On Thu, Jul 28, 2022, 23:06 Satyen Dhamankar <[email protected]> wrote:
> Hello, > > I am running some very simple SPCE water simulations in VOTCA. I am > testing out IBI. > I have to primary questions: > 1. *How do I check the extent of convergence of the IBI?* > This my settings.xml file: > > <cg> > <!-- example for a non-bonded interaction entry --> > <non-bonded> > <!-- name of the interaction --> > <name>CG-CG</name> > <!-- types involved in this interaction --> > <type1>Bead1</type1> > <type2>Bead1</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.0</min> > <max>0.9</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf) --> > <target>CG-CG.dist.tgt</target> > <lammps> > <!-- name of the table for lammps run --> > <table>CG_CG.pot</table> > <!-- nm to angstrom --> > <scale>10</scale> > <!-- kJ/mol to kcal/mol --> > <y_scale>0.239006</y_scale> > <table_begin>0.20</table_begin> > <table_bins>0.002</table_bins> > </lammps> > </inverse> > </non-bonded> > > <!-- general options for inverse script --> > <inverse> > <!-- votca units 300*0.00831451 kJ/mol --> > <kBT>2.47772398</kBT> > <!-- use lammps as simulation program --> > <program>lammps</program> > <!-- lammps specific options --> > <lammps> > <!-- lammps script to run !--> > <script>cg.spce.in</script> > <!-- topology to be used by csg_stat !--> > <topol>cg.spce.data</topol> > <!-- traj file created by lammps !--> > <traj>traj.dump</traj> > </lammps> > <initial_configuration>maindir</initial_configuration> > <!-- these files are copied for each new run --> > <filelist>cg.spce.data cg.spce.in</filelist> > <!-- do so many iterations --> > <iterations_max>300</iterations_max> > <convergence_check> > limit>0.0001</limit> > </convergence_check> > <!-- ibi: inverse biltzmann imc: inverse monte carlo --> > <method>ibi</method> > </inverse> > </cg> > > In <inverse> I have plugged <convergence_check> and put a limit of 1e-4, > although, I have no idea how it is being processed by the system. > You will need to add the "convergence" task in the post_add list of each interaction you want to consider, that is missing in your listing above. > 2. *How do I make sure that LAMMPS is multithreading the process? * > > I am running these CG simulations with LAMMPS, and I want to make sure > that I am using all the threads that are available to me. For a usual > lammps simulation, I would do > > srun --ntasks=96 lmp_exe -in in.simulation > > But how do I translate the above resource allocation to csg_inverse or > csg_fmatch? > csg_fmatch has a --nt option and for csg_inverse it is usually automatic, but can overwrite the number of threads to use in the settings file. Additional you can tell Votca to run lammps with a specific command. For srun submission you need to allocate the resources, but then run csg_inverse serially and then override the number of threads in the XML settings file and use a special lammps command. Christoph > > > > Thank you for taking the time to read my question! > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/40cc6de3-c363-4f8a-91ff-4a484c31f983n%40googlegroups.com > <https://groups.google.com/d/msgid/votca/40cc6de3-c363-4f8a-91ff-4a484c31f983n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e65CtYK177%3Dmz9DbLaDAKZ%2BSmsD43qZT5REh2OdRhOcqA%40mail.gmail.com.
