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Merged
awvwgk merged 1 commit into from
May 4, 2022
Merged

Add support for 1D and 2D periodic boundary conditions #18

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96 changes: 63 additions & 33 deletions src/dftd3/cutoff.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -55,69 +55,99 @@ subroutine get_lattice_points(periodic, lat, rthr, trans)
real(wp), intent(in) :: rthr
real(wp), intent(in) :: lat(:, :)
real(wp), allocatable, intent(out) :: trans(:, :)
real(wp) :: vec(size(lat, 2)), norms(size(lat, 1), size(lat, 2))
integer :: rep(3)
integer :: itr, ix, iy, iz

if (.not.any(periodic)) then
allocate(trans(3, 1))
trans(:, :) = 0.0_wp
else
return
end if

if (all(periodic)) then
call get_translations(lat, rthr, rep)
allocate(trans(3, product(2*rep+1)))
itr = 0
do ix = -rep(1), rep(1)
do iy = -rep(2), rep(2)
do iz = -rep(3), rep(3)
itr = itr + 1
trans(:, itr) = lat(:, 1)*ix + lat(:, 2)*iy + lat(:, 3)*iz
end do
else if (count(periodic) == 1) then
vec = sqrt(sum(lat**2, 1))
where(periodic)
rep = ceiling(rthr / vec)
elsewhere
rep = 0
endwhere
else if (count(periodic) == 2) then
call get_normals(lat, norms)
where(spread(periodic, 2, 3))
norms = lat
endwhere
call get_translations(norms, rthr, rep)
where(.not.periodic)
rep = 0
endwhere
end if

allocate(trans(3, product(2*rep+1)))
itr = 0
do ix = -rep(1), rep(1)
do iy = -rep(2), rep(2)
do iz = -rep(3), rep(3)
itr = itr + 1
trans(:, itr) = lat(:, 1)*ix + lat(:, 2)*iy + lat(:, 3)*iz
end do
end do
end if
end do

end subroutine get_lattice_points


subroutine get_normals(lattice, normal)
real(wp), intent(in) :: lattice(:, :)
real(wp), intent(out) :: normal(:, :)

integer :: itr
do itr = 1, 3
call crossproduct(lattice(:, mod(itr, 3) + 1), lattice(:, mod(itr + 1, 3) + 1), &
& normal(:, itr))
end do
end subroutine get_normals


!> generate a supercell based on a realspace cutoff, this subroutine
! doesn't know anything about the convergence behaviour of the
! associated property.
pure subroutine get_translations(lat, rthr, rep)
real(wp), intent(in) :: rthr
real(wp), intent(in) :: lat(3, 3)
integer, intent(out) :: rep(3)
real(wp) :: normx(3), normy(3), normz(3)
real(wp) :: norm(3, 3), normy(3), normz(3)
real(wp) :: cos10, cos21, cos32

! find normal to the plane...
call crossproduct(lat(:, 2), lat(:, 3), normx)
call crossproduct(lat(:, 3), lat(:, 1), normy)
call crossproduct(lat(:, 1), lat(:, 2), normz)
call crossproduct(lat(:, 2), lat(:, 3), norm(:, 1))
call crossproduct(lat(:, 3), lat(:, 1), norm(:, 2))
call crossproduct(lat(:, 1), lat(:, 2), norm(:, 3))
! ...normalize it...
normx = normx/norm2(normx)
normy = normy/norm2(normy)
normz = normz/norm2(normz)
norm(:, 1) = norm(:, 1)/norm2(norm(:, 1))
norm(:, 2) = norm(:, 2)/norm2(norm(:, 2))
norm(:, 3) = norm(:, 3)/norm2(norm(:, 3))
! cos angles between normals and lattice vectors
cos10 = sum(normx*lat(:, 1))
cos21 = sum(normy*lat(:, 2))
cos32 = sum(normz*lat(:, 3))
cos10 = sum(norm(:, 1)*lat(:, 1))
cos21 = sum(norm(:, 2)*lat(:, 2))
cos32 = sum(norm(:, 3)*lat(:, 3))
rep(1) = ceiling(abs(rthr/cos10))
rep(2) = ceiling(abs(rthr/cos21))
rep(3) = ceiling(abs(rthr/cos32))

contains

pure subroutine crossproduct(a, b, c)
real(wp), intent(in) :: a(3), b(3)
real(wp), intent(out) :: c(3)
real(wp) :: x, y, z

x=a(2)*b(3)-b(2)*a(3)
y=a(3)*b(1)-b(3)*a(1)
z=a(1)*b(2)-b(1)*a(2)
c=(/x, y, z/)
end subroutine crossproduct

end subroutine get_translations

pure subroutine crossproduct(a, b, c)
real(wp), intent(in) :: a(3), b(3)
real(wp), intent(out) :: c(3)
real(wp) :: x, y, z

x = a(2)*b(3)-b(2)*a(3)
y = a(3)*b(1)-b(3)*a(1)
z = a(1)*b(2)-b(1)*a(2)
c = [x, y, z]
end subroutine crossproduct

end module dftd3_cutoff
108 changes: 106 additions & 2 deletions test/unit/test_periodic.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ module test_periodic
use mctc_env, only : wp
use mctc_env_testing, only : new_unittest, unittest_type, error_type, check, &
& test_failed
use mctc_io, only : structure_type
use mctc_io, only : structure_type, new
use mstore, only : get_structure
use dftd3
implicit none
Expand Down Expand Up @@ -50,11 +50,13 @@ subroutine collect_periodic(testsuite)
& new_unittest("BLYP-D3(0)", test_blypd3zero_benzene), &
& new_unittest("M06L-D3(0)", test_m06ld3zero_cyanamide), &
& new_unittest("rPW86PBE-D3(0)", test_rpw86pbed3zero_co2), &
& new_unittest("revSSB-D3(0)", test_revssbd3zero_cytosine) &
& new_unittest("revSSB-D3(0)", test_revssbd3zero_cytosine), &
! new_unittest("HSEsol-D3(BJ)-ATM", test_hsesold3bjatm_oxacb), &
! new_unittest("PWGGA-D3(BJ)-ATM", test_pwggad3bjatm_pyrazine), &
! new_unittest("B3PW91-D3(0)-ATM", test_b3pw91d3zeroatm_urea), &
! new_unittest("RPBE-D3(0)-ATM", test_rpbed3zeroatm_hexamine) &
& new_unittest("revPBE-D3(BJ)", test_revpbed3bj_1d), &
& new_unittest("BP86-D3(0)", test_bp86d3zero_2d) &
& ]

end subroutine collect_periodic
Expand Down Expand Up @@ -397,4 +399,106 @@ subroutine test_rpbed3zeroatm_hexamine(error)
end subroutine test_rpbed3zeroatm_hexamine


subroutine test_revpbed3bj_1d(error)
!> Error handling
type(error_type), allocatable, intent(out) :: error

integer, parameter :: nat = 32
integer, parameter :: num(nat) = 6
real(wp), parameter :: xyz(3, nat) = reshape([&
& 1.36794785746435_wp, 13.45808943446053_wp, 8.83754983226359_wp, &
& 3.69183290816438_wp, 13.13552229161569_wp, 10.16652201690950_wp, &
& 1.36792668081267_wp, 10.38660504434782_wp, 13.04411926632965_wp, &
& 3.69180534781206_wp, 11.55414582295511_wp, 12.33193380846742_wp, &
& 1.36791549262702_wp, 3.53066844289674_wp, 10.38660588677206_wp, &
& 1.36792046664920_wp, 7.73723910626293_wp, 13.45809224934817_wp, &
& 3.69181279359489_wp, 6.40826717723392_wp, 13.13552570942280_wp, &
& 1.36792009865062_wp, 3.11669712338516_wp, 7.73723850632628_wp, &
& 3.69181515738094_wp, 3.43926499914873_wp, 6.40826580885474_wp, &
& 3.69178443989294_wp, 4.24285720771059_wp, 11.55415026712869_wp, &
& 1.36790824853106_wp, 6.18818490375705_wp, 3.53066863732142_wp, &
& 3.69178194163078_wp, 5.02063901427657_wp, 4.24285736953327_wp, &
& 1.36794124909207_wp, 13.04411858182861_wp, 6.18818324080182_wp, &
& 1.36792249732236_wp, 8.83755133592807_wp, 3.11669686076913_wp, &
& 3.69182456413952_wp, 10.16652118921143_wp, 3.43926084011816_wp, &
& 3.69181444966104_wp, 12.33193631088573_wp, 5.02063847821044_wp, &
& 6.01572566324028_wp, 13.45790756713123_wp, 8.83752222635545_wp, &
& 8.33965926123256_wp, 13.13576644753615_wp, 10.16660228658307_wp, &
& 6.01574747573805_wp, 10.38654070512969_wp, 13.04391961251944_wp, &
& 8.33964066450677_wp, 11.55427002850905_wp, 12.33211653730939_wp, &
& 6.01574728097580_wp, 3.53087013230607_wp, 10.38654217813321_wp, &
& 6.01568913853645_wp, 7.73726406411719_wp, 13.45790864082374_wp, &
& 8.33963586549168_wp, 6.40818371470975_wp, 13.13576911116618_wp, &
& 6.01568179676984_wp, 3.11688332536281_wp, 7.73726611148835_wp, &
& 8.33963704688671_wp, 3.43902559351770_wp, 6.40818390180453_wp, &
& 8.33962496288127_wp, 4.24267007149867_wp, 11.55427031066552_wp, &
& 6.01573464280675_wp, 6.18824653544318_wp, 3.53086861480278_wp, &
& 8.33961857277245_wp, 5.02052001792996_wp, 4.24267413625204_wp, &
& 6.01575677304189_wp, 13.04392044501564_wp, 6.18824448603611_wp, &
& 6.01568344836224_wp, 8.83752193432504_wp, 3.11688171781516_wp, &
& 8.33964228963694_wp, 10.16660428027860_wp, 3.43902155668011_wp, &
& 8.33965118613331_wp, 12.33211762632282_wp, 5.02051902430387_wp],&
& shape(xyz))
logical, parameter :: periodic(3) = [.true., .false., .false.]
real(wp), parameter :: lattice(3, 3) = reshape([&
& 9.2955628527586_wp, 0.0_wp, 0.0_wp, 0.0_wp, 1.0_wp, 0.0_wp, 0.0_wp, 0.0_wp, 1.0_wp], &
& shape(lattice))
real(wp), parameter :: lattice_vac(3, 3) = reshape([&
& 9.2955628527586_wp, 0.0_wp, 0.0_wp, 0.0_wp, 100.0_wp, 0.0_wp, 0.0_wp, 0.0_wp, 100.0_wp], &
& shape(lattice))
type(structure_type) :: mol
type(rational_damping_param) :: param
type(d3_param) :: inp = d3_param(&
& s6 = 1.0_wp, s9 = 0.0_wp, alp = 14.0_wp, &
& a1 = 0.5238_wp, s8 = 2.3550_wp, a2 = 3.5016_wp)

call new(mol, num, xyz, periodic=periodic, lattice=lattice)
call new_rational_damping(param, inp)
call test_dftd3_gen(error, mol, param, -0.25436101196186600_wp)

call new(mol, num, xyz, periodic=[.true.], lattice=lattice_vac)
call test_dftd3_gen(error, mol, param, -0.25436101196186600_wp)

end subroutine test_revpbed3bj_1d


subroutine test_bp86d3zero_2d(error)
!> Error handling
type(error_type), allocatable, intent(out) :: error

integer, parameter :: nat = 4
integer, parameter :: num(nat) = 6
real(wp), parameter :: xyz(3, nat) = reshape([&
& -0.12918412100093_wp, 0.06210659750976_wp, -2.13384498734326_wp, &
& 0.12856915667443_wp, -0.07403227791901_wp, 4.02358027265954_wp, &
& -0.12317720857511_wp, 2.75170732207802_wp, -2.13345350602279_wp, &
& 2.44816466162280_wp, 1.28612566399214_wp, 4.02317048854901_wp],&
& shape(xyz))
logical, parameter :: periodic(3) = [.true., .true., .false.]
real(wp), parameter :: lattice(3, 3) = reshape([&
& 4.68837849314507_wp, 0.00000000000000_wp, 0.00000000000000_wp, &
& -2.36282788044783_wp, 4.04978545156612_wp, 0.00000000000000_wp, &
& 0.00000000000000_wp, 0.00000000000000_wp, 1.00000000000000_wp],&
& shape(lattice))
real(wp), parameter :: lattice_vac(3, 3) = reshape([&
& 4.68837849314507_wp, 0.00000000000000_wp, 0.00000000000000_wp, &
& -2.36282788044783_wp, 4.04978545156612_wp, 0.00000000000000_wp, &
& 0.00000000000000_wp, 0.00000000000000_wp, 100.000000000000_wp],&
& shape(lattice))
type(structure_type) :: mol
type(zero_damping_param) :: param
type(d3_param) :: inp = d3_param(&
& s6 = 1.0_wp, s9 = 0.0_wp, alp = 14.0_wp, &
& rs6 = 1.139_wp, s8 = 1.683_wp)

call new(mol, num, xyz, periodic=periodic, lattice=lattice)
call new_zero_damping(param, inp)
call test_dftd3_gen(error, mol, param, -1.5983949078995030E-2_wp)

call new(mol, num, xyz, periodic=[.true.], lattice=lattice_vac)
call test_dftd3_gen(error, mol, param, -1.5983949078995030E-2_wp)

end subroutine test_bp86d3zero_2d


end module test_periodic