	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.

Calculate 3rd order Steinhardt parameters.

The 3rd order Steinhardt parameters allow us to measure the degree to which the first coordination shell around an atom is ordered. The Steinhardt parameter for atom, \(i\) is complex vector whose components are calculated using the following formula:

\[ q_{3m}(i) = \frac{\sum_j \sigma( r_{ij} ) Y_{3m}(\mathbf{r}_{ij}) }{\sum_j \sigma( r_{ij} ) } \]

where \(Y_{3m}\) is one of the 3rd order spherical harmonics so \(m\) is a number that runs from \(-3\) to \(+3\). The function \(\sigma( r_{ij} )\) is a switchingfunction that acts on the distance between atoms \(i\) and \(j\). The parameters of this function should be set so that it the function is equal to one when atom \(j\) is in the first coordination sphere of atom \(i\) and is zero otherwise.

The Steinhardt parameters can be used to measure the degree of order in the system in a variety of different ways. The simplest way of measuring whether or not the coordination sphere is ordered is to simply take the norm of the above vector i.e.

\[ Q_3(i) = \sqrt{ \sum_{m=-3}^3 q_{3m}(i)^{*} q_{3m}(i) } \]

This norm is small when the coordination shell is disordered and larger when the coordination shell is ordered. Furthermore, when the keywords LESS_THAN, MIN, MAX, HISTOGRAM, MEAN and so on are used with this colvar it is the distribution of these normed quantities that is investigated.

Other measures of order can be taken by averaging the components of the individual \(q_3\) vectors individually or by taking dot products of the \(q_{3}\) vectors on adjacent atoms. More information on these variables can be found in the documentation for LOCAL_Q3, LOCAL_AVERAGE and NLINKS.

Examples

The following command calculates the average Q3 parameter for the 64 atoms in a box of Lennard Jones and prints this quantity to a file called colvar:

Click on the labels of the actions for more information on what each action computes

q3: Q3 SPECIESthis keyword is used for colvars such as coordination number. 
=1-64 D_0 could not find this keyword 
=1.3 R_0 could not find this keyword 
=0.2 MEANtake the mean of these variables. 
 The Q3 action with label q3 calculates a single scalar value
PRINT ARGthe input for this action is the scalar output from one or more other actions. 
=q3.mean FILEthe name of the file on which to output these quantities 
=colvar The PRINT action with label

The following command calculates the histogram of Q3 parameters for the 64 atoms in a box of Lennard Jones and prints these quantities to a file called colvar:

Click on the labels of the actions for more information on what each action computes

q3: Q3 SPECIESthis keyword is used for colvars such as coordination number.
=1-64 D_0 could not find this keyword
=1.3 R_0 could not find this keyword
=0.2 HISTOGRAMcalculate how many of the values fall in each of the bins of a histogram.
={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} The Q3 action with label q3 calculates the following quantities:

Quantity Description
q3.between-1 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. This is the 1th of these quantities
q3.between-2 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. This is the 2th of these quantities
q3.between-3 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. This is the 3th of these quantities
q3.between-4 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. This is the 4th of these quantities
q3.between-5 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. This is the 5th of these quantities
q3.between-6 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. This is the 6th of these quantities
q3.between-7 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. This is the 7th of these quantities
q3.between-8 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. This is the 8th of these quantities
q3.between-9 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. This is the 9th of these quantities
q3.between-10 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. This is the 10th of these quantities
q3.between-11 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. This is the 11th of these quantities
q3.between-12 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. This is the 12th of these quantities
q3.between-13 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. This is the 13th of these quantities
q3.between-14 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. This is the 14th of these quantities
q3.between-15 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. This is the 15th of these quantities
q3.between-16 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. This is the 16th of these quantities
q3.between-17 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. This is the 17th of these quantities
q3.between-18 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. This is the 18th of these quantities
q3.between-19 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. This is the 19th of these quantities
q3.between-20 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. This is the 20th of these quantities

PRINT ARGthe input for this action is the scalar output from one or more other actions.
=q3.* FILEthe name of the file on which to output these quantities
=colvar The PRINT action with label

The following command could be used to measure the Q3 parameters that describe the arrangement of chlorine ions around the sodium atoms in sodium chloride. The imagined system here is composed of 64 NaCl formula units and the atoms are arranged in the input with the 64 Na \(^+\) ions followed by the 64 Cl \(-\) ions. Once again the average Q3 parameter is calculated and output to a file called colvar

Click on the labels of the actions for more information on what each action computes

q3: Q3 SPECIESAthis keyword is used for colvars such as the coordination number. 
=1-64 SPECIESBthis keyword is used for colvars such as the coordination number. 
=65-128 D_0 could not find this keyword 
=1.3 R_0 could not find this keyword 
=0.2 MEANtake the mean of these variables. 
 The Q3 action with label q3 calculates a single scalar value
PRINT ARGthe input for this action is the scalar output from one or more other actions. 
=q3.mean FILEthe name of the file on which to output these quantities 
=colvar The PRINT action with label

If you simply want to examine the values of the Q3 parameters for each of the atoms in your system you can do so by exploiting the command DUMPMULTICOLVAR as shown in the example below. The following output file will output a file in an extended xyz format called q3.xyz for each frame of the analyzed MD trajectory. The first column in this file will contain a dummy name for each of the atoms, columns 2-4 will then contain the x, y and z positions of the atoms, column 5 will contain the value of the Q3 parameter, columns 6-12 will contain the real parts of the director of the \(q_{3m}\) vector while columns 12-19 will contain the imaginary parts of this director.

Click on the labels of the actions for more information on what each action computes

q3: Q3 SPECIESAthis keyword is used for colvars such as the coordination number. 
=1-64 SPECIESBthis keyword is used for colvars such as the coordination number. 
=65-128 D_0 could not find this keyword 
=1.3 R_0 could not find this keyword 
=0.2 MEANtake the mean of these variables. 
 The Q3 action with label q3 calculates a single scalar value
DUMPMULTICOLVAR DATAcompulsory keyword 
certain actions in plumed work by calculating a list of variables and summing over
them. 
=q3 FILEcompulsory keyword 
file on which to output coordinates 
=q3.xyz The DUMPMULTICOLVAR action with label

Glossary of keywords and components

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 vectors 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. All 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 the label for the components. As such by using the LABEL keyword in the description of the keyword input you can customize the component name. In addition, you can calculate all of these scalar functions for one particular component of the calculated vector by making use of the COMPONENT keyword. The first component is used to refer to the norm of the vector. The individual components can then be referenced using the numbers 2, 3, and so on. So as an example MEAN1={COMPONENT=1} calculates the average vector norm. MEAN2={COMPONENT=2} by contrast calculates the mean for all of the first components of the vectors.

Quantity	Keyword	Description
vmean	VMEAN	the norm of the mean vector. The output component can be referred to elsewhere in the input file by using the label.vmean
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
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=12 ) 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

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
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...
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...
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...
VMEAN	calculate the norm of the mean vector. The final value can be referenced using label.vmean. You can use multiple instances of this keyword i.e. VMEAN1, VMEAN2, VMEAN3... The corresponding values are then referenced using label.vmean-1, label.vmean-2, label.vmean-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...
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...
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

Quantity	Description
q3.between-1	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. This is the 1th of these quantities
q3.between-2	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. This is the 2th of these quantities
q3.between-3	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. This is the 3th of these quantities
q3.between-4	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. This is the 4th of these quantities
q3.between-5	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. This is the 5th of these quantities
q3.between-6	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. This is the 6th of these quantities
q3.between-7	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. This is the 7th of these quantities
q3.between-8	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. This is the 8th of these quantities
q3.between-9	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. This is the 9th of these quantities
q3.between-10	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. This is the 10th of these quantities
q3.between-11	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. This is the 11th of these quantities
q3.between-12	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. This is the 12th of these quantities
q3.between-13	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. This is the 13th of these quantities
q3.between-14	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. This is the 14th of these quantities
q3.between-15	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. This is the 15th of these quantities
q3.between-16	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. This is the 16th of these quantities
q3.between-17	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. This is the 17th of these quantities
q3.between-18	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. This is the 18th of these quantities
q3.between-19	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. This is the 19th of these quantities
q3.between-20	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. This is the 20th of these quantities