Action: DUMPDERIVATIVES

Module	generic
Description	Usage
Dump the derivatives with respect to the input parameters for scalar values (generally CVs, functions or biases).
This action outputs data to a file. You can read more about how PLUMED manages output files here

Details and examples

Dump the derivatives with respect to the input parameters for scalar values (generally CVs, functions or biases).

You can use this command to output the derivatives of a scalar with respect to whatever input parameters are used to calculate that scalar. For example, the following input instructs plumed to write a file called deriv that contains both the analytical and numerical derivatives of the distance between atoms 1 and 2.

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

distanceThe DISTANCE action with label distance calculates the following quantities: Quantity    Type    Description  
distance scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
distanceNThe DISTANCE action with label distanceN calculates the following quantities: Quantity    Type    Description  
distanceN scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 NUMERICAL_DERIVATIVES calculate the derivatives for these quantities numerically
DUMPDERIVATIVESDump the derivatives with respect to the input parameters for scalar values (generally CVs, functions or biases). More details ARGthe labels of the values whose derivatives should be output=distance,distanceN STRIDE the frequency with which the derivatives should be output=1 FILEthe name of the file on which to output the derivatives=deriv

This input outputs the derivative of the distance with respect to the atom positions and the cell vectors (virial-like form). It will thus output 15 deriatives for the two quantities output - the derivatives with respect to the x,y and z components of the input atoms and the 9 components of the virial.

By contast the following input will only output 1 derivative; namely, the derivative of the switching function, f, with respect to the input distance, d.

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

dThe DISTANCE action with label d calculates the following quantities: Quantity    Type    Description  
d scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
fThe LESS_THAN action with label f calculates the following quantities: Quantity    Type    Description  
f scalar a function that is one if the input is less than a threshold: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=d SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.2}
DUMPDERIVATIVESDump the derivatives with respect to the input parameters for scalar values (generally CVs, functions or biases). More details ARGthe labels of the values whose derivatives should be output=f STRIDE the frequency with which the derivatives should be output=1 FMT the format with which the derivatives should be output=%8.4f FILEthe name of the file on which to output the derivatives=deriv

You can only use this command to output the derivatives of rank 0 (scalar) values. You cannot use it to output derivatives of vector, matrix of function values.

RESTART, UPDATE_FROM and UPDATE_UNTIL

Notice that the RESTART, UPDATE_FROM and UPDATE_UNTIL keywords keywords can be used in this action in the same way as they are used for PRINT. Consequently, if you would like to append derivatives to an existing file called deriv instead of backing that file up at the start of the calculation and outputting the data from the calculation on a new file called deriv you would use an input like the one shown below:

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

distanceThe DISTANCE action with label distance calculates the following quantities: Quantity    Type    Description  
distance scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
DUMPDERIVATIVESDump the derivatives with respect to the input parameters for scalar values (generally CVs, functions or biases). More details ARGthe labels of the values whose derivatives should be output=distance STRIDE the frequency with which the derivatives should be output=1 FILEthe name of the file on which to output the derivatives=deriv RESTARTallows per-action setting of restart (YES/NO/AUTO)=YES

Similarly, if you want to only output the derivatives during the 400 ps time interval after the first 100 ps of the simulation you would use an input like the one shown below:

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

distanceThe DISTANCE action with label distance calculates the following quantities: Quantity    Type    Description  
distance scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
DUMPDERIVATIVESDump the derivatives with respect to the input parameters for scalar values (generally CVs, functions or biases). More details ARGthe labels of the values whose derivatives should be output=distance STRIDE the frequency with which the derivatives should be output=1 FILEthe name of the file on which to output the derivatives=deriv UPDATE_FROMOnly update this action from this time=100 UPDATE_UNTILOnly update this action until this time=500

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 values whose derivatives should be output

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 values whose derivatives should be output
STRIDE	compulsory	1	the frequency with which the derivatives should be output
FILE	compulsory	none	the name of the file on which to output the derivatives
FMT	compulsory	%15.10f	the format with which the derivatives should be output
RESTART	optional	not used	allows per-action setting of restart (YES/NO/AUTO)
UPDATE_FROM	optional	not used	Only update this action from this time
UPDATE_UNTIL	optional	not used	Only update this action until this time

Quantity	Type	Description
distance	scalar	the DISTANCE between this pair of atoms