VOTCA with LAMMPS

[Sudeep Maheshwari]

Hello All

I am new to installing and using VOTCA. We dont use Gromacs in our group and i have to make VOTCA work with LAMMPS.
Could someone please point out how to use build.sh to make Votca on my computer with LAMMPS as the MD software and not Gromacs.
Any hint in this direction would be very valuable. Also if someone could comment on how good does LAMMPS work with VOTCA would be nice.

cheers
sudeep

[Christoph Junghans]

Sudeep,

2017-09-29 9:02 GMT-06:00 Sudeep Maheshwari <sudeep....@gmail.com>:
> Hello All
>
> I am new to installing and using VOTCA. We dont use Gromacs in our group and
> i have to make VOTCA work with LAMMPS.
> Could someone please point out how to use build.sh to make Votca on my
> computer with LAMMPS as the MD software and not Gromacs.

You can compile VOTCA with -DWITH_GMX=OFF to disable the gromacs backend.

> Any hint in this direction would be very valuable. Also if someone could
> comment on how good does LAMMPS work with VOTCA would be nice.

There are a couple of tutorials using LAMMPS in csg-tutorials:
$ ls -d */*lammps*
spce/ibi_lammps spce/realtime_lammps spce/re_lammps

And searching the mailing also has some help on LAMMPS:
<https://groups.google.com/forum/#!searchin/votca/lammps%7Csort:relevance>
there are even a version of the propane/ibi tutorial for LAMMPS:
<https://groups.google.com/d/msg/votca/FeFw9xYgU6k/aQoDwIqGwaoJ>

If you need something specific just ask!

Christoph
>
> cheers
> sudeep
>
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Christoph Junghans
Web: http://www.compphys.de

[Sudeep Maheshwari]

Thanks a lot for the reply christoph

I am facing some more problem in compiling VOTCA, as compiling without sqlite3 is not working and i figured out that i might need gromacs somewhere down the line

Could you please tell me how to force search location for gromacs and sqlite3 while building votca.

I was trying the following command but now i want to specify location of gromacs and sqlite3 while building
./build.sh --prefix ~/votca --dev -DWITH_GMX=OFF tools csg kmc moo ctp ctp-tutorials ctp-manual

cheers
sudeep

[Sudeep Maheshwari]

I found the web page showing the commands to force search locations, i am able to include commands for the location of SQLITE but the GROMACS is installed as a module which works when i load it using "module load gromacs" on the cluster.
Also after even after specifying the locations for the directory of sqlite, the program is not able to detect it and shuts out with the error of No package sqlite3 found.

Could you please suggest me some solution of both of these problems
I am using the command ./build.sh --prefix ~/votca --dev -DSQLITE_INCLUDE_DIR=/home/smaheshwari/bin/include -DSQLITE_LIBRARY=/home/smaheshwari/bin/lib -DWITH_GMX=OFF tools csg kmc moo ctp ctp-tutorials ctp-manual

sudeep

[Christoph Junghans]

2017-10-02 4:08 GMT-06:00 Sudeep Maheshwari <sudeep....@gmail.com>:
> I found the web page showing the commands to force search locations, i am
> able to include commands for the location of SQLITE but the GROMACS is
> installed as a module which works when i load it using "module load gromacs"
> on the cluster.
> Also after even after specifying the locations for the directory of sqlite,
> the program is not able to detect it and shuts out with the error of No
> package sqlite3 found.
>
> Could you please suggest me some solution of both of these problems
> I am using the command ./build.sh --prefix ~/votca --dev
> -DSQLITE_INCLUDE_DIR=/home/smaheshwari/bin/include
> -DSQLITE_LIBRARY=/home/smaheshwari/bin/lib -DWITH_GMX=OFF tools csg kmc moo
> ctp ctp-tutorials ctp-manual

If don't need ctp, you also don't need sqlite3 as well and can disable
it with the "-DWITH_SQLITE3=OFF" option, csg works without sqlite3.

If you need ctp, you will need to add
-DSQLITE3_INCLUDE_DIR="/home/smaheshwari/bin/include" and
-DSQLITE3_LIBRARY="/home/smaheshwari/bin/lib/libsqlite3.so"
Please note, that we are requiring sqlite3 for ctp and hence both
variables are called SQLITE3 (note the "3"), and cmake wants
SQLITE3_LIBRARY to be that path to the library, incl. the library name
itself.

You can use cmake-gui to see all variables:
$ export CMAKE=cmake-gui
$ ./build.sh --prefix ~/votca --dev ....

For more hints see: https://github.com/votca/csg/wiki/Installing

Christoph

[Sudeep Maheshwari]

Dear Christoph

Thanks a lot for your reply and hints
I was able to build VOTCA successfully
I used sqlite3 because i want to perform ctp and xtp calculations
I have one more question, for running the ibi_lammps example in csg_tutorials/spce
I am trying to supply the location of my lammps executable in the settings.xml but i think i am making a mistake there
I want to use the lmp_mpi executable to run my jobs in parallel

I am writing it like this
  <!-- general options for inverse script -->
  <inverse>
    <!-- 300*0.00831451 lammps units -->
    <kBT>2.49435</kBT>
    <!-- use lammps as simulation program -->
    <program>/home/smaheshwari/lammpspimd/lammps-17Nov16/src/lmp_mpi</program>
    <!-- lammps specific options -->
    <lammps>
      <!-- lammps script to run !-->
      <script>spce.in</script>
      <!-- topology to be used by  csg_stat !-->
      <topol>topol.xml</topol>
      <!-- traj file created by lammps !-->
      <traj>traj.dump</traj>
    </lammps>


Could you please point out what is the mistake that i am making

sincerely
sudeep

[Christoph Junghans]

2017-10-03 7:58 GMT-06:00 Sudeep Maheshwari <sudeep....@gmail.com>:
> Dear Christoph
>
> Thanks a lot for your reply and hints
> I was able to build VOTCA successfully
> I used sqlite3 because i want to perform ctp and xtp calculations
> I have one more question, for running the ibi_lammps example in
> csg_tutorials/spce
> I am trying to supply the location of my lammps executable in the
> settings.xml but i think i am making a mistake there
> I want to use the lmp_mpi executable to run my jobs in parallel
>
> I am writing it like this
> <!-- general options for inverse script -->
> <inverse>
> <!-- 300*0.00831451 lammps units -->
> <kBT>2.49435</kBT>
> <!-- use lammps as simulation program -->
>
> <program>/home/smaheshwari/lammpspimd/lammps-17Nov16/src/lmp_mpi</program>

The program is still "lammps". Program has to be "gromacs", "lammps"
or something like that.

> <!-- lammps specific options -->
> <lammps>

You need to add
<command>/home/smaheshwari/lammpspimd/lammps-17Nov16/src/lmp_mpi</command>
in the <lammps> block here, see Section 10.4 (pg 55) of
<http://votca.github.io/doxygen/manual.pdf>

Christoph