PLUMED-NEST

Project ID: plumID:23.036
Source: melt/plumed.dat
Originally used with PLUMED version: 2.8.1
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

#spib_learned_cv
#
#RESTART
  
q6The Q6 action with label q6 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6
vector
the norms of the vectors of spherical harmonic coefficients
q6_mean
scalar
the mean of the colvars: 
Q6
Calculate sixth order Steinhardt parameters. This action is a shortcut. More details
 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.33 D_MAX=0.6} 
SPECIESA
this keyword is used for colvars such as the coordination number
=1-256 
SPECIESB
this keyword is used for colvars such as the coordination number
=257-512 
MEAN
 calculate the mean of all the quantities
 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
# PLUMED interprets the command:
# q6: Q6 SWITCH={RATIONAL R_0=0.33 D_MAX=0.6} SPECIESA=1-256 SPECIESB=257-512 MEAN LOWMEM
# as follows (Click the red comment above to revert to the short version of the input):
q6_grpThe GROUP action with label q6_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_grp
atoms
indices of atoms specified in GROUP: 
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
=1-256
q6_matThe CONTACT_MATRIX action with label q6_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_mat.w
matrix
a matrix containing the weights for the bonds between each pair of atoms
q6_mat.x
matrix
the projection of the bond on the x axis
q6_mat.y
matrix
the projection of the bond on the y axis
q6_mat.z
matrix
the projection of the bond on the z axis: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
GROUPA
=1-256 
GROUPB
=257-512 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=0.33 D_MAX=0.6} 
COMPONENTS
 also calculate the components of the vector connecting the atoms in the contact matrix
q6_shThe SPHERICAL_HARMONIC action with label q6_sh calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_sh.rm-n6
matrix
the real parts of the spherical harmonic values with the m value given  This is the n6th of these quantities
q6_sh.rm-n5
matrix
the real parts of the spherical harmonic values with the m value given  This is the n5th of these quantities
q6_sh.rm-n4
matrix
the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q6_sh.rm-n3
matrix
the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q6_sh.rm-n2
matrix
the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q6_sh.rm-n1
matrix
the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q6_sh.rm-0
matrix
the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q6_sh.rm-p1
matrix
the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q6_sh.rm-p2
matrix
the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q6_sh.rm-p3
matrix
the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q6_sh.rm-p4
matrix
the real parts of the spherical harmonic values with the m value given  This is the p4th of these quantities
q6_sh.rm-p5
matrix
the real parts of the spherical harmonic values with the m value given  This is the p5th of these quantities
q6_sh.rm-p6
matrix
the real parts of the spherical harmonic values with the m value given  This is the p6th of these quantities
q6_sh.im-n6
matrix
the real parts of the spherical harmonic values with the m value given  This is the n6th of these quantities
q6_sh.im-n5
matrix
the real parts of the spherical harmonic values with the m value given  This is the n5th of these quantities
q6_sh.im-n4
matrix
the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q6_sh.im-n3
matrix
the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q6_sh.im-n2
matrix
the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q6_sh.im-n1
matrix
the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q6_sh.im-0
matrix
the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q6_sh.im-p1
matrix
the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q6_sh.im-p2
matrix
the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q6_sh.im-p3
matrix
the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q6_sh.im-p4
matrix
the real parts of the spherical harmonic values with the m value given  This is the p4th of these quantities
q6_sh.im-p5
matrix
the real parts of the spherical harmonic values with the m value given  This is the p5th of these quantities
q6_sh.im-p6
matrix
the real parts of the spherical harmonic values with the m value given  This is the p6th of these quantities: 
SPHERICAL_HARMONIC
Calculate the values of all the spherical harmonic funtions for a particular value of l. More details
 
ARG
the values input to this function
=q6_mat.x,q6_mat.y,q6_mat.z,q6_mat.w 
L
the value of the angular momentum
=6
q6_denom_onesThe CONSTANT action with label q6_denom_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_denom_ones
vector
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=256
q6_denomThe MATRIX_VECTOR_PRODUCT action with label q6_denom calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_denom
vector
the vector that is obtained by taking the product between the matrix and the vector that were input: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the label for the matrix and the vector/scalar that are being multiplied
=q6_mat.w,q6_denom_ones
q6_spThe MATRIX_VECTOR_PRODUCT action with label q6_sp calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_sp.rm-n6
vector
the product of the matrix q6_sh.rm-n6 and the vector q6_denom_ones
q6_sp.rm-n5
vector
the product of the matrix q6_sh.rm-n5 and the vector q6_denom_ones
q6_sp.rm-n4
vector
the product of the matrix q6_sh.rm-n4 and the vector q6_denom_ones
q6_sp.rm-n3
vector
the product of the matrix q6_sh.rm-n3 and the vector q6_denom_ones
q6_sp.rm-n2
vector
the product of the matrix q6_sh.rm-n2 and the vector q6_denom_ones
q6_sp.rm-n1
vector
the product of the matrix q6_sh.rm-n1 and the vector q6_denom_ones
q6_sp.rm-0
vector
the product of the matrix q6_sh.rm-0 and the vector q6_denom_ones
q6_sp.rm-p1
vector
the product of the matrix q6_sh.rm-p1 and the vector q6_denom_ones
q6_sp.rm-p2
vector
the product of the matrix q6_sh.rm-p2 and the vector q6_denom_ones
q6_sp.rm-p3
vector
the product of the matrix q6_sh.rm-p3 and the vector q6_denom_ones
q6_sp.rm-p4
vector
the product of the matrix q6_sh.rm-p4 and the vector q6_denom_ones
q6_sp.rm-p5
vector
the product of the matrix q6_sh.rm-p5 and the vector q6_denom_ones
q6_sp.rm-p6
vector
the product of the matrix q6_sh.rm-p6 and the vector q6_denom_ones
q6_sp.im-n6
vector
the product of the matrix q6_sh.im-n6 and the vector q6_denom_ones
q6_sp.im-n5
vector
the product of the matrix q6_sh.im-n5 and the vector q6_denom_ones
q6_sp.im-n4
vector
the product of the matrix q6_sh.im-n4 and the vector q6_denom_ones
q6_sp.im-n3
vector
the product of the matrix q6_sh.im-n3 and the vector q6_denom_ones
q6_sp.im-n2
vector
the product of the matrix q6_sh.im-n2 and the vector q6_denom_ones
q6_sp.im-n1
vector
the product of the matrix q6_sh.im-n1 and the vector q6_denom_ones
q6_sp.im-0
vector
the product of the matrix q6_sh.im-0 and the vector q6_denom_ones
q6_sp.im-p1
vector
the product of the matrix q6_sh.im-p1 and the vector q6_denom_ones
q6_sp.im-p2
vector
the product of the matrix q6_sh.im-p2 and the vector q6_denom_ones
q6_sp.im-p3
vector
the product of the matrix q6_sh.im-p3 and the vector q6_denom_ones
q6_sp.im-p4
vector
the product of the matrix q6_sh.im-p4 and the vector q6_denom_ones
q6_sp.im-p5
vector
the product of the matrix q6_sh.im-p5 and the vector q6_denom_ones
q6_sp.im-p6
vector
the product of the matrix q6_sh.im-p6 and the vector q6_denom_ones: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the label for the matrix and the vector/scalar that are being multiplied
=q6_sh.*,q6_denom_ones
q6_norm2The COMBINE action with label q6_norm2 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_norm2
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
POWERS
 the powers to which you are raising each of the arguments in your function
=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 
ARG
the values input to this function
=q6_sp.rm-n6,q6_sp.im-n6,q6_sp.rm-n5,q6_sp.im-n5,q6_sp.rm-n4,q6_sp.im-n4,q6_sp.rm-n3,q6_sp.im-n3,q6_sp.rm-n2,q6_sp.im-n2,q6_sp.rm-n1,q6_sp.im-n1,q6_sp.rm-0,q6_sp.im-0,q6_sp.rm-p1,q6_sp.im-p1,q6_sp.rm-p2,q6_sp.im-p2,q6_sp.rm-p3,q6_sp.im-p3,q6_sp.rm-p4,q6_sp.im-p4,q6_sp.rm-p5,q6_sp.im-p5,q6_sp.rm-p6,q6_sp.im-p6
q6_normThe CUSTOM action with label q6_norm calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_norm
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_norm2 
FUNC
the function you wish to evaluate
=sqrt(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6The CUSTOM action with label q6 calculates the following quantities:
 Quantity   
 Type   
 Description  
q6
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q6_norm,q6_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q6_meanThe MEAN action with label q6_mean calculates the following quantities:
 Quantity   
 Type   
 Description  
q6_mean
scalar
the mean of all the elements in the input vector: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the values input to this function
=q6 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# --- End of included input --- 
q4The Q4 action with label q4 calculates the following quantities:
 Quantity   
 Type   
 Description  
q4
vector
the norms of the vectors of spherical harmonic coefficients
q4_mean
scalar
the mean of the colvars: 
Q4
Calculate fourth order Steinhardt parameters. This action is a shortcut. More details
 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.33 D_MAX=0.6} 
SPECIESA
this keyword is used for colvars such as the coordination number
=1-256 
SPECIESB
this keyword is used for colvars such as the coordination number
=257-512 
MEAN
 calculate the mean of all the quantities
 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
# PLUMED interprets the command:
# q4: Q4 SWITCH={RATIONAL R_0=0.33 D_MAX=0.6} SPECIESA=1-256 SPECIESB=257-512 MEAN LOWMEM
# as follows (Click the red comment above to revert to the short version of the input):
q4_grpThe GROUP action with label q4_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
q4_grp
atoms
indices of atoms specified in GROUP: 
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
=1-256
q4_matThe CONTACT_MATRIX action with label q4_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
q4_mat.w
matrix
a matrix containing the weights for the bonds between each pair of atoms
q4_mat.x
matrix
the projection of the bond on the x axis
q4_mat.y
matrix
the projection of the bond on the y axis
q4_mat.z
matrix
the projection of the bond on the z axis: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
GROUPA
=1-256 
GROUPB
=257-512 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=0.33 D_MAX=0.6} 
COMPONENTS
 also calculate the components of the vector connecting the atoms in the contact matrix
q4_shThe SPHERICAL_HARMONIC action with label q4_sh calculates the following quantities:
 Quantity   
 Type   
 Description  
q4_sh.rm-n4
matrix
the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q4_sh.rm-n3
matrix
the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q4_sh.rm-n2
matrix
the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q4_sh.rm-n1
matrix
the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q4_sh.rm-0
matrix
the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q4_sh.rm-p1
matrix
the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q4_sh.rm-p2
matrix
the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q4_sh.rm-p3
matrix
the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q4_sh.rm-p4
matrix
the real parts of the spherical harmonic values with the m value given  This is the p4th of these quantities
q4_sh.im-n4
matrix
the real parts of the spherical harmonic values with the m value given  This is the n4th of these quantities
q4_sh.im-n3
matrix
the real parts of the spherical harmonic values with the m value given  This is the n3th of these quantities
q4_sh.im-n2
matrix
the real parts of the spherical harmonic values with the m value given  This is the n2th of these quantities
q4_sh.im-n1
matrix
the real parts of the spherical harmonic values with the m value given  This is the n1th of these quantities
q4_sh.im-0
matrix
the real parts of the spherical harmonic values with the m value given  This is the 0th of these quantities
q4_sh.im-p1
matrix
the real parts of the spherical harmonic values with the m value given  This is the p1th of these quantities
q4_sh.im-p2
matrix
the real parts of the spherical harmonic values with the m value given  This is the p2th of these quantities
q4_sh.im-p3
matrix
the real parts of the spherical harmonic values with the m value given  This is the p3th of these quantities
q4_sh.im-p4
matrix
the real parts of the spherical harmonic values with the m value given  This is the p4th of these quantities: 
SPHERICAL_HARMONIC
Calculate the values of all the spherical harmonic funtions for a particular value of l. More details
 
ARG
the values input to this function
=q4_mat.x,q4_mat.y,q4_mat.z,q4_mat.w 
L
the value of the angular momentum
=4
q4_denom_onesThe CONSTANT action with label q4_denom_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
q4_denom_ones
vector
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=256
q4_denomThe MATRIX_VECTOR_PRODUCT action with label q4_denom calculates the following quantities:
 Quantity   
 Type   
 Description  
q4_denom
vector
the vector that is obtained by taking the product between the matrix and the vector that were input: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the label for the matrix and the vector/scalar that are being multiplied
=q4_mat.w,q4_denom_ones
q4_spThe MATRIX_VECTOR_PRODUCT action with label q4_sp calculates the following quantities:
 Quantity   
 Type   
 Description  
q4_sp.rm-n4
vector
the product of the matrix q4_sh.rm-n4 and the vector q4_denom_ones
q4_sp.rm-n3
vector
the product of the matrix q4_sh.rm-n3 and the vector q4_denom_ones
q4_sp.rm-n2
vector
the product of the matrix q4_sh.rm-n2 and the vector q4_denom_ones
q4_sp.rm-n1
vector
the product of the matrix q4_sh.rm-n1 and the vector q4_denom_ones
q4_sp.rm-0
vector
the product of the matrix q4_sh.rm-0 and the vector q4_denom_ones
q4_sp.rm-p1
vector
the product of the matrix q4_sh.rm-p1 and the vector q4_denom_ones
q4_sp.rm-p2
vector
the product of the matrix q4_sh.rm-p2 and the vector q4_denom_ones
q4_sp.rm-p3
vector
the product of the matrix q4_sh.rm-p3 and the vector q4_denom_ones
q4_sp.rm-p4
vector
the product of the matrix q4_sh.rm-p4 and the vector q4_denom_ones
q4_sp.im-n4
vector
the product of the matrix q4_sh.im-n4 and the vector q4_denom_ones
q4_sp.im-n3
vector
the product of the matrix q4_sh.im-n3 and the vector q4_denom_ones
q4_sp.im-n2
vector
the product of the matrix q4_sh.im-n2 and the vector q4_denom_ones
q4_sp.im-n1
vector
the product of the matrix q4_sh.im-n1 and the vector q4_denom_ones
q4_sp.im-0
vector
the product of the matrix q4_sh.im-0 and the vector q4_denom_ones
q4_sp.im-p1
vector
the product of the matrix q4_sh.im-p1 and the vector q4_denom_ones
q4_sp.im-p2
vector
the product of the matrix q4_sh.im-p2 and the vector q4_denom_ones
q4_sp.im-p3
vector
the product of the matrix q4_sh.im-p3 and the vector q4_denom_ones
q4_sp.im-p4
vector
the product of the matrix q4_sh.im-p4 and the vector q4_denom_ones: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
 
ARG
the label for the matrix and the vector/scalar that are being multiplied
=q4_sh.*,q4_denom_ones
q4_norm2The COMBINE action with label q4_norm2 calculates the following quantities:
 Quantity   
 Type   
 Description  
q4_norm2
vector
the vector obtained by doing an element-wise application of a linear compbination to the input vectors: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
POWERS
 the powers to which you are raising each of the arguments in your function
=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 
ARG
the values input to this function
=q4_sp.rm-n4,q4_sp.im-n4,q4_sp.rm-n3,q4_sp.im-n3,q4_sp.rm-n2,q4_sp.im-n2,q4_sp.rm-n1,q4_sp.im-n1,q4_sp.rm-0,q4_sp.im-0,q4_sp.rm-p1,q4_sp.im-p1,q4_sp.rm-p2,q4_sp.im-p2,q4_sp.rm-p3,q4_sp.im-p3,q4_sp.rm-p4,q4_sp.im-p4
q4_normThe CUSTOM action with label q4_norm calculates the following quantities:
 Quantity   
 Type   
 Description  
q4_norm
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q4_norm2 
FUNC
the function you wish to evaluate
=sqrt(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q4The CUSTOM action with label q4 calculates the following quantities:
 Quantity   
 Type   
 Description  
q4
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=q4_norm,q4_denom 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
q4_meanThe MEAN action with label q4_mean calculates the following quantities:
 Quantity   
 Type   
 Description  
q4_mean
scalar
the mean of all the elements in the input vector: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the values input to this function
=q4 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# --- End of included input --- 

eneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the internal energy: 
ENERGY
Calculate the total potential energy of the simulation box. More details
volThe VOLUME action with label vol calculates the following quantities:
 Quantity   
 Type   
 Description  
vol
scalar
the volume of simulation box: 
VOLUME
Calculate the volume of the simulation box. More details


COMBINE
Calculate a polynomial combination of a set of other variables. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=enthalpyThe COMBINE action with label enthalpy calculates the following quantities:
 Quantity   
 Type   
 Description  
enthalpy
scalar
a linear compbination
 
ARG
the values input to this function
=ene,vol
 
COEFFICIENTS
 the coefficients of the arguments in your function
=1.0,0.060221409
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE

COMBINE
Calculate a polynomial combination of a set of other variables. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=hThe COMBINE action with label h calculates the following quantities:
 Quantity   
 Type   
 Description  
h
scalar
a linear compbination
 
ARG
the values input to this function
=enthalpy
 
POWERS
 the powers to which you are raising each of the arguments in your function
=1
 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.00926
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE


COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details
 ...
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.33 D_MAX=0.6}
SPECIESA
this keyword is used for colvars such as the coordination number
=1-256 
SPECIESB
this keyword is used for colvars such as the coordination number
=257-512
MEAN
 calculate the mean of all the quantities
MOMENTS
the list of moments that you would like to calculate
=2
MORE_THAN1
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=4.0 D_MAX=5.0}
MORE_THAN2
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=5.0 D_MAX=6.0}
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cnThe COORDINATIONNUMBER action with label cn calculates the following quantities:
 Quantity   
 Type   
 Description  
cn
vector
the coordination numbers of the specified atoms
cn_morethan-1
scalar
the number of colvars that have a value more than a threshold
cn_morethan-2
scalar
the number of colvars that have a value more than a threshold
cn_mean
scalar
the mean of the colvars
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility
... COORDINATIONNUMBER
# PLUMED interprets the command:
# COORDINATIONNUMBER ...
# SWITCH={RATIONAL R_0=0.33 D_MAX=0.6}
# SPECIESA=1-256 SPECIESB=257-512
# MEAN
# MOMENTS=2
# MORE_THAN1={RATIONAL R_0=4.0 D_MAX=5.0}
# MORE_THAN2={RATIONAL R_0=5.0 D_MAX=6.0}
# LABEL=cn
# LOWMEM
# ... COORDINATIONNUMBER
# as follows (Click the red comment above to revert to the short version of the input):
cn_grpThe GROUP action with label cn_grp calculates the following quantities:
 Quantity   
 Type   
 Description  
cn_grp
atoms
indices of atoms specified in GROUP: 
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
=1-256
cn_matThe CONTACT_MATRIX action with label cn_mat calculates the following quantities:
 Quantity   
 Type   
 Description  
cn_mat
matrix
a matrix containing the weights for the bonds between each pair of atoms: 
CONTACT_MATRIX
Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details
 
GROUPA
=1-256 
GROUPB
=257-512 
SWITCH
specify the switching function to use between two sets of indistinguishable atoms
={RATIONAL R_0=0.33 D_MAX=0.6}
cn_onesThe CONSTANT action with label cn_ones calculates the following quantities:
 Quantity   
 Type   
 Description  
cn_ones
vector
the constant value that was read from the plumed input: 
ONES
Create a constant vector with all elements equal to one More details
 
SIZE
the number of ones that you would like to create
=256
cnThe MATRIX_VECTOR_PRODUCT action with label cn calculates the following quantities:
 Quantity   
 Type   
 Description  
cn
vector
the vector that is obtained by taking the product between the matrix and the vector that were input: 
MATRIX_VECTOR_PRODUCT
Calculate the product of the matrix and the vector More details
  
ARG
the label for the matrix and the vector/scalar that are being multiplied
=cn_mat,cn_ones
cn_caverageThe MEAN action with label cn_caverage calculates the following quantities:
 Quantity   
 Type   
 Description  
cn_caverage
scalar
the mean of all the elements in the input vector: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the values input to this function
=cn 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
cn_diffpow-2The CUSTOM action with label cn_diffpow-2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn_diffpow-2
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values input to this function
=cn,cn_caverage 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
FUNC
the function you wish to evaluate
=(x-y)^2
cn_moment-2The MEAN action with label cn_moment-2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn_moment-2
scalar
the mean of all the elements in the input vector: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the values input to this function
=cn_diffpow-2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
cn_mt1The MORE_THAN action with label cn_mt1 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn_mt1
vector
the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: 
MORE_THAN
Use a switching function to determine how many of the input variables are more than a certain cutoff. More details
 
ARG
the values input to this function
=cn 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={RATIONAL R_0=4.0 D_MAX=5.0}
cn_morethan-1The SUM action with label cn_morethan-1 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn_morethan-1
scalar
the sum of all the elements in the input vector: 
SUM
Calculate the sum of the arguments More details
 
ARG
the values input to this function
=cn_mt1 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
cn_mt2The MORE_THAN action with label cn_mt2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn_mt2
vector
the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: 
MORE_THAN
Use a switching function to determine how many of the input variables are more than a certain cutoff. More details
 
ARG
the values input to this function
=cn 
SWITCH
This keyword is used if you want to employ an alternative to the continuous swiching function defined above
={RATIONAL R_0=5.0 D_MAX=6.0}
cn_morethan-2The SUM action with label cn_morethan-2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cn_morethan-2
scalar
the sum of all the elements in the input vector: 
SUM
Calculate the sum of the arguments More details
 
ARG
the values input to this function
=cn_mt2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
cn_meanThe MEAN action with label cn_mean calculates the following quantities:
 Quantity   
 Type   
 Description  
cn_mean
scalar
the mean of all the elements in the input vector: 
MEAN
Calculate the arithmetic mean of the elements in a vector More details
 
ARG
the values input to this function
=cn 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# --- End of included input --- 
cv1_lThe COMBINE action with label cv1_l calculates the following quantities:
 Quantity   
 Type   
 Description  
cv1_l
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the values input to this function
=q4.mean,q6.mean,cn.mean,cn.moment-2,cn.morethan-1,cn.morethan-2,h 
COEFFICIENTS
 the coefficients of the arguments in your function
=8.77874,-11.6973,0.157351,0.0816257,0.00418239,-0.0177146,-0.0163215 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

cv2_lThe COMBINE action with label cv2_l calculates the following quantities:
 Quantity   
 Type   
 Description  
cv2_l
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the values input to this function
=q4.mean,q6.mean,cn.mean,cn.moment-2,cn.morethan-1,cn.morethan-2,h 
COEFFICIENTS
 the coefficients of the arguments in your function
=20.4484,12.8081,-1.74684,0.763133,-0.00471387,0.0117218,0.000533273 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

cv1The MATHEVAL action with label cv1 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv1
scalar
an arbitrary function: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the values input to this function
=cv1_l 
FUNC
the function you wish to evaluate
=x-28.139110 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 

cv2The MATHEVAL action with label cv2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv2
scalar
an arbitrary function: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG
the values input to this function
=cv2_l 
FUNC
the function you wish to evaluate
=x-8.283814 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 

metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).: 
METAD
Used to performed metadynamics on one or more collective variables. This action has hidden defaults. More details
 
ARG
the labels of the scalars on which the bias will act
=cv1,cv2 
SIGMA
the widths of the Gaussian hills
=0.15,0.15 
HEIGHT
the heights of the Gaussian hills
=5 
PACE
the frequency for hill addition
=1000 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=100 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=1125 
GRID_MIN
the lower bounds for the grid
=-6,-7 
GRID_MAX
the upper bounds for the grid
=4,7 
GRID_BIN
the number of bins for the grid
=150,175 
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
metad: 
METAD
Used to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details
 
ARG
the labels of the scalars on which the bias will act
=cv1,cv2 
SIGMA
the widths of the Gaussian hills
=0.15,0.15 
HEIGHT
the heights of the Gaussian hills
=5 
PACE
the frequency for hill addition
=1000 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=100 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=1125 
GRID_MIN
the lower bounds for the grid
=-6,-7 
GRID_MAX
the upper bounds for the grid
=4,7 
GRID_BIN
the number of bins for the grid
=150,175 
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
  
FILE
 a file in which the list of added hills is stored
=HILLS
PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
=cv1,cv2,q4.mean,q6.mean,cn.mean,cn.moment-2,cn.morethan-1,cn.morethan-2,h,metad.bias,metad.rbias 
FILE
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=100