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426 lines (411 loc) · 16.4 KB
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!*****************************************************************************************
subroutine elim_white_space(string)
implicit none
character(256), intent(inout):: string
!local variables
integer:: i, j
do i=1,256
if(string(1:1)==' ') then
do j=1,256-i
string(j:j)=string(j+1:j+1)
enddo
string(256-i+1:256-i+1)=''
else
exit
endif
enddo
end subroutine elim_white_space
!*****************************************************************************************
function delta_kronecker(i,j) result(delta)
implicit none
integer, intent(in):: i, j
!local variables
real(8):: delta
if(i==j) then
delta=1.d0
else
delta=0.d0
endif
end function delta_kronecker
!*****************************************************************************************
!This subroutine will transform back all atoms into the periodic cell
!defined by the 3 lattice vectors in latvec=[v1.v2.v3]
subroutine backtocell_alborz(nat,latvec,rxyz_red)
implicit none
integer, intent(in):: nat
real(8), intent(in):: latvec(3,3)
real(8), intent(inout):: rxyz_red(3,nat)
!local variables
real(8):: vol
integer:: iat
!First check if the volume is positive
call getvol_alborz(latvec,vol)
if(vol.le.0.d0) stop "Negative volume during backtocell_alborz"
do iat=1,nat
rxyz_red(1,iat)=modulo(modulo(rxyz_red(1,iat),1.d0),1.d0)
rxyz_red(2,iat)=modulo(modulo(rxyz_red(2,iat),1.d0),1.d0)
rxyz_red(3,iat)=modulo(modulo(rxyz_red(3,iat),1.d0),1.d0)
enddo
end subroutine backtocell_alborz
!*****************************************************************************************
subroutine getvol_alborz(cellvec,vol)
implicit none
real(8), intent(in):: cellvec(3,3)
real(8), intent(out):: vol
vol=cellvec(1,1)*cellvec(2,2)*cellvec(3,3)-cellvec(1,1)*cellvec(2,3)*cellvec(3,2)- &
cellvec(1,2)*cellvec(2,1)*cellvec(3,3)+cellvec(1,2)*cellvec(2,3)*cellvec(3,1)+ &
cellvec(1,3)*cellvec(2,1)*cellvec(3,2)-cellvec(1,3)*cellvec(2,2)*cellvec(3,1)
if(vol<0.d0) stop 'ERROR: Negative volume!'
end subroutine getvol_alborz
!*****************************************************************************************
!This routine computes the distance of the reduced coordinates xred_1 and xred_2 and applies
!periodic boundary conditions to them and computes the squared distance
subroutine pbc_distance1_alborz(cellvec,xred_1,xred_2,distance2,dxyz)
implicit none
real(8), intent(in):: cellvec(3,3), xred_1(3), xred_2(3)
real(8), intent(inout):: distance2, dxyz(3)
!local variables
integer:: i
real(8):: diff(3)
diff(1:3)=xred_2(1:3)-xred_1(1:3)
do i=1,3
if(.not. diff(i)>-0.5d0) then
diff(i)=diff(i)+1.d0
elseif(diff(i)>0.5d0) then
diff(i)=diff(i)-1.d0
endif
enddo
!dxyz=matmul(cellvec,diff)
dxyz(1)=cellvec(1,1)*diff(1)+cellvec(1,2)*diff(2)+cellvec(1,3)*diff(3)
dxyz(2)=cellvec(2,1)*diff(1)+cellvec(2,2)*diff(2)+cellvec(2,3)*diff(3)
dxyz(3)=cellvec(3,1)*diff(1)+cellvec(3,2)*diff(2)+cellvec(3,3)*diff(3)
distance2=dxyz(1)*dxyz(1)+dxyz(2)*dxyz(2)+dxyz(3)*dxyz(3)
end subroutine pbc_distance1_alborz
!*****************************************************************************************
!This subroutine will return how many periodic expansions for each lattice vector
!direction are necessary for the periodic boundary conditions
!with for the given rcut. nec1,nec2,nec3 for latvec(:,1),latvec(:,2),latvec(:,3)
subroutine n_rep_dim_alborz(cellvec,rcut,nec1,nec2,nec3)
implicit none
real(8), intent(in):: cellvec(3,3), rcut
integer, intent(out):: nec1, nec2, nec3
!local variables
real(8):: zero(3), dist(3)
real(8):: vn(3,3) !normalized normal vector of the planes form by cell vectors
integer:: i
nec1=0 ; nec2=0 ; nec3=0
call nveclatvec_alborz(cellvec,vn)
zero=(/0.d0,0.d0,0.d0/)
do i=1,3
call dist2plane_alborz(cellvec(1,mod(i+1,3)+1),vn(1,i),zero,dist(i))
!write(*,*) "rcut",i,rcut, dist
enddo
nec1=int(rcut/dist(2))+1
nec2=int(rcut/dist(3))+1
nec3=int(rcut/dist(1))+1
end subroutine n_rep_dim_alborz
!*****************************************************************************************
!Will calculate the normalized normal vector to the 3 planes of the cell
subroutine nveclatvec_alborz(cellvec,vn)
implicit none
real(8), intent(in) :: cellvec(3,3)
real(8), intent(out):: vn(3,3)
!local variables
real(8):: v(3), vnorm
integer:: i
do i=1,3
call cross_product_alborz(cellvec(1,i),cellvec(1,mod(i,3)+1),v)
vnorm=sqrt(v(1)*v(1)+v(2)*v(2)+v(3)*v(3))
vn(1,i)=v(1)/vnorm
vn(2,i)=v(2)/vnorm
vn(3,i)=v(3)/vnorm
enddo
end subroutine nveclatvec_alborz
!*****************************************************************************************
!This subroutine will calculate the distance between a plane and a point in space
!The point is 'r1', the normalized normal vector of the plane is 'nvec',
!'r0' is an arbitrary point on the plane !and the output is the distance 'dist'
subroutine dist2plane_alborz(r1,vn,r0,dist)
implicit none
real(8), intent(in):: r1(3), vn(3), r0(3)
real(8), intent(out):: dist
!local variables
real(8):: rd(3)
rd(1)=r1(1)-r0(1)
rd(2)=r1(2)-r0(2)
rd(3)=r1(3)-r0(3)
dist=abs(rd(1)*vn(1)+rd(2)*vn(2)+rd(3)*vn(3))
end subroutine dist2plane_alborz
!*****************************************************************************************
!This routine will write the file "filename" in ascii file format
!The input unit will always be in atomic units (bohr, hartree), but the output can be specified by the vaule in "units"
!So if units==angstroem, the file will be converted to angstroem
! if units==bohr, the positions will not be changed
subroutine write_atomic_file_ascii_alborz(filename,nat,xred,latvec0,energy,pressure,printval1,printval2,kinds)
implicit none
integer:: nat,natin,iat
character(40):: filename,units
real(8):: pos(3,nat),xred(3,nat),latvec(3,3),latvec0(3,3),dproj(6),rotmat(3,3),v(3,3),ucvol
real(8):: angbohr,hartree2ev,in_GPA,in_ang3,int_press
real(8):: energy, etotal, enthalpy, enthalpy_at,pressure,printval1,printval2
integer:: Kinds(nat)
if(trim(units)=="angstroem") then
angbohr=1.d0/1.889725989d0
hartree2ev=27.211396132d0
in_GPA=29421.033d0
in_ang3=0.148184743d0
int_press=160.217646200d0
elseif(trim(units)=="bohr") then
angbohr=1.d0
hartree2ev=1.d0
in_GPA=1.d0
in_ang3=1.d0
int_press=1.d0
else
angbohr=1.d0
hartree2ev=1.d0
in_GPA=1.d0
in_ang3=1.d0
int_press=1.d0
endif
!latvec(:,1)=acell(1)*rprim(:,1)
!latvec(:,2)=acell(2)*rprim(:,2)
!latvec(:,3)=acell(3)*rprim(:,3)
latvec=latvec0
do iat=1,nat
pos(:,iat)=matmul(latvec,xred(:,iat))
enddo
call latvec2dproj_alborz(dproj,latvec,rotmat,pos,nat)
!Compute cell volume
v=latvec
ucvol= v(1,1)*v(2,2)*v(3,3)-v(1,1)*v(2,3)*v(3,2)-v(1,2)*v(2,1)*v(3,3)+&
v(1,2)*v(2,3)*v(3,1)+v(1,3)*v(2,1)*v(3,2)-v(1,3)*v(2,2)*v(3,1)
!Convert units
!!!The second entry in the first line is the enthalpy in atomic units
!!enthalpy_at=energy+pressure*ucvol
dproj=dproj*angbohr
pos=pos*angbohr
etotal=energy*hartree2ev
enthalpy=energy*hartree2ev+pressure*in_GPA/int_press*ucvol*in_ang3
ucvol=ucvol*in_ang3
open(unit=46,file=trim(filename))
write(46,'(i4,1x,es25.15,1x,es25.15,1x,a20,es15.7,a14,es15.7,a13,es15.7)')&
& nat,printval1,printval2," energy(Ha)=",etotal," enthalpy(Ha)=",enthalpy,&
&" ucvol(bhr3)=",ucvol
write(46,*) dproj(1:3)
write(46,*) dproj(4:6)
do iat=1,nat
if(kinds(iat)==1) write(46,'(3(1x,es25.15),2x,a2)') pos(:,iat),"A "
if(kinds(iat)==2) write(46,'(3(1x,es25.15),2x,a2)') pos(:,iat),"B "
enddo
close(46)
end subroutine write_atomic_file_ascii_alborz
!*****************************************************************************************
!This subroutine will convert the distance and projective representation of
!a periodic cell (dxx,dyx,dyy,dzx,dzy,dzz) into a
!lattice vektor format (vec1(:,1),vec2(:,2),vec3(:,3)) with dxx oriented into x direction
subroutine dproj2latvec_alborz(dproj,cellvec)
implicit none
real(8), intent(in):: dproj(6)
real(8), intent(out):: cellvec(3,3)
!local variables
cellvec(1,1)=dproj(1) ; cellvec(1,2)=dproj(2) ; cellvec(1,3)=dproj(4)
cellvec(2,1)=0.d0 ; cellvec(2,2)=dproj(3) ; cellvec(2,3)=dproj(5)
cellvec(3,1)=0.d0 ; cellvec(3,2)=0.d0 ; cellvec(3,3)=dproj(6)
end subroutine dproj2latvec_alborz
!*****************************************************************************************
!This subroutine will convert the lattice vector representation of thei
!periodic cell (vec1,vec2,vec3) into the projective representation (dxx,dyx,dyy,dzx,dzy,dzz)
!The cell will thus be rotated. The rotational matrix is stored in rotmat as an operator rotmat
!and the atomic position rxyz are transformed into the new coordination sizstem as well
subroutine latvec2dproj_alborz(dproj,latvec,rotmat,rxyz,nat)
implicit none
integer, intent(in):: nat
real(8),intent(inout):: dproj(6), latvec(3,3), rotmat(3,3), rxyz(3,nat)
!local variables
real(8):: tempvec(3), rotmat1(3,3), rotmat2(3,3), crossp(3), alpha, latvect(3,3)
real(8):: eps,axe(3), anrm,rxyzt(3), rotmatt(3,3)
integer:: iat,i
eps=1.d-6
!Calculating dxx
dproj(1)=sqrt(latvec(1,1)*latvec(1,1)+latvec(2,1)*latvec(2,1)+latvec(3,1)*latvec(3,1))
!Calculate the first rotation to align the first axis in x direction
rotmat1(:,:)=0.d0
do i=1,3
rotmat1(i,i)=1.d0
enddo
tempvec(:)=0.d0
tempvec(1)=1.d0
!tempvec is the x-unit vector
call cross_product_alborz(latvec(:,1),tempvec,crossp)
if (abs(crossp(1)).lt.eps*1.d-1 .and. abs(crossp(2)).lt.eps*1.d-1 .and. abs(crossp(3)).lt.eps*1.d-1) goto 1001 !no rotation needed
anrm=sqrt(crossp(1)*crossp(1)+crossp(2)*crossp(2)+crossp(3)*crossp(3))
axe(:)=crossp(:)/anrm
alpha=dacos(dot_product(tempvec,latvec(:,1))/dproj(1))
call rotation_alborz(alpha,axe,rotmat1)
latvec(:,:)=matmul(rotmat1(:,:),latvec(:,:))
! call DGEMM('N','N',3,3,3,1.d0,rotmat,3,latvec,3,0.d0,latvect,3)
! latvec=latvect
1001 continue
if(latvec(2,1).gt.eps .or. latvec(3,1).gt.eps) then
write(*,*) "Error in 1. rotation",latvec(2,1),latvec(3,1)
stop
endif
!Calculate the second rotation to align the second axis in xy plane
rotmat2(:,:)=0.d0
do i=1,3
rotmat2(i,i)=1.d0
enddo
! axe(:)=0.d0
! axe(1)=1.d0
tempvec(:)=latvec(:,2)
tempvec(1)=0.d0
call cross_product_alborz(tempvec,(/0.d0,1.d0,0.d0/),axe)
if (abs(axe(1)).lt.eps*1.d-1 .and. abs(axe(2)).lt.eps*1.d-1 .and. abs(axe(3)).lt.eps*1.d-1 .and. tempvec(2).gt.0.d0) goto 1002 !no rotation needed
anrm=sqrt(axe(1)*axe(1)+axe(2)*axe(2)+axe(3)*axe(3))
axe=axe/anrm
call cross_product_alborz(axe,latvec(:,2),crossp)
if (abs(crossp(1)).lt.eps*1.d-1 .and. abs(crossp(2)).lt.eps*1.d-1 .and. crossp(3).gt.0.d0) goto 1002 !no rotation needed
anrm=sqrt(tempvec(2)*tempvec(2)+tempvec(3)*tempvec(3))
alpha=dot_product((/0.d0,1.d0,0.d0/),tempvec(:))/anrm
alpha=dacos(alpha)
call rotation_alborz(alpha,axe,rotmat2)
latvec(:,:)=matmul(rotmat2(:,:),latvec(:,:))
! call DGEMM('N','N',3,3,3,1.d0,rotmat,3,latvec,3,0.d0,latvect,3)
! latvec=latvect
1002 continue
if(latvec(3,2).gt.eps) then! stop "Error in 2. rotation"
! write(*,*) latvec(:,1)
! write(*,*) latvec(:,2)
write(*,*) "Error in 2. rotation"
stop
endif
if(latvec(3,3).lt.0.d0) stop "Error in orientation of the cell"
!The total rotational matrix:
rotmat=matmul(rotmat2(:,:),rotmat1(:,:))
! call DGEMM('N','N',3,3,3,1.d0,rotmat2,3,rotmat1,3,0.d0,rotmatt,3)
! rotmat=rotmatt
!Apply rotation on all atoms
do iat=1,nat
rxyz(:,iat)=matmul(rotmat,rxyz(:,iat))
! call DGEMM('N','N',3,3,3,1.d0,rotmat,3,latvec,3,0.d0,latvect,3)
! rxyz(:,iat)=rxyzt(:)
enddo
!Calculate all other elements of dproj
dproj(2)=latvec(1,2)
dproj(3)=latvec(2,2)
dproj(4)=latvec(1,3)
dproj(5)=latvec(2,3)
dproj(6)=latvec(3,3)
end subroutine latvec2dproj_alborz
!*****************************************************************************************
!a very simple implementation of the cross product
subroutine cross_product_alborz(a,b,c)
implicit none
real(8), intent(in):: a(3), b(3)
real(8), intent(out):: c(3)
c(1)=a(2)*b(3)-a(3)*b(2)
c(2)=a(3)*b(1)-a(1)*b(3)
c(3)=a(1)*b(2)-a(2)*b(1)
end subroutine cross_product_alborz
!*****************************************************************************************
!This subroutine will calculate the rotational matrix rotmat for a
!3-dim vector around an axis 'axe' by the angle 'angle'.
subroutine rotation_alborz(angle,axe,rotmat)
implicit none
real(8), intent(in):: angle
real(8), intent(in):: axe(3)
real(8), intent(out):: rotmat(3,3)
!local variables
!Define Rotation Matrix
rotmat(1,1)=cos(angle)+(axe(1)**2)*(1.d0-cos(angle))
rotmat(1,2)=axe(1)*axe(2)*(1.d0-cos(angle))-axe(3)*dsin(angle)
rotmat(1,3)=axe(1)*axe(3)*(1.d0-cos(angle))+axe(2)*dsin(angle)
rotmat(2,1)=axe(2)*axe(1)*(1.d0-cos(angle))+axe(3)*dsin(angle)
rotmat(2,2)=cos(angle)+(axe(2)**2)*(1.d0-cos(angle))
rotmat(2,3)=axe(2)*axe(3)*(1.d0-cos(angle))-axe(1)*dsin(angle)
rotmat(3,1)=axe(3)*axe(1)*(1.d0-cos(angle))-axe(2)*dsin(angle)
rotmat(3,2)=axe(3)*axe(2)*(1.d0-cos(angle))+axe(1)*dsin(angle)
rotmat(3,3)=cos(angle)+(axe(3)**2)*(1.d0-cos(angle))
!do i=1,3
! vector2(i)=rotator(i,1)*vector(1)+rotator(i,2)*vector(2)+rotator(i,3)*vector(3)
!enddo
!vector(:)=vector2(:)
end subroutine rotation_alborz
!*****************************************************************************************
!This subrtouine will transform theforces initially in the cartesian system into the
!internal coordinates with respect to the cell vectors provided in the cv
subroutine fxyz_cart2int_alborz(nat,v_cart,cv,v_int)
implicit none
integer, intent(in):: nat
real(8), intent(in):: v_cart(3,nat), cv(3,3)
real(8), intent(out):: v_int(3,nat)
!local variables
integer:: iat
do iat=1,nat
v_int(1,iat)=cv(1,1)*v_cart(1,iat)+cv(2,1)*v_cart(2,iat)+cv(3,1)*v_cart(3,iat)
v_int(2,iat)=cv(1,2)*v_cart(1,iat)+cv(2,2)*v_cart(2,iat)+cv(3,2)*v_cart(3,iat)
v_int(3,iat)=cv(1,3)*v_cart(1,iat)+cv(2,3)*v_cart(2,iat)+cv(3,3)*v_cart(3,iat)
enddo
end subroutine fxyz_cart2int_alborz
!*****************************************************************************************
subroutine fxyz_red2cart(nat,fint,cv,fcart)
implicit none
integer, intent(in):: nat
real(8), intent(in):: fint(3,nat), cv(3,3)
real(8), intent(out):: fcart(3,nat)
!local variables
integer:: iat
real(8):: cvinv(3,3)
call invertmat_alborz(cv,cvinv)
do iat=1,nat
fcart(1,iat)=cvinv(1,1)*fint(1,iat)+cvinv(2,1)*fint(2,iat)+cvinv(3,1)*fint(3,iat)
fcart(2,iat)=cvinv(1,2)*fint(1,iat)+cvinv(2,2)*fint(2,iat)+cvinv(3,2)*fint(3,iat)
fcart(3,iat)=cvinv(1,3)*fint(1,iat)+cvinv(2,3)*fint(2,iat)+cvinv(3,3)*fint(3,iat)
enddo
end subroutine fxyz_red2cart
!*****************************************************************************************
subroutine count_words(str,n)
implicit none
character(*), intent(in):: str
integer, intent(out):: n
!local variables
integer:: ind, k
character(50):: word
character(256):: str2
str2=str
n=0
word=''
do
str2=adjustl(str2)
read(str2,*,iostat=k) word
!write(*,'(i3,1x,a,i5)') n,trim(word),len_trim(word)
if(len_trim(word)==0) return
ind=index(str2,trim(word))
!write(*,'(2i3)') ind,ind+len_trim(word)-1
str2(ind:ind+len_trim(word)-1)=' '
!write(*,*) 'updated str2',trim(str2)
n=n+1
word=''
!write(*,*)
enddo
end subroutine count_words
!*****************************************************************************************
subroutine count_substring(str1,str2,n)
implicit none
character(*), intent(in) :: str1, str2
integer, intent(out):: n
!local variables
integer:: m, ind
stop 'ERROR: this subroutine is not tested'
n=0
if(len(str2)==0) return
m=1
do
ind=index(str1(m:),str2)
if(ind==0) return
n=n+1
m=m+ind+len(str2)
enddo
end subroutine count_substring
!*****************************************************************************************
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