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Hi everyone! Please recommend literature that reviews the topological analysis of the ELF, LOL and Laplacian functions. The meaning of the critical points (3;+1), (3;-1) and (3;+3) in the context of these functions is not entirely clear
Will a function for outputting a .wfn file with promolecular wavefunction be added someday so that only xyz and "atomwfn" can be used to generate this file, and not a .wfn file with real wavefunction, calculated in the same basis as the atoms in "atomwfn"?
Hello! i need to use aspherical atomic density to build promolecular density, but i dont understand how to do it, because function 100(hidden option) > 10 give spherical avaraged density even if i use atom.wfn file with aspherical density. i rewrote subroutine sphatmraddens to get values for all (r;theta;phi) points, but i dont understand how to use this data for building promolecular density. i attach my code and file density.txt for some atom which i get with the help of my code. should i create new lagintpol in (r,theta,phi) space to use my data in building promolecular density with calcprodens(x,y,z,0)? or what? help me please
subroutine sphatmraddens
use defvar
use util
use functions
implicit real*8 (a-h,o-z)
! Declare variables
real*8, allocatable :: radx(:), rady(:), radz(:), radpos(:), density(:)
integer :: ntheta, nphi
real*8 :: theta, phi
integer :: irad, itheta, iphi, idx
real*8 :: rad, x, y, z
integer :: ifinish, iprogstp, iprogcrit, nradpt
integer :: itmp
parameter (truncrho = 1D-8, rlow = 0D0, rhigh = 12D0, nradpt = 200, ntheta = 50, nphi = 100)
! Allocate arrays
allocate(radx(nradpt), rady(nradpt), radz(nradpt), radpos(nradpt), density(nradpt*ntheta*nphi))
ifinish = 0
iprogstp = 20
iprogcrit = iprogstp
write(*,*) "Calculating..."
! Parallel loop
!$OMP PARALLEL DO SHARED(density, radpos, ifinish, iprogcrit) PRIVATE(irad, itheta, iphi, rad, x, y, z, theta, phi, idx) schedule(dynamic) NUM_THREADS(nthreads)
do irad = 1, nradpt
rad = rlow + (rhigh - rlow) * (irad - 1) / (nradpt - 1)
radpos(irad) = rad
do itheta = 0, ntheta-1
theta = pi * itheta / (ntheta - 1) ! theta ranges from 0 to pi
do iphi = 0, nphi-1
phi = 2 * pi * iphi / nphi ! phi ranges from 0 to 2*pi
x = rad * sin(theta) * cos(phi)
y = rad * sin(theta) * sin(phi)
z = rad * cos(theta)
idx = (irad - 1) * ntheta * nphi + itheta * nphi + iphi + 1
! Compute density
density(idx) = fdens(x, y, z)
end do
end do
ifinish = ifinish + 1
if (ifinish >= iprogcrit) then
call showprog(ifinish, nradpt)
iprogcrit = iprogcrit + iprogstp
end if
end do
!$OMP END PARALLEL DO
! Output results
open(10, file="density.txt", status="replace")
itmp = 0
do irad = 1, nradpt
do itheta = 0, ntheta-1
theta = pi * itheta / (ntheta - 1)
do iphi = 0, nphi-1
phi = 2 * pi * iphi / nphi
idx = (irad - 1) * ntheta * nphi + itheta * nphi + iphi + 1
if (density(idx) > truncrho) then
itmp = itmp + 1
write(10, "(' r=', f12.6, ' theta=', f12.6, ' phi=', f12.6, ' density=', f25.10, 'D0')") radpos(irad), theta, phi, density(idx)
end if
end do
end do
end do
close(10)
write(*,*) "The result has been output to density.txt in the current folder"
end subroutine sphatmraddensi get correct values for all (r,theta,phi) points with this code, but i need to construct density with this values (do not pay attention that the density values are small, in my case it should be so)
file: https://drive.google.com/file/d/136n0jN … sp=sharing
p.s. may be my way to build promolecular density with aspherical atomic densities is bad? is there other way to do it?
i need to use molecule.xyz input and then analyze promolecular density, so 1000>17 doesnt suit me because i need molecule.wfn file for it
i need to modify this part of 'calchessmat_prodens' subroutine to get good promolecular density and calculate its derivatives for all elements. the following part of code doesnt calculate derivatives in the nuclear positions (but value of promolecular density is good calculated), however, in non-nuclear positions the derivative is calculated normally, what should I write in the following code to get derivatives in nuclear positionsn? (i ask this because if i use "output prop in point" for the iuserfunc==-2 function then i get derivatives at nuclear positions, but in the case below (elerho from my new calchessmat_prodens) i don't get derivatives of elerho in nuclear positions, only value)
if (iele>=1) then
if (r>atmrhocut(iele)) cycle
call genatmraddens(iele,rhoarr,npt) !Extract spherically averaged radial density of corresponding element at specific grids
if (idohess==0) then
call lagintpol(atmradpos(1:npt),rhoarr(1:npt),npt,r,term,der1r,der2r,2)
else if (idohess==1) then
call lagintpol(atmradpos(1:npt),rhoarr(1:npt),npt,r,term,der1r,der2r,3)
end if
elerho=elerho+term
der1rdr=der1r/r
derx=derx+der1rdr*rx
dery=dery+der1rdr*ry
derz=derz+der1rdr*rz
if (idohess==1) then
tmpval=(der2r-der1rdr)/r2
dxx=dxx+der1rdr+tmpval*rx2
dyy=dyy+der1rdr+tmpval*ry2
dzz=dzz+der1rdr+tmpval*rz2
dxy=dxy+tmpval*rx*ry
dyz=dyz+tmpval*ry*rz
dxz=dxz+tmpval*rx*rz
end if
end ifthank you soooo much
but so, im following to your advice to modife calchessmat_prodens code to generate good promoldens
i did this:
(i changed 'if ele<=18' to 'if ele >=118)
subroutine calchessmat_prodens(xin,yin,zin,elerho,elegrad,elehess)
use util
real*8 elerho,xin,yin,zin
real*8,optional :: elegrad(3),elehess(3,3)
real*8 posarr(200),rhoarr(200),tvec(3)
elerho=0D0
derx=0D0
dery=0D0
derz=0D0
dxx=0D0
dyy=0D0
dzz=0D0
dxy=0D0
dyz=0D0
dxz=0D0
idohess=0
if (present(elehess)) idohess=1
call getpointcell(xin,yin,zin,ic,jc,kc)
do icell=ic-PBCnx,ic+PBCnx
? ? do jcell=jc-PBCny,jc+PBCny
? ? ? ? do kcell=kc-PBCnz,kc+PBCnz
? ? ? ? ? ? call tvec_PBC(icell,jcell,kcell,tvec)
? ? ? ? ? ? do i=1,nfragatm
? ?? ? ? ? ? ? ?iatm=fragatm(i)
? ?? ? ? ? ? ? ?iele=a(iatm)%index
? ?? ? ? ? ? ? ?!rx=a(iatm)%x+tvec(1)-xin !Wrong code, older than 2022-Sep-18
? ?? ? ? ? ? ? ?!ry=a(iatm)%y+tvec(2)-yin
? ?? ? ? ? ? ? ?!rz=a(iatm)%z+tvec(3)-zin
? ?? ? ? ? ? ? ?rx=xin-tvec(1)-a(iatm)%x !Relative x
? ?? ? ? ? ? ? ?ry=yin-tvec(2)-a(iatm)%y
? ?? ? ? ? ? ? ?rz=zin-tvec(3)-a(iatm)%z
? ?? ? ? ? ? ? ?rx2=rx*rx
? ?? ? ? ? ? ? ?ry2=ry*ry
? ?? ? ? ? ? ? ?rz2=rz*rz
? ?? ? ? ? ? ? ?r2=rx2+ry2+rz2
? ?? ? ? ? ? ? ?r=dsqrt(r2)
? ?? ? ? ? ? ? ?if (iele>=118) then !H~Ar, use Weitao Yang's fitted parameters as original RDG paper
? ?? ? ? ? ? ? ? ? ?if (atomdenscut==1) then !Tight cutoff, for CHNO corresponding to cutoff at rho=0.00001
? ? ? ?? ? ? ? ? ? ? ? ?if (iele==1.and.r2>25D0) then !H, 6.63^2=43.9569. But this seems to be unnecessarily large, so I use 5^2=25
? ? ? ? ? ?? ? ? ? ? ? ? ? ?cycle
? ? ? ?? ? ? ? ? ? ? ? ?else if (iele==6.and.r2>58.6756D0) then !C, 7.66^2=58.6756
? ? ? ? ? ?? ? ? ? ? ? ? ? ?cycle
? ? ? ?? ? ? ? ? ? ? ? ?else if (iele==7.and.r2>43.917129D0) then !N, 6.627^2=43.917129
? ? ? ? ? ?? ? ? ? ? ? ? ? ?cycle
? ? ? ?? ? ? ? ? ? ? ? ?else if (iele==8.and.r2>34.9281D0) then !O, 5.91^2=34.9281
? ? ? ? ? ?? ? ? ? ? ? ? ? ?cycle
? ? ? ?? ? ? ? ? ? ? ? ?else if (r2>(2.5D0*vdwr(iele))**2) then !Other cases, larger than 2.5 times of its vdw radius will be skipped
? ? ? ? ? ?? ? ? ? ? ? ? ? ?cycle
? ? ? ?? ? ? ? ? ? ? ? ?end if
? ?? ? ? ? ? ? ? ? ?else if (atomdenscut==2) then !Medium cutoff, the result may be not as accurate as atomdenscut==1, but much more cheaper
? ? ? ?? ? ? ? ? ? ? ? ?if (r2>(2.2D0*vdwr(iele))**2) cycle
? ?? ? ? ? ? ? ? ? ?else if (atomdenscut==3) then !Loose cutoff, the most inaccurate
? ? ? ?? ? ? ? ? ? ? ? ?if (r2>(1.8D0*vdwr(iele))**2) cycle
? ?? ? ? ? ? ? ? ? ?else if (atomdenscut==4) then !Foolish cutoff, you need to know what you are doing
? ? ? ?? ? ? ? ? ? ? ? ?if (r2>(1.5D0*vdwr(iele))**2) cycle
? ?? ? ? ? ? ? ? ? ?end if
? ? ? ?? ? ? ? ? ? ?r2_1d5=r2**1.5D0
? ? ? ?? ? ? ? ? ? ?do iSTO=1,3
? ? ? ? ? ?? ? ? ? ? ? ?if (YWTatomcoeff(iele,iSTO)==0D0) cycle
? ? ? ? ? ?? ? ? ? ? ? ?expterm=YWTatomexp(iele,iSTO)
? ? ? ? ? ?? ? ? ? ? ? ?term=YWTatomcoeff(iele,iSTO)*dexp(-r/expterm)
? ? ? ? ? ?? ? ? ? ? ? ?elerho=elerho+term
? ? ? ? ? ?? ? ? ? ? ? ?if (r==0D0) cycle !Derivative of STO at nuclei is pointless
? ? ? ? ? ?? ? ? ? ? ? ?tmp=term/expterm/r
? ? ? ? ? ?? ? ? ? ? ? ?derx=derx-tmp*rx !Calculating gradient doesn't cost detectable time, so always calculate it
? ? ? ? ? ?? ? ? ? ? ? ?dery=dery-tmp*ry
? ? ? ? ? ?? ? ? ? ? ? ?derz=derz-tmp*rz
? ? ? ? ? ?? ? ? ? ? ? ?if (idohess==1) then
? ? ? ? ? ? ? ?? ? ? ? ? ? ?tmp1=1/r2_1d5/expterm
? ? ? ? ? ? ? ?? ? ? ? ? ? ?tmp2=1/r2/(expterm*expterm)
? ? ? ? ? ? ? ?? ? ? ? ? ? ?dxx=dxx+term*(tmp1*rx2-1/r/expterm+tmp2*rx2)
? ? ? ? ? ? ? ?? ? ? ? ? ? ?dyy=dyy+term*(tmp1*ry2-1/r/expterm+tmp2*ry2)
? ? ? ? ? ? ? ?? ? ? ? ? ? ?dzz=dzz+term*(tmp1*rz2-1/r/expterm+tmp2*rz2)
? ? ? ? ? ? ? ?? ? ? ? ? ? ?tmp=term*(tmp1+tmp2)
? ? ? ? ? ? ? ?? ? ? ? ? ? ?dxy=dxy+rx*ry*tmp
? ? ? ? ? ? ? ?? ? ? ? ? ? ?dyz=dyz+ry*rz*tmp
? ? ? ? ? ? ? ?? ? ? ? ? ? ?dxz=dxz+rx*rz*tmp
? ? ? ? ? ?? ? ? ? ? ? ?end if
? ? ? ?? ? ? ? ? ? ?end do
? ?? ? ? ? ? ? ?else !Heavier than Ar
? ? ? ? ? ? ? ? ? ? if (r>atmrhocut(iele)) cycle
? ? ? ?? ? ? ? ? ? ?call genatmraddens(iele,rhoarr,npt) !Extract spherically averaged radial density of corresponding element at specific grids
? ? ? ?? ? ? ? ? ? ?if (idohess==0) then
? ? ? ? ? ? ? ? ? ? ? ? call lagintpol(atmradpos(1:npt),rhoarr(1:npt),npt,r,term,der1r,der2r,2)
? ? ? ?? ? ? ? ? ? ?else if (idohess==1) then
? ? ? ? ? ? ? ? ? ? ? ? call lagintpol(atmradpos(1:npt),rhoarr(1:npt),npt,r,term,der1r,der2r,3)
? ? ? ? ? ? ? ? ? ? end if
? ? ? ?? ? ? ? ? ? ?elerho=elerho+term
? ? ? ?? ? ? ? ? ? ?der1rdr=der1r/r
? ? ? ?? ? ? ? ? ? ?derx=derx+der1rdr*rx
? ? ? ?? ? ? ? ? ? ?dery=dery+der1rdr*ry
? ? ? ?? ? ? ? ? ? ?derz=derz+der1rdr*rz
? ? ? ?? ? ? ? ? ? ?if (idohess==1) then !See promolecular_grid routine in props.f90 of NCIplot
? ? ? ? ? ?? ? ? ? ? ? ?tmpval=(der2r-der1rdr)/r2
? ? ? ? ? ?? ? ? ? ? ? ?dxx=dxx+der1rdr+tmpval*rx2
? ? ? ? ? ?? ? ? ? ? ? ?dyy=dyy+der1rdr+tmpval*ry2
? ? ? ? ? ?? ? ? ? ? ? ?dzz=dzz+der1rdr+tmpval*rz2
? ? ? ? ? ?? ? ? ? ? ? ?dxy=dxy+tmpval*rx*ry
? ? ? ? ? ?? ? ? ? ? ? ?dyz=dyz+tmpval*ry*rz
? ? ? ? ? ?? ? ? ? ? ? ?dxz=dxz+tmpval*rx*rz
? ? ? ?? ? ? ? ? ? ?end if
? ?? ? ? ? ? ? ?end if
? ? ? ? ? ? end do
? ? ? ? end do
? ? end do
end do
if (present(elegrad)) then
? ? elegrad(1)=derx
? ? elegrad(2)=dery
? ? elegrad(3)=derz
end if
if (idohess==1) then
? ? elehess(1,1)=dxx
? ? elehess(2,2)=dyy
? ? elehess(3,3)=dzz
? ? elehess(1,2)=dxy
? ? elehess(2,3)=dyz
? ? elehess(1,3)=dxz
? ? elehess(2,1)=dxy
? ? elehess(3,2)=dyz
? ? elehess(3,1)=dxz
end if
end subroutineand if i try to "Output all properties at a point" (point is the O atom in H2O) i get follow for promolecular density (promolecular density is good calculated, but its derivatives are not calculated)
Density of electrons:? 0.3441456709E+00
Reduced density gradient:? 0.1000000000E+03
Note: Matrix diagonalization exceed max cycle before convergence
Sign(lambda2)*rho:? ? ? ? ? ? ? ?NaN
ESP from nuclear charges:? 0.1000000000E+04
van der Waals potential (probe atom: C ):? 0.1280973043+126 kcal/mol
User-defined real space function:? ? ? ? ? ? ? ?NaN
Note: Below information are for electron density
Components of gradient in x/y/z are:
? ? ? ? ? ? ? ?NaN? ? ? ? ? ? ? ?NaN? ? ? ? ? ? ? ?NaN
Norm of gradient is:? ? ? ? ? ? ? ?NaN
Components of Laplacian in x/y/z are:
? ? ? ? ? ? ? ?NaN? ? ? ? ? ? ? ?NaN? ? ? ? ? ? ? ?NaN
Total:? ? ? ? ? ? ? ?NaN
Hessian matrix:
? ? ? ? ? ? ? ?NaN? ? ? ? ? ? ? ?NaN? ? ? ? ? ? ? ?NaN
? ? ? ? ? ? ? ?NaN? ? ? ? ? ? ? ?NaN? ? ? ? ? ? ? ?NaN
? ? ? ? ? ? ? ?NaN? ? ? ? ? ? ? ?NaN? ? ? ? ? ? ? ?NaNI create my own function that creates promolecular density (input file xyz) with calcprodens(x,y,z,0) and then analyze it. should i use subroutine gencalchessmat to calc promolgrad and hess?
sorry))
is it possible to use calcprodens(x,y,z,0) to generate "good" promolecular density and then analyze it? And could you please tell me, what function/subroutine is used for topological analysis of iuserfunc==-2(calcprodens) How are derivatives and the Hessian matrix calculated?
а нельзя использовать функцию calcprodens(x,y,z,0) для генерации хорошей промолекулярной плотности а потом использовать ее для анализа? And could you please tell me, щn the basis of what function is topological analysis done iuserfunc==-2(calcprodens) How are derivatives and the Hessian matrix calculated?
could you please explain to me what is the difference between calchessmat_dens_promol and calchessmat_prodens? which function i need to use to calculate promolecular density with built-in spherical atomic densities and then analyze it (calculate gradient, lapl on promolecular density)?
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