dump_modify command¶

Syntax¶

dump_modify dump-ID keyword values ...

• dump-ID = ID of dump to modify
• one or more keyword/value pairs may be appended
• these keywords apply to various dump styles
• keyword = append or buffer or element or every or fileper or first or flush or format or image or label or nfile or pad or precision or region or scale or sort or thresh or unwrap or binary or compressor

append arg = yes or no
buffer arg = yes or no
binary arg = yes or no (VTK dumps only)
compressor arg = none or zlib or lz4 (VTK dumps only)
element args = E1 E2 ... EN, where N = # of atom types
  E1,...,EN = element name, e.g. C or Fe or Ga
every arg = N
  N = dump every this many timesteps
  N can be a variable (see below)
fileper arg = Np
  Np = write one file for every this many processors
first arg = yes or no
format arg = C-style format string for one line of output
flush arg = yes or no
image arg = yes or no
label arg = string
  string = character string (e.g. BONDS) to use in header of dump local file
nfile arg = Nf
  Nf = write this many files, one from each of Nf processors
pad arg = Nchar = # of characters to convert timestep to
precision arg = power-of-10 value from 10 to 1000000
region arg = region-ID or "none"
scale arg = yes or no
sort arg = off or id or N or -N
   off = no sorting of per-atom lines within a snapshot
   id = sort per-atom lines by atom ID
   N = sort per-atom lines in ascending order by the Nth column
   -N = sort per-atom lines in descending order by the Nth column
thresh args = attribute operation value
  attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
  operation = "<" or "<=" or ">" or ">=" or "==" or "!="
  value = numeric value to compare to
  these 3 args can be replaced by the word "none" to turn off thresholding
unwrap arg = yes or no

• these keywords apply only to the image and movie styles
• keyword = acolor or adiam or amap or bcolor or bdiam or backcolor or boxcolor or color or bitrate or framerate

acolor args = type color
  type = atom type or range of types (see below)
  color = name of color or color1/color2/...
adiam args = type diam
  type = atom type or range of types (see below)
  diam = diameter of atoms of that type (distance units)
amap args = lo hi style delta N entry1 entry2 ... entryN
  lo = number or min = lower bound of range of color map
  hi = number or max = upper bound of range of color map
  style = 2 letters = "c" or "d" or "s" plus "a" or "f"
    "c" for continuous
    "d" for discrete
    "s" for sequential
    "a" for absolute
    "f" for fractional
  delta = binsize (only used for style "s", otherwise ignored)
    binsize = range is divided into bins of this width
  N = # of subsequent entries
  entry = value color (for continuous style)
    value = number or min or max = single value within range
    color = name of color used for that value
  entry = lo hi color (for discrete style)
    lo/hi = number or min or max = lower/upper bound of subset of range
    color = name of color used for that subset of values
  entry = color (for sequential style)
    color = name of color used for a bin of values
backcolor arg = color
  color = name of color for background
bcolor args = type color
  type = bond type or range of types (see below)
  color = name of color or color1/color2/...
bdiam args = type diam
  type = bond type or range of types (see below)
  diam = diameter of bonds of that type (distance units)
bitrate arg = rate
  rate = target bitrate for movie in kbps
boxcolor arg = color
  color = name of color for box lines
color args = name R G B
  name = name of color
  R,G,B = red/green/blue numeric values from 0.0 to 1.0
framerate arg = fps
  fps = frames per second for movie

Examples¶

dump_modify 1 format "%d %d %20.15g %g %g" scale yes
dump_modify myDump image yes scale no flush yes
dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
dump_modify xtcdump precision 10000
dump_modify 1 every 1000 nfile 20
dump_modify 1 every v_myVar
dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red

Description¶

Modify the parameters of a previously defined dump command. Not all parameters are relevant to all dump styles.

These keywords apply to various dump styles, including the dump image and dump movie styles. The description gives details.

The append keyword applies to all dump styles except cfg and xtc and dcd. It also applies only to text output files, not to binary or gzipped or image/movie files. If specified as yes, then dump snapshots are appended to the end of an existing dump file. If specified as no, then a new dump file will be created which will overwrite an existing file with the same name. This keyword can only take effect if the dump_modify command is used after the dump command, but before the first command that causes dump snapshots to be output, e.g. a run or minimize command. Once the dump file has been opened, this keyword has no further effect.

The buffer keyword applies only to dump styles atom, custom, local, and xyz. It also applies only to text output files, not to binary or gzipped files. If specified as yes, which is the default, then each processor writes its output into an internal text buffer, which is then sent to the processor(s) which perform file writes, and written by those processors(s) as one large chunk of text. If specified as no, each processor sends its per-atom data in binary format to the processor(s) which perform file wirtes, and those processor(s) format and write it line by line into the output file.

The buffering mode is typically faster since each processor does the relatively expensive task of formatting the output for its own atoms. However it requires about twice the memory (per processor) for the extra buffering.

If dump_modify binary is used, 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.

dump_modify compressor can be used to specify the writing of compressed binary data (automatically sets dump_modify binary yes). Options for compressors include:

none: No compression
zlib: Zlib compression
lz4: Lz4 compression (VTK >= 8.0 required)

The element keyword applies only to the the dump cfg, xyz, and image styles. It associates element names (e.g. H, C, Fe) with LIGGGHTS(R)-PUBLIC atom types. See the list of element names at the bottom of this page.

In the case of dump cfg, this allows the AtomEye visualization package to read the dump file and render atoms with the appropriate size and color.

In the case of dump image, the output images will follow the same AtomEye convention. An element name is specified for each atom type (1 to Ntype) in the simulation. The same element name can be given to multiple atom types.

In the case of xyz format dumps, there are no restrictions to what label can be used as an element name. Any whitespace separated text will be accepted.

The every keyword changes the dump frequency originally specified by the dump command to a new value. The every keyword can be specified in one of two ways. It can be a numeric value in which case it must be > 0. Or it can be an equal-style variable, which should be specified as v_name, where name is the variable name.

In this case, the variable is evaluated at the beginning of a run to determine the next timestep at which a dump snapshot will be written out. On that timestep the variable will be evaluated again to determine the next timestep, etc. Thus the variable should return timestep values. See the stagger() and logfreq() and stride() math functions for equal-style variables, as examples of useful functions to use in this context. Other similar math functions could easily be added as options for equal-style variables. Also see the next() function, which allows use of a file-style variable which reads successive values from a file, each time the variable is evaluated. Used with the every keyword, if the file contains a list of ascending timesteps, you can output snapshots whenever you wish.

Note that when using the variable option with the every keyword, you need to use the first option if you want an initial snapshot written to the dump file. The every keyword cannot be used with the dump dcd style.

For example, the following commands will write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:

variable     s equal logfreq(10,3,10)
dump         1 all atom 100 tmp.dump
dump_modify  1 every v_s first yes

The following commands would write snapshots at the timesteps listed in file tmp.times:

variable        f file tmp.times
variable     s equal next(f)
dump         1 all atom 100 tmp.dump
dump_modify  1 every v_s

The first keyword determines whether a dump snapshot is written on the very first timestep after the dump command is invoked. This will always occur if the current timestep is a multiple of N, the frequency specified in the dump command, including timestep 0. But if this is not the case, a dump snapshot will only be written if the setting of this keyword is yes. If it is no, which is the default, then it will not be written.

The flush keyword determines whether a flush operation is invoked after a dump snapshot is written to the dump file. A flush insures the output in that file is current (no buffering by the OS), even if LIGGGHTS(R)-PUBLIC halts before the simulation completes. Flushes cannot be performed with dump style xtc.

The text-based dump styles have a default C-style format string which simply specifies %d for integers and %g for real values. The format keyword can be used to override the default with a new C-style format string. Do not include a trailing “n” newline character in the format string. This option has no effect on the dcd and xtc dump styles since they write binary files. Note that for the cfg style, the first two fields (atom id and type) are not actually written into the CFG file, though you must include formats for them in the format string.

The fileper keyword is documented below with the nfile keyword.

The image keyword applies only to the dump atom style. If the image value is yes, 3 flags are appended to each atom’s coords which are the absolute box image of the atom in each dimension. For example, an x image flag of -2 with a normalized coord of 0.5 means the atom is in the center of the box, but has passed thru the box boundary 2 times and is really 2 box lengths to the left of its current coordinate. Note that for dump style custom these various values can be printed in the dump file by using the appropriate atom attributes in the dump command itself.

The label keyword applies only to the dump local style. When it writes local information, such as bond or angle topology to a dump file, it will use the specified label to format the header. By default this includes 2 lines:

ITEM: NUMBER OF ENTRIES
ITEM: ENTRIES ...

The word “ENTRIES” will be replaced with the string specified, e.g. BONDS or ANGLES.

The nfile or fileper keywords can be used in conjunction with the “%” wildcard character in the specified dump file name, for all dump styles except the dcd, image, movie, xtc, and xyz styles (for which “%” is not allowed). As explained on the dump command doc page, the “%” character causes the dump file to be written in pieces, one piece for each of P processors. By default P = the number of processors the simulation is running on. The nfile or fileper keyword can be used to set P to a smaller value, which can be more efficient when running on a large number of processors.

The nfile keyword sets P to the specified Nf value. For example, if Nf = 4, and the simulation is running on 100 processors, 4 files will be written, by processors 0,25,50,75. Each will collect information from itself and the next 24 processors and write it to a dump file.

For the fileper keyword, the specified value of Np means write one file for every Np processors. For example, if Np = 4, every 4th processor (0,4,8,12,etc) will collect information from itself and the next 3 processors and write it to a dump file.

The pad keyword only applies when the dump filename is specified with a wildcard “*” character which becomes the timestep. If pad is 0, which is the default, the timestep is converted into a string of unpadded length, e.g. 100 or 12000 or 2000000. When pad is specified with Nchar > 0, the string is padded with leading zeroes so they are all the same length = Nchar. For example, pad 7 would yield 0000100, 0012000, 2000000. This can be useful so that post-processing programs can easily read the files in ascending timestep order.

The precision keyword only applies to the dump xtc style. A specified value of N means that coordinates are stored to 1/N nanometer accuracy, e.g. for N = 1000, the coordinates are written to 1/1000 nanometer accuracy.

The region keyword only applies to the dump custom, cfg, image, and movie styles. If specified, only atoms in the region will be written to the dump file or included in the image/movie. Only one region can be applied as a filter (the last one specified). See the region command for more details. Note that a region can be defined as the “inside” or “outside” of a geometric shape, and it can be the “union” or “intersection” of a series of simpler regions.

The scale keyword applies only to the dump atom style. A scale value of yes means atom coords are written in normalized units from 0.0 to 1.0 in each box dimension. If the simluation box is triclinic (tilted), then all atom coords will still be between 0.0 and 1.0. A value of no means they are written in absolute distance units (e.g. Angstroms or sigma).

The sort keyword determines whether lines of per-atom output in a snapshot are sorted or not. A sort value of off means they will typically be written in indeterminate order, either in serial or parallel. This is the case even in serial if the atom_modify sort option is turned on, which it is by default, to improve performance. A sort value of id means sort the output by atom ID. A sort value of N or -N means sort the output by the value in the Nth column of per-atom info in either ascending or descending order.

The dump local style cannot be sorted by atom ID, since there are typically multiple lines of output per atom. Some dump styles, such as dcd and xtc, require sorting by atom ID to format the output file correctly. If multiple processors are writing the dump file, via the “%” wildcard in the dump filename, then sorting cannot be performed.

The thresh keyword only applies to the dump custom, cfg, image, and movie styles. Multiple thresholds can be specified. Specifying “none” turns off all threshold criteria. If thresholds are specified, only atoms whose attributes meet all the threshold criteria are written to the dump file or included in the image. The possible attributes that can be tested for are the same as those that can be specified in the dump custom command, with the exception of the element attribute, since it is not a numeric value. Note that different attributes can be output by the dump custom command than are used as threshold criteria by the dump_modify command. E.g. you can output the coordinates and stress of atoms whose energy is above some threshold.

The unwrap keyword only applies to the dump dcd and xtc styles. If set to yes, coordinates will be written “unwrapped” by the image flags for each atom. Unwrapped means that if the atom has passed thru a periodic boundary one or more times, the value is printed for what the coordinate would be if it had not been wrapped back into the periodic box. Note that these coordinates may thus be far outside the box size stored with the snapshot.

These keywords apply only to the dump image and dump movie styles. Any keyword that affects an image, also affects a movie, since the movie is simply a collection of images. Some of the keywords only affect the dump movie style. The description gives details.

The acolor keyword can be used with the dump image command, when its atom color setting is type, to set the color that atoms of each type will be drawn in the image.

The specified type should be an integer from 1 to Ntypes = the number of atom types. A wildcard asterisk can be used in place of or in conjunction with the type argument to specify a range of atom types. This takes the form “*” or “n” or “n” or “m*n”. If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive).

The specified color can be a single color which is any of the 140 pre-defined colors (see below) or a color name defined by the dump_modify color option. Or it can be two or more colors separated by a “/” character, e.g. red/green/blue. In the former case, that color is assigned to all the specified atom types. In the latter case, the list of colors are assigned in a round-robin fashion to each of the specified atom types.

The adiam keyword can be used with the dump image command, when its atom diameter setting is type, to set the size that atoms of each type will be drawn in the image. The specified type should be an integer from 1 to Ntypes. As with the acolor keyword, a wildcard asterisk can be used as part of the type argument to specify a range of atomt types. The specified diam is the size in whatever distance units the input script is using, e.g. Angstroms.

The amap keyword can be used with the dump image command, with its atom keyword, when its atom setting is an atom-attribute, to setup a color map. The color map is used to assign a specific RGB (red/green/blue) color value to an individual atom when it is drawn, based on the atom’s attribute, which is a numeric value, e.g. its x-component of velocity if the atom-attribute “vx” was specified.

The basic idea of a color map is that the atom-attribute will be within a range of values, and that range is associated with a a series of colors (e.g. red, blue, green). An atom’s specific value (vx = -3.2) can then mapped to the series of colors (e.g. halfway between red and blue), and a specific color is determined via an interpolation procedure.

There are many possible options for the color map, enabled by the amap keyword. Here are the details.

The lo and hi settings determine the range of values allowed for the atom attribute. If numeric values are used for lo and/or hi, then values that are lower/higher than that value are set to the value. I.e. the range is static. If lo is specified as min or hi as max then the range is dynamic, and the lower and/or upper bound will be calculated each time an image is drawn, based on the set of atoms being visualized.

The style setting is two letters, such as “ca”. The first letter is either “c” for continuous, “d” for discrete, or “s” for sequential. The second letter is either “a” for absolute, or “f” for fractional.

A continuous color map is one in which the color changes continuously from value to value within the range. A discrete color map is one in which discrete colors are assigned to sub-ranges of values within the range. A sequential color map is one in which discrete colors are assigned to a sequence of sub-ranges of values covering the entire range.

An absolute color map is one in which the values to which colors are assigned are specified explicitly as values within the range. A fractional color map is one in which the values to which colors are assigned are specified as a fractional portion of the range. For example if the range is from -10.0 to 10.0, and the color red is to be assigned to atoms with a value of 5.0, then for an absolute color map the number 5.0 would be used. But for a fractional map, the number 0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0.

The delta setting must be specified for all styles, but is only used for the sequential style; otherwise the value is ignored. It specifies the bin size to use within the range for assigning consecutive colors to. For example, if the range is from -10.0 to 10.0 and a delta of 1.0 is used, then 20 colors will be assigned to the range. The first will be from -10.0 <= color1 < -9.0, then 2nd from -9.0 <= color2 < -8.0, etc.

The N setting is how many entries follow. The format of the entries depends on whether the color map style is continuous, discrete or sequential. In all cases the color setting can be any of the 140 pre-defined colors (see below) or a color name defined by the dump_modify color option.

For continuous color maps, each entry has a value and a color. The value is either a number within the range of values or min or max. The value of the first entry must be min and the value of the last entry must be max. Any entries in between must have increasing values. Note that numeric values can be specified either as absolute numbers or as fractions (0.0 to 1.0) of the range, depending on the “a” or “f” in the style setting for the color map.

Here is how the entries are used to determine the color of an individual atom, given the value X of its atom attribute. X will fall between 2 of the entry values. The color of the atom is linearly interpolated (in each of the RGB values) between the 2 colors associated with those entries. For example, if X = -5.0 and the 2 surrounding entries are “red” at -10.0 and “blue” at 0.0, then the atom’s color will be halfway between “red” and “blue”, which happens to be “purple”.

For discrete color maps, each entry has a lo and hi value and a color. The lo and hi settings are either numbers within the range of values or lo can be min or hi can be max. The lo and hi settings of the last entry must be min and max. Other entries can have any lo and hi values and the sub-ranges of different values can overlap. Note that numeric lo and hi values can be specified either as absolute numbers or as fractions (0.0 to 1.0) of the range, depending on the “a” or “f” in the style setting for the color map.

Here is how the entries are used to determine the color of an individual atom, given the value X of its atom attribute. The entries are scanned from first to last. The first time that lo <= X <= hi, X is assigned the color associated with that entry. You can think of the last entry as assigning a default color (since it will always be matched by X), and the earlier entries as colors that override the default. Also note that no interpolation of a color RGB is done. All atoms will be drawn with one of the colors in the list of entries.

For sequential color maps, each entry has only a color. Here is how the entries are used to determine the color of an individual atom, given the value X of its atom attribute. The range is partitioned into N bins of width binsize. Thus X will fall in a specific bin from 1 to N, say the Mth bin. If it falls on a boundary between 2 bins, it is considered to be in the higher of the 2 bins. Each bin is assigned a color from the E entries. If E < N, then the colors are repeated. For example if 2 entries with colors red and green are specified, then the odd numbered bins will be red and the even bins green. The color of the atom is the color of its bin. Note that the sequential color map is really a shorthand way of defining a discrete color map without having to specify where all the bin boundaries are.

The backcolor sets the background color of the images. The color name can be any of the 140 pre-defined colors (see below) or a color name defined by the dump_modify color option.

The bcolor keyword can be used with the dump image command, with its bond keyword, when its color setting is type, to set the color that bonds of each type will be drawn in the image.

The specified type should be an integer from 1 to Nbondtypes = the number of bond types. A wildcard asterisk can be used in place of or in conjunction with the type argument to specify a range of bond types. This takes the form “*” or “n” or “n” or “m*n”. If N = the number of bond types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to N (inclusive). A middle asterisk means all types from m to n (inclusive).

The specified color can be a single color which is any of the 140 pre-defined colors (see below) or a color name defined by the dump_modify color option. Or it can be two or more colors separated by a “/” character, e.g. red/green/blue. In the former case, that color is assigned to all the specified bond types. In the latter case, the list of colors are assigned in a round-robin fashion to each of the specified bond types.

The bdiam keyword can be used with the dump image command, with its bond keyword, when its diam setting is type, to set the diameter that bonds of each type will be drawn in the image. The specified type should be an integer from 1 to Nbondtypes. As with the bcolor keyword, a wildcard asterisk can be used as part of the type argument to specify a range of bond types. The specified diam is the size in whatever distance units you are using, e.g. Angstroms.

The bitrate keyword can be used with the dump movie command to define the size of the resulting movie file and its quality via setting how many kbits per second are to be used for the movie file. Higher bitrates require less compression and will result in higher quality movies. The quality is also determined by the compression format and encoder. The default setting is 2000 kbit/s, which will result in average quality with older compression formats.

The boxcolor keyword sets the color of the simulation box drawn around the atoms in each image. See the “dump image box” command for how to specify that a box be drawn. The color name can be any of the 140 pre-defined colors (see below) or a color name defined by the dump_modify color option.

The color keyword allows definition of a new color name, in addition to the 140-predefined colors (see below), and associates 3 red/green/blue RGB values with that color name. The color name can then be used with any other dump_modify keyword that takes a color name as a value. The RGB values should each be floating point values between 0.0 and 1.0 inclusive.

When a color name is converted to RGB values, the user-defined color names are searched first, then the 140 pre-defined color names. This means you can also use the color keyword to overwrite one of the pre-defined color names with new RBG values.

The framerate keyword can be used with the dump movie command to define the duration of the resulting movie file. Movie files written by the dump movie command have a default frame rate of 24 frames per second and the images generated will be converted at that rate. Thus a sequence of 1000 dump images will result in a movie of about 42 seconds. To make a movie run longer you can either generate images more frequently or lower the frame rate. To speed a movie up, you can do the inverse. Using a frame rate higher than 24 is not recommended, as it will result in simply dropping the rendered images. It is more efficient to dump images less frequently.

Restrictions¶

none

Related commands¶

dump, dump image, undump

Default¶

The option defaults are

• append = no
• buffer = yes for dump styles atom, custom, loca, and xyz
• element = “C” for every atom type
• every = whatever it was set to via the dump command
• fileper = # of processors
• first = no
• flush = yes
• format = %d and %g for each integer or floating point value
• image = no
• label = ENTRIES
• nfile = 1
• pad = 0
• precision = 1000
• region = none
• scale = yes
• sort = off for dump styles atom, custom, cfg, and local
• sort = id for dump styles dcd, xtc, and xyz
• thresh = none
• unwrap = no
• acolor = * red/green/blue/yellow/aqua/cyan
• adiam = * 1.0
• amap = min max cf 0.0 2 min blue max red
• backcolor = black
• bcolor = * red/green/blue/yellow/aqua/cyan
• bdiam = * 0.5
• bitrate = 2000
• boxcolor = yellow
• color = 140 color names are pre-defined as listed below
• framerate = 24

These are the standard 109 element names that LIGGGHTS(R)-PUBLIC pre-defines for use with the dump image and dump_modify commands.

• 1-10 = “H”, “He”, “Li”, “Be”, “B”, “C”, “N”, “O”, “F”, “Ne”
• 11-20 = “Na”, “Mg”, “Al”, “Si”, “P”, “S”, “Cl”, “Ar”, “K”, “Ca”
• 21-30 = “Sc”, “Ti”, “V”, “Cr”, “Mn”, “Fe”, “Co”, “Ni”, “Cu”, “Zn”
• 31-40 = “Ga”, “Ge”, “As”, “Se”, “Br”, “Kr”, “Rb”, “Sr”, “Y”, “Zr”
• 41-50 = “Nb”, “Mo”, “Tc”, “Ru”, “Rh”, “Pd”, “Ag”, “Cd”, “In”, “Sn”
• 51-60 = “Sb”, “Te”, “I”, “Xe”, “Cs”, “Ba”, “La”, “Ce”, “Pr”, “Nd”
• 61-70 = “Pm”, “Sm”, “Eu”, “Gd”, “Tb”, “Dy”, “Ho”, “Er”, “Tm”, “Yb”
• 71-80 = “Lu”, “Hf”, “Ta”, “W”, “Re”, “Os”, “Ir”, “Pt”, “Au”, “Hg”
• 81-90 = “Tl”, “Pb”, “Bi”, “Po”, “At”, “Rn”, “Fr”, “Ra”, “Ac”, “Th”
• 91-100 = “Pa”, “U”, “Np”, “Pu”, “Am”, “Cm”, “Bk”, “Cf”, “Es”, “Fm”
• 101-109 = “Md”, “No”, “Lr”, “Rf”, “Db”, “Sg”, “Bh”, “Hs”, “Mt”

These are the 140 colors that LIGGGHTS(R)-PUBLIC pre-defines for use with the dump image and dump_modify commands. Additional colors can be defined with the dump_modify color command. The 3 numbers listed for each name are the RGB (red/green/blue) values. Divide each value by 255 to get the equivalent 0.0 to 1.0 value.