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03-list.f90
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03-list.f90
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module mo_list
!
! verlet list, see more at page 147 of <computer simulation of liquids>
!
use mo_syst
use mo_config
implicit none
! global constants.
!! skin
real(8), private, parameter :: set_nlcut = 0.70d0
!! for sake of memory saving, we consider listmax neighbor of one particle at most
!! enlarge this if you study 3D system or high volume fraction system
integer, private, parameter :: listmax = 32
! neighbor list of one particle
type listone_t
! neighbor number
integer :: nbsum
! neighbor index
integer :: nblist(listmax)
! precalculated relative relation, used for distance calculation in perodical cell
integer(1) :: iround(free,listmax)
integer(1) :: cory(listmax)
!
real(4) :: con0(free)
end type
! neighbor list struct of system
type list_t
integer :: natom
type(listone_t), allocatable, dimension(:) :: list
! contact number
integer, allocatable, dimension(:) :: nbi
! tag particle is rattler or not
integer, allocatable, dimension(:) :: rattlerflag
real(8) :: nlcut
end type
type(list_t) :: nb
! voronoi cell
type voro_one_t
integer :: nbsum
integer :: nblist(listmax)
integer :: vid1(listmax), vid2(listmax)
end type
type voro_t
integer :: natom
type(voro_one_t), allocatable, dimension(:) :: list
real(8), allocatable, dimension(:,:) :: center, vertex
real(8) :: la(free), strain
contains
procedure :: init => init_voro
procedure :: decompose => calc_voro
end type
type(voro_t) :: voro
contains
subroutine init_list(tnb, tcon)
!
! allocate memory
!
implicit none
! para list
type(list_t), intent(inout) :: tnb
type(con_t), intent(in) :: tcon
! local
integer :: tnatom
tnatom = tcon%natom
tnb%natom = tnatom
tnb%nlcut = set_nlcut
if ( allocated(tnb%list) ) then
if ( size(tnb%list) /= tnatom ) then
deallocate( tnb%list )
allocate( tnb%list(tnatom) )
end if
else
allocate( tnb%list(tnatom) )
end if
end subroutine
subroutine make_list(tnb, tcon)
!
! make list of system
!
implicit none
! para list
type(con_t), intent(in) :: tcon
type(list_t), intent(inout) :: tnb
! local
real(8) :: lainv(free), dra(free), rai(free), raj(free), ri, rj, rij2, dij
integer :: cory, iround(free)
integer :: i, j, k, itemp
associate( &
natom => tcon%natom, &
ra => tcon%ra, &
r => tcon%r, &
la => tcon%la, &
strain => tcon%strain, &
list => tnb%list, &
nlcut => tnb%nlcut &
)
nlcut = set_nlcut
lainv = 1.d0 / la
! set nbsum to zero
list(:)%nbsum = 0
do i=1, natom
list(i)%con0 = ra(:,i)
rai = ra(:,i)
ri = r(i)
do j=i+1, natom
raj = ra(:,j)
rj = r(j)
dra = raj - rai
cory = nint( dra(free) * lainv(free) )
dra(1) = dra(1) - strain * la(free) * cory
do k=1, free-1
iround(k) = nint( dra(k) * lainv(k) )
end do
iround(free) = cory
do k=1, free
dra(k) = dra(k) - iround(k) * la(k)
end do
rij2 = sum( dra**2 )
dij = ri + rj
if ( rij2 > ( dij+nlcut )**2 ) cycle
if ( list(i)%nbsum < listmax ) then
itemp = list(i)%nbsum
itemp = itemp + 1
list(i)%nbsum = itemp
list(i)%nblist(itemp) = j
list(i)%iround(:,itemp) = iround
list(i)%cory(itemp) = cory
end if
end do
end do
end associate
end subroutine
subroutine one_make_list( tnb, tcon, tn )
!
! make list for one particle
!
implicit none
! para list
type(con_t), intent(in) :: tcon
type(list_t), intent(inout) :: tnb
integer, intent(in) :: tn
! local
real(8) :: lainv(free), dra(free), rai(free), raj(free), ri, rj, rij2, dij
integer :: cory, iround(free)
integer :: i, j, k, itemp
associate( &
natom => tcon%natom, &
ra => tcon%ra, &
r => tcon%r, &
la => tcon%la, &
strain => tcon%strain, &
list => tnb%list, &
nlcut => tnb%nlcut &
)
lainv = 1.d0 / la
i = tn
list(i)%nbsum = 0
list(i)%con0 = ra(:,i)
rai = ra(:,i)
ri = r(i)
do j = 1, natom
raj = ra(:,j)
rj = r(j)
dra = raj - rai
cory = nint( dra(free) * lainv(free) )
dra(1) = dra(1) - strain * la(free) * cory
do k = 1, free-1
iround(k) = nint( dra(k) * lainv(k) )
end do
iround(free) = cory
do k = 1, free
dra(k) = dra(k) - iround(k) * la(k)
end do
rij2 = sum( dra**2 )
dij = ri + rj
if ( rij2 > ( dij+nlcut )**2 ) cycle
if ( list(i)%nbsum < listmax ) then
itemp = list(i)%nbsum
itemp = itemp + 1
list(i)%nbsum = itemp
list(i)%nblist(itemp) = j
list(i)%iround(:,itemp) = iround
list(i)%cory(itemp) = cory
end if
if ( list(j)%nbsum < listmax ) then
itemp = list(j)%nbsum
if ( all( list(j)%nblist(1:itemp) /= i ) ) then
itemp = itemp + 1
list(j)%nbsum = itemp
list(j)%nblist(itemp) = i
list(j)%iround(:,itemp) = - iround
list(j)%cory(itemp) = - cory
end if
end if
end do
end associate
end subroutine
subroutine full_make_list( tnb, tcon )
!
! make list for all the particles
!
implicit none
! para list
type(con_t), intent(in) :: tcon
type(list_t), intent(inout) :: tnb
! local
real(8) :: lainv(free), dra(free), rai(free), raj(free), ri, rj, rij2, dij
integer :: cory, iround(free)
integer :: i, j, k, itemp
associate( &
natom => tcon%natom, &
ra => tcon%ra, &
r => tcon%r, &
la => tcon%la, &
strain => tcon%strain, &
list => tnb%list, &
nlcut => tnb%nlcut &
)
nlcut = set_nlcut
lainv = 1.d0 / la
! set nbsum to zero
list(:)%nbsum = 0
do i=1, natom
list(i)%con0 = ra(:,i)
rai = ra(:,i)
ri = r(i)
do j=i+1, natom
raj = ra(:,j)
rj = r(j)
dra = raj - rai
cory = nint( dra(free) * lainv(free) )
dra(1) = dra(1) - strain * la(free) * cory
do k=1, free-1
iround(k) = nint( dra(k) * lainv(k) )
end do
iround(free) = cory
do k=1, free
dra(k) = dra(k) - iround(k) * la(k)
end do
rij2 = sum( dra**2 )
dij = ri + rj
if ( rij2 > ( dij+nlcut )**2 ) cycle
if ( list(i)%nbsum < listmax ) then
itemp = list(i)%nbsum
itemp = itemp + 1
list(i)%nbsum = itemp
list(i)%nblist(itemp) = j
list(i)%iround(:,itemp) = iround
list(i)%cory(itemp) = cory
end if
if ( list(j)%nbsum < listmax ) then
itemp = list(j)%nbsum
itemp = itemp + 1
list(j)%nbsum = itemp
list(j)%nblist(itemp) = i
list(j)%iround(:,itemp) = - iround
list(j)%cory(itemp) = - cory
end if
end do
end do
end associate
end subroutine
subroutine calc_z( tnb, tcon )
!
! calculate coordination number
!
implicit none
! para list
type(con_t), intent(in) :: tcon
type(list_t), intent(inout) :: tnb
! local
real(8) :: dra(free), rai(free), raj(free), ri, rj, rij2, dij
integer :: cory, iround(free)
integer :: i, j, k, jj
if ( allocated( tnb%nbi ) .and. size(tnb%nbi) /= tcon%natom ) then
deallocate( tnb%nbi )
end if
if ( .not. allocated( tnb%nbi ) ) then
allocate( tnb%nbi(tcon%natom) )
end if
associate( &
natom => tcon%natom, &
ra => tcon%ra, &
r => tcon%r, &
la => tcon%la, &
strain => tcon%strain, &
list => tnb%list, &
nbi => tnb%nbi &
)
! set nbsum to zero
nbi = 0
do i=1, natom
rai = ra(:,i)
ri = r(i)
do jj=1, list(i)%nbsum
j = list(i)%nblist(jj)
raj = ra(:,j)
rj = r(j)
dra = raj - rai
cory = list(i)%cory(jj)
iround = list(i)%iround(:,jj)
dra(1) = dra(1) - strain * la(free) * cory
do k=1, free
dra(k) = dra(k) - iround(k) * la(k)
end do
rij2 = sum( dra**2 )
dij = ri + rj
if ( rij2 > ( dij )**2 ) cycle
nbi(i) = nbi(i) + 1
nbi(j) = nbi(j) + 1
end do
end do
end associate
end subroutine
function check_list( tnb, tcon ) result(flag)
!
! determine remake list or not
!
implicit none
! para list
type(list_t), intent(in) :: tnb
type(con_t), intent(in) :: tcon
! result
logical :: flag
! local
real(8) :: maxdis, dra(free), dr2
integer :: i
associate( &
natom => tcon%natom, &
ra => tcon%ra, &
nlcut => tnb%nlcut &
)
maxdis = 0.d0
do i=1, tcon%natom
dra = tcon%ra(:,i) - tnb%list(i)%con0
dr2 = sum( dra**2 )
if ( maxdis < dr2 ) maxdis = dr2
end do
flag = .false.
if ( maxdis > 0.25 * nlcut**2 ) flag = .true.
end associate
end function
! ToDo
! subroutine check_rattler
function calc_rattler( tcon, tnblist ) result(flag)
implicit none
! para list
type(con_t), intent(in) :: tcon
type(list_t), intent(in), optional :: tnblist
! result
integer, dimension(tcon%natom) :: flag
! local
type(list_t) :: lclist
integer :: i
if ( present(tnblist) ) then
lclist = tnblist
else
call init_list( lclist, tcon )
call make_list( lclist, tcon )
end if
call calc_z( lclist, tcon )
flag = 0
do i=1, lclist%natom
if ( lclist%nbi(i) == 0 ) then
flag(i) = 1
elseif ( lclist%nbi(i) <= (free-1) ) then
write(*,*) "Warning: The coordination number of a certain particle is less than 2, please reconsider whether your model is correct."
! If you are sure that's okay, please delete the next line and recompile your project.
stop
end if
end do
end function
! voro
subroutine init_voro( this, tcon )
implicit none
! para list
class(voro_t), intent(inout) :: this
type(con_t), intent(in) :: tcon
this%natom = tcon%natom
this%center = tcon%ra
this%la = tcon%la
this%strain = tcon%strain
if( .not. allocated(this%list) ) then
allocate( this%list(this%natom) )
else if( size(this%list) /= tcon%natom ) then
deallocate( this%list )
allocate( this%list(tcon%natom) )
end if
end subroutine
subroutine calc_voro( this )
implicit none
! para list
class(voro_t), intent(inout) :: this
! local
integer, parameter :: maxcan = 200
integer, dimension(maxcan) :: verts
real(8), dimension(maxcan) :: px, py, ps
integer, dimension(maxcan) :: tag
real(8), parameter :: rcut = 3.5
real(8) :: rai(free), raij(free), rijsq
integer :: i, j, k, cory, ncan
associate( natom => this%natom, &
list => this%list, &
con => this%center, &
la => this%la, &
strain => this%strain &
)
list(:)%nbsum = 0
! main loop
do i=1, natom
rai = con(:,i)
k = 0
do j=1, natom
if ( i == j ) cycle
raij = con(:,j) - rai
cory = nint( raij(2) / la(2) )
raij(1) = raij(1) - cory * strain * la(2)
raij(:) = raij(:) - anint( raij(:) / la ) * la
rijsq = sum(raij**2)
if ( rijsq < rcut**2 ) then
if ( k == maxcan ) then
write(*,*) k
cycle
end if
k = k + 1
px(k) = raij(1)
py(k) = raij(2)
ps(k) = rijsq
tag(k) = j
end if
end do
ncan = k
call sortps( px, py, ps, tag, ncan )
call calc_voro_single( px, py, ps, maxcan, ncan, verts )
do k=1, ncan
if ( verts(k) /= 0 ) then
list(i)%nbsum = list(i)%nbsum + 1
list(i)%nblist(list(i)%nbsum) = tag(k)
end if
end do
end do
end associate
end subroutine
subroutine sortps( px, py, ps, tag, ncan )
use mo_math, only: swap
implicit none
! para list
integer :: ncan
real(8), dimension(ncan) :: px, py, ps
integer, dimension(ncan) :: tag
! local
integer :: i, imin
do i=1, ncan-1
imin = minloc( ps(i:ncan), 1 ) + i - 1
if ( i == imin ) cycle
call swap( px(i), px(imin) )
call swap( py(i), py(imin) )
call swap( ps(i), ps(imin) )
call swap( tag(i), tag(imin) )
end do
end subroutine
subroutine calc_voro_single( px, py, ps, maxcan, ncan, verts )
implicit none
integer :: maxcan, ncan, nv, ne
real(8), dimension(maxcan) :: px, py, ps
integer, dimension(maxcan) :: verts
integer, parameter :: maxv = 200
real(8), dimension(maxv) :: vx, vy
integer, dimension(maxv) :: iv, jv
logical :: flag
real(8) :: ai,bi,ci, aj,bj,cj, det, detinv
real(8) :: vxij, vyij
real(8), parameter :: tol=1.d-8
integer :: i, j, l, v
!-- check
if ( ncan < 3 ) then
write(*,'('' less than 3 points given to work '',i5)') ncan
stop
end if
v = 0
do i=1, ncan-1
ai = px(i)
bi = py(i)
ci = -ps(i)
do j=i+1, ncan
aj = px(j)
bj = py(j)
cj = -ps(j)
det = ai*bj - aj*bi
if( abs(det) >= tol ) then
detinv = 1.d0 / det
vxij = ( bi * cj - bj * ci ) * detinv
vyij = ( aj * ci - ai * cj ) * detinv
flag = .true.
l = 1
do while( flag .and. l < ncan )
if ( l /= i .and. l /= j ) then
flag = ( ( px(l) * vxij + py(l) * vyij ) .le. ps(l) )
end if
l = l + 1
end do
if ( flag ) then
v = v + 1
if ( v > maxv ) stop 'too many vertices'
iv(v) = i
jv(v) = j
vx(v) = 0.5 * vxij
vy(v) = 0.5 * vyij
end if
end if
end do
end do
nv = v ! total vertex found
if ( nv < 3 ) then
write(*,'('' less than 3 vertices found in work '',i5)') nv
stop
end if
verts(1:ncan) = 0
do i = 1, nv
verts(iv(i)) = verts(iv(i)) + 1
verts(jv(i)) = verts(jv(i)) + 1
end do
flag = .true.
ne = 0
do i = 1, ncan
if ( verts(i) > 0 ) then
ne = ne + 1
if ( verts(i) /= 2 ) then ! it is supposed that every neighbor contribute 2 vertex
flag = .false.
end if
end if
end do
if ( flag .eqv. .false. ) then
write (*,'('' **** vertex error: degeneracy ? **** '')')
end if
if ( ne /= nv ) then
write(*,'('' **** edge error: degeneracy ? **** '')')
end if
end subroutine
end module