Project ID: plumID:19.052
Source: plumed.dat
Originally used with PLUMED version: not specified
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
UNITSThis command sets the internal units for the code. More details NATURAL use natural units
The UNITS action with label calculates somethingcellThe CELL action with label cell calculates the following quantities:| Quantity | Type | Description |
| cell.ax | scalar | the ax component of the cell matrix |
| cell.ay | scalar | the ay component of the cell matrix |
| cell.az | scalar | the az component of the cell matrix |
| cell.bx | scalar | the bx component of the cell matrix |
| cell.by | scalar | the by component of the cell matrix |
| cell.bz | scalar | the bz component of the cell matrix |
| cell.cx | scalar | the cx component of the cell matrix |
| cell.cy | scalar | the cy component of the cell matrix |
| cell.cz | scalar | the cz component of the cell matrix |
: CELLGet the components of the simulation cell More details
cubThe FCCUBIC action with label cub calculates the following quantities:| Quantity | Type | Description |
| cub | vector | the symmetry function for each of the specified atoms |
| cub_morethan-1 | scalar | the number of colvars that have a value more than a threshold |
| cub_mean | scalar | the mean of the colvars |
: FCCUBICMeasure how similar the environment around atoms is to that found in a FCC structure. 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=2-23329 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.={CUBIC D_0=1.2 D_MAX=1.5} ALPHA The alpha parameter of the angular function that is used for FCCUBIC=27 MEAN calculate the mean of all the quantities 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.={SMAP R_0=0.45 D_0=0.0 A=8 B=8}
cub: FCCUBICMeasure how similar the environment around atoms is to that found in a FCC structure. 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=2-23329 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.={CUBIC D_0=1.2 D_MAX=1.5} ALPHA The alpha parameter of the angular function that is used for FCCUBIC=27 MEAN calculate the mean of all the quantities 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.={SMAP R_0=0.45 D_0=0.0 A=8 B=8} PHI The Euler rotational angle phi=0.0 THETA The Euler rotational angle theta=0.0 PSI The Euler rotational angle psi=0.0
# cub: FCCUBIC SPECIES=2-23329 SWITCH={CUBIC D_0=1.2 D_MAX=1.5} ALPHA=27 MEAN MORE_THAN1={SMAP R_0=0.45 D_0=0.0 A=8 B=8}
cub_grpThe GROUP action with label cub_grp calculates the following quantities:| Quantity | Type | Description |
| cub_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=2-23329
cub_matThe CONTACT_MATRIX action with label cub_mat calculates the following quantities:| Quantity | Type | Description |
| cub_mat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
| cub_mat.x | matrix | the projection of the bond on the x axis |
| cub_mat.y | matrix | the projection of the bond on the y axis |
| cub_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 GROUPspecifies the list of atoms that should be assumed indistinguishable=2-23329 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.={CUBIC D_0=1.2 D_MAX=1.5} COMPONENTS also calculate the components of the vectors connecting the atoms in the contact matrix
cub_vfuncThe FCCUBIC_FUNC action with label cub_vfunc calculates the following quantities:| Quantity | Type | Description |
| cub_vfunc | matrix | the matrix obtained by doing an element-wise application of a function that measures the similarity with an fcc environment to the input matrix |
: FCCUBIC_FUNCMeasure how similar the environment around atoms is to that found in a FCC structure. More details ARGthe values input to this function=cub_mat.x,cub_mat.y,cub_mat.z ALPHA The alpha parameter of the angular function=27
cub_wvfuncThe CUSTOM action with label cub_wvfunc calculates the following quantities:| Quantity | Type | Description |
| cub_wvfunc | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cub_vfunc,cub_mat.w 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
cub_onesThe CONSTANT action with label cub_ones calculates the following quantities:| Quantity | Type | Description |
| cub_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=23328
cubThe MATRIX_VECTOR_PRODUCT action with label cub calculates the following quantities:| Quantity | Type | Description |
| cub | 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=cub_wvfunc,cub_ones
cub_denomThe MATRIX_VECTOR_PRODUCT action with label cub_denom calculates the following quantities:| Quantity | Type | Description |
| cub_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=cub_mat.w,cub_ones
cub_nThe CUSTOM action with label cub_n calculates the following quantities:| Quantity | Type | Description |
| cub_n | 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=cub,cub_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
cub_mt1The MORE_THAN action with label cub_mt1 calculates the following quantities:| Quantity | Type | Description |
| cub_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=cub_n SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={SMAP R_0=0.45 D_0=0.0 A=8 B=8}
cub_morethan-1The SUM action with label cub_morethan-1 calculates the following quantities:| Quantity | Type | Description |
| cub_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=cub_mt1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cub_meanThe MEAN action with label cub_mean calculates the following quantities:| Quantity | Type | Description |
| cub_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=cub_n PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
metadThe METAD action with label metad calculates the following quantities:| Quantity | Type | Description |
| metad.bias | scalar | the instantaneous value of the bias potential |
: METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=cub.morethan-1
PACEthe frequency for hill addition=1000 HEIGHTthe heights of the Gaussian hills=0.3 SIGMAthe widths of the Gaussian hills=600 FILE a file in which the list of added hills is stored=HILLS TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=0.58 BIASFACTORuse well tempered metadynamics and use this bias factor=400
ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=300 SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.1
...
fixmaxThe UPPER_WALLS action with label fixmax calculates the following quantities:| Quantity | Type | Description |
| fixmax.bias | scalar | the instantaneous value of the bias potential |
| fixmax.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cub.morethan-1 ATthe positions of the wall=2500 KAPPAthe force constant for the wall=0.1
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=10 ARGthe labels of the values that you would like to print to the file=cell.ax,cub.*,metad.bias,fixmax.bias FILEthe name of the file on which to output these quantities=COLVAR
ENDPLUMEDTerminate plumed input. More details
