> --
> Anton Kokalj
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
> (tel: +386-1-477-3523 // fax:+386-1-477-3822)
>
> Please, if possible, avoid sending me Word or PowerPoint attachments.
> See:  http://www.gnu.org/philosophy/no-word-attachments.html
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

[Pw_forum] xcrysden

[Tone Kokalj]

On Tue, 2012-03-27 at 11:38 +0100, ramzi alaya wrote:
> Dear all,
> 
>  
> I have a file input structure Zinc blenbe relaxed, do I draw this
> structure with xcrysden?
> Can you help me out?

You would like to visualize the structure from your pw.x input file or
what?

If so you may try with: xcrysden --pwi filename

Regards, Tone

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html

[Pw_forum] xcrysden

[ramzi alaya]

Dear all,
 
I have a file input structure Zinc blenbe relaxed, do I draw this structure 
with xcrysden?
Can you help me out?

 
Thank you.

Regards.
 
 
 
**
Ramzi Alaya
E-mail : ramzialaya at hotmail.fr
Facult? des Sciences de Gab?s, Cit? Erriadh 6072 Gab?s- Tunisie
Unit? de Recherche sur les H?t?ro-Epitaxies et Applications

  
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20120327/d89188f3/attachment-0001.htm
 

[Pw_forum] [xcrysden]:how to get the output structure file as xyz format

[chengyu yang]

Dear Everyone,
  I have a very simple question: I set up a structure and repeat it
in Xcrysden, and then I want to get the structure file for the whole
periodic structure as xyz file. How could I do that?
  I can only find .xsf format and other formats.
  Can you help me out?
  Thank you.
Regards.

Chengyu Yang
MMAE,University of Central Florida
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20120326/5faf9bc4/attachment.htm
 

[Pw_forum] XCrysDen & Animation Capture

[Tone Kokalj]

On Sun, 2011-11-06 at 11:50 -0500, Axel Kohlmeyer wrote:
> hi paul,
> 
> On Sat, Nov 5, 2011 at 8:46 PM, W2AGZ  wrote:
> It seems that the mpeg_encode and whirlgif packages are no
> longer available for XCrysDen, and their old source codes are
> ?un-make-able,? at least within the current release of Ubuntu.
> Any advice on how to ?capture? the animation sequence of,
> e.g., structure relaxation, for use in an presentation format
> such as Powerpoint or Impress?
> 
> 
> 
> 
> have you checked out one of the following programs?
> - ppmtompeg (part of the netpbm package)
> - mencoder (part of the mplayer suite)
> - gifsicle (best gif encoder i know)
> - convert (part of the ImageMagik package, worst gif encoder i know)
> 
> 
> all of those were already supported by XCrySDen many years ago,
> so i would assume they still are.

Which, indeed, they still are. The mpeg_encode and whirlgif are not used
anymore for years.

It is true that sometimes making a movie can be tricky, but xcrysden
gives you a possibility to edit the movie encoding script before the
encoding, which can be useful when and if the default route fails.

Regards, Tone

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html

[Pw_forum] XCrysDen & Animation Capture

[W2AGZ]

Thanks, Arles and Axel.  I'll check out your suggestions.

 

Axel, maybe you should consider publishing a review of all tools available
for use on Quantum-Espresso ;-)

 

Cheers, -Paul

 

Paul Grant

W2AGZ Technologies (www.w2agz.com)

Staff Associate, JPL-NASA

 

-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/2006/7bc1c633/attachment.htm
 

[Pw_forum] XCrysDen & Animation Capture

[Axel Kohlmeyer]

hi paul,

On Sat, Nov 5, 2011 at 8:46 PM, W2AGZ  wrote:

> It seems that the mpeg_encode and whirlgif packages are no longer
> available for XCrysDen, and their old source codes are ?un-make-able,? at
> least within the current release of Ubuntu.  Any advice on how to ?capture?
> the animation sequence of, e.g., structure relaxation, for use in an
> presentation format such as Powerpoint or Impress?
>

have you checked out one of the following programs?
- ppmtompeg (part of the netpbm package)
- mencoder (part of the mplayer suite)
- gifsicle (best gif encoder i know)
- convert (part of the ImageMagik package, worst gif encoder i know)

all of those were already supported by XCrySDen many years ago,
so i would assume they still are.

cheers,
axel.


>
> ** **
>
> -Paul Grant
>
> W2AGZ Technologies (www.w2agz.com)
>
> Staff Associate, JPL-NASA
>
> ** **
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com  http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/2006/eaf6fddc/attachment.htm
 

[Pw_forum] XCrysDen & Animation Capture

[Arles V. Gil Rebaza]

You can use Jmol, this program read a XYZ file..

Best

PhD stud. Arles V. Gil Rebaza
IFLP - Argentina

2011/11/5 W2AGZ 

> It seems that the mpeg_encode and whirlgif packages are no longer
> available for XCrysDen, and their old source codes are ?un-make-able,? at
> least within the current release of Ubuntu.  Any advice on how to ?capture?
> the animation sequence of, e.g., structure relaxation, for use in an
> presentation format such as Powerpoint or Impress?
>
> ** **
>
> -Paul Grant
>
> W2AGZ Technologies (www.w2agz.com)
>
> Staff Associate, JPL-NASA
>
> ** **
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
###->   Arles V.   <-###
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/2005/02546444/attachment-0001.htm
 

[Pw_forum] XCrysDen & Animation Capture

[W2AGZ]

It seems that the mpeg_encode and whirlgif packages are no longer available
for XCrysDen, and their old source codes are "un-make-able," at least within
the current release of Ubuntu.  Any advice on how to "capture" the animation
sequence of, e.g., structure relaxation, for use in an presentation format
such as Powerpoint or Impress?

 

-Paul Grant

W2AGZ Technologies (www.w2agz.com)

Staff Associate, JPL-NASA

 

-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/2005/d8b19bb5/attachment.htm
 

[Pw_forum] Xcrysden crashes!

[Lorenzo Paulatto]

In data 01 settembre 2009 alle ore 20:52:43, Bertrand SITAMTZE
 ha scritto:
> 4240 Aborted


Dear Bertran,
I found the solution to several months ago, but posted it in the xcrysden
mailing list. Have a look here:
http://www.democritos.it/pipermail/xcrysden/2009-February/000564.html

cheers

-- 
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/



  SISSA Webmail https://webmail.sissa.it/
  Powered by SquirrelMail http://www.squirrelmail.org/

[Pw_forum] Xcrysden crashes!

[Gabriele Sclauzero]

Dear Bertrand,

Bertrand SITAMTZE wrote:
> I found that somebody got the same problem in 2007. See the link:
> 
> http://www..democritos.it/pipermail/xcrysden/2007-December/000440.html
> 
> I went through the forum and I didn't got any solution.

Did you mean that you already posted on the xcrysden users forum and got no 
solution? I 
think that the correct forum to search for a solution to your problem is the 
xcrysden 
mailing list, although many people from the QE community uses xcrysden.

You can subscribe (and then post) to the xcrysden forum through this link:

http://www.democritos.it/mailman/listinfo/xcrysden

In order to help the troubleshooting you should give more details (version of 
the program, 
static binaries or compiled by yourself, on which HW/SW, ...).

Regards,

GS


> 
> Thanking for any help
> 
> 
> 
> Bertrand SITAMTZE
> PhD student
> Department of Physics
> University of Yaounde
>  I-Cameroon
> *
> 
> 
> 
> 
> 
> --- En date de : *Mar 1.9.09, Lorenzo Paulatto //* a 
> ?crit :
> 
> 
> De: Lorenzo Paulatto 
> Objet: Re: [Pw_forum] Re : Re:Pseudopotential for Li
> ?: "PWSCF Forum" 
> Date: Mardi 1 Septembre 2009, 12h16
> 
> In data 01 settembre 2009 alle ore 12:11:33, Bertrand SITAMTZE 
> > ha scritto:
>  > Please, I would like you to help with the section concerning the
> 1 1S, 2 
>  > 2S and 2 2P reference states. I mean, what should I put in the
> following 
>  > section?
> 
> That's exactly what I told you in the other email: you need two
> reference 
> wavefunction per value of l
> e.g. you could do something like this:
> 
> 5
> 1S  1  0  2.00   0.00   0.750  1.100
> 2S  2  0  0.80   0.00   0.750  1.100
> 2S  2  0  0.00   0.10   0.750  1.100
> 2P  2  1  0.20   0.00   0.750  1.100
> 2P  2  1  0.00   0.10   0.750  1.100
> 
> for the second reference (that one that does not have the eigenvalue 
> energy) occupation must be zero. The reference energy (in my example
> 0.10) 
> has to be chosen by testing and error; it will likely be in the range 
> -0.20 to 1.0
> 
> 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 mailing list
> Pw_forum at pwscf.org 
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> start: 2008-09-03 end: -00-00
> 
> 
> 
> 
> ___
> 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] Xcrysden crashes!

[Bertrand SITAMTZE]

Dear all,

I downloaded Xcrysden and installed it on one of our computer without any 
problem. But? I have not been able to do it with the other computer. The 
./xcConfigure message does well, but running the executable xcryxden crashes 
with a message similar to this:/XCrySDen/xcrysden: line 163:  4240 Aborted 
(core dumped) ${XCRYSDEN_TOPDIR}/bin/xcrys 
${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPD
DIR $XCRYSDEN_SCRATCH $ARGS > /dev/null

I found that somebody got the same problem in 2007. See the link:

http://www.democritos.it/pipermail/xcrysden/2007-December/000440.html

I went through the forum and I didn't got any solution.

Thanking for any help



Bertrand SITAMTZE
PhD student
Department of Physics
University of Yaounde I-Cameroon
*




--- En date de?: Mar 1.9.09, Lorenzo Paulatto  a ?crit?:

De: Lorenzo Paulatto 
Objet: Re: [Pw_forum] Re : Re:Pseudopotential for Li
?: "PWSCF Forum" 
Date: Mardi 1 Septembre 2009, 12h16

In data 01 settembre 2009 alle ore 12:11:33, Bertrand SITAMTZE? 
 ha scritto:
> Please, I would like you to help with the section concerning the 1 1S, 2? 
> 2S and 2 2P reference states. I mean, what should I put in the following? 
> section?

That's exactly what I told you in the other email: you need two reference? 
wavefunction per value of l
e.g. you could do something like this:

5
1S? 1? 0? 2.00???0.00???0.750? ? ? 1.100
2S? 2? 0? 0.80???0.00???0.750? ? ? 1.100
2S? 2? 0? 0.00???0.10???0.750? ? ? 1.100
2P? 2? 1? 0.20???0.00???0.750? ? ? 1.100
2P? 2? 1? 0.00???0.10???0.750? ? ? 1.100

for the second reference (that one that does not have the eigenvalue? 
energy) occupation must be zero. The reference energy (in my example 0.10)? 
has to be chosen by testing and error; it will likely be in the range? 
-0.20 to 1.0

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 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/20090901/98ae7736/attachment-0001.htm
 

[Pw_forum] XCrysDen

[MAHASIN ALAM]

Dear Lorenzo Paulatto,
?
Thank you very much for your help.
?
Regards
?
Mahasin

--- On Tue, 14/7/09, Lorenzo Paulatto  wrote:


From: Lorenzo Paulatto <paula...@sissa.it>
Subject: Re: [Pw_forum] XCrysDen
To: "PWSCF Forum" 
Date: Tuesday, 14 July, 2009, 3:06 PM


In data 14 luglio 2009 alle ore 11:21:45, MAHASIN ALAM? 
 ha scritto:
> I am trying to install the "XCrysDen" software in MS-Windows, I have? 
> downloaded the specified file from the "Quantum Espresso" site. But when? 
> I unzipped the file, the error message showing is that the "xcConfigure"? 
> file is not created. Can any one please help me how to install the? 
> software.

Dear Mahasin,
you should really just read xcrysden documentation, where the installation? 
procedure is explained in details.
Nevertheless, I would advice you to use the 1.6 pre-release version of? 
xcrysden, instead, which does not involve any installation procedure and? 
is more compatible with the newer versions of QE:? 
<http://www.xcrysden.org/Download.html#__toc__1>

cheers


-- 
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 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/20090714/7ee6f87b/attachment.htm
 

[Pw_forum] XCrysDen

[Lorenzo Paulatto]

In data 14 luglio 2009 alle ore 11:21:45, MAHASIN ALAM  
 ha scritto:
> I am trying to install the "XCrysDen" software in MS-Windows, I have  
> downloaded the specified file from the "Quantum Espresso" site. But when  
> I unzipped the file, the error message showing is that the "xcConfigure"  
> file is not created. Can any one please help me how to install the  
> software.

Dear Mahasin,
you should really just read xcrysden documentation, where the installation  
procedure is explained in details.
Nevertheless, I would advice you to use the 1.6 pre-release version of  
xcrysden, instead, which does not involve any installation procedure and  
is more compatible with the newer versions of QE:  


cheers


-- 
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] XCrysDen

[MAHASIN ALAM]

Dear All,
?
I am trying to install the "XCrysDen" software in MS-Windows, I have downloaded 
the specified file from the "Quantum Espresso" site. But when I unzipped the 
file, the error message showing is that the "xcConfigure" file is not created. 
Can any one please help me how to install the software.
?
Warm regards
?
Sk Mahasin Alam


  
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090714/b1a8e133/attachment.htm
 

[Pw_forum] Xcrysden

[lan haiping]

On Fri, Apr 3, 2009 at 7:43 PM, S. K. S.  wrote:

> Dear Users,
>
> I have a couple of questions  regarding  Xcrysden.
> 1. Usually xcrysden files use the following format:
>
>  PRIMVEC
>5.52460788000.000.00
>0.003.90648780400.00
>0.000.00   19.5324384880
>  PRIMCOORD
>  14 1
>  31  0.3031580950 0.00-0.3114762280
>  31  2.6436116560 1.9532436370-1.8580462820
>  31 -0.0518106620 0.00-3.8817233780
>  31  2.7623039400 1.9532436370-5.8597314410
>  31  0.00 0.00-7.8129756070
>  31  2.7623039400 1.9532436370-9.7662192440
>  33  1.4763662580 1.9532436370 0.3364242780
>
> where atomic positions  are not written in crystal co-ordinates.
> Is it possible to specify atomic positions in crystal co-ordinates in any
> of .xyz or .xsf  xcrysden input files (except .pwi or .pwo files).
>

Yes, you can, please have a look at the format of XSF file.

>
> 2. How to print the thermometer in Xcrysden???
> Everytime I get an error saying "could not execute /usr/bin/convert".
>
You should install GIMP, a GNU image processor.

>
> I'll be highly obliged if anyone kindly discuss the above issues.
> regards,
> SKS
> JNCASR
> Bangalore
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20090403/bccfe097/attachment.htm
 

[Pw_forum] Xcrysden

[S. K. S.]

Dear all,

Thanks a lot for your kind and helpful reply.
Few things about Xcrysden are yet to be known.

1. Now I can print the thermometer after installing
ImageMagick. However, it prints the thermometer
separately. Please have a look on  the attached file.
Is it possible in XCrysden to print the thermometer  together
with the background  "Xcrysden charge-density" plot


2.  >No! XSF uses Carthesian coordinates (Angstrom units).

 Then,  is there any other smart way to change Angstrom  coordinates
  to crystal coordinates in Xcrysden??? The usual pen and paper
  (analytical and manual) method is not always time-saving especially for
  non-cubic  (for instance, hexagonal) systems.

 3.  Another thing I would like  to know, whether it is possible to increase
  the size of the "XYZ co-ordinate symbol" in Xcrysden???
  One can easily zoom the picture of a molecule or a crystal in the
  Xcrysden and print  the larger size picture because   Xcrysden's print is
  an XWD window dump.  But what about  co-ordinate symbol???
  Is it possible to make its size bigger?

  regards,
  SKS
-- next part --
A non-text attachment was scrubbed...
Name: mol-urea2D.jpg
Type: image/jpeg
Size: 4822 bytes
Desc: not available
Url : 
http://www.democritos.it/pipermail/pw_forum/attachments/20090403/fe5fcd38/attachment-0001.jpg
 

[Pw_forum] Xcrysden

[Tone Kokalj]

On Fri, 2009-04-03 at 19:04 +0530, S. K. S. wrote:
> Dear all,
> 
> Thanks a lot for your kind and helpful reply.
> Few things about Xcrysden are yet to be known.
> 
> 1. Now I can print the thermometer after installing
> ImageMagick. However, it prints the thermometer
> separately. Please have a look on  the attached file.
> Is it possible in XCrysden to print the thermometer  together
> with the background  "Xcrysden charge-density" plot

This is why image manipulation or some other presentation programs are
used for. Take as many "primitive" images as you like and assemble a
master image there.

> 2.  >No! XSF uses Carthesian coordinates (Angstrom units).
> 
>  Then,  is there any other smart way to change Angstrom  coordinates
>   to crystal coordinates in Xcrysden??? The usual pen and paper
>   (analytical and manual) method is not always time-saving especially for
>   non-cubic  (for instance, hexagonal) systems.

There is! 

Instead of making XSF, make a plain pw.x input file and specify
ATOMIC_POSITIONS in crystal units, then load that pw.x input file into
xcrysden. Now you can pass to Carthesian if you wish so (i.e. save the
loaded file as XSF).


> 
>  3.  Another thing I would like  to know, whether it is possible to increase
>   the size of the "XYZ co-ordinate symbol" in Xcrysden???
>   One can easily zoom the picture of a molecule or a crystal in the
>   Xcrysden and print  the larger size picture because   Xcrysden's print is
>   an XWD window dump.  But what about  co-ordinate symbol???
>   Is it possible to make its size bigger?

Unfortunately not. (you can make it manual though: print it as it is so
that you will have the directions, and then make a new one in some image
processing program)

Regards, Tone
-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html

[Pw_forum] Xcrysden

[Tone Kokalj]

On Fri, 2009-04-03 at 17:13 +0530, S. K. S. wrote:
> Dear Users,
> 
> I have a couple of questions  regarding  Xcrysden.
> 1. Usually xcrysden files use the following format:
> 
>  PRIMVEC
> 5.52460788000.000.00
> 0.003.90648780400.00
> 0.000.00   19.5324384880
>  PRIMCOORD
>  14 1
>  31  0.3031580950 0.00-0.3114762280
>  31  2.6436116560 1.9532436370-1.8580462820
>  31 -0.0518106620 0.00-3.8817233780
>  31  2.7623039400 1.9532436370-5.8597314410
>  31  0.00 0.00-7.8129756070
>  31  2.7623039400 1.9532436370-9.7662192440
>  33  1.4763662580 1.9532436370 0.3364242780
> 
> where atomic positions  are not written in crystal co-ordinates.
> Is it possible to specify atomic positions in crystal co-ordinates in any
> of .xyz or .xsf  xcrysden input files

No! XSF uses Carthesian coordinates (Angstrom units).

> 2. How to print the thermometer in Xcrysden???
> Everytime I get an error saying "could not execute /usr/bin/convert".

You need  ImageMagick suite of programs (convert is a member of it) for
"printing" in xcrysden (actually the new xcrysden version will also try
to use netbpm if image-magick is missing).

For ImageMagick see: http://www.imagemagick.org
Note however that (probably) all linux distributions have it. So you may
find the package corresponding to your distribution.

Regards, Tone
-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html

[Pw_forum] xcrysden+cygwin can't display relax process

[Tone Kokalj]

On Fri, 2009-03-13 at 09:04 +0100, Paolo Giannozzi wrote:
> Dr. Shu-jun Hu wrote:
> 
> > The string '0   0   0' means the position of corresponding ions has been 
> > fix. When
> > such strings have been removed from the output file, the whole relax 
> > process can
> > be displayed correctly. I suggest removing the 0 0 0 string from the output 
> > file
> > or fix the bug of xcrysden.
> 
> which version of xcrysden are you using? I think this is fixed
> in the most recent versions

It is!

Regards, Tone

PS: If the error still persists in the new versions, follow the guidelines of 
Gabriele: send the output file.

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html

[Pw_forum] xcrysden+cygwin can't display relax process

[Paolo Giannozzi]

Dr. Shu-jun Hu wrote:

> The string '0   0   0' means the position of corresponding ions has been fix. 
> When
> such strings have been removed from the output file, the whole relax process 
> can
> be displayed correctly. I suggest removing the 0 0 0 string from the output 
> file
> or fix the bug of xcrysden.

which version of xcrysden are you using? I think this is fixed
in the most recent versions

P.
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

[Pw_forum] xcrysden+cygwin can't display relax process

[Gabriele Sclauzero]

Dr. Shu-jun Hu wrote:
> Dear All,
> 
> When I use the xcyrsden installed on cygwin to display the relaxing process, 
> it
> just shows the initio structure (only one slide) rather than the whole 
> process.
> Since some ions have been fixed in the input file, the new structure after 
> each
> dynamic step is like:
> 
> *
>  atom 140 type  1   force = 0.00621763   -0.00424409   -0.00889158
> 
>  Total force = 0.061794 Total SCF correction = 0.002797
> 
>  Entering Dynamics:iteration =27
> 
>   =   0.99727388
> 
> ATOMIC_POSITIONS (angstrom)
> Zn   0.0   0.0   0.00   0   0
> Zn   2.81560   1.62560   0.00   0   0
> O0.0   0.0   1.986200   0   0
> ***
> 
> The string '0   0   0' means the position of corresponding ions has been fix. 
> When
> such strings have been removed from the output file, the whole relax process 
> can
> be displayed correctly. I suggest removing the 0 0 0 string from the output 
> file
> or fix the bug of xcrysden.

Which bug? For me (on Linux...) xcrysden works perfectly in displaying the 
atomic 
coordinates of relax calculations.
If you have clear evidence that this is a bug (and it has not been solved 
already in a 
later release... BTW, you did not mention which version of Xcrysden you're 
using, I 
suppose you already tried the last one) and it is reproducible, please send a 
pw output 
file that gives the error to the xcrysden mailing list (which is not this one).
Removing that string from pw output is not good idea, since the atomic 
positions on the 
output can be reused as starting configuration for a successive relaxation in 
case one is 
obliged to restart from_scratch for some reason.

Cheers

GS




> 
> Best 
> 
> Shujun
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ___
> 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] xcrysden+cygwin can't display relax process

[Dr. Shu-jun Hu]

Dear All,

When I use the xcyrsden installed on cygwin to display the relaxing process, it
just shows the initio structure (only one slide) rather than the whole process.
Since some ions have been fixed in the input file, the new structure after each
dynamic step is like:

*
 atom 140 type  1   force = 0.00621763   -0.00424409   -0.00889158

 Total force = 0.061794 Total SCF correction = 0.002797

 Entering Dynamics:iteration =27

  =   0.99727388

ATOMIC_POSITIONS (angstrom)
Zn   0.0   0.0   0.00   0   0
Zn   2.81560   1.62560   0.00   0   0
O0.0   0.0   1.986200   0   0
***

The string '0   0   0' means the position of corresponding ions has been fix. 
When
such strings have been removed from the output file, the whole relax process can
be displayed correctly. I suggest removing the 0 0 0 string from the output file
or fix the bug of xcrysden.

Best 

Shujun

[Pw_forum] xcrysden+cygwin can't display relax process

[Lex Kemper]

Hello Dr. Hu,

XCrysDen uses an awk script to parse the relaxation output file. It 
doesn't like the 0 0 0 because it searches (as I recall) for lines that 
have 4 entries. It's relatively easy to change it so it'll search for 
lines that have 4 OR 7 entries.

Cheers,

Lex Kemper
Department of Physics
University of Florida


Dr. Shu-jun Hu wrote:
> Dear All,
> 
> When I use the xcyrsden installed on cygwin to display the relaxing process, 
> it
> just shows the initio structure (only one slide) rather than the whole 
> process.
> Since some ions have been fixed in the input file, the new structure after 
> each
> dynamic step is like:
> 
> *
>  atom 140 type  1   force = 0.00621763   -0.00424409   -0.00889158
> 
>  Total force = 0.061794 Total SCF correction = 0.002797
> 
>  Entering Dynamics:iteration =27
> 
>   =   0.99727388
> 
> ATOMIC_POSITIONS (angstrom)
> Zn   0.0   0.0   0.00   0   0
> Zn   2.81560   1.62560   0.00   0   0
> O0.0   0.0   1.986200   0   0
> ***
> 
> The string '0   0   0' means the position of corresponding ions has been fix. 
> When
> such strings have been removed from the output file, the whole relax process 
> can
> be displayed correctly. I suggest removing the 0 0 0 string from the output 
> file
> or fix the bug of xcrysden.
> 
> Best 
> 
> Shujun
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

[Pw_forum] XCRYSDEN problem readinf PW4 output

[Tone Kokalj]

On Mon, 2008-10-13 at 10:03 +0200, Marcello Rosini wrote:
> Hi everybody,
> I had a problem with xcrysden when reading the output of a pw 4.* 
> relaxation. The problem is that in the output also the fixed flags of 
> the atom coordinates are present, while it was not so in the previous 
> versions.

Indeed so. The xcrysden 1.4.* version cannot handle it due to the reason
you describe, but the "latest-snapshot" version can
http://www.xcrysden.org/download/xc-latest-linuxPC-semishared.tar.gz

> I modified few lines in the source code, in order to make xcrysden able 
> to work in this case.
> You can find the modified code here:
> http://cdm.unimo.it/home/fisica/rosini.marcello/scr.tar.gz

Very good!

Regards, Tone
-- 
Tone Kokalj 
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)

[Pw_forum] XCRYSDEN problem readinf PW4 output

[Marcello Rosini]

Hi everybody,
I had a problem with xcrysden when reading the output of a pw 4.* 
relaxation. The problem is that in the output also the fixed flags of 
the atom coordinates are present, while it was not so in the previous 
versions.
I modified few lines in the source code, in order to make xcrysden able 
to work in this case.
You can find the modified code here:
http://cdm.unimo.it/home/fisica/rosini.marcello/scr.tar.gz

One you have installed xcrysden, extract the modified files in the 
directory "scripts" of the xcrysden root directory and it should work.

Marcello

[Pw_forum] xcrysden problem "error couldn't change working directory to "Y/xc_23632": no such file or directory

[xu yuehua]

thank  you for your kindly help (even if in the condition of  the server is
down. )
2008/10/10 Paolo Giannozzi 

> xu yuehua wrote:
>
> > the whole progress of installation:
>
> I do not see where XCRYSDEN_SCRATCH is set. You need to:
> - remove everything Xcrysden-related from everywhere,
>   including .bashrc
> - reinstall from scratch
>
> > [..] is there any other problem ?
>
> I have no problem at all! (well, actually I have one:
> some genius has cut the electricity and the mail server
> of the physics department is down...)
>
> 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
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20081010/62ef8438/attachment.htm
 

[Pw_forum] xcrysden problem "error couldn't change working directory to "Y/xc_23632": no such file or directory

[xu yuehua]

 the whole progress of installation:

 jdong at sgi4700:~/xyh/XCrySDen-pre1.5bbin-static> ./xcConfigure
more: unknown option "-m"
usage: more [-dflpcsu] [+linenum | +/pattern] name1 name2 ...
more: unknown option "-m"
usage: more [-dflpcsu] [+linenum | +/pattern] name1 name2 ...
Press   to continue ...
   I am about to create the $HOME/.xcrysden directory and copy XCRYSDEN
   definition/customization files to it. See the XCRYSDEN  documentation
   for further instructions about XCRYSDEN customization.
   Press  to continue ...
   
 Please answer to following QUESTIONS!!!
   

CRYSTAL-95/98/03 is an electronic structure program for periodic systems.
(http://www.crystal.unito.it/)
Do you have a CRYSTAL-95/98/03 package ([y]es/[n]o): n
Specify printing command (default: lpr -h):
more: unknown option "-m"
usage: more [-dflpcsu] [+linenum | +/pattern] name1 name2 ...
Do you want to enable the "babel" program ([y]es/[n]o): n
Do you want to enable the ImageMagick's "convert" program ([y]es/[n]o): n
Do you want to enable the "whirlgif" program ([y]es/[n]o): n
Do you want to enable the "mpeg_encode" program ([y]es/[n]o): n

 
   You have specified the following definitions:
 
Print Command: lpr -h
Is this correct ([y]es/[n]o): y
creating /disk2/jdong/.xcrysden/custom-definitions ... OK
Would you like to edit ~/.xcrysden/custom-definitions file now
([y]es/[n]o):n
copying /disk2/jdong/xyh/XCrySDen-pre1.5bbin-static/Tcl/Xcrysden_defaults
... OK
more: unknown option "-m"
usage: more [-dflpcsu] [+linenum | +/pattern] name1 name2 ...
--
is there any other  problem ?



2008/10/10 Paolo Giannozzi 

> xu yuehua wrote:
>
> > the problem is so strange. Y is what ?
> > i have not specify any directory named  as  "Y"
>
> sure? really? didn't you answer "Y" to any question
> during installation?
>
> 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
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20081010/68d88c6e/attachment.htm
 

[Pw_forum] xcrysden problem "error couldn't change working directory to "Y/xc_23632": no such file or directory

[xu yuehua]

the former.
the problem is so strange. Y is what ?
i have not specify any directory named  as  "Y"
 and i
ls  -al  found the
 drwxr-xr-x 4  jdong phys96 2008-10-10 17:56 Y
and the same  xcryden software in another machine is rather ok.and the ls
-al

drwxrwxr-x  46 xyh  xyh  4096 Oct 10 10:07 xcrys_tmp

maybe the reason is Y.where is Y ???

2008/10/10 Tone Kokalj 

> On Fri, 2008-10-10 at 20:54 +0800, xu yuehua wrote:
> > yes ,i get the information :
> > jdong at sgi4700:~> env | grep XCRYSDEN
> > XCRYSDEN_SCRATCH=/disk2/jdong/xyh/xcrys_tmp
> > XCRYSDEN_TOPDIR=/disk2/jdong/xyh/XCrySDen-pre1.5bbin-static
>
> This looks OK.
>
> Are you sure you still get "Y/xc_***: no such file or directory" message
> or is the message different now?
>
> or does it says: "/disk2/jdong/xyh/xcrys_tmp/xc_***: ... no such file or
> directory"
>
> If it is the latter, it can be the problem related to write permission
> of /disk2/jdong/xyh/xcrys_tmp or to full disk.
>
> Regards, Tone
>
> --
> Tone Kokalj 
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
> +386-1-477-3523 // fax:+386-1-477-3822)
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20081010/9d976198/attachment.htm
 

[Pw_forum] xcrysden problem "error couldn't change working directory to "Y/xc_23632": no such file or directory

[xu yuehua]

yes ,i get the information :
jdong at sgi4700:~> env | grep XCRYSDEN
XCRYSDEN_SCRATCH=/disk2/jdong/xyh/xcrys_tmp
XCRYSDEN_TOPDIR=/disk2/jdong/xyh/XCrySDen-pre1.5bbin-static



2008/10/10 Tone Kokalj 

> On Fri, 2008-10-10 at 18:09 +0800, xu yuehua wrote:
> > en,en
> > i have set the absolute path XCRYSDEN_SCRATCH. but   the error stills
> > is the problem
> > of pre-compile ? i  found the errors are the same whether i run
> > the ./xcconfire or not (directly run xcrysden after tar xf the
> > package).
> >
> > the bashrc :
> >
> > ulimit -s unlimited
> > export PATH=~/bin/:$PATH
> > alias q=qstat
> > #
> > # this is for XCRYSDEN pre1.5b; added by XCRYSDEN installation on
> > # Fri Oct 10 09:32:28 UTC 2008
> > #
> > XCRYSDEN_TOPDIR=/disk2/jdong/xyh/XCrySDen-pre1.5bbin-static
> > XCRYSDEN_SCRATCH=/disk2/jdong/xyh/xcrys_tmp
> > export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH
> > PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:
> > $XCRYSDEN_TOPDIR/util"
>
> This definition is not compatible with "error couldn't change working
> directory to "Y/xc_23632"
>
> Can you execute: env | grep XCRYSDEN
>
> You should get something like:
>
> XCRYSDEN_TOPDIR=/disk2/jdong/xyh/XCrySDen-pre1.5bbin-static
> XCRYSDEN_SCRATCH=/disk2/jdong/xyh/xcrys_tmp
>
>  Regards, Tone
>
> --
> Tone Kokalj 
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
> +386-1-477-3523 // fax:+386-1-477-3822)
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20081010/b2e2930c/attachment-0001.htm
 

[Pw_forum] xcrysden problem "error couldn't change working directory to "Y/xc_23632": no such file or directory

[xu yuehua]

en,en
i have set the absolute path XCRYSDEN_SCRATCH. but   the error stills  is
the problem
of pre-compile ? i  found the errors are the same whether i run the
./xcconfire or not (directly run xcrysden after tar xf the package).

the bashrc :

ulimit -s unlimited
export PATH=~/bin/:$PATH
alias q=qstat
#
# this is for XCRYSDEN pre1.5b; added by XCRYSDEN installation on
# Fri Oct 10 09:32:28 UTC 2008
#
XCRYSDEN_TOPDIR=/disk2/jdong/xyh/XCrySDen-pre1.5bbin-static
XCRYSDEN_SCRATCH=/disk2/jdong/xyh/xcrys_tmp
export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH
PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/util"


2008/10/10 Tone Kokalj 

> On Fri, 2008-10-10 at 10:44 +0800, xu yuehua wrote:
> > hi everyone here:
> > i have installed the xcrysden (XCrySDen-pre1.5bbin-static) to linux
> > system .and when I ran   xcrysden, the
> >  graphic interface can appear, but could open any file ,when i open
> > some file ,the error message is below "error couldn't change working
> > directory to "Y/xc_23632": no such file or directory"
> > AND  i found out the Y  directory is generated automatically  in the
> > directory  where the software is running .
>
> You have specified relative pathname for XCRYSDEN_SCRATCH. A very bad
> idea. Thatwhy the "Y" directory is created in current directory. Please
> set XCRYSDEN_SCRATCH as absolute pathname, e.g., something
> like /scratch/$USER/xcrys_tmp
>
> Regards, Tone
>
> --
> Tone Kokalj 
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
> +386-1-477-3523 // fax:+386-1-477-3822)
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20081010/63504012/attachment.htm
 

[Pw_forum] xcrysden problem "error couldn't change working directory to "Y/xc_23632": no such file or directory

[Paolo Giannozzi]

xu yuehua wrote:

> the whole progress of installation:

I do not see where XCRYSDEN_SCRATCH is set. You need to:
- remove everything Xcrysden-related from everywhere,
   including .bashrc
- reinstall from scratch

> [..] is there any other problem ?

I have no problem at all! (well, actually I have one:
some genius has cut the electricity and the mail server
of the physics department is down...)

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

[Pw_forum] xcrysden problem "error couldn't change working directory to "Y/xc_23632": no such file or directory

[Tone Kokalj]

On Fri, 2008-10-10 at 21:28 +0800, xu yuehua wrote:
> the former.
> the problem is so strange. Y is what ?

Probably a symbol for "unknown" ...#@!#...

> i have not specify any directory named  as  "Y"
>  and i  
> ls  -al  found the 
>  drwxr-xr-x 4  jdong phys96 2008-10-10 17:56 Y
> 
> and the same  xcryden software in another machine is rather ok.and the
> ls -al 
> 
> drwxrwxr-x  46 xyh  xyh  4096 Oct 10 10:07 xcrys_tmp
>  
> maybe the reason is Y.where is Y ???

This is very awkward!

Wait, both Y and xcrys_tmp seems like a relative paths. From which
dirrectory you executed "ls" command?

What about the owenrship of scratch directory. On onw machine it is
jdongh:phys on the other xyh:xyh. Note that each user should create its
own scratch directory.

Regards, Tone

PS: Let us try to solve this via private channel not to populate
pw_forum too much ...

-- 
Tone Kokalj 
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)

[Pw_forum] xcrysden problem "error couldn't change working directory to "Y/xc_23632": no such file or directory

[Paolo Giannozzi]

xu yuehua wrote:

> the problem is so strange. Y is what ?
> i have not specify any directory named  as  "Y"

sure? really? didn't you answer "Y" to any question
during installation?

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

[Pw_forum] xcrysden problem "error couldn't change working directory to "Y/xc_23632": no such file or directory

[Tone Kokalj]

On Fri, 2008-10-10 at 20:54 +0800, xu yuehua wrote:
> yes ,i get the information :
> jdong at sgi4700:~> env | grep XCRYSDEN
> XCRYSDEN_SCRATCH=/disk2/jdong/xyh/xcrys_tmp
> XCRYSDEN_TOPDIR=/disk2/jdong/xyh/XCrySDen-pre1.5bbin-static

This looks OK. 

Are you sure you still get "Y/xc_***: no such file or directory" message
or is the message different now?

or does it says: "/disk2/jdong/xyh/xcrys_tmp/xc_***: ... no such file or
directory"

If it is the latter, it can be the problem related to write permission
of /disk2/jdong/xyh/xcrys_tmp or to full disk.

Regards, Tone

-- 
Tone Kokalj 
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)

[Pw_forum] xcrysden problem "error couldn't change working directory to "Y/xc_23632": no such file or directory

[Tone Kokalj]

On Fri, 2008-10-10 at 18:09 +0800, xu yuehua wrote:
> en,en  
> i have set the absolute path XCRYSDEN_SCRATCH. but   the error stills
> is the problem 
> of pre-compile ? i  found the errors are the same whether i run
> the ./xcconfire or not (directly run xcrysden after tar xf the
> package).
>  
> the bashrc :
> 
> ulimit -s unlimited
> export PATH=~/bin/:$PATH
> alias q=qstat
> #
> # this is for XCRYSDEN pre1.5b; added by XCRYSDEN installation on
> # Fri Oct 10 09:32:28 UTC 2008
> #
> XCRYSDEN_TOPDIR=/disk2/jdong/xyh/XCrySDen-pre1.5bbin-static
> XCRYSDEN_SCRATCH=/disk2/jdong/xyh/xcrys_tmp
> export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH
> PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:
> $XCRYSDEN_TOPDIR/util"

This definition is not compatible with "error couldn't change working
directory to "Y/xc_23632"

Can you execute: env | grep XCRYSDEN

You should get something like:

XCRYSDEN_TOPDIR=/disk2/jdong/xyh/XCrySDen-pre1.5bbin-static
XCRYSDEN_SCRATCH=/disk2/jdong/xyh/xcrys_tmp

Regards, Tone

-- 
Tone Kokalj 
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)

[Pw_forum] xcrysden problem "error couldn't change working directory to "Y/xc_23632": no such file or directory

[Tone Kokalj]

On Fri, 2008-10-10 at 10:44 +0800, xu yuehua wrote:
> hi everyone here:
> i have installed the xcrysden (XCrySDen-pre1.5bbin-static) to linux
> system .and when I ran   xcrysden, the
>  graphic interface can appear, but could open any file ,when i open
> some file ,the error message is below "error couldn't change working
> directory to "Y/xc_23632": no such file or directory"
> AND  i found out the Y  directory is generated automatically  in the
> directory  where the software is running . 

You have specified relative pathname for XCRYSDEN_SCRATCH. A very bad
idea. Thatwhy the "Y" directory is created in current directory. Please
set XCRYSDEN_SCRATCH as absolute pathname, e.g., something
like /scratch/$USER/xcrys_tmp

Regards, Tone

-- 
Tone Kokalj 
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel:
+386-1-477-3523 // fax:+386-1-477-3822)

[Pw_forum] xcrysden problem "error couldn't change working directory to "Y/xc_23632": no such file or directory

[xu yuehua]

hi everyone here:
i have installed the xcrysden (XCrySDen-pre1.5bbin-static) to linux system
.and *when I ran   xcrysden, the
** graphic interface can appear, but could open any file ,when i open some
file ,the error message is below "error couldn't change working directory to
"Y/xc_23632": no such file or directory"*
*AND  i found out the Y  directory is generated automatically  in the
directory  where the software is running . i have specified the
XCRYSDEN_SCRATCH  ,it seems the right place to store such files as
xc_23632.but it do not work. *
**
-- 
Xu Yuehua
physics Department of Nanjing university
China
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20081010/eb20eb2b/attachment.htm
 

[Pw_forum] xcrysden problem "error couldn't change working directory to "Y/xc_23632": no such file or directory

[Paolo Giannozzi]

xu yuehua wrote:

> "error couldn't change working directory to "Y/xc_23632": 
>  no such file or directory"

likely you did something wrong during installation. Remove
everything and try to reinstall

Paolo
-- 
Paolo Giannozzi, Democritos and University of Udine, Italy

[Pw_forum] XCRYSDEN

[S. K. S.]

  Dear PWscf Users,

  Is there any option in XCRYSDEN software where
  we can  increase the size or the font of  the
 "Coordinate System"  logo which usually
  comes below in the
  left side corner of any XCRYSDEN Picture?

  regards,

  S. K. S.
  JNCASR
  Bangalore
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20080522/5a5411ed/attachment.htm
 

[Pw_forum] XCrySDen question

[Ary Junior]

Hi, when I try:

xcrysden --pwi input.pw.inp

I get an error. I've checked my "xcrys_tmp/" directory and the "
pwi2xsf.xsf_out" for the structure was generated, but the "
pwi2xsf.xsf_out.raw" was not... Anybody can help me? The error is:

Running on platform: unix
Executing: /opt/XCrySDen-1.4.1bin-static/bin/ftnunit

*** the hardware does not support the stereo ***

TEXT-WIDGET: .a1.f1.t
Executing: sh /opt/XCrySDen-1.4.1bin-static/scripts/pwi2xsf.sh
/home/aryjr/DFT-GFQSI-ARY/Praticas/semicondutores/si-modelo.pw.inp
Error in startup script: error opening files:
~/xcrys_tmp/xc_4618/pwi2xsf.xsf_out and
~/xcrys_tmp/xc_4618/pwi2xsf.xsf_out.raw
while executing
"exec $system(BINDIR)/xsf2xsf $filedir $filedir.raw 3"
("eval" body line 1)
invoked from within
"eval {exec $system(BINDIR)/xsf2xsf $filedir $filedir.raw}
$xcMisc(reduce_to)"
(procedure "xsfOpen" line 26)
invoked from within
"xsfOpen $program_output .mesa"
(procedure "openExtStruct" line 183)
invoked from within
"openExtStruct 3 crystal external  [list sh
$system(TOPDIR)/scripts/pwi2xsf.sh]  pwi2xsf.xsf_out  {PWSCF Input File}
ANGS  -file $filedir  -preset pwIn..."
invoked from within
"if [file exists $filedir] {
# pop-up Viewer
ViewMol .
openExtStruct 3 crystal external  [list sh
$system(TOPDIR)/scripts/pwi2xsf.sh]  pwi2xsf..."
("--pwi" arm line 2)
invoked from within
"switch -glob -- $tag {
"-a" -
"--attrib*" {
set load_attributes 1
set file_attributes $filedir
}

"--xsf" -
"--xcr..."
(procedure "parseComLinArg" line 44)
invoked from within
"parseComLinArg [lrange $argv 2 end]"
invoked from within
"if { [llength $argv] > 2 } {
parseComLinArg [lrange $argv 2 end]
} else {
ViewMol .
}"
(file "/opt/XCrySDen-1.4.1bin-static/Tcl/xcInit.tcl" line 532)

Thanks very much!!!

Ary Junior
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20080212/71ca4c4d/attachment.htm
 

[Pw_forum] xcrysden error:***.rx.in is not pwscf input file

[xu yuehua]

about the format in my inputfile,you see a whitespace,it is just
effect here ,in my compute,it is rather in order .i can enclose it if you
could accept it .



2007/11/27, Tone Kokalj :
>
>
> On Tue, 2007-11-27 at 21:19 +0800, xu yuehua wrote:
> > ok .i will put my ***.rx.in here :i put it into XCRYSDEN.BUT
> > THE ERROR SAYS::**,rx.in is not pwscf input file !
>
> On my computer  xcrysden says:
>
> invalid number: incomprehensible list input
> apparent state: internal I/O
> lately reading sequential formatted internal IO
>
> Luckily xcrysden is picky enough to complain against your input file,
> because there is typo therein. In particular:
>
> > ATOMIC_POSITIONS { crystal }
> >  H0.1102739014   -0.07742902990.6115517241
> >  H0.1389927901   -0.04350134551.0285862069
> >  H   -0.10546646010.02154511120.6018620690
> >  H   -0.1078330245   -0.04130626000.2584827586
> >  H   -0.1324180.12410553951.0127586207
> >  H   - 0.07190011570.10953916680.5982068966
>
> Notice the whitespace after minus sign for last x-coordinate:
> - 0.0719001157
>
> Regards, Tone
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20071127/c39ad7d7/attachment.htm
 

[Pw_forum] xcrysden error:***.rx.in is not pwscf input file

[lan haiping]

 this part is so strange to me !!
CELL_PARAMETERS
33.0694,19.0926 0
 0.0 38.1852 0.0
 0.0  0.0 5.4820

On Nov 27, 2007 9:19 PM, xu yuehua  wrote:

> ok .i will put my ***.rx.in here :i put it into XCRYSDEN.BUT
> THE ERROR SAYS::**,rx.in is not pwscf input file !
> 
>   calculation  = "relax",
>   prefix   = "h2o",
>   pseudo_dir   = "/home/xyh/intel_espresso-3.2/pseudo",
>   outdir   = "/home/xyh/intel_espresso-3.2/tmp",
> /
> 
>   ibrav = 0,
>   nat   = 15,
>   ntyp  = 2,
>   ecutwfc   = 29.98744D0,
>   ecutrho   =200
>   occupations = "smearing",
>   smearing= "gauss",
>   degauss = 0.003D0,
> /
> 
>   conv_thr= 1.D-9,
>   mixing_beta = 0.2D0,
> /
> 
>   pot_extrapolation = "second_order",
>   wfc_extrapolation = "second_order",
> /
> CELL_PARAMETERS
> 33.0694,19.0926 0
>  0.0 38.1852 0.0
>  0.0  0.0 5.4820
> ATOMIC_SPECIES
> H  1.0  H.pbe-van_bm.UPF
> O 15.999 O.pbe-van_bm.UPF
> ATOMIC_POSITIONS { crystal }
>  H0.1102739014   -0.07742902990.6115517241
>  H0.1389927901   -0.04350134551.0285862069
>  H   -0.10546646010.02154511120.6018620690
>  H   -0.1078330245   -0.04130626000.2584827586
>  H   -0.1324180.12410553951.0127586207
>  H   - 0.07190011570.10953916680.5982068966
>  H0.0005944993   -0.09475764570.7058965517
>  H0.0681044664   -0.14812649061.07
>  H0.01635444670.12481782610.2592758621
>  H0.0639829858 0.05074118040.5938965517
>  O0.1321617646   -0.04395216940.6873103448
>  O   -0.0925246679   -0.03294558680.5714137931
>  O   -0.12000311090.10963521880.6811034483
>  O0.0571462440   -0.1256424289 0.753000
>  O0.01422796850.09913354050.5491724138
> K_POINTS {automatic}
> 1 1 6 0 0 0
>
>
>
> 2007/11/27, Tone Kokalj :
>
> >
> > On Tue, 2007-11-27 at 17:00 +0800, xu yuehua wrote:
> > > hi everyone:
> > > I have complete the relaxed work ,and want to see the details ,but
> > > when i put my input file **.rx.in into crysden  ,and the error message
> > > says:**,rx.in is not pwscf infut file !
> >
> > How can anybody say?
> > It is impossible to say anything without the input file that produces
> > the error !
> >
> > Regards, Tone
> >
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Xu Yuehua
> physics Department of Nanjing university
> China
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20071127/877326e4/attachment-0001.htm
 

[Pw_forum] xcrysden error:***.rx.in is not pwscf input file

[xu yuehua]

ok .i will put my ***.rx.in here :i put it into XCRYSDEN.BUT
THE ERROR SAYS::**,rx.in is not pwscf input file !

  calculation  = "relax",
  prefix   = "h2o",
  pseudo_dir   = "/home/xyh/intel_espresso-3.2/pseudo",
  outdir   = "/home/xyh/intel_espresso-3.2/tmp",
/

  ibrav = 0,
  nat   = 15,
  ntyp  = 2,
  ecutwfc   = 29.98744D0,
  ecutrho   =200
  occupations = "smearing",
  smearing= "gauss",
  degauss = 0.003D0,
/

  conv_thr= 1.D-9,
  mixing_beta = 0.2D0,
/

  pot_extrapolation = "second_order",
  wfc_extrapolation = "second_order",
/
CELL_PARAMETERS
33.0694,19.0926 0
 0.0 38.1852 0.0
 0.0  0.0 5.4820
ATOMIC_SPECIES
H  1.0  H.pbe-van_bm.UPF
O 15.999 O.pbe-van_bm.UPF
ATOMIC_POSITIONS { crystal }
 H0.1102739014   -0.07742902990.6115517241
 H0.1389927901   -0.04350134551.0285862069
 H   -0.10546646010.02154511120.6018620690
 H   -0.1078330245   -0.04130626000.2584827586
 H   -0.1324180.12410553951.0127586207
 H   -0.07190011570.10953916680.5982068966
 H0.0005944993   -0.09475764570.7058965517
 H0.0681044664   -0.14812649061.07
 H0.01635444670.12481782610.2592758621
 H0.06398298580.05074118040.5938965517
 O0.1321617646   -0.04395216940.6873103448
 O   -0.0925246679   -0.03294558680.5714137931
 O   -0.12000311090.10963521880.6811034483
 O0.0571462440   -0.12564242890.753000
 O0.01422796850.09913354050.5491724138
K_POINTS {automatic}
1 1 6 0 0 0



2007/11/27, Tone Kokalj :
>
>
> On Tue, 2007-11-27 at 17:00 +0800, xu yuehua wrote:
> > hi everyone:
> > I have complete the relaxed work ,and want to see the details ,but
> > when i put my input file **.rx.in into crysden  ,and the error message
> > says:**,rx.in is not pwscf infut file !
>
> How can anybody say?
> It is impossible to say anything without the input file that produces
> the error !
>
> Regards, Tone
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20071127/2b6a3429/attachment.htm
 

[Pw_forum] xcrysden error:***.rx.in is not pwscf input file

[xu yuehua]

hi everyone:
I have complete the relaxed work ,and want to see the details ,but when i
put my input file **.rx.in into crysden  ,and the error message says:**,
rx.in is not pwscf infut file !
and i want to ask what is input file in pwscf?
why **.rx.in is not ?
i need your help
bests

-- 
Xu Yuehua
physics Department of Nanjing university
China
-- next part --
An HTML attachment was scrubbed...
URL: 
http://www.democritos.it/pipermail/pw_forum/attachments/20071127/1cc483c1/attachment.htm
 

[Pw_forum] xcrysden error:***.rx.in is not pwscf input file

[Tone Kokalj]

On Tue, 2007-11-27 at 21:19 +0800, xu yuehua wrote:
> ok .i will put my ***.rx.in here :i put it into XCRYSDEN.BUT 
> THE ERROR SAYS::**,rx.in is not pwscf input file !

On my computer  xcrysden says:

invalid number: incomprehensible list input
apparent state: internal I/O
lately reading sequential formatted internal IO

Luckily xcrysden is picky enough to complain against your input file,
because there is typo therein. In particular:

> ATOMIC_POSITIONS { crystal }
>  H0.1102739014   -0.07742902990.6115517241 
>  H0.1389927901   -0.04350134551.0285862069
>  H   -0.10546646010.02154511120.6018620690
>  H   -0.1078330245   -0.04130626000.2584827586
>  H   -0.1324180.12410553951.0127586207
>  H   - 0.07190011570.10953916680.5982068966

Notice the whitespace after minus sign for last x-coordinate: 
- 0.0719001157

Regards, Tone

[Pw_forum] xcrysden error:***.rx.in is not pwscf input file

[Paolo Giannozzi]

On Nov 27, 2007, at 14:34 , lan haiping wrote:

>  this part is so strange to me !!
> CELL_PARAMETERS
> 33.0694,19.0926 0
>  0.0 38.1852 0.0
>  0.0  0.0 5.4820

it is a perfectly acceptable syntax
---
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] xcrysden error:***.rx.in is not pwscf input file

[Tone Kokalj]

On Tue, 2007-11-27 at 17:00 +0800, xu yuehua wrote:
> hi everyone: 
> I have complete the relaxed work ,and want to see the details ,but
> when i put my input file **.rx.in into crysden  ,and the error message
> says:**,rx.in is not pwscf infut file !

How can anybody say?
It is impossible to say anything without the input file that produces
the error !

Regards, Tone