PLUMED-NEST

Project ID: plumID:21.011
Source: NaCl_at_graphite-cmumd/coordination-profiles.plmd
Originally used with PLUMED version: 2.5.1
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

# Define atom groups
gra: 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=1-9152:1 
The GROUP action with label gra calculates somethingwat: 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=9153-43319:3
The GROUP action with label wat calculates somethingsod: 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=43320-43737:1
The GROUP action with label sod calculates somethingchl: 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=43738-44155:1
The GROUP action with label chl calculates somethingslt: 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=43320-44155:1
The GROUP action with label slt calculates somethingsln: 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=9153-44155:1 

# Set a virtual atom at the origin and in the 'bulk'
The GROUP action with label sln calculates somethingp0: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.696525,2.75872,7.403535
The FIXEDATOM action with label p0 calculates somethingp1: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.696525,2.75872,11.403535

# Get the coordination number distributions
The FIXEDATOM action with label p1 calculates somethingcn0:  COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=sod SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=chl 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=0.355 NN=32 MM=64}
The COORDINATIONNUMBER action with label cn0 calculates the following quantities:
 Quantity   
 Description  
cn0.value
the coordination numbers of the specified atomscn1:  COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=sod SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=wat 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=0.325 NN=32 MM=64}
The COORDINATIONNUMBER action with label cn1 calculates the following quantities:
 Quantity   
 Description  
cn1.value
the coordination numbers of the specified atomscn2:  COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=chl SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=wat 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=0.385 NN=32 MM=64}
The COORDINATIONNUMBER action with label cn2 calculates the following quantities:
 Quantity   
 Description  
cn2.value
the coordination numbers of the specified atomscn3:  COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=sod SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=gra 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=0.365 NN=32 MM=64}
The COORDINATIONNUMBER action with label cn3 calculates the following quantities:
 Quantity   
 Description  
cn3.value
the coordination numbers of the specified atomsips: MFILTER_MOREApply one minus a switching function to the input vector. More details DATAthe vector you wish to transform=cn0 SWITCHthe switching function that transform={GAUSSIAN D_0=0.9999 R_0=0.00001}

The MFILTER_MORE action with label ips calculates the following quantities:
 Quantity   
 Description  densnacl: MULTICOLVARDENSEvaluate the average value of a multicolvar on a grid. More details DATAthe multicolvar which you would like to calculate the density profile for=cn0 ORIGINwe will use the position of this atom as the origin=p0 DIRthe direction in which to calculate the density profile=z NBINSthe number of bins to use in each direction (alternative to GRID_NBIN)=1480 KERNEL the kernel function you are using=GAUSSIAN BANDWIDTHthe bandwidths for kernel density esimtation=0.03 NORMALIZATIONset true/false to determine how to the data is normalised=true STRIDE the frequency with which to accumulate the densities=1
The MULTICOLVARDENS action with label densnacl calculates the following quantities:
 Quantity   
 Description  
densnacl.value
the average value of the order parameters at each point on the griddensnaow: MULTICOLVARDENSEvaluate the average value of a multicolvar on a grid. More details DATAthe multicolvar which you would like to calculate the density profile for=cn1 ORIGINwe will use the position of this atom as the origin=p0 DIRthe direction in which to calculate the density profile=z NBINSthe number of bins to use in each direction (alternative to GRID_NBIN)=1480 KERNEL the kernel function you are using=GAUSSIAN BANDWIDTHthe bandwidths for kernel density esimtation=0.03 NORMALIZATIONset true/false to determine how to the data is normalised=true STRIDE the frequency with which to accumulate the densities=1
The MULTICOLVARDENS action with label densnaow calculates the following quantities:
 Quantity   
 Description  
densnaow.value
the average value of the order parameters at each point on the griddensclow: MULTICOLVARDENSEvaluate the average value of a multicolvar on a grid. More details DATAthe multicolvar which you would like to calculate the density profile for=cn2 ORIGINwe will use the position of this atom as the origin=p0 DIRthe direction in which to calculate the density profile=z NBINSthe number of bins to use in each direction (alternative to GRID_NBIN)=1480 KERNEL the kernel function you are using=GAUSSIAN BANDWIDTHthe bandwidths for kernel density esimtation=0.03 NORMALIZATIONset true/false to determine how to the data is normalised=true STRIDE the frequency with which to accumulate the densities=1
The MULTICOLVARDENS action with label densclow calculates the following quantities:
 Quantity   
 Description  
densclow.value
the average value of the order parameters at each point on the griddensnagra: MULTICOLVARDENSEvaluate the average value of a multicolvar on a grid. More details DATAthe multicolvar which you would like to calculate the density profile for=cn3 ORIGINwe will use the position of this atom as the origin=p0 DIRthe direction in which to calculate the density profile=z NBINSthe number of bins to use in each direction (alternative to GRID_NBIN)=1480 KERNEL the kernel function you are using=GAUSSIAN BANDWIDTHthe bandwidths for kernel density esimtation=0.03 NORMALIZATIONset true/false to determine how to the data is normalised=true STRIDE the frequency with which to accumulate the densities=1
The MULTICOLVARDENS action with label densnagra calculates the following quantities:
 Quantity   
 Description  
densnagra.value
the average value of the order parameters at each point on the griddensips: MULTICOLVARDENSEvaluate the average value of a multicolvar on a grid. More details DATAthe multicolvar which you would like to calculate the density profile for=ips ORIGINwe will use the position of this atom as the origin=p0 DIRthe direction in which to calculate the density profile=z NBINSthe number of bins to use in each direction (alternative to GRID_NBIN)=1480 KERNEL the kernel function you are using=GAUSSIAN BANDWIDTHthe bandwidths for kernel density esimtation=0.03 NORMALIZATIONset true/false to determine how to the data is normalised=true STRIDE the frequency with which to accumulate the densities=1

The MULTICOLVARDENS action with label densips calculates the following quantities:
 Quantity   
 Description  
densips.value
the average value of the order parameters at each point on the gridDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=densnacl FILE the file on which to write the grid=DENSna-cl.dat
The DUMPGRID action with label  calculates somethingDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=densnaow FILE the file on which to write the grid=DENSna-ow.dat
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=densclow FILE the file on which to write the grid=DENScl-ow.dat
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=densnagra FILE the file on which to write the grid=DENSna-gra.dat
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=densips FILE the file on which to write the grid=DENSips.dat