xmd-support Mailing List for xmd (Page 7)

hi,everyone
I also met some trouble in melting,by using morse potential table inversed from the Energy table created by CASTEP,I found several alloys could not melt until 6000k,but our potentials are pretty well in atomic site preference calculation,and if simulate those alloys, it's also hard to find out equalibrium melting point,and after melted at high temperature,then we quench them, or clamp at  a lower temperature(such as 10k),system potential energy are continuing decreased and could hardly reach an equalibrium state.
 
If anyone know the reason for such phenomena? or how to solve them?
> Date: Mon, 14 Jul 2008 16:51:40 +0530> From: kau...@ya...> To: xmd...@li...> Subject: [Xmd-support] difference between perfect lattice and some defect.> > hello sir> regarding my previous querry you said that perfect lattice should not be used for melting point calculation because due to nucleation difficulty it will be super heating. but when we use any potential wich is semi empirical where we input elastic constant, melting point e.t.c apart from some data from first principle calculation to generate the potential table. and since we r using this potential in our calculation some defects are inherently there. so will it we correct to consider as perfect.> > another point is that for gold i am getting close to actual 1350 K, for Ni it is 200 K higher and for tungsten even it is not melting at 4000K. > > > > Bollywood, fun, friendship, sports and more. You name it, we have it on http://in.promos.yahoo.com/groups/bestofyahoo/> > -------------------------------------------------------------------------> Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW!> Studies have shown that voting for your favorite open source project,> along with a healthy diet, reduces your potential for chronic lameness> and boredom. Vote Now at http://www.sourceforge.net/community/cca08> _______________________________________________> Xmd-support mailing list> Xmd...@li...> https://lists.sourceforge.net/lists/listinfo/xmd-support
_________________________________________________________________
这里好多好玩的视频，用鼠标点到视频看看，有惊喜！
http://cnweb.search.live.com/video/results.aspx?q=%E5%A5%A5%E8%BF%90%E5%9C%A3%E7%81%AB&mkt=zh-cn&FORM=WLMTWC

Hello Kaush Gaya!

What method are you using to calculate the meting point? I suggest this one:

http://prola.aps.org/abstract/PRB/v49/i5/p3109_1

Good Day!

hello sir
regarding my previous querry you said that perfect lattice should not be used for melting point calculation because due to nucleation difficulty it will be super heating. but when we use any potential wich is semi empirical where we input elastic constant, melting point e.t.c apart from some data from first principle calculation to generate the potential table. and since we r using this potential in our calculation some defects are inherently there. so will it we correct to consider as perfect.

another point is that for gold i am getting close to actual 1350 K, for Ni it is 200 K higher and for tungsten even it is not melting at 4000K. 



      Bollywood, fun, friendship, sports and more. You name it, we have it on http://in.promos.yahoo.com/groups/bestofyahoo/

>1. i am not able to generate stress-strain curve on any metal for e.g
> Ni or gold?
 
Did you strain the lattice and write out the stress?  See the examples 
  http://xmd.sourceforge.net/examples/econst.xm.txt
  http://xmd.sourceforge.net/examples/econst2.xm.txt
which describe how to strain the lattice.  You can then use the WRITE
STRESS command to print the stress.


> 2. while calculating the melting point of metals i am not able to get
> consistent result. i am ploting energy vs temperature and the change
> is sudden energy i am considering to be the phase transformation.
> what else i do to get consistent result.

The melting point it very sensitive to the initial defects.  If you have
a perfect lattice, you will have to superheat the sample to start
melting, and then because of the superheated temperature, the melting
will happen very quickly.

Try putting a free surface or even an dislocation in your sample before
you try to melt it.


Hope that helps.

- Jon

On Fri, 2008-07-04 at 12:07 +0530, singh kaush wrote:
> hello
> 
> i have two question?
> 1. i am not able to generate stress-strain curve on any metal for e.g Ni or gold?
> 
> 2. while calculating the melting point of metals i am not able to get consistent result. i am ploting energy vs temperature and the change is sudden energy i am considering to be the phase transformation.
> what else i do to get consistent result.
> 
> 
> 
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hello

i have two question?
1. i am not able to generate stress-strain curve on any metal for e.g Ni or gold?

2. while calculating the melting point of metals i am not able to get consistent result. i am ploting energy vs temperature and the change is sudden energy i am considering to be the phase transformation.
what else i do to get consistent result.



      Meet people who discuss and share your passions. Go to http://in.promos.yahoo.com/groups/bestofyahoo/

Respected Sir,
                Thanks to your suggestion , I was able to scale them
differently. I was  trying the second method you mentioned while your mail
came . Another problem I am facing is I have to measure the cutting  and
thrust forces on the workpiece which are exerted due to its interaction with
the tool material during machining  . (  These forces are just the
components of external force on the workpiece due to the tool) .  When I use
the command " write extforce "  on the workpiece it is saying that it gives
this force only when you initialize an external force . I would be grateful
if you could suggest a way to write the external force components on
workpiece atoms arising only due to the interaction with tool atoms .
                Also I have been using the "potential eval" command to
create morse potential table values . Though I have got the parameter values
, the  cut off radius is not being mentioned in most of the scientific
articles that I refer to . Can you please suggest whether I can use the same
cut off radius value for interaction between workpiece atoms and for
interaction between workpiece and tool atoms. ( In the articles they don't
specify for which interaction the cut off radius has been specified . )
                             Thanking you Sir,

Yours sincerely,
                                                           S.Santosh.

Hi Santosh -


There are two ways to do this.  First, you could use the FILL command.
This can set the lattice constant you want when you create the
particles, so you won't need to scale them after.

The second way is to use the MOVE command; it can scale positions.  For
example, if you want to scale a group of selected particles in the X
direction, while at the same time leaving the particle at X=5 unmoved,
you could do this, 

  MOVE  1.1*(x-5) 0 0

Hope that helps.

- Jon



On Thu, 2008-04-17 at 01:00 +0530, santosh jeevan wrote:
> Hi,
>     I am S.Santosh.I am trying to do MDS of nano machining. Here I
> have to scale two different lattices  ( workpiece and tool ) by
> different scale factors . But in XMD using scale command,a ll atoms
> are scaled.Can someone please suggest a way to selectively scale
> atoms.
> 
>              Thanks in advance,
>                                                             Yours
> sincerely, 
>                                                                santosh
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Hi,
    I am S.Santosh.I am trying to do MDS of nano machining. Here I have to
scale two different lattices  ( workpiece and tool ) by different scale
factors . But in XMD using scale command,a ll atoms are scaled.Can someone
please suggest a way to selectively scale atoms.

             Thanks in advance,
                                                            Yours sincerely,

                                                               santosh

Hi,
    I am S.Santosh.I am trying to do MDS of nano machining.I need to scale
two materials(tool and workpiece) with different scale factors.But in XMD
when I scale , all particles are scaled. Is there any method to selectively
scale the particles?
                                                               Thanks in
advance,

                                                                santosh.

Hi,
    This is S.Santosh.I have been trying to carry MDS for nano machining
.For this I need to scale the tool and workpiece with different scale
factors.But in XMD

Dear All

I tried use VC++ 6.0 to compile xmd. It is OK but i don't know how to open 
the parallel process capability.
Later, I installed Cygwin which is a Unix emulator in window and installed 
GCC.

Section 6.2 of documentation tells me that to compile the parallel version, 
you must edit the Makefile and uncomment the following lines,
#THREAD_LIB=-lpthread
#DEF=-DUSE_THREAD_LIB -D_REENTRANT $(INTEL_PATCH)I cannot find the above two 
lines in makefile under /srcI hope to run the parallel computation in window 
platformPlease give me more instruction. ThanksWingkin 

Did you use the pre-compiled Windows version or did you compile from
source code?  If you used the Windows version, I would recommend trying
the version that you compile yourself.

If you did use the compiled version, could you send me your input files
so that I can test the program?

- Jon

On Sun, 2007-08-19 at 13:40 -0500, rohini yerram wrote:
> Hello Dr. Jon Rifkin,
>  
>             When i executed the crack  (companion program)
> http://xmd.sourceforge.net/other/crack/crack.html, after executing the
> crack command, in the output file, i didnt get 
> # Theoretical Critical Stress Intensity (erg/cm^2.5) 5.421088e
> +07         
>    # Applied Stress Intensity              (erg/cm^2.5) 5.421088e+07
> values. i got  the output file only with perfect lattice positions and
> displacements,with out any theoretical critical stress intensity and
> applied stress intensity. can you suggest me or give me some ideas
> regarding how to calculate stress intensity factors using crack
> command.
>  
> Rohini Yerram

Hello Dr. Jon Rifkin,

            When i executed the crack  (companion program)
http://xmd.sourceforge.net/other/crack/crack.html, after executing the crack
command, in the output file, i didnt get
# Theoretical Critical Stress Intensity (erg/cm^2.5) 5.421088e+07
   # Applied Stress Intensity              (erg/cm^2.5) 5.421088e+07
values. i got  the output file only with perfect lattice positions and
displacements,with out any theoretical critical stress intensity and applied
stress intensity. can you suggest me or give me some ideas regarding how to
calculate stress intensity factors using crack command.

Rohini Yerram

You can use the PLOT command to produce plots of the atoms in postscript
output.

- Jon

On Wed, 2007-08-01 at 18:54 -0500, rohini yerram wrote:
> hello XMD users,
> 
>  
> 
> I exexuted XMD for 3d stress program. 
> 
>  
> 
> clamp 300 
> 
> itemp 300
> 
> cmd 1000
> 
>  
> 
> i exexuted the MD simulation with the help of vmoviec and wmoviec. i
> want to take snapshots during the molecular dynamic simulation. 
> 
>  
> 
> please explain me how can i take snapshots for a particular time
> during the molecular dynamic simulation.
> 
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2 week ago I write.

 

Dear XMD users!

 

I have execute XMD for 3d MD simulation:

 

:

itemp 1000

clamp 1000

eunit K

esave 100 TK.txt

cmd 100000

...

 

I found that average value of kinetic energy is 1250.

If I set any other value for clamp, scale factor is the same - 1.25.

Please, explain my why.

 

My wondering was due to value of scale factor =1.25 < 1.5  (3/2).

Sorry for disturbance, 

I found that difference is due to my boundary condition.

 

 

hello XMD users,



I exexuted XMD for 3d stress program.



clamp 300

itemp 300

cmd 1000



i exexuted the MD simulation with the help of vmoviec and wmoviec. i want to
take snapshots during the molecular dynamic simulation.



please explain me how can i take snapshots for a particular time during the
molecular dynamic simulation.

Dear XMD users!

 

I have execute XMD for 3d MD simulation:

 

.

itemp 1000

clamp 1000

eunit K

esave 100 TK.txt

cmd 100000

...

 

I found that average value of kinetic energy is 1250.

If I set any other value for clamp, scale factor is the same - 1.25.

Please, explain my why.

 

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Ny0wNy0xMyANCg==

How can we obtain the engineering stress from the stress result in XMD ?

       
---------------------------------
Building a website is a piece of cake. 
Yahoo! Small Business gives you all the tools to get online.

> in XMD, basic thermostat is berendsen. (right?)

It is similar to the Berendsen thermostat, but not exactly. 
The Berendsen thermostat scales the atomic velocities by the factor 

sqrt(1 + (dt/L) * (T/T0-1))

where dt is the simulation time step, T0 is the thermostat setting, T is
the instantaneous temperature, the L is the "rise time".

In XMD, we use the following velocity scaling factor, 

sqrt((T/T0)^(dt/L))

where the value dt/L is called CSTEP in the CLAMP command.


> Is it possible to use another thermostat like Nose-Hoover?

Sorry, Nose-Hoover is not included in the XMD code.

- Jon

aW4gWE1ELCBiYXNpYyB0aGVybW9zdGF0IGlzIGJlcmVuZHNlbi4gKHJpZ2h0PykNCklzIGl0IHBv
c3NpYmxlIHRvIHVzZSBhbm90aGVyIHRoZXJtb3N0YXQgbGlrZSBOb3NlLUhvb3Zlcj8NCg==

Hi,

I found the attached was scrubbed. I do not whether somebody could 
receive it, let me paste it here.

# Reference:
# Fabrizio Cleri and Vittorio Rosato
# Tight-binding potentials for transition metals and alloys
# Physical Review B48, 22(1993)
# -----start--------
#Parameters for Ag
    eunit eV
    potential set eam 1
          calc A=0.1028
          calc Y=1.178
          calc p=10.928
      calc q=3.139
      calc a0=4.085
      calc r0=a0*sqrt(2.0)/2
    potential formula pair 1 1 5000 1.0 5.8
          2*A*exp(-p*(r/r0-1.0))
    potential formula dens 1 5000 1.0 5.8
          Y*Y*exp(-2*q*(r/r0-1.0))
    potential formula embed 1 50000 1e-8 2000
          -sqrt(r)
#    potential write plot pair 1 1
#   potential write plot dens 1
#    potential write plot embed 1
#--------end--------

Best,

Dr. Hongbo Liu

xmd...@li... wrote:
> Send Xmd-support mailing list submissions to
> 	xmd...@li...
>
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://lists.sourceforge.net/lists/listinfo/xmd-support
> or, via email, send a message with subject or body 'help' to
> 	xmd...@li...
>
> You can reach the person managing the list at
> 	xmd...@li...
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Xmd-support digest..."
>
>
> Today's Topics:
>
>    1. Re: Xmd-support Digest, Vol 7, Issue 1 SMTB potential
>       (Dr. Hong Bo Liu)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 10 Apr 2007 08:23:24 -0500
> From: "Dr. Hong Bo Liu" <hb...@im...>
> Subject: Re: [Xmd-support] Xmd-support Digest, Vol 7, Issue 1 SMTB
> 	potential
> To: xmd...@li...
> Message-ID: <461...@im...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> Attached is SMTB potential for silver. It is a text file and can be used 
> directly in the XMD input file.
>
> Best,
>
> Dr. Hongbo Liu
>
> xmd...@li... wrote:
>   
>> Send Xmd-support mailing list submissions to
>> 	xmd...@li...
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> 	https://lists.sourceforge.net/lists/listinfo/xmd-support
>> or, via email, send a message with subject or body 'help' to
>> 	xmd...@li...
>>
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>> 	xmd...@li...
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Xmd-support digest..."
>>
>>
>> Today's Topics:
>>
>>    1. EAM potential (Justo Rojas Tapia)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Wed, 04 Apr 2007 13:55:21 -0500
>> From: Justo Rojas Tapia <jr...@ip...>
>> Subject: [Xmd-support] EAM potential
>> To: xmd...@li...
>> Message-ID: <117...@jr...>
>> Content-Type: text/plain;	charset="iso-8859-1"
>>
>> Hello everybody,
>>
>> I need to obtain the EAM potential of silver in appropriate format for
>> the XMD. Could anybody  help me?
>>
>> Thanks in advance
>>
>> Justo Rojas
>>
>> Instituto Peruano de Enegia Nuclear
>>
>>
>>
>>
>> Este mensaje electr?nico y sus documentos adjuntos, s?lo son para conocimiento y uso de la persona(s) y/o Instituci?n a quien va dirigido.
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>> End of Xmd-support Digest, Vol 7, Issue 1
>> *****************************************
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>>   
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>   

Hi,

Attached is SMTB potential for silver. It is a text file and can be used 
directly in the XMD input file.

Best,

Dr. Hongbo Liu

xmd...@li... wrote:
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> 	xmd...@li...
>
> To subscribe or unsubscribe via the World Wide Web, visit
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> or, via email, send a message with subject or body 'help' to
> 	xmd...@li...
>
> You can reach the person managing the list at
> 	xmd...@li...
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Xmd-support digest..."
>
>
> Today's Topics:
>
>    1. EAM potential (Justo Rojas Tapia)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 04 Apr 2007 13:55:21 -0500
> From: Justo Rojas Tapia <jr...@ip...>
> Subject: [Xmd-support] EAM potential
> To: xmd...@li...
> Message-ID: <117...@jr...>
> Content-Type: text/plain;	charset="iso-8859-1"
>
> Hello everybody,
>
> I need to obtain the EAM potential of silver in appropriate format for
> the XMD. Could anybody  help me?
>
> Thanks in advance
>
> Justo Rojas
>
> Instituto Peruano de Enegia Nuclear
>
>
>
>
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Hello everybody,

I need to obtain the EAM potential of silver in appropriate format for
the XMD. Could anybody  help me?

Thanks in advance

Justo Rojas

Instituto Peruano de Enegia Nuclear




Este mensaje electr=F3nico y sus documentos adjuntos, s=F3lo son para =
conocimiento y uso de la persona(s) y/o Instituci=F3n a quien va =
dirigido.
 Si usted no es el destinatario(s), agradeceremos se abstenga de =
copiarlos, divulgarlos o usarlos, as=ED como agradeceremos comunique =
este error a la siguiente direcci=F3n pos...@ip... y borre de =
su equipo este mensaje y los documentos adjuntos en caso contenga =
alguno.
 La lectura de este mensaje presupone que usted comprende y acepta los =
t=E9rminos de este aviso

Frank -

> i sent this patch to jon.rifkin but got no answer so far. i wonder
whether he is still maintaining xmd. that's why i decided to send the
patch to the mailinglist, too.

I didn't respond to your original email because I din't get a chanced to
check my mail on Friday, but I'm glad you followed up on the mailing list.

> please find attached a patch to fix the macro for the derivative of f_a.
> this could be the reason for the 'factor 2 off' concerning
> BondStrengthD, and if that's for sure, you most probably want to skip
the > correction.
Thanks for the tip.  I will correct the code.  However, the code you
corrected has no effect on BoundStrengthD, because is not used in the
program, since the only call to that MACRO is inactive because it lies
between the directives
  #if 0
  #endif

My recollection is that I disabled that MACRO code because it didn't work.
 And, it probably didn't work because of the error you found.

> i would be very thankful for any information concerning analytical
> calculation of the virial for tersoff potentials (dV_ij / dr x r_ij). as
> far as i understood, you do the pressure calc numerically by variation
> of the site lengths. any ideas?
XMD calculates virial term you cite for the Tersoff potential using an
analytically derived formula.  Unfortunately, I don't have the derivation
on hand.  Basically, it the expressing the system potential energy as a
sum of the atomic positions of the Tersoff functional form, and then
expressing the  atomic positions as a function of a uniform system strain,
and then finally taking the derivate of that as a function of the strain.

I hope that helps.

- Jon