COLVARS package

[akram]

Dear experts,
I want to use the “group2ndx” command to create an index file where the IDs of the any atoms belonging to a certain group is determined.
This command needs to install the COLVARS package, but I can’t compile Lammps after installing this package because I get the following error when using “make mpi”:

makefile.package.setting:4: …/…/lib/colvars/Makefile.lammps: No such file or directory.

My first question is, isn’t there another way to create an index file of atomic groups in which the IDs of the atoms belonging to each individual type are lined up like below:
[type1]
1,4,6,10,24,45,…

[type2]
2,3,9,11,14,18,34,…

[type3]
5,7,12,20,22,…

And the second question is: How can I compile Lammps after installing the COLVARS package and not encounter the above error?
MY LAMMPS VERSION: 23 JUNE2022

[akohlmey]

@akram

How can I compile Lammps after installing the COLVARS package and not encounter the above error?

Very simple. You need to follow the installation instructions (which you didn’t, since you are using the traditional make build procedure, you need to click on the “Traditional make” tab).
To use the COLVARS package, you first need to compile the colvars library. That will create the file that is missing and avoid the compilation error.

If you would compile with CMake instead, this would not be necessary, since the CMake scripting integrates both build steps into one.

[akram]

@akohlmey

Very simple. You need to follow the installation instructions (which you didn’t, since you are using the traditional make build procedure, you need to click on the “Traditional make” tab).
To use the COLVARS package, you first need to compile the colvars library. That will create the file that is missing and avoid the compilation error.

If you would compile with CMake instead, this would not be necessary, since the CMake scripting integrates both build steps into one

Dear akohlmey,
Thanks for your reply. when I use :
make lib-colvars args=“-m mpi”

I encounter the below:
Installing lib colvars
/bin/bash: line 2: python: command not found

[hothello]

@akram

/bin/bash: line 2: python: command not found

Read 10 times the above line and try to figure out the meaning.

[akram]

@hothello

Read 10 times the above line and try to figure out the meaning.

Read the following sentence 20 times:
"Every person should learn how to behave with someone who is new to software or package, otherwise his behavior will be very unprofessional!

[akohlmey]

@akram

"Every person should learn how to behave with someone who is new to software or package, otherwise his behavior will be very unprofessional!

Please no flame wars.

Being a beginner in LAMMPS, however, is no excuse for not doing your homework.
The error message you get is not really a LAMMPS thing but a general Linux thing.
You apparently have no program called “python” installed, however, that is a prerequisite for building LAMMPS the way you have chosen to build.
Using a web search, you could have easily figured out what it means, rather than complaining.

The LAMMPS developers generally recommend people that have limited experience with compiling, makefiles, and running commands on the command line to use the CMake build process. It has many checks, does many things automatically, and will tell you when something is missing. The traditional build system assumes that people know what they are doing, and that rarely applies to beginners.

[akram]

Dear akohlmey,
Thank you for your friendly reply.
I found out the cause of the error and I am installing the package.
Best regards,
Akram

[hothello]

I apologise for being mean!
However, if we allow using the forum as a substitute for reading the docs, or learning how to turn a computer on, we turn thematic channels into a dump of uninteresting conversations from which there is little to learn from.