Modar manpage

  • The man page can be printed by command “./modar -h”


./modar  [options] [modar_inputfile.inp] [-o <output/log file>]



./modar run.inp




-vl <number>

for declare verbose level, default value is 0, bigger means louder



-np <number>

for declare the # of threads for OpenMP.

Modar can detect # of cores available automatically

So you don't need to set this opt if you have no idea



-o <log file>

to tell the log file name, by default,  Modar will create a log file using the same filename of input




to print log message to screen rather than to the default log file




to enable instant flushing for output/log file




to tell debug dumping file path, for debug only




to enable Replica Exchange Simulation rather than parallel




to enable share memory for MPI communication




to enable domain decomposing method for parallel dividing, this is the default parallel dividing method used in MoDaR




to use FFT decomposing method parallel dividing




to enable spatial decomposing method for parallel dividing



-tabnp <number>

or -tabscale <number>

to set # of control points per angstrom for spline interpolation, default value is 100, which is good enough for approximation




to disable lookup table for all case, by default lookup table is alway on for Ewald terms for CPU base          while for GPU base, the default value is false, and it also turns nonbonded optimization off




to disable nonbonded optimization



-nnbopt <number>

to set total # of atomtype for nonbonded optimization, default value is 20, which is enough for most system




to disable file backup, MODAR backups all files existed by default, backup function will be disabled for restart case




to disable termination signal handling policy,          MODAR handles termination signals internal by default,          use this flag to turn off the handling policy




to enable continuously restarting write out,              rather than to create new files, see following -mds -rst -nstep –nstepmore, for more detail about to do a restart MD run



-mds <mds file>

the Modar .mds file, i.e. the whole MD system setup packed in a binary file



-rst <rst file>

the Modar restarting state in a binary file



-nstep <number>

the total step MD will run



-nstepmore <number>

the number of step MD will be continued





Modar can detect file format automatically, for instance, to launch a 1ns more restart run simply by command:

./modar -restart run.mds run.rst -nstepmore 500000 -o more_1.log




to print version information




to print this manpage


-cuda <on/off>

To enable/disable CUDA GPU speedup for cuda build only




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