Outputs - hyschive/gamer-fork GitHub Wiki

This page describes various data formats and options for storing simulation snapshots. For simulation logs recording, for example, performance, load balancing, and memory consumption, see Simulation Logs .

Compilation Options

Related options: --hdf5  

Runtime Parameters

Parameters described on this page: OPT__OUTPUT_TOTAL,   OPT__OUTPUT_PART,   OPT__OUTPUT_TEXT_FORMAT_FLT,   OPT__OUTPUT_USER,   OPT__OUTPUT_PAR_MODE,   OPT__OUTPUT_PAR_MESH,   OPT__OUTPUT_BASEPS,   OPT__OUTPUT_BASE,   OPT__OUTPUT_POT,   OPT__OUTPUT_PAR_DENS,   OPT__OUTPUT_CC_MAG,   OPT__OUTPUT_PRES,   OPT__OUTPUT_TEMP,   OPT__OUTPUT_ENTR,   OPT__OUTPUT_CS,   OPT__OUTPUT_DIVVEL,   OPT__OUTPUT_MACH,   OPT__OUTPUT_DIVMAG,   OPT__OUTPUT_LORENTZ,   OPT__OUTPUT_3VELOCITY,   OPT__OUTPUT_ENTHALPY,   OPT__OUTPUT_USER_FIELD,   OPT__OUTPUT_MODE,   OPT__OUTPUT_RESTART,   OUTPUT_STEP,   OUTPUT_DT,   OUTPUT_WALLTIME,   OUTPUT_WALLTIME_UNIT,   OUTPUT_PART_X,   OUTPUT_PART_Y,   OUTPUT_PART_Z,   INIT_DUMPID,  

Other related parameters: none

Parameters below are shown in the format:   Name   (Valid Values)   [Default Value]

  • OPT__OUTPUT_TOTAL   (0=off, 1=HDF5, 2=C-binary)   [1]

    • Description: Output the simulation snapshots in the specified binary format (HDF5 or simple C-binary), which will store all simulation information such as grid data, particle data, tree structure, runtime parameters, and compilation options. These snapshots can be used for restarting simulations . The snapshot filename is currently fixed to Data_%06d. See also OPT__OUTPUT_MODE for specifying the data dump frequency.
    • Restriction: OPT__OUTPUT_TOTAL=1 is only applicable when enabling the compilation option --hdf5 . Data analysis with yt is currently only supported for the HDF5 snapshots of GAMER.

  • OPT__OUTPUT_PART   (0=off, 1=xy, 2=yz, 3=xz, 4=x, 5=y, 6=z, 7=diagonal)   [0]

  • OPT__OUTPUT_TEXT_FORMAT_FLT   (%XX.YYe)   [%24.16e]

  • OPT__OUTPUT_USER   (0=off, 1=on)   [0]

  • OPT__OUTPUT_PAR_MODE   (0=off, 1=text files, 2=C-binary files)   [0]

    • Description: Output particle data in either the text or binary format. This option is mainly for debugging purposes since the simulation snapshots (with the option OPT__OUTPUT_TOTAL) already store particle data.
    • Restriction:

  • OPT__OUTPUT_PAR_MESH   (0=off, 1=on)   [1]

    • Description: Map mesh attributes to tracer particles and output them in the HDF5 snapshots. Edit Input__Par_Mesh to specify the desired mesh attributes. An example file can be found at example/input/Input__Par_Mesh.
    • Restriction: Only applicable when enabling --tracer and setting OPT__OUTPUT_TOTAL to 1.

  • OPT__OUTPUT_BASEPS   (0=off, 1=on)   [0]

    • Description: Output the mass density power spectrum on the root level.
    • Restriction:

  • OPT__OUTPUT_BASE   (0=off, 1=on)   [0]

    • Description: Only output the base-level (i.e., root level) data for OPT__OUTPUT_PART.
    • Restriction:

  • OPT__OUTPUT_POT   (0=off, 1=on)   [1]

    • Description: Output the gravitational potential data on grids.
    • Restriction:

  • OPT__OUTPUT_PAR_DENS   (0=off, 1=particle mass density, 2=total mass density)   [0]

    • Description: Store the particle or total mass density on grids in the simulation snapshots. The particle interpolation scheme is set by PAR_INTERP .
    • Restriction: Only applicable when enabling OPT__OUTPUT_TOTAL.

  • OPT__OUTPUT_CC_MAG   (0=off, 1=on)   [1]

    • Description: Output the cell-centered magnetic field (mandatory for yt analysis).
    • Restriction: For --mhd only.

  • OPT__OUTPUT_PRES   (0=off, 1=on)   [0]

    • Description: Output the gas pressure (or gas + cosmic-ray pressure when enabling --cosmic_ray ) on grids. Magnetic pressure is always excluded.
    • Restriction:

  • OPT__OUTPUT_TEMP   (0=off, 1=on)   [0 for HD, 1 for SRHD]

    • Description: Output the gas temperature on grids.
    • Restriction:

  • OPT__OUTPUT_ENTR   (0=off, 1=on)   [0]

    • Description: Output the gas entropy on grids.
    • Restriction: Mainly used by the gamma-law EoS.

  • OPT__OUTPUT_CS   (0=off, 1=on)   [0]

    • Description: Output the sound speed on grids.
    • Restriction:

  • OPT__OUTPUT_DIVVEL   (0=off, 1=on)   [0]

    • Description: Output the divergence of gas velocity on grids.
    • Restriction:

  • OPT__OUTPUT_MACH   (0=off, 1=on)   [0]

    • Description: Output the Mach number on grids.
    • Restriction:

  • OPT__OUTPUT_DIVMAG   (0=off, 1=on)   [0]

    • Description: Output $|\nabla \cdot B| \Delta h / |B|$, where $B$ is the magnetic field and $\Delta h$ is cell width.
    • Restriction: For --mhd only.

  • OPT__OUTPUT_LORENTZ   (0=off, 1=on)   [0]

    • Description: Output the SRHD Lorentz factor on grids.
    • Restriction: For --srhd only.

  • OPT__OUTPUT_3VELOCITY   (0=off, 1=on)   [0]

    • Description: Output the SRHD three-velocity on grids.
    • Restriction: For --srhd only.

  • OPT__OUTPUT_ENTHALPY   (0=off, 1=on)   [1]

    • Description: Output the SRHD reduced enthalpy on grids.
    • Restriction: For --srhd only.

  • OPT__OUTPUT_RESTART   (0=off, 1=on)   [0]

    • Description: Output a snapshot immediately after restarting a simulation. It can be useful if some physical quantities change during restart (e.g., new particles are added).
    • Restriction:

  • OUTPUT_STEP   (>0)   [none]

  • OUTPUT_DT   (>0.0)   [none]

  • OUTPUT_WALLTIME_UNIT   (0=second, 1=minute, 2=hour, 3=day)   [0]

  • OUTPUT_PART_X   (within the simulation domain)   [-1.0]

  • OUTPUT_PART_Y   (within the simulation domain)   [-1.0]

  • OUTPUT_PART_Z   (within the simulation domain)   [-1.0]

  • INIT_DUMPID   (≥0; <0 → set to default)   [-1]

    • Description: Set the first data dump ID. Note that it is unnecessary to set this value in most cases, even when restarting simulations, unless you want to overwrite the default value.
    • Restriction:

Remarks

Enforcing Outputs

Typically, the simulation output interval is controlled by OUTPUT_STEP, OUTPUT_DT, or the timetable Input__DumpTable depending on OPT__OUTPUT_MODE. One can also enforce output by creating a file named DUMP_GAMER_DUMP (e.g., using touch DUMP_GAMER_DUMP) in the same directory as the executable gamer. The program will check the existence of this file after every root-level update. If it is detected, the program will output data (assuming at least one of the output options described on this page is enabled) and delete the file DUMP_GAMER_DUMP. Note that this functionality is supported only when the runtime parameter OPT__MANUAL_CONTROL is on.

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