lammps-users Digest, Vol 81, Issue 65

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Today's Topics:

   1. Re: why respa level for outer == kspace? (Steve Plimpton)
   2. Re: How to dump some energy into the system efficiently
      (Steve Plimpton)
   3. Re: why respa level for outer == kspace? (Axel Kohlmeyer)
   4. Re: Go-like interactions in LAMMPS (Steve Plimpton)
   5. Re: Elastic constant script and minimize command (Steve Plimpton)
   6. Re: ?hybrid full sphere? for ?atom_style? (Steve Plimpton)
   7. Re: MEAM potential- B1 reference structure (Grigory Smirnov)
   8. Re: why respa level for outer == kspace? (Steve Plimpton)
   9. bond/break (Saikat Basu)
  10. Re: why respa level for outer == kspace? (Axel Kohlmeyer)
  11. OMP package in the lammps-22Feb13 version problem
      (Rolf Isele-Holder)
  12. Re: enthalpy and equation of state (Carlos Campana)
  13. Re: bond/break (Samuel Palato)
  14. Re: OMP package in the lammps-22Feb13 version problem
      (Axel Kohlmeyer)
  15. Re: bond/break (Vikas Varshney)
  16. Kspace slab correction with compute group/group (Chen Wei)

----------------------------------------------------------------------

Message: 1
Date: Tue, 26 Feb 2013 05:17:23 -0700
From: Steve Plimpton <[email protected]>
Subject: Re: [lammps-users] why respa level for outer == kspace?
To: Axel Kohlmeyer <[email protected]>
Cc: LAMMPS Users Mailing List <[email protected]>
Message-ID:
  <[email protected]...>
Content-Type: text/plain; charset=ISO-8859-1

run_style respa 3 2 2 inner 1 5.0 6.0 outer 2 kspace 3

This command specifies 4 levels, and you are asking that
KSpace be at level 3, not the outermost 4. Am I
missing something?

Steve

Not sure what the point of not putting
KSpace at the outer level would be,
since nothing is more outer?

i *do* want to put kspace at the outermost level, but i want to it
less frequently than the outer non-bonded calculations.
as i wrote, it works fine, if i don't split non-bonded into inner and
outer.

axel.

Steve

hi,

does anybody know the reason why run_style respa allows this:

run_style respa 2 2 pair 1 kspace 2

and this:

run_style respa 2 2 inner 1 5.0 6.0 outer 2

but not this:

run_style respa 3 2 2 inner 1 5.0 6.0 outer 2 kspace 3

it would be trivial to change the source code to allow it, but i
presume there is a reason for this choice and i am curious to learn
it.

thanks in advance,
     axel.

--
Dr. Axel Kohlmeyer [email protected] http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

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--
Dr. Axel Kohlmeyer [email protected] http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

------------------------------

Message: 2
Date: Tue, 26 Feb 2013 05:18:39 -0700
From: Steve Plimpton <[email protected]>
Subject: Re: [lammps-users] How to dump some energy into the system
  efficiently
To: Vikas Varshney <[email protected]...>
Cc: [email protected]
Message-ID:
  <[email protected]...>
Content-Type: text/plain; charset=ISO-8859-1

Regions can be dynamic - see the region doc page.

Steve

Dear Steve,

As per your suggestion, I looked over fix heat and the code by itself is
almost clear to me. After thinking a bit, one issue that I figured in
using
"fix" based methodology is that my group of atoms over which heat is
being
dissipated varies over time. In addition, the region over which I
distribute
the energy will change with time (think of a photon whose absortion
point
(X,Y,Z) will be detemined in stochastic way). In that case, I cannot
even
use group "all" with some region id as region itself will change. So, I
was
thinking to adapt the fix heat code to something which is not invoked
repeatedly but only when I asked it to with different group definitions
or
region definitions. The idea is as follows. Lets say we call it
dump_energy
command

0. Run A steps (where A is variable)
1. Define a region of radius R around stochastically chosen point x,y,z
point.
2. Define the group of atoms.
3. Use dump energy command as follows
    dump_energy group energy (energy units) distribution
(unform,gaussian,others)
4. Delete the group
5. Delete the region
6. Go to step 0

Please guide if this makes more sense.

Your second suggestion regarding using lib interface also has merit. But
in
that case as well, I would need to calculate/extract KE/mass of the
group of
atoms, calculate/extract center of mass velocity and then rescale the
K.E.
energy accordingly. In my opinion, writing a module based on fix heat
and
calling it from the C++ as a command line would be a more systematic way
to
go.

Please guide.

Best Regards,
Vikas

Dear Steve,

Thank you for all of your suggestions. All of them are makes sense now.
I
will start from fix heat as you suggested and will try to modify it
according to your suggestions.

Best Regards,
Vikas

There are several ways to approach this problem.

(1) look at fix heat, which may do exactly what you want,
or which could be adapted by you to deposit its energy
according to some other formula

(2) The lib interface has a lammps_extract_atom() function
which returns the ptr on each processor to the data for
x,v,whatever. There is no gather/scatter overhead to
using that. Then each proc can loop over its local atoms,
determine if you want to rescale its velocity, and just do
directly. This is the same way something like fix heat operates.

(3) It is not hard to give a fix (fix heat or one you write) an
arg that is an equal-style variable that returns a value for
the next timestep on which you want to invoke it. Thus
if you can write an equal-style variable that generates
the sequence of timesteps you want to invoke your operation,
you can use it. See the dump_modify every v_foo command
as an example. And there are several variable functions
that allow you to generate irregular sequences of timesteps.
Or you could simply code the calculalation of the next timestep
into the fix, have the fix be invoked every step, and simply
return if it is not the "next" timestep.

Steve

> Dear Steve, Users,
>
> I plan to add thermal enregy into my system of interest in only
> selected
> region (think of a local photon absorbtion on the surface region). I
am
> running my simulations using lammps as library. One of the ways to
do
> it is
> to user lammps_gather_atoms to extract the cooridnates and
velocities,
> Update the velocities (using some factor) of the atoms which are in
> certain
> region and then use lammps_scatter_atom function to feed it back to
> lammps.
>
> As the lammps_gather_atoms command extract the information of "all"
the
> atoms, I will need to calculate the distance of each atom from the
> center of
> photon absorption site to decide whether to update its velocity. If
> that
> region is small and my overall system is large, my concern is that
it
> might
> not be efficient.
>
> I am thinking if I could write a routine in lammps itself which will
do
> a
> similar thing locally on requesting in input script. The inputs will
be
> group (based on region) and the energy (to be distributed) and
possibly
> how
> the energy needs to be distributed (gaussian, uniform), etc. As this
is
> not
> going to be happen at constant time intervals, write a fix probably
> won't
> work.
>
> Another thing could be to write something along the lines of
> lammps_gather_atom_group in which we specify the group and extract
the
> information of atoms only for that group. For preallocation, we can
get
> the
> array size from using variable count(group) feature. But after going
> through
> library.cpp, it seem to me that atoms "tagging" (which atom goes
where
> in
> copy array) could create problems when MPI_Allreduce is called?
>
> Your suggestions are welcome. What is more efficient? What templete
> routines
> should I look over. (displace_atoms.cpp?) Please guide.
>
> Best Regards,
> Vikas
>
>
>
> ------------------------------------------------------------------------------
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------------------------------

Message: 3
Date: Tue, 26 Feb 2013 13:23:35 +0100
From: Axel Kohlmeyer <[email protected]>
Subject: Re: [lammps-users] why respa level for outer == kspace?
To: Steve Plimpton <[email protected]>
Cc: LAMMPS Users Mailing List <[email protected]>
Message-ID:
  <[email protected]...>
Content-Type: text/plain; charset=ISO-8859-1

run_style respa 3 2 2 inner 1 5.0 6.0 outer 2 kspace 3

This command specifies 4 levels, and you are asking that

sorry, but it doesn't. the numbers in the respa command are all 1
based not zero based.

KSpace be at level 3, not the outermost 4. Am I
missing something?

i am asking for 3 levels. level 1 being executed twice for every
evaluation of level 2
level 2 in turn being execute twice for every evaluation of level 3.

i'm assigning bond, angle, dihedral, improper and inner to level 1,
i'm skipping middle, assigning outer to level 2 and kspace to level 3,
which is the outermost level. but the code in respa.cpp doesn't allow
me to do the factor 2 between outer non-bonded a kspace. however,
i can run a factor 2 between pair and kspace, if i run all of pair
together.

axel.

Steve

Not sure what the point of not putting
KSpace at the outer level would be,
since nothing is more outer?

i *do* want to put kspace at the outermost level, but i want to it
less frequently than the outer non-bonded calculations.
as i wrote, it works fine, if i don't split non-bonded into inner and
outer.

axel.

Steve

hi,

does anybody know the reason why run_style respa allows this:

run_style respa 2 2 pair 1 kspace 2

and this:

run_style respa 2 2 inner 1 5.0 6.0 outer 2

but not this:

run_style respa 3 2 2 inner 1 5.0 6.0 outer 2 kspace 3

it would be trivial to change the source code to allow it, but i
presume there is a reason for this choice and i am curious to learn
it.

thanks in advance,
     axel.

--
Dr. Axel Kohlmeyer [email protected] http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

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--
Dr. Axel Kohlmeyer [email protected] http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

--
Dr. Axel Kohlmeyer [email protected] http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

------------------------------

Message: 4
Date: Tue, 26 Feb 2013 05:25:37 -0700
From: Steve Plimpton <[email protected]>
Subject: Re: [lammps-users] Go-like interactions in LAMMPS
To: [email protected]...
Cc: Dan Hinckley <[email protected]...>, lammps
  <[email protected]>
Message-ID:
  <[email protected]...>
Content-Type: text/plain; charset=windows-1252

I suggest you write a pair_go.cpp pair style that
computes the interactions you want. You'd still
need to define the param for each atom, which you
could do either with a new atom_style (also not hard
to create). Or with a fix that stored the additional
values/atom. The fix could read the definitions out
of the data file. There is a hook in read_data to enable
that. The fix could also store the per-atom bond/angle
params, used by a bond_go.cpp style, etc.

Steve

Hi, Dan:

There isn't a good way to attach a specific set of sigma and epsilon
values
to individual atoms; most LAMMPS pair potentials are geared to using
atom
"types" to determine the coefficients.

So you'd need to assign each atom to its own type, tinker with the
software
to store the pair potential as part of the atom type, or find some way
to
"import" this information and make it part of the pair potential
calculation
(the way parameter information is read in for the EAM or ReaxFF pair
styles). This would require a decent amount of coding, although it is
possible.

?AEI

Hello,

Does LAMMPS have the capability to easily simulate Go-like
interactions?
By Go-like, I mean:

1) Non-bonded interactions with parameters (epsilon, sigma) that are
unique to atom i and atom j (atom ID not type).
2) Bonded interactions (bonds, angles, dihedrals) with equilibrium
distances and angles that are unique to the atom IDs of the
constitutive
atoms.

Obviously, one might specify a unique type for every bond and provide
the
corresponding coefficients; however, that seems rather crude.

Thank you,

Dan

--
Dan Hinckley
Molecular Thermodynamics and Statistical Mechanics Research Group
Department of Chemical and Biological Engineering
University of Wisconsin-Madison
Email: [email protected]...
Phone: 801-400-4391

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--

Ahmed E. Ismail
[email protected]...
[email protected]...

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------------------------------

Message: 5
Date: Tue, 26 Feb 2013 05:29:27 -0700
From: Steve Plimpton <[email protected]>
Subject: Re: [lammps-users] Elastic constant script and minimize
  command
To: Prithwish Nandi <[email protected]...>
Cc: [email protected]
Message-ID:
  <[email protected]...>
Content-Type: text/plain; charset=ISO-8859-1

Comments below.

Steve

Hi,
I am using the elastic constant script provided in the LAMMPS
distribution.

I have a question about the "minimize" command. In the "in.elastic" file
it
is given as :

minimize \{etol\} {ftol} \{maxiter\} {maxeval}

The values of these variable as given in the "init.mod" file are as
follows:

variable etol equal 0.0
variable ftol equal 1.0e-10
variable maxiter equal 100
variable maxeval equal 1.0e-2

Now, in LAMMPS manual ( http://lammps.sandia.gov/doc/minimize.html ), we
can
see the following :

"Either or both of the etol and ftol values can be set to 0.0, in which
case
some other criterion will terminate the minimization."

What does it mean ?

Just what it says. A setting of zero for ftol (or etol) means
that setting is ignored when deciding to end the minimization.
The other criteria are still considered.

Doe it mean that if either 'etol' or 'ftol' equals to zero (as in the
above
case mentioned), the stopping criterion will be decided by either
'maxiter'
or 'maxeval' ?

In that case, how can we guarantee that the structure is relaxed
properly ?

That's up to you. There is no simple definition of "relaxed properly".
LAMMPS uses the criteria you define.

I have another question:

I want to calculate elastic constants for a damaged system (having lot
of
lattice defects like frenkel pairs, dislocations, stacking faults etc)
using
this script.

In that case, attending a stopping criterion like ftol= 1.0e-10 will be
very
difficult.

So, how can we judiciously choose these parameters in such cases ?

Again, that's not a LAMMPS Q. That's a conceptual Q. I suggest
you try your system and see how it works.

Thanks,

--

Prithwish

--
--
Prithwish K. Nandi
Department of Nuclear Engineering
North Carolina State University
Raleigh, NC, USA 27695
E-mail: [email protected]...
Cell: +1 (919) 985-3715

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------------------------------

Message: 6
Date: Tue, 26 Feb 2013 05:33:10 -0700
From: Steve Plimpton <[email protected]>
Subject: Re: [lammps-users] ?hybrid full sphere? for ?atom_style?
To: fatemeh hosseinzadeh <[email protected]...>
Cc: "[email protected]"
  <[email protected]>
Message-ID:
  <[email protected]...>
Content-Type: text/plain; charset=windows-1252

The following are defined parameter values in data file.
atom-ID , atom-type , x , y , z , molecule-ID , q , diameter , density
Then I used dump to read this parameter.

I don't understand what you mean by using the dump
to command to read the data file. If you can
run the simulation, then you used the read_data command,
which is thus working fine. If you dumped to a dump
file during the simulation, then the dump command is
working fine.

Steve

Dear all,
Hello

I used ?hybrid full sphere? for ?atom_style?.
The following are defined parameter values in data file.
atom-ID , atom-type , x , y , z , molecule-ID , q , diameter , density
Then I used dump to read this parameter.
dump 1 all custom 100 dump.xyz id type x y z mol q diameter

I got a strange result, lammps output q column as mol and output density
column(last column value) as q!!!!!!!!!!!
Then I changed the columns in data file, but lammps understood that last
column couldn?t get negative value(q)..!
So I think the sequence of parameter is true but I can?t understand why
this
happen.

Thanks in advance,
Fatemeh

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------------------------------

Message: 7
Date: Tue, 26 Feb 2013 16:42:44 +0400
From: Grigory Smirnov <[email protected]...>
Subject: Re: [lammps-users] MEAM potential- B1 reference structure
To: mohammad sharif <[email protected]...>
Cc: "[email protected]"
  <[email protected]>
Message-ID:
  <[email protected]...>
Content-Type: text/plain; charset="iso-8859-1"

Dear Mohammad,

I guess your input script is incorrect. I have attached the input file
that
works for me. Hope it will help you.

Grigory Smirnov
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------------------------------

Message: 8
Date: Tue, 26 Feb 2013 05:49:53 -0700
From: Steve Plimpton <[email protected]>
Subject: Re: [lammps-users] why respa level for outer == kspace?
To: Axel Kohlmeyer <[email protected]>
Cc: LAMMPS Users Mailing List <[email protected]>
Message-ID:
  <[email protected]...>
Content-Type: text/plain; charset=ISO-8859-1

oops - I misread the doc page, that is 3 levels, not 4.

I think changing the test to level_kspace < level_outer
should be fine. Our thinking may have been that some
portion of the pairwise should be done with the KSpace
since they are complementary, but I don't think
it is a requirement. I see that the code will even
allow you to not put KSpace at the outermost level
(just throws a warning), which is what I thought you
were doing if there were 4 levels defined.

Steve

run_style respa 3 2 2 inner 1 5.0 6.0 outer 2 kspace 3

This command specifies 4 levels, and you are asking that

sorry, but it doesn't. the numbers in the respa command are all 1
based not zero based.

KSpace be at level 3, not the outermost 4. Am I
missing something?

i am asking for 3 levels. level 1 being executed twice for every
evaluation of level 2
level 2 in turn being execute twice for every evaluation of level 3.

i'm assigning bond, angle, dihedral, improper and inner to level 1,
i'm skipping middle, assigning outer to level 2 and kspace to level 3,
which is the outermost level. but the code in respa.cpp doesn't allow
me to do the factor 2 between outer non-bonded a kspace. however,
i can run a factor 2 between pair and kspace, if i run all of pair
together.

axel.

Steve

Not sure what the point of not putting
KSpace at the outer level would be,
since nothing is more outer?

i *do* want to put kspace at the outermost level, but i want to it
less frequently than the outer non-bonded calculations.
as i wrote, it works fine, if i don't split non-bonded into inner and
outer.

axel.

Steve

hi,

does anybody know the reason why run_style respa allows this:

run_style respa 2 2 pair 1 kspace 2

and this:

run_style respa 2 2 inner 1 5.0 6.0 outer 2

but not this:

run_style respa 3 2 2 inner 1 5.0 6.0 outer 2 kspace 3

it would be trivial to change the source code to allow it, but i
presume there is a reason for this choice and i am curious to learn
it.

thanks in advance,
     axel.

--
Dr. Axel Kohlmeyer [email protected] http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
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_______________________________________________
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--
Dr. Axel Kohlmeyer [email protected] http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

--
Dr. Axel Kohlmeyer [email protected] http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

------------------------------

Message: 9
Date: Tue, 26 Feb 2013 18:54:58 +0530
From: "Saikat Basu" <[email protected]...>
Subject: [lammps-users] bond/break
To: [email protected]
Message-ID:
  <[email protected]...>
Content-Type: text/plain;charset=iso-8859-1

Hi,

I have some queries regarding the bond/break command .

1. As it is documented in LAMMPS site :"This fix is part of the MC
package. It is only enabled if LAMMPS was built with that
package....Currently, there are 2 restrictions for using this fix".

So what exact package is required for this command to work with ?

2. Now,say,I have a system where 'the no of bond types'='no of bonds'.
   And moreover all the bonds have different bond length.

For this case if I want to impose bond/break, I have to mention the
'bond-type' in the fix. Basically it has to be executed over all bond
types.then what value have to be written ?

Any comment is welcome.

Thanking you,

Best,
******************
Saikat Basu
Junior Research Fellow
Department of Solid State Physics
IACS,Kolkata
Kolkata-700032
Ph no- 03324734971(extn- 2114)

------------------------------

Message: 10
Date: Tue, 26 Feb 2013 14:11:22 +0100
From: Axel Kohlmeyer <[email protected]>
Subject: Re: [lammps-users] why respa level for outer == kspace?
To: Steve Plimpton <[email protected]>
Cc: LAMMPS Users Mailing List <[email protected]>
Message-ID:
  <[email protected]...>
Content-Type: text/plain; charset=ISO-8859-1

oops - I misread the doc page, that is 3 levels, not 4.

I think changing the test to level_kspace < level_outer
should be fine. Our thinking may have been that some
portion of the pairwise should be done with the KSpace
since they are complementary, but I don't think
it is a requirement. I see that the code will even

in fact, this kind of scheme is what people do in NAMD to get the best
performance.

allow you to not put KSpace at the outermost level
(just throws a warning), which is what I thought you
were doing if there were 4 levels defined.

that seems to be working fine, though.
i made some tests for that, too. e.g.:

using:

run_style respa 2 1 pair 1 kspace 1

run_style respa 2 1 pair 1 kspace 2

and

run_style verlet

all give identical trajectories for 100 MD steps

only

run_style respa 1 pair 1 kspace 1

doesn't work.

axel.

Steve

run_style respa 3 2 2 inner 1 5.0 6.0 outer 2 kspace 3

This command specifies 4 levels, and you are asking that

sorry, but it doesn't. the numbers in the respa command are all 1
based not zero based.

KSpace be at level 3, not the outermost 4. Am I
missing something?

i am asking for 3 levels. level 1 being executed twice for every
evaluation of level 2
level 2 in turn being execute twice for every evaluation of level 3.

i'm assigning bond, angle, dihedral, improper and inner to level 1,
i'm skipping middle, assigning outer to level 2 and kspace to level 3,
which is the outermost level. but the code in respa.cpp doesn't allow
me to do the factor 2 between outer non-bonded a kspace. however,
i can run a factor 2 between pair and kspace, if i run all of pair
together.

axel.

Steve

Not sure what the point of not putting
KSpace at the outer level would be,
since nothing is more outer?

i *do* want to put kspace at the outermost level, but i want to it
less frequently than the outer non-bonded calculations.
as i wrote, it works fine, if i don't split non-bonded into inner and
outer.

axel.

Steve

hi,

does anybody know the reason why run_style respa allows this:

run_style respa 2 2 pair 1 kspace 2

and this:

run_style respa 2 2 inner 1 5.0 6.0 outer 2

but not this:

run_style respa 3 2 2 inner 1 5.0 6.0 outer 2 kspace 3

it would be trivial to change the source code to allow it, but i
presume there is a reason for this choice and i am curious to learn
it.

thanks in advance,
     axel.

--
Dr. Axel Kohlmeyer [email protected] http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

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Dr. Axel Kohlmeyer [email protected] http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

--
Dr. Axel Kohlmeyer [email protected] http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

--
Dr. Axel Kohlmeyer [email protected] http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

------------------------------

Message: 11
Date: Tue, 26 Feb 2013 15:06:36 +0100
From: Rolf Isele-Holder <[email protected]...>
Subject: [lammps-users] OMP package in the lammps-22Feb13 version
  problem
To: [email protected]
Message-ID: <[email protected]...>
Content-Type: text/plain; charset=us-ascii

Dear all,

I have problems with using the OMP package in the lammps-22Feb13 version.
I compiled the code with a Makefile that worked well for the
lammps-14Feb13 version
including the OMP package.

The beginning of my LAMMPS input script looks like this:

  echo both
  units real
  atom_style full

  atom_style full
  bond_style harmonic
  angle_style harmonic
  dihedral_style opls

  package omp 4 force/neigh

  read_restart e0.rs

  thermo_style custom step etotal press fnorm fmax
  ...

I get the following output on the screen:

  LAMMPS (22 Feb 2013)
      using 4 OpenMP thread(s) per MPI task
  units real
  atom_style full

  atom_style full
  bond_style harmonic
  angle_style harmonic
  dihedral_style opls

  package omp 4 force/neigh

The code then stops (there is no additional output on the
screen for several minutes).

Has anyone encountered similar problems?

Best,

Rolf

------------------------------

Message: 12
Date: Tue, 26 Feb 2013 09:07:17 -0500
From: Carlos Campana <[email protected]...>
Subject: Re: [lammps-users] enthalpy and equation of state
To: Oscar Guerrero <[email protected]...>
Cc: "[email protected]"
  <[email protected]>
Message-ID:
  <[email protected]...>
Content-Type: text/plain; charset=ISO-8859-1

Oscar
The loop is easy to implement using a loop type variable in lammps.
The variable link show one example:
http://lammps.sandia.gov/doc/variable.html
Carlos

Hi Carlos,

Your right, The problem arise when i try to compare (H vs P) for
different
phases. The output data for the two phases are not evenly spaced, thus
its
impossible to compare the solid-solid transition I came with another
approach that might work: How about Using xmgrace and then do
interpolation/spline (cubic splne) to the data sets. This way i can
define
the low/hight limit and the length, Using this mehod then the sets will
be
of same size and then i can compare Hfcc - Hhcp and find the pressure
(P) in
which the phase transition occours i.e Hfcc - Hhcp = 0

I Read your comment and your make me realice that when using fix deform
i'm
comparing the two phases, but I created two different lattice and thus
the
value of pressure are not going to be equal (duh!) . Please Let me think
about the FOR/Loop feature (I follow you idear) and hopefuly i may be
able
to implent an script, ...

Thanks
Oscar Guerrero

Oscar,
If I understand correctly your problem with the H vs P plot arises
because the variable that you modify with fix deform is the cell shape
(volume), and thus you get different pressure values when considering
different phases. Right?
Have you tried instead to place the fix box/relax combined with
minimization in a loop where you set the pressure within the fix
box/relax and then extract your other variables from the thermo info?
Carlos

> Hi lammps users,
>
>
>
> im trying to calculate the equation of state (EOS) (T=0) for
different
> structures eg. BCC, FCC, HCP. Please find the script below. I'm using
> fix
> deform and storing Etotal/atom and VOL/Vo.
>
> The plot of (E vs V) I believe make sence because the minimum of
energy
> is
> equal to the Ecohesive. Foe example lets use Cu EAM Potential Mishin
Cu
> EAM1
> PRB(2001)63:224106
>
>
>
> I'm also trying to find Enthalpy vs Pressure for different phases.
I'm
> trying to Compare FCC enthalpy vc HCP enthalpy at T=0 .
>
> Unfourtounately my script is wrong. In order to compare two data
sets,
> the
> data sets should be of same lenght and the values space evenly i.e
Equal
> values of Pressure P correspong to different values of Enthalpy "H"
>
> Example ENTHALPHY VS P (BCC) P=10 , H=1 ENTHALPHY VS P (HCP) P=10
,
> H=23
> (values are spaces evenly in pressure)
>
>
>
> Can someone please tell me how to find Enthalpy vs Pressure (T=0) for
> different Phases using Lammps ?
>
> Any information will be grealy appreciate
>
>
>
> Thanks alot for your help and advise
>
> Oscar Guerrero
>
>
>
> # ---------- Initialize Simulation ---------------------
>
> clear
>
> units metal
>
> dimension 3
>
> boundary p p p
>
> atom_style atomic
>
> atom_modify map array
>
> # ---------- define variables -------------------------------
>
> timestep 0.005
>
>
>
> # ---------- Create Atoms ------------------------------------
>
> lattice bcc 3.615 origin 0.0 0.0 0.0 orient x 1 0 0 orient y
0
> 1 0
> orient z 0 0 1
>
> # lattice fcc 3.615 origin 0.0 0.0 0.0 orient x 1 0 0 orient y
0
> 1 0
> orient z 0 0 1
>
> # lattice hcp 3.615 origin 0.0 0.0 0.0 orient x 1 0 0 orient y
0
> 1 0
> orient z 0 0 1
>
> region box block 0 5 0 5 0 5 units lattice
>
> create_box 1 box
>
> create_atoms 1 box
>
> # ---------- Define Interatomic Potential ---------------------
>
> pair_style eam/alloy
>
> pair_coeff * * Cu_mishin1.eam.alloy Cu
>
> # ---------- Define Settings ----------------------------------
>
> compute eng all pe/atom
>
> compute kiene all ke/atom
>
> compute pre all stress/atom
>
> compute eatoms all reduce sum c_eng
>
> # ---------- Print Atoms ----------------------------------
>
> reset_timestep 0
>
> dump 1 all cfg 2 lattice.dump.*.cfg id type xs ys zs
>
> run 1
>
> undump 1
>
> # ---------- FIND MINIMUM ENERGY LEVEL -------------------------
>
> reset_timestep 0
>
> fix 1 all box/relax iso 0.0 vmax 0.001
>
> thermo 0
>
> thermo_style custom step pe lx ly lz vol press pxx pyy pzz c_eatoms
>
> min_style cg
>
> minimize 1e-25 1e-25 5000 10000
>
> unfix 1
>
> #--------------STORE TEMPORARY VARIABLES ----------------------------
>
> # Store final volume/atom for further calculations
>
> variable tmp equal "vol/count(all)"
>
> variable V0 equal \{tmp\} &gt; &gt; print &quot;Volume per atom, V0: {V0}"
>
> # Store final length for further calculations
>
> variable tmp equal "lx"
>
> variable L0 equal \{tmp\} &gt; &gt; print &quot;Initial Length, L0: {L0}"
>
> # ---------- DEFORMATION STEPS ARE HERE
> ----------------------------------
>
> reset_timestep 0
>
> # RUN SIMULATION AT 0K
>
> fix 1 all deform 1 x erate -0.10 remap x
>
> # ---------- FIND EQUATION OF STATE
------------------------------------
>
> thermo 0
>
> thermo_style custom step etotal enthalpy lx ly lz vol press pxx pyy
pzz
> temp
>
> variable natoms equal "count(all)" # NUMBER
> ATOMS
>
> variable H equal "enthalpy/v_natoms" # ENTHALPY
>
> variable strain equal "-(lx - v_L0)/v_L0" # STRAIN
>
> variable shear equal "0.5*(pxx - 0.5*(pyy + pzz))/10000" # SHEAR
> CALCULATION
>
> variable out1 equal "(vol/v_natoms)/v_V0" # VOLUME
PER
> ATOM
>
> variable out2 equal "etotal/v_natoms" # TOTAL
> ENERGY
> PER/ATOM
>
> variable out3 equal "pxx/10000" # PRESSURE
> PXX
> (GPA UNITS)
>
> variable out4 equal "pyy/10000" # PRESSURE
> PYY
> (GPA UNITS)
>
> variable out5 equal "pzz/10000" # PRESSURE
> PZZ
> (GPA UNITS)
>
> variable out6 equal "press/10000" # TENSOR
> PRESSURE
> (GPA UNITS)
>
> variable out7 equal "temp" #
TEMPERATURE
>
> variable out8 equal "lx" # lx
>
> variable out9 equal "ly" # ly
>
> variable out10 equal "lz" # lz
>
> fix def1 all print 2 "\{strain\} {shear}" file shear.dat screen no
>
> fix def2 all print 2 "\{out1\} {out2} \{out3\} {out4} \{out5\} {out6}
> \{out7\} {out8} \{out9\} {out10} \{H\} &quot; file eos\.dat screen no &gt; &gt; fix def3 all print 2 &quot;{out6} ${H} " file enthalpy.dat screen no
>
> run 1200
>
> unfix 1
>
> unfix def1
>
> unfix def2
>
> unfix def3
>
> # SIMULATION DONE
>
> clear
>
> print "creo ya esta =)"
>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> _______________________________________________
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> [email protected]
> https://lists.sourceforge.net/lists/listinfo/lammps-users
>

--

//******************************
Address = "UTSA PHYSICS";

Name = "Oscar Guerrero" ;
Phone = null ;

extension = null ;
//*******************************

------------------------------

Message: 13
Date: Tue, 26 Feb 2013 09:10:43 -0500
From: Samuel Palato <[email protected]...>
Subject: Re: [lammps-users] bond/break
To: [email protected]
Message-ID: <[email protected]...>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Le 2013-02-26 08:24, Saikat Basu a ?crit :

Hi,

  I have some queries regarding the bond/break command .

  1. As it is documented in LAMMPS site :"This fix is part of the MC
package. It is only enabled if LAMMPS was built with that
package....Currently, there are 2 restrictions for using this fix".

  So what exact package is required for this command to work with ?

You need the 'mc' package. For instructions about how to build LAMMPS
with optional packages (Linux):
http://lammps.sandia.gov/doc/Section_start.html#start_3_2
You can also play with 'make' in your source directory.

When I am implementing this 'fix' and trying to start a run
the error flashed is regarding the declaration of 'bond type'.
So, I think there may not be too much issues regarding the package.

Thanks for your comment.

  2. Now,say,I have a system where 'the no of bond types'='no of bonds'.
    And moreover all the bonds have different bond length.

  For this case if I want to impose bond/break, I have to mention the
'bond-type' in the fix. Basically it has to be executed over all bond
  types.then what value have to be written ?

  Any comment is welcome.

Thanking you,

Best,
******************
Saikat Basu
Junior Research Fellow
Department of Solid State Physics
IACS,Kolkata
Kolkata-700032
Ph no- 03324734971(extn- 2114)

------------------------------------------------------------------------------
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I don't know 'bond/break', so I'll leave it to someone else to answer
point 2.

Samuel Palato

------------------------------

Message: 14
Date: Tue, 26 Feb 2013 15:21:28 +0100
From: Axel Kohlmeyer <[email protected]>
Subject: Re: [lammps-users] OMP package in the lammps-22Feb13 version
  problem
To: Rolf Isele-Holder <[email protected]...>
Cc: LAMMPS Users Mailing List <[email protected]>
Message-ID:
  <[email protected]...>
Content-Type: text/plain; charset=ISO-8859-1

Dear all,

I have problems with using the OMP package in the lammps-22Feb13
version.

[...]

I get the following output on the screen:

        LAMMPS (22 Feb 2013)
                using 4 OpenMP thread(s) per MPI task
        units real
        atom_style full

        atom_style full
        bond_style harmonic
        angle_style harmonic
        dihedral_style opls

        package omp 4 force/neigh

The code then stops (there is no additional output on the
screen for several minutes).

Has anyone encountered similar problems?

this is due to a stupid bug that was introduced in the latest patch to
the USER-OMP code when trying to refactor the argument handling of the
package omp command to for future changes in the code.

here is a patch. you can also leave out the force/neigh flag. it is
the default anyway.
diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp
index bac0017..e160660 100644
--- a/src/USER-OMP/fix_omp.cpp
+++ b/src/USER-OMP/fix_omp.cpp
@@ -108,6 +108,7 @@ FixOMP::FixOMP(LAMMPS *lmp, int narg, char **arg)
       _mixed = false;
     else
       error->all(FLERR,"Illegal package omp mode requested");
+ ++iarg;
   }

   // print summary of settings

at the current state of affairs, the package omp command is rarely
needed. it will automatically be inserted when you use -sf omp or
-suffix omp with the number of threads defaulting to the value of the
OMP_NUM_THREADS environment variable.

axel.

Best,

Rolf

------------------------------------------------------------------------------
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--
Dr. Axel Kohlmeyer [email protected] http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

------------------------------

Message: 15
Date: Tue, 26 Feb 2013 09:46:28 -0500
From: Vikas Varshney <[email protected]...>
Subject: Re: [lammps-users] bond/break
To: Samuel Palato <[email protected]...>
Cc: [email protected]
Message-ID:
  <[email protected]...>
Content-Type: text/plain; charset="iso-8859-1"

For the second answer,
If you want to all bond types to be eligible then have the fix multiple
times with different values of bond_type.

This will be a mammoth task.. In my system, I have 30K bonds. Writing
it so many times is unnecessary ..

I think, there should be an option (like 1*,<=N etc which is familiar
to other type declaration in LAMMPS input script) to do it in a simple
fashion.

Is there anybody to render some clues ..

Thanks
Saikat

Regards
Vikas

Le 2013-02-26 08:24, Saikat Basu a ?crit :
> Hi,
>
> I have some queries regarding the bond/break command .
>
> 1. As it is documented in LAMMPS site :"This fix is part of the MC
> package. It is only enabled if LAMMPS was built with that
> package....Currently, there are 2 restrictions for using this fix".
>
> So what exact package is required for this command to work with ?
>

You need the 'mc' package. For instructions about how to build LAMMPS
with optional packages (Linux):
http://lammps.sandia.gov/doc/Section_start.html#start_3_2
You can also play with 'make' in your source directory.

> 2. Now,say,I have a system where 'the no of bond types'='no of
bonds'.
> And moreover all the bonds have different bond length.
>
> For this case if I want to impose bond/break, I have to mention the
> 'bond-type' in the fix. Basically it has to be executed over all bond
> types.then what value have to be written ?
>
> Any comment is welcome.
>
> Thanking you,
>
> Best,
> ******************
> Saikat Basu
> Junior Research Fellow
> Department of Solid State Physics
> IACS,Kolkata
> Kolkata-700032
> Ph no- 03324734971(extn- 2114)
>
>
>
------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> _______________________________________________
> lammps-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/lammps-users
>

I don't know 'bond/break', so I'll leave it to someone else to answer
point 2.

Samuel Palato

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------------------------------

Message: 16
Date: Tue, 26 Feb 2013 14:56:25 +0000
From: Chen Wei <[email protected]...>
Subject: [lammps-users] Kspace slab correction with compute
  group/group
To: "[email protected]"
  <[email protected]>
Message-ID:
  <[email protected]...>
Content-Type: text/plain; charset="windows-1252"

Dear Lammps-users,

I want to do the MD of waters confined by non-uniformly charged surfaces,
I'm interested in the force between water molecules and one surface, the
commands are:

?...

kspace_style ewald 1.0e-4

kspace_modify slab 3.0

?...

compute Force spce group/group topsurface kspace yes

?...

But Lammps reports :

ERROR: Cannot (yet) use Kspace slab correction with compute group/group
(ewald.cpp:991),

I also tried to use 3D ewald directly assuming a periodicity in the z
direction

with a simulation box size of 10 times of the distance between the
surfaces. It does not work well.

Is there any other way to compute the force in Lammps? All suggestions are
welcomed.

Thank you very much,

Wei
-------------- next part --------------
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------------------------------

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End of lammps-users Digest, Vol 81, Issue 65
********************************************

Thanking you,

Best,

2

please do everybody a favor when replying to a digested e-mail trim
down the content to the relevant message and follow the advice quoted
below that is given in every digest that you receive.

thanks,
      axel.

[...]