OPT_DUMMY

	This is part of the ves module
	It is only available if you configure PLUMED with ./configure –enable-modules=ves . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

Dummy optimizer for debugging.

This is dummy optimizer that can be used for debugging. It will not update the coefficients but can be used to monitor the gradient and Hessian for a given VES bias.

Examples

In the following input we use the OPT_DUMMY to monitor the gradient and Hessian for a given VES bias every 1 iteration.

Click on the labels of the actions for more information on what each action computes

phi: TORSION ATOMSthe four atoms involved in the torsional angle =5,7,9,15 The TORSION action with label phi calculates a single scalar value
bf1: BF_FOURIER ORDERcompulsory keyword 
The order of the basis function expansion. =5 MINIMUMcompulsory keyword 
The minimum of the interval on which the basis functions are defined. =-pi MAXIMUMcompulsory keyword 
The maximum of the interval on which the basis functions are defined. =pi The BF_FOURIER action with label bf1
ves1: VES_LINEAR_EXPANSION ...
   ARGthe input for this action is the scalar output from one or more other actions. =phi 
   BASIS_FUNCTIONScompulsory keyword 
the label of the one dimensional basis functions that should be used. =bf1 
   
   TEMPthe system temperature - this is needed if the MD code does not pass the temperature
to PLUMED. =300.0 
   GRID_BINSthe number of bins used for the grid. =100 
...The VES_LINEAR_EXPANSION action with label ves1 calculates the following quantities:

 Quantity   
 Description  
ves1.bias
the instantaneous value of the bias potential
ves1.force2
the instantaneous value of the squared force due to this bias potential.


o1: OPT_DUMMY ...
   BIAScompulsory keyword 
the label of the VES bias to be optimized =ves1 
   STRIDEcompulsory keyword 
the frequency of updating the coefficients given in the number of MD steps. =1000 
   
   MONITOR_HESSIAN( default=off ) also monitor the Hessian  
   GRADIENT_FILEthe name of output file for the gradient =gradient.data 
   GRADIENT_OUTPUThow often the gradient should be written to file. =1 
   GRADIENT_FMTspecify format for gradient file(s) (useful for decrease the number of digits in
regtests) =%12.6f 
   HESSIAN_FILEthe name of output file for the Hessian =hessian.data 
   HESSIAN_OUTPUThow often the Hessian should be written to file. =1 
   HESSIAN_FMTspecify format for hessian file(s) (useful for decrease the number of digits in regtests)
=%12.6f 
...The OPT_DUMMY action with label o1

Glossary of keywords and components

Description of components

By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Keyword	Description
gradrms	MONITOR_INSTANTANEOUS_GRADIENT	the root mean square value of the coefficient gradient. For multiple biases this component is labeled using the number of the bias as gradrms-#.
gradmax	MONITOR_INSTANTANEOUS_GRADIENT	the largest absolute value of the coefficient gradient. For multiple biases this component is labeled using the number of the bias as gradmax-#.
avergradrms	MONITOR_AVERAGE_GRADIENT	the root mean square value of the averaged coefficient gradient. For multiple biases this component is labeled using the number of the bias as gradrms-#.
avergradmax	MONITOR_AVERAGE_GRADIENT	the largest absolute value of the averaged coefficient gradient. For multiple biases this component is labeled using the number of the bias as gradmax-#.

Compulsory keywords

BIAS	the label of the VES bias to be optimized
STRIDE	the frequency of updating the coefficients given in the number of MD steps.
COEFFS_FILE	( default=coeffs.data ) the name of output file for the coefficients
COEFFS_OUTPUT	( default=100 ) how often the coefficients should be written to file. This parameter is given as the number of iterations.

Options

MONITOR_INSTANTANEOUS_GRADIENT	( default=off ) if quantities related to the instantaneous gradient should be outputted.
MULTIPLE_WALKERS	( default=off ) if optimization is to be performed using multiple walkers connected via MPI
MONITOR_AVERAGE_GRADIENT	( default=off ) if the averaged gradient should be monitored and quantities related to it should be outputted.
MONITOR_HESSIAN	( default=off ) also monitor the Hessian
COEFFS_FMT	specify format for coefficient file(s) (useful for decrease the number of digits in regtests)
COEFFS_SET_ID_PREFIX	suffix to add to the filename given in FILE to identify the bias, should only be given if a single filename is given in FILE when optimizing multiple biases.
INITIAL_COEFFS	the name(s) of file(s) with the initial coefficients
TARGETDIST_AVERAGES_FILE	the name of output file for the target distribution averages. By default it is targetdist-averages.data.
TARGETDIST_AVERAGES_OUTPUT	how often the target distribution averages should be written out to file. Note that the value is given in terms of coefficient iterations. If no value is given are the averages only written at the beginning of the optimization
BIAS_OUTPUT	how often the bias(es) should be written out to file. Note that the value is given in terms of coefficient iterations.
FES_OUTPUT	how often the FES(s) should be written out to file. Note that the value is given in terms of coefficient iterations.
FES_PROJ_OUTPUT	how often the projections of the FES(s) should be written out to file. Note that the value is given in terms of coefficient iterations.
RESTART	allows per-action setting of restart (YES/NO/AUTO)
UPDATE_FROM	Only update this action from this time
UPDATE_UNTIL	Only update this action until this time
MONITOR_AVERAGES_GRADIENT_EXP_DECAY	use an exponentially decaying averaging with a given time constant when monitoring the averaged gradient