dump command

Ref: dump image command

Syntax:

dump ID style select-ID N file args

  • ID = user-assigned name for the dump

  • style = particle or grid or surf or image

  • select-ID = which particles, grid cells, surface elements to dump

    • for dump style = particle or image, use a mixture ID

    • for style = grid, use a grid group ID

    • for style = surf, use a surface group ID

  • N = dump every this many timesteps

  • file = name of file to write dump info to

  • args = list of arguments for a particular style

    • particle args = list of particle attributes

      possible attributes = id, type, proc, x, y, z, xs, ys, zs, vx, vy, vz, ke, erot, evib, p_ID, p_ID[N], c_ID, c_ID[N], f_ID, f_ID[N], v_name

      • id = particle ID

      • type = particle species

      • proc = ID of owning processor

      • x,y,z = unscaled particle coordinates

      • xs,ys,zs = scaled particle coordinates

      • vx,vy,vz = particle velocities

      • ke,erot,evib = translational, rotational, and vibrational energy

      • p_ID = custom per-particle vector with ID

      • p_ID[N] = Nth column of custom per-particle array with ID

      • c_ID = per-particle vector calculated by a compute with ID

      • c_ID[N] = Nth column of per-particle array calculated by a compute, with ID, N can include wildcard (see below)

      • f_ID = per-particle vector calculated by a fix with ID

      • f_ID[N] = Nth column of per-particle array calculated by a fix. With ID, N can include wildcard (see below)

      • v_name = per-particle vector calculated by a particle-style variable with name

    • grid args = list of grid attributes

      possible attributes = id, idstr, proc, xlo, ylo, zlo, xhi, yhi, zhi, c_ID, c_ID[N], f_ID, f_ID[N], v_name

      • id = integer form of grid cell ID

      • idstr = string form of grid cell ID

      • proc = processor that owns grid cell

      • xlo,ylo,zlo = coords of lower left corner of grid cell

      • xhi,yhi,zhi = coords of lower left corner of grid cell

      • xc,yc,zc = coords of center of grid cell

      • vol = flow volume of grid cell (area in 2d)

      • c_ID = per-grid vector calculated by a compute with ID

      • c_ID[N] = Nth column of per-grid array calculated by a compute with ID, N can include wildcard (see below)

      • f_ID = per-grid vector calculated by a fix with ID

      • f_ID[N] = Nth column of per-grid array calculated by a fix with ID, N can include wildcard (see below)

      • v_name = per-grid vector calculated by a grid-style variable with name

    • surf args = list of surf attributes

      possible attributes = id, v1x, v1y, v1z, v2x, v2y, v2z, v3x, v3y, v3z, c_ID, c_ID[N], f_ID, f_ID[N], v_name

      • id = surface element ID

      • v1x,v1y,v1z = coords of 1st vertex in surface element

      • v1x,v1y,v1z = coords of 2nd vertex in surface element

      • v1x,v1y,v1z = coords of 3rd vertex in surface element

      • c_ID = per-surf vector calculated by a compute with ID

      • c_ID[N] = Nth column of per-surf array calculated by a compute with ID, I can include wildcard (see below)

      • f_ID = per-surf vector calculated by a fix with ID

      • f_ID[N] = Nth column of per-surf array calculated by a fix with ID, N can include wildcard (see below)

      • v_name = per-surf vector calculated by a surf-style variable with name

    • image args

      Discussed on dump image doc page

Examples:

dump 1 particle all 100 dump.myforce.* id type x y vx fx
dump 2 particle inflow 100 dump.%.myforce id type c_myF[3] v_ke
dump 3 grid all 1000 tmp.grid id proc xlo ylo zlo xhi yhi zhi

Description:

Dump a snapshot of simulation quantities to one or more files every N timesteps in one of several styles. The image style is the exception; it creates a JPG or PPM image file of the simulation configuration every N timesteps, as discussed on the dump image doc page.

The ID for a dump is used to identify the dump in other commands. Each dump ID must be unique. The ID can only contain alphanumeric characters and underscores. You can specify multiple dumpes of the same style so long as they have different IDs. A dump can be deleted with the undump command, after which its ID can be re-used.

The style setting determines what quantities are written to the file and in what format. The particle, grid, surf options are for particles, grid cells, or surface elements. Settings made via the dump_modify command can also alter what info is included in the file and the format of individual values.

The select-ID setting determines which particles, grid cells, or surface elements are output. For style = particle, the select-ID is a mixture ID as defined by the mixture command. Only particles whose species are part of the mixture are output. For style = grid, the select-ID is for a grid group, as defined by the group grid command. Only grid cells in the group are output. For style = surf, the select-ID is for a surface eleemnt group, as defined by the group surf command. Only surface elements in the group are output.

As described below, the filename determines the kind of output (text or binary or gzipped, one big file or one per timestep, one big file or one per processor).

The precision of values output to text-based dump files can be controlled by the dump_modify format command and its options.

The particle and grid and surf styles create files in a simple text format that is self-explanatory when viewing a dump file. Many of the SPARTA post-processing tools, including Pizza.py, work with this format.

For post-processing purposes the text files are self-describing in the following sense.

The dimensions of the simulation box are included in each snapshot. This information is formatted as:

ITEM: BOX BOUNDS xx yy zz
xlo xhi
ylo yhi
zlo zhi

where xlo,xhi are the maximum extents of the simulation box in the x-dimension, and similarly for y and z. The “xx yy zz” represent 6 characters that encode the style of boundary for each of the 6 simulation box boundaries (xlo,xhi and ylo,yhi and zlo,zhi). Each of the 6 characters is either o = outflow, p = periodic, or s = specular. See the boundary command for details.

The “ITEM: NUMBER OF ATOMS” or “ITEM: NUMBER OF CELLS” or “ITEM: NUMBER OF SURFS” entry in each snapshot gives the number of particles, grid cells, surfaces to follow.

The “ITEM: ATOMS” or “ITEM: CELLS” or “ITEM: SURFS” entry in each snapshot lists column descriptors for the per-particle or per-grid or per-surf lines that follow. The descriptors are the attributes specied in the dump command for the style. Possible attributes are listed above and will appear in the order specified. An explanation of the possible attributes is given below.

Dumps are performed on timesteps that are a multiple of N (including timestep 0). Note that this means a dump will not be performed on the initial timestep after the dump command is invoked, if the current timestep is not a multiple of N. This behavior can be changed via the dump_modify first command. N can be changed between runs by using the dump_modify every command.

The specified filename determines how the dump file(s) is written. The default is to write one large text file, which is opened when the dump command is invoked and closed when an undump command is used or when SPARTA exits.

Dump filenames can contain two wildcard characters. If a “*” character appears in the filename, then one file per snapshot is written and the “*” character is replaced with the timestep value. For example, tmp.dump.* becomes tmp.dump.0, tmp.dump.10000, tmp.dump.20000, etc. Note that the dump_modify pad command can be used to insure all timestep numbers are the same length (e.g. 00010), which can make it easier to read a series of dump files in order by some post-processing tools.

If a “%” character appears in the filename, then one file is written for each processor and the “%” character is replaced with the processor ID from 0 to P-1. For example, tmp.dump.% becomes tmp.dump.0, tmp.dump.1, …, tmp.dump.P-1, etc. This creates smaller files and can be a fast mode of output on parallel machines that support parallel I/O for output.

Note that the “*” and “%” characters can be used together to produce a large number of small dump files!

If the filename ends with “.bin”, the dump file (or files, if “*” or “%” is also used) is written in binary format. A binary dump file will be about the same size as a text version, but will typically write out much faster. Of course, when post-processing, you will need to convert it back to text format or write your own code to read the binary file. The format of the binary file can be understood by looking at the tools/binary2txt.cpp file.

Warning

The file “binary2txt.cpp” is not currently shipped with SPARTA

If the filename ends with “.gz”, the dump file (or files, if “*” or “%” is also used) is written in gzipped format. A gzipped dump file will be about 3x smaller than the text version, but will also take longer to write.

Note that in the discussion which follows, for styles which can reference values from a compute or fix, like the particle, grid, or surf styles, the bracketed index I can be specified using a wildcard asterisk with the index to effectively specify multiple values. This takes the form “*” or “n” or “n” or “m*n”. If N = the size of the vector (for mode = scalar) or the number of columns in the array (for mode = vector), then an asterisk with no numeric values means all indices from 1 to N. A leading asterisk means all indices from 1 to n (inclusive). A trailing asterisk means all indices from n to N (inclusive). A middle asterisk means all indices from m to n (inclusive).

Using a wildcard is the same as if the individual columns of the array had been listed one by one. E.g. these 2 dump commands are equivalent, since the compute grid command creates a per-grid array with 3 columns:

compute myGrid all all u v w
dump 2 grid all 100 tmp.dump id c_myGrid[*]
dump 2 grid all 100 tmp.dump id c_myGrid[1] c_myGrid[2] c_myGrid[3]

Particle attributes

This section explains the particle attributes that can be specified as part of the particle style.

Id is the particle ID. Type is an integer index representing the particle species. It is a value from 1 to Nspecies, The value corresponds to the order in which species were defined via the species command. Proc is the ID of the processor which currently owns the particle.

The x, y, z attributes write particle coordinates “unscaled”, in the appropriate distance units. Use xs, ys, zs to “scale” the coordinates to the box size, so that each value is 0.0 to 1.0.

Vx, Vy, Vz are components of particle velocity. The ke, erot, and evib attributes are the kinetic, rotational, and vibrational energies of the particle. A particle’s kinetic energy is given by 1/2 m (vx^2 + vy^2 + vz^2). The way that rotational and vibrational energy is treated in collisions and stored by particles is affected by the collide_modify command.

The p_ID and p_ID[N] attributes allow custom per-particle vectors or arrays defined by a fix command to be output. The ID in the attribute should be replaced by the actual ID of the custom particle attribute that the fix defines. See individal fix commands for details, e.g. the fix ambipolar command which defines the custom vector “ionambi” and the custom array “velambi”.

If p_ID is used as an attribute, the custom attribute must be a vector, and it is output. If p_ID[N] is used, the custom attribute must be an array, and N must be in the range from 1-M, which will output the Nth column of the M-column array.

The c_ID and c_ID[I] attributes allow per-particle vectors or arrays calculated by a compute to be output. The ID in the attribute should be replaced by the actual ID of the compute that has been defined previously in the input script. See the compute command for details.

If c_ID is used as an attribute, the compute must calculate a per-particle vector, and it is output. If c_ID[I] is used, the compute must calculate a per-particle array, and I must be in the range from 1-M, which will output the Ith column of the M-column array. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values.

The f_ID and f_ID[I] attributes allow vector or array per-particle quantities calculated by a fix to be output. The ID in the attribute should be replaced by the actual ID of the fix that has been defined previously in the input script.

If f_ID is used as an attribute, the fix must calculate a per-particle vector, and it is output. If f_ID[I] is used, the fix must calculate a per-particle array, and I must be in the range from 1-M, which will output the Ith column of the M-column array. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values.

The v_name attribute allows per-particle vectors calculated by a variable to be output. The name in the attribute should be replaced by the actual name of the variable that has been defined previously in the input script. Only a particle-style variable can be referenced, since it is the only style that generates per-particle values. Variables of style particle can reference per-particle attributes, stats keywords, or invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of creating quantities to output to a dump file.

See Section 10 of the manual for information on how to add new compute and fix styles to SPARTA to calculate per-particle quantities which could then be output into dump files.

Grid Attributes

This section explains the grid cell attributes that can be specified as part of the grid style.

Note that dump grid will output one line (per snapshot) for 3 kinds of child cells: unsplit cells, cut cells, and sub cells of split cells. Section 6.8 of the manual gives details of how SPARTA defines child, unsplit, cut, split, and sub cells. This is different than compute or fix commands that produce per grid information, which also include split cells in their output. The dump grid command discards that output since the sub cells of a split cell provide the needed information for further processing and visualization. Note that unsplit cells can be outside (in the flow) or inside surface objects, if they exist.

Id and idstr are two different forms of the grid cell ID. In SPARTA each grid cell is assigned a unique ID which represents its location, in a topological sense, within the hierarchical grid. This ID is stored as an integer such as 5774983, but can also be decoded into a string such as 33-4-6, which makes it easier to understand the grid hierarchy. In this case it means the grid cell is at the 3rd level of the hierarchy. Its grandparent cell was 33 at the 1st level, its parent was cell 4 (at level 2) within cell 33, and the cell itself is cell 6 (at level 3) within cell 4 within cell 33. If you specify id, the ID is printed directly as an integer. If you specify idstr, it is printed as a string.

Proc is the ID of the processor which currently owns the grid cell.

The xlo, ylo, zlo attributes write the coordinates of the lower-left corner of the grid cell in the appropriate distance units. The xhi, yhi, zhi attributes write the coordinates of the upper-right corner of the grid cell. The xc, yc, zc attributes write the coordinates of the center point of the grid cell. The zlo, zhi, zc attributes cannot be used for a 2d simulation.

The vol attribute is the flow volume of the grid cell (or area in 2d) for unsplit or cut or sub cells. Section 4.8 of the manual gives details of how SPARTA defines unsplit and sub cells. Flow volume is the portion of the grid cell that is accessible to particles, i.e. outside any closed surface that may intersect the cell. Note that unsplit cells which are inside a surface object will have a flow volume of 0.0. Likewise a cut cell which is inside a suface object but which is intersected by surface element(s) which only touch a face, edge, or corner point of the grid cell, will have a flow volume of 0.0.

The c_ID and c_ID[I] attributes allow per-grid vectors or arrays calculated by a compute to be output. The ID in the attribute should be replaced by the actual ID of the compute that has been defined previously in the input script. See the compute command for details.

If c_ID is used as an attribute, and the compute calculates a per-grid vector, then the per-grid vector is output. If c_ID[I] is used, then I must be in the range from 1-M, which will output the Ith column of the M-column per-grid array calculated by the compute. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values.

The f_ID and f_ID[I] attributes allow per-grid vectors or arrays calculated by a fix to be output. The ID in the attribute should be replaced by the actual ID of the fix that has been defined previously in the input script.

If f_ID is used as an attribute, and the fix calculates a per-grid vector, then the per-grid vector is output. If f_ID[I] is used, then I must be in the range from 1-M, which will output the Ith column of the M-columne per-grid array calculated by the fix. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values.

The v_name attribute allows per-grid vectors calculated by a variable to be output. The name in the attribute should be replaced by the actual name of the variable that has been defined previously in the input script. Only a grid-style variable can be referenced, since it is the only style that generates per-grid values. Variables of style grid can reference per-grid attributes, stats keywords, or invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of creating quantities to output to a dump file.

See Section 10 of the manual for information on how to add new compute and fix styles to SPARTA to calculate per-grid quantities which could then be output into dump files.

Surface attributes

This section explains the surface element attributes that can be specified as part of the surf style. For 2d simulations, a surface element is a line segment with 2 end points. Crossing the unit +z vector into the vector (v2-v1) determines the outward normal of the line segment. For 3d simulations, a surface element is a triangle with 3 corner points. Crossing (v2-v1) into (v3-v1) determines the outward normal of the triangle.

Id is the surface element ID.

The v1x, v1y, v1z, v2x, v2y, v2z, v3x, v3y, v3z attributes write the coordinates of the vertices of the end or corner points of the surface element. The v1z, v2z, v3x, v3y, and v3z attributes cannot be used for a 2d simulation.

The c_ID and c_ID[I] attributes allow per-surf vectors or arrays calculated by a compute to be output. The ID in the attribute should be replaced by the actual ID of the compute that has been defined previously in the input script. See the compute command for details.

If c_ID is used as an attribute, and the compute calculates a per-srf vector, then the per-surf vector is output. If c_ID[I] is used, then I must be in the range from 1-M, which will output the Ith column of the M-column per-surf array calculated by the compute. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values.

The f_ID and f_ID[I] attributes allow per-surf vectors or arrays calculated by a fix to be output. The ID in the attribute should be replaced by the actual ID of the fix that has been defined previously in the input script.

If f_ID is used as an attribute, and the fix calculates a per-surf vector, then the per-surf vector is output. If f_ID[I] is used, then I must be in the range from 1-M, which will output the Ith column of the M-column per-surf array calculated by the fix. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values.

The v_name attribute allows per-surf vectors calculated by a variable to be output. The name in the attribute should be replaced by the actual name of the variable that has been defined previously in the input script. Only a surf-style variable can be referenced, since it is the only style that generates per-surf values. Variables of style surf can reference per-surf attributes, stats keywords, or invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of creating quantities to output to a dump file.

Important

Surf-style variables have not yet been implemented in SPARTA.

See Section 10 of the manual for information on how to add new compute and fix styles to SPARTA to calculate per-surf quantities which could then be output into dump files.

Restrictions:

To write gzipped dump files, you must compile SPARTA with the -DSPARTA_GZIP option - see the Making SPARTA section of the documentation.

Default:

The defaults for the image style are listed on the dump image doc page.