fullkern (c47b2)
Full Kernel Module
VERSON 1 06.07.2020
by
Marco Pezzella
Debasish Koner
Markus Meuwly
FULLKERN provides a way to flexibly implement RKHS based potentials for small molecules
inside CHARMM. At the moment the interactions between atoms are set to zero, with the
aim of automatically setting to zero internally the intramolecular interactions.The
PSF remains unchanged.The new interactions are not explicitly added to the PSF file and
only exist for the duration of a CHARMM run. FULLKERN is called via the FLMK keyword.
References:
[1] D. Koner and M. Meuwly arXiv prepint https://arxiv.org/abs/2005.04667v2
Syntax :: Syntax of the FULLKERN module.
Description :: A brief description of the module and how it works.
Generation of the potential :: How to generate the new potential.
How to run with your potential :: Shows how to compile charmm with the desired
potential and run it.
How to to generate the coefficents :: Brief description of how to store the coefficients.
Example :: Description of the example: Acetone.
!--------------------------------Syntax--------------------------------!
FLMK { READ {UNIT (integer) NATOMS (integer) DIMSYS (integer) DIMKERN (integer)
NCOEFF (integer) ATOM1 (integer) ATOMN (integer) DATAFILE (char)} }
READ option will activate the module, reading all the parameters needed for
storing and usage of the module.
UNIT: units needed for reading the data file;
NATOMS: number of atoms treated with the kernels;
DIMSYS: number of interatomic distances in the system;
DIMKERN: number of 1D kernel basis functions;
NCOEFF: number of the coefficients in datafile;
ATOM1: index of the first atom treated by kernels;
ATOMN: index of the last atom treated by kernels;
DATAFILEe: name of the data file containing the coefficients.
!--------------------------------Description-------------------------------!
FULLKERN is invoked by the FLMK command. At first the module reads the parameters for
the molecules and the atoms involved. These information will be considered only for
the present run of CHARMM, no modifications will be applied to the PSF file.
Under the current implementation, force field parameters need to be set to zero.
No compatibility issues with other modules in CHARMM are registered.
!-----------------------------Generation of the potential -----------------------------!
The fortran code for the RKHS potential and calculation of the coefficients are
generated using a python script which takes care of the permutationally invariant
symmetry of the molecule. Information regrading this will be made available in github.
!-------------------------How to run with your potential-------------------------!
TOOO (NEED TO BE DISCUSSED)
!------------------------- How to to generate the coefficents -------------------------!
Calculate ab initio energies and cartesian gradients of the system for sample structures
using normal mode sampling (randomly displacing the cordinates along the normal mode
vectors). The coordinates, energy and gradients are then used to calculate the coefficients
for the kernal polynomial using a least square fit. Corresponding codes for this will be
made available in github
!-----------------------------------Example-----------------------------------!
Acetone dynamics.
----------------------------------------- Needed improvements
1- Remove properly the intratomic interactions inside the subroutine.
2- Include the keywords for better recognition of the variable and make the code more general.
3- Make a flexible implementation?
I would say that for point 1 and point 4 we can ask advise to Joshua.
1- Optional flag for the installation of FULLKERN, via the "-a FLMK".
2- Make the module verbose.
3- Insert the deallocation module.
VERSON 1 06.07.2020
by
Marco Pezzella
Debasish Koner
Markus Meuwly
FULLKERN provides a way to flexibly implement RKHS based potentials for small molecules
inside CHARMM. At the moment the interactions between atoms are set to zero, with the
aim of automatically setting to zero internally the intramolecular interactions.The
PSF remains unchanged.The new interactions are not explicitly added to the PSF file and
only exist for the duration of a CHARMM run. FULLKERN is called via the FLMK keyword.
References:
[1] D. Koner and M. Meuwly arXiv prepint https://arxiv.org/abs/2005.04667v2
Syntax :: Syntax of the FULLKERN module.
Description :: A brief description of the module and how it works.
Generation of the potential :: How to generate the new potential.
How to run with your potential :: Shows how to compile charmm with the desired
potential and run it.
How to to generate the coefficents :: Brief description of how to store the coefficients.
Example :: Description of the example: Acetone.
!--------------------------------Syntax--------------------------------!
FLMK { READ {UNIT (integer) NATOMS (integer) DIMSYS (integer) DIMKERN (integer)
NCOEFF (integer) ATOM1 (integer) ATOMN (integer) DATAFILE (char)} }
READ option will activate the module, reading all the parameters needed for
storing and usage of the module.
UNIT: units needed for reading the data file;
NATOMS: number of atoms treated with the kernels;
DIMSYS: number of interatomic distances in the system;
DIMKERN: number of 1D kernel basis functions;
NCOEFF: number of the coefficients in datafile;
ATOM1: index of the first atom treated by kernels;
ATOMN: index of the last atom treated by kernels;
DATAFILEe: name of the data file containing the coefficients.
!--------------------------------Description-------------------------------!
FULLKERN is invoked by the FLMK command. At first the module reads the parameters for
the molecules and the atoms involved. These information will be considered only for
the present run of CHARMM, no modifications will be applied to the PSF file.
Under the current implementation, force field parameters need to be set to zero.
No compatibility issues with other modules in CHARMM are registered.
!-----------------------------Generation of the potential -----------------------------!
The fortran code for the RKHS potential and calculation of the coefficients are
generated using a python script which takes care of the permutationally invariant
symmetry of the molecule. Information regrading this will be made available in github.
!-------------------------How to run with your potential-------------------------!
TOOO (NEED TO BE DISCUSSED)
!------------------------- How to to generate the coefficents -------------------------!
Calculate ab initio energies and cartesian gradients of the system for sample structures
using normal mode sampling (randomly displacing the cordinates along the normal mode
vectors). The coordinates, energy and gradients are then used to calculate the coefficients
for the kernal polynomial using a least square fit. Corresponding codes for this will be
made available in github
!-----------------------------------Example-----------------------------------!
Acetone dynamics.
----------------------------------------- Needed improvements
1- Remove properly the intratomic interactions inside the subroutine.
2- Include the keywords for better recognition of the variable and make the code more general.
3- Make a flexible implementation?
I would say that for point 1 and point 4 we can ask advise to Joshua.
1- Optional flag for the installation of FULLKERN, via the "-a FLMK".
2- Make the module verbose.
3- Insert the deallocation module.