Action: OPT_DUMMY

Module	ves
Description	Usage
Dummy optimizer for debugging.
output value	type
a scalar	scalar

Details and examples

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

phiThe TORSION action with label phi calculates the following quantities: Quantity    Type    Description  
phi scalar the TORSION involving these atoms:   TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,15

bf1: BF_FOURIERFourier basis functions. More details ORDERThe order of the basis function expansion=5 MINIMUMThe minimum of the interval on which the basis functions are defined=-pi MAXIMUMThe maximum of the interval on which the basis functions are defined=pi

The BF_FOURIER action with label bf1 calculates somethingVES_LINEAR_EXPANSIONLinear basis set expansion bias. This action has hidden defaults. More details ...
 ARGthe labels of the scalars on which the bias will act=phi
 BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1
 LABELa label for the action so that its output can be referenced in the input to other actions=ves1The VES_LINEAR_EXPANSION action with label ves1 calculates the following quantities: Quantity    Type    Description  
ves1.bias scalar the instantaneous value of the bias potential
ves1.force2 scalar the instantaneous value of the squared force due to this bias potential.
 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
... VES_LINEAR_EXPANSION
VES_LINEAR_EXPANSIONLinear basis set expansion bias. This action uses the defaults shown here. More details ...
 ARGthe labels of the scalars on which the bias will act=phi
 BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1
 LABELa label for the action so that its output can be referenced in the input to other actions=ves1
 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
 GRID_FMT the format to use when outputting the numbers in the grids=%14.9f
... VES_LINEAR_EXPANSION

OPT_DUMMYDummy optimizer for debugging. This action has hidden defaults. More details ...
  BIASthe label of the VES bias to be optimized=ves1
  STRIDEthe frequency of updating the coefficients given in the number of MD steps=1000
  LABELa label for the action so that its output can be referenced in the input to other actions=o1
  MONITOR_HESSIAN 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
... OPT_DUMMY
The OPT_DUMMY action with label o1 calculates the following quantities: Quantity    Description  
o1.value a scalarOPT_DUMMYDummy optimizer for debugging. This action uses the defaults shown here. More details ...
  BIASthe label of the VES bias to be optimized=ves1
  STRIDEthe frequency of updating the coefficients given in the number of MD steps=1000
  LABELa label for the action so that its output can be referenced in the input to other actions=o1
  MONITOR_HESSIAN 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
 COEFFS_FILE the name of output file for the coefficients=coeffs.data COEFFS_OUTPUT how often the coefficients should be written to file=100
... OPT_DUMMY

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
gradrms	scalar	MONITOR_INSTANTANEOUS_GRADIENT	the root mean square value of the coefficient gradient
gradmax	scalar	MONITOR_INSTANTANEOUS_GRADIENT	the largest absolute value of the coefficient gradient
avergradrms	scalar	MONITOR_AVERAGE_GRADIENT	the root mean square value of the averaged coefficient gradient
avergradmax	scalar	MONITOR_AVERAGE_GRADIENT	the largest absolute value of the averaged coefficient gradient

Full list of keywords

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

Keyword	Type	Default	Description
BIAS	compulsory	none	the label of the VES bias to be optimized
STRIDE	compulsory	none	the frequency of updating the coefficients given in the number of MD steps
COEFFS_FILE	compulsory	coeffs.data	the name of output file for the coefficients
COEFFS_OUTPUT	compulsory	100	how often the coefficients should be written to file
COEFFS_FMTThis keyword do not have examples	optional	not used	specify format for coefficient file(s) (useful for decrease the number of digits in regtests)
COEFFS_SET_ID_PREFIXThis keyword do not have examples	optional	not used	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_COEFFSThis keyword do not have examples	optional	not used	the name(s) of file(s) with the initial coefficients
MONITOR_INSTANTANEOUS_GRADIENTThis keyword do not have examples	optional	false	if quantities related to the instantaneous gradient should be outputted
TARGETDIST_AVERAGES_FILEThis keyword do not have examples	optional	not used	the name of output file for the target distribution averages
TARGETDIST_AVERAGES_OUTPUTThis keyword do not have examples	optional	not used	how often the target distribution averages should be written out to file
BIAS_OUTPUTThis keyword do not have examples	optional	not used	how often the bias(es) should be written out to file
FES_OUTPUTThis keyword do not have examples	optional	not used	how often the FES(s) should be written out to file
FES_PROJ_OUTPUTThis keyword do not have examples	optional	not used	how often the projections of the FES(s) should be written out to file
RESTARTThis keyword do not have examples	optional	not used	allows per-action setting of restart (YES/NO/AUTO)
UPDATE_FROMThis keyword do not have examples	optional	not used	Only update this action from this time
UPDATE_UNTILThis keyword do not have examples	optional	not used	Only update this action until this time
MULTIPLE_WALKERSThis keyword do not have examples	optional	false	if optimization is to be performed using multiple walkers connected via MPI
MONITOR_AVERAGE_GRADIENTThis keyword do not have examples	optional	false	if the averaged gradient should be monitored and quantities related to it should be outputted
MONITOR_AVERAGES_GRADIENT_EXP_DECAYThis keyword do not have examples	optional	not used	use an exponentially decaying averaging with a given time constant when monitoring the averaged gradient
MONITOR_HESSIAN	optional	false	also monitor the Hessian

Quantity	Type	Description
phi	scalar	the TORSION involving these atoms