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: GROUPDefine 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 ATOMSthe 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: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=grp SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.0 D_MAX=8.0} LOWMEM this flag does nothing and is present only to ensure back-compatibility MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={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 the following quantities:
 Quantity   
 Description  
cn.morethan
the number of colvars that have a value more than a threshold
cn.value
the coordination numbers of the specified atomsq6: Q6Calculate sixth order Steinhardt parameters. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=grp SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={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 the following quantities:
 Quantity   
 Description  
q6.value
the norms of the vectors of spherical harmonic coefficientslq6: LOCAL_Q6Calculate 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 SPECIESthe label of the action that computes the Steinhardt parameters for which you would like to calculate local steinhardt parameters=q6 SWITCHThis 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 the following quantities:
 Quantity   
 Description  
lq6.value
the values of the local steinhardt parameters for the input atomsflq6: MFILTER_MOREApply one minus a switching function to the input vector. More details DATAthe vector you wish to transform=lq6 SWITCHthe 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 the following quantities:
 Quantity   
 Description  cnq6: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=flq6 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=7.0 D_MAX=8.0} MEAN calculate the mean of all the quantities MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=11.0 D_MAX=13.0}

The COORDINATIONNUMBER action with label cnq6 calculates the following quantities:
 Quantity   
 Description  
cnq6.morethan
the number of colvars that have a value more than a threshold
cnq6.mean
the mean of the colvars
cnq6.value
the coordination numbers of the specified atomsPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cn.morethan,cnq6.morethan STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=cn.mod.dat