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Action: TTMETAD

Module ttsketch
Description Usage
Performs metadynamics with a tensor-train representation of the bias potential. used in 0 tutorialsused in 0 eggs

Details and examples

Performs metadynamics with a tensor-train representation of the bias potential.

This action runs metadynamics while periodically compressing the accumulated Gaussian hills into a low-rank tensor train (TT) using the TT-Sketch algorithm. The TT representation keeps memory and evaluation cost bounded throughout long simulations, in contrast to standard metadynamics where cost grows linearly with the number of deposited hills.

Examples

The following input runs TT-MetaD on two distances. Hills are deposited every 500 steps and compressed into a TT every 1e6 steps with target rank 10.

Click on the labels of the actions for more information on what each action computes
tested on2.11
d1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
d2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,4
TTMETADPerforms metadynamics with a tensor-train representation of the bias potential. This action has hidden defaults. More details ...
  ARGthe labels of the scalars on which the bias will act=d1,d2
  SIGMAthe widths of the Gaussian hills=0.1,0.1
  HEIGHTthe heights of the Gaussian hills=1.0
  PACEthe frequency for hill addition=500
  SKETCH_PACE The frequency for TT Vbias updates=1000000
  SKETCH_RANKTarget rank for TTSketch algorithm - compulsory if SKETCH_CUTOFF is not specified=10
  SKETCH_INITRANKInitial rank for TTSketch algorithm=50
  INTERVAL_MINLower limits, outside the limits the system will not feel the biasing force=0.0,0.0
  INTERVAL_MAXUpper limits, outside the limits the system will not feel the biasing force=3.0,3.0
  FILE a file in which the list of added hills is stored=HILLS
  LABELa label for the action so that its output can be referenced in the input to other actions=tt
... TTMETAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=tt.bias 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

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword Type Description
ARG scalar the labels of the scalars on which the bias will act

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword Type Default Description
ARG input none the labels of the scalars on which the bias will act
SIGMA compulsory none the widths of the Gaussian hills
PACE compulsory none the frequency for hill addition
FILE compulsory HILLS a file in which the list of added hills is stored
HEIGHT compulsory none the heights of the Gaussian hills
SKETCH_INITRANK compulsory none Initial rank for TTSketch algorithm
SKETCH_PACE compulsory 1e6 The frequency for TT Vbias updates
INTERVAL_MIN compulsory none Lower limits, outside the limits the system will not feel the biasing force
INTERVAL_MAX compulsory none Upper limits, outside the limits the system will not feel the biasing force
SKETCH_NBASIS compulsory 20 Number of basis functions per dimension
SKETCH_ALPHA compulsory 0.05 Weight coefficient for random tensor train construction
NUMERICAL_DERIVATIVESThis keyword do not have examples optional false calculate the derivatives for these quantities numerically
KERNEL_BASISThis keyword do not have examples optional false Specifies that local kernel basis should be used instead of Fourier basis
FMTThis keyword do not have examples optional not used specify format for HILLS files (useful for decrease the number of digits in regtests)
BIASFACTORThis keyword do not have examples optional not used use well tempered metadynamics and use this bias factor
TEMPThis keyword do not have examples optional not used the system temperature - this is only needed if you are doing well-tempered metadynamics
WALKERS_MPIThis keyword do not have examples optional false To be used when gromacs + multiple walkers are used
WALKERS_DIRThis keyword do not have examples optional not used shared directory with the hills files from all the walkers
RESTARTThis keyword do not have examples optional not used allows per-action setting of restart (YES/NO/AUTO)
SKETCH_RANK optional not used Target rank for TTSketch algorithm - compulsory if SKETCH_CUTOFF is not specified
SKETCH_CUTOFFThis keyword do not have examples optional not used Truncation error cutoff for singular value decomposition - compulsory if SKETCH_RANK is not specified
SKETCH_UNTILThis keyword do not have examples optional not used After this time, the bias potential freezes
SKETCH_WIDTHThis keyword do not have examples optional not used Width of Gaussian kernels for smoothing
KERNEL_DXThis keyword do not have examples optional not used Width of basis function kernels
NONINTRUSIVEThis keyword do not have examples optional false Sketching uses previous exact sum of Gaussians instead of TT approximation
DETERMINISTICThis keyword do not have examples optional false Use a fixed random seed for TT sketch construction, ensuring reproducible results