MBX reading of xyz coordinates and definition of all dim-s and trim-s

[Yevhen Horbatenko]

Dear developers of MBX:

I am trying to go through some parts of the MBX code, to find the place (if any) where the MBX reading of xyz coordinates occurs during LAMMPS MD run,

as well as the place (if any) where all possible dimers and trimers are defined within a given simulation box, e.g., of bulk water.

Regarding the latter, probably, it is done with GetPairList (from system.cpp) that calls AddClustersParallel (from system.cpp) that, in turn, calls AddClusters (from sys_tools.cpp).  However, i am not sure, since i am new to c++. 

I would appreciate any response/explanation.

Yevhen Horbatenko

- -

Research Professor,

Room 219, IBS CMSD, 

R&D Center at Korea University,

Anam-ro 145, Seoul, Republic of Korea

Tel: + 82-10-2779-5440

E-mail: papilio.p...@gmail.com

[Francesco Paesani]

Dear Yevhen,

To answer your question about the dimers/trimers extraction from LAMMPS, it will be difficult to do it directly from LAMMPS. However, the System class contains an interface function called GetPairList() that find all dimers or trimers in the system and return the indexes of their monomers. To use this function, you will have to create a new C++ executable in which you load the NRG file into a System instance (see src/main/single_point.cpp for example of loading NRG file into System instance), and then call GetPairList() and print the results. As a word of caution, this function will ONLY return the monomer indexes, not the coordinates. To get the coordinates of the dimers and trimers, pass the monomer indices returned by GetPairList() to GetFirstInd() to get the index of the first atom of each monomer in the coordinate array which can be obtained by calling GetRealXYZ(). All of the functions in the System class are properly documented in system.h.

Thank you,
Marc, Ethan, and Francesco

[Yevhen Horbatenko]

Dear all:

Thank you for your reply and your suggestion.

Let me check it and try after coupling MBX with LAMMPS-QUIP

(succeeded partially within these days).

Kind regards,

Yevhen Horbatenko