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 at or buffer or delay or element or every or fileper or first or flush or format or image or label or maxfiles or nfile or pad or pbc or precision or region or refresh or scale or sfactor or sort or tfactor or thermo or thresh or time or units or unwrap
append arg = yes or no at arg = N N = index of frame written upon first dump buffer arg = yes or no delay arg = Dstep Dstep = delay output until this timestep 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 flush arg = yes or no format args = line string, int string, float string, M string, or none string = C-style format string M = integer from 1 to N, where N = # of per-atom quantities being output image arg = yes or no label arg = string string = character string (e.g. BONDS) to use in header of dump local file maxfiles arg = Fmax Fmax = keep only the most recent Fmax snapshots (one snapshot per file) nfile arg = Nf Nf = write this many files, one from each of Nf processors pad arg = Nchar = # of characters to convert timestep to pbc arg = yes or no = remap atoms via periodic boundary conditions precision arg = power-of-10 value from 10 to 1000000 region arg = region-ID or "none" refresh arg = c_ID = compute ID that supports a refresh operation scale arg = yes or no sfactor arg = coordinate scaling factor (> 0.0) 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 tfactor arg = time scaling factor (> 0.0) thermo arg = yes or no time arg = yes or no thresh args = attribute operator value attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" value = numeric value to compare to, or LAST these 3 args can be replaced by the word "none" to turn off thresholding units arg = yes or no unwrap arg = yes or no
these keywords apply only to the image and movie styles
keyword = acolor or adiam or amap or backcolor or bcolor or bdiam or boxcolor or color or bitrate or framerate or header
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) boxcolor arg = color color = name of color for simulation box lines and processor sub-domain 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 bitrate arg = rate rate = target bitrate for movie in kbps framerate arg = fps fps = frames per second for movie header arg = yes or no yes to write the header no to not write the headerthese keywords apply only to the /gz and /zstd dump styles
keyword = compression_level
compression_level args = level level = integer specifying the compression level that should be used (see below for supported levels)
these keywords apply only to the /zstd dump styles
keyword = compression_level
checksum args = yes or no (add checksum at end of zst file)
Examples¶
dump_modify 1 format line "%d %d %20.15g %g %g" scale yes
dump_modify 1 format float %20.15g 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 sfactor 0.1
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.
As explained on the dump doc page, the atom/mpiio, custom/mpiio, and xyz/mpiio dump styles are identical in command syntax and in the format of the dump files they create, to the corresponding styles without “mpiio”, except the single dump file they produce is written in parallel via the MPI-IO library. Thus if a dump_modify option below is valid for the atom style, it is also valid for the atom/mpiio style, and similarly for the other styles which allow for use of MPI-IO.
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.
The at keyword only applies to the netcdf dump style. It can only be used if the append yes keyword is also used. The N argument is the index of which frame to append to. A negative value can be specified for N, which means a frame counted from the end of the file. The at keyword can only be used if the dump_modify command is 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, cfg, 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.
The delay keyword applies to all dump styles. No snapshots will be output until the specified Dstep timestep or later. Specifying Dstep < 0 is the same as turning off the delay setting. This is a way to turn off unwanted output early in a simulation, for example, during an equilibration phase.
The element keyword applies only to the dump cfg, xyz, and image styles. It associates element names (e.g. H, C, Fe) with LAMMPS 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 white-space 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
Note
When using a file-style variable with the every keyword, the file of timesteps must list a first timestep that is beyond the current timestep (e.g. it cannot be 0). And it must list one or more timesteps beyond the length of the run you perform. This is because the dump command will generate an error if the next timestep it reads from the file is not a value greater than the current timestep. Thus if you wanted output on steps 0,15,100 of a 100-timestep run, the file should contain the values 15,100,101 and you should also use the dump_modify first command. Any final value > 100 could be used in place of 101.
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 LAMMPS halts before the simulation completes. Flushes cannot be performed with dump style xtc.
The format keyword can be used to change the default numeric format output by the text-based dump styles: atom, local, custom, cfg, and xyz styles, and their MPIIO variants. Only the line or none options can be used with the atom and xyz styles.
All the specified format strings are C-style formats, e.g. as used by the C/C++ printf() command. The line keyword takes a single argument which is the format string for an entire line of output for each atom (do not include a trailing “n”), with N fields, which you must enclose in quotes if it is more than one field. The int and float keywords take a single format argument and are applied to all integer or floating-point quantities output. The setting for M string also takes a single format argument which is used for the Mth value output in each line, e.g. the fifth column is output in high precision for “format 5 %20.15g”.
Note
When using the line keyword for the cfg style, the first two fields (atom ID and type) are not actually written into the CFG file, however you must include formats for them in the format string.
The format keyword can be used multiple times. The precedence is that for each value in a line of output, the M format (if specified) is used, else the int or float setting (if specified) is used, else the line setting (if specified) for that value is used, else the default setting is used. A setting of none clears all previous settings, reverting all values to their default format.
Note
Atom and molecule IDs are stored internally as 4-byte or 8-byte signed integers, depending on how LAMMPS was compiled. When specifying the format int option you can use a “%d”-style format identifier in the format string and LAMMPS will convert this to the corresponding 8-byte form if it is needed when outputting those values. However, when specifying the line option or format M string option for those values, you should specify a format string appropriate for an 8-byte signed integer, e.g. one with “%ld”, if LAMMPS was compiled with the -DLAMMPS_BIGBIG option for 8-byte IDs.
Note
Any value written to a text-based dump file that is a per-atom quantity calculated by a compute or fix is stored internally as a floating-point value. If the value is actually an integer and you wish it to appear in the text dump file as a (large) integer, then you need to use an appropriate format. For example, these commands:
compute 1 all property/local batom1 batom2
dump 1 all local 100 tmp.bonds index c_1[1] c_1[2]
dump_modify 1 format line "%d %0.0f %0.0f"
will output the two atom IDs for atoms in each bond as integers. If the dump_modify command were omitted, they would appear as floating-point values, assuming they were large integers (more than 6 digits). The “index” keyword should use the “%d” format since it is not generated by a compute or fix, and is stored internally as an integer.
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 through 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 maxfiles keyword can only be used when a ‘*’ wildcard is included in the dump file name, i.e. when writing a new file(s) for each snapshot. The specified Fmax is how many snapshots will be kept. Once this number is reached, the file(s) containing the oldest snapshot is deleted before a new dump file is written. If the specified Fmax <= 0, then all files are retained.
This can be useful for debugging, especially if you don’t know on what timestep something bad will happen, e.g. when LAMMPS will exit with an error. You can dump every timestep, and limit the number of dump files produced, even if you run for 1000s of steps.
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 fourth 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 pbc keyword applies to all the dump styles. As explained on the dump doc page, atom coordinates in a dump file may be slightly outside the simulation box. This is because periodic boundary conditions are enforced only on timesteps when neighbor lists are rebuilt, which will not typically coincide with the timesteps dump snapshots are written. If the setting of this keyword is set to yes, then all atoms will be remapped to the periodic box before the snapshot is written, then restored to their original position. If it is set to no they will not be. The no setting is the default because it requires no extra computation.
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 refresh keyword only applies to the dump custom, cfg, image, and movie styles. It allows an “incremental” dump file to be written, by refreshing a compute that is used as a threshold for determining which atoms are included in a dump snapshot. The specified c_ID gives the ID of the compute. It is prefixed by “c_” to indicate a compute, which is the only current option. At some point, other options may be added, e.g. fixes or variables.
Note
This keyword can only be specified once for a dump. Refreshes of multiple computes cannot yet be performed.
The definition and motivation of an incremental dump file is as follows. Instead of outputting all atoms at each snapshot (with some associated values), you may only wish to output the subset of atoms with a value that has changed in some way compared to the value the last time that atom was output. In some scenarios this can result in a dramatically smaller dump file. If desired, by post-processing the sequence of snapshots, the values for all atoms at all timesteps can be inferred.
A concrete example is a simulation of atom diffusion in a solid, represented as atoms on a lattice. Diffusive hops are rare. Imagine that when a hop occurs an atom moves more than a distance Dhop. For any snapshot we only want to output atoms that have hopped since the last snapshot. This can be accomplished with something the following commands:
variable Dhop equal 0.6
variable check atom "c_dsp[4] > v_Dhop"
compute dsp all displace/atom refresh check
dump 1 all custom 20 tmp.dump id type x y z
dump_modify 1 append yes thresh c_dsp[4] > ${Dhop} refresh c_dsp
The compute displace/atom command calculates the displacement of each atom from its reference position. The “4” index is the scalar displacement; 1,2,3 are the xyz components of the displacement. The dump_modify thresh command will cause only atoms that have displaced more than 0.6 Angstroms to be output on a given snapshot (assuming metal units). However, note that when an atom is output, we also need to update the reference position for that atom to its new coordinates. So that it will not be output in every snapshot thereafter. That reference position is stored by compute displace/atom. So the dump_modify refresh option triggers a call to compute displace/atom at the end of every dump to perform that update. The refresh check option shown as part of the compute displace/atom command enables the compute to respond to the call from the dump command, and update the appropriate reference positions. This is done be defining an atom-style variable, check in this example, which calculates a Boolean value (0 or 1) for each atom, based on the same criterion used by dump_modify thresh.
See the compute displace/atom command for more details, including an example of how to produce output that includes an initial snapshot with the reference position of all atoms.
Note that only computes with a refresh option will work with dump_modify refresh. See individual compute doc pages for details. Currently, only compute displace/atom supports this option. Others may be added at some point. If you use a compute that does not support refresh operations, LAMMPS will not complain; dump_modify refresh will simply do nothing.
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 simulation 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 sfactor and tfactor keywords only apply to the dump xtc style. They allow customization of the unit conversion factors used when writing to XTC files. By default they are initialized for whatever units style is being used, to write out coordinates in nanometers and time in picoseconds. I.e. for real units, LAMMPS defines sfactor = 0.1 and tfactor = 0.001, since the Angstroms and fs used by real units are 0.1 nm and 0.001 ps respectively. If you are using a units system with distance and time units far from nm and ps, you may wish to write XTC files with different units, since the compression algorithm used in XTC files is most effective when the typical magnitude of position data is between 10.0 and 0.1.
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.
Note
Unless it is required by the dump style, sorting dump file output requires extra overhead in terms of CPU and communication cost, as well as memory, versus unsorted output.
The thermo keyword only applies the dump netcdf style. It triggers writing of thermo information to the dump file alongside per-atom data. The values included in the dump file are identical to the values specified by thermo_style.
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 a different attributes can be used than those output by the dump custom command. E.g. you can output the coordinates and stress of atoms whose energy is above some threshold.
If an atom-style variable is used as the attribute, then it can produce continuous numeric values or effective Boolean 0/1 values which may be useful for the comparison operator. Boolean values can be generated by variable formulas that use comparison or Boolean math operators or special functions like gmask() and rmask() and grmask(). See the variable command page for details.
The specified value must be a simple numeric value or the word LAST. If LAST is used, it refers to the value of the attribute the last time the dump command was invoked to produce a snapshot. This is a way to only dump atoms whose attribute has changed (or not changed). Three examples follow.
dump_modify ... thresh ix != LAST
This will dump atoms which have crossed the periodic x boundary of the simulation box since the last dump. (Note that atoms that crossed once and then crossed back between the two dump timesteps would not be included.)
region foo sphere 10 20 10 15
variable inregion atom rmask(foo)
dump_modify ... thresh v_inregion |^ LAST
This will dump atoms which crossed the boundary of the spherical region since the last dump.
variable charge atom "(q > 0.5) || (q < -0.5)"
dump_modify ... thresh v_charge |^ LAST
This will dump atoms whose charge has changed from an absolute value less than 1/2 to greater than 1/2 (or vice versa) since the last dump. E.g. due to reactions and subsequent charge equilibration in a reactive force field.
The choice of operators listed above are the usual comparison operators. The XOR operation (exclusive or) is also included as “|^”. In this context, XOR means that if either the attribute or value is 0.0 and the other is non-zero, then the result is “true” and the threshold criterion is met. Otherwise it is not met.
The time keyword only applies to the dump atom, custom, and local styles (and their COMPRESS package versions atom/gz, custom/gz and local/gz). If set to yes, each frame will will contain two extra lines before the “ITEM: TIMESTEP” entry:
ITEM: TIME <elapsed time>
This will output the current elapsed simulation time in current time units equivalent to the thermo keyword time. This is to simplify post-processing of trajectories using a variable time step, e.g. when using fix dt/reset. The default setting is no.
The units keyword only applies to the dump atom, custom, and local styles (and their COMPRESS package versions atom/gz, custom/gz and local/gz). If set to yes, each individual dump file will contain two extra lines at the very beginning with:
ITEM: UNITS <units style>
This will output the current selected units style to the dump file and thus allows visualization and post-processing tools to determine the choice of units of the data in the dump file. The default setting is no.
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 through 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 descriptions give 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 atom 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 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 second 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.
Here is an example of using a sequential color map to color all the atoms in individual molecules with a different color. See the examples/pour/in.pour.2d.molecule input script for an example of how this is used.
variable colors string &
"red green blue yellow white &
purple pink orange lime gray"
variable mol atom mol%10
dump 1 all image 250 image.*.jpg v_mol type &
zoom 1.6 adiam 1.5
dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors}
In this case, 10 colors are defined, and molecule IDs are mapped to one of the colors, even if there are 1000s of molecules.
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.
Note
Not all movie file formats supported by dump movie allow the bitrate to be set. If not, the setting is silently ignored.
The boxcolor keyword sets the color of the simulation box drawn around the atoms in each image as well as the color of processor sub-domain boundaries. See the “dump image box” command for how to specify that a box be drawn via the box keyword, and the sub-domain boundaries via the subbox keyword. 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.
The header keyword toggles whether the dump file will include a header. Excluding a header will reduce the size of the dump file for fixes such as fix pair/tracker which do not require the information typically written to the header.
The COMPRESS package offers both GZ and Zstd compression variants of styles
atom, custom, local, cfg, and xyz. When using these styles the compression
level can be controlled by the compression_level parameter. File names
with these styles have to end in either .gz or .zst.
GZ supports compression levels from -1 (default), 0 (no compression), and 1 to
9. 9 being the best compression. The COMPRESS /gz styles use 9 as
default compression level.
Zstd offers a wider range of compression levels, including negative levels that sacrifice compression for performance. 0 is the default, positive levels are 1 to 22, with 22 being the most expensive compression. Zstd promises higher compression/decompression speeds for similar compression ratios. For more details see http://facebook.github.io/zstd/.
In addition, Zstd compressed files can have a checksum of the entire
contents. The Zstd enabled dump styles enable this feature by default and it
can be disabled with the checksum parameter.
Restrictions¶
none
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
maxfiles = -1
nfile = 1
pad = 0
pbc = no
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
units = no
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
compression_level = 9 (gz variants)
compression_level = 0 (zstd variants)
checksum = yes (zstd variants)
These are the standard 109 element names that LAMMPS 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 LAMMPS 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.
aliceblue = 240, 248, 255 |
antiquewhite = 250, 235, 215 |
aqua = 0, 255, 255 |
aquamarine = 127, 255, 212 |
azure = 240, 255, 255 |
beige = 245, 245, 220 |
bisque = 255, 228, 196 |
black = 0, 0, 0 |
blanchedalmond = 255, 255, 205 |
blue = 0, 0, 255 |
blueviolet = 138, 43, 226 |
brown = 165, 42, 42 |
burlywood = 222, 184, 135 |
cadetblue = 95, 158, 160 |
chartreuse = 127, 255, 0 |
chocolate = 210, 105, 30 |
coral = 255, 127, 80 |
cornflowerblue = 100, 149, 237 |
cornsilk = 255, 248, 220 |
crimson = 220, 20, 60 |
cyan = 0, 255, 255 |
darkblue = 0, 0, 139 |
darkcyan = 0, 139, 139 |
darkgoldenrod = 184, 134, 11 |
darkgray = 169, 169, 169 |
darkgreen = 0, 100, 0 |
darkkhaki = 189, 183, 107 |
darkmagenta = 139, 0, 139 |
darkolivegreen = 85, 107, 47 |
darkorange = 255, 140, 0 |
darkorchid = 153, 50, 204 |
darkred = 139, 0, 0 |
darksalmon = 233, 150, 122 |
darkseagreen = 143, 188, 143 |
darkslateblue = 72, 61, 139 |
darkslategray = 47, 79, 79 |
darkturquoise = 0, 206, 209 |
darkviolet = 148, 0, 211 |
deeppink = 255, 20, 147 |
deepskyblue = 0, 191, 255 |
dimgray = 105, 105, 105 |
dodgerblue = 30, 144, 255 |
firebrick = 178, 34, 34 |
floralwhite = 255, 250, 240 |
forestgreen = 34, 139, 34 |
fuchsia = 255, 0, 255 |
gainsboro = 220, 220, 220 |
ghostwhite = 248, 248, 255 |
gold = 255, 215, 0 |
goldenrod = 218, 165, 32 |
gray = 128, 128, 128 |
green = 0, 128, 0 |
greenyellow = 173, 255, 47 |
honeydew = 240, 255, 240 |
hotpink = 255, 105, 180 |
indianred = 205, 92, 92 |
indigo = 75, 0, 130 |
ivory = 255, 240, 240 |
khaki = 240, 230, 140 |
lavender = 230, 230, 250 |
lavenderblush = 255, 240, 245 |
lawngreen = 124, 252, 0 |
lemonchiffon = 255, 250, 205 |
lightblue = 173, 216, 230 |
lightcoral = 240, 128, 128 |
lightcyan = 224, 255, 255 |
lightgoldenrodyellow = 250, 250, 210 |
lightgreen = 144, 238, 144 |
lightgrey = 211, 211, 211 |
lightpink = 255, 182, 193 |
lightsalmon = 255, 160, 122 |
lightseagreen = 32, 178, 170 |
lightskyblue = 135, 206, 250 |
lightslategray = 119, 136, 153 |
lightsteelblue = 176, 196, 222 |
lightyellow = 255, 255, 224 |
lime = 0, 255, 0 |
limegreen = 50, 205, 50 |
linen = 250, 240, 230 |
magenta = 255, 0, 255 |
maroon = 128, 0, 0 |
mediumaquamarine = 102, 205, 170 |
mediumblue = 0, 0, 205 |
mediumorchid = 186, 85, 211 |
mediumpurple = 147, 112, 219 |
mediumseagreen = 60, 179, 113 |
mediumslateblue = 123, 104, 238 |
mediumspringgreen = 0, 250, 154 |
mediumturquoise = 72, 209, 204 |
mediumvioletred = 199, 21, 133 |
midnightblue = 25, 25, 112 |
mintcream = 245, 255, 250 |
mistyrose = 255, 228, 225 |
moccasin = 255, 228, 181 |
navajowhite = 255, 222, 173 |
navy = 0, 0, 128 |
oldlace = 253, 245, 230 |
olive = 128, 128, 0 |
olivedrab = 107, 142, 35 |
orange = 255, 165, 0 |
orangered = 255, 69, 0 |
orchid = 218, 112, 214 |
palegoldenrod = 238, 232, 170 |
palegreen = 152, 251, 152 |
paleturquoise = 175, 238, 238 |
palevioletred = 219, 112, 147 |
papayawhip = 255, 239, 213 |
peachpuff = 255, 239, 213 |
peru = 205, 133, 63 |
pink = 255, 192, 203 |
plum = 221, 160, 221 |
powderblue = 176, 224, 230 |
purple = 128, 0, 128 |
red = 255, 0, 0 |
rosybrown = 188, 143, 143 |
royalblue = 65, 105, 225 |
saddlebrown = 139, 69, 19 |
salmon = 250, 128, 114 |
sandybrown = 244, 164, 96 |
seagreen = 46, 139, 87 |
seashell = 255, 245, 238 |
sienna = 160, 82, 45 |
silver = 192, 192, 192 |
skyblue = 135, 206, 235 |
slateblue = 106, 90, 205 |
slategray = 112, 128, 144 |
snow = 255, 250, 250 |
springgreen = 0, 255, 127 |
steelblue = 70, 130, 180 |
tan = 210, 180, 140 |
teal = 0, 128, 128 |
thistle = 216, 191, 216 |
tomato = 253, 99, 71 |
turquoise = 64, 224, 208 |
violet = 238, 130, 238 |
wheat = 245, 222, 179 |
white = 255, 255, 255 |
whitesmoke = 245, 245, 245 |
yellow = 255, 255, 0 |
yellowgreen = 154, 205, 50 |