34 use,
intrinsic :: iso_fortran_env
64 real(real64),
allocatable :: c6free(:)
65 real(real64),
allocatable :: dpfree(:)
66 real(real64),
allocatable :: r0free(:)
67 real(real64),
allocatable :: c6abfree(:, :)
68 real(real64),
allocatable :: volfree(:)
69 real(real64),
allocatable :: c6ab(:, :)
70 real(real64) :: cutoff
71 real(real64) :: damping
74 real(real64),
allocatable :: derivative_coeff(:)
80 type(vdw_ts_t),
intent(out) :: this
81 type(namespace_t),
intent(in) :: namespace
82 type(ions_t),
intent(in) :: ions
84 integer :: ispecies, jspecies
85 real(real64) :: num, den
123 safe_allocate(this%c6free(1:ions%nspecies))
124 safe_allocate(this%dpfree(1:ions%nspecies))
125 safe_allocate(this%r0free(1:ions%nspecies))
126 safe_allocate(this%volfree(1:ions%nspecies))
127 safe_allocate(this%c6abfree(1:ions%nspecies, 1:ions%nspecies))
128 safe_allocate(this%c6ab(1:ions%natoms, 1:ions%natoms))
129 safe_allocate(this%derivative_coeff(1:ions%natoms))
131 do ispecies = 1, ions%nspecies
132 call get_vdw_param(namespace, ions%species(ispecies)%s%get_label(), &
133 this%c6free(ispecies), this%dpfree(ispecies), this%r0free(ispecies))
134 select type(spec=>ions%species(ispecies)%s)
142 do ispecies = 1, ions%nspecies
143 do jspecies = 1, ions%nspecies
144 num =
m_two*this%c6free(ispecies)*this%c6free(jspecies)
145 den = (this%dpfree(jspecies)/this%dpfree(ispecies))*this%c6free(ispecies) &
146 + (this%dpfree(ispecies)/this%dpfree(jspecies))*this%c6free(jspecies)
147 this%c6abfree(ispecies, jspecies) = num/den
156 type(vdw_ts_t),
intent(inout) :: this
160 safe_deallocate_a(this%c6free)
161 safe_deallocate_a(this%dpfree)
162 safe_deallocate_a(this%r0free)
163 safe_deallocate_a(this%volfree)
164 safe_deallocate_a(this%c6abfree)
165 safe_deallocate_a(this%c6ab)
166 safe_deallocate_a(this%derivative_coeff)
173 subroutine vdw_ts_calculate(this, namespace, space, latt, atom, natoms, pos, mesh, nspin, density, energy, potential, force)
174 type(
vdw_ts_t),
intent(inout) :: this
176 class(
space_t),
intent(in) :: space
178 type(
atom_t),
intent(in) :: atom(:)
179 integer,
intent(in) :: natoms
180 real(real64),
intent(in) :: pos(1:space%dim,1:natoms)
181 class(
mesh_t),
intent(in) :: mesh
182 integer,
intent(in) :: nspin
183 real(real64),
intent(in) :: density(:, :)
184 real(real64),
intent(out) :: energy
185 real(real64),
contiguous,
intent(out) :: potential(:)
186 real(real64),
intent(out) :: force(:, :)
189 subroutine f90_vdw_calculate(natoms, dd, sr, zatom, coordinates, vol_ratio, &
190 energy, force, derivative_coeff)
191 use,
intrinsic :: iso_fortran_env
193 integer,
intent(in) :: natoms
194 real(real64),
intent(in) :: dd
195 real(real64),
intent(in) :: sr
196 integer,
intent(in) :: zatom
197 real(real64),
intent(in) :: coordinates
198 real(real64),
intent(in) :: vol_ratio
199 real(real64),
intent(out) :: energy
200 real(real64),
intent(out) :: force
201 real(real64),
intent(out) :: derivative_coeff
202 end subroutine f90_vdw_calculate
206 integer :: iatom, jatom, ispecies, jspecies, jcopy, ip
207 real(real64) :: rr, rr6, dffdr0, ee, ff, dee, dffdrab, dffdvra, deabdvra
208 real(real64),
allocatable :: coordinates(:,:), vol_ratio(:), dvadens(:), dvadrr(:), &
209 dr0dvra(:), r0ab(:,:)
211 integer,
allocatable :: zatom(:)
212 real(real64) :: x_j(space%dim)
216 safe_allocate(vol_ratio(1:natoms))
217 safe_allocate(dvadens(1:mesh%np))
218 safe_allocate(dvadrr(1:3))
219 safe_allocate(dr0dvra(1:natoms))
222 force(1:space%dim, 1:natoms) =
m_zero
223 this%derivative_coeff(1:natoms) =
m_zero
224 call hirshfeld_init(hirshfeld, mesh, namespace, space, latt, atom, natoms, pos, nspin)
231 ispecies = atom(iatom)%species%get_index()
234 jspecies = atom(jatom)%species%get_index()
235 this%c6ab(iatom,jatom) = vol_ratio(iatom)*vol_ratio(jatom)*this%c6abfree(ispecies,jspecies)
239 if (space%is_periodic())
then
240 safe_allocate(r0ab(1:natoms,1:natoms))
244 ispecies = atom(iatom)%species%get_index()
246 jspecies = atom(jatom)%species%get_index()
248 r0ab(iatom,jatom) = (vol_ratio(iatom)**(
m_one/
m_three))*this%r0free(ispecies) &
249 + (vol_ratio(jatom)**(
m_one/
m_three))*this%r0free(jspecies)
255 jspecies = atom(jatom)%species%get_index()
257 do jcopy = 1, latt_iter%n_cells
258 x_j = pos(:, jatom) + latt_iter%get(jcopy)
261 ispecies = atom(iatom)%species%get_index()
262 rr = norm2(x_j - pos(:, iatom))
265 if (rr < 1.0e-10_real64) cycle
267 ee =
exp(-this%damping * ((rr / (this%sr*r0ab(iatom, jatom))) -
m_one))
272 dffdrab = (this%damping/(this%sr*r0ab(iatom, jatom)))*dee
274 dffdr0 = -this%damping*rr/(this%sr*r0ab(iatom, jatom)**2)*dee
276 energy = energy -
m_half*ff*this%c6ab(iatom, jatom)/rr6
279 dffdvra = dffdr0*dr0dvra(iatom)
282 deabdvra = (dffdvra*this%c6ab(iatom, jatom) + ff*vol_ratio(jatom)*this%c6abfree(ispecies, jspecies))/rr6
284 this%derivative_coeff(iatom) = this%derivative_coeff(iatom) + deabdvra
290 safe_deallocate_a(r0ab)
292 safe_allocate(coordinates(1:space%dim, 1:natoms))
293 safe_allocate(zatom(1:natoms))
296 coordinates(:, iatom) = pos(:, iatom)
297 zatom(iatom) = int(atom(iatom)%species%get_z())
301 call f90_vdw_calculate(natoms, this%damping, this%sr, zatom(1), coordinates(1, 1), &
302 vol_ratio(1), energy, force(1, 1), this%derivative_coeff(1))
305 safe_deallocate_a(coordinates)
306 safe_deallocate_a(zatom)
313 call lalg_axpy(mesh%np, -this%derivative_coeff(iatom), dvadens, potential)
322 safe_deallocate_a(vol_ratio)
323 safe_deallocate_a(dvadens)
324 safe_deallocate_a(dvadrr)
325 safe_deallocate_a(dr0dvra)
335 type(
ions_t),
intent(in) :: ions
336 real(real64),
intent(inout) :: force_vdw(1:ions%space%dim, 1:ions%natoms)
337 class(
mesh_t),
intent(in) :: mesh
338 integer,
intent(in) :: nspin
339 real(real64),
intent(in) :: density(:, :)
344 integer :: iatom, jatom, ispecies, jspecies, jcopy
345 real(real64) :: rr, rr6, dffdr0, ee, ff, dee, dffdvra, deabdvra, deabdrab, x_j(ions%space%dim)
346 real(real64),
allocatable :: vol_ratio(:), dvadrr(:), dr0dvra(:), r0ab(:,:), derivative_coeff(:), c6ab(:,:)
352 safe_allocate(vol_ratio(1:ions%natoms))
353 safe_allocate(dvadrr(1:3))
354 safe_allocate(dr0dvra(1:ions%natoms))
355 safe_allocate(r0ab(1:ions%natoms,1:ions%natoms))
356 safe_allocate(derivative_coeff(1:ions%natoms))
357 safe_allocate(c6ab(1:ions%natoms,1:ions%natoms))
360 force_vdw(1:ions%space%dim, 1:ions%natoms) =
m_zero
361 derivative_coeff(1:ions%natoms) =
m_zero
362 c6ab(1:ions%natoms,1:ions%natoms) =
m_zero
363 r0ab(1:ions%natoms,1:ions%natoms) =
m_zero
364 dr0dvra(1:ions%natoms) =
m_zero
365 dvadrr(1:ions%space%dim) =
m_zero
366 vol_ratio(1:ions%natoms) =
m_zero
369 call hirshfeld_init(hirshfeld, mesh, ions%namespace, ions%space, ions%latt, ions%atom, ions%natoms, ions%pos, nspin)
372 do iatom = 1, ions%natoms
376 do iatom = 1, ions%natoms
377 ispecies = ions%atom(iatom)%species%get_index()
379 do jatom = 1, ions%natoms
380 jspecies = ions%atom(jatom)%species%get_index()
381 c6ab(iatom, jatom) = vol_ratio(iatom)*vol_ratio(jatom)*this%c6abfree(ispecies, jspecies)
386 do iatom = 1, ions%natoms
387 ispecies = ions%atom(iatom)%species%get_index()
388 do jatom = iatom, ions%natoms
389 jspecies = ions%atom(jatom)%species%get_index()
391 r0ab(iatom, jatom) = (vol_ratio(iatom)**(
m_one/
m_three))*this%r0free(ispecies) &
392 + (vol_ratio(jatom)**(
m_one/
m_three))*this%r0free(jspecies)
393 if (iatom /= jatom) r0ab(jatom, iatom) = r0ab(iatom, jatom)
398 do jatom = 1, ions%natoms
399 jspecies = ions%atom(jatom)%species%get_index()
401 do jcopy = 1, latt_iter%n_cells
402 x_j = ions%pos(:, jatom) + latt_iter%get(jcopy)
403 do iatom = 1, ions%natoms
404 ispecies = ions%atom(iatom)%species%get_index()
405 rr = norm2(x_j - ions%pos(:, iatom))
410 ee =
exp(-this%damping*(rr/(this%sr*r0ab(iatom, jatom)) -
m_one))
414 dffdr0 = -this%damping*rr/( this%sr*r0ab(iatom, jatom)**2)*dee
416 deabdrab = c6ab(iatom,jatom)*(this%damping/(this%sr*r0ab(iatom, jatom))*dee - 6.0_real64*ff/rr)/rr6
418 dffdvra = dffdr0*dr0dvra(iatom)
420 deabdvra = (dffdvra*c6ab(iatom, jatom) + ff*vol_ratio(jatom)*this%c6abfree(ispecies, jspecies))/rr6
422 derivative_coeff(iatom) = derivative_coeff(iatom) + deabdvra
425 deabdrab = c6ab(iatom, jatom)*(this%damping/(this%sr*r0ab(iatom, jatom))*dee - 6.0_real64*ff/rr)/rr6
426 force_vdw(:, iatom) = force_vdw(:, iatom) +
m_half*deabdrab*(ions%pos(:, iatom) - x_j)/rr
431 do iatom = 1, ions%natoms
432 do jatom = 1, ions%natoms
434 force_vdw(:, jatom)= force_vdw(:, jatom) + derivative_coeff(iatom)*dvadrr
440 safe_deallocate_a(vol_ratio)
441 safe_deallocate_a(dvadrr)
442 safe_deallocate_a(dr0dvra)
443 safe_deallocate_a(r0ab)
444 safe_deallocate_a(derivative_coeff)
445 safe_deallocate_a(c6ab)
455 type(
vdw_ts_t) ,
intent(inout) :: this
456 type(
ions_t),
intent(in) :: ions
457 character(len=*),
intent(in) :: dir, fname
460 integer :: iunit, iatom, jatom
466 iunit =
io_open(trim(dir) //
"/" // trim(fname), namespace, action=
'write')
467 write(iunit,
'(a)')
' # Atom1 Atom2 C6_{12}^{eff}'
470 do iatom = 1, ions%natoms
471 do jatom = 1, ions%natoms
472 write(iunit,
'(3x, i5, i5, e15.6)') iatom, jatom, this%c6ab(iatom, jatom)
488 character(len=*),
intent(in) :: atom
489 real(real64),
intent(out) :: c6
490 real(real64),
intent(out) :: alpha
491 real(real64),
intent(out) :: r0
495 select case (trim(atom))
498 alpha = 4.500000_real64
503 alpha = 1.380000_real64
508 alpha = 164.200000_real64
509 c6 = 1387.000000_real64
513 alpha = 38.000000_real64
514 c6 = 214.000000_real64
518 alpha = 21.000000_real64
519 c6 = 99.500000_real64
523 alpha = 12.000000_real64
524 c6 = 46.600000_real64
528 alpha = 7.400000_real64
529 c6 = 24.200000_real64
533 alpha = 5.400000_real64
534 c6 = 15.600000_real64
538 alpha = 3.800000_real64
543 alpha = 2.670000_real64
548 alpha = 162.700000_real64
549 c6 = 1556.000000_real64
553 alpha = 71.000000_real64
554 c6 = 627.000000_real64
558 alpha = 60.000000_real64
559 c6 = 528.000000_real64
563 alpha = 37.000000_real64
564 c6 = 305.000000_real64
568 alpha = 25.000000_real64
569 c6 = 185.000000_real64
573 alpha = 19.600000_real64
574 c6 = 134.000000_real64
578 alpha = 15.000000_real64
579 c6 = 94.600000_real64
583 alpha = 11.100000_real64
584 c6 = 64.300000_real64
588 alpha = 292.900000_real64
589 c6 = 3897.000000_real64
593 alpha = 160.000000_real64
594 c6 = 2221.000000_real64
598 alpha = 120.000000_real64
599 c6 = 1383.000000_real64
603 alpha = 98.000000_real64
604 c6 = 1044.000000_real64
608 alpha = 84.000000_real64
609 c6 = 832.000000_real64
613 alpha = 78.000000_real64
614 c6 = 602.000000_real64
618 alpha = 63.000000_real64
619 c6 = 552.000000_real64
623 alpha = 56.000000_real64
624 c6 = 482.000000_real64
628 alpha = 50.000000_real64
629 c6 = 408.000000_real64
633 alpha = 48.000000_real64
634 c6 = 373.000000_real64
638 alpha = 42.000000_real64
639 c6 = 253.000000_real64
643 alpha = 40.000000_real64
644 c6 = 284.000000_real64
648 alpha = 60.000000_real64
649 c6 = 498.000000_real64
653 alpha = 41.000000_real64
654 c6 = 354.000000_real64
658 alpha = 29.000000_real64
659 c6 = 246.000000_real64
663 alpha = 25.000000_real64
664 c6 = 210.000000_real64
668 alpha = 20.000000_real64
669 c6 = 162.000000_real64
673 alpha = 16.800000_real64
674 c6 = 129.600000_real64
678 alpha = 319.200000_real64
679 c6 = 4691.000000_real64
683 alpha = 199.000000_real64
684 c6 = 3170.000000_real64
693 alpha = 23.680000_real64
694 c6 = 157.500000_real64
698 alpha = 50.600000_real64
699 c6 = 339.000000_real64
713 alpha = 35.000000_real64
714 c6 = 385.000000_real64
718 alpha = 27.300000_real64
719 c6 = 285.900000_real64
759 call messages_write(
'vdw ts: reference free atom parameters not available for species '//trim(atom))
constant times a vector plus a vector
double exp(double __x) __attribute__((__nothrow__
type(debug_t), save, public debug
real(real64), parameter, public m_two
real(real64), parameter, public m_zero
real(real64), parameter, public m_half
real(real64), parameter, public m_one
real(real64), parameter, public m_three
subroutine, public hirshfeld_init(this, mesh, namespace, space, latt, atom, natoms, pos, nspin)
real(real64), parameter, public tol_hirshfeld
subroutine, public hirshfeld_end(this)
subroutine, public hirshfeld_density_derivative(this, iatom, ddensity)
subroutine, public hirshfeld_position_derivative(this, space, iatom, jatom, density, dposition)
subroutine, public hirshfeld_volume_ratio(this, iatom, density, volume_ratio)
subroutine, public dio_function_output(how, dir, fname, namespace, space, mesh, ff, unit, ierr, pos, atoms, grp, root)
Top-level IO routine for functions defined on the mesh.
subroutine, public io_close(iunit, grp)
subroutine, public io_mkdir(fname, namespace, parents)
integer function, public io_open(file, namespace, action, status, form, position, die, recl, grp)
This module defines the meshes, which are used in Octopus.
subroutine, public messages_fatal(no_lines, only_root_writes, namespace)
logical function mpi_grp_is_root(grp)
Is the current MPI process of grpcomm, root.
type(mpi_grp_t), public mpi_world
subroutine, public profiling_out(label)
Increment out counter and sum up difference between entry and exit time.
subroutine, public profiling_in(label, exclude)
Increment in counter and save entry time.
real(real64) function, public ps_density_volume(ps, namespace)
brief This module defines the class unit_t which is used by the unit_systems_oct_m module.
This module defines the unit system, used for input and output.
type(unit_system_t), public units_inp
the units systems for reading and writing
type(unit_t), public unit_one
some special units required for particular quantities
Tkatchenko-Scheffler pairwise method for van der Waals (vdW, dispersion) interactions.
subroutine, public vdw_ts_init(this, namespace, ions)
subroutine, public vdw_ts_calculate(this, namespace, space, latt, atom, natoms, pos, mesh, nspin, density, energy, potential, force)
Calculate the potential for the Tatchenko-Scheffler vdW correction as described in Phys....
subroutine, public vdw_ts_write_c6ab(this, ions, dir, fname, namespace)
subroutine get_vdw_param(namespace, atom, c6, alpha, r0)
subroutine, public vdw_ts_force_calculate(this, force_vdw, ions, mesh, nspin, density)
subroutine, public vdw_ts_end(this)
The following class implements a lattice iterator. It allows one to loop over all cells that are with...
Describes mesh distribution to nodes.