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libgeneral.f90
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libgeneral.f90
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MODULE GLOB
!! Syntaxis
!! ctct: contact
!! ctcts : contacts
!! set: set
!! verl: verlet
!! ns: neighbors
!! gd: grid
!! gdns: grid neighbors
!! upd: update
!! filt: filter
!! cell: cell
!! ctoff: cutoff
!! ats: atoms
!! num: number
!! numat: number of atoms
!! glob: global magnitude
!! diff: different
INTEGER,DIMENSION(:),ALLOCATABLE::cl_ind,cl_start !! indices fortran
DOUBLE PRECISION,DIMENSION(:),ALLOCATABLE::cl_val
INTEGER::mx_c,my_c,mz_c !num_cells in x,y,z
DOUBLE PRECISION::lx_c,ly_c,lz_c !length cells in x,y,z
INTEGER::mtot_c,mx_my_c !num total cells, var aux
INTEGER::nscxcell !number neighbor cells per cell
LOGICAL,DIMENSION(:),ALLOCATABLE::cell_upd !cell needs update
INTEGER,DIMENSION(:,:),ALLOCATABLE::nsc_cell !cell neighbors of a cell
LOGICAL,DIMENSION(:),ALLOCATABLE::cell_pbc !cell with none or any pbc requirement
LOGICAL,DIMENSION(:,:),ALLOCATABLE::nsc_cell_pbc !neighbor cell requires pbc
INTEGER,DIMENSION(:),ALLOCATABLE::gns_head,gns_list,gns_at_cell ! grid neighbors -atoms-
!### Verlet neighbours lists should be this way, but f2py does not support derived types yet.
!TYPE I_NO_RECT_MAT
! INTEGER,DIMENSION(:),ALLOCATABLE::column
! INTEGER::dim
!END TYPE I_NO_RECT_MAT
!TYPE(I_NO_RECT_MAT),DIMENSION(:),ALLOCATABLE::ver_ic_ind,ver_oc_ind !! indices fortran
INTEGER,DIMENSION(:,:),ALLOCATABLE::ver_ic_ind,ver_oc_ind !! indices fortran
INTEGER,DIMENSION(:),ALLOCATABLE::ver_ic_dim,ver_oc_dim
INTEGER::dim_ic,dim_oc
LOGICAL,DIMENSION(:,:),ALLOCATABLE::filt_sets_ns_ind
DOUBLE PRECISION,DIMENSION(:,:),ALLOCATABLE::pos_ant
INTEGER,DIMENSION(:,:),ALLOCATABLE::hbs_out
DOUBLE PRECISION,DIMENSION(:),ALLOCATABLE::hbs_vals_out
CONTAINS
SUBROUTINE PERPENDICULAR_NORMED_VECT (vect1,vect2,vect_out)
DOUBLE PRECISION,DIMENSION(3),INTENT(IN)::vect1,vect2
DOUBLE PRECISION,DIMENSION(3),INTENT(OUT)::vect_out
CALL PRODUCT_VECT(vect1,vect2,vect_out)
CALL NORMALIZE_VECT(vect_out)
END SUBROUTINE PERPENDICULAR_NORMED_VECT
SUBROUTINE PRODUCT_VECT(a,b,normal)
DOUBLE PRECISION,DIMENSION(3),INTENT(IN)::a,b
DOUBLE PRECISION,DIMENSION(3),INTENT(OUT)::normal
normal(1)=a(2)*b(3)-a(3)*b(2)
normal(2)=-a(1)*b(3)+a(3)*b(1)
normal(3)=a(1)*b(2)-a(2)*b(1)
END SUBROUTINE PRODUCT_VECT
SUBROUTINE NORMALIZE_VECT (a)
DOUBLE PRECISION,DIMENSION(3),INTENT(INOUT)::a
DOUBLE PRECISION::norm
norm=sqrt(dot_product(a,a))
a=a/norm
END SUBROUTINE NORMALIZE_VECT
!!!!!!!!MINE!!!!!!
SUBROUTINE NOT_CUBIC(box,coor,vector)
IMPLICIT NONE
DOUBLE PRECISION,dimension(3,3),intent(IN)::box
DOUBLE PRECISION,dimension(3)::vect
DOUBLE PRECISION,dimension(3),INTENT(IN)::coor
integer::k,l,m,counter,pos_min
real::dist
DOUBLE PRECISION,dimension(27)::dist_list
DOUBLE PRECISION,dimension(3),intent(OUT)::vector
DOUBLE PRECISION,dimension(27,3)::vector_list
counter=1
do k=-1,1
do l=-1,1
do m=-1,1
vect(:)=coor(:)+box(1,:)*k+box(2,:)*l+box(3,:)*m
vector_list(counter,:)=vect(:)
dist_list(counter)=sqrt(dot_product(vect,vect))
counter=counter+1
end do
end do
end do
dist=minval(dist_list(:))
pos_min=minloc(dist_list(:),DIM=1)
vector=vector_list(pos_min,:)
END SUBROUTINE NOT_CUBIC
!!!!!!!!!END MINE!!!!!!!!
SUBROUTINE PBC(vector,box,ortho)
IMPLICIT NONE
DOUBLE PRECISION,DIMENSION(3),INTENT(INOUT)::vector
DOUBLE PRECISION,DIMENSION(3,3),INTENT(IN)::box
DOUBLE PRECISION,DIMENSION(3)::aux
INTEGER,INTENT(IN)::ortho
INTEGER::i
DOUBLE PRECISION::x,L,Lhalf
IF (ortho==1) THEN
DO i=1,3
L=box(i,i)
Lhalf=0.50d0*L
x=vector(i)
IF (abs(x)>Lhalf) THEN
IF (x>Lhalf) THEN
x=x-L
ELSE
x=x+L
END IF
vector(i)=x
END IF
END DO
ELSE
!SUBROUTINE NOT_CUBIC(box,vector,vector)
CALL NOT_CUBIC(box,vector,aux)
vector=aux
print*, 'Corrections on PBC not implemented with a non-cubic box.'
END IF
END SUBROUTINE PBC
SUBROUTINE CENTER_OF_MASS (pbc_opt,list_com,coors,box,ortho,numat_com,numat_glob,com)
IMPLICIT NONE
INTEGER,INTENT(IN)::pbc_opt,ortho,numat_com,numat_glob
DOUBLE PRECISION,DIMENSION(numat_glob,3),INTENT(IN)::coors
DOUBLE PRECISION,DIMENSION(3,3),INTENT(IN)::box
INTEGER,DIMENSION(numat_com),INTENT(IN)::list_com
DOUBLE PRECISION,DIMENSION(3),INTENT(OUT)::com
INTEGER::ii,jj,kk,nn
DOUBLE PRECISION,DIMENSION(:),ALLOCATABLE::pix,vect_aux,old_ref
DOUBLE PRECISION,DIMENSION(:,:),ALLOCATABLE::comaux
DOUBLE PRECISION::theta,pi
DOUBLE PRECISION::x,y,z,Lx,Ly,Lz
com=0.0d0
IF (pbc_opt==0) THEN
DO ii=1,numat_com
jj=list_com(ii)+1
com(:)=com(:)+coors(jj,:)
END DO
com(:)=com(:)/(numat_com*1.0d0)
ELSE
IF (ortho==1) THEN
! Bai, Linge; Breen, David (2008). "Calculating Center of Mass in an Unbounded 2D Environment".
! Journal of Graphics, GPU, and Game Tools 13 (4): 53–60. doi:10.1080/2151237X.2008.10129266
ALLOCATE(comaux(3,2),vect_aux(3),pix(3),old_ref(3))
comaux=0.0d0
vect_aux=0.0d0
pi=3.1415926535897931*2.0d0
DO ii=1,3
pix(ii)=box(ii,ii)/pi
END DO
DO ii=1,numat_com
jj=list_com(ii)+1
DO kk=1,3
theta=coors(jj,kk)/pix(kk)
comaux(kk,1)=comaux(kk,1)+pix(kk)*dcos(theta)
comaux(kk,2)=comaux(kk,2)+pix(kk)*dsin(theta)
END DO
END DO
comaux(:,:)=comaux(:,:)/(numat_com*1.0d0)
theta=3.1415926535897931
DO ii=1,3
com(ii)=datan2(-comaux(ii,2),-comaux(ii,1))+theta
com(ii)=pix(ii)*com(ii)
END DO
DEALLOCATE(comaux,pix)
! Recompute com with new reference
old_ref=com
com=0.0d0
Lx=box(1,1)
Ly=box(2,2)
Lz=box(3,3)
vect_aux(1)=(Lx/2.0d0)-old_ref(1)
vect_aux(2)=(Ly/2.0d0)-old_ref(2)
vect_aux(3)=(Lz/2.0d0)-old_ref(3)
DO ii=1,numat_com
jj=list_com(ii)+1
x=coors(jj,1)+vect_aux(1)
y=coors(jj,2)+vect_aux(2)
z=coors(jj,3)+vect_aux(3)
IF (x<0.0d0) THEN
nn=CEILING(abs(x)/Lx)
x=x+nn*Lx
ELSE IF (x>=Lx) THEN
nn=INT(x/Lx)
x=x-nn*Lx
END IF
IF (y<0.0d0) THEN
nn=CEILING(abs(y)/Ly)
y=y+nn*Ly
ELSE IF (y>=Ly) THEN
nn=INT(y/Ly)
y=y-nn*Ly
END IF
IF (z<0.0d0) THEN
nn=CEILING(abs(z)/Lz)
z=z+nn*Lz
ELSE IF (z>=Lz) THEN
nn=INT(z/Lz)
z=z-nn*Lz
END IF
x=x-vect_aux(1)
y=y-vect_aux(2)
z=z-vect_aux(3)
com(:)=com(:)+(/x,y,z/)
END DO
com=com/(numat_com*1.0d0)
x=com(1)
y=com(2)
z=com(3)
IF (x<0.0d0) THEN
nn=CEILING(abs(x)/Lx)
x=x+nn*Lx
ELSE IF (x>=Lx) THEN
nn=INT(x/Lx)
x=x-nn*Lx
END IF
IF (y<0.0d0) THEN
nn=CEILING(abs(y)/Ly)
y=y+nn*Ly
ELSE IF (y>=Ly) THEN
nn=INT(y/Ly)
y=y-nn*Ly
END IF
IF (z<0.0d0) THEN
nn=CEILING(abs(z)/Lz)
z=z+nn*Lz
ELSE IF (z>=Lz) THEN
nn=INT(z/Lz)
z=z-nn*Lz
END IF
com(:)=(/x,y,z/)
DEALLOCATE(vect_aux,old_ref)
ELSE
print*,'Function not implemented for not orthorhombic unit cells.'
END IF
END IF
END SUBROUTINE CENTER_OF_MASS
SUBROUTINE CENTER (pbc_opt,wrap_opt,list_com,list_mov,coors,box,ortho,numat_com,numat_mov,numat_glob)
IMPLICIT NONE
INTEGER,INTENT(IN)::pbc_opt,wrap_opt,numat_com,numat_mov,numat_glob,ortho
DOUBLE PRECISION,DIMENSION(numat_glob,3),INTENT(INOUT)::coors
DOUBLE PRECISION,DIMENSION(3,3),INTENT(IN)::box
INTEGER,DIMENSION(numat_com),INTENT(IN)::list_com
INTEGER,DIMENSION(numat_mov),INTENT(IN)::list_mov
INTEGER::ii,jj,kk,nn
DOUBLE PRECISION,DIMENSION(:),ALLOCATABLE::com
DOUBLE PRECISION::x,y,z,Lx,Ly,Lz
Lx=box(1,1)
Ly=box(2,2)
Lz=box(3,3)
ALLOCATE(com(3))
com=0.0d0
CALL CENTER_OF_MASS(pbc_opt,list_com,coors,box,ortho,numat_com,numat_glob,com)
com(1)=box(1,1)/2.0d0-com(1)
com(2)=box(2,2)/2.0d0-com(2)
com(3)=box(3,3)/2.0d0-com(3)
DO ii=1,numat_glob
jj=list_mov(ii)+1
coors(jj,:)=coors(jj,:)+com(:)
END DO
IF (wrap_opt==1) THEN
IF (ortho==1) THEN
DO ii=1,numat_glob
jj=list_mov(ii)+1
x=coors(jj,1)
y=coors(jj,2)
z=coors(jj,3)
IF (x<0.0d0) THEN
nn=CEILING(abs(x)/Lx)
x=x+nn*Lx
ELSE IF (x>=Lx) THEN
nn=INT(x/Lx)
x=x-nn*Lx
END IF
IF (y<0.0d0) THEN
nn=CEILING(abs(y)/Ly)
y=y+nn*Ly
ELSE IF (y>=Ly) THEN
nn=INT(y/Ly)
y=y-nn*Ly
END IF
IF (z<0.0d0) THEN
nn=CEILING(abs(z)/Lz)
z=z+nn*Lz
ELSE IF (z>=Lz) THEN
nn=INT(z/Lz)
z=z-nn*Lz
END IF
coors(jj,:)=(/x,y,z/)
END DO
END IF
END IF
DEALLOCATE(com)
END SUBROUTINE CENTER
INTEGER FUNCTION CELL_INDEX(ix,iy,iz)
IMPLICIT NONE
INTEGER,INTENT(IN)::ix,iy,iz
cell_index=1+MOD(ix+mx_c,mx_c)+MOD(iy+my_c,my_c)*mx_c+MOD(iz+mz_c,mz_c)*mx_my_c
END FUNCTION CELL_INDEX
LOGICAL FUNCTION CELLS_PBC(icell,ncell)
IMPLICIT NONE
INTEGER,INTENT(IN)::icell,ncell
INTEGER::ix,iy,iz
INTEGER::nx,ny,nz
INTEGER::ll,lx,lxy
ll=icell-1
ix=MOD(ll,mx_c)
lx=INT(ll/mx_c)
iy=MOD(lx,my_c)
lxy=INT(ll/mx_my_c)
iz=MOD(lxy,mz_c)
ll=ncell-1
nx=MOD(ll,mx_c)
lx=INT(ll/mx_c)
ny=MOD(lx,my_c)
lxy=INT(ll/mx_my_c)
nz=MOD(lxy,mz_c)
cells_pbc=.FALSE.
IF ((1.0d0*(abs(nx-ix)+1))>((1.0d0*mx_c)/2.0d0)) cells_pbc=.TRUE.
IF ((1.0d0*(abs(ny-iy)+1))>((1.0d0*my_c)/2.0d0)) cells_pbc=.TRUE.
IF ((1.0d0*(abs(nz-iz)+1))>((1.0d0*mz_c)/2.0d0)) cells_pbc=.TRUE.
END FUNCTION CELLS_PBC
LOGICAL FUNCTION CHECK_CELL(rcut,ix,iy,iz)
IMPLICIT NONE
DOUBLE PRECISION,INTENT(IN)::rcut
INTEGER,INTENT(IN)::ix,iy,iz
INTEGER::aix,aiy,aiz
INTEGER::ii,jj,kk,pp,qq,rr
DOUBLE PRECISION,DIMENSION(3)::o1,o2,vect
DOUBLE PRECISION::val_aux,rcut2
LOGICAL::filter
check_cell=.FALSE.
rcut2=rcut*rcut
aix=abs(ix)
aiy=abs(iy)
aiz=abs(iz)
filter=.FALSE.
DO ii=0,1
DO jj=0,1
DO kk=0,1
o1(:)=(/ii*lx_c,jj*ly_c,kk*lz_c/)
DO pp=0,1
DO qq=0,1
DO rr=0,1
o2(:)=(/pp*lx_c,qq*ly_c,rr*lz_c/)
vect=o2-o1
val_aux=dot_product(vect,vect)
IF (val_aux<rcut2) THEN
filter=.TRUE.
EXIT
END IF
END DO
IF (filter.eqv..TRUE.) EXIT
END DO
IF (filter.eqv..TRUE.) EXIT
END DO
IF (filter.eqv..TRUE.) EXIT
END DO
IF (filter.eqv..TRUE.) EXIT
END DO
IF (filter.eqv..TRUE.) EXIT
END DO
check_cell=filter
END FUNCTION CHECK_CELL
SUBROUTINE MAKE_CELL_NS (rcell,rcut,box,natom)
INTEGER,INTENT(IN)::natom
DOUBLE PRECISION,INTENT(IN)::rcell,rcut
double precision,DIMENSION(3,3),INTENT(IN)::box
INTEGER::ii,jj,kk,gg,ix,iy,iz,deltx,delty,deltz
INTEGER::icell,ncell
LOGICAL::filter,filter2
LOGICAL,DIMENSION(:,:,:),ALLOCATABLE::aux_mask
mx_c=FLOOR(box(1,1)/rcell)
lx_c=box(1,1)/mx_c
my_c=FLOOR(box(2,2)/rcell)
ly_c=box(2,2)/my_c
mz_c=FLOOR(box(3,3)/rcell)
lz_c=box(3,3)/mz_c
mx_my_c=mx_c*my_c
mtot_c=mx_my_c*mz_c
!print*,mx_c,my_c,mz_c
!print*,box(1,1)/mx_c,box(2,2)/my_c,box(3,3)/mz_c
!
!print*,((natom*1.0d0)/(mtot_c*1.0d0))
deltx=CEILING(rcut/lx_c)
delty=CEILING(rcut/ly_c)
deltz=CEILING(rcut/lz_c)
!print*,mtot_c
!print*,mx_c,my_c,mz_c
!print*,lx_c,ly_c,lz_c
!print*,'================='
!print*,'( -',deltx,',',deltx,' )'
!print*,'( -',delty,',',delty,' )'
!print*,'( -',deltz,',',deltz,' )'
ALLOCATE(aux_mask(-deltx:deltx,-delty:delty,-deltz:deltz))
aux_mask=.FALSE.
gg=0
DO ii=-deltx,deltx
DO jj=-delty,delty
DO kk=-deltz,deltz
IF (check_cell(rcut,ii,jj,kk)) THEN
aux_mask(ii,jj,kk)=.TRUE.
gg=gg+1
END IF
END DO
END DO
END DO
nscxcell=gg
!print*,nscxcell,'out of',(2*deltx+1)*(2*delty+1)*(2*deltz+1)
IF (ALLOCATED(nsc_cell)) DEALLOCATE(nsc_cell)
IF (ALLOCATED(cell_upd)) DEALLOCATE(cell_upd)
IF (ALLOCATED(cell_pbc)) DEALLOCATE(cell_pbc)
IF (ALLOCATED(nsc_cell_pbc)) DEALLOCATE(nsc_cell_pbc)
ALLOCATE(nsc_cell(mtot_c,nscxcell),nsc_cell_pbc(mtot_c,nscxcell))
ALLOCATE(cell_upd(mtot_c),cell_pbc(mtot_c))
cell_pbc=.FALSE.
DO ix=0,mx_c-1
DO iy=0,my_c-1
DO iz=0,mz_c-1
icell=cell_index(ix,iy,iz)
filter=.false.
gg=0
DO ii=-deltx,deltx
DO jj=-delty,delty
DO kk=-deltz,deltz
IF (aux_mask(ii,jj,kk).eqv..TRUE.) THEN
gg=gg+1
ncell=cell_index(ix+ii,iy+jj,iz+kk)
nsc_cell(icell,gg)=ncell
filter2=cells_pbc(icell,ncell)
IF (filter2.eqv..TRUE.) filter=.TRUE.
nsc_cell_pbc(icell,gg)=filter2
END IF
END DO
END DO
END DO
cell_pbc(icell)=filter
END DO
END DO
END DO
!PRINT*,COUNT(cell_pbc),'cells with pbc'
DEALLOCATE(aux_mask)
IF (ALLOCATED(gns_head)) DEALLOCATE(gns_head)
IF (ALLOCATED(gns_list)) DEALLOCATE(gns_list)
IF (ALLOCATED(gns_at_cell)) DEALLOCATE(gns_at_cell)
ALLOCATE(gns_head(mtot_c))
ALLOCATE(gns_list(natom))
ALLOCATE(gns_at_cell(natom))
END SUBROUTINE MAKE_CELL_NS
SUBROUTINE GRID_NS_LIST (coors,box,natom)
IMPLICIT NONE
INTEGER,INTENT(IN)::natom
DOUBLE PRECISION,DIMENSION(natom,3),INTENT(in)::coors
DOUBLE PRECISION,DIMENSION(3,3),INTENT(IN)::box
DOUBLE PRECISION::mx_c_L,my_c_L,mz_c_L
INTEGER::ii,icell
mx_c_L=(mx_c*1.0d0)/box(1,1)
my_c_L=(my_c*1.0d0)/box(2,2)
mz_c_L=(mz_c*1.0d0)/box(3,3)
gns_head=0
DO ii=1,natom
icell=1+int(coors(ii,1)*mx_c_L)+int(coors(ii,2)*my_c_L)*mx_c+int(coors(ii,3)*mz_c_L)*mx_my_c
gns_at_cell(ii)=icell
gns_list(ii)=gns_head(icell)
gns_head(icell)=ii
END DO
END SUBROUTINE GRID_NS_LIST
SUBROUTINE MAKE_VERLET_LIST_GRID_NS (r_ic,r_oc,pbc_opt,coors,box,vol,ortho,natom)
IMPLICIT NONE
DOUBLE PRECISION,INTENT(IN)::r_ic,r_oc
INTEGER,INTENT(IN)::pbc_opt,ortho
INTEGER,INTENT(IN)::natom
DOUBLE PRECISION,INTENT(IN)::vol
DOUBLE PRECISION,DIMENSION(natom,3),intent(in)::coors
DOUBLE PRECISION,DIMENSION(3,3),INTENT(IN)::box
DOUBLE PRECISION::r_ic2,r_oc2
DOUBLE PRECISION,DIMENSION(3)::vect,vect_aux
DOUBLE PRECISION::val_aux,pi,fact
!!! Hasta aqui 7.2 seg 1000 frames (3 min 25000)
INTEGER::ii,jj,gg,ll,kk,icell,ncell
INTEGER::gg_ic,gg_oc
INTEGER::gg2_ic,gg2_oc
LOGICAL::filter
CALL GRID_NS_LIST(coors,box,natom)
r_ic2=r_ic*r_ic
r_oc2=r_oc*r_oc
pi=acos(-1.0d0)
fact=(natom/vol)*(4.0d0*pi/3.0d0)*2.0d0 !! factor 1.50 to be safe, since f2py does not support derived types
dim_ic=CEILING(fact*(r_ic2*r_ic))+1
dim_oc=CEILING(fact*(r_oc2*r_oc))+1
IF (ALLOCATED(ver_ic_ind)) DEALLOCATE(ver_ic_ind)
IF (ALLOCATED(ver_ic_dim)) DEALLOCATE(ver_ic_dim)
IF (ALLOCATED(ver_oc_ind)) DEALLOCATE(ver_oc_ind)
IF (ALLOCATED(ver_oc_dim)) DEALLOCATE(ver_oc_dim)
IF (ALLOCATED(pos_ant)) DEALLOCATE(pos_ant)
ALLOCATE(ver_ic_ind(natom,dim_ic),ver_oc_ind(natom,dim_oc))
ALLOCATE(ver_ic_dim(natom),ver_oc_dim(natom))
ALLOCATE(pos_ant(natom,3))
pos_ant=coors
ver_ic_dim=0
ver_oc_dim=0
DO ii=1,natom
vect_aux=coors(ii,:)
icell=gns_at_cell(ii)
gg_oc=ver_oc_dim(ii)
gg_ic=ver_ic_dim(ii)
IF (cell_pbc(icell)) THEN
DO jj=1,nscxcell
ncell=nsc_cell(icell,jj)
filter=nsc_cell_pbc(icell,jj)
kk=gns_head(ncell)
DO
IF (kk==0) EXIT
IF (kk>ii) THEN
vect=(coors(kk,:)-vect_aux)
IF (filter) CALL PBC (vect,box,ortho)
val_aux=dot_product(vect,vect)
IF (val_aux<=r_oc2) THEN
gg_oc=gg_oc+1
ver_oc_ind(ii,gg_oc)=kk
gg2_oc=ver_oc_dim(kk)+1
ver_oc_ind(kk,gg2_oc)=ii
ver_oc_dim(kk)=gg2_oc
IF (val_aux<=r_ic2) THEN
gg_ic=gg_ic+1
ver_ic_ind(ii,gg_ic)=kk
gg2_ic=ver_ic_dim(kk)+1
ver_ic_ind(kk,gg2_ic)=ii
ver_ic_dim(kk)=gg2_ic
END IF
END IF
END IF
kk=gns_list(kk)
END DO
END DO
ELSE
DO jj=1,nscxcell
ncell=nsc_cell(icell,jj)
kk=gns_head(ncell)
DO
IF (kk==0) EXIT
IF (kk>ii) THEN
vect=(coors(kk,:)-vect_aux)
val_aux=dot_product(vect,vect)
IF (val_aux<=r_oc2) THEN
gg_oc=gg_oc+1
ver_oc_ind(ii,gg_oc)=kk
gg2_oc=ver_oc_dim(kk)+1
ver_oc_ind(kk,gg2_oc)=ii
ver_oc_dim(kk)=gg2_oc
IF (val_aux<=r_ic2) THEN
gg_ic=gg_ic+1
ver_ic_ind(ii,gg_ic)=kk
gg2_ic=ver_ic_dim(kk)+1
ver_ic_ind(kk,gg2_ic)=ii
ver_ic_dim(kk)=gg2_ic
END IF
END IF
END IF
kk=gns_list(kk)
END DO
END DO
END IF
ver_oc_dim(ii)=gg_oc
ver_ic_dim(ii)=gg_ic
END DO
END SUBROUTINE MAKE_VERLET_LIST_GRID_NS
SUBROUTINE UPDATE_VERLET_LIST_GRID_NS (r_ic,r_oc,pbc_opt,coors,box,vol,ortho,natom)
IMPLICIT NONE
DOUBLE PRECISION,INTENT(IN)::r_ic,r_oc
INTEGER,INTENT(IN)::pbc_opt,ortho
INTEGER,INTENT(IN)::natom
DOUBLE PRECISION,INTENT(IN)::vol
DOUBLE PRECISION,DIMENSION(natom,3),intent(in)::coors
DOUBLE PRECISION,DIMENSION(3,3),INTENT(IN)::box
LOGICAL::update,filter
INTEGER::ii,jj,kk,icell,ncell
DOUBLE PRECISION::val_aux
DOUBLE PRECISION::r_diff,drneimax,drneimax2,r_ic2,r_oc2
DOUBLE PRECISION,DIMENSION(3)::vect,vect_aux
INTEGER::gg_ic,gg_oc
INTEGER::gg2_ic,gg2_oc
update=.FALSE.
drneimax=0.0
drneimax2=0.0
r_oc2=r_oc*r_oc
r_ic2=r_ic*r_ic
r_diff=r_oc-r_ic
DO ii=1,natom
vect=pos_ant(ii,:)-coors(ii,:)
CALL PBC (vect,box,ortho)
val_aux=dot_product(vect,vect)
IF (val_aux > drneimax) THEN
drneimax2=drneimax
drneimax=val_aux
ELSE
IF (val_aux > drneimax2) THEN
drneimax2=val_aux
END IF
END IF
END DO
IF ((sqrt(drneimax)+sqrt(drneimax2))>r_diff) THEN
update=.TRUE.
END IF
IF (update) THEN
CALL GRID_NS_LIST(coors,box,natom)
pos_ant=coors
ver_ic_dim=0
ver_oc_dim=0
DO ii=1,natom
vect_aux=coors(ii,:)
icell=gns_at_cell(ii)
gg_oc=ver_oc_dim(ii)
gg_ic=ver_ic_dim(ii)
IF (cell_pbc(icell)) THEN
DO jj=1,nscxcell
ncell=nsc_cell(icell,jj)
filter=nsc_cell_pbc(icell,jj)
kk=gns_head(ncell)
DO
IF (kk==0) EXIT
IF (kk>ii) THEN
vect=(coors(kk,:)-vect_aux)
IF (filter) CALL PBC (vect,box,ortho)
val_aux=dot_product(vect,vect)
IF (val_aux<=r_oc2) THEN
gg_oc=gg_oc+1
ver_oc_ind(ii,gg_oc)=kk
gg2_oc=ver_oc_dim(kk)+1
ver_oc_ind(kk,gg2_oc)=ii
ver_oc_dim(kk)=gg2_oc
IF (val_aux<=r_ic2) THEN
gg_ic=gg_ic+1
ver_ic_ind(ii,gg_ic)=kk
gg2_ic=ver_ic_dim(kk)+1
ver_ic_ind(kk,gg2_ic)=ii
ver_ic_dim(kk)=gg2_ic
END IF
END IF
END IF
kk=gns_list(kk)
END DO
END DO
ELSE
DO jj=1,nscxcell
ncell=nsc_cell(icell,jj)
kk=gns_head(ncell)
DO
IF (kk==0) EXIT
IF (kk>ii) THEN
vect=(coors(kk,:)-vect_aux)
val_aux=dot_product(vect,vect)
IF (val_aux<=r_oc2) THEN
gg_oc=gg_oc+1
ver_oc_ind(ii,gg_oc)=kk
gg2_oc=ver_oc_dim(kk)+1
ver_oc_ind(kk,gg2_oc)=ii
ver_oc_dim(kk)=gg2_oc
IF (val_aux<=r_ic2) THEN
gg_ic=gg_ic+1
ver_ic_ind(ii,gg_ic)=kk
gg2_ic=ver_ic_dim(kk)+1
ver_ic_ind(kk,gg2_ic)=ii
ver_ic_dim(kk)=gg2_ic
END IF
END IF
END IF
kk=gns_list(kk)
END DO
END DO
END IF
ver_oc_dim(ii)=gg_oc
ver_ic_dim(ii)=gg_ic
END DO
ELSE
ver_ic_dim=0
DO ii=1,natom
vect_aux=coors(ii,:)
gg_ic=ver_ic_dim(ii)
icell=gns_at_cell(ii)
IF (cell_pbc(icell)) THEN
DO jj=1,ver_oc_dim(ii)
kk=ver_oc_ind(ii,jj)
IF (kk>ii) THEN
vect=(coors(kk,:)-vect_aux)
CALL PBC (vect,box,ortho)
val_aux=dot_product(vect,vect)
IF (val_aux<=r_ic2) THEN
gg_ic=gg_ic+1
ver_ic_ind(ii,gg_ic)=kk
gg2_ic=ver_ic_dim(kk)+1
ver_ic_ind(kk,gg2_ic)=ii
ver_ic_dim(kk)=gg2_ic
END IF
END IF
END DO
ver_ic_dim(ii)=gg_ic
ELSE
DO jj=1,ver_oc_dim(ii)
kk=ver_oc_ind(ii,jj)
IF (kk>ii) THEN
vect=(coors(kk,:)-vect_aux)
val_aux=dot_product(vect,vect)
IF (val_aux<=r_ic2) THEN
gg_ic=gg_ic+1
ver_ic_ind(ii,gg_ic)=kk
gg2_ic=ver_ic_dim(kk)+1
ver_ic_ind(kk,gg2_ic)=ii
ver_ic_dim(kk)=gg2_ic
END IF
END IF
END DO
ver_ic_dim(ii)=gg_ic
END IF
END DO
END IF
END SUBROUTINE UPDATE_VERLET_LIST_GRID_NS
SUBROUTINE EXTRACT_NS_LIST_SETS(diff_sets,list1,list2,n1,n2,numat_glob)
IMPLICIT NONE
INTEGER,INTENT(IN)::diff_sets,n1,n2,numat_glob
INTEGER,DIMENSION(n1),INTENT(IN)::list1
INTEGER,DIMENSION(n2),INTENT(IN)::list2
INTEGER::ii,jj,ai
LOGICAL,DIMENSION(:),ALLOCATABLE::filter
IF (ALLOCATED(filt_sets_ns_ind)) DEALLOCATE(filt_sets_ns_ind)
ALLOCATE(filt_sets_ns_ind(numat_glob,dim_ic))
filt_sets_ns_ind=.FALSE.
IF (diff_sets==1) THEN
ALLOCATE(filter(numat_glob))
filter=.FALSE.
DO ii=1,n2
filter(list2(ii)+1)=.TRUE.
END DO
DO ii=1,n1
ai=list1(ii)+1
DO jj=1,ver_ic_dim(ai)
IF (filter(ver_ic_ind(ai,jj))) THEN
filt_sets_ns_ind(ai,jj)=.TRUE.
END IF
END DO
END DO
filter=.FALSE.
DO ii=1,n1
filter(list1(ii)+1)=.TRUE.
END DO
DO ii=1,n2
ai=list2(ii)+1
DO jj=1,ver_ic_dim(ai)
IF (filter(ver_ic_ind(ai,jj))) THEN
filt_sets_ns_ind(ai,jj)=.TRUE.
END IF
END DO
END DO
DEALLOCATE(filter)
ELSE
ALLOCATE(filter(numat_glob))
filter=.FALSE.
DO ii=1,n2
filter(list2(ii)+1)=.TRUE.
END DO
DO ii=1,n1
ai=list1(ii)+1
DO jj=1,ver_ic_dim(ai)
IF (filter(ver_ic_ind(ai,jj))) THEN
filt_sets_ns_ind(ai,jj)=.TRUE.
END IF
END DO
END DO
DEALLOCATE(filter)
END IF
END SUBROUTINE EXTRACT_NS_LIST_SETS
SUBROUTINE DISTANCE (diff_syst,diff_set,pbc_opt,list1,coors1,box1,ortho1,list2,coors2,n1,n2,natom1,natom2,matrix)
IMPLICIT NONE
INTEGER,INTENT(IN)::diff_syst,diff_set,pbc_opt,ortho1
integer,intent(in)::n1,n2,natom1,natom2
INTEGER,DIMENSION(n1),INTENT(IN)::list1
INTEGER,DIMENSION(n2),INTENT(IN)::list2
double precision,dimension(natom1,3),intent(in)::coors1
double precision,DIMENSION(3,3),INTENT(IN)::box1
double precision,dimension(natom2,3),intent(in)::coors2
double precision,dimension(n1,n2),intent(out)::matrix
integer::i,j,ai,aj
double precision,dimension(:),allocatable::vect,vect_aux
integer,dimension(:),allocatable::llist1,llist2
double precision::val_aux
ALLOCATE(vect(3),vect_aux(3))
ALLOCATE(llist1(n1),llist2(n2))
llist1=list1+1
llist2=list2+1
matrix=0.0d0
IF ((diff_syst==1) .or. (diff_set==1)) THEN
IF (pbc_opt==1) THEN
do i=1,n1
ai=llist1(i)
vect_aux=coors1(ai,:)
do j=1,n2
aj=llist2(j)
vect=(coors2(aj,:)-vect_aux)
CALL PBC (vect,box1,ortho1)
val_aux=sqrt(dot_product(vect,vect))
matrix(i,j)=val_aux
end do
end do
ELSE
do i=1,n1
ai=llist1(i)
vect_aux=coors1(ai,:)
do j=1,n2
aj=llist2(j)
vect=(coors2(aj,:)-vect_aux)
val_aux=sqrt(dot_product(vect,vect))
matrix(i,j)=val_aux