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Cc: jnkim@uiuc.edu
Subject: [Ohmms-dev] AntiSymTensor
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Should AntiSymTensor and SymTensor behave
like Tensor when used in ParticleAttirb<>?

Specifically,  consider code fragment:

   typedef Tensor<double,3> Tensor_t;
   typedef AntiSymTensor<double,3> AntiSymTensor_t;

   ParticleAttrib<Tensor_t> tensor;
   ParticleAttrib<AntiSymTensor_t> antisymtensor;

   t =3D 0.0e0;=20
   antisymtensor =3D 0.0e0;

The last assignment triggers error.  Above is a mock version
of problem.  I can forward exact source if necessary.  Can
you verify that above should work?

Compile-time error is particularly nasty, but maybe it will
shed some light.  This is real error, not from toy problem above.
In real example I am using AntiSymTensor for torque.  When I
switch Torque_t to a simple Tensor<> compiles fine (but torque
is not a tensor, so not a solution).

g++ -DHAVE_CONFIG_H -I. -I../../src -I. -I../../src/OOMPI    =
-ftemplate-depth-60 -DADD_  -I/usr/include/libxml2 -c -o =
FFHydroSDPotential.o `test -f 'StokesianDynamics/FFHydroSDPotential.cpp' =
|| echo '../../src/'`StokesianDynamics/FFHydroSDPotential.cpp
../../src/PETE/OperatorTags.h: In member function `BinaryReturn<T1, T2,
   OpAssign>::Type_t OpAssign::operator()(const T1&, const T2&) const =
[with T1
   =3D AntiSymTensor<Scalar_t, 3>, T2 =3D double]':
../../src/ParticleBase/ParticleAttrib.cpp:1135:   instantiated from =
`void evaluate(ParticleAttrib<T1>&, const Op&, const Expression<T2>&) =
[with T =3D AntiSymTensor<Scalar_t, 3>, Op =3D OpAssign, RHS =3D =
Scalar<double>]'
../../src/ParticleBase/ParticleAttrib.cpp:974:   instantiated from =
`ParticleAttrib<T1>& assign(ParticleAttrib<T1>&, const RHS&) [with T1 =
=3D AntiSymTensor<Scalar_t, 3>, RHS =3D double]'
../../src/ParticleBase/ParticleAttrib.h:139:   instantiated from =
`ParticleAttrib<T>& ParticleAttrib<T>::operator=3D(const RHS&) [with RHS =
=3D double, T =3D AntiSymTensor<Scalar_t, 3>]'
../../src/StokesianDynamics/FFHydroSDPotential.cpp:57:   instantiated =
from here
../../src/PETE/OperatorTags.h:757: could not convert =
`(++a)->AntiSymTensor<T,
   D>::operator=3D(const T&) [with T =3D Scalar_t, unsigned int D =3D =
3]((+b))' to `
   AntiSymTensor<Scalar_t, 3>&'




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<DIV><FONT face=3DArial size=3D2>Should AntiSymTensor and SymTensor=20
behave</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>like Tensor when used in=20
ParticleAttirb&lt;&gt;?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Specifically,&nbsp; consider code=20
fragment:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>&nbsp;&nbsp; typedef =
Tensor&lt;double,3&gt;=20
Tensor_t;</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>&nbsp;&nbsp; typedef =
AntiSymTensor&lt;double,3&gt;=20
AntiSymTensor_t;</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>&nbsp;&nbsp; =
ParticleAttrib&lt;Tensor_t&gt;=20
tensor;</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>&nbsp;&nbsp; =
ParticleAttrib&lt;AntiSymTensor_t&gt;=20
antisymtensor;</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>&nbsp;&nbsp; t =3D 0.0e0; </FONT></DIV>
<DIV><FONT face=3DArial size=3D2>&nbsp;&nbsp; antisymtensor =3D =
0.0e0;</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>The last assignment triggers =
error.&nbsp; Above is=20
a mock version</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>of problem.&nbsp; I can forward exact =
source if=20
necessary.&nbsp; Can</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>you verify that above should =
work?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Compile-time error is particularly =
nasty, but maybe=20
it will</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>shed some light.&nbsp; This is real =
error, not from=20
toy problem above.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>In real example I am using =
AntiSymTensor for=20
torque.&nbsp; When I</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>switch Torque_t to a simple =
Tensor&lt;&gt; compiles=20
fine (but torque</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>is not a tensor, so not a =
solution).</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>g++ -DHAVE_CONFIG_H -I. -I../../src -I. =

-I../../src/OOMPI&nbsp;&nbsp;&nbsp; -ftemplate-depth-60 -DADD_&nbsp;=20
-I/usr/include/libxml2 -c -o FFHydroSDPotential.o `test -f=20
'StokesianDynamics/FFHydroSDPotential.cpp' || echo=20
'../../src/'`StokesianDynamics/FFHydroSDPotential.cpp<BR>../../src/PETE/O=
peratorTags.h:=20
In member function `BinaryReturn&lt;T1, T2,<BR>&nbsp;&nbsp; =
OpAssign&gt;::Type_t=20
OpAssign::operator()(const T1&amp;, const T2&amp;) const [with=20
T1<BR>&nbsp;&nbsp; =3D AntiSymTensor&lt;Scalar_t, 3&gt;, T2 =3D=20
double]':<BR>../../src/ParticleBase/ParticleAttrib.cpp:1135:&nbsp;&nbsp; =

instantiated from `void evaluate(ParticleAttrib&lt;T1&gt;&amp;, const =
Op&amp;,=20
const Expression&lt;T2&gt;&amp;) [with T =3D AntiSymTensor&lt;Scalar_t, =
3&gt;, Op=20
=3D OpAssign, RHS =3D=20
Scalar&lt;double&gt;]'<BR>../../src/ParticleBase/ParticleAttrib.cpp:974:&=
nbsp;&nbsp;=20
instantiated from `ParticleAttrib&lt;T1&gt;&amp;=20
assign(ParticleAttrib&lt;T1&gt;&amp;, const RHS&amp;) [with T1 =3D=20
AntiSymTensor&lt;Scalar_t, 3&gt;, RHS =3D=20
double]'<BR>../../src/ParticleBase/ParticleAttrib.h:139:&nbsp;&nbsp;=20
instantiated from `ParticleAttrib&lt;T&gt;&amp;=20
ParticleAttrib&lt;T&gt;::operator=3D(const RHS&amp;) [with RHS =3D =
double, T =3D=20
AntiSymTensor&lt;Scalar_t,=20
3&gt;]'<BR>../../src/StokesianDynamics/FFHydroSDPotential.cpp:57:&nbsp;&n=
bsp;=20
instantiated from here<BR>../../src/PETE/OperatorTags.h:757: could not =
convert=20
`(++a)-&gt;AntiSymTensor&lt;T,<BR>&nbsp;&nbsp; D&gt;::operator=3D(const =
T&amp;)=20
[with T =3D Scalar_t, unsigned int D =3D 3]((+b))' to `<BR>&nbsp;&nbsp;=20
AntiSymTensor&lt;Scalar_t, 3&gt;&amp;'<BR></FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV></BODY></HTML>

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From jnkim@ncsa.uiuc.edu  Tue Apr 27 16:15:10 2004
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To: "david richie" <drichie@hpti.com>, <ohmms-dev@mcc.uiuc.edu>
From: Jeongnim Kim <jnkim@ncsa.uiuc.edu>
Subject: Re: [Ohmms-dev] AntiSymTensor
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Let me know if you can compile

antisymtesor[0] = 0.0;

At 05:02 PM 4/27/2004 -0400, david richie wrote:
>Should AntiSymTensor and SymTensor behave
>like Tensor when used in ParticleAttirb<>?
>
>Specifically,  consider code fragment:
>
>    typedef Tensor<double,3> Tensor_t;
>    typedef AntiSymTensor<double,3> AntiSymTensor_t;
>
>    ParticleAttrib<Tensor_t> tensor;
>    ParticleAttrib<AntiSymTensor_t> antisymtensor;
>
>    t = 0.0e0;
>    antisymtensor = 0.0e0;
>
>The last assignment triggers error.  Above is a mock version
>of problem.  I can forward exact source if necessary.  Can
>you verify that above should work?
>
>Compile-time error is particularly nasty, but maybe it will
>shed some light.  This is real error, not from toy problem above.
>In real example I am using AntiSymTensor for torque.  When I
>switch Torque_t to a simple Tensor<> compiles fine (but torque
>is not a tensor, so not a solution).
>
>g++ -DHAVE_CONFIG_H -I. -I../../src -I. 
>-I../../src/OOMPI    -ftemplate-depth-60 -DADD_  -I/usr/include/libxml2 -c 
>-o FFHydroSDPotential.o `test -f 
>'StokesianDynamics/FFHydroSDPotential.cpp' || echo 
>'../../src/'`StokesianDynamics/FFHydroSDPotential.cpp
>../../src/PETE/OperatorTags.h: In member function `BinaryReturn<T1, T2,
>    OpAssign>::Type_t OpAssign::operator()(const T1&, const T2&) const 
> [with T1
>    = AntiSymTensor<Scalar_t, 3>, T2 = double]':
>../../src/ParticleBase/ParticleAttrib.cpp:1135:   instantiated from `void 
>evaluate(ParticleAttrib<T1>&, const Op&, const Expression<T2>&) [with T = 
>AntiSymTensor<Scalar_t, 3>, Op = OpAssign, RHS = Scalar<double>]'
>../../src/ParticleBase/ParticleAttrib.cpp:974:   instantiated from 
>`ParticleAttrib<T1>& assign(ParticleAttrib<T1>&, const RHS&) [with T1 = 
>AntiSymTensor<Scalar_t, 3>, RHS = double]'
>../../src/ParticleBase/ParticleAttrib.h:139:   instantiated from 
>`ParticleAttrib<T>& ParticleAttrib<T>::operator=(const RHS&) [with RHS = 
>double, T = AntiSymTensor<Scalar_t, 3>]'
>../../src/StokesianDynamics/FFHydroSDPotential.cpp:57:   instantiated from 
>here
>../../src/PETE/OperatorTags.h:757: could not convert `(++a)->AntiSymTensor<T,
>    D>::operator=(const T&) [with T = Scalar_t, unsigned int D = 3]((+b))' 
> to `
>    AntiSymTensor<Scalar_t, 3>&'
>
>
>_______________________________________________
>Ohmms-dev mailing list
>Ohmms-dev@mcc.uiuc.edu
>http://mcc0.mcc.uiuc.edu/mailman/listinfo/ohmms-dev

Best wishes,
Jeongnim Kim

---------------------------------------------------------------
Jeongnim Kim                           e-mail: jnkim@uiuc.edu
NCSA                                   Tel: 217-244-6319 (NCSA)
Beckman Institute                           217-244-4971 (MCC)
405 N Mathews Av.                      Fax: 217-244-2909
Urbana, IL 61801
---------------------------------------------------------------


From DRichie@HPTI.com  Wed Apr 28 15:46:07 2004
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Subject: [Ohmms-dev] exp() and ParticleAttrib<TinyVector<double,3> >
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does there exist support for using exp() function on ParticleAttirb<> =
container?
If not, can you suggest closest function to use as starting point in =
OhmmsPETE/

Example:

   typedef TinyVector<double,3> Position_t;
   typedef ParticleAttrib<Position_t> ParticlePosition_t;
   double alpha =3D 0.9;
   ParticlePosition_t& R1,R2;

   R1 =3D something
   R2 =3D exp(-R1/alpha);

???

-David



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<DIV><FONT face=3DArial size=3D2>does there exist support for using =
exp() function=20
on ParticleAttirb&lt;&gt; container?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>If not, can you suggest closest =
function to use as=20
starting point in OhmmsPETE/</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Example:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>&nbsp;&nbsp; typedef =
TinyVector&lt;double,3&gt;=20
Position_t;</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>&nbsp;&nbsp; typedef=20
ParticleAttrib&lt;Position_t&gt; ParticlePosition_t;</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>&nbsp;&nbsp; double alpha =3D =
0.9;</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>&nbsp;&nbsp; ParticlePosition_t&amp;=20
R1,R2;</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>&nbsp;&nbsp; R1 =3D =
something</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>&nbsp;&nbsp; R2 =3D =
exp(-R1/alpha);</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>???</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>-David</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
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Download is updated:

http://www.mcc.uiuc.edu/ohmms/sw/archive.html

I will use mailing list for such information from now on.


Best wishes,
Jeongnim Kim

---------------------------------------------------------------
Jeongnim Kim                           e-mail: jnkim@uiuc.edu
NCSA                                   Tel: 217-244-6319 (NCSA)
Beckman Institute                           217-244-4971 (MCC)
405 N Mathews Av.                      Fax: 217-244-2909
Urbana, IL 61801
---------------------------------------------------------------


From jnkim@ncsa.uiuc.edu  Fri Jul 23 10:46:38 2004
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Subject: [Ohmms-dev] a patch is uploaded
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Check out for a patch
http://www.mcc.uiuc.edu/ohmms/sw/archive.html

Ohmms-v0.2.4-patch-20040723.tar

a patch for cmake and ParticleIO. Apply it in the top directory.

Contains:
         CMakeLists.txt
         CMake/FindLapack.cmake
         src/FortranLib/CMakeLists.txt
         src/ParticleIO/RecordParticleAttrib.h
         src/ParticleIO/RecordParticle.cpp


Best wishes,
Jeongnim Kim

---------------------------------------------------------------
Jeongnim Kim                           e-mail: jnkim@uiuc.edu
NCSA                                   Tel: 217-244-6319 (NCSA)
Beckman Institute                           217-244-4971 (MCC)
405 N Mathews Av.                      Fax: 217-244-2909
Urbana, IL 61801
---------------------------------------------------------------


From jnkim@ncsa.uiuc.edu  Fri Jul 23 11:09:26 2004
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Cc: Richard Hennig <rhennig@pacific.mps.ohio-state.edu>
Subject: [Ohmms-dev] Re: lattice.set
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I was aware of the potential problem but let it go until you point it out.
I added to the patch and updated cvs.
Use
myPtcl->Lattice.update(h0);

instead of set.

At 11:42 AM 7/23/2004 -0400, you wrote:
>Hi Jeongnim,
>
>I added my name to the ohmms e-mail list and will let the others here know
>about it.
>
>Forget about my comment on the restart file.  I used a wrong stride value
>and ohmms did not write out the last MD step results.  Now I use stride=1
>and it writes out the correct lattice parameters.  But the potential
>routine still does not get the correct NN list.
>
>Thanks for your help.
>
>Cheers,
>  Richard
>
>
>On Fri, 23 Jul 2004, Jeongnim Kim wrote:
>
> > I know why your xyz file was wrong. Forgot to use reference, since I
> > totally forgot that you may change the lattice! I fixed them.
> >
> > For your question: I do not understand what you mean by the last one.
> > Not having the original lattice is okay if you have changed it:
> > If you have set it with a new value, the restart will use the value set 
> by it.
> > But, what is the last one?
> >
> > BTW, tell people to subscribe to the mailing list. I will notice any cvs
> > update that may affect to the calculations, like this case.
> >
> > mcc0.mcc.uiuc.edu/mailman/listinfo/ohmms-dev
> >
> > I will probably ignore any e-mail about the code and documentation sent to
> > me directly. Or, at least, I will answer to the mailing list not to the
> > questioner.
> >
> > At 11:29 AM 7/23/2004 -0400, you wrote:
> > >Hi Jeongnim,
> > >
> > >The restart file contains the lattice parameter after the first MD step,
> > >not the last one and also not the original lattice parameter either!
> > >That is strange.  Do you understand this?
> > >
> > >Richard
> > >
> > >
> > >
> > >
> > >On Fri, 23 Jul 2004, Jeongnim Kim wrote:
> > >
> > > > Can you check the restart.xml file?
> > > >
> > > > At 10:47 AM 7/23/2004 -0400, you wrote:
> > > > >Hi Jeongnim,
> > > > >
> > > > >I am debugging the EPN propagator using your latest ohmms version 2.4.
> > > > >Using the lattice.set function, I still do not get the correct nearest
> > > > >neighbor list in my potential evaluation after the unit cell has
> > > > >changed shape.  Also, when I am looking at the output xyz file, the
> > > > >lattice vectors never change.
> > > > >
> > > > >I added a few debug print statements to EPNVerlet.cpp and
> > > > >Lattice/CrystalLattice.cpp to see how the variables change and 
> that the
> > > > >lattice gets updated.  From what I can tell the lattice gets set in
> > > > >Lattice.set correctly but when it is written out into the xyz file it
> > > > >still writes the original value.  This old value also seems to be 
> used in
> > > > >the NNEngine.
> > > > >
> > > > >Do you have any idea what I am doing wrong here. Thanks for your help.
> > > > >
> > > > >Cheers,
> > > > >  Richard
> > > >
> > > > Best wishes,
> > > > Jeongnim Kim
> > > >
> > > > ---------------------------------------------------------------
> > > > Jeongnim Kim                           e-mail: jnkim@uiuc.edu
> > > > NCSA                                   Tel: 217-244-6319 (NCSA)
> > > > Beckman Institute                           217-244-4971 (MCC)
> > > > 405 N Mathews Av.                      Fax: 217-244-2909
> > > > Urbana, IL 61801
> > > > ---------------------------------------------------------------
> > > >
> >
> > Best wishes,
> > Jeongnim Kim
> >
> > ---------------------------------------------------------------
> > Jeongnim Kim                           e-mail: jnkim@uiuc.edu
> > NCSA                                   Tel: 217-244-6319 (NCSA)
> > Beckman Institute                           217-244-4971 (MCC)
> > 405 N Mathews Av.                      Fax: 217-244-2909
> > Urbana, IL 61801
> > ---------------------------------------------------------------
> >

Best wishes,
Jeongnim Kim

---------------------------------------------------------------
Jeongnim Kim                           e-mail: jnkim@uiuc.edu
NCSA                                   Tel: 217-244-6319 (NCSA)
Beckman Institute                           217-244-4971 (MCC)
405 N Mathews Av.                      Fax: 217-244-2909
Urbana, IL 61801
---------------------------------------------------------------


From jnkim@ncsa.uiuc.edu  Fri Jul 23 13:11:24 2004
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It is correct. Something is not working with sprng. Even though autoconfig 
finds it, it does not link it correctly. Using sprng is the hardest one and 
I have not fully autoconfig-ed or cmake-ed it.

A practical fix:
add -lsprng to LIBS in src/OhmmsApp/Makefile
or

you can have LIBS="-lsprng" with the configuration. It is supposed to append.

Will find a better fix soon.

At 01:42 PM 7/23/2004 -0400, you wrote:
>Jeongnim,
>
>I have succesfully compiled Ohmms-v2.4.0.  However, to compile properly, I
>must use --without-sprng.  If I try to compile with sprng, I get errors
>like "double_rng not found", etc.  The installed sprng library on the
>local linuces here is very old -- could this be the problem, or am I
>doing something wrong.
>
>Here's the configure options I use to try to enable sprng:
>
>../configure --with-cxx=gcc --with-sprng=/usr/local
>--with-sprng-include=/usr/local/include --with-sprng-libdir=/usr/local/lib
>
>To repeat, is the problem my configure options or is it a problem with the
>installed libraries?
>
>Cheers,
>~Kaden
>
>Office phone:  (614) 292-2887

Best wishes,
Jeongnim Kim

---------------------------------------------------------------
Jeongnim Kim                           e-mail: jnkim@uiuc.edu
NCSA                                   Tel: 217-244-6319 (NCSA)
Beckman Institute                           217-244-4971 (MCC)
405 N Mathews Av.                      Fax: 217-244-2909
Urbana, IL 61801
---------------------------------------------------------------


From jnkim@ncsa.uiuc.edu  Fri Jul 23 14:28:29 2004
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Cc: Dallas Trinkle <trinkle@pacific.mps.ohio-state.edu>
Subject: [Ohmms-dev] Re: getting out the forces from a run
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Check out src/ParticleTags.cpp
or code documentation.

force does not exist but "f" does.

At 03:21 PM 7/23/2004 -0400, you wrote:
>   So I'm trying to modify the bulksi example to have it spit out the
>forces as well as the atom positions; so I modified part of the xml to
>look like this...
>
>       <loop blocks="5" steps="1000">
>         <record name="ensemble" stride="100" />
>         <record name="particle" format="ascii" stride="500">
>           <attrib name="position" datatype="xmolArray"></attrib>
>           <attrib name="force" datatype="xmolArray"></attrib>
>           <attrib name="e" datatype="scalarArray"></attrib>
>         </record>
>         <record name="particle" stride="500" condition="overwrite" />
>       </loop>
>
>...by adding the <attrib name="force"...> line.  I got a file, but it's
>all zeroes... which makes me think that I'm not using the right name for
>the attribute.
>
>   Is there a place in the documentation where the attributes of a particle
>are listed, so that I could find what name I'm supposed to use to get
>particle forces?  I was probably looking at the wrong documentation on the
>ohmms website.  Thanks; --d

Best wishes,
Jeongnim Kim

---------------------------------------------------------------
Jeongnim Kim                           e-mail: jnkim@uiuc.edu
NCSA                                   Tel: 217-244-6319 (NCSA)
Beckman Institute                           217-244-4971 (MCC)
405 N Mathews Av.                      Fax: 217-244-2909
Urbana, IL 61801
---------------------------------------------------------------


From hazzard@pacific.mps.ohio-state.edu  Fri Jul 23 14:35:36 2004
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Jeongnim,

I have tried several variations on this theme: in the makefile, at the end
of the configure command, etc..  No luck, even though -lsprng is there in
many ways.  Can you have a look at what I'm doing?

/oahu/disk2/hazzard/inter/Ohmms-v2.4.0.DuTest2/linuxkadenbin

Cheers,
~Kaden

Office phone:  (614) 292-2887

On Fri, 23 Jul 2004, Jeongnim Kim wrote:

> It is correct. Something is not working with sprng. Even though autoconfig
> finds it, it does not link it correctly. Using sprng is the hardest one and
> I have not fully autoconfig-ed or cmake-ed it.
>
> A practical fix:
> add -lsprng to LIBS in src/OhmmsApp/Makefile
> or
>
> you can have LIBS="-lsprng" with the configuration. It is supposed to append.
>
> Will find a better fix soon.

From jnkim@ncsa.uiuc.edu  Fri Jul 23 15:37:21 2004
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I found out a very simple trick after many trials and errors with numerous 
libraries.

This applies to any package that uses autoconf/automake.  You can always 
set the values like

LIBS
CXXFLAGS

to by-pass potential problems during configure. A typical problem is with 
sprng/hdf5 installed in the standard directories: /usr/local/include and 
/usr/local/lib (don't know why but I'm also very new with autoconf/automake).

For example, this will get you somewhere:

configure --with-cxx=gcc LIBS="-lsprng -lgmp"


Best wishes,
Jeongnim Kim

---------------------------------------------------------------
Jeongnim Kim                           e-mail: jnkim@uiuc.edu
NCSA                                   Tel: 217-244-6319 (NCSA)
Beckman Institute                           217-244-4971 (MCC)
405 N Mathews Av.                      Fax: 217-244-2909
Urbana, IL 61801
---------------------------------------------------------------


From jnkim@ncsa.uiuc.edu  Mon Jul 26 18:17:27 2004
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Hi All,

I have made a package called ohmmscore which contains only the base classes.
It is used for abstraction penalty timing analysis and I plan to add more 
test codes. If you are interested in, check out

http://www.mcc.uiuc.edu/ohmms/others/ohmmscore.html


Best wishes,
Jeongnim Kim

---------------------------------------------------------------
Jeongnim Kim                           e-mail: jnkim@uiuc.edu
NCSA                                   Tel: 217-244-6319 (NCSA)
Beckman Institute                           217-244-4971 (MCC)
405 N Mathews Av.                      Fax: 217-244-2909
Urbana, IL 61801
---------------------------------------------------------------


From jnkim@ncsa.uiuc.edu  Tue Aug  3 09:01:45 2004
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cvs update include:

i) FreeEnergyMC by Hazzard and Welch. This package is excluded from public 
distributions.
ii) Breaking up Particle/ParticleSet.cpp. This was done to speed up 
compilations on IBM clusters.
iii) --with-hdf5=DIR --with-hdf5-libs to configure HDF5 library.
iv) --with-sprng=DIR --with-sprng-libs to configure sprng library
v) cmake update: cmake is a preferred way to configure ohmms on IBM 
clusters.  Many GNU tools are either broken or outdated.


Best wishes,
Jeongnim Kim

---------------------------------------------------------------
Jeongnim Kim                           e-mail: jnkim@uiuc.edu
NCSA                                   Tel: 217-244-6319 (NCSA)
Beckman Institute                           217-244-4971 (MCC)
405 N Mathews Av.                      Fax: 217-244-2909
Urbana, IL 61801
---------------------------------------------------------------


From jnkim@ncsa.uiuc.edu  Thu Aug 12 14:26:27 2004
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Find Ohmms-v0.2.4-daily-20040812.tgz
at
http://www.mcc.uiuc.edu/ohmms/sw/archive.html

It contains the changes due to removal of IonID from ParticleBase.
A more neutral name GroupID is used for the codes and all the changes are 
made accordingly.


Best wishes,
Jeongnim Kim

---------------------------------------------------------------
Jeongnim Kim                           e-mail: jnkim@uiuc.edu
NCSA                                   Tel: 217-244-6319 (NCSA)
Beckman Institute                           217-244-4971 (MCC)
405 N Mathews Av.                      Fax: 217-244-2909
Urbana, IL 61801
---------------------------------------------------------------


From rhennig@pacific.mps.ohio-state.edu  Tue Nov  9 13:45:37 2004
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---------- Forwarded message ----------
Date: Tue, 9 Nov 2004 13:42:02 -0500 (EST)
From: Du Yaojun <dyj@pacific.mps.ohio-state.edu>
To: rhennig@campbell.mps.ohio-state.edu
Subject: question MD with Ohmms

Hey Richard


I run the MD with 2840 atom at /king/home/dyj/OHMMS/MD/I4c+36i

/oahu/disk2/dyj/tvn.10.xml is the script

/oahu/disk2/dyj/sample are the first 300 output.

It seems that some of atoms blow away from the bulk.

What shall I add in the script in order to keep every atom in the bulk?

Thanks
Yaojun

From jnkim@ncsa.uiuc.edu  Tue Jan 18 17:04:39 2005
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Hi all,

i) I'm very close to release a revised version of the code.
There isn't any change as far as "how-to-use" is concerned, i.e., the input 
files of the version 0.2.4 should work as they do with the old code.

However, internal codes underwent significant changes: much cleaner and 
more efficient. And, renewal of OpenMP machines (32-way IBM and big SGI 
Altix) inspired me to improve the parallel performance.

Anyway, if you are interested in testing the code, contact me.

ii) wiki is available. http://www.mcc.uiuc.edu/cgi-bin/wiki/ohmms.pl

There is nothing there yet but I think I will use wiki mainly instead of 
the mailing list. Anyone can edit the wiki.  The main page has the link to 
the wiki.

I would appreciate any suggestion or comment.


Best wishes,
Jeongnim Kim

---------------------------------------------------------------
Jeongnim Kim                           e-mail: jnkim@uiuc.edu
NCSA                                   Tel: 217-244-6319 (NCSA)
Beckman Institute                           217-244-4971 (MCC)
405 N Mathews Av.                      Fax: 217-244-2909
Urbana, IL 61801
---------------------------------------------------------------


From gorse@mps.ohio-state.edu  Tue Jan 18 17:33:08 2005
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Subject: Re: [Ohmms-dev] release of a new version
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I am willing to run some quick tests on my DP 2 GHz G5.  =)

Cheers,
Joe

On Jan 18, 2005, at 6:04 PM, Jeongnim Kim wrote:

> Hi all,
>
> i) I'm very close to release a revised version of the code.
> There isn't any change as far as "how-to-use" is concerned, i.e., the 
> input files of the version 0.2.4 should work as they do with the old 
> code.
>
> However, internal codes underwent significant changes: much cleaner 
> and more efficient. And, renewal of OpenMP machines (32-way IBM and 
> big SGI Altix) inspired me to improve the parallel performance.
>
> Anyway, if you are interested in testing the code, contact me.
>
> ii) wiki is available. http://www.mcc.uiuc.edu/cgi-bin/wiki/ohmms.pl
>
> There is nothing there yet but I think I will use wiki mainly instead 
> of the mailing list. Anyone can edit the wiki.  The main page has the 
> link to the wiki.
>
> I would appreciate any suggestion or comment.
>
>
> Best wishes,
> Jeongnim Kim
>
> ---------------------------------------------------------------
> Jeongnim Kim                           e-mail: jnkim@uiuc.edu
> NCSA                                   Tel: 217-244-6319 (NCSA)
> Beckman Institute                           217-244-4971 (MCC)
> 405 N Mathews Av.                      Fax: 217-244-2909
> Urbana, IL 61801
> ---------------------------------------------------------------
>
> _______________________________________________
> Ohmms-dev mailing list
> Ohmms-dev@mcc.uiuc.edu
> http://mcc0.mcc.uiuc.edu/mailman/listinfo/ohmms-dev
>


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i strongly support use of wiki (which says a lot since i am generally =
cynical about such things).
=20
once you get going with it, it would be good to have a quick start link =
to help people
figure out how to use it.  usually there are 4 or 5 basic things people =
need to know.
however, general documentation will cover 10,000 other topics, leading =
to confusion.
=20
one thing i would like to know is how i could easily spawn a wiki page =
from the main
one.  as an example, you, Joe and i are trying to do something with =
StormRT.  how
could i create a page and post the response i sent in an email awhile =
back?  that would
be really valuable to be able to do.  the page would have become the =
ongoing discussion
and facts pertaining to what we are working through.
=20
this is much better way to collaborate than email.
=20
-david

________________________________

From: ohmms-dev-bounces@mcc.uiuc.edu on behalf of Jeongnim Kim
Sent: Tue 1/18/2005 6:04 PM
To: ohmms-dev@mcc.uiuc.edu
Subject: [Ohmms-dev] release of a new version



Hi all,

i) I'm very close to release a revised version of the code.
There isn't any change as far as "how-to-use" is concerned, i.e., the =
input
files of the version 0.2.4 should work as they do with the old code.

However, internal codes underwent significant changes: much cleaner and
more efficient. And, renewal of OpenMP machines (32-way IBM and big SGI
Altix) inspired me to improve the parallel performance.

Anyway, if you are interested in testing the code, contact me.

ii) wiki is available. http://www.mcc.uiuc.edu/cgi-bin/wiki/ohmms.pl

There is nothing there yet but I think I will use wiki mainly instead of
the mailing list. Anyone can edit the wiki.  The main page has the link =
to
the wiki.

I would appreciate any suggestion or comment.


Best wishes,
Jeongnim Kim

---------------------------------------------------------------
Jeongnim Kim                           e-mail: jnkim@uiuc.edu
NCSA                                   Tel: 217-244-6319 (NCSA)
Beckman Institute                           217-244-4971 (MCC)
405 N Mathews Av.                      Fax: 217-244-2909
Urbana, IL 61801
---------------------------------------------------------------

_______________________________________________
Ohmms-dev mailing list
Ohmms-dev@mcc.uiuc.edu
http://mcc0.mcc.uiuc.edu/mailman/listinfo/ohmms-dev



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<DIV dir=3Dltr><FONT face=3DArial size=3D2>one thing i would like to =
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<FONT face=3DTahoma size=3D2><B>From:</B> ohmms-dev-bounces@mcc.uiuc.edu =
on behalf =0A=
of Jeongnim Kim<BR><B>Sent:</B> Tue 1/18/2005 6:04 PM<BR><B>To:</B> =0A=
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version<BR></FONT><BR></DIV>=0A=
<DIV>=0A=
<P><FONT size=3D2>Hi all,<BR><BR>i) I'm very close to release a revised =
version of =0A=
the code.<BR>There isn't any change as far as "how-to-use" is concerned, =
i.e., =0A=
the input<BR>files of the version 0.2.4 should work as they do with the =
old =0A=
code.<BR><BR>However, internal codes underwent significant changes: much =
cleaner =0A=
and<BR>more efficient. And, renewal of OpenMP machines (32-way IBM and =
big =0A=
SGI<BR>Altix) inspired me to improve the parallel =
performance.<BR><BR>Anyway, if =0A=
you are interested in testing the code, contact me.<BR><BR>ii) wiki is =0A=
available. <A =0A=
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mailing list. Anyone can edit the wiki.&nbsp; The main page has the link =0A=
to<BR>the wiki.<BR><BR>I would appreciate any suggestion or =0A=
comment.<BR><BR><BR>Best wishes,<BR>Jeongnim =0A=
Kim<BR><BR>--------------------------------------------------------------=
-<BR>Jeongnim =0A=
Kim&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp; =0A=
e-mail: =0A=
jnkim@uiuc.edu<BR>NCSA&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
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Tel: 217-244-6319 (NCSA)<BR>Beckman =0A=
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217-244-4971 (MCC)<BR>405 N Mathews =0A=
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p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =0A=
Fax: 217-244-2909<BR>Urbana, IL =0A=
61801<BR>---------------------------------------------------------------<=
BR><BR>_______________________________________________<BR>Ohmms-dev =0A=
mailing list<BR>Ohmms-dev@mcc.uiuc.edu<BR><A =0A=
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From gorse@mps.ohio-state.edu  Thu Jan 20 19:03:14 2005
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Subject: Re: [Ohmms-dev] release of a new version
Date: Thu, 20 Jan 2005 20:03:09 -0500
To: "Richie, David" <DRichie@HPTI.com>
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Forums are good for that, too.  Though the wiki will serve the same=20
purpose, I supposed.

To some extent, I did that with the Wilkins twiki, but I have drifted=20
toward laziness and haven't kept up with the editing and posting of=20
emails.  Perhaps with collaboration it will be less tedious.  =3D)

Cheers,
Joe


On Jan 20, 2005, at 1:11 PM, Richie, David wrote:

> i strongly support use of wiki (which says a lot since i am generally=20=

> cynical about such things).
> =A0
> once you get going with it, it would be good to have a quick start=20
> link to help people
> figure out how to use it.=A0 usually there are 4 or 5 basic things=20
> people need to know.
> however, general documentation will cover 10,000 other topics, leading=20=

> to confusion.
> =A0
> one thing i would like to know is how i could easily spawn a wiki page=20=

> from the main
> one.=A0 as an example, you, Joe and i are trying to do something with=20=

> StormRT.=A0 how
> could i create a page and post the response i sent in an email awhile=20=

> back?=A0 that would
> be really valuable to be able to do.=A0 the page would have become the=20=

> ongoing discussion
> and facts pertaining to what we are working through.
> =A0
> this is much better way to collaborate than email.
> =A0
> -david
>
>
> From: ohmms-dev-bounces@mcc.uiuc.edu on behalf of Jeongnim Kim
> Sent: Tue 1/18/2005 6:04 PM
> To: ohmms-dev@mcc.uiuc.edu
> Subject: [Ohmms-dev] release of a new version
>
>
> Hi all,
>
> i) I'm very close to release a revised version of the code.
> There isn't any change as far as "how-to-use" is concerned, i.e., the=20=

> input
> files of the version 0.2.4 should work as they do with the old code.
>
> However, internal codes underwent significant changes: much cleaner =
and
> more efficient. And, renewal of OpenMP machines (32-way IBM and big =
SGI
> Altix) inspired me to improve the parallel performance.
>
> Anyway, if you are interested in testing the code, contact me.
>
> ii) wiki is available. http://www.mcc.uiuc.edu/cgi-bin/wiki/ohmms.pl
>
> There is nothing there yet but I think I will use wiki mainly instead=20=

> of
> the mailing list. Anyone can edit the wiki.=A0 The main page has the=20=

> link to
> the wiki.
>
> I would appreciate any suggestion or comment.
>
>
> Best wishes,
> Jeongnim Kim
>
> ---------------------------------------------------------------
> Jeongnim Kim=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0 e-mail: jnkim@uiuc.edu
> NCSA=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Tel: 217-244-6319 (NCSA)
> Beckman Institute=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0=A0 217-244-4971 (MCC)
> 405 N Mathews Av.=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0 Fax: 217-244-2909
> Urbana, IL 61801
> ---------------------------------------------------------------
>
> _______________________________________________
> Ohmms-dev mailing list
> Ohmms-dev@mcc.uiuc.edu
> http://mcc0.mcc.uiuc.edu/mailman/listinfo/ohmms-dev
> _______________________________________________
> Ohmms-dev mailing list
> Ohmms-dev@mcc.uiuc.edu
> http://mcc0.mcc.uiuc.edu/mailman/listinfo/ohmms-dev