Shortcut: DOPS

Module	crystdistrib
Description	Usage
Calculate DOPS order parameter for molecules.
output value	type
the values of the DOPS order parameters	vector

Details and examples

Calculate DOPS order parameter for molecules.

DOPS is a shortcut to calculate the Distance Order Parameters that are described in the paper below. As arguments, DOPS takes a list of atoms, a cutoff, and a kernel file detailing the means, variances, and normalization factors of probability distributions. DOPS returns a vector of order parameters.

The DOPS kernel file has FIELDS height, mu, and sigma corresponding to the normalization factor, mean, and variance of the gaussian distributions used in the order parameters. The SET kerneltype is gaussian.

DOPS returns one order parameter per atom given, evaluated over each atom's neighbors within the cutoff given. The kernel file defines a radial distribution function. The order parameter is obtained by evaluating the RDF at each neighbor's position within the cutoff, and summing them up.

This example file calculates the DOPS for a system of 3 molecules.

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

#SETTINGS INPUTFILES=regtest/crystdistrib/rt-dops-forces/kernels.dat
dopsThe DOPS action with label dops calculates the following quantities: Quantity    Type    Description  
dops vector the values of the DOPS order parameters: DOPSCalculate DOPS order parameter for molecules. This action is a shortcut. More details SPECIESthe list of atoms for which the DOPS are being calculated and the atoms that can be in the environments=1,4,7 CUTOFF to make the calculation faster we calculate a cutoff value on the distances=7.4 KERNELFILEthe file containing the list of kernel parameters=regtest/crystdistrib/rt-dops-forces/kernels.dat Click here to see an extract from this file.
    ×  FILE: regtest/crystdistrib/rt-dops-forces/kernels.dat
    #! FIELDS height mu sigma
#! SET kerneltype gaussian
2.26628554234 6.37235632777 0.17603354605920524374
2.26598891932 6.37243472055 0.17605658924421270294
2.83246817245 6.94118069019 0.14084616529226330342
2.23141032403 6.87945090447 0.17878481429679151024
2.26563347801 6.81645001966 0.17608420968034740280
2.26829869206 6.37245683771 0.17587731359970688385
2.26856314184 6.37237895273 0.17585681131941429581
2.84313122015 6.94216988399 0.14031792749263861615
2.21827805142 6.87753705648 0.17984322576025361650
2.27474509536 6.8181064339  0.17537889463529058575
  
# PLUMED interprets the command:
# dops: DOPS SPECIES=1,4,7 CUTOFF=7.4 KERNELFILE=regtest/crystdistrib/rt-dops-forces/kernels.dat
# as follows (Click the red comment above to revert to the short version of the input):
dops_cmatThe DISTANCE_MATRIX action with label dops_cmat calculates the following quantities: Quantity    Type    Description  
dops_cmat matrix a matrix containing the weights for the bonds between each pair of atoms: DISTANCE_MATRIXCalculate a matrix of distances between atoms. More details  GROUPthe atoms for which you would like to calculate the adjacency matrix=1,4,7 CUTOFF ignore distances that have a value larger than this cutoff=34.359
dops_kvalThe CUSTOM action with label dops_kval calculates the following quantities: Quantity    Type    Description  
dops_kval matrix the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dops_cmat PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=2.26629*exp(-(x-6.37236)^2/0.0619756)+2.26599*exp(-(x-6.37243)^2/0.0619918)+2.83247*exp(-(x-6.94118)^2/0.0396753)+2.23141*exp(-(x-6.87945)^2/0.063928)+2.26563*exp(-(x-6.81645)^2/0.0620113)+2.2683*exp(-(x-6.37246)^2/0.0618657)+2.26856*exp(-(x-6.37238)^2/0.0618512)+2.84313*exp(-(x-6.94217)^2/0.0393782)+2.21828*exp(-(x-6.87754)^2/0.0646872)+2.27475*exp(-(x-6.81811)^2/0.0615155)
dops_onesThe CONSTANT action with label dops_ones calculates the following quantities: Quantity    Type    Description  
dops_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=3
dopsThe MATRIX_VECTOR_PRODUCT action with label dops calculates the following quantities: Quantity    Type    Description  
dops vector the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=dops_kval,dops_ones
# --- End of included input ---

If you want to calculate DOPS from the radial distribution function of the GROUPB atoms around the GROUPA atoms you use an input like the one shown below:

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

#SETTINGS INPUTFILES=regtest/crystdistrib/rt-dops-forces/kernels.dat
dopsThe DOPS action with label dops calculates the following quantities: Quantity    Type    Description  
dops vector the values of the DOPS order parameters: DOPSCalculate DOPS order parameter for molecules. This action is a shortcut. More details ...
  SPECIESAthe list of atoms for which DOPS are being calculated=1,4,7 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the DOPS are being calculated=10,13,16,19 CUTOFF to make the calculation faster we calculate a cutoff value on the distances=7.4
  KERNELFILEthe file containing the list of kernel parameters=regtest/crystdistrib/rt-dops-forces/kernels.dat Click here to see an extract from this file.
    ×  FILE: regtest/crystdistrib/rt-dops-forces/kernels.dat
    #! FIELDS height mu sigma
#! SET kerneltype gaussian
2.26628554234 6.37235632777 0.17603354605920524374
2.26598891932 6.37243472055 0.17605658924421270294
2.83246817245 6.94118069019 0.14084616529226330342
2.23141032403 6.87945090447 0.17878481429679151024
2.26563347801 6.81645001966 0.17608420968034740280
2.26829869206 6.37245683771 0.17587731359970688385
2.26856314184 6.37237895273 0.17585681131941429581
2.84313122015 6.94216988399 0.14031792749263861615
2.21827805142 6.87753705648 0.17984322576025361650
2.27474509536 6.8181064339  0.17537889463529058575
  
...
# PLUMED interprets the command:
# dops: DOPS ...
#   SPECIESA=1,4,7 SPECIESB=10,13,16,19 CUTOFF=7.4
#   KERNELFILE=regtest/crystdistrib/rt-dops-forces/kernels.dat
# ...
# as follows (Click the red comment above to revert to the short version of the input):
dops_cmatThe DISTANCE_MATRIX action with label dops_cmat calculates the following quantities: Quantity    Type    Description  
dops_cmat matrix a matrix containing the weights for the bonds between each pair of atoms: DISTANCE_MATRIXCalculate a matrix of distances between atoms. More details  GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=1,4,7 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=10,13,16,19 CUTOFF ignore distances that have a value larger than this cutoff=34.359
dops_kvalThe CUSTOM action with label dops_kval calculates the following quantities: Quantity    Type    Description  
dops_kval matrix the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dops_cmat PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=2.26629*exp(-(x-6.37236)^2/0.0619756)+2.26599*exp(-(x-6.37243)^2/0.0619918)+2.83247*exp(-(x-6.94118)^2/0.0396753)+2.23141*exp(-(x-6.87945)^2/0.063928)+2.26563*exp(-(x-6.81645)^2/0.0620113)+2.2683*exp(-(x-6.37246)^2/0.0618657)+2.26856*exp(-(x-6.37238)^2/0.0618512)+2.84313*exp(-(x-6.94217)^2/0.0393782)+2.21828*exp(-(x-6.87754)^2/0.0646872)+2.27475*exp(-(x-6.81811)^2/0.0615155)
dops_onesThe CONSTANT action with label dops_ones calculates the following quantities: Quantity    Type    Description  
dops_ones vector the constant value that was read from the plumed input: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=4
dopsThe MATRIX_VECTOR_PRODUCT action with label dops calculates the following quantities: Quantity    Type    Description  
dops vector the vector that is obtained by taking the product between the matrix and the vector that were input: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=dops_kval,dops_ones
# --- End of included input ---

Input

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

Keyword	Type	Description
SPECIES	atoms	the list of atoms for which the DOPS are being calculated and the atoms that can be in the environments
SPECIESA	atoms	the list of atoms for which DOPS are being calculated
SPECIESB	atoms	the list of atoms that can be in the environments of each of the atoms for which the DOPS are being calculated

Full list of keywords

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

Keyword	Type	Default	Description
SPECIES	input	none	the list of atoms for which the DOPS are being calculated and the atoms that can be in the environments
SPECIESA	input	none	the list of atoms for which DOPS are being calculated
SPECIESB	input	none	the list of atoms that can be in the environments of each of the atoms for which the DOPS are being calculated
KERNELFILE	compulsory	none	the file containing the list of kernel parameters
CUTOFF	compulsory	6.25	to make the calculation faster we calculate a cutoff value on the distances

References

More information about how this action can be used is available in the following articles:

E. E. Santiso, B. L. Trout, A general set of order parameters for molecular crystals. The Journal of Chemical Physics. 134 (2011)

Quantity	Type	Description
dops	vector	the values of the DOPS order parameters