Shortcut: Q3
| Module | symfunc |
|---|---|
| Description | Usage |
| Calculate 3rd order Steinhardt parameters. |   |
| output value | type |
| the norms of the vectors of spherical harmonic coefficients | vector |
Details and examples
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, is complex vector whose components are calculated using the following formula:
where is one of the 3rd order spherical harmonics so is a number that runs from to . The function is a switching function that acts on the distance between atoms and . The parameters of this function should be set so that it the function is equal to one when atom is in the first coordination sphere of atom and is zero otherwise.
As discussed on this page, 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.
This norm is small when the coordination shell is disordered and larger when the coordination shell is ordered. The following input illustrates how by averaging the value of this norm over all the atoms in the system you can measure the global degree of order in the system:
Click on the labels of the actions for more information on what each action computes
q3The Q3 action with label q3 calculates the following quantities:: Q3Calculate 3rd order Steinhardt parameters. This action is a shortcut and it has hidden defaults. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-64 D_0 The d_0 parameter of the switching function=1.3 R_0The r_0 parameter of the switching function=0.2 q3: Q3Calculate 3rd order Steinhardt parameters. This action is a shortcut and uses the defaults shown here. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-64 D_0 The d_0 parameter of the switching function=1.3 R_0The r_0 parameter of the switching function=0.2 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0 # PLUMED interprets the command: # q3: Q3 SPECIES=1-64 D_0=1.3 R_0=0.2 # as follows (Click the red comment above to revert to the short version of the input): q3_grpThe GROUP action with label q3_grp calculates the following quantities:
Quantity Type Description q3 vector the norms of the vectors of spherical harmonic coefficients : 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=1-64 q3_matThe CONTACT_MATRIX action with label q3_mat calculates the following quantities:
Quantity Type Description q3_grp atoms indices of atoms specified in GROUP : CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-64 R_0The r_0 parameter of the switching function=0.2 D_0 The d_0 parameter of the switching function=1.3 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0 COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix q3_shThe SPHERICAL_HARMONIC action with label q3_sh calculates the following quantities:
Quantity Type Description q3_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms q3_mat.x matrix the projection of the bond on the x axis q3_mat.y matrix the projection of the bond on the y axis q3_mat.z matrix the projection of the bond on the z axis : SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q3_mat.x,q3_mat.y,q3_mat.z,q3_mat.w Lthe value of the angular momentum=3 q3_denom_onesThe CONSTANT action with label q3_denom_ones calculates the following quantities:
Quantity Type Description q3_sh.rm-n3 matrix the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities q3_sh.rm-n2 matrix the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities q3_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities q3_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities q3_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities q3_sh.rm-p2 matrix the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities q3_sh.rm-p3 matrix the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities q3_sh.im-n3 matrix the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities q3_sh.im-n2 matrix the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities q3_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities q3_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities q3_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities q3_sh.im-p2 matrix the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities q3_sh.im-p3 matrix the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities : ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64 q3_denomThe MATRIX_VECTOR_PRODUCT action with label q3_denom calculates the following quantities:
Quantity Type Description q3_denom_ones vector the constant value that was read from the plumed input : MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q3_mat.w,q3_denom_ones q3_spThe MATRIX_VECTOR_PRODUCT action with label q3_sp calculates the following quantities:
Quantity Type Description q3_denom vector the vector that is obtained by taking the product between the matrix and the vector that were input : MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q3_sh.*,q3_denom_ones q3_norm2The COMBINE action with label q3_norm2 calculates the following quantities:
Quantity Type Description q3_sp.rm-n3 vector the product of the matrix q3_sh.rm-n3 and the vector q3_denom_ones q3_sp.rm-n2 vector the product of the matrix q3_sh.rm-n2 and the vector q3_denom_ones q3_sp.rm-n1 vector the product of the matrix q3_sh.rm-n1 and the vector q3_denom_ones q3_sp.rm-0 vector the product of the matrix q3_sh.rm-0 and the vector q3_denom_ones q3_sp.rm-p1 vector the product of the matrix q3_sh.rm-p1 and the vector q3_denom_ones q3_sp.rm-p2 vector the product of the matrix q3_sh.rm-p2 and the vector q3_denom_ones q3_sp.rm-p3 vector the product of the matrix q3_sh.rm-p3 and the vector q3_denom_ones q3_sp.im-n3 vector the product of the matrix q3_sh.im-n3 and the vector q3_denom_ones q3_sp.im-n2 vector the product of the matrix q3_sh.im-n2 and the vector q3_denom_ones q3_sp.im-n1 vector the product of the matrix q3_sh.im-n1 and the vector q3_denom_ones q3_sp.im-0 vector the product of the matrix q3_sh.im-0 and the vector q3_denom_ones q3_sp.im-p1 vector the product of the matrix q3_sh.im-p1 and the vector q3_denom_ones q3_sp.im-p2 vector the product of the matrix q3_sh.im-p2 and the vector q3_denom_ones q3_sp.im-p3 vector the product of the matrix q3_sh.im-p3 and the vector q3_denom_ones : COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif 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 ARGthe values input to this function=q3_sp.rm-n3,q3_sp.im-n3,q3_sp.rm-n2,q3_sp.im-n2,q3_sp.rm-n1,q3_sp.im-n1,q3_sp.rm-0,q3_sp.im-0,q3_sp.rm-p1,q3_sp.im-p1,q3_sp.rm-p2,q3_sp.im-p2,q3_sp.rm-p3,q3_sp.im-p3 q3_normThe CUSTOM action with label q3_norm calculates the following quantities:
Quantity Type Description q3_norm2 vector the vector obtained by doing an element-wise application of a linear combination to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3The CUSTOM action with label q3 calculates the following quantities:
Quantity Type Description q3_norm vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_norm,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # --- End of included input --- q3_meanThe MEAN action with label q3_mean calculates the following quantities:
Quantity Type Description q3 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=q3_mean FILEthe name of the file on which to output these quantities=colvar
Quantity Type Description q3_mean scalar the MEAN of the elements in the input value
In the above input the rational switching function with the parameters above. We would recommend using SWITCH syntax rather than the syntax above when giving the parameters for the switching function as you can then use any of the switching functions described in the documentation for LESS_THAN. More importantly, however, using this syntax allows you to set the D_MAX parameter for the switching function as demonstrated below:
Click on the labels of the actions for more information on what each action computes
q3The Q3 action with label q3 calculates the following quantities:: Q3Calculate 3rd order Steinhardt parameters. This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-64 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 D_0=1.3 R_0=0.2 D_MAX=3.0} # PLUMED interprets the command: # q3: Q3 SPECIES=1-64 SWITCH={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0} # as follows (Click the red comment above to revert to the short version of the input): q3_grpThe GROUP action with label q3_grp calculates the following quantities:
Quantity Type Description q3 vector the norms of the vectors of spherical harmonic coefficients : 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=1-64 q3_matThe CONTACT_MATRIX action with label q3_mat calculates the following quantities:
Quantity Type Description q3_grp atoms indices of atoms specified in GROUP : CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-64 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=1.3 R_0=0.2 D_MAX=3.0} COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix q3_shThe SPHERICAL_HARMONIC action with label q3_sh calculates the following quantities:
Quantity Type Description q3_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms q3_mat.x matrix the projection of the bond on the x axis q3_mat.y matrix the projection of the bond on the y axis q3_mat.z matrix the projection of the bond on the z axis : SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q3_mat.x,q3_mat.y,q3_mat.z,q3_mat.w Lthe value of the angular momentum=3 q3_denom_onesThe CONSTANT action with label q3_denom_ones calculates the following quantities:
Quantity Type Description q3_sh.rm-n3 matrix the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities q3_sh.rm-n2 matrix the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities q3_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities q3_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities q3_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities q3_sh.rm-p2 matrix the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities q3_sh.rm-p3 matrix the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities q3_sh.im-n3 matrix the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities q3_sh.im-n2 matrix the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities q3_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities q3_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities q3_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities q3_sh.im-p2 matrix the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities q3_sh.im-p3 matrix the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities : ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64 q3_denomThe MATRIX_VECTOR_PRODUCT action with label q3_denom calculates the following quantities:
Quantity Type Description q3_denom_ones vector the constant value that was read from the plumed input : MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q3_mat.w,q3_denom_ones q3_spThe MATRIX_VECTOR_PRODUCT action with label q3_sp calculates the following quantities:
Quantity Type Description q3_denom vector the vector that is obtained by taking the product between the matrix and the vector that were input : MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q3_sh.*,q3_denom_ones q3_norm2The COMBINE action with label q3_norm2 calculates the following quantities:
Quantity Type Description q3_sp.rm-n3 vector the product of the matrix q3_sh.rm-n3 and the vector q3_denom_ones q3_sp.rm-n2 vector the product of the matrix q3_sh.rm-n2 and the vector q3_denom_ones q3_sp.rm-n1 vector the product of the matrix q3_sh.rm-n1 and the vector q3_denom_ones q3_sp.rm-0 vector the product of the matrix q3_sh.rm-0 and the vector q3_denom_ones q3_sp.rm-p1 vector the product of the matrix q3_sh.rm-p1 and the vector q3_denom_ones q3_sp.rm-p2 vector the product of the matrix q3_sh.rm-p2 and the vector q3_denom_ones q3_sp.rm-p3 vector the product of the matrix q3_sh.rm-p3 and the vector q3_denom_ones q3_sp.im-n3 vector the product of the matrix q3_sh.im-n3 and the vector q3_denom_ones q3_sp.im-n2 vector the product of the matrix q3_sh.im-n2 and the vector q3_denom_ones q3_sp.im-n1 vector the product of the matrix q3_sh.im-n1 and the vector q3_denom_ones q3_sp.im-0 vector the product of the matrix q3_sh.im-0 and the vector q3_denom_ones q3_sp.im-p1 vector the product of the matrix q3_sh.im-p1 and the vector q3_denom_ones q3_sp.im-p2 vector the product of the matrix q3_sh.im-p2 and the vector q3_denom_ones q3_sp.im-p3 vector the product of the matrix q3_sh.im-p3 and the vector q3_denom_ones : COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif 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 ARGthe values input to this function=q3_sp.rm-n3,q3_sp.im-n3,q3_sp.rm-n2,q3_sp.im-n2,q3_sp.rm-n1,q3_sp.im-n1,q3_sp.rm-0,q3_sp.im-0,q3_sp.rm-p1,q3_sp.im-p1,q3_sp.rm-p2,q3_sp.im-p2,q3_sp.rm-p3,q3_sp.im-p3 q3_normThe CUSTOM action with label q3_norm calculates the following quantities:
Quantity Type Description q3_norm2 vector the vector obtained by doing an element-wise application of a linear combination to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3The CUSTOM action with label q3 calculates the following quantities:
Quantity Type Description q3_norm vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_norm,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # --- End of included input --- q3_meanThe MEAN action with label q3_mean calculates the following quantities:
Quantity Type Description q3 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=q3_mean FILEthe name of the file on which to output these quantities=colvar
Quantity Type Description q3_mean scalar the MEAN of the elements in the input value
Setting the D_MAX can substantially improve PLUMED performance as it turns on the linked list algorithm that is discussed in the optimisation details part
of the documentation for CONTACT_MATRIX.
Working with two types of atoms
The command below 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
q3The Q3 action with label q3 calculates the following quantities:: Q3Calculate 3rd order Steinhardt parameters. This action is a shortcut and it has hidden defaults. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=1-64 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=65-128 D_0 The d_0 parameter of the switching function=1.3 R_0The r_0 parameter of the switching function=0.2 q3: Q3Calculate 3rd order Steinhardt parameters. This action is a shortcut and uses the defaults shown here. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=1-64 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=65-128 D_0 The d_0 parameter of the switching function=1.3 R_0The r_0 parameter of the switching function=0.2 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0 # PLUMED interprets the command: # q3: Q3 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 # as follows (Click the red comment above to revert to the short version of the input): q3_grpThe GROUP action with label q3_grp calculates the following quantities:
Quantity Type Description q3 vector the norms of the vectors of spherical harmonic coefficients : 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=1-64 q3_matThe CONTACT_MATRIX action with label q3_mat calculates the following quantities:
Quantity Type Description q3_grp atoms indices of atoms specified in GROUP : CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=1-64 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=65-128 R_0The r_0 parameter of the switching function=0.2 D_0 The d_0 parameter of the switching function=1.3 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0 COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix q3_shThe SPHERICAL_HARMONIC action with label q3_sh calculates the following quantities:
Quantity Type Description q3_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms q3_mat.x matrix the projection of the bond on the x axis q3_mat.y matrix the projection of the bond on the y axis q3_mat.z matrix the projection of the bond on the z axis : SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q3_mat.x,q3_mat.y,q3_mat.z,q3_mat.w Lthe value of the angular momentum=3 q3_denom_onesThe CONSTANT action with label q3_denom_ones calculates the following quantities:
Quantity Type Description q3_sh.rm-n3 matrix the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities q3_sh.rm-n2 matrix the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities q3_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities q3_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities q3_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities q3_sh.rm-p2 matrix the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities q3_sh.rm-p3 matrix the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities q3_sh.im-n3 matrix the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities q3_sh.im-n2 matrix the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities q3_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities q3_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities q3_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities q3_sh.im-p2 matrix the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities q3_sh.im-p3 matrix the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities : ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64 q3_denomThe MATRIX_VECTOR_PRODUCT action with label q3_denom calculates the following quantities:
Quantity Type Description q3_denom_ones vector the constant value that was read from the plumed input : MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q3_mat.w,q3_denom_ones q3_spThe MATRIX_VECTOR_PRODUCT action with label q3_sp calculates the following quantities:
Quantity Type Description q3_denom vector the vector that is obtained by taking the product between the matrix and the vector that were input : MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q3_sh.*,q3_denom_ones q3_norm2The COMBINE action with label q3_norm2 calculates the following quantities:
Quantity Type Description q3_sp.rm-n3 vector the product of the matrix q3_sh.rm-n3 and the vector q3_denom_ones q3_sp.rm-n2 vector the product of the matrix q3_sh.rm-n2 and the vector q3_denom_ones q3_sp.rm-n1 vector the product of the matrix q3_sh.rm-n1 and the vector q3_denom_ones q3_sp.rm-0 vector the product of the matrix q3_sh.rm-0 and the vector q3_denom_ones q3_sp.rm-p1 vector the product of the matrix q3_sh.rm-p1 and the vector q3_denom_ones q3_sp.rm-p2 vector the product of the matrix q3_sh.rm-p2 and the vector q3_denom_ones q3_sp.rm-p3 vector the product of the matrix q3_sh.rm-p3 and the vector q3_denom_ones q3_sp.im-n3 vector the product of the matrix q3_sh.im-n3 and the vector q3_denom_ones q3_sp.im-n2 vector the product of the matrix q3_sh.im-n2 and the vector q3_denom_ones q3_sp.im-n1 vector the product of the matrix q3_sh.im-n1 and the vector q3_denom_ones q3_sp.im-0 vector the product of the matrix q3_sh.im-0 and the vector q3_denom_ones q3_sp.im-p1 vector the product of the matrix q3_sh.im-p1 and the vector q3_denom_ones q3_sp.im-p2 vector the product of the matrix q3_sh.im-p2 and the vector q3_denom_ones q3_sp.im-p3 vector the product of the matrix q3_sh.im-p3 and the vector q3_denom_ones : COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif 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 ARGthe values input to this function=q3_sp.rm-n3,q3_sp.im-n3,q3_sp.rm-n2,q3_sp.im-n2,q3_sp.rm-n1,q3_sp.im-n1,q3_sp.rm-0,q3_sp.im-0,q3_sp.rm-p1,q3_sp.im-p1,q3_sp.rm-p2,q3_sp.im-p2,q3_sp.rm-p3,q3_sp.im-p3 q3_normThe CUSTOM action with label q3_norm calculates the following quantities:
Quantity Type Description q3_norm2 vector the vector obtained by doing an element-wise application of a linear combination to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3The CUSTOM action with label q3 calculates the following quantities:
Quantity Type Description q3_norm vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_norm,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # --- End of included input --- q3_meanThe MEAN action with label q3_mean calculates the following quantities:
Quantity Type Description q3 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=q3_mean FILEthe name of the file on which to output these quantities=colvar
Quantity Type Description q3_mean scalar the MEAN of the elements in the input value
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 DUMPATOMS 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 vector while columns 13-19 will contain the imaginary parts of this director.
Click on the labels of the actions for more information on what each action computes
q3The Q3 action with label q3 calculates the following quantities:: Q3Calculate 3rd order Steinhardt parameters. This action is a shortcut and it has hidden defaults. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=1-64 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=65-128 D_0 The d_0 parameter of the switching function=1.3 R_0The r_0 parameter of the switching function=0.2 MEAN calculate the mean of all the quantities q3: Q3Calculate 3rd order Steinhardt parameters. This action is a shortcut and uses the defaults shown here. More details SPECIESAthe list of atoms for which the symmetry function is being calculated=1-64 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=65-128 D_0 The d_0 parameter of the switching function=1.3 R_0The r_0 parameter of the switching function=0.2 MEAN calculate the mean of all the quantities NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0 # PLUMED interprets the command: # q3: Q3 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN # as follows (Click the red comment above to revert to the short version of the input): q3_grpThe GROUP action with label q3_grp calculates the following quantities:
Quantity Type Description q3 vector the norms of the vectors of spherical harmonic coefficients q3_mean scalar the mean of the colvars : 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=1-64 q3_matThe CONTACT_MATRIX action with label q3_mat calculates the following quantities:
Quantity Type Description q3_grp atoms indices of atoms specified in GROUP : CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=1-64 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=65-128 R_0The r_0 parameter of the switching function=0.2 D_0 The d_0 parameter of the switching function=1.3 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0 COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix q3_shThe SPHERICAL_HARMONIC action with label q3_sh calculates the following quantities:
Quantity Type Description q3_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms q3_mat.x matrix the projection of the bond on the x axis q3_mat.y matrix the projection of the bond on the y axis q3_mat.z matrix the projection of the bond on the z axis : SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q3_mat.x,q3_mat.y,q3_mat.z,q3_mat.w Lthe value of the angular momentum=3 q3_denom_onesThe CONSTANT action with label q3_denom_ones calculates the following quantities:
Quantity Type Description q3_sh.rm-n3 matrix the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities q3_sh.rm-n2 matrix the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities q3_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities q3_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities q3_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities q3_sh.rm-p2 matrix the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities q3_sh.rm-p3 matrix the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities q3_sh.im-n3 matrix the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities q3_sh.im-n2 matrix the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities q3_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities q3_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities q3_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities q3_sh.im-p2 matrix the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities q3_sh.im-p3 matrix the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities : ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64 q3_denomThe MATRIX_VECTOR_PRODUCT action with label q3_denom calculates the following quantities:
Quantity Type Description q3_denom_ones vector the constant value that was read from the plumed input : MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q3_mat.w,q3_denom_ones q3_spThe MATRIX_VECTOR_PRODUCT action with label q3_sp calculates the following quantities:
Quantity Type Description q3_denom vector the vector that is obtained by taking the product between the matrix and the vector that were input : MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q3_sh.*,q3_denom_ones q3_norm2The COMBINE action with label q3_norm2 calculates the following quantities:
Quantity Type Description q3_sp.rm-n3 vector the product of the matrix q3_sh.rm-n3 and the vector q3_denom_ones q3_sp.rm-n2 vector the product of the matrix q3_sh.rm-n2 and the vector q3_denom_ones q3_sp.rm-n1 vector the product of the matrix q3_sh.rm-n1 and the vector q3_denom_ones q3_sp.rm-0 vector the product of the matrix q3_sh.rm-0 and the vector q3_denom_ones q3_sp.rm-p1 vector the product of the matrix q3_sh.rm-p1 and the vector q3_denom_ones q3_sp.rm-p2 vector the product of the matrix q3_sh.rm-p2 and the vector q3_denom_ones q3_sp.rm-p3 vector the product of the matrix q3_sh.rm-p3 and the vector q3_denom_ones q3_sp.im-n3 vector the product of the matrix q3_sh.im-n3 and the vector q3_denom_ones q3_sp.im-n2 vector the product of the matrix q3_sh.im-n2 and the vector q3_denom_ones q3_sp.im-n1 vector the product of the matrix q3_sh.im-n1 and the vector q3_denom_ones q3_sp.im-0 vector the product of the matrix q3_sh.im-0 and the vector q3_denom_ones q3_sp.im-p1 vector the product of the matrix q3_sh.im-p1 and the vector q3_denom_ones q3_sp.im-p2 vector the product of the matrix q3_sh.im-p2 and the vector q3_denom_ones q3_sp.im-p3 vector the product of the matrix q3_sh.im-p3 and the vector q3_denom_ones : COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif 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 ARGthe values input to this function=q3_sp.rm-n3,q3_sp.im-n3,q3_sp.rm-n2,q3_sp.im-n2,q3_sp.rm-n1,q3_sp.im-n1,q3_sp.rm-0,q3_sp.im-0,q3_sp.rm-p1,q3_sp.im-p1,q3_sp.rm-p2,q3_sp.im-p2,q3_sp.rm-p3,q3_sp.im-p3 q3_normThe CUSTOM action with label q3_norm calculates the following quantities:
Quantity Type Description q3_norm2 vector the vector obtained by doing an element-wise application of a linear combination to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3The CUSTOM action with label q3 calculates the following quantities:
Quantity Type Description q3_norm vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_norm,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_meanThe MEAN action with label q3_mean calculates the following quantities:
Quantity Type Description q3 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # --- End of included input --- DUMPATOMSDump selected atoms on a file. More details ATOMSthe atom indices whose positions you would like to print out=q3 ARGthe labels of vectors that should be output in the xyz file=q3 FILEfile on which to output coordinates; extension is automatically detected=q3.xyz
Quantity Type Description q3_mean scalar the MEAN of the elements in the input value
The MASK keyword
You can use the MASK keyword with this action in the same way that it is used with COORDINATIONNUMBER. This keyword thus expects a vector in input, which tells Q3 that it is safe not to calculate the Q3 parameter for some of the atoms. As illustrated below, this is useful if you are using functionality from the volumes module to calculate the average value of the Q3 parameter for only those atoms that lie in a certain part of the simulation box.
Click on the labels of the actions for more information on what each action computes
# Fixed virtual atom which serves as the probe volume's center (pos. in nm) centerThe FIXEDATOM action with label center calculates the following quantities:: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.5,2.5,2.5 center: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=2.5,2.5,2.5 SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0 # Vector in which element i is one if atom i is in sphere of interest and zero otherwise sphereThe INSPHERE action with label sphere calculates the following quantities:
Quantity Type Description center atoms virtual atom calculated by FIXEDATOM action : INSPHEREThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. More details ATOMSthe group of atoms that you would like to investigate=1-400 CENTERthe atom whose vicinity we are interested in examining=center RADIUSthe switching function that tells us the extent of the sphereical region of interest. Options for this keyword are explained in the documentation for LESS_THAN.={GAUSSIAN D_0=0.5 R_0=0.01 D_MAX=0.52} # Calculate the fccubic parameter of the atoms ccThe Q3 action with label cc calculates the following quantities:
Quantity Type Description sphere vector vector of numbers between 0 and 1 that measure the degree to which each atom is within the volume of interest : Q3Calculate 3rd order Steinhardt parameters. This action is a shortcut. More details ... SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-400 MASKthe label for a vector that is used to determine which rows of the matrix are computed=sphere 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 D_0=3.0 R_0=1.5 D_MAX=6.0} ... # PLUMED interprets the command: # cc: Q3 ... # SPECIES=1-400 MASK=sphere # SWITCH={RATIONAL D_0=3.0 R_0=1.5 D_MAX=6.0} # ... # as follows (Click the red comment above to revert to the short version of the input): cc_grpThe GROUP action with label cc_grp calculates the following quantities:
Quantity Type Description cc vector the norms of the vectors of spherical harmonic coefficients : 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=1-400 cc_matThe CONTACT_MATRIX action with label cc_mat calculates the following quantities:
Quantity Type Description cc_grp atoms indices of atoms specified in GROUP : CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-400 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=3.0 R_0=1.5 D_MAX=6.0} COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix MASKa vector that is used to used to determine which rows of the adjancency matrix to compute=sphere cc_shThe SPHERICAL_HARMONIC action with label cc_sh calculates the following quantities:
Quantity Type Description cc_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms cc_mat.x matrix the projection of the bond on the x axis cc_mat.y matrix the projection of the bond on the y axis cc_mat.z matrix the projection of the bond on the z axis : SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=cc_mat.x,cc_mat.y,cc_mat.z,cc_mat.w Lthe value of the angular momentum=3 cc_denom_onesThe CONSTANT action with label cc_denom_ones calculates the following quantities:
Quantity Type Description cc_sh.rm-n3 matrix the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities cc_sh.rm-n2 matrix the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities cc_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities cc_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities cc_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities cc_sh.rm-p2 matrix the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities cc_sh.rm-p3 matrix the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities cc_sh.im-n3 matrix the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities cc_sh.im-n2 matrix the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities cc_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities cc_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities cc_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities cc_sh.im-p2 matrix the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities cc_sh.im-p3 matrix the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities : ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=400 cc_denomThe MATRIX_VECTOR_PRODUCT action with label cc_denom calculates the following quantities:
Quantity Type Description cc_denom_ones vector the constant value that was read from the plumed input : MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=cc_mat.w,cc_denom_ones cc_spThe MATRIX_VECTOR_PRODUCT action with label cc_sp calculates the following quantities:
Quantity Type Description cc_denom vector the vector that is obtained by taking the product between the matrix and the vector that were input : MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=cc_sh.*,cc_denom_ones cc_norm2The COMBINE action with label cc_norm2 calculates the following quantities:
Quantity Type Description cc_sp.rm-n3 vector the product of the matrix cc_sh.rm-n3 and the vector cc_denom_ones cc_sp.rm-n2 vector the product of the matrix cc_sh.rm-n2 and the vector cc_denom_ones cc_sp.rm-n1 vector the product of the matrix cc_sh.rm-n1 and the vector cc_denom_ones cc_sp.rm-0 vector the product of the matrix cc_sh.rm-0 and the vector cc_denom_ones cc_sp.rm-p1 vector the product of the matrix cc_sh.rm-p1 and the vector cc_denom_ones cc_sp.rm-p2 vector the product of the matrix cc_sh.rm-p2 and the vector cc_denom_ones cc_sp.rm-p3 vector the product of the matrix cc_sh.rm-p3 and the vector cc_denom_ones cc_sp.im-n3 vector the product of the matrix cc_sh.im-n3 and the vector cc_denom_ones cc_sp.im-n2 vector the product of the matrix cc_sh.im-n2 and the vector cc_denom_ones cc_sp.im-n1 vector the product of the matrix cc_sh.im-n1 and the vector cc_denom_ones cc_sp.im-0 vector the product of the matrix cc_sh.im-0 and the vector cc_denom_ones cc_sp.im-p1 vector the product of the matrix cc_sh.im-p1 and the vector cc_denom_ones cc_sp.im-p2 vector the product of the matrix cc_sh.im-p2 and the vector cc_denom_ones cc_sp.im-p3 vector the product of the matrix cc_sh.im-p3 and the vector cc_denom_ones : COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif 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 ARGthe values input to this function=cc_sp.rm-n3,cc_sp.im-n3,cc_sp.rm-n2,cc_sp.im-n2,cc_sp.rm-n1,cc_sp.im-n1,cc_sp.rm-0,cc_sp.im-0,cc_sp.rm-p1,cc_sp.im-p1,cc_sp.rm-p2,cc_sp.im-p2,cc_sp.rm-p3,cc_sp.im-p3 cc_normThe CUSTOM action with label cc_norm calculates the following quantities:
Quantity Type Description cc_norm2 vector the vector obtained by doing an element-wise application of a linear combination to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cc_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ccThe CUSTOM action with label cc calculates the following quantities:
Quantity Type Description cc_norm vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cc_norm,cc_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # --- End of included input --- # Multiply fccubic parameters numbers by sphere vector prodThe CUSTOM action with label prod calculates the following quantities:
Quantity Type Description cc vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cc,sphere FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # Sum of coordination numbers for atoms that are in the sphere of interest numerThe SUM action with label numer calculates the following quantities:
Quantity Type Description prod vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=prod PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # Number of atoms that are in sphere of interest denomThe SUM action with label denom calculates the following quantities:
Quantity Type Description numer scalar the SUM of the elements in the input value : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=sphere PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # Average coordination number for atoms in sphere of interest avThe CUSTOM action with label av calculates the following quantities:
Quantity Type Description denom scalar the SUM of the elements in the input value : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=numer,denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # And print out final CV to a file PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=av FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=1
Quantity Type Description av scalar an arbitrary function
This input calculate the average value of the Q3 parameter for only those atoms that are within a spherical region that is centered on the point .
Deprecated syntax
More information on the deprecated keywords that are given below is available in the documentation for the DISTANCES command. Below is an example where these deprecated keywords are used to calculate the histogram of Q3 parameters for the 64 atoms in a box of Lennard Jones print them to a file called colvar:
Click on the labels of the actions for more information on what each action computes
q3The Q3 action with label q3 calculates the following quantities:: Q3Calculate 3rd order Steinhardt parameters. This action is a shortcut and it has hidden defaults. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-64 D_0 The d_0 parameter of the switching function=1.3 R_0The r_0 parameter of the switching function=0.2 HISTOGRAMcalculate a discretized histogram of the distribution of values={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} q3: Q3Calculate 3rd order Steinhardt parameters. This action is a shortcut and uses the defaults shown here. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-64 D_0 The d_0 parameter of the switching function=1.3 R_0The r_0 parameter of the switching function=0.2 HISTOGRAMcalculate a discretized histogram of the distribution of values={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0 # PLUMED interprets the command: # q3: Q3 SPECIES=1-64 D_0=1.3 R_0=0.2 HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} # as follows (Click the red comment above to revert to the short version of the input): q3_grpThe GROUP action with label q3_grp calculates the following quantities:
Quantity Type Description q3 vector the norms of the vectors of spherical harmonic coefficients q3_between-1 scalar the number of colvars that have a value that lies in a particular interval q3_between-2 scalar the number of colvars that have a value that lies in a particular interval q3_between-3 scalar the number of colvars that have a value that lies in a particular interval q3_between-4 scalar the number of colvars that have a value that lies in a particular interval q3_between-5 scalar the number of colvars that have a value that lies in a particular interval q3_between-6 scalar the number of colvars that have a value that lies in a particular interval q3_between-7 scalar the number of colvars that have a value that lies in a particular interval q3_between-8 scalar the number of colvars that have a value that lies in a particular interval q3_between-9 scalar the number of colvars that have a value that lies in a particular interval q3_between-10 scalar the number of colvars that have a value that lies in a particular interval q3_between-11 scalar the number of colvars that have a value that lies in a particular interval q3_between-12 scalar the number of colvars that have a value that lies in a particular interval q3_between-13 scalar the number of colvars that have a value that lies in a particular interval q3_between-14 scalar the number of colvars that have a value that lies in a particular interval q3_between-15 scalar the number of colvars that have a value that lies in a particular interval q3_between-16 scalar the number of colvars that have a value that lies in a particular interval q3_between-17 scalar the number of colvars that have a value that lies in a particular interval q3_between-18 scalar the number of colvars that have a value that lies in a particular interval q3_between-19 scalar the number of colvars that have a value that lies in a particular interval q3_between-20 scalar the number of colvars that have a value that lies in a particular interval : 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=1-64 q3_matThe CONTACT_MATRIX action with label q3_mat calculates the following quantities:
Quantity Type Description q3_grp atoms indices of atoms specified in GROUP : CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-64 R_0The r_0 parameter of the switching function=0.2 D_0 The d_0 parameter of the switching function=1.3 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0 COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix q3_shThe SPHERICAL_HARMONIC action with label q3_sh calculates the following quantities:
Quantity Type Description q3_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms q3_mat.x matrix the projection of the bond on the x axis q3_mat.y matrix the projection of the bond on the y axis q3_mat.z matrix the projection of the bond on the z axis : SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q3_mat.x,q3_mat.y,q3_mat.z,q3_mat.w Lthe value of the angular momentum=3 q3_denom_onesThe CONSTANT action with label q3_denom_ones calculates the following quantities:
Quantity Type Description q3_sh.rm-n3 matrix the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities q3_sh.rm-n2 matrix the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities q3_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities q3_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities q3_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities q3_sh.rm-p2 matrix the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities q3_sh.rm-p3 matrix the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities q3_sh.im-n3 matrix the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities q3_sh.im-n2 matrix the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities q3_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities q3_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities q3_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities q3_sh.im-p2 matrix the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities q3_sh.im-p3 matrix the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities : ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64 q3_denomThe MATRIX_VECTOR_PRODUCT action with label q3_denom calculates the following quantities:
Quantity Type Description q3_denom_ones vector the constant value that was read from the plumed input : MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q3_mat.w,q3_denom_ones q3_spThe MATRIX_VECTOR_PRODUCT action with label q3_sp calculates the following quantities:
Quantity Type Description q3_denom vector the vector that is obtained by taking the product between the matrix and the vector that were input : MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q3_sh.*,q3_denom_ones q3_norm2The COMBINE action with label q3_norm2 calculates the following quantities:
Quantity Type Description q3_sp.rm-n3 vector the product of the matrix q3_sh.rm-n3 and the vector q3_denom_ones q3_sp.rm-n2 vector the product of the matrix q3_sh.rm-n2 and the vector q3_denom_ones q3_sp.rm-n1 vector the product of the matrix q3_sh.rm-n1 and the vector q3_denom_ones q3_sp.rm-0 vector the product of the matrix q3_sh.rm-0 and the vector q3_denom_ones q3_sp.rm-p1 vector the product of the matrix q3_sh.rm-p1 and the vector q3_denom_ones q3_sp.rm-p2 vector the product of the matrix q3_sh.rm-p2 and the vector q3_denom_ones q3_sp.rm-p3 vector the product of the matrix q3_sh.rm-p3 and the vector q3_denom_ones q3_sp.im-n3 vector the product of the matrix q3_sh.im-n3 and the vector q3_denom_ones q3_sp.im-n2 vector the product of the matrix q3_sh.im-n2 and the vector q3_denom_ones q3_sp.im-n1 vector the product of the matrix q3_sh.im-n1 and the vector q3_denom_ones q3_sp.im-0 vector the product of the matrix q3_sh.im-0 and the vector q3_denom_ones q3_sp.im-p1 vector the product of the matrix q3_sh.im-p1 and the vector q3_denom_ones q3_sp.im-p2 vector the product of the matrix q3_sh.im-p2 and the vector q3_denom_ones q3_sp.im-p3 vector the product of the matrix q3_sh.im-p3 and the vector q3_denom_ones : COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif 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 ARGthe values input to this function=q3_sp.rm-n3,q3_sp.im-n3,q3_sp.rm-n2,q3_sp.im-n2,q3_sp.rm-n1,q3_sp.im-n1,q3_sp.rm-0,q3_sp.im-0,q3_sp.rm-p1,q3_sp.im-p1,q3_sp.rm-p2,q3_sp.im-p2,q3_sp.rm-p3,q3_sp.im-p3 q3_normThe CUSTOM action with label q3_norm calculates the following quantities:
Quantity Type Description q3_norm2 vector the vector obtained by doing an element-wise application of a linear combination to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3The CUSTOM action with label q3 calculates the following quantities:
Quantity Type Description q3_norm vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_norm,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt1The BETWEEN action with label q3_bt1 calculates the following quantities:
Quantity Type Description q3 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0 UPPER=0.05 SMEAR=0.1} q3_between-1The SUM action with label q3_between-1 calculates the following quantities:
Quantity Type Description q3_bt1 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt2The BETWEEN action with label q3_bt2 calculates the following quantities:
Quantity Type Description q3_between-1 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.05 UPPER=0.1 SMEAR=0.1} q3_between-2The SUM action with label q3_between-2 calculates the following quantities:
Quantity Type Description q3_bt2 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt3The BETWEEN action with label q3_bt3 calculates the following quantities:
Quantity Type Description q3_between-2 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.1 UPPER=0.15 SMEAR=0.1} q3_between-3The SUM action with label q3_between-3 calculates the following quantities:
Quantity Type Description q3_bt3 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt4The BETWEEN action with label q3_bt4 calculates the following quantities:
Quantity Type Description q3_between-3 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.15 UPPER=0.2 SMEAR=0.1} q3_between-4The SUM action with label q3_between-4 calculates the following quantities:
Quantity Type Description q3_bt4 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt5The BETWEEN action with label q3_bt5 calculates the following quantities:
Quantity Type Description q3_between-4 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.2 UPPER=0.25 SMEAR=0.1} q3_between-5The SUM action with label q3_between-5 calculates the following quantities:
Quantity Type Description q3_bt5 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt6The BETWEEN action with label q3_bt6 calculates the following quantities:
Quantity Type Description q3_between-5 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.25 UPPER=0.3 SMEAR=0.1} q3_between-6The SUM action with label q3_between-6 calculates the following quantities:
Quantity Type Description q3_bt6 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt7The BETWEEN action with label q3_bt7 calculates the following quantities:
Quantity Type Description q3_between-6 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.3 UPPER=0.35 SMEAR=0.1} q3_between-7The SUM action with label q3_between-7 calculates the following quantities:
Quantity Type Description q3_bt7 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt7 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt8The BETWEEN action with label q3_bt8 calculates the following quantities:
Quantity Type Description q3_between-7 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.35 UPPER=0.4 SMEAR=0.1} q3_between-8The SUM action with label q3_between-8 calculates the following quantities:
Quantity Type Description q3_bt8 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt8 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt9The BETWEEN action with label q3_bt9 calculates the following quantities:
Quantity Type Description q3_between-8 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.4 UPPER=0.45 SMEAR=0.1} q3_between-9The SUM action with label q3_between-9 calculates the following quantities:
Quantity Type Description q3_bt9 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt9 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt10The BETWEEN action with label q3_bt10 calculates the following quantities:
Quantity Type Description q3_between-9 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.45 UPPER=0.5 SMEAR=0.1} q3_between-10The SUM action with label q3_between-10 calculates the following quantities:
Quantity Type Description q3_bt10 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt10 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt11The BETWEEN action with label q3_bt11 calculates the following quantities:
Quantity Type Description q3_between-10 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.5 UPPER=0.55 SMEAR=0.1} q3_between-11The SUM action with label q3_between-11 calculates the following quantities:
Quantity Type Description q3_bt11 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt11 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt12The BETWEEN action with label q3_bt12 calculates the following quantities:
Quantity Type Description q3_between-11 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.55 UPPER=0.6 SMEAR=0.1} q3_between-12The SUM action with label q3_between-12 calculates the following quantities:
Quantity Type Description q3_bt12 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt12 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt13The BETWEEN action with label q3_bt13 calculates the following quantities:
Quantity Type Description q3_between-12 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.6 UPPER=0.65 SMEAR=0.1} q3_between-13The SUM action with label q3_between-13 calculates the following quantities:
Quantity Type Description q3_bt13 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt13 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt14The BETWEEN action with label q3_bt14 calculates the following quantities:
Quantity Type Description q3_between-13 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.65 UPPER=0.7 SMEAR=0.1} q3_between-14The SUM action with label q3_between-14 calculates the following quantities:
Quantity Type Description q3_bt14 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt14 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt15The BETWEEN action with label q3_bt15 calculates the following quantities:
Quantity Type Description q3_between-14 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.7 UPPER=0.75 SMEAR=0.1} q3_between-15The SUM action with label q3_between-15 calculates the following quantities:
Quantity Type Description q3_bt15 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt15 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt16The BETWEEN action with label q3_bt16 calculates the following quantities:
Quantity Type Description q3_between-15 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.75 UPPER=0.8 SMEAR=0.1} q3_between-16The SUM action with label q3_between-16 calculates the following quantities:
Quantity Type Description q3_bt16 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt16 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt17The BETWEEN action with label q3_bt17 calculates the following quantities:
Quantity Type Description q3_between-16 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.8 UPPER=0.85 SMEAR=0.1} q3_between-17The SUM action with label q3_between-17 calculates the following quantities:
Quantity Type Description q3_bt17 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt17 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt18The BETWEEN action with label q3_bt18 calculates the following quantities:
Quantity Type Description q3_between-17 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.85 UPPER=0.9 SMEAR=0.1} q3_between-18The SUM action with label q3_between-18 calculates the following quantities:
Quantity Type Description q3_bt18 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt18 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt19The BETWEEN action with label q3_bt19 calculates the following quantities:
Quantity Type Description q3_between-18 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.9 UPPER=0.95 SMEAR=0.1} q3_between-19The SUM action with label q3_between-19 calculates the following quantities:
Quantity Type Description q3_bt19 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt19 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_bt20The BETWEEN action with label q3_bt20 calculates the following quantities:
Quantity Type Description q3_between-19 scalar the SUM of the elements in the input value : BETWEENUse a switching function to determine how many of the input variables are within a certain range. More details ARGthe values input to this function=q3 SWITCHThis keyword is used if you want to employ an alternative to the continuous function defined above={GAUSSIAN LOWER=0.95 UPPER=1 SMEAR=0.1} q3_between-20The SUM action with label q3_between-20 calculates the following quantities:
Quantity Type Description q3_bt20 vector the vector obtained by doing an element-wise application of a function that is one if the input falls within a particular range and zero otherwise to the input vectors : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_bt20 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=q3.* FILEthe name of the file on which to output these quantities=colvar
Quantity Type Description q3_between-20 scalar the SUM of the elements in the input value
The following example illustrates how you can use VSUM to calculate a global vector of values as follows:
where the sum runs over all the atoms. You can then take these values and compute the following norm:
The VMEAN command that is also used in the input below performs a similar operations. The only difference is that we divide the sums in the first expression above by the number of atoms.
Click on the labels of the actions for more information on what each action computes
q3The Q3 action with label q3 calculates the following quantities:: Q3Calculate 3rd order Steinhardt parameters. This action is a shortcut and it has hidden defaults. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-64 D_0 The d_0 parameter of the switching function=1.3 R_0The r_0 parameter of the switching function=0.2 VMEAN calculate the norm of the mean vector VSUM calculate the norm of the sum of all the vectors q3: Q3Calculate 3rd order Steinhardt parameters. This action is a shortcut and uses the defaults shown here. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-64 D_0 The d_0 parameter of the switching function=1.3 R_0The r_0 parameter of the switching function=0.2 VMEAN calculate the norm of the mean vector VSUM calculate the norm of the sum of all the vectors NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0 # PLUMED interprets the command: # q3: Q3 SPECIES=1-64 D_0=1.3 R_0=0.2 VMEAN VSUM # as follows (Click the red comment above to revert to the short version of the input): q3_grpThe GROUP action with label q3_grp calculates the following quantities:
Quantity Type Description q3 vector the norms of the vectors of spherical harmonic coefficients : 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=1-64 q3_matThe CONTACT_MATRIX action with label q3_mat calculates the following quantities:
Quantity Type Description q3_grp atoms indices of atoms specified in GROUP : CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-64 R_0The r_0 parameter of the switching function=0.2 D_0 The d_0 parameter of the switching function=1.3 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0 COMPONENTS also calculate the components of the vector connecting the atoms in the contact matrix q3_shThe SPHERICAL_HARMONIC action with label q3_sh calculates the following quantities:
Quantity Type Description q3_mat.w matrix a matrix containing the weights for the bonds between each pair of atoms q3_mat.x matrix the projection of the bond on the x axis q3_mat.y matrix the projection of the bond on the y axis q3_mat.z matrix the projection of the bond on the z axis : SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q3_mat.x,q3_mat.y,q3_mat.z,q3_mat.w Lthe value of the angular momentum=3 q3_denom_onesThe CONSTANT action with label q3_denom_ones calculates the following quantities:
Quantity Type Description q3_sh.rm-n3 matrix the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities q3_sh.rm-n2 matrix the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities q3_sh.rm-n1 matrix the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities q3_sh.rm-0 matrix the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities q3_sh.rm-p1 matrix the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities q3_sh.rm-p2 matrix the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities q3_sh.rm-p3 matrix the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities q3_sh.im-n3 matrix the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities q3_sh.im-n2 matrix the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities q3_sh.im-n1 matrix the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities q3_sh.im-0 matrix the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities q3_sh.im-p1 matrix the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities q3_sh.im-p2 matrix the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities q3_sh.im-p3 matrix the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities : ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=64 q3_denomThe MATRIX_VECTOR_PRODUCT action with label q3_denom calculates the following quantities:
Quantity Type Description q3_denom_ones vector the constant value that was read from the plumed input : MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q3_mat.w,q3_denom_ones q3_spThe MATRIX_VECTOR_PRODUCT action with label q3_sp calculates the following quantities:
Quantity Type Description q3_denom vector the vector that is obtained by taking the product between the matrix and the vector that were input : MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q3_sh.*,q3_denom_ones q3_rmn-n3The CUSTOM action with label q3_rmn-n3 calculates the following quantities:
Quantity Type Description q3_sp.rm-n3 vector the product of the matrix q3_sh.rm-n3 and the vector q3_denom_ones q3_sp.rm-n2 vector the product of the matrix q3_sh.rm-n2 and the vector q3_denom_ones q3_sp.rm-n1 vector the product of the matrix q3_sh.rm-n1 and the vector q3_denom_ones q3_sp.rm-0 vector the product of the matrix q3_sh.rm-0 and the vector q3_denom_ones q3_sp.rm-p1 vector the product of the matrix q3_sh.rm-p1 and the vector q3_denom_ones q3_sp.rm-p2 vector the product of the matrix q3_sh.rm-p2 and the vector q3_denom_ones q3_sp.rm-p3 vector the product of the matrix q3_sh.rm-p3 and the vector q3_denom_ones q3_sp.im-n3 vector the product of the matrix q3_sh.im-n3 and the vector q3_denom_ones q3_sp.im-n2 vector the product of the matrix q3_sh.im-n2 and the vector q3_denom_ones q3_sp.im-n1 vector the product of the matrix q3_sh.im-n1 and the vector q3_denom_ones q3_sp.im-0 vector the product of the matrix q3_sh.im-0 and the vector q3_denom_ones q3_sp.im-p1 vector the product of the matrix q3_sh.im-p1 and the vector q3_denom_ones q3_sp.im-p2 vector the product of the matrix q3_sh.im-p2 and the vector q3_denom_ones q3_sp.im-p3 vector the product of the matrix q3_sh.im-p3 and the vector q3_denom_ones : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_sp.rm-n3,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_imn-n3The CUSTOM action with label q3_imn-n3 calculates the following quantities:
Quantity Type Description q3_rmn-n3 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_sp.im-n3,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rmn-n2The CUSTOM action with label q3_rmn-n2 calculates the following quantities:
Quantity Type Description q3_imn-n3 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_sp.rm-n2,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_imn-n2The CUSTOM action with label q3_imn-n2 calculates the following quantities:
Quantity Type Description q3_rmn-n2 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_sp.im-n2,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rmn-n1The CUSTOM action with label q3_rmn-n1 calculates the following quantities:
Quantity Type Description q3_imn-n2 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_sp.rm-n1,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_imn-n1The CUSTOM action with label q3_imn-n1 calculates the following quantities:
Quantity Type Description q3_rmn-n1 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_sp.im-n1,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rmn-0The CUSTOM action with label q3_rmn-0 calculates the following quantities:
Quantity Type Description q3_imn-n1 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_sp.rm-0,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_imn-0The CUSTOM action with label q3_imn-0 calculates the following quantities:
Quantity Type Description q3_rmn-0 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_sp.im-0,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rmn-p1The CUSTOM action with label q3_rmn-p1 calculates the following quantities:
Quantity Type Description q3_imn-0 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_sp.rm-p1,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_imn-p1The CUSTOM action with label q3_imn-p1 calculates the following quantities:
Quantity Type Description q3_rmn-p1 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_sp.im-p1,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rmn-p2The CUSTOM action with label q3_rmn-p2 calculates the following quantities:
Quantity Type Description q3_imn-p1 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_sp.rm-p2,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_imn-p2The CUSTOM action with label q3_imn-p2 calculates the following quantities:
Quantity Type Description q3_rmn-p2 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_sp.im-p2,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rmn-p3The CUSTOM action with label q3_rmn-p3 calculates the following quantities:
Quantity Type Description q3_imn-p2 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_sp.rm-p3,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_imn-p3The CUSTOM action with label q3_imn-p3 calculates the following quantities:
Quantity Type Description q3_rmn-p3 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_sp.im-p3,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rms-n3The MEAN action with label q3_rms-n3 calculates the following quantities:
Quantity Type Description q3_imn-p3 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_rmn-n3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_ims-n3The MEAN action with label q3_ims-n3 calculates the following quantities:
Quantity Type Description q3_rms-n3 scalar the MEAN of the elements in the input value : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_imn-n3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rms-n2The MEAN action with label q3_rms-n2 calculates the following quantities:
Quantity Type Description q3_ims-n3 scalar the MEAN of the elements in the input value : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_rmn-n2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_ims-n2The MEAN action with label q3_ims-n2 calculates the following quantities:
Quantity Type Description q3_rms-n2 scalar the MEAN of the elements in the input value : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_imn-n2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rms-n1The MEAN action with label q3_rms-n1 calculates the following quantities:
Quantity Type Description q3_ims-n2 scalar the MEAN of the elements in the input value : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_rmn-n1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_ims-n1The MEAN action with label q3_ims-n1 calculates the following quantities:
Quantity Type Description q3_rms-n1 scalar the MEAN of the elements in the input value : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_imn-n1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rms-0The MEAN action with label q3_rms-0 calculates the following quantities:
Quantity Type Description q3_ims-n1 scalar the MEAN of the elements in the input value : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_rmn-0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_ims-0The MEAN action with label q3_ims-0 calculates the following quantities:
Quantity Type Description q3_rms-0 scalar the MEAN of the elements in the input value : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_imn-0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rms-p1The MEAN action with label q3_rms-p1 calculates the following quantities:
Quantity Type Description q3_ims-0 scalar the MEAN of the elements in the input value : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_rmn-p1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_ims-p1The MEAN action with label q3_ims-p1 calculates the following quantities:
Quantity Type Description q3_rms-p1 scalar the MEAN of the elements in the input value : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_imn-p1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rms-p2The MEAN action with label q3_rms-p2 calculates the following quantities:
Quantity Type Description q3_ims-p1 scalar the MEAN of the elements in the input value : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_rmn-p2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_ims-p2The MEAN action with label q3_ims-p2 calculates the following quantities:
Quantity Type Description q3_rms-p2 scalar the MEAN of the elements in the input value : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_imn-p2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rms-p3The MEAN action with label q3_rms-p3 calculates the following quantities:
Quantity Type Description q3_ims-p2 scalar the MEAN of the elements in the input value : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_rmn-p3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_ims-p3The MEAN action with label q3_ims-p3 calculates the following quantities:
Quantity Type Description q3_rms-p3 scalar the MEAN of the elements in the input value : MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_imn-p3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_vmean2The COMBINE action with label q3_vmean2 calculates the following quantities:
Quantity Type Description q3_ims-p3 scalar the MEAN of the elements in the input value : COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif 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 ARGthe values input to this function=q3_rms-n3,q3_ims-n3,q3_rms-n2,q3_ims-n2,q3_rms-n1,q3_ims-n1,q3_rms-0,q3_ims-0,q3_rms-p1,q3_ims-p1,q3_rms-p2,q3_ims-p2,q3_rms-p3,q3_ims-p3 q3_vmeanThe CUSTOM action with label q3_vmean calculates the following quantities:
Quantity Type Description q3_vmean2 scalar a linear combination : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_vmean2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rmz-n3The SUM action with label q3_rmz-n3 calculates the following quantities:
Quantity Type Description q3_vmean scalar an arbitrary function : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_rmn-n3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_imz-n3The SUM action with label q3_imz-n3 calculates the following quantities:
Quantity Type Description q3_rmz-n3 scalar the SUM of the elements in the input value : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_imn-n3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rmz-n2The SUM action with label q3_rmz-n2 calculates the following quantities:
Quantity Type Description q3_imz-n3 scalar the SUM of the elements in the input value : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_rmn-n2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_imz-n2The SUM action with label q3_imz-n2 calculates the following quantities:
Quantity Type Description q3_rmz-n2 scalar the SUM of the elements in the input value : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_imn-n2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rmz-n1The SUM action with label q3_rmz-n1 calculates the following quantities:
Quantity Type Description q3_imz-n2 scalar the SUM of the elements in the input value : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_rmn-n1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_imz-n1The SUM action with label q3_imz-n1 calculates the following quantities:
Quantity Type Description q3_rmz-n1 scalar the SUM of the elements in the input value : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_imn-n1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rmz-0The SUM action with label q3_rmz-0 calculates the following quantities:
Quantity Type Description q3_imz-n1 scalar the SUM of the elements in the input value : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_rmn-0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_imz-0The SUM action with label q3_imz-0 calculates the following quantities:
Quantity Type Description q3_rmz-0 scalar the SUM of the elements in the input value : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_imn-0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rmz-p1The SUM action with label q3_rmz-p1 calculates the following quantities:
Quantity Type Description q3_imz-0 scalar the SUM of the elements in the input value : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_rmn-p1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_imz-p1The SUM action with label q3_imz-p1 calculates the following quantities:
Quantity Type Description q3_rmz-p1 scalar the SUM of the elements in the input value : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_imn-p1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rmz-p2The SUM action with label q3_rmz-p2 calculates the following quantities:
Quantity Type Description q3_imz-p1 scalar the SUM of the elements in the input value : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_rmn-p2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_imz-p2The SUM action with label q3_imz-p2 calculates the following quantities:
Quantity Type Description q3_rmz-p2 scalar the SUM of the elements in the input value : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_imn-p2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_rmz-p3The SUM action with label q3_rmz-p3 calculates the following quantities:
Quantity Type Description q3_imz-p2 scalar the SUM of the elements in the input value : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_rmn-p3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_imz-p3The SUM action with label q3_imz-p3 calculates the following quantities:
Quantity Type Description q3_rmz-p3 scalar the SUM of the elements in the input value : SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=q3_imn-p3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_vsum2The COMBINE action with label q3_vsum2 calculates the following quantities:
Quantity Type Description q3_imz-p3 scalar the SUM of the elements in the input value : COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif 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 ARGthe values input to this function=q3_rmz-n3,q3_imz-n3,q3_rmz-n2,q3_imz-n2,q3_rmz-n1,q3_imz-n1,q3_rmz-0,q3_imz-0,q3_rmz-p1,q3_imz-p1,q3_rmz-p2,q3_imz-p2,q3_rmz-p3,q3_imz-p3 q3_vsumThe CUSTOM action with label q3_vsum calculates the following quantities:
Quantity Type Description q3_vsum2 scalar a linear combination : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_vsum2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3_norm2The COMBINE action with label q3_norm2 calculates the following quantities:
Quantity Type Description q3_vsum scalar an arbitrary function : COMBINECalculate a polynomial combination of a set of other variables. More details PERIODICif 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 ARGthe values input to this function=q3_sp.rm-n3,q3_sp.im-n3,q3_sp.rm-n2,q3_sp.im-n2,q3_sp.rm-n1,q3_sp.im-n1,q3_sp.rm-0,q3_sp.im-0,q3_sp.rm-p1,q3_sp.im-p1,q3_sp.rm-p2,q3_sp.im-p2,q3_sp.rm-p3,q3_sp.im-p3 q3_normThe CUSTOM action with label q3_norm calculates the following quantities:
Quantity Type Description q3_norm2 vector the vector obtained by doing an element-wise application of a linear combination to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_norm2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO q3The CUSTOM action with label q3 calculates the following quantities:
Quantity Type Description q3_norm vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors : CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q3_norm,q3_denom FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=q3.* FILEthe name of the file on which to output these quantities=colvar
Quantity Type Description q3 vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors
Input
The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.
| Keyword | Type | Description |
|---|---|---|
| SPECIES | atoms | the list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments |
| SPECIESA | atoms | the list of atoms for which the symmetry function is being calculated |
| SPECIESB | atoms | the list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated |
Output components
This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.
| Name | Type | Keyword | Description |
|---|---|---|---|
| lessthan | scalar | LESS_THAN | the number of colvars that have a value less than a threshold |
| morethan | scalar | MORE_THAN | the number of colvars that have a value more than a threshold |
| altmin | scalar | ALT_MIN | the minimum value of the cv |
| min | scalar | MIN | the minimum colvar |
| max | scalar | MAX | the maximum colvar |
| between | scalar | BETWEEN | the number of colvars that have a value that lies in a particular interval |
| highest | scalar | HIGHEST | the largest of the colvars |
| lowest | scalar | LOWEST | the smallest of the colvars |
| sum | scalar | SUM | the sum of the colvars |
| mean | scalar | MEAN | the mean of the colvars |
| _vmean | scalar | VMEAN | the norm of the mean vector |
| _vsum | scalar | VSUM | the norm of the mean vector |
Full list of keywords
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| SPECIES | input | none | the list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments |
| SPECIESA | input | none | the list of atoms for which the symmetry function is being calculated |
| SPECIESB | input | none | the list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated |
| NN | compulsory | 6 | The n parameter of the switching function |
| MM | compulsory | 0 | The m parameter of the switching function; 0 implies 2*NN |
| D_0 | compulsory | 0.0 | The d_0 parameter of the switching function |
| R_0 | compulsory | none | The r_0 parameter of the switching function |
| SWITCH | optional | not used | the switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN. |
| MASK | optional | not used | the label for a vector that is used to determine which rows of the matrix are computed |
| VMEAN | optional | false | calculate the norm of the mean vector |
| VSUM | optional | false | calculate the norm of the sum of all the vectors |
| USEGPUThis keyword do not have examples | optional | false | run part of this calculation on the GPU |
deprecated keywords
The keywords in the following table can still be used with this action but have been deprecated
| Keyword | Description |
|---|---|
| LESS_THAN | calculate the number of variables that are less than a certain target value |
| MORE_THAN | calculate the number of variables that are more than a certain target value |
| ALT_MIN | calculate the minimum value |
| MIN | calculate the minimum value |
| MAX | calculate the maximum value |
| BETWEEN | calculate the number of values that are within a certain range |
| HIGHEST | this flag allows you to recover the highest of these variables |
| HISTOGRAM | calculate a discretized histogram of the distribution of values |
| LOWEST | this flag allows you to recover the lowest of these variables |
| SUM | calculate the sum of all the quantities |
| MEAN | calculate the mean of all the quantities |
| LOWMEM | Including this keyword in the input to this action makes no difference to the calculation performed it was used in older versions of PLUMED and is provided here for back compatibility only |
References
More information about how this action can be used is available in the following articles: