ICONST
In the ICONST file, geometric parameters are defined, which are then monitored or controlled in a molecular-dynamics simulation. For instance, the distance between two sites can be constrained or affected by the action of a bias potential. Finally, VASP writes the output to the REPORT file.
Overview
Two kinds of geometric parameters can be defined: primitive parameters (e.g., bond lengths or angles), and complex parameters (i.e., linear combinations of primitive coordinates). Each line defines one coordinate, and the complex coordinates must be defined after all primitive ones. The syntax reads as follows:
flag item(1) ... item(N) status ... ... flag c_1 ... c_M status
where flag
specifies the type of primitive coordinate, item(1) ... item(N)
is a space-separated list of integers that, e.g., specifies the ions enumerated in the order they appear in the POSCAR file (starting at 1), and status
is an integer that sets the status, e.g., constrained or monitored. Here, the first line defines the syntax of a primitive coordinates . Assuming that primitive coordinates were specified on the first lines of the ICONST file, the last line defines a complex coordinate, where c_1 ... c_M
is a space-separated list of the coefficients for the primitive coordinate defined in line .
For instance, the following ICONST file defines two primitive coordinates and one complex coordinate.
R 1 6 0 R 1 5 0 S 1 -1 0
The first two lines define the bonds between atom and atom , and between atom and . The complex coordinate is the difference between the two bond lengths, which is defined on the third line.
Settings for flag
In case of primitive coordinates
flag
= R: interatomic distance between atomsitem(1)
anditem(2)
.flag
= A: angle defined by atomsitem(1)
,item(2)
anditem(3)
(with the atomitem(2)
being the apex).flag
= T: torsional angle defined by atomsitem(1)
,item(2)
,item(3)
anditem(4)
.flag
= M: distance between atomitem(1)
and the center of bond between atomsitem(2)
anditem(3)
.flag
= B: distance between the center of bond between atomsitem(1)
anditem(2)
and the center of bond between atomsitem(3)
anditem(4)
flag
= P: ratio of length of the bond between atomsitem(1)
anditem(2)
and the length of the bond between atomsitem(3)
anditem(4)
flag
= W: function with being the bond length (in ) between the atomsitem(1)
anditem(2)
, is the reference bond length specified asitem(3)
, and the exponents and are defined asitem(4)
anditem(5)
, respectively.flag
= X, Y, and Z: fractional (direct) coordinates linked with the lattice vectors , , and .flag
= cX, cY, and cZ: Cartesian coordinates , , and .flag
= LR: length of lattice vectoritem(1)
flag
= LA: angle between lattice vectorsitem(1)
anditem(2)
flag
= LV: cell volume (noitem(i)
is defined in this case)
In case of complex coordinates
flag
= S: simple linear combination of primitive coordinates, i.e., .flag
= C: norm of the vector of primitive coordinates, which reads .flag
= D: coordination number^{[1]}, i.e., .flag
= IS: path-based coordinate^{[2]} measuring progress along discretized path represented by points predefined in file IRCCAR, i.e.,flag
= IZ: path-based coordinate^{[2]} measuring orthogonal distance from the path predefined in file IRCCAR, i.e., with
as defined above The complex coordinates are functions defined in the space spanned by the primitive coordinates.
Mind: All complex coordinates must be defined after the last primitive coordinate. Whenever complex coordinates are defined, the primitive coordinates are only the basis for their definition, and their status is ignored. |
Settings for item(i)
It depends on the setting of flag
. In most cases, item(i)
is an integer specifying either the position of the atom or the lattice vector in the POSCAR file. Mind that two atoms are needed to define a bond length, three atoms are required for a bonding angle, etc. In the special case of the flag W
, also some additional parameters, i.e., the reference bond length (generally a floating-point number) and exponents used in the definition (integers) are defined via item(i)
. See the description of the corresponding flag
.
Settings for status
status
= 0: the coordinate is constrained.status
= 4: the coordinate is affected by a Fermi-type step functionstatus
= 5: the coordinate defines the collective variable in metadynamicsstatus
= 7: the coordinate is monitoredstatus
= 8: the coordinate is affected by a harmonic potential
Use cases and examples
Define two constraints
The following constrains the bond lengths between atoms 1 and 5, and between atoms 1 and 6.
R 1 5 0 R 1 6 0
Use complex coordinates
Consider, for instance, the ICONST file with the following lines:
R 1 6 0 R 1 5 0 S 1 -1 0
The first two lines define two primitive coordinates - bonds between the atoms and , and between the atoms and . The complex coordinate is the difference between the two bond lengths which is defined on the third line. Mind that whenever complex coordinates are defined, the primitives are used only as a basis for their definition. Consequently, the two primitive coordinates are not constrained in the simulation (despite status
=0). Thus, the only controlled parameter is the complex coordinate. Therefore, to fix the first bond length and the complex coordinate at the same time, the ICONST file should be modified as follows:
R 1 6 0 R 1 5 0 S 1 -1 0 S 1 0 0
Consider the same system as discussed above and assume that the reference distance for the bond between atoms 1 and 6 is 1.1 , while that for the bond between 1 and 5 is 1.5 . The coordination number can be fixed in two equivalent ways. The first definition makes use of the complex type D, in which case the corresponding ICONST would be written like this:
R 1 6 0 R 1 5 0 D 1.1 1.5 0
In this case, the exponents appearing in numerator and denominator of the defining formula for D (see above) are fixed at the values 9 and 14, respectively. Alternatively, one can fix the same coordination number using the W primitive and S complex coordinates. This can be accomplished as follows:
W 1 6 1.1 9 14 0 W 1 5 1.5 9 14 0 S 1 1 0
The advantage of this format is that the coefficients M and N (see above the definition of W) can be set for each distance separately. Moreover, this format allows for an easy and intuitive definition of scaled sums of (and/or differences between) multiple coordination numbers - simply via a suitable choice of coefficients linked with S, which can be positive, negative, or zero.
Restrictions on the volume and/or shape of the simulation cell
In the context of a molecular dynamics simulation in NpT ensemble, the ICONST file can be used to impose restrictions on the volume and/or shape of the simulation cell. The following examples cover some of the most important scenarios:
1.) Simulation with a constant cell volume and variable shape.
LV 0
2.) Variable lengths of lattice vectors but fixed lattice angles.
LA 1 2 0 LA 1 3 0 LA 2 3 0
3.) A cubic cell with variable volume but fixed shape. Note that the S type constraints involving the lengths of the lattice vectors () are chosen so as to preserve ratios , as required by the cubic shape.
LA 1 2 0 LA 1 3 0 LA 2 3 0 LR 1 0 LR 2 0 LR 3 0 S 1 0 0 0 0 0 0 S 0 1 0 0 0 0 0 S 0 0 1 0 0 0 0 S 0 0 0 1 -1 0 0 S 0 0 0 1 0 -1 0 S 0 0 0 0 1 -1 0
4.) An orthorhombic cell with variable volume but fixed shape. Here, in order to fix ratios between the lengths of the lattice vectors (), we define the constraints of the form . For instance, if the cell vectors are such that the relative proportions of their lengths are , the following ICONST can be used:
LA 1 2 0 LA 1 3 0 LA 2 3 0 LR 1 0 LR 2 0 LR 3 0 S 1 0 0 0 0 0 0 S 0 1 0 0 0 0 0 S 0 0 1 0 0 0 0 S 0 0 0 1.5 -1.0 0.0 0 S 0 0 0 2.0 0.0 -1.0 0 S 0 0 0 0.0 4.0 -3.0 0
Related tags and articles
SHAKETOL, SHAKEMAXITER, MDALGO, REPORT