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Fix xtb/docking test #1173

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merged 6 commits into from
Feb 12, 2025
+12 −9
Merged

Fix xtb/docking test #1173

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1881ef0
Skip i==j for avoiding division by zero
foxtran Feb 1, 2025
1e86c83
Skip close atoms for avoiding division by zero as well as avoid compl…
foxtran Feb 1, 2025
c4ca5d4
Close files properly
foxtran Feb 1, 2025
1800109
Cycle after filling gab1/gab2
foxtran Feb 10, 2025
a56dc82
Avoid division by zero by updating expression
foxtran Feb 10, 2025
fb2aba3
Use r2 instead of r*r
foxtran Feb 10, 2025
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3 changes: 2 additions & 1 deletion src/docking/search_nci.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -966,6 +966,7 @@ END SUBROUTINE Quicksort
call generateFileName(fin_name, 'best', '', comb%ftype)
call open_file(ifinal, fin_name, 'w')
call writeMolecule(comb, ifinal, energy=final_e(1))
call close_file(ifinal)
!If not xyz then best.xyz is written to not have api break
if(comb%ftype /= 1)then
call open_file(ifinal, 'best.xyz', 'w')
Expand All @@ -975,8 +976,8 @@ END SUBROUTINE Quicksort
write (ifinal, '(a4,2x,3f20.14)') comb%sym(j), xyz_opt(1, j, 1)*autoang, &
& xyz_opt(2, j, 1)*autoang, xyz_opt(3, j, 1)*autoang
end do
call close_file(ifinal)
end if
call close_file(ifinal)


call delete_file(set%opt_logfile)
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12 changes: 6 additions & 6 deletions src/iff/iff_energy.f90
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Expand Up @@ -275,16 +275,16 @@ subroutine iff_e(env, n, n1, n2, at1, at2, neigh, A1, c02, q01, q02, c6ab,&
r2 = (AL1(1, i) - AL2(1, j))**2&
&+ (AL1(2, i) - AL2(2, j))**2&
&+ (AL1(3, i) - AL2(3, j))**2
r = dble(sqrt(real(r2)))
esl = esl + AL1(4, i)*AL2(4, j)/(r + r0tmp(jat, iat)/r)
r = sqrt(r2)
esl = esl + AL1(4, i)*AL2(4, j)*r/(r2 + r0tmp(jat, iat))
end do
! LP atom corrections
do j = 1, n2
r2 = (A2(1, j) - AL1(1, i))**2&
&+ (A2(2, j) - AL1(2, i))**2&
&+ (A2(3, j) - AL1(3, i))**2
r = dble(sqrt(real(r2)))
esl = esl + AL1(4, i)*q2(j)/(r + r0tmp(j, iat)/r)
r = sqrt(r2)
esl = esl + AL1(4, i)*q2(j)*r/(r2 + r0tmp(j, iat))
end do
end do
! LP atom corrections
Expand All @@ -294,8 +294,8 @@ subroutine iff_e(env, n, n1, n2, at1, at2, neigh, A1, c02, q01, q02, c6ab,&
r2 = (A1(1, j) - AL2(1, i))**2&
&+ (A1(2, j) - AL2(2, i))**2&
&+ (A1(3, j) - AL2(3, i))**2
r = dble(sqrt(real(r2)))
esl = esl + AL2(4, i)*q1(j)/(r + r0tmp(iat, j)/r)
r = sqrt(r2)
esl = esl + AL2(4, i)*q1(j)*r/(r2 + r0tmp(iat, j))
end do
end do

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6 changes: 4 additions & 2 deletions src/iff/iff_ini.f90
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Expand Up @@ -217,11 +217,12 @@ subroutine init_iff(env,n1,n2,at1,at2,neigh,xyz1,xyz2,q1,q2,c6ab,z1,z2,&
&(xyz1(3, j) - xyz1(3, i))**2
r0 = sqrt(rr)
gab1(j, i) = 1.0d0/(r0 + 1./sqrt(gam(at1(i))*gam(at1(j))))
if (j .eq. i) cycle
ai = alp0(i)**(1./3)
aj = alp0(j)**(1./3)
rrr = 1.13*2.6*(ai + aj)*0.5/r0
tmp = 1.0d0/(1.d0 + 6.d0*rrr**14)
if (j .ne. i .and. tmp .gt. 0.90 .and. r0 .lt. thr) then
if (tmp .gt. 0.90 .and. r0 .lt. thr) then
k = k + 1
neigh(k, i) = j
end if
Expand All @@ -239,11 +240,12 @@ subroutine init_iff(env,n1,n2,at1,at2,neigh,xyz1,xyz2,q1,q2,c6ab,z1,z2,&
&(xyz2(3, j) - xyz2(3, i))**2
r0 = sqrt(rr)
gab2(j, i) = 1.0d0/(r0 + 1./sqrt(gam(at2(i))*gam(at2(j))))
if (j .eq. i) cycle
ai = alp0(i + n1)**(1./3)
aj = alp0(j + n1)**(1./3)
rrr = 1.13*2.6*(ai + aj)*0.5/r0
tmp = 1.0d0/(1.d0 + 6.d0*rrr**14)
if (j .ne. i .and. tmp .gt. 0.90 .and. r0 .lt. thr) then
if (tmp .gt. 0.90 .and. r0 .lt. thr) then
k = k + 1
neigh(k, i + n1) = j
end if
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