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.
In the following input we use the OPT_DUMMY to monitor the gradient and Hessian for a given VES bias every 1 iteration.
phi: TORSIONATOMS=5,7,9,15 bf1: BF_FOURIERthe four atoms involved in the torsional angleORDER=5compulsory keyword The order of the basis function expansion.MINIMUM=-picompulsory keyword The minimum of the interval on which the basis functions are defined.MAXIMUM=pi ves1: VES_LINEAR_EXPANSION ...compulsory keyword The maximum of the interval on which the basis functions are defined.ARG=phicompulsory keyword the labels of the scalars on which the bias will actBASIS_FUNCTIONS=bf1compulsory keyword the label of the one dimensional basis functions that should be used.TEMP=300.0the system temperature - this is needed if the MD code does not pass the temperature to PLUMED.GRID_BINS=100 ... o1: OPT_DUMMY ...the number of bins used for the grid.BIAS=ves1compulsory keyword the label of the VES bias to be optimizedSTRIDE=1000compulsory keyword the frequency of updating the coefficients given in the number of MD steps.MONITOR_HESSIAN( default=off ) also monitor the HessianGRADIENT_FILE=gradient.datathe name of output file for the gradientGRADIENT_OUTPUT=1how often the gradient should be written to file.GRADIENT_FMT=%12.6fspecify format for gradient file(s) (useful for decrease the number of digits in regtests)HESSIAN_FILE=hessian.datathe name of output file for the HessianHESSIAN_OUTPUT=1how often the Hessian should be written to file.HESSIAN_FMT=%12.6f ...specify format for hessian file(s) (useful for decrease the number of digits in regtests)
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 | Description |
.#!value | a scalar |
In addition the following quantities can be calculated by employing the keywords listed 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-#. |
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. |
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 |