PLUMED-NEST

Project ID: plumID:23.026
Source: plumed_analytical.dat
Originally used with PLUMED version: 2.5.2
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

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

### PLUMED input file to analyse LAMMPS sims of colloids

### atoms of interest
grp: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-421

### calculate the coordination number distributions for particles in grp and find those with CN>3 and CN>11
The GROUP action with label grp calculates somethingcn: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 
SPECIES
this keyword is used for colvars such as coordination number
=grp 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=7.0 D_MAX=8.0} 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=3.0 D_MAX=13.0}

### calculate the number of particles with crystalline order (first shell geometries)
The COORDINATIONNUMBER action with label cn calculates somethingq6: 
Q6
Calculate sixth order Steinhardt parameters. More details
 
SPECIES
this keyword is used for colvars such as coordination number
=grp 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=7.0 D_MAX=8.0} 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
The Q6 action with label q6 calculates somethinglq6: 
LOCAL_Q6
Calculate the local degree of order around an atoms by taking the average dot product between the q_6 vector on the central atom and the q_6 vector on the atoms in the first coordination sphere. More details
 
SPECIES
=q6 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={RATIONAL R_0=7.0 D_MAX=8.0} 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
The LOCAL_Q6 action with label lq6 calculates somethingflq6: 
MFILTER_MORE
Basically equivalent to MORE_THAN. More details
 
DATA
the vector you wish to transform
=lq6 
SWITCH
the switching function that transform
={GAUSSIAN R_0=0.69 D_MAX=0.70} 

### calculate the coordination number distributions for these crystalline particles and count them
The MFILTER_MORE action with label flq6 calculates somethingcnq6: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 
SPECIES
this keyword is used for colvars such as coordination number
=flq6 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=7.0 D_MAX=8.0} 
MEAN
 calculate the mean of all the quantities
 
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=11.0 D_MAX=13.0}

The COORDINATIONNUMBER action with label cnq6 calculates something
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cn.morethan,cnq6.morethan 
STRIDE
 the frequency with which the quantities of interest should be output
=1 
FILE
the name of the file on which to output these quantities
=cn.mod.dat