# dump_modify command # [dump_modify](dump_image) command for image/movie options ## Syntax ``` LAMMPS 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 *balance* or *buffer* or *colname* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *skip* 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 *balance* arg = *yes* or *no* *buffer* arg = *yes* or *no* *colname* values = ID string, or *default* string = new column header name ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output *or* a custom dump keyword or reference to compute, fix, property or variable. *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 on timesteps which are a multiple of N N can be a variable (see below) *every/time* arg = Delta Delta = dump once every Delta interval of simulation time (time units) Delta 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, ID string, or *none* string = C-style format string ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output *or* a custom dump keyword or reference to compute, fix, property or variable. *header* arg = *yes* or *no* *yes* to write the header *no* to not write the header *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) *skip* arg = v_name v_name = variable with name which evaluates to non-zero (skip) or 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](dump_image) - keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate* see the `dump image `__ doc page for details - these 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 = *checksum* *checksum* args = *yes* or *no* (add checksum at end of zst file) ## Examples ``` LAMMPS 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 fx >= 3.2 dump_modify xtcdump precision 10000 sfactor 0.1 dump_modify 1 every 1000 nfile 20 dump_modify 1 every v_myVar ``` ## Description Modify the parameters of a previously defined dump command. Not all parameters are relevant to all dump styles. As explained on the [dump](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. ------------------------------------------------------------------------ Unless otherwise noted, the following keywords apply to all the various dump styles, including the [dump image](dump_image) and [dump movie](dump_image) styles. ------------------------------------------------------------------------ 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](run) or [minimize](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. ------------------------------------------------------------------------ ::: versionadded 4May2022 ::: The *colname* keyword can be used to change the default header keyword for dump styles: *atom*, *custom*, *cfg*, and *local* and their compressed, ADIOS, and MPIIO variants. The setting for *ID string* replaces the default text with the provided string. *ID* can be a positive integer when it represents the column number counting from the left, a negative integer when it represents the column number from the right (i.e. -1 is the last column/keyword), or a custom dump keyword (or compute, fix, property, or variable reference) and then it replaces the string for that specific keyword. For *atom* dump styles only the keywords \"id\", \"type\", \"x\", \"y\", \"z\", \"ix\", \"iy\", \"iz\" can be accessed via string regardless of whether scaled or unwrapped coordinates were enabled or disabled, and it always assumes 8 columns for indexing regardless of whether image flags are enabled or not. For dump style *cfg* only changes to the \"auxiliary\" keywords (6th or later keyword) will become visible. The *colname* keyword can be used multiple times. If multiple *colname* settings refer to the same keyword, the last setting has precedence. A setting of *default* clears all previous settings, reverting all values to their default names. Using the *scale* or *image* keyword will also reset all header keywords to their default values. ------------------------------------------------------------------------ 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](http://li.mit.edu/Archive/Graphics/A/)\_ 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](http://li.mit.edu/Archive/Graphics/A/)\_ 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 can be used with any dump style except the *dcd* and *xtc* styles. It specifies that the output of dump snapshots will now be performed on timesteps which are a multiple of a new $N$ value, This overrides the dump frequency originally specified by the [dump](dump) command. 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](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](variable), as examples of useful functions to use in this context. Other similar math functions could easily be added as options for [equal-style variables](variable). 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: ``` LAMMPS 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: ``` LAMMPS variable f file tmp.times variable s equal next(f) dump 1 all atom 100 tmp.dump dump_modify 1 every v_s ``` :::: note ::: title 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. :::: ------------------------------------------------------------------------ ::: versionadded 7Jan2022 ::: The *every/time* keyword can be used with any dump style except the *dcd* and *xtc* styles. It changes the frequency of dump snapshots from being based on the current timestep to being determined by elapsed simulation time, i.e. in time units of the [units](units) command, and specifies *Delta* for the interval between snapshots. This can be useful when the timestep size varies during a simulation run, e.g. by use of the [fix dt/reset](fix_dt_reset) command. The default is to perform output on timesteps which a multiples of specified timestep value $N$; see the *every* keyword. The *every/time* keyword can be used with any dump style except the *dcd* and *xtc* styles. It does two things. It specifies that the interval between dump snapshots will be set in simulation time (i.e. in time units of the [units](units) command). This can be useful when the timestep size varies during a simulation run (e.g., by use of the [fix dt/reset](fix_dt_reset) command). The default is to specify the interval in timesteps; see the *every* keyword. The *every/time* command also sets the interval value. :::: note ::: title Note ::: If you wish dump styles *atom*, *custom*, *local*, or *xyz* to include the simulation time as a field in the header portion of each snapshot, you also need to use the dump_modify *time* keyword with a setting of *yes*. See its documentation below. :::: Note that since snapshots are output on simulation steps, each snapshot will be written on the first timestep whose associated simulation time is \>= the exact snapshot time value. As with the *every* option, the *Delta* value can be specified in one of two ways. It can be a numeric value in which case it must be \> 0.0. Or it can be an [equal-style variable](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 simulation time at which a dump snapshot will be written out. On that timestep the variable will be evaluated again to determine the next simulation time, etc. Thus the variable should return values in time units. Note the current timestep or simulation time can be used in an [equal-style variables](variable) since they are both thermodynamic keywords. 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/time* keyword, if the file contains a list of ascending simulation times, you can output snapshots whenever you wish. Note that when using the variable option with the *every/time* keyword, you need to use the *first* option if you want an initial snapshot written to the dump file. The *every/time* keyword cannot be used with the dump *dcd* style. For example, the following commands will write snapshots at successive simulation times which grow by a factor of 1.5 with each interval. The dt value used in the variable is to avoid a zero result when the initial simulation time is 0.0. ``` LAMMPS variable increase equal 1.5*(time+dt) dump 1 all atom 100 tmp.dump dump_modify 1 every/time v_increase first yes ``` The following commands would write snapshots at the times listed in file tmp.times: ``` LAMMPS variable f file tmp.times variable s equal next(f) dump 1 all atom 100 tmp.dump dump_modify 1 every/time v_s ``` :::: note ::: title Note ::: When using a file-style variable with the *every/time* keyword, the file of timesteps must list a first time that is beyond the time associated with the current timestep (e.g., it cannot be 0.0). And it must list one or more times beyond the length of the run you perform. This is because the dump command will generate an error if the next time it reads from the file is not a value greater than the current time. Thus if you wanted output at times 0,15,100 of a run of length 100 in simulation time, 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](dump) command or [dump_modify every](dump_modify) command, including timestep 0. It will also always occur if the current simulation time is a multiple of *Delta*, the time interval specified in the [dump_modify every/time](dump_modify) command. 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. Note that if the argument to the [dump_modify every](dump_modify) [dump_modify every/time](dump_modify) commands is a variable and not a numeric value, then specifying *first yes* is the only way to write a dump snapshot on the first timestep after the dump command is invoked. ------------------------------------------------------------------------ The *flush* keyword determines whether a flush operation is invoked after a dump snapshot is written to the dump file. A flush ensures 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, such 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 there 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 $M$th value output in each line (e.g., the fifth column is output in high precision by \"format 5 %20.15g\"). :::: note ::: title 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 ::: title 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 ::: title Note ::: Any value written to a text-based dump file that is a per-atom quantity calculated by a [compute](compute) or [fix](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: :::: ``` LAMMPS 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 six 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 *header* keyword toggles whether the dump file will include a header. Excluding a header will reduce the size of the dump file for data produced by [pair tracker](pair_tracker) or [bpm bond styles](Howto_bpm) which may not require the information typically written to the header. ------------------------------------------------------------------------ The *image* keyword applies only to the dump *atom* style. If the image value is *yes*, three 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 twice and is really two 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. Using this keyword will reset all custom header names set with *dump_modify colname* to their respective default values. ------------------------------------------------------------------------ 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 two 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 $\text{Fmax} \le 0$, then all files are retained. This can be useful for debugging, especially if you do not know on what timestep something bad will happen (e.g., when LAMMPS will exit with an error). You can dump every time step and limit the number of dump files produced, even if you run for thousands 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](dump) command doc page, the \"%\" character causes the dump file to be written in pieces, one piece for each of $P$ processors. By default, $P$ is 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 $N_f$ value. For example, if $N_f = 4$, and the simulation is running on 100 processors, four files will be written by processors 0, 25, 50, and 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 $N_p$ means write one file for every $N_p$ processors. For example, if $N_p = 4$, every fourth processor (0, 4, 8, 12, etc.) will collect information from itself and the next three 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](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 ::: title 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: ``` LAMMPS 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](compute_displace_atom) command calculates the displacement of each atom from its reference position. The \"4\" index is the scalar displacement; 1, 2, and 3 are the $xyz$ components of the displacement. The [dump_modify thresh](dump_modify) command will cause only atoms that have displaced more than $0.6~\AA$ 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](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](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](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](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](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., $\AA$ or $\sigma$). Using this keyword will reset all custom header names set with *dump_modify colname* to their respective default values. ------------------------------------------------------------------------ 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](units) style is being used, to write out coordinates in nanometers and time in picoseconds. For example, for *real* units, LAMMPS defines *sfactor* = 0.1 and *tfactor* = 0.001, since the $\AA$ 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. ------------------------------------------------------------------------ ::: versionadded 15Sep2022 ::: The *skip* keyword can be used with all dump styles. It allows a dump snapshot to be skipped (not written to the dump file), if a condition is met. The condition is computed by an [equal-style variable](variable), which should be specified as v_name, where name is the variable name. If the variable evaluation returns a non-zero value, then the dump snapshot is skipped. If it returns zero, the dump proceeds as usual. Note that [equal-style variable](variable) can contain Boolean operators which effectively evaluate as a true (non-zero) or false (zero) result. The *skip* keyword can be useful for debugging purposes, e.g. to dump only on a particular timestep. Or to limit output to conditions of interest, e.g. only when the force on some atom exceeds a threshold value. ------------------------------------------------------------------------ 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](atom_modify) 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 $N$th 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 and the *nfile* or *fileper* keywords are set to non-default values (i.e., the number of dump file pieces is not equal to the number of procs), then sorting cannot be performed. In a parallel run, the per-processor dump file pieces can have significant imbalance in number of lines of per-atom info. The *balance* keyword determines whether the number of lines in each processor snapshot are balanced to be nearly the same. A balance value of *no* means no balancing will be done, while *yes* means balancing will be performed. This balancing preserves dump sorting order. For a serial run, this option is ignored since the output is already balanced. :::: note ::: title 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 styles *netcdf* and *yaml*. It triggers writing of [thermo](thermo) information to the dump file alongside per-atom data. The values included in the dump file are cached values from the last thermo output and include the exact same the values as specified by the [thermo_style](thermo_style) command. Because these are cached values, they are only up-to-date when dump output is on a timestep that also has thermo output. Dump style *yaml* will skip thermo output on incompatible steps. ------------------------------------------------------------------------ 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](dump) 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](dump) command. For example, 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](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. ``` LAMMPS 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.) ``` LAMMPS 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. ``` LAMMPS 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 $\frac12$ to greater than $\frac12$ (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*, *local*, and *xyz* styles (and their COMPRESS package versions *atom/gz*, *custom/gz* and *local/gz*). For the first three styles, if set to *yes*, each frame will will contain two extra lines before the \"ITEM: TIMESTEP\" entry: ITEM: TIME \ For the *xyz* style, the simulation time is included on the same line as the timestep value. This will output the current elapsed simulation time in current time units equivalent to the [thermo keyword](thermo_style) *time*. This is to simplify post-processing of trajectories using a variable time step (e.g., when using [fix dt/reset](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 \ This will output the current selected [units](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. ------------------------------------------------------------------------ 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` keyword. 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 [https://facebook.github.io/zstd/]{.title-ref}. In addition, Zstd compressed files can include a checksum of the entire contents. The Zstd enabled dump styles enable this feature by default and it can be disabled with the `checksum` keyword. ------------------------------------------------------------------------ ## Restrictions Not all *dump_modify* options can be applied to all dump styles. Details are in the discussions of the individual options. ## Related commands [dump](dump), [dump image](dump_image), [undump](undump) ## Default The option defaults are - append = no - balance = 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](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 - compression_level = 9 (gz variants) - compression_level = 0 (zstd variants) - checksum = yes (zstd variants)