You can see
Note: Below information are for electron densityIf currently wavefunction information is not available, then the data must be NaN.
If you want to obtain derivative information for e.g. real space function 100 (current user-defined function), you can enter main function 1, input f100, then input the coordinate of interest, and then various data at this point will be printed, and derivative information (like gradient and Hessian) will also be printed for the real space function 100.
thank 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 NaNIf your function doesn't have capability of calculating analytic gradient and Hessian, you do not need to modify gencalchessmat. The gradient and Hessian will be calculated numerically and automatically in gencalchessmat.
I 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?
Yes, calcprodens(x,y,z,0) is exactly what you need.
In "real*8 function userfunc(x,y,z)", you can find
case (-2) !Promolecular density userfunc=calcprodens(x,y,z,0)So, if you set iuserfunc=-2 and perform topology analysis for user-defined function, then it is equivalent to perform topology analysis on promolecular density. In this case, the derivatives are evaluated fully numerically.
The topology analysis module calls "subroutine gencalchessmat" to obtain needed derivatives (gradient and possibly Hessian). If you find there is no specific code in this subroutine for evaluating analytic derivatives, that means the derivatives will be evaluated numerically automatically.
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?
Please fully speak in English, otherwise I cannot exactly understand your question.
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?
You should use calchessmat_prodens. Note that currently for element index <=18, the proatomic density in RDG original paper is used in this subroutine, while for others, the proatomic density constructed by me is used. The quality of the former is much poorer than the latter, but faster to evaluate. If you need good promolecular density, I suggest modifying this subroutine to use the latter for all elements.
calchessmat_dens_promol is used to calculate density and derivatives based on promolecular wavefunction combined from isolated atomic wavefunction. In contrast, calchessmat_prodens only requires atomic coordinates and element information.
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)?