Fortran interface: core routines

Functions/Subroutines
subroutine	ddx::ddfromfile (fname, ddx_data, tol, charges, ddx_error)
	Read the configuration from ddX input file and return a ddx_data structure. More...
subroutine	ddx::ddinit (model, nsph, coords, radii, eps, ddx_data, ddx_error, force, kappa, eta, shift, lmax, ngrid, incore, maxiter, jacobi_ndiis, enable_fmm, pm, pl, nproc, logfile, adjoint, eps_int)
	Wrapper to the initialization routine which supports optional arguments. This will make future maintenance easier. More...
subroutine	ddx::ddrun (ddx_data, state, electrostatics, psi, tol, esolv, ddx_error, force, read_guess)
	Main solver routine. More...
subroutine	ddx::setup (params, constants, workspace, state, electrostatics, psi, ddx_error)
	Setup the state for the different models. More...
subroutine	ddx::fill_guess (params, constants, workspace, state, tol, ddx_error)
	Do a guess for the primal linear system for the different models. More...
subroutine	ddx::fill_guess_adjoint (params, constants, workspace, state, tol, ddx_error)
	Do a guess for the adjoint linear system for the different models. More...
subroutine	ddx::solve (params, constants, workspace, state, tol, ddx_error)
	Solve the primal linear system for the different models. More...
subroutine	ddx::solve_adjoint (params, constants, workspace, state, tol, ddx_error)
	Solve the adjoint linear system for the different models. More...
subroutine	ddx::energy (params, constants, workspace, state, solvation_energy, ddx_error)
	Compute the energy for the different models. More...
subroutine	ddx::solvation_force_terms (params, constants, workspace, state, electrostatics, force, ddx_error)
	Compute the solvation terms of the forces (solute aspecific) for the different models. This must be summed to the solute specific term to get the full forces. More...
subroutine	ddx_core::allocate_electrostatics (params, constants, electrostatics, ddx_error)
	Given the chosen model, find the required electrostatic properties, and allocate the arrays for them in the container. More...
subroutine	ddx_core::deallocate_electrostatics (electrostatics, ddx_error)
	Deallocate the electrostatic properties. More...
subroutine	ddx_core::allocate_state (params, constants, state, ddx_error)
	Initialize the ddx_state object. More...
subroutine	ddx_core::deallocate_state (state, ddx_error)
	Deallocate the ddx_state object. More...
subroutine	ddx_core::get_banner (string)
	Print the ddX logo. More...

Detailed Description

Function/Subroutine Documentation

ddfromfile()

subroutine ddx::ddfromfile	(	character(len=*), intent(in)	fname,
		type(ddx_type), intent(out)	ddx_data,
		real(dp), intent(out)	tol,
		real(dp), dimension(:), intent(out), allocatable	charges,
		type(ddx_error_type), intent(inout)	ddx_error
	)

Read the configuration from ddX input file and return a ddx_data structure.

Parameters

[in]	fname	Filename containing all the required info
[out]	ddx_data	Object containing all inputs
[out]	tol	tolerance for iterative solvers
[out]	charges	charge array, size(nsph)
[in,out]	ddx_error	ddX error

Definition at line 25 of file ddx.f90.

ddinit()

subroutine ddx::ddinit	(	integer, intent(in)	model,
		integer, intent(in)	nsph,
		real(dp), dimension(3, nsph), intent(in)	coords,
		real(dp), dimension(nsph), intent(in)	radii,
		real(dp), intent(in)	eps,
		type(ddx_type), intent(out), target	ddx_data,
		type(ddx_error_type), intent(inout)	ddx_error,
		integer, intent(in), optional	force,
		real(dp), intent(in), optional	kappa,
		real(dp), intent(in), optional	eta,
		real(dp), intent(in), optional	shift,
		integer, intent(in), optional	lmax,
		integer, intent(in), optional	ngrid,
		integer, intent(in), optional	incore,
		integer, intent(in), optional	maxiter,
		integer, intent(in), optional	jacobi_ndiis,
		integer, intent(in), optional	enable_fmm,
		integer, intent(in), optional	pm,
		integer, intent(in), optional	pl,
		integer, intent(in), optional	nproc,
		character(len=255), intent(in), optional	logfile,
		integer, intent(in), optional	adjoint,
		real(dp), intent(in), optional	eps_int
	)

Wrapper to the initialization routine which supports optional arguments. This will make future maintenance easier.

Parameters

[in]	model	1 for COSMO, 2 for PCM and 3 for LPB
[in]	nsph	number of spheres n > 0
[in]	coords	coordinates of the spheres, size (3, nsph)
[in]	radii	radii of the spheres, size (nsph)
[in]	eps	relative dielectric permittivity eps > 1
[out]	ddx_data	Container for ddX data structures
[in,out]	ddx_error	ddX error
	[in,optional]	force: 1 if forces are required and 0 otherwise
	[in,optional]	kappa: Debye-H"{u}ckel parameter
	[in,optional]	eta: regularization parameter 0 < eta <= 1
	[in,optional]	shift: shift of characteristic function -1 for interior, 0 for centered and 1 for outer regularization
	[in,optional]	lmax: Maximal degree of modeling spherical harmonics, lmax >= 0
	[in,optional]	ngrid: Number of Lebedev grid points ngrid >= 0
	[in,optional]	incore: handling of the sparse matrices, 1 for precomputing them and keeping them in memory, 0 for assembling the matrix-vector products on-the-fly
	[in,optional]	maxiter: Maximum number of iterations for the iterative solver, maxiter > 0
	[in,optional]	jacobi_ndiis: Number of extrapolation points for the Jacobi/DIIS solver, ndiis >= 0
	[in,optional]	enable_fmm: 1 to use FMM acceleration and 0 otherwise
	[in,optional]	pm: Maximal degree of multipole spherical harmonics. Ignored in the case fmm=0. Value -1 means no far-field FMM interactions are computed, pm >= -1
	[in,optional]	pl: Maximal degree of local spherical harmonics. Ignored in the case fmm=0. Value -1 means no far-field FMM interactions are computed, pl >= -1
	[in,optional]	nproc: Number of OpenMP threads, nproc >= 0.
	[in,optional]	logfile: file name for log information.

Definition at line 243 of file ddx.f90.

ddrun()

subroutine ddx::ddrun	(	type(ddx_type), intent(inout)	ddx_data,
		type(ddx_state_type), intent(inout)	state,
		type(ddx_electrostatics_type), intent(in)	electrostatics,
		real(dp), dimension(ddx_data % constants % nbasis, ddx_data % params % nsph), intent(in)	psi,
		real(dp), intent(in)	tol,
		real(dp), intent(out)	esolv,
		type(ddx_error_type), intent(inout)	ddx_error,
		real(dp), dimension(3, ddx_data % params % nsph), intent(out), optional	force,
		logical, intent(in), optional	read_guess
	)

Main solver routine.

Solves the solvation problem, computes the energy, and if required computes the forces.

Parameters

[in]	ddx_data	ddX object with all input information
[in,out]	state	ddx state (contains RHSs and solutions)
[in]	electrostatics	electrostatic property container
[in]	psi	RHS of the adjoint problem
[in]	tol	tolerance for the linear system solvers
[out]	esolv	solvation energy
[in,out]	ddx_error	ddX error
[out]	force	Analytical forces (optional argument, only if required)
[in]	read_guess	optional argument, if true read the guess from the state object

Definition at line 362 of file ddx.f90.

setup()

subroutine ddx::setup	(	type(ddx_params_type), intent(in)	params,
		type(ddx_constants_type), intent(inout)	constants,
		type(ddx_workspace_type), intent(inout)	workspace,
		type(ddx_state_type), intent(inout)	state,
		type(ddx_electrostatics_type), intent(in)	electrostatics,
		real(dp), dimension(constants % nbasis, params % nsph), intent(in)	psi,
		type(ddx_error_type), intent(inout)	ddx_error
	)

Setup the state for the different models.

Parameters

[in]	params	User specified parameters
[in]	constants	Precomputed constants
[in,out]	workspace	Preallocated workspaces
[in,out]	state	ddx state (contains solutions and RHSs)
[in]	electrostatics	electrostatic property container
[in]	psi	Representation of the solute potential in spherical harmonics, size (nbasis, nsph)
[in,out]	ddx_error	ddX error

Definition at line 471 of file ddx.f90.

fill_guess()

subroutine ddx::fill_guess	(	type(ddx_params_type), intent(in)	params,
		type(ddx_constants_type), intent(inout)	constants,
		type(ddx_workspace_type), intent(inout)	workspace,
		type(ddx_state_type), intent(inout)	state,
		real(dp), intent(in)	tol,
		type(ddx_error_type), intent(inout)	ddx_error
	)

Do a guess for the primal linear system for the different models.

Parameters

[in]	params	User specified parameters
[in,out]	constants	Precomputed constants
[in,out]	workspace	Preallocated workspaces
[in,out]	state	ddx state (contains solutions and RHSs)
[in]	tol	tolerance
[in,out]	ddx_error	ddX error

Definition at line 509 of file ddx.f90.

fill_guess_adjoint()

subroutine ddx::fill_guess_adjoint	(	type(ddx_params_type), intent(in)	params,
		type(ddx_constants_type), intent(inout)	constants,
		type(ddx_workspace_type), intent(inout)	workspace,
		type(ddx_state_type), intent(inout)	state,
		real(dp), intent(in)	tol,
		type(ddx_error_type), intent(inout)	ddx_error
	)

Do a guess for the adjoint linear system for the different models.

Parameters

[in]	params	User specified parameters
[in,out]	constants	Precomputed constants
[in,out]	workspace	Preallocated workspaces
[in,out]	state	ddx state (contains solutions and RHSs)
[in]	tol	tolerance
[in,out]	ddx_error	ddX error

Definition at line 541 of file ddx.f90.

solve()

subroutine ddx::solve	(	type(ddx_params_type), intent(in)	params,
		type(ddx_constants_type), intent(inout)	constants,
		type(ddx_workspace_type), intent(inout)	workspace,
		type(ddx_state_type), intent(inout)	state,
		real(dp), intent(in)	tol,
		type(ddx_error_type), intent(inout)	ddx_error
	)

Solve the primal linear system for the different models.

Parameters

[in]	params	: General options
[in]	constants	: Precomputed constants
[in,out]	workspace	: Preallocated workspaces
[in,out]	state	: Solutions, guesses and relevant quantities
[in]	tol	: Tolerance for the iterative solvers
[in,out]	ddx_error	ddX error

Definition at line 573 of file ddx.f90.

solve_adjoint()

subroutine ddx::solve_adjoint	(	type(ddx_params_type), intent(in)	params,
		type(ddx_constants_type), intent(inout)	constants,
		type(ddx_workspace_type), intent(inout)	workspace,
		type(ddx_state_type), intent(inout)	state,
		real(dp), intent(in)	tol,
		type(ddx_error_type), intent(inout)	ddx_error
	)

Solve the adjoint linear system for the different models.

Parameters

[in]	params	: General options
[in]	constants	: Precomputed constants
[in,out]	workspace	: Preallocated workspaces
[in,out]	state	: Solutions, guesses and relevant quantities
[in]	tol	: Tolerance for the iterative solvers
[in,out]	ddx_error	ddX error

Definition at line 605 of file ddx.f90.

energy()

subroutine ddx::energy	(	type(ddx_params_type), intent(in)	params,
		type(ddx_constants_type), intent(in)	constants,
		type(ddx_workspace_type), intent(in)	workspace,
		type(ddx_state_type), intent(in)	state,
		real(dp), intent(out)	solvation_energy,
		type(ddx_error_type), intent(inout)	ddx_error
	)

Compute the energy for the different models.

Parameters

[in]	params	General options
[in]	constants	Precomputed constants
[in,out]	workspace	Preallocated workspaces
[in]	state	ddx state (contains solutions and RHSs)
[out]	solvation_energy	resulting energy
[in,out]	ddx_error	ddX error

Definition at line 637 of file ddx.f90.

solvation_force_terms()

subroutine ddx::solvation_force_terms	(	type(ddx_params_type), intent(in)	params,
		type(ddx_constants_type), intent(in)	constants,
		type(ddx_workspace_type), intent(inout)	workspace,
		type(ddx_state_type), intent(inout)	state,
		type(ddx_electrostatics_type), intent(in)	electrostatics,
		real(dp), dimension(3, params % nsph), intent(out)	force,
		type(ddx_error_type), intent(inout)	ddx_error
	)

Compute the solvation terms of the forces (solute aspecific) for the different models. This must be summed to the solute specific term to get the full forces.

Parameters

[in]	params	General options
[in]	constants	Precomputed constants
[in,out]	workspace	Preallocated workspaces
[in,out]	state	Solutions and relevant quantities
[in]	electrostatics	Electrostatic properties container.
[out]	force	Geometrical contribution to the forces
[in,out]	ddx_error	ddX error

Definition at line 675 of file ddx.f90.

allocate_electrostatics()

subroutine ddx_core::allocate_electrostatics	(	type(ddx_params_type), intent(in)	params,
		type(ddx_constants_type), intent(in)	constants,
		type(ddx_electrostatics_type), intent(out)	electrostatics,
		type(ddx_error_type), intent(inout)	ddx_error
	)

Given the chosen model, find the required electrostatic properties, and allocate the arrays for them in the container.

Parameters

[in]	params	ddx parameters
[in]	constants	ddx constants
[out]	electrostatics,ddX	electrostatic properties container
[in,out]	ddx_error	ddX error

Definition at line 340 of file ddx_core.f90.

deallocate_electrostatics()

subroutine ddx_core::deallocate_electrostatics	(	type(ddx_electrostatics_type), intent(inout)	electrostatics,
		type(ddx_error_type), intent(inout)	ddx_error
	)

Deallocate the electrostatic properties.

Parameters

[out]	electrostatics,ddX	electrostatic properties container
[in,out]	ddx_error	ddX error

Definition at line 406 of file ddx_core.f90.

allocate_state()

subroutine ddx_core::allocate_state	(	type(ddx_params_type), intent(in)	params,
		type(ddx_constants_type), intent(in)	constants,
		type(ddx_state_type), intent(out)	state,
		type(ddx_error_type), intent(inout)	ddx_error
	)

Initialize the ddx_state object.

Parameters

[in]	params	User specified parameters
[in]	constants	Precomputed constants
[in,out]	state	ddx state (contains solutions and RHSs)
[in,out]	ddx_error	ddX error

Definition at line 446 of file ddx_core.f90.

deallocate_state()

subroutine ddx_core::deallocate_state	(	type(ddx_state_type), intent(inout)	state,
		type(ddx_error_type), intent(inout)	ddx_error
	)

Deallocate the ddx_state object.

Parameters

[in,out]	state	ddx state (contains solutions and RHSs)
[in,out]	ddx_error	ddX error

Definition at line 774 of file ddx_core.f90.

get_banner()

subroutine ddx_core::get_banner

(

character (len=2047), intent(out)

string

)

Print the ddX logo.

Parameters

[out]

string

container for the logo

Definition at line 2788 of file ddx_core.f90.