PLUMED: I cannot understand line: Q4 SPECIES=1-512 SWITCH=RATIONAL D_0=1.3 R_0=0.2 LABEL=q4

[bin.chr...@gmail.com]

Hello,

Today I just installed PLUMED 2.1 with LAMMPS 2Apr-13. I am just testing it on the cubic ice. PLUMED seemed to have run and correctly read the UNITS command. But it failed at the command above in the subject line. I wonder what I missed in the installation. 

Thank you for help.

Bin

[gareth....@gmail.com]

You need curly braces around the switch part. Also you need to go to the directory

plumed2/src/

And type

touch crystallization.on. Once you have done this recompile.

Gareth

Sent from my iPad

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[Bin Song]

Hello Gareth,

Thank you for response.  I have done touch crystallization.on in src/. And I recompiled PLUMED and LAMMPS. But I still got the same error message. 

And the curly brackets were in my plumed input file, somehow in the output file the curly brackets were not shown. Does this mean the PLUMED was reading the command wrong?

Another question is when I compiled PLUMED I used mpic++, which seems not to support 'long long'. I let this slide. Could this be a problem?

A third question is that I may want to use local_average q4 to drive the same simulations with umbrella sampling, I think it is not implemented yet. Am I right?

Thank you.

Bin

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[gareth....@gmail.com]

Hello

Not sure what is going on. If you do

ls src/crystallization 

Are there object files? Files such as Q6.o? Also check how I spelt crystallization I can't remember if I did it uk (crystallisation) or usa style (crystallization)? The spelling of the .on file should be the same as the name of the directory.

You can use the local average of q4 to drive simulations. The derivatives are there. 

Gareth

Sent from my iPad

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[Bin Song]

The object files in there. The folder was in US spelling. 

I plan to run it outside lammps. But the lammps driver < trjfile seems to not recognize my trajectory file. My trajectory file is in has only id, type, and x y z in scaled units.

Thanks for your quick response.

Bin 

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[gareth....@gmail.com]

Not sure I understand your last email sorry. Based on your previous email is it linking in the q4.o when it builds plumed?

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[xx w]

HI

how do you solve the problem?

在 2014年12月23日星期二 UTC+1上午1:42:06，bin.chr...@gmail.com写道：

[Gareth Tribello]

What problem?  Do you have any error messages, do you have an example for what you are trying to do with plumed or do you have a problem with lammps.  If you look this email thread in my last email I said that I didn’t understand what problem you were having.  If you provide more information I might be able to help.  

 

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[debi...@gmail.com]

Hello Bin,

I understand that it's a very old problem. But I am facing the same error, PLUMED: I cannot understand line: Q6 LABEL=tq6 SPECIES=1-30 SWITCH=RATIONAL R_0=0.01 D_0=0.3 D_MAX=0.35

As I am new user of PLUMED in lammps, could you kindly share how you solved this problem. I have tried many things but nothing worked is this because plumed is not properly compiled? 

Thank you very much

Debdas

On Tuesday, 23 December 2014 18:16:25 UTC-7, Bin Song wrote:

The object files in there. The folder was in US spelling. 

I plan to run it outside lammps. But the lammps driver < trjfile seems to not recognize my trajectory file. My trajectory file is in has only id, type, and x y z in scaled units.

Thanks for your quick response.

Bin 

On Dec 23, 2014, at 6:12 PM, gareth....@gmail.com wrote:

Hello

Not sure what is going on. If you do

ls src/crystallization 

Are there object files? Files such as Q6.o? Also check how I spelt crystallization I can't remember if I did it uk (crystallisation) or usa style (crystallization)? The spelling of the .on file should be the same as the name of the directory.

You can use the local average of q4 to drive simulations. The derivatives are there. 

Gareth

Sent from my iPad

On 23 Dec 2014, at 21:24, Bin Song <bin.ch...@gmail.com> wrote:

Hello Gareth,

Thank you for response.  I have done touch crystallization.on in src/. And I recompiled PLUMED and LAMMPS. But I still got the same error message. 

And the curly brackets were in my plumed input file, somehow in the output file the curly brackets were not shown. Does this mean the PLUMED was reading the command wrong?

Another question is when I compiled PLUMED I used mpic++, which seems not to support 'long long'. I let this slide. Could this be a problem?

A third question is that I may want to use local_average q4 to drive the same simulations with umbrella sampling, I think it is not implemented yet. Am I right?

Thank you.

Bin

On Dec 23, 2014, at 1:16 AM, gareth....@gmail.com wrote:

You need curly braces around the switch part. Also you need to go to the directory

plumed2/src/

And type

touch crystallization.on. Once you have done this recompile.

Gareth

Sent from my iPad

On 23 Dec 2014, at 00:42, bin.ch...@gmail.com wrote:

Hello,

Today I just installed PLUMED 2.1 with LAMMPS 2Apr-13. I am just testing it on the cubic ice. PLUMED seemed to have run and correctly read the UNITS command. But it failed at the command above in the subject line. I wonder what I missed in the installation. 

Thank you for help.

Bin

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[Gareth Tribello]

When you compiled plumed did you do

./configure --enable-modules=all

If you didn't do that it would explain your problem. 

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[Bin Song]

Hello Debdas,

I did not get it working at the time and just wrote my own code to
compute Q4 at the time. However, my issue was older versions of lammps
and plumed. I have been using newer versions of plumed and have no
issue. It would be helpful if you gave the log file of the plumed
command and configure log when you compiled plumed.

Best luck,
Bin

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[Debdas Dhabal]

Dear Gareth and Bin,

I am able to solve the problem. I was making a stupid mistake, the version of the library for the PLUMED was different from what I intended. It was an older version where all the modules were not compiled may be. 

Anyways thank you very much both of you for your prompt response. 

With regards

Debdas

 

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Debdas Dhabal

Postdoctoral Researcher.

SEAS, Department of Chemical and Biomolecular Engineering,

The University of Pennsylvania, Philadelphia, PA 19104, USA.