neb_utils Module Reference

Module with utility for Nudged Elastic Band Calculation. More...

Functions/Subroutines
subroutine, public	build_replica_coords (neb_section, particle_set, coords, vels, neb_env, iw, globenv, para_env)
	Constructs or Read the coordinates for all replica. More...
subroutine, public	neb_calc_energy_forces (rep_env, neb_env, coords, energies, forces, particle_set, output_unit)
	Driver to compute energy and forces within a NEB, Based on the use of the replica_env. More...
subroutine, public	reorient_images (rotate_frames, particle_set, coords, vels, iw, distances, number_of_replica)
	Reorient iteratively all images of the NEB chain in order to have always the smaller RMSD between two following images. More...
subroutine, public	reparametrize_images (reparametrize_frames, spline_order, smoothing, coords, sline, distances)
	Reparametrization of the replica for String Method with splines. More...
logical function, public	check_convergence (neb_env, Dcoords, forces)
	Checks for convergence criteria during a NEB run. More...

Detailed Description

Module with utility for Nudged Elastic Band Calculation.

Note

Numerical accuracy for parallel runs: Each replica starts the SCF run from the one optimized in a previous run. It may happen then energies and derivatives of a serial run and a parallel run could be slightly different 'cause of a different starting density matrix. Exact results are obtained using: EXTRAPOLATION USE_GUESS in QS section (Teo 09.2006)

Author

Teodoro Laino 10.2006

Function/Subroutine Documentation

build_replica_coords()

subroutine, public neb_utils::build_replica_coords	(	type(section_vals_type), pointer	neb_section,
		type(particle_type), dimension(:), pointer	particle_set,
		type(neb_var_type), pointer	coords,
		type(neb_var_type), pointer	vels,
		type(neb_type), pointer	neb_env,
		integer, intent(in)	iw,
		type(global_environment_type), pointer	globenv,
		type(mp_para_env_type), pointer	para_env
	)

Constructs or Read the coordinates for all replica.

Parameters

neb_section	...
particle_set	...
coords	...
vels	...
neb_env	...
iw	...
globenv	...
para_env	...

Author

Teodoro Laino 09.2006

Definition at line 138 of file neb_utils.F.

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neb_calc_energy_forces()

subroutine, public neb_utils::neb_calc_energy_forces	(	type(replica_env_type), pointer	rep_env,
		type(neb_type), optional, pointer	neb_env,
		type(neb_var_type), pointer	coords,
		real(kind=dp), dimension(:), intent(out)	energies,
		type(neb_var_type), pointer	forces,
		type(particle_type), dimension(:), pointer	particle_set,
		integer, intent(in)	output_unit
	)

Driver to compute energy and forces within a NEB, Based on the use of the replica_env.

Parameters

rep_env	...
neb_env	...
coords	...
energies	...
forces	...
particle_set	...
output_unit	...

Author

Teodoro Laino 09.2006

Definition at line 365 of file neb_utils.F.

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reorient_images()

subroutine, public neb_utils::reorient_images	(	logical, intent(in)	rotate_frames,
		type(particle_type), dimension(:), optional, pointer	particle_set,
		type(neb_var_type), pointer	coords,
		type(neb_var_type), pointer	vels,
		integer, intent(in)	iw,
		real(kind=dp), dimension(:), optional	distances,
		integer, intent(in)	number_of_replica
	)

Reorient iteratively all images of the NEB chain in order to have always the smaller RMSD between two following images.

Parameters

rotate_frames	...
particle_set	...
coords	...
vels	...
iw	...
distances	...
number_of_replica	...

Author

Teodoro Laino 09.2006

Definition at line 875 of file neb_utils.F.

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reparametrize_images()

subroutine, public neb_utils::reparametrize_images	(	logical, intent(in)	reparametrize_frames,
		integer, intent(in)	spline_order,
		real(kind=dp), intent(in)	smoothing,
		real(kind=dp), dimension(:, :), pointer	coords,
		real(kind=dp), dimension(:, :), pointer	sline,
		real(kind=dp), dimension(:)	distances
	)

Reparametrization of the replica for String Method with splines.

Parameters

reparametrize_frames	...
spline_order	...
smoothing	...
coords	...
sline	...
distances	...

Author

Teodoro Laino - Rodolphe Vuilleumier 09.2008

Definition at line 928 of file neb_utils.F.

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check_convergence()

logical function, public neb_utils::check_convergence	(	type(neb_type), pointer	neb_env,
		type(neb_var_type), pointer	Dcoords,
		type(neb_var_type), pointer	forces
	)

Checks for convergence criteria during a NEB run.

Parameters

neb_env	...
Dcoords	...
forces	...

Returns

...

Author

Teodoro Laino 10.2006

Definition at line 993 of file neb_utils.F.

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