Plumed with LAMMPS problem

[karen...@yandex.ru]

Hello,

I'm trying to use LAMMPS with Plumed and for this purpose I've patched Lammps according to Plumed instruction. The code have been compiled without errors, and I checked that Lammps linker has "fix_plumed.o" in the list of object files. However, when I try to use this fix, Lammps says that fix style is incorrect. What can be the reason for such error?
( I've tried Plumed 2.0.2 and 2.1.0 and Lammps 22Nov13 and 1Feb14 )

Another question: I'd really like to see some examples of LAMMPS+Plumed script, because I don't have the clear understanding of how to write it. So I'd be very grateful if you gave me some simple working script.

Thanks for help!

______________

Karen Fidanyan,

Joint Institute of High Temperature,

Russian Academy of Science

[Paolo Raiteri]

Hi Karen,

I'm trying to use LAMMPS with Plumed and for this purpose I've patched Lammps according to Plumed instruction. The code have been compiled without errors, and I checked that Lammps linker has "fix_plumed.o" in the list of object files. However, when I try to use this fix, Lammps says that fix style is incorrect. What can be the reason for such error?

It's aways hard to gauge where the error is without seeing the input files...

My first guess would be that your fix plumed command in the lammps input is incorrect.

This is how it should look like:

fix 22 all plumed plumedfile plumed.inp outfile plumed.out

Another question: I'd really like to see some examples of LAMMPS+Plumed script, because I don't have the clear understanding of how to write it. So I'd be very grateful if you gave me some simple working script.

The PLUMED input file is completely independent from LAMMPS.

Every example you can find in the manual and/or in the mailing list will work with LAMMPS

The only thing you have to be careful is to specify the correct units in the PLUMED input file so that everything is compatible.

Paolo

[karen...@yandex.ru]

Hi Paolo, thanks for reply!

This is my input script, i've just changed the fix in the simplest Lammps example "melt":

"

# 3d Lennard-Jones melt

units lj

atom_style atomic

lattice fcc 0.8442

region box block 0 10 0 10 0 10

create_box 1 box

create_atoms 1 box

mass 1 1.0

velocity all create 3.0 87287

pair_style lj/cut 2.5

pair_coeff 1 1 1.0 1.0 2.5

neighbor 0.3 bin

neigh_modify every 20 delay 0 check no

fix     3 all plumed     plumedfile  /home/karen/lammps_folder/plumed_2.0.2/spring_2014/first.plmd        outfile ../first.log

"

Fix syntax seems to be correct...

Maybe I made mistakes during the patching procedure?

What I did:

1. compiled Plumed and installed it

2. compiled pure Lammps and checked it

3. from Lammps root directory called plumed patch -p

4. typed    make yes-user-plumed

5. recompiled Lammps (there were no problems)

6. tried to launch this script and received  "ERROR: Invalid fix style"

[Bashpy]

Check to see if you are using the right LAMMPS executable. Type the following:

lammps_executable -h

You should see plumed in the Fix styles section.  

[karen...@yandex.ru]

Thanks for advice, I checked it: there is no plumed. Do you have any idea what could be the reason for such problem?

[botuve...@gmail.com]

It is surprising that LAMMPS patched with PLUMED compiles correctly and the fix doesn't show up. Let me ask the following just to be sure:

1. after patching lammps did type make yes-user-plumed? 

2. did you copy the new executable compiled after patching LAMMPS to your path? you could still be using the old executable without knowing it. 

Regards,