typically produce a 0.0 if the string is not a numeric string, which is likely not what you want. The formula for an atom-style variable can use any style of variable, including other atom-style or atomfile-style variables.
Examples of different kinds of variable references are as follows. There is no ambiguity as to what a reference means, since variables produce only a global scalar or a per-atom vector, never both.
v_name v_name[I] scalar, or per-atom vector atom I's value in per-atom vector Immediate Evaluation of Variables:
There is a difference between referencing a variable with a leading $ sign (e.g. $x or ${abc}) versus with a leading \(e.g. v_x or v_abc). The former can be used in any input script command, including a variable command. The input script parser evaluates the reference variable immediately and substitutes its value into the command. As explained in Section commands 3.2 for \reference such as $((xlo+xhi)/2+sqrt(v_area)) evaluates the string between the parenthesis as an equal-style variable. Referencing a variable with a leading \fix ave/spatial or dump custom or thermo_style commands) if you wish it to evaluate a variable periodically during a run. It can also be used in a variable formula if you wish to reference a second variable. The second variable will be evaluated whenever the first variable is evaluated.
As an example, suppose you use this command in your input script to define the variable \variable v equal vol
before a run where the simulation box size changes. You might think this will assign the initial volume to the variable \That is not the case. Rather it assigns a formula which evaluates the volume (using the thermo_style keyword \the variable \fix ave/time then the current volume of the box will be evaluated continuously during the run.
If you want to store the initial volume of the system, you can do it this way: variable v equal vol variable v0 equal $v
The second command will force \Thus the command
thermo_style custom step v_v v_v0
would print out both the current and initial volume periodically during the run.
Note that it is a mistake to enclose a variable formula in double quotes if it contains variables preceeded by $ signs. For example,
variable vratio equal \
This is because the quotes prevent variable substitution (see this section on parsing input script commands), and thus an error will occur when the formula for \
Variable Accuracy:
Obviously, LAMMPS attempts to evaluate variables containing formulas (equal and atom style variables) accurately whenever the evaluation is performed. Depending on what is included in the formula, this may require invoking
a compute, either directly or indirectly via a thermo keyword, or accessing a value previously calculated by a compute, or accessing a value calculated and stored by afix. If the compute is one that calculates the pressure or energy of the system,
then these quantities need to be tallied during the evaluation of the interatomic potentials (pair, bond, etc) on timesteps that the variable will need the values.
LAMMPS keeps track of all of this during a run or energy minimization. An error will be generated if you attempt to evaluate a variable on timesteps when it cannot produce accurate values. For example, if a thermo_style custom command prints a variable which accesses values stored by a fix ave/time command and the timesteps on which thermo output is generated are not multiples of the averaging frequency used in the fix command, then an error will occur.
An input script can also request variables be evaluated before or after or in between runs, e.g. by including them in a print command. In this case, if a compute is needed to evaluate a variable (either directly or indirectly), LAMMPS will not invoke the compute, but it will use a value previously calculated by the compute, and can do this only if it was
invoked on the current timestep. Fixes will always provide a quantity needed by a variable, but the quantity may or may not be current. This leads to one of three kinds of behavior:
(1) The variable may be evaluated accurately. If it contains references to a compute or fix, and these values were
calculated on the last timestep of a preceeding run, then they will be accessed and used by the variable and the result will be accurate.
(2) LAMMPS may not be able to evaluate the variable and will generate an error message stating so. For example, if the variable requires a quantity from a compute that has not been invoked on the current timestep, LAMMPS will generate an error. This means, for example, that such a variable cannot be evaluated before the first run has occurred. Likewise, in between runs, a variable containing a compute cannot be evaluated unless the compute was invoked on the last timestep of the preceding run, e.g. by thermodynamic output.
One way to get around this problem is to perform a 0-timestep run before using the variable. For example, these commands
variable t equal temp
print \run 1000
will generate an error if the run is the first run specified in the input script, because generating a value for the \requires a compute for calculating the temperature to be invoked. However, this sequence of commands would be fine:
run 0
variable t equal temp
print \run 1000
The 0-timestep run initializes and invokes various computes, including the one for temperature, so that the value it stores is current and can be accessed by the variable \the state of the system, so it does not change the input state for the 1000-timestep run that follows. Also note that the 0-timestep run must actually use and invoke the compute in question (e.g. via thermo or dump output) in order for it to enable the compute to be used in a variable after the run. Thus if you are trying to print a variable that uses a compute you have defined, you can insure it is invoked on the last timestep of the preceding run by including it in thermodynamic output.
Unlike computes, fixes will never generate an error if their values are accessed by a variable in between runs. They always return some value to the variable. However, the value may not be what you expect if the fix has not yet calculated the quantity of interest or it is not current. For example, the fix indent command stores the force on the indenter. But this is not computed until a run is performed. Thus if a variable attempts to print this value before the first run, zeroes will be output. Again, performing a 0-timestep run before printing the variable has the desired effect.
(3) The variable may be evaluated incorrectly and LAMMPS may have no way to detect this has occurred. Consider the following sequence of commands: pair_coeff 1 1 1.0 1.0
run 1000
pair_coeff 1 1 1.5 1.0 variable e equal pe
print \
The first run is performed using one setting for the pairwise potential defined by the pair_style and pair_coeff commands. The potential energy is evaluated on the final timestep and stored by thecompute pe compute (this is done by
the thermo_style command). Then a pair coefficient is changed, altering the potential energy of the system. When the potential energy is printed via the \compute pe compute, thinking it is current. There are many other commands which could alter the state of the system between runs, causing a variable to evaluate incorrectly.
The solution to this issue is the same as for case (2) above, namely perform a 0-timestep run before the variable is evaluated to insure the system is up-to-date. For example, this sequence of commands would print a potential energy that reflected the changed pairwise coefficient: pair_coeff 1 1 1.0 1.0 run 1000
pair_coeff 1 1 1.5 1.0 run 0
variable e equal pe
print \
Restrictions:
Indexing any formula element by global atom ID, such as an atom value, requires the atom style to use a global mapping in order to look up the vector indices. By default, only atom styles with molecular information create global maps. The atom_modify map command can override the default.
All universe- and uloop-style variables defined in an input script must have the same number of values. Related commands:
next, jump, include, temper, fix print, print Default: none
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands
read_data command Syntax:
read_data file keyword args ...
file = name of data file to read in
? zero or more keyword/arg pairs may be appended ? keyword = fix
? fix args = fix-ID header-string section-string
? fix-ID = ID of fix to process header lines and sections of data file
? header-string = header lines containing this string will be passed to fix ? section-string = section names with this string will be passed to fix Examples:
?
read_data data.lj
read_data ../run7/data.polymer.gz
read_data data.protein fix mycmap crossterm CMAP Description:
Read in a data file containing information LAMMPS needs to run a simulation. The file can be ASCII text or a gzipped text file (detected by a .gz suffix). This is one of 3 ways to specify initial atom coordinates; see the read_restart and create_atoms commands for alternative methods.
The structure of the data file is important, though many settings and sections are optional or can come in any order. See the examples directory for sample data files for different problems.
A data file has a header and a body. The header appears first. The first line of the header is always skipped; it typically contains a description of the file. Then lines are read one at a time. Lines can have a trailing comment starting with '#' that is ignored. If the line is blank (only whitespace after comment is deleted), it is skipped. If the line contains a header keyword, the corresponding value(s) is read from the line. If it doesn't contain a header keyword, the line begins the body of the file.
The body of the file contains zero or more sections. The first line of a section has only a keyword. This line can have a trailing comment starting with '#' that is either ignored or can be used to check for a style match, as described below. The next line is skipped. The remaining lines of the section contain values. The number of lines depends on the section keyword as described below. Zero or more blank lines can be used between sections. Sections can appear in any order, with a few exceptions as noted below.
The keyword fix can be used one or more times. Each usage specifies a fix that will be used to process a specific portion of the data file. Any header line containing header-string and any section with a name containing section-string will be passed to the specified fix. See the fix property/atom command for an example of a fix that operates in this manner. The doc page for the fix defines the syntax of the header line(s) and section(s) that it reads from the data file. Note that the header-string can be specified as NULL, in which case no header lines are passed to the fix. This means that it can infer the length of its Section from standard header settings, such as the number of atoms.
The formatting of individual lines in the data file (indentation, spacing between words and numbers) is not important except that header and section keywords (e.g. atoms, xlo xhi, Masses, Bond Coeffs) must be capitalized as shown and can't have extra white space between their words - e.g. two spaces or a tab between the 2 words in \words in \
These are the recognized header keywords. Header lines can come in any order. The value(s) are read from the beginning of the line. Thus the keyword atoms should be in a line like \ylo yhi should be in a line like \10.0 10.0 ylo yhi\xy xz yz should be in a line like \of 0, except the lo/hi box size defaults are -0.5 and 0.5. A line need only appear if the value is different than the default.
? ? ? ? ? ? ? ? ? ? ? ? ? ?
atoms = # of atoms in system bonds = # of bonds in system angles = # of angles in system
dihedrals = # of dihedrals in system impropers = # of impropers in system atom types = # of atom types in system bond types = # of bond types in system angle types = # of angle types in system
dihedral types = # of dihedral types in system improper types = # of improper types in system
extra bond per atom = leave space for this many new bonds per atom extra angle per atom = leave space for this many new angles per atom
extra dihedral per atom = leave space for this many new dihedrals per atom extra improper per atom = leave space for this many new impropers per atom
extra special per atom = leave space for this many new special bonds per atom ? ellipsoids = # of ellipsoids in system ? lines = # of line segments in system ? triangles = # of triangles in system ? bodies = # of bodies in system
? xlo xhi = simulation box boundaries in x dimension ? ylo yhi = simulation box boundaries in y dimension ? zlo zhi = simulation box boundaries in z dimension ? xy xz yz = simulation box tilt factors for triclinic system
The initial simulation box size is determined by the lo/hi settings. In any dimension, the system may be periodic or non-periodic; see the boundary command. When the simulation box is created it is also partitioned into a regular 3d grid of rectangular bricks, one per processor, based on the number of processors being used and the settings of the processors command. The partitioning can later be changed by the balance or fix balance commands.
?
If the xy xz yz line does not appear, LAMMPS will set up an axis-aligned (orthogonal) simulation box. If the line does appear, LAMMPS creates a non-orthogonal simulation domain shaped as a parallelepiped with triclinic symmetry. The parallelepiped has its \xlo,0,0); B = (xy,yhi-ylo,0); C = (xz,yz,zhi-zlo). Xy,xz,yz can be 0.0 or positive or negative values and are called \because they are the amount of displacement applied to faces of an originally orthogonal box to transform it into the parallelepiped.
The tilt factors (xy,xz,yz) can not skew the box more than half the distance of the corresponding parallel box length. For example, if xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt factor must be between -5 and 5. Similarly, both xz and yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation, since if the maximum tilt factor is 5 (as in this example), then configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all geometrically equivalent.
See Section_howto 12 of the doc pages for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations.
When a triclinic system is used, the simulation domain must be periodic in any dimensions with a non-zero tilt factor, as defined by the boundary command. I.e. if the xy tilt factor is non-zero, then both the x and y dimensions must be periodic. Similarly, x and z must be periodic if xz is non-zero and y and z must be periodic if yz is non-zero. Also note that if your simulation will tilt the box, e.g. via the fix deform command, the simulation box must be defined as triclinic, even if the tilt factors are initially 0.0.
For 2d simulations, the zlo zhi values should be set to bound the z coords for atoms that appear in the file; the default of -0.5 0.5 is valid if all z coords are 0.0. For 2d triclinic simulations, the xz and yz tilt factors must be 0.0.
If the system is periodic (in a dimension), then atom coordinates can be outside the bounds (in that dimension); they will be remapped (in a periodic sense) back inside the box.
IMPORTANT NOTE: If the system is non-periodic (in a dimension), then all atoms in the data file must have coordinates (in that dimension) that are \periodic dimension is of style \boundary command), then the atom coords must be strictly \hi value, due to the way LAMMPS assign atoms to processors. Note that you should not make the lo/hi values radically smaller/larger than the extent of the atoms. For example, if your atoms extend from 0 to 50, you should not specify the box bounds as -10000 and 10000. This is because LAMMPS uses the specified box size to layout the 3d grid of processors. A huge (mostly empty) box will be sub-optimal for performance when using \boundary command). When using \boundary command), a huge (mostly empty) box may cause a parallel simulation to lose atoms the first time that LAMMPS shrink-wraps the box around the atoms.
The \will be added to the system when a simulation runs, e.g. by using the fix bond/create command. This will pre-allocate space in LAMMPS data structures for storing the new bonds (angles, dihedrals, impropers).