Project ID: plumID:23.036
Source: aq/plumed.dat
Originally used with PLUMED version: 2.8.1
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
Click on the labels of the actions for more information on what each action computes
q6The Q6 action with label q6 calculates the following quantities:| Quantity | Type | Description |
| q6 | vector | the norms of the vectors of spherical harmonic coefficients |
| q6_mean | scalar | the mean of the colvars |
: Q6Calculate sixth order Steinhardt parameters. This action is a shortcut and it has hidden defaults. More details R_0The r_0 parameter of the switching function=0.33 SPECIESAthe list of atoms for which the symmetry function is being calculated=1-256 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=257-512 MEAN calculate the mean of all the quantities LOWMEM this flag does nothing and is present only to ensure back-compatibility
q6: Q6Calculate sixth order Steinhardt parameters. This action is a shortcut and uses the defaults shown here. More details R_0The r_0 parameter of the switching function=0.33 SPECIESAthe list of atoms for which the symmetry function is being calculated=1-256 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=257-512 MEAN calculate the mean of all the quantities LOWMEM this flag does nothing and is present only to ensure back-compatibility D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
# q6: Q6 R_0=0.33 SPECIESA=1-256 SPECIESB=257-512 MEAN LOWMEM
q6_grpThe GROUP action with label q6_grp calculates the following quantities:| Quantity | Type | Description |
| q6_grp | atoms | indices of atoms specified in GROUP |
: 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=1-256
q6_matThe CONTACT_MATRIX action with label q6_mat calculates the following quantities:| Quantity | Type | Description |
| q6_mat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
| q6_mat.x | matrix | the projection of the bond on the x axis |
| q6_mat.y | matrix | the projection of the bond on the y axis |
| q6_mat.z | matrix | the projection of the bond on the z axis |
: CONTACT_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=1-256 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=257-512 R_0The r_0 parameter of the switching function=0.33 D_0 The d_0 parameter of the switching function=0.0 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 vectors connecting the atoms in the contact matrix
q6_shThe SPHERICAL_HARMONIC action with label q6_sh calculates the following quantities:| Quantity | Type | Description |
| q6_sh.rm-n6 | matrix | the real parts of the spherical harmonic values with the m value given This is the n6th of these quantities |
| q6_sh.rm-n5 | matrix | the real parts of the spherical harmonic values with the m value given This is the n5th of these quantities |
| q6_sh.rm-n4 | matrix | the real parts of the spherical harmonic values with the m value given This is the n4th of these quantities |
| q6_sh.rm-n3 | matrix | the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities |
| q6_sh.rm-n2 | matrix | the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities |
| q6_sh.rm-n1 | matrix | the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities |
| q6_sh.rm-0 | matrix | the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities |
| q6_sh.rm-p1 | matrix | the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities |
| q6_sh.rm-p2 | matrix | the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities |
| q6_sh.rm-p3 | matrix | the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities |
| q6_sh.rm-p4 | matrix | the real parts of the spherical harmonic values with the m value given This is the p4th of these quantities |
| q6_sh.rm-p5 | matrix | the real parts of the spherical harmonic values with the m value given This is the p5th of these quantities |
| q6_sh.rm-p6 | matrix | the real parts of the spherical harmonic values with the m value given This is the p6th of these quantities |
| q6_sh.im-n6 | matrix | the real parts of the spherical harmonic values with the m value given This is the n6th of these quantities |
| q6_sh.im-n5 | matrix | the real parts of the spherical harmonic values with the m value given This is the n5th of these quantities |
| q6_sh.im-n4 | matrix | the real parts of the spherical harmonic values with the m value given This is the n4th of these quantities |
| q6_sh.im-n3 | matrix | the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities |
| q6_sh.im-n2 | matrix | the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities |
| q6_sh.im-n1 | matrix | the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities |
| q6_sh.im-0 | matrix | the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities |
| q6_sh.im-p1 | matrix | the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities |
| q6_sh.im-p2 | matrix | the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities |
| q6_sh.im-p3 | matrix | the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities |
| q6_sh.im-p4 | matrix | the real parts of the spherical harmonic values with the m value given This is the p4th of these quantities |
| q6_sh.im-p5 | matrix | the real parts of the spherical harmonic values with the m value given This is the p5th of these quantities |
| q6_sh.im-p6 | matrix | the real parts of the spherical harmonic values with the m value given This is the p6th of these quantities |
: SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q6_mat.x,q6_mat.y,q6_mat.z,q6_mat.w Lthe value of the angular momentum=6
q6_denom_onesThe CONSTANT action with label q6_denom_ones calculates the following quantities:| Quantity | Type | Description |
| q6_denom_ones | vector | the constant value that was read from the plumed input |
: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=256
q6_denomThe MATRIX_VECTOR_PRODUCT action with label q6_denom calculates the following quantities:| Quantity | Type | Description |
| q6_denom | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q6_mat.w,q6_denom_ones
q6_spThe MATRIX_VECTOR_PRODUCT action with label q6_sp calculates the following quantities:| Quantity | Type | Description |
| q6_sp.rm-n6 | vector | the product of the matrix q6_sh.rm-n6 and the vector q6_denom_ones |
| q6_sp.rm-n5 | vector | the product of the matrix q6_sh.rm-n5 and the vector q6_denom_ones |
| q6_sp.rm-n4 | vector | the product of the matrix q6_sh.rm-n4 and the vector q6_denom_ones |
| q6_sp.rm-n3 | vector | the product of the matrix q6_sh.rm-n3 and the vector q6_denom_ones |
| q6_sp.rm-n2 | vector | the product of the matrix q6_sh.rm-n2 and the vector q6_denom_ones |
| q6_sp.rm-n1 | vector | the product of the matrix q6_sh.rm-n1 and the vector q6_denom_ones |
| q6_sp.rm-0 | vector | the product of the matrix q6_sh.rm-0 and the vector q6_denom_ones |
| q6_sp.rm-p1 | vector | the product of the matrix q6_sh.rm-p1 and the vector q6_denom_ones |
| q6_sp.rm-p2 | vector | the product of the matrix q6_sh.rm-p2 and the vector q6_denom_ones |
| q6_sp.rm-p3 | vector | the product of the matrix q6_sh.rm-p3 and the vector q6_denom_ones |
| q6_sp.rm-p4 | vector | the product of the matrix q6_sh.rm-p4 and the vector q6_denom_ones |
| q6_sp.rm-p5 | vector | the product of the matrix q6_sh.rm-p5 and the vector q6_denom_ones |
| q6_sp.rm-p6 | vector | the product of the matrix q6_sh.rm-p6 and the vector q6_denom_ones |
| q6_sp.im-n6 | vector | the product of the matrix q6_sh.im-n6 and the vector q6_denom_ones |
| q6_sp.im-n5 | vector | the product of the matrix q6_sh.im-n5 and the vector q6_denom_ones |
| q6_sp.im-n4 | vector | the product of the matrix q6_sh.im-n4 and the vector q6_denom_ones |
| q6_sp.im-n3 | vector | the product of the matrix q6_sh.im-n3 and the vector q6_denom_ones |
| q6_sp.im-n2 | vector | the product of the matrix q6_sh.im-n2 and the vector q6_denom_ones |
| q6_sp.im-n1 | vector | the product of the matrix q6_sh.im-n1 and the vector q6_denom_ones |
| q6_sp.im-0 | vector | the product of the matrix q6_sh.im-0 and the vector q6_denom_ones |
| q6_sp.im-p1 | vector | the product of the matrix q6_sh.im-p1 and the vector q6_denom_ones |
| q6_sp.im-p2 | vector | the product of the matrix q6_sh.im-p2 and the vector q6_denom_ones |
| q6_sp.im-p3 | vector | the product of the matrix q6_sh.im-p3 and the vector q6_denom_ones |
| q6_sp.im-p4 | vector | the product of the matrix q6_sh.im-p4 and the vector q6_denom_ones |
| q6_sp.im-p5 | vector | the product of the matrix q6_sh.im-p5 and the vector q6_denom_ones |
| q6_sp.im-p6 | vector | the product of the matrix q6_sh.im-p6 and the vector q6_denom_ones |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q6_sh.*,q6_denom_ones
q6_norm2The COMBINE action with label q6_norm2 calculates the following quantities:| Quantity | Type | Description |
| q6_norm2 | vector | the vector obtained by doing an element-wise application of a linear compbination to the input vectors |
: 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=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 ARGthe values input to this function=q6_sp.rm-n6,q6_sp.im-n6,q6_sp.rm-n5,q6_sp.im-n5,q6_sp.rm-n4,q6_sp.im-n4,q6_sp.rm-n3,q6_sp.im-n3,q6_sp.rm-n2,q6_sp.im-n2,q6_sp.rm-n1,q6_sp.im-n1,q6_sp.rm-0,q6_sp.im-0,q6_sp.rm-p1,q6_sp.im-p1,q6_sp.rm-p2,q6_sp.im-p2,q6_sp.rm-p3,q6_sp.im-p3,q6_sp.rm-p4,q6_sp.im-p4,q6_sp.rm-p5,q6_sp.im-p5,q6_sp.rm-p6,q6_sp.im-p6
q6_normThe CUSTOM action with label q6_norm calculates the following quantities:| Quantity | Type | Description |
| q6_norm | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q6_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
q6The CUSTOM action with label q6 calculates the following quantities:| Quantity | Type | Description |
| q6 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q6_norm,q6_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
q6_meanThe MEAN action with label q6_mean calculates the following quantities:| Quantity | Type | Description |
| q6_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q6 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
q4The Q4 action with label q4 calculates the following quantities:| Quantity | Type | Description |
| q4 | vector | the norms of the vectors of spherical harmonic coefficients |
| q4_mean | scalar | the mean of the colvars |
: Q4Calculate fourth order Steinhardt parameters. This action is a shortcut and it has hidden defaults. More details R_0The r_0 parameter of the switching function=0.33 SPECIESAthe list of atoms for which the symmetry function is being calculated=1-256 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=257-512 MEAN calculate the mean of all the quantities LOWMEM this flag does nothing and is present only to ensure back-compatibility
q4: Q4Calculate fourth order Steinhardt parameters. This action is a shortcut and uses the defaults shown here. More details R_0The r_0 parameter of the switching function=0.33 SPECIESAthe list of atoms for which the symmetry function is being calculated=1-256 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=257-512 MEAN calculate the mean of all the quantities LOWMEM this flag does nothing and is present only to ensure back-compatibility D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
# q4: Q4 R_0=0.33 SPECIESA=1-256 SPECIESB=257-512 MEAN LOWMEM
q4_grpThe GROUP action with label q4_grp calculates the following quantities:| Quantity | Type | Description |
| q4_grp | atoms | indices of atoms specified in GROUP |
: 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=1-256
q4_matThe CONTACT_MATRIX action with label q4_mat calculates the following quantities:| Quantity | Type | Description |
| q4_mat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
| q4_mat.x | matrix | the projection of the bond on the x axis |
| q4_mat.y | matrix | the projection of the bond on the y axis |
| q4_mat.z | matrix | the projection of the bond on the z axis |
: CONTACT_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=1-256 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=257-512 R_0The r_0 parameter of the switching function=0.33 D_0 The d_0 parameter of the switching function=0.0 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 vectors connecting the atoms in the contact matrix
q4_shThe SPHERICAL_HARMONIC action with label q4_sh calculates the following quantities:| Quantity | Type | Description |
| q4_sh.rm-n4 | matrix | the real parts of the spherical harmonic values with the m value given This is the n4th of these quantities |
| q4_sh.rm-n3 | matrix | the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities |
| q4_sh.rm-n2 | matrix | the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities |
| q4_sh.rm-n1 | matrix | the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities |
| q4_sh.rm-0 | matrix | the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities |
| q4_sh.rm-p1 | matrix | the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities |
| q4_sh.rm-p2 | matrix | the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities |
| q4_sh.rm-p3 | matrix | the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities |
| q4_sh.rm-p4 | matrix | the real parts of the spherical harmonic values with the m value given This is the p4th of these quantities |
| q4_sh.im-n4 | matrix | the real parts of the spherical harmonic values with the m value given This is the n4th of these quantities |
| q4_sh.im-n3 | matrix | the real parts of the spherical harmonic values with the m value given This is the n3th of these quantities |
| q4_sh.im-n2 | matrix | the real parts of the spherical harmonic values with the m value given This is the n2th of these quantities |
| q4_sh.im-n1 | matrix | the real parts of the spherical harmonic values with the m value given This is the n1th of these quantities |
| q4_sh.im-0 | matrix | the real parts of the spherical harmonic values with the m value given This is the 0th of these quantities |
| q4_sh.im-p1 | matrix | the real parts of the spherical harmonic values with the m value given This is the p1th of these quantities |
| q4_sh.im-p2 | matrix | the real parts of the spherical harmonic values with the m value given This is the p2th of these quantities |
| q4_sh.im-p3 | matrix | the real parts of the spherical harmonic values with the m value given This is the p3th of these quantities |
| q4_sh.im-p4 | matrix | the real parts of the spherical harmonic values with the m value given This is the p4th of these quantities |
: SPHERICAL_HARMONICCalculate the values of all the spherical harmonic funtions for a particular value of l. More details ARGthe values input to this function=q4_mat.x,q4_mat.y,q4_mat.z,q4_mat.w Lthe value of the angular momentum=4
q4_denom_onesThe CONSTANT action with label q4_denom_ones calculates the following quantities:| Quantity | Type | Description |
| q4_denom_ones | vector | the constant value that was read from the plumed input |
: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=256
q4_denomThe MATRIX_VECTOR_PRODUCT action with label q4_denom calculates the following quantities:| Quantity | Type | Description |
| q4_denom | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q4_mat.w,q4_denom_ones
q4_spThe MATRIX_VECTOR_PRODUCT action with label q4_sp calculates the following quantities:| Quantity | Type | Description |
| q4_sp.rm-n4 | vector | the product of the matrix q4_sh.rm-n4 and the vector q4_denom_ones |
| q4_sp.rm-n3 | vector | the product of the matrix q4_sh.rm-n3 and the vector q4_denom_ones |
| q4_sp.rm-n2 | vector | the product of the matrix q4_sh.rm-n2 and the vector q4_denom_ones |
| q4_sp.rm-n1 | vector | the product of the matrix q4_sh.rm-n1 and the vector q4_denom_ones |
| q4_sp.rm-0 | vector | the product of the matrix q4_sh.rm-0 and the vector q4_denom_ones |
| q4_sp.rm-p1 | vector | the product of the matrix q4_sh.rm-p1 and the vector q4_denom_ones |
| q4_sp.rm-p2 | vector | the product of the matrix q4_sh.rm-p2 and the vector q4_denom_ones |
| q4_sp.rm-p3 | vector | the product of the matrix q4_sh.rm-p3 and the vector q4_denom_ones |
| q4_sp.rm-p4 | vector | the product of the matrix q4_sh.rm-p4 and the vector q4_denom_ones |
| q4_sp.im-n4 | vector | the product of the matrix q4_sh.im-n4 and the vector q4_denom_ones |
| q4_sp.im-n3 | vector | the product of the matrix q4_sh.im-n3 and the vector q4_denom_ones |
| q4_sp.im-n2 | vector | the product of the matrix q4_sh.im-n2 and the vector q4_denom_ones |
| q4_sp.im-n1 | vector | the product of the matrix q4_sh.im-n1 and the vector q4_denom_ones |
| q4_sp.im-0 | vector | the product of the matrix q4_sh.im-0 and the vector q4_denom_ones |
| q4_sp.im-p1 | vector | the product of the matrix q4_sh.im-p1 and the vector q4_denom_ones |
| q4_sp.im-p2 | vector | the product of the matrix q4_sh.im-p2 and the vector q4_denom_ones |
| q4_sp.im-p3 | vector | the product of the matrix q4_sh.im-p3 and the vector q4_denom_ones |
| q4_sp.im-p4 | vector | the product of the matrix q4_sh.im-p4 and the vector q4_denom_ones |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=q4_sh.*,q4_denom_ones
q4_norm2The COMBINE action with label q4_norm2 calculates the following quantities:| Quantity | Type | Description |
| q4_norm2 | vector | the vector obtained by doing an element-wise application of a linear compbination to the input vectors |
: 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=2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2 ARGthe values input to this function=q4_sp.rm-n4,q4_sp.im-n4,q4_sp.rm-n3,q4_sp.im-n3,q4_sp.rm-n2,q4_sp.im-n2,q4_sp.rm-n1,q4_sp.im-n1,q4_sp.rm-0,q4_sp.im-0,q4_sp.rm-p1,q4_sp.im-p1,q4_sp.rm-p2,q4_sp.im-p2,q4_sp.rm-p3,q4_sp.im-p3,q4_sp.rm-p4,q4_sp.im-p4
q4_normThe CUSTOM action with label q4_norm calculates the following quantities:| Quantity | Type | Description |
| q4_norm | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q4_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
q4The CUSTOM action with label q4 calculates the following quantities:| Quantity | Type | Description |
| q4 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=q4_norm,q4_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
q4_meanThe MEAN action with label q4_mean calculates the following quantities:| Quantity | Type | Description |
| q4_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=q4 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
eneThe ENERGY action with label ene calculates the following quantities:| Quantity | Type | Description |
| ene | scalar | the internal energy |
: ENERGYCalculate the total potential energy of the simulation box. More details
volThe VOLUME action with label vol calculates the following quantities:| Quantity | Type | Description |
| vol | scalar | the volume of simulation box |
: VOLUMECalculate the volume the simulation box. More details
COMBINECalculate a polynomial combination of a set of other variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=enthalpyThe COMBINE action with label enthalpy calculates the following quantities:| Quantity | Type | Description |
| enthalpy | scalar | a linear compbination |
ARGthe values input to this function=ene,vol
COEFFICIENTS the coefficients of the arguments in your function=1.0,0.060221409
PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... COMBINE
COMBINECalculate a polynomial combination of a set of other variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=hThe COMBINE action with label h calculates the following quantities:| Quantity | Type | Description |
| h | scalar | a linear compbination |
ARGthe values input to this function=enthalpy
POWERS the powers to which you are raising each of the arguments in your function=1
COEFFICIENTS the coefficients of the arguments in your function=0.00926
PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... COMBINE
COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details ...
SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.33 D_MAX=0.6}
SPECIESAthe list of atoms for which the symmetry function is being calculated=1-256 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=257-512
MEAN calculate the mean of all the quantities
MOMENTSthe list of moments that you would like to calculate=2
MORE_THAN1calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=4.0}
MORE_THAN2calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=5.0}
LABELa label for the action so that its output can be referenced in the input to other actions=cnThe COORDINATIONNUMBER action with label cn calculates the following quantities:| Quantity | Type | Description |
| cn | vector | the coordination numbers of the specified atoms |
| cn_morethan-1 | scalar | the number of colvars that have a value more than a threshold |
| cn_morethan-2 | scalar | the number of colvars that have a value more than a threshold |
| cn_mean | scalar | the mean of the colvars |
LOWMEM this flag does nothing and is present only to ensure back-compatibility
... COORDINATIONNUMBER
# COORDINATIONNUMBER ...
cn_grpThe GROUP action with label cn_grp calculates the following quantities:| Quantity | Type | Description |
| cn_grp | atoms | indices of atoms specified in GROUP |
: 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=1-256
cn_matThe CONTACT_MATRIX action with label cn_mat calculates the following quantities:| Quantity | Type | Description |
| cn_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: CONTACT_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=1-256 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=257-512 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 R_0=0.33 D_MAX=0.6}
cn_onesThe CONSTANT action with label cn_ones calculates the following quantities:| Quantity | Type | Description |
| cn_ones | vector | the constant value that was read from the plumed input |
: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=256
cnThe MATRIX_VECTOR_PRODUCT action with label cn calculates the following quantities:| Quantity | Type | Description |
| cn | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=cn_mat,cn_ones
cn_caverageThe MEAN action with label cn_caverage calculates the following quantities:| Quantity | Type | Description |
| cn_caverage | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=cn PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cn_diffpow-2The CUSTOM action with label cn_diffpow-2 calculates the following quantities:| Quantity | Type | Description |
| cn_diffpow-2 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cn,cn_caverage PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=(x-y)^2
cn_moment-2The MEAN action with label cn_moment-2 calculates the following quantities:| Quantity | Type | Description |
| cn_moment-2 | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=cn_diffpow-2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cn_mt1The MORE_THAN action with label cn_mt1 calculates the following quantities:| Quantity | Type | Description |
| cn_mt1 | vector | the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors |
: MORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=cn SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=4.0}
cn_morethan-1The SUM action with label cn_morethan-1 calculates the following quantities:| Quantity | Type | Description |
| cn_morethan-1 | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=cn_mt1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cn_mt2The MORE_THAN action with label cn_mt2 calculates the following quantities:| Quantity | Type | Description |
| cn_mt2 | vector | the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors |
: MORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=cn SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=5.0}
cn_morethan-2The SUM action with label cn_morethan-2 calculates the following quantities:| Quantity | Type | Description |
| cn_morethan-2 | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=cn_mt2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cn_meanThe MEAN action with label cn_mean calculates the following quantities:| Quantity | Type | Description |
| cn_mean | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=cn PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
cv1_lThe COMBINE action with label cv1_l calculates the following quantities:| Quantity | Type | Description |
| cv1_l | scalar | a linear compbination |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=q4.mean,q6.mean,cn.mean,cn.moment-2,cn.morethan-1,cn.morethan-2,h COEFFICIENTS the coefficients of the arguments in your function=0.676064,-0.720446,-1.56094,0.706886,-0.030074,-0.0025326,6.20144e-05 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cv2_lThe COMBINE action with label cv2_l calculates the following quantities:| Quantity | Type | Description |
| cv2_l | scalar | a linear compbination |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=q4.mean,q6.mean,cn.mean,cn.moment-2,cn.morethan-1,cn.morethan-2,h COEFFICIENTS the coefficients of the arguments in your function=-2.00895,1.89549,-3.15277,-0.432,0.00841427,0.0416259,-0.00289463 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cv1The MATHEVAL action with label cv1 calculates the following quantities:| Quantity | Type | Description |
| cv1 | scalar | an arbitrary function |
: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cv1_l FUNCthe function you wish to evaluate=x+2.809855 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cv2The MATHEVAL action with label cv2 calculates the following quantities:| Quantity | Type | Description |
| cv2 | scalar | an arbitrary function |
: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cv2_l FUNCthe function you wish to evaluate=x-3.756015 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
metadThe METAD action with label metad calculates the following quantities:| Quantity | Type | Description |
| metad.bias | scalar | the instantaneous value of the bias potential |
| metad.rbias | scalar | the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram. |
| metad.rct | scalar | the reweighting factor c(t). |
: METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=cv1,cv2 SIGMAthe widths of the Gaussian hills=0.15,0.24 HEIGHTthe heights of the Gaussian hills=5 PACEthe frequency for hill addition=1000 BIASFACTORuse well tempered metadynamics and use this bias factor=100 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 GRID_MINthe lower bounds for the grid=-4.5,-7 GRID_MAXthe upper bounds for the grid=3,5 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
metad: METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=cv1,cv2 SIGMAthe widths of the Gaussian hills=0.15,0.24 HEIGHTthe heights of the Gaussian hills=5 PACEthe frequency for hill addition=1000 BIASFACTORuse well tempered metadynamics and use this bias factor=100 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 GRID_MINthe lower bounds for the grid=-4.5,-7 GRID_MAXthe upper bounds for the grid=3,5 CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] FILE a file in which the list of added hills is stored=HILLS
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cv1,cv2,q4.mean,q6.mean,cn.mean,cn.moment-2,cn.morethan-1,cn.morethan-2,h,metad.bias,metad.rbias FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=100
