questions about msd/chunk

Dear developers,

I am trying to calculate msd for multiatomic molecules. I have tried with monatomic particles.

compute chunkCX CX chunk/atom molecule nchunk once ids once units box

–> producing chunkID for each chunk, which is regarded as each molecule.

compute diffCX CX msd/chunk chunkCX

–> caculating MSD of the center of mass for each chunk. The output is supposed to be global array.

I wonder how I can print out the vaules of c_diffCX.

For monatomic particles,
I have used
fix msdCa Ca ave/time 1 1 10 v_ttime c_diffCa[1] c_diffCa[2] c_diffCa[3] c_diffCa[4] ave one file msd_Ca.txt

But, this way does not work for msd/chunk.
How can I print out the average values of c_diffCX[*]? assuming the number of atoms in each chunk is constant.

Thank you for your help.

Baek

Dear Baek,

Since you computed msd for “all” the “n” types of atom, diffCX is a 2-dimentional n*4 array. Thus, for example, c_diffCX[2][3] gives you the z-component of msd for atom type 2.

Regards

MN

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Do the example script lines given on the compute msd/chunk doc

page not work correctly?

Steve

Dear Nejatolahi,

Thanks for your help.

c_diffCX[2][3] gives you the z-component of msd for atom type 2.

–> For clarity, is the “AVERAGE” of the z-component of mad for atom type 2?

In addition, I have included only one type of atom in CX, assuming type = 2. Even in case, do I need to specify like c_diffCX[2][3] ?

Baek

According to Doc,

The simplest way to output the results of the compute com/msd calculation to a file is to use the fix ave/time command, for example:

compute cc1 all chunk/atom molecule
compute myChunk all com/msd cc1
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector

I cannot find out “compute com/msd” command and document (I am using 30Jul2016 Ver.) and this guidance did not work for my case.

I cannot find out “compute com/msd” command and document (I am using 30Jul2016 Ver.) and this guidance >did not work for my case.

I don’t know what this means. What can you not

find, and what did not work?

Steve