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bonds_ref.f90
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bonds_ref.f90
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! CARACAL - Ring polymer molecular dynamics and rate constant calculations
! on black-box generated potential energy surfaces
!
! Copyright (c) 2023 by Julien Steffen ([email protected])
! Stefan Grimme ([email protected]) (QMDFF code)
!
! Permission is hereby granted, free of charge, to any person obtaining a
! copy of this software and associated documentation files (the "Software"),
! to deal in the Software without restriction, including without limitation
! the rights to use, copy, modify, merge, publish, distribute, sublicense,
! and/or sell copies of the Software, and to permit persons to whom the
! Software is furnished to do so, subject to the following conditions:
!
! The above copyright notice and this permission notice shall be included in
! all copies or substantial portions of the Software.
!
! THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
! IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
! FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
! THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
! LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
! FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
! DEALINGS IN THE SOFTWARE.
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! subroutine bonds_ref: calculate reference bondlengths
! of the forming and breaking bonds at the TS to define
! the s1 dividing surface for the rpmd rate calculation
! program
! For unimolecular reactions, also define reference
! bond lengths of the s0 reactant surface
!
! part of EVB
!
subroutine bonds_ref
use general
use evb_mod
implicit none
integer::i,j ! loop indices
integer::atom1,atom2 ! the current atom numbers
real(kind=8)::Rx,Ry,Rz
!
! calculate the forming bonds
!
if (form_num .gt. 0) then
allocate(form_ref(form_num))
end if
do i=1,form_num
atom1=bond_form(i,1)
atom2=bond_form(i,2)
Rx=ts_ref(1,atom1)-ts_ref(1,atom2)
Ry=ts_ref(2,atom1)-ts_ref(2,atom2)
Rz=ts_ref(3,atom1)-ts_ref(3,atom2)
form_ref(i)=sqrt(Rx*Rx+Ry*Ry+Rz*Rz)
end do
!
! calculate the breaking bonds
!
if (break_num .gt. 0) then
allocate(break_ref(break_num))
end if
do i=1,break_num
atom1=bond_break(i,1)
atom2=bond_break(i,2)
Rx=ts_ref(1,atom1)-ts_ref(1,atom2)
Ry=ts_ref(2,atom1)-ts_ref(2,atom2)
Rz=ts_ref(3,atom1)-ts_ref(3,atom2)
break_ref(i)=sqrt(Rx*Rx+Ry*Ry+Rz*Rz)
end do
!
! For unimolecular reactions:
! calculate the forming and breaking bonds
! at the transition state
!
if ((umbr_type .eq. "CYCLOREVER") .or. (umbr_type .eq. "REARRANGE") .or.&
& (umbr_type .eq. "DECOM_1BOND") .or. (umbr_type .eq. "ELIMINATION")) then
allocate(form_reac(form_num),break_reac(break_num))
if (size(reac_ref) .lt. 2) then
write(*,*) "Please add the keyword REACTANTS_STRUC!"
call fatal
end if
do i=1,form_num
atom1=bond_form(i,1)
atom2=bond_form(i,2)
Rx=reac_ref(1,atom1)-reac_ref(1,atom2)
Ry=reac_ref(2,atom1)-reac_ref(2,atom2)
Rz=reac_ref(3,atom1)-reac_ref(3,atom2)
form_reac(i)=sqrt(Rx*Rx+Ry*Ry+Rz*Rz)
end do
!
! calculate the breaking bonds
!
do i=1,break_num
atom1=bond_break(i,1)
atom2=bond_break(i,2)
Rx=reac_ref(1,atom1)-reac_ref(1,atom2)
Ry=reac_ref(2,atom1)-reac_ref(2,atom2)
Rz=reac_ref(3,atom1)-reac_ref(3,atom2)
break_reac(i)=sqrt(Rx*Rx+Ry*Ry+Rz*Rz)
end do
end if
return
end subroutine bonds_ref