FCCUBIC
This is part of the crystallization module
It is only available if you configure PLUMED with ./configure –enable-modules=crystallization . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

Measure how similar the environment around atoms is to that found in a FCC structure.

This CV was introduced in this article [3] and again in this article [35] This CV essentially determines whether the environment around any given atom is similar to that found in the FCC structure or not. The function that is used to make this determination is as follows:

\[ s_i = \frac{ \sum_{i \ne j} \sigma(r_{ij}) \left\{ a\left[ \frac{(x_{ij}y_{ij})^4 + (x_{ij}z_{ij})^4 + (y_{ij}z_{ij})^4}{r_{ij}^8} - \frac{\alpha (x_{ij}y_{ij}z_{ij})^4}{r_{ij}^{12}} \right] + b \right\} }{ \sum_{i \ne j} \sigma(r_{ij}) } \]

In this expression \(x_{ij}\), \(y_{ij}\) and \(z_{ij}\) are the \(x\), \(y\) and \(z\) components of the vector connecting atom \(i\) to atom \(j\) and \(r_{ij}\) is the magnitude of this vector. \(\sigma(r_{ij})\) is a switchingfunction that acts on the distance between atom \(i\) and atom \(j\) and its inclusion in the numerator and the denominator of the above expression as well as the fact that we are summing over all of the other atoms in the system ensures that we are calculating an average of the function of \(x_{ij}\), \(y_{ij}\) and \(z_{ij}\) for the atoms in the first coordination sphere around atom \(i\). Lastly, \(\alpha\) is a parameter that can be set by the user, which by default is equal to three. The values of \(a\) and \(b\) are calculated from \(\alpha\) using:

\[ a = \frac{ 80080}{ 2717 + 16 \alpha} \qquad \textrm{and} \qquad b = \frac{ 16(\alpha - 143) }{2717 + 16\alpha} \]

This quantity is once again a multicolvar so you can compute it for multiple atoms using a single PLUMED action and then compute the average value for the atoms in your system, the number of atoms that have an \(s_i\) value that is more that some target and so on. Notice also that you can rotate the reference frame if you are using a non-standard unit cell.

Description of components

When the label of this action is used as the input for a second you are not referring to a scalar quantity as you are in regular collective variables. The label is used to reference the full set of quantities calculated by the action. This is usual when using MultiColvar functions. Generally when doing this the previously calculated multicolvar will be referenced using the DATA keyword rather than ARG.

This Action can be used to calculate the following scalar quantities directly. These quantities are calculated by employing the keywords listed below. These quantities can then be referenced elsewhere in the input file by using this Action's label followed by a dot and the name of the quantity. Some of them can be calculated multiple times with different parameters. In this case the quantities calculated can be referenced elsewhere in the input by using the name of the quantity followed by a numerical identifier e.g. label.lessthan-1, label.lessthan-2 etc. When doing this and, for clarity we have made it so that the user can set a particular label for each of the components. As such by using the LABEL keyword in the description of the keyword input you can customize the component name

Quantity Keyword Description
altmin ALT_MIN the minimum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
between BETWEEN the number/fraction of values within a certain range. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
highest HIGHEST the highest of the quantities calculated by this action
lessthan LESS_THAN the number of values less than a target value. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
lowest LOWEST the lowest of the quantities calculated by this action
max MAX the maximum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
mean MEAN the mean value. The output component can be referred to elsewhere in the input file by using the label.mean
min MIN the minimum value. This is calculated using the formula described in the description of the keyword so as to make it continuous.
moment MOMENTS the central moments of the distribution of values. The second moment would be referenced elsewhere in the input file using label.moment-2, the third as label.moment-3, etc.
morethan MORE_THAN the number of values more than a target value. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters.
The atoms involved can be specified using
SPECIES this keyword is used for colvars such as coordination number. In that context it specifies that plumed should calculate one coordination number for each of the atoms specified. Each of these coordination numbers specifies how many of the other specified atoms are within a certain cutoff of the central atom. You can specify the atoms here as another multicolvar action or using a MultiColvarFilter or ActionVolume action. When you do so the quantity is calculated for those atoms specified in the previous multicolvar. This is useful if you would like to calculate the Steinhardt parameter for those atoms that have a coordination number more than four for example
Or alternatively by using
SPECIESA this keyword is used for colvars such as the coordination number. In that context it species that plumed should calculate one coordination number for each of the atoms specified in SPECIESA. Each of these coordination numbers specifies how many of the atoms specifies using SPECIESB is within the specified cutoff. As with the species keyword the input can also be specified using the label of another multicolvar
SPECIESB this keyword is used for colvars such as the coordination number. It must appear with SPECIESA. For a full explanation see the documentation for that keyword
Compulsory keywords
NN ( default=6 ) The n parameter of the switching function
MM ( default=0 ) The m parameter of the switching function; 0 implies 2*NN
D_0 ( default=0.0 ) The d_0 parameter of the switching function
R_0 The r_0 parameter of the switching function
PHI ( default=0.0 ) The Euler rotational angle phi
THETA ( default=0.0 ) The Euler rotational angle theta
PSI ( default=0.0 ) The Euler rotational angle psi
ALPHA ( default=3.0 ) The alpha parameter of the angular function
Options
NUMERICAL_DERIVATIVES ( default=off ) calculate the derivatives for these quantities numerically
NOPBC ( default=off ) ignore the periodic boundary conditions when calculating distances
SERIAL ( default=off ) do the calculation in serial. Do not use MPI
LOWMEM ( default=off ) lower the memory requirements
TIMINGS ( default=off ) output information on the timings of the various parts of the calculation
UNORMALIZED

( default=off ) calculate the sum of the components of the vector rather than the mean

SWITCH This keyword is used if you want to employ an alternative to the continuous switching function defined above. The following provides information on the switchingfunction that are available. When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.
MEAN take the mean of these variables. The final value can be referenced using label.mean. You can use multiple instances of this keyword i.e. MEAN1, MEAN2, MEAN3... The corresponding values are then referenced using label.mean-1, label.mean-2, label.mean-3...
MORE_THAN calculate the number of variables more than a certain target value. This quantity is calculated using \(\sum_i 1.0 - \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction. The final value can be referenced using label.morethan. You can use multiple instances of this keyword i.e. MORE_THAN1, MORE_THAN2, MORE_THAN3... The corresponding values are then referenced using label.morethan-1, label.morethan-2, label.morethan-3...
LESS_THAN calculate the number of variables less than a certain target value. This quantity is calculated using \(\sum_i \sigma(s_i)\), where \(\sigma(s)\) is a switchingfunction. The final value can be referenced using label.lessthan. You can use multiple instances of this keyword i.e. LESS_THAN1, LESS_THAN2, LESS_THAN3... The corresponding values are then referenced using label.lessthan-1, label.lessthan-2, label.lessthan-3...
MAX calculate the maximum value. To make this quantity continuous the maximum is calculated using \( \textrm{max} = \beta \log \sum_i \exp\left( \frac{s_i}{\beta}\right) \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\)) The final value can be referenced using label.max. You can use multiple instances of this keyword i.e. MAX1, MAX2, MAX3... The corresponding values are then referenced using label.max-1, label.max-2, label.max-3...
MIN calculate the minimum value. To make this quantity continuous the minimum is calculated using \( \textrm{min} = \frac{\beta}{ \log \sum_i \exp\left( \frac{\beta}{s_i} \right) } \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\)) The final value can be referenced using label.min. You can use multiple instances of this keyword i.e. MIN1, MIN2, MIN3... The corresponding values are then referenced using label.min-1, label.min-2, label.min-3...
BETWEEN calculate the number of values that are within a certain range. These quantities are calculated using kernel density estimation as described on histogrambead. The final value can be referenced using label.between. You can use multiple instances of this keyword i.e. BETWEEN1, BETWEEN2, BETWEEN3... The corresponding values are then referenced using label.between-1, label.between-2, label.between-3...
HISTOGRAM calculate how many of the values fall in each of the bins of a histogram. This shortcut allows you to calculates NBIN quantities like BETWEEN. The final value can be referenced using label.histogram. You can use multiple instances of this keyword i.e. HISTOGRAM1, HISTOGRAM2, HISTOGRAM3... The corresponding values are then referenced using label.histogram-1, label.histogram-2, label.histogram-3...
MOMENTS calculate the moments of the distribution of collective variables. The mth moment of a distribution is calculated using \(\frac{1}{N} \sum_{i=1}^N ( s_i - \overline{s} )^m \), where \(\overline{s}\) is the average for the distribution. The moments keyword takes a lists of integers as input or a range. Each integer is a value of \(m\). The final calculated values can be referenced using moment- \(m\). You can use the COMPONENT keyword in this action but the syntax is slightly different. If you would like the second and third moments of the third component you would use MOMENTS={COMPONENT=3 MOMENTS=2-3}. The moments would then be referred to using the labels moment-3-2 and moment-3-3. This syntax is also required if you are using numbered MOMENT keywords i.e. MOMENTS1, MOMENTS2...
ALT_MIN calculate the minimum value. To make this quantity continuous the minimum is calculated using \( \textrm{min} = -\frac{1}{\beta} \log \sum_i \exp\left( -\beta s_i \right) \) The value of \(\beta\) in this function is specified using (BETA= \(\beta\)). The final value can be referenced using label.altmin. You can use multiple instances of this keyword i.e. ALT_MIN1, ALT_MIN2, ALT_MIN3... The corresponding values are then referenced using label.altmin-1, label.altmin-2, label.altmin-3...
LOWEST this flag allows you to recover the lowest of these variables. The final value can be referenced using label.lowest
HIGHEST this flag allows you to recover the highest of these variables. The final value can be referenced using label.highest
Examples

The following input calculates the FCCUBIC parameter for the 64 atoms in the system and then calculates and prints the average value for this quantity.

FCCUBIC SPECIES=1-64 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN LABEL=d
PRINT ARG=d.* FILE=colv