Run the code

The execution of RMPCDMD is controlled via a single command-line program, rmpcdmd. RMPCDMD must be built before using this tool, see the Install documentation.

rmpcdmd run

Usage:

rmpcdmd run program input output seed

Arguments

  • program one of the simulation program coming with RMPCMD (i.e. single_dimer_pbc)
  • input text file with simulation parameters
  • output filename for the output data
  • seed a signed 64-bit integer value. seed can be set to the value auto, a seed will the be generated from the /dev/urandom device.

When run with no argument, rmpcdmd run will list the parameters and the possible values for program.

The simulation programs (see Programs) can also be executed directly at the command-line with the syntax:

./program input output seed

Where the arguments are the same as when using rmpcdmd, with the differences

  • For seed the keyword auto cannot be used.
  • The ./ must be replaced by the full path to the build directory when executing from another directory.
  • Less information is available in the output (start and end times, value of OMP_NUM_THREADS environment variable.

rmpcdmd plot

Usage:

rmpcdmd plot [-h] datafile [--obs OBSERVABLE] [--traj GROUP/TRAJECTORY]

Arguments

  • -h display the the full command-line syntax and exit
  • datafile a datafile produced by one of the simulation programs

One of [--obs OBSERVABLE] or [--traj GROUP/TRAJECTORY] can be given to display an observable or a trajectory from the file.

rmpcdmd seeder

Usage:

rmpcdmd seeder

Returns a signed 64-bit integer seed.

rmpcdmd timers

Usage:

rmpcdmd timers [-h] datafile [--plot]

Arguments

  • -h display the the full command-line syntax and exit
  • datafile a datafile produced by one of the simulation programs
  • --plot plots the timers data as a bargraph instead of printing to the terminal.

Prints (or plot in the --plot option is given) the value of the timers in the simulation file datafile.

experiments/ directory

The execution of some RMPCDMD simulations is illustrated in the directory experiments/, using makefiles for simplicity. An example simulation session is given below

user@pc$~$ cd /tmp/RMPCDMD/
user@pc$/tmp/RMPCDMD$ cd experiments/01-single-dimer/
user@pc$/tmp/RMPCDMD/experiments/01-single-dimer$ ls
dimer.parameters  Makefile  plot_histogram.py  plot_velocity.py
ruckner-kapral.parameters
user@pc$/tmp/RMPCDMD/experiments/01-single-dimer$ make simulation
/tmp/RMPCDMD/experiments/01-single-dimer/../../build/rmpcdmd run single_dimer_pbc
dimer.parameters dimer.h5 auto
RMPCDMD running single_dimer_pbc
OMP_NUM_THREADS not set
Start time -- Thu Jun 16 13:40:08 CEST 2016
single_dimer_pbc dimer.parameters dimer.h5 3589052620060159831

 Running for         100 loops
 mass   1130.9733867645264        1130.9733867645264
    5   10   15   20   25   30   35   40   45   50   55   60   65   70   75   80   85
   90   95  100
 n extra sorting         747

real    3m25.006s
user    10m13.496s
sys     0m0.988s
End time -- Thu Jun 16 13:43:33 CEST 2016
205s elapsed
user@pc$/tmp/RMPCDMD/experiments/01-single-dimer$