Basic File Format

Merger trees are stored in HDF5 files for portability and convenience. Additionally, the format is intended to be sufficiently flexible to allow it to desribe merger trees obtained in a wide variety of ways, including Monte Carlo algorithms (e.g. extended Press-Schechter algorithms) and from N-body simulations.

Flexibility and Extensibility

All of the groups/datasets in the file except for the forestIndex and forestHalos groups are, in principle, optional. This does not mean that a file created without some of these optional groups/datasets will be useable by a given code. It is the responsibility of a given code to check that all data that it requires is present in the file. You are therefore encouraged to include as much information as possible when constructing merger tree files.

Additionally, the file format is intended to be extensible. It is permissible to add additional datasets, for example to describe some other properties of nodes in each tree. Additional datasets should follow the structure of currently defined datasets, i.e. they should be stored as a single dataset combining all trees with nodes listed in the same order as for other datasets. For additional datasets which might be of general use you are encouraged to contact us and recommend them for inclusion in the standard—this allows their name to be standardized.

A Note on Scalar Attributes

Many of the HDF5 attributes discussed in this document are indicated to be scalar (rank 0) attributes. It is allowable within the standard that these be pseudo-scalars (rank 1 arrays contaning a single element). This allows such attributes to be created using the h5lt API for example.

Example File Structure

An example of the structure of such a file, called “example.hdf5” is shown below using the format of h5dump. Each of the groups is described in detail in the following sections.

HDF5 "example.hdf5" {
GROUP "/" {
   ATTRIBUTE "formatVersion"
   GROUP "cosmology" {
   }
   GROUP "groupFinder" {
   }
   GROUP "forestHalos" {
   }
   GROUP "forests" {
   }
   GROUP "particles" {
   }
   GROUP "provenance" {
   }
   GROUP "simulation" {
   }
   GROUP "forestIndex" {
   }
   GROUP "units" {
   }
}

Format Version Attribute

The formatVersion attribute specifies which version of the merger tree file format this file follows. The current standard is version 2.

Cosmology Group

The cosmology group describes the cosmological model within which the merger trees contained in the file were constructed. An example of this group, showing standard attributes, is given below.

GROUP "cosmology" {
   ATTRIBUTE "HubbleParam" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SCALAR
      DATA {
      (0): 0.73
      }
   }
   ATTRIBUTE "OmegaMatter" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SCALAR
      DATA {
      (0): 0.25
      }
   }
   ATTRIBUTE "OmegaLambda" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SCALAR
      DATA {
      (0): 0.75
      }
   }
   ATTRIBUTE "OmegaBaryon" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SCALAR
      DATA {
      (0): 0.045
      }
   }
   ATTRIBUTE "powerSpectrumIndex" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SCALAR
      DATA {
      (0): 1
      }
   }
   ATTRIBUTE "sigma_8" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SCALAR
      DATA {
      (0): 0.9
      }
   }
   ATTRIBUTE "transferFunction" {
      DATATYPE  H5T_STRING {
            STRSIZE 7;
            STRPAD H5T_STR_SPACEPAD;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
      DATASPACE  SCALAR
      DATA {
      (0): "CAMB"
      }
   }
}

Standard Attributes

The following are standard attributes in the cosmology group (others may be added as desired).

HubbleParam: The Hubble parameter in units of 100 km/s/Mpc at z=0, h₀;

OmegaMatter:The density of matter (both dark and baryonic matter) in units of the critical density at z=0, Ω_M;

OmegaLambda: The density of dark energy in units of the critical density at z=0, Ω_Λ;

OmegaBaryon: The density of matter (both dark and baryonic matter) in units of the critical density at z=0, Ω_b;

powerSpectrumIndex: The index of the primordial power spectrum of matter fluctuations, i.e. n_s for power spectrum P(k) ∝ k^n_s;

sigma_8: The root-variance of mass fluctuations in real space top-hat spheres of radius 8 h^-1 Mpc computed from the z=0 linear theory power spectrum, σ₈;

transferFunction: A descriptor of the transfer function used to compute the power spectrum.

Group Finder Group

This group, typically relevant only for merger trees derived from N-body simulations, describes the characteristics of the group finding algorithm that was used to find halos in the simulation. An example of this group, showing standard attributes, is given below.

GROUP "groupFinder" {
   COMMENT "Group finder parameters."
   ATTRIBUTE "code" {
      DATATYPE  H5T_STRING {
            STRSIZE 7;
            STRPAD H5T_STR_SPACEPAD;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
      DATASPACE  SCALAR
      DATA {
      (0): "SUBFIND"
      }
   }
   ATTRIBUTE "linkingLength" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SCALAR
      DATA {
      (0): 0.2
      }
   }
   ATTRIBUTE "minimumParticleNumber" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SCALAR
      DATA {
      (0): 20
      }
   }
}

Standard Attributes

The following are standard attributes in the groupFinder group (others may be added as desired).

code: The name of the group finding code used in the construction of these merger trees;

linkingLength: For friends-of-friends group finding algorithms the dimensionless (i.e. in units of the mean interparticle spacing) linking length used;

minimumParticleNumber: The minimum number of particles that a group was required to have in order to be included in a merger tree.

Simulation Group

This group, typically relevant only for merger trees derived from N-body simulations, describes the characteristics of the simulation from which the trees were derived. An example of this group, showing standard attributes, is given below.

 GROUP "simulation" {
   COMMENT "Simulation parameters."
   ATTRIBUTE "ErrTolIntAccuracy" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SCALAR
      DATA {
      (0): 0.02
      }
   }
   ATTRIBUTE "TypeOfTimestepCriterion" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SCALAR
      DATA {
      (0): 0
      }
   }
   ATTRIBUTE "boxSize" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SCALAR
      DATA {
      (0): 500
      }
   }
   ATTRIBUTE "code" {
      DATATYPE  H5T_STRING {
            STRSIZE 8;
            STRPAD H5T_STR_SPACEPAD;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
      DATASPACE  SCALAR
      DATA {
      (0): "GADGET-2"
      }
   }
   ATTRIBUTE "initialConditions" {
      DATATYPE  H5T_STRING {
            STRSIZE 5;
            STRPAD H5T_STR_SPACEPAD;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
      DATASPACE  SCALAR
      DATA {
      (0): "glass"
      }
   }
   ATTRIBUTE "softeningKernel" {
      DATATYPE  H5T_STRING {
            STRSIZE 6;
            STRPAD H5T_STR_SPACEPAD;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
      DATASPACE  SCALAR
      DATA {
      (0): "spline"
      }
   }
   ATTRIBUTE "softeningPlummerEquivalent" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SCALAR
      DATA {
      (0): 0.005
      }
   }
   ATTRIBUTE "startRedshift" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SCALAR
      DATA {
      (0): 127
      }
   }
}

Standard Attributes

The following are standard attributes in the simulation group (others may be added as desired).

boxSize: Relevant for cubic volumes typical of cosmological simulations, this attributes gives the length of the box in whatever unit system the file used (see Units Group);

code: The name of the code used to run the simulation;

initialConditions: A description of the initial conditions;

softeningKernel: A description of the softening kernel used;

softeningPlummerEquivalent: The equivalent Plummer softening length;

startRedshift: The redshift at which the simulation was begun.

Gadget-specific Standard Attributes

The following are standard attributes in the simulation group specifically relevant to simulations run with the Gadget code. They typically reflect the values of parameters used by that code.

ErrTolIntAccuracy: The integration accuracy used by Gadget;

TypeOfTimestepCriterion: The type of timestepping criterion used by Gadget;

SofteningGas: Specifies the (comoving) softening of the first particle group in Gadget;

SofteningHalo: Specifies the (comoving) softening of the second particle group in Gadget;

SofteningDisk: Specifies the (comoving) softening of the third particle group in Gadget;

SofteningBulge: Specifies the (comoving) softening of the fourth particle group in Gadget;

SofteningStars: Specifies the (comoving) softening of the fifth particle group in Gadget;

SofteningBndry: Specifies the (comoving) softening of the sixth particle group in Gadget;

SofteningGasMaxPhys: Specifies the maximum physical softening of the first particle group in Gadget;

SofteningHaloMaxPhys: Specifies the maximum physical softening of the second particle group in Gadget;

SofteningDiskMaxPhys: Specifies the maximum physical softening of the third particle group in Gadget;

SofteningBulgeMaxPhys: Specifies the maximum physical softening of the fourth particle group in Gadget;

SofteningStarsMaxPhys: Specifies the maximum physical softening of the fifth particle group in Gadget;

SofteningBndryMaxPhys: Specifies the maximum physical softening of the sixth particle group in Gadget.

Units Group

This group describes the unit system used throughout the file. Attributes should be included for length, mass and velocity units. In each case, three attributes are required to describe the units used (in the following quantity refers to length, mass, time or velocity):

quantityUnitsInSI: The units of this quantity expressed in the SI system;

quantityHubbleExponent: The exponent of the reduced Hubble constant, h, appearing in the units for this quantity;

quantityScaleFactorExponent: The exponent, n, of the expansion factor, a, required to convert this quantity into physical units. That is, multiplying this quantity by aⁿ will give the quantity in physical units.

For example, if lengths in the file are expressed in units of comoving h^-1 Mpc, then we would have

     lengthUnitsInSI           =  3.08568e+22
     lengthHubbleExponent      = -1
     lengthScaleFactorExponent =  1

This allows a code reading the data from a merger tree file to automatically convert it into whatever unit/coordinate system it chooses.

An example of this group, showing standard attributes, is given below.

   ATTRIBUTE "lengthHubbleExponent" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SCALAR
      DATA {
      (0): -1
      }
   }
   ATTRIBUTE "lengthScaleFactorExponent" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SCALAR
      DATA {
      (0): 1
      }
   }
   ATTRIBUTE "lengthUnitsInSI" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SCALAR
      DATA {
      (0): 3.08568e+22
      }
   }
   ATTRIBUTE "massHubbleExponent" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SCALAR
      DATA {
      (0): -1
      }
   }
   ATTRIBUTE "massScaleFactorExponent" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SCALAR
      DATA {
      (0): 0
      }
   }
   ATTRIBUTE "massUnitsInSI" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SCALAR
      DATA {
      (0): 1.98892e+40
      }
   }
   ATTRIBUTE "timeHubbleExponent" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SCALAR
      DATA {
      (0): 0
      }
   }
   ATTRIBUTE "timeScaleFactorExponent" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SCALAR
      DATA {
      (0): 0
      }
   }
   ATTRIBUTE "timeUnitsInSI" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SCALAR
      DATA {
      (0): 3.1556926e+16
      }
   }
}   ATTRIBUTE "velocityHubbleExponent" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SCALAR
      DATA {
      (0): 0
      }
   }
   ATTRIBUTE "velocityScaleFactorExponent" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SCALAR
      DATA {
      (0): 0
      }
   }
   ATTRIBUTE "velocityUnitsInSI" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SCALAR
      DATA {
      (0): 1000
      }
   }
}

Forest Halos Group

The forestHalos group contains the data describing the actual merger tree forests. Nodes from each forest must be stored contiguously. An example of this group is given below. In this example, <nodeCount> is the total number of nodes in all merger tree forests.

GROUP "forestHalos" {
   ATTRIBUTE "haloMassesIncludeSubhalos" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SCALAR
      DATA {
      (0): 0
      }
   }
   ATTRIBUTE "haloAngularMomentaIncludeSubhalos" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SCALAR
      DATA {
      (0): 0
      }
   }
   ATTRIBUTE "forestsAreSelfContained" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SCALAR
      DATA {
      (0): 1
      }
   }
   ATTRIBUTE "treesHaveSubhalos" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SCALAR
      DATA {
      (0): 1
      }
   }
   ATTRIBUTE "velocitiesIncludeHubbleFlow" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SCALAR
      DATA {
      (0): 0
      }
   }
   ATTRIBUTE "positionsArePeriodic" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SCALAR
      DATA {
      (0): 0
      }
   }
   DATASET "descendantIndex" {
   COMMENT "The index of each descendant node."
      DATATYPE  H5T_STD_I64LE
      DATASPACE  SIMPLE { ( <nodeCount> ) / ( <nodeCount> ) }
   }
   DATASET "expansionFactor" {
   COMMENT "The expansion factor of each node."
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <nodeCount> ) / ( <nodeCount> ) }
   }
   DATASET "halfMassRadius" {
   COMMENT "The half mass radius of each node."
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <nodeCount> ) / ( <nodeCount> ) }
   }
   DATASET "hostIndex" {
   COMMENT "The index of each host node."
      DATATYPE  H5T_STD_I64LE
      DATASPACE  SIMPLE { ( <nodeCount> ) / ( <nodeCount> ) }
   }
   DATASET "nodeIndex" {
   COMMENT "The index of each node."
      DATATYPE  H5T_STD_I64LE
      DATASPACE  SIMPLE { ( <nodeCount> ) / ( <nodeCount> ) }
   }
   DATASET "nodeMass" {
   COMMENT "The mass of each node."
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <nodeCount> ) / ( <nodeCount> ) }
   }
   DATASET "particleCount" {
   COMMENT "The number of entries within the particles group for this node."
      DATATYPE  H5T_STD_I64LE
      DATASPACE  SIMPLE { ( <nodeCount> ) / ( <nodeCount> ) }
   }
   DATASET "particleStart" {
   COMMENT "The index within the particles group at which the particle data for this node is stored."
      DATATYPE  H5T_STD_I64LE
      DATASPACE  SIMPLE { ( <nodeCount> ) / ( <nodeCount> ) }
   }
   DATASET "position" {
   COMMENT "The position of each node."
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <nodeCount>, 3 ) / ( <nodeCount>, 3 ) }
   }
   DATASET "scaleRadius" {
   COMMENT "The scale radius of each node."
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <nodeCount> ) / ( <nodeCount> ) }
   }
   DATASET "redshift" {
   COMMENT "The redshift of each node."
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <nodeCount> ) / ( <nodeCount> ) }
   }
   DATASET "spin" {
   COMMENT "The spin of each node."
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <nodeCount>, 3 ) / ( <nodeCount>, 3 ) }
   }
   DATASET "time" {
   COMMENT "The time of each node."
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <nodeCount> ) / ( <nodeCount> ) }
   }
   DATASET "velocity" {
   COMMENT "The velocity of each node."
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <nodeCount>, 3 ) / ( <nodeCount>, 3 ) }
   }
}

Standard Attributes

The following are standard attributes in the forestHalos group (others may be added as desired).

haloMassesIncludeSubhalos: Indicates whether or not the masses of halos include the masses of any subhalos that they may contain. A value of 0 implies that halo masses do not include masses of subhalos, while a value of 1 indicates that they do;

haloAngularMomentaIncludeSubhalos: Indicates whether or not the angular momenta of halos include the angular momenta contributed by any subhalos that they may contain. A value of 0 implies that halo masses do not include the contribution of subhalos, while a value of 1 indicates that they do. If this attribute is not present it is assumed to be equal to the haloMassesIncludeSubhalos attribute;

forestsAreSelfContained: Indicates whether or not forests are self-contained, in the sense that nodes never transfer from one forest to another. A value of 0 implies that nodes can move from one tree to another, while a value of 1 implies that they can not;

treesHaveSubhalos: Indicates whether or not trees contain information on subhalos. A value of 0 implies that they do not, while a value of 1 implies that they do. This attribute is a convenience, as subhalo presence can be determined from the node data directly;

velocitiesIncludeHubbleFlow: Indicates whether or not velocities include the Hubble flow. A value of 0 indicates that they do not, while a value of 1 indicates that they do. See here for important notes on velocity definitions in .

positionsArePeriodic: Indicates whether or not positions are periodic (as in a cosmological cube simulation). A value of 0 indicates that they are not, while a value of 1 indicates that they are periodic, with a period of boxSize.

Standard Datasets

The following are standard datasets in the forestHalos group.

angularMomentum: The angular momentum of the halo. This can be either the magnitude of the angular momentum or a 3-D vector;

expansionFactor: The expansion factor (normalized to unity at the present day) at which this node is identified (note that only one of the expansionFactor, redshift and time datasets is required, since they are simply related, but multiple can be present);

descendantIndex: The nodeIndex of the descendant of this node in the merger tree, or -1 if there is no descendant;

halfMassRadius: The radius containing half the mass of the node;

hostIndex: The nodeIndex of the node which hosts this node. For nodes that are self-hosting (i.e. that are not subhalos inside another halo), the value of hostIndex should be set equal to the node’s own nodeIndex;

nodeIndex: An ID number for the node, unique at least within each tree. If nodes are able to move from one tree to another, the ID must be unique within all trees. No other constraints are placed on nodeIndex (e.g. it does not have to be monotonically increasing within the file for example);

nodeMass: The mass of the node;

position: The three dimensional position of this node;

redshift: The redshift at which this node is identified (note that only one of the expansionFactor, redshift and time datasets is required, since they are simply related, but multiple can be present);

scaleRadius: The characteristic scale radius in the node (typically, but not necessarily, the NFW scale radius);

spin: The spin parameter, λ, of the halo. This can be either the spin magnitude or a 3-D vector;

time: The time at which this node is identified (note that only one of the expansionFactor, redshift and time datasets is required, since they are simply related, but multiple can be present);

velocity: The three dimensional velocity of the node. See here for important notes on velocity definitions in ;

particleIndexStart: If the particles group is included, this dataset should give the index of the first entry in the particle datasets that corresponds to the particle associated with this node;

particleIndexCount: If the particles group is included, this dataset should give the number of entries in particle datasets that correspond to the particle associated with this node;

Note that, internally, uses a different naming convention for the links between nodes. Specifically, an isolated node’s descendant is known as its parent, while a satellite node’s host is also referred to as the parent. By default, will output a parentIndex dataset, which therefore specifies either the descendant or host, depending on whether the node in question is isolated or not. To additionally output information which matches the use of “descendant” and “host” in these merger tree files, set both of the input parameters and to true. This will result in the output of two additional datasets, descendantIndex and hostIndex which correspond to the definitions used in the merger tree file.

Forest Index Group

The forestIndex group contains indexing information which describes which sections of the datasets in the forestHalos group belong to each forest. An example of this group is given below.

GROUP "forestIndex" {
   DATASET "firstNode" {
   COMMENT "Position of the first node in each forest in the forestHalos datasets."
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SIMPLE { ( <forestCount> ) / ( <forestCount> ) }
   }
   DATASET "numberOfNodes" {
   COMMENT "Number of nodes in each forst."
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SIMPLE { ( <forestCount> ) / ( <forestCount> ) }
   }
   DATASET "forestIndex" {
   COMMENT "Unique index of forst."
      DATATYPE  H5T_STD_I64LE
      DATASPACE  SIMPLE { ( <forestCount> ) / ( <forestCount> ) }
   }
   DATASET "forestWeight" {
   COMMENT "The number of such forests required per unit volume to create a representative sample."
      DATATYPE  H5T_STD_F64LE
      DATASPACE  SIMPLE { ( <forestCount> ) / ( <forestCount> ) }
   }
}

Standard Datasets

firstNode: For each forest, gives the position¹ in the forestHalos datasets of the first node in the forest (note that dataset indexing begins at 0). This does not necessarily have to be a root node of the forest—nodes in a single forest can be stored in any order in the forestHalos datasets, providing that they are contiguous;

numberOfNodes: For each forest, gives the number of nodes in the forest;

forestIndex: A unique ID number for each forest;

forestWeight: A weight factor specifying the number density of each forest required to construct a representative sample. If not present, it is acceptable to assume that the weight is 1/boxSize³ if that attribute is present in the simulation group. In cases where a simulation has been split into multiple subvolumes, the forestWeight should still be the weight required to construct a representative sample from the entire volume. That is, for a cubic simulation of side length $L$ split into $N$ equal-volume subvolumes, forestWeight should be $1/L^3$ in each subvolume's merger tree file, not $N/L^3$.

Forests Group

The forests group is optional and provides a convenience method for accessing the properties of individual forests. If present, it contains one group for each tree in the file, named forest<forestID> where <forestID> is the ID of the forest. Each of these groups should contain a set of scalar references to the sections of the datasets in the forestHalos group to which this forest corresponds. For example, the descendantIndex reference for the forest with ID number 89 would be as follows:

GROUP "forests/forest89" {
   DATASET "descendantIndex" {
      DATATYPE  H5T_REFERENCE
      DATASPACE  SCALAR
      DATA {
         DATASET /forestHalos/descendantIndex {(<indexBegin>)-(<indexEnd>)}
      }
   }
}

Particles Group

The particles group is optional and contains information on particle trajectories. It is intended for use with merger trees derived from N-body simulations for which it is often useful to track the location of, for example, the most bound particle associated with a subhalo even after that subhalo can no longer be tracked in the simulation. An example of this group is given below. In this example, <particleCount> is the total number of particles included in the group.

GROUP "particles" {
   DATASET "particleID" {
   COMMENT "The ID of each particle."
      DATATYPE  H5T_STD_I64LE
      DATASPACE  SIMPLE { ( <particleCount> ) / ( <particleCount> ) }
   }
   DATASET "redshift" {
   COMMENT "The redshift of each particle."
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <particleCount> ) / ( <particleCount> ) }
   }
   DATASET "time" {
   COMMENT "The time of each particle."
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <particleCount> ) / ( <particleCount> ) }
   }
   DATASET "expansionFactor" {
   COMMENT "The expansion factor of each particle."
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <particleCount> ) / ( <particleCount> ) }
   }
   DATASET "position" {
   COMMENT "The position of each node."
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <particleCount>, 3 ) / ( <particleCount>, 3 ) }
   }
   DATASET "velocity" {
   COMMENT "The velocity of each node."
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( <particleCount>, 3 ) / ( <particleCount>, 3 ) }
   }
}

Each particle should be stored contiguously (i.e. entries with the same particleID should be consecutive) and it is frequently convenient (although not required) that entries for each particle be arranged in order of increasing cosmic time.

Standard Datasets

particleID: An ID, unique within the entire simulation, for each particle;

redshift: The redshift at which the particle is recorded (a single particle can appear in these datasets at multiple times);

time: The time at which the particle is recorded (a single particle can appear in these datasets multiple times at different redshifts);

expansionFactor: The expansion factor at which the particle is recorded (a single particle can appear in these datasets multiple times at different expansion factors);

position: The spatial position of the particle;

velocity: The velocity of the particle. See here for important notes on velocity definitions in .

Note that only one of the expansionFactor, time and redshift datasets is required, as they are simply related, but multiple of them can be present.

[1]: That is, it gives the array index of the first node of the forest in the forestHalos/nodeIndex dataset for example. It does not give the nodeIndex of the first node in the forest.

Merger Tree File Format - galacticusorg/galacticus GitHub Wiki

Basic File Format

Flexibility and Extensibility

A Note on Scalar Attributes

Example File Structure

Format Version Attribute

Cosmology Group

Standard Attributes

Group Finder Group

Standard Attributes

Simulation Group

Standard Attributes

Gadget-specific Standard Attributes

Units Group

Forest Halos Group

Standard Attributes

Standard Datasets

Forest Index Group

Standard Datasets

Forests Group

Particles Group

Standard Datasets

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Merger Tree File Format - galacticusorg/galacticus GitHub Wiki

Basic File Format

Flexibility and Extensibility

A Note on Scalar Attributes

Example File Structure

Format Version Attribute

Cosmology Group

Standard Attributes

Group Finder Group

Standard Attributes

Simulation Group

Standard Attributes

Gadget-specific Standard Attributes

Units Group

Forest Halos Group

Standard Attributes

Standard Datasets

Forest Index Group

Standard Datasets

Forests Group

Particles Group

Standard Datasets

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